PT AU BA BE GP AF BF CA TI SO SE BS LA DT CT CY CL SP HO DE ID AB C1 RP EM RI OI FU FX CR NR TC Z9 U1 U2 PU PI PA SN EI BN J9 JI PD PY VL IS PN SU SI MA BP EP AR DI D2 EA PG WC SC GA UT PM OA HC HP DA J Ksiazek, TG; Erdman, D; Goldsmith, CS; Zaki, SR; Peret, T; Emery, S; Tong, SX; Urbani, C; Comer, JA; Lim, W; Rollin, PE; Dowell, SF; Ling, AE; Humphrey, CD; Shieh, WJ; Guarner, J; Paddock, CD; Rota, P; Fields, B; DeRisi, J; Yang, JY; Cox, N; Hughes, JM; LeDuc, JW; Bellini, WJ; Anderson, LJ Ksiazek, TG; Erdman, D; Goldsmith, CS; Zaki, SR; Peret, T; Emery, S; Tong, SX; Urbani, C; Comer, JA; Lim, W; Rollin, PE; Dowell, SF; Ling, AE; Humphrey, CD; Shieh, WJ; Guarner, J; Paddock, CD; Rota, P; Fields, B; DeRisi, J; Yang, JY; Cox, N; Hughes, JM; LeDuc, JW; Bellini, WJ; Anderson, LJ SARS Working Grp A novel coronavirus associated with severe acute respiratory syndrome NEW ENGLAND JOURNAL OF MEDICINE English Article PORCINE EPIDEMIC DIARRHEA; VIRUS; INFECTION; PROPAGATION; DISEASE; FEVER BACKGROUND A worldwide outbreak of severe acute respiratory syndrome (SARS) has been associated with exposures originating from a single ill health care worker from Guangdong Province, China. We conducted studies to identify the etiologic agent of this outbreak. METHODS We received clinical specimens from patients in seven countries and tested them, using virus-isolation techniques, electron-microscopical and histologic studies, and molecular and serologic assays, in an attempt to identify a wide range of potential pathogens. RESULTS None of the previously described respiratory pathogens were consistently identified. However, a novel coronavirus was isolated from patients who met the case definition of SARS. Cytopathological features were noted in Vero E6 cells inoculated with a throat-swab specimen. Electron-microscopical examination revealed ultrastructural features characteristic of coronaviruses. Immunohistochemical and immunofluorescence staining revealed reactivity with group I coronavirus polyclonal antibodies. Consensus coronavirus primers designed to amplify a fragment of the polymerase gene by reverse transcription-polymerase chain reaction (RT-PCR) were used to obtain a sequence that clearly identified the isolate as a unique coronavirus only distantly related to previously sequenced coronaviruses. With specific diagnostic RT-PCR primers we identified several identical nucleotide sequences in 12 patients from several locations, a finding consistent with a point-source outbreak. Indirect fluorescence antibody tests and enzyme-linked immunosorbent assays made with the new isolate have been used to demonstrate a virus-specific serologic response. This virus may never before have circulated in the U.S. population. CONCLUSIONS A novel coronavirus is associated with this outbreak, and the evidence indicates that this virus has an etiologic role in SARS. Because of the death of Dr. Carlo Urbani, we propose that our first isolate be named the Urbani strain of SARS-associated coronavirus. Ctr Dis Control & Prevent, Special Pathogens Branch, Natl Ctr Infect Dis, Atlanta, GA 30333 USA; Ctr Dis Control & Prevent, Resp & Enter Virus Brach, Natl Ctr Infect Dis, Atlanta, GA USA; Ctr Dis Control & Prevent, Infect Dis Pathol Act, Natl Ctr Infect Dis, Atlanta, GA USA; Ctr Dis Control & Prevent, Influenza Branch, Natl Ctr Infect Dis, Atlanta, GA USA; Ctr Dis Control & Prevent, Div Bacterial & Mycot Dis, Natl Ctr Infect Dis, Atlanta, GA USA; Ctr Dis Control & Prevent, Off Director, Div Viral & Rickettsial Dis, Natl Ctr Infect Dis, Atlanta, GA USA; WHO, Hanoi, Vietnam; Queen Mary Hosp, Govt Virus Unit, Hong Kong, Hong Kong, Peoples R China; Int Emerging Infect Dis Program, Bangkok, Thailand; Univ Calif San Francisco, San Francisco, CA 94143 USA; Singapore Gen Hosp, Dept Pathol, Singapore, Singapore; Ctr Dis Control, Dept Hlth, Taipei, Taiwan Ksiazek, TG (reprint author), Ctr Dis Control & Prevent, Special Pathogens Branch, Natl Ctr Infect Dis, Atlanta, GA 30333 USA. 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MAY 15 2003 348 20 1953 1966 10.1056/NEJMoa030781 14 Medicine, General & Internal General & Internal Medicine 677TJ WOS:000182823400004 12690092 Bronze 2020-04-01 J Drosten, C; Gunther, S; Preiser, W; van der Werf, S; Brodt, HR; Becker, S; Rabenau, H; Panning, M; Kolesnikova, L; Fouchier, RAM; Berger, A; Burguiere, AM; Cinatl, J; Eickmann, M; Escriou, N; Grywna, K; Kramme, S; Manuguerra, JC; Muller, S; Rickerts, V; Sturmer, M; Vieth, S; Klenk, HD; Osterhaus, ADME; Schmitz, H; Doerr, HW Drosten, C; Gunther, S; Preiser, W; van der Werf, S; Brodt, HR; Becker, S; Rabenau, H; Panning, M; Kolesnikova, L; Fouchier, RAM; Berger, A; Burguiere, AM; Cinatl, J; Eickmann, M; Escriou, N; Grywna, K; Kramme, S; Manuguerra, JC; Muller, S; Rickerts, V; Sturmer, M; Vieth, S; Klenk, HD; Osterhaus, ADME; Schmitz, H; Doerr, HW Identification of a novel coronavirus in patients with severe acute respiratory syndrome NEW ENGLAND JOURNAL OF MEDICINE English Article LASSA VIRUS; FEVER BACKGROUND The severe acute respiratory syndrome (SARS) has recently been identified as a new clinical entity. SARS is thought to be caused by an unknown infectious agent. METHODS Clinical specimens from patients with SARS were searched for unknown viruses with the use of cell cultures and molecular techniques. RESULTS A novel coronavirus was identified in patients with SARS. The virus was isolated in cell culture, and a sequence 300 nucleotides in length was obtained by a polymerase-chain-reaction (PCR)-based random-amplification procedure. Genetic characterization indicated that the virus is only distantly related to known coronaviruses (identical in 50 to 60 percent of the nucleotide sequence). On the basis of the obtained sequence, conventional and real-time PCR assays for specific and sensitive detection of the novel virus were established. Virus was detected in a variety of clinical specimens from patients with SARS but not in controls. High concentrations of viral RNA of up to 100 million molecules per milliliter were found in sputum. Viral RNA was also detected at extremely low concentrations in plasma during the acute phase and in feces during the late convalescent phase. Infected patients showed seroconversion on the Vero cells in which the virus was isolated. CONCLUSIONS The novel coronavirus might have a role in causing SARS. Bernhard Nocht Inst Trop Med, Dept Virol, Natl Reference Ctr Trop Infect Dis, D-20359 Hamburg, Germany; Univ Frankfurt, Inst Med Virol, D-6000 Frankfurt, Germany; Univ Frankfurt, Med Clin 3, D-6000 Frankfurt, Germany; Univ Marburg, Inst Virol, D-3550 Marburg, Germany; Inst Pasteur, Natl Influenza Ctr No France, Paris, France; Erasmus Univ, Inst Virol, Rotterdam, Netherlands Drosten, C (reprint author), Bernhard Nocht Inst Trop Med, Dept Virol, Natl Reference Ctr Trop Infect Dis, Bernhard Nocht Str 74, D-20359 Hamburg, Germany. Panning, Marcus/I-7889-2016; Preiser, Wolfgang/J-4875-2016; Fouchier, Ron A/A-1911-2014; Escriou, Nicolas/A-2392-2016; Fouchier, Ron/Y-3755-2019; Becker, Stephan/A-1065-2010 Preiser, Wolfgang/0000-0002-0254-7910; Fouchier, Ron A/0000-0001-8095-2869; Escriou, Nicolas/0000-0002-1224-6839; Fouchier, Ron/0000-0001-8095-2869; Becker, Stephan/0000-0002-2794-5659; van der WERF, Sylvie/0000-0002-1148-4456; , Simon/0000-0002-2765-1589; Gunther, Stephan/0000-0002-6562-0230; Osterhaus, Albert/0000-0002-6074-1172; Sturmer, Martin/0000-0003-4300-9315 Cho KO, 2001, AM J VET RES, V62, P1436, DOI 10.2460/ajvr.2001.62.1436; Cossart Y, 1998, LANCET, V352, P164, DOI 10.1016/S0140-6736(05)77802-8; Drosten C, 2002, J CLIN MICROBIOL, V40, P2323, DOI 10.1128/JCM.40.7.2323-2330.2002; FELSENSTEIN J, 2000, PHYLIP PHYLOGENY INF; Gunther S, 2000, EMERG INFECT DIS, V6, P466, DOI 10.3201/eid0605.000504; KEW MC, 1996, LANCET S2, V348, P10; Makela MJ, 1998, J CLIN MICROBIOL, V36, P539; POUTANEN SM, 2003, NEW ENGL J MED, V348, P1993; Stephensen CB, 1999, VIRUS RES, V60, P181, DOI 10.1016/S0168-1702(99)00017-9; TSANG KW, 2003, NEW ENGL J MED, V348, P1975; *WHO, 2003, CUM NUMB REP CAS SEV; 2003, WKLY EPIDEMIOL REC, V78, P81; 2003, WKLY EPIDEMIOL REC, V78, P73 13 1762 2025 79 205 MASSACHUSETTS MEDICAL SOC/NEJM WALTHAM WALTHAM WOODS CENTER, 860 WINTER ST,, WALTHAM, MA 02451-1413 USA 0028-4793 NEW ENGL J MED N. 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MAY 15 2003 348 20 1967 1976 10.1056/NEJMoa030747 10 Medicine, General & Internal General & Internal Medicine 677TJ WOS:000182823400005 12690091 Green Published, Bronze 2020-04-01 J Rota, PA; Oberste, MS; Monroe, SS; Nix, WA; Campagnoli, R; Icenogle, JP; Penaranda, S; Bankamp, B; Maher, K; Chen, MH; Tong, SX; Tamin, A; Lowe, L; Frace, M; DeRisi, JL; Chen, Q; Wang, D; Erdman, DD; Peret, TCT; Burns, C; Ksiazek, TG; Rollin, PE; Sanchez, A; Liffick, S; Holloway, B; Limor, J; McCaustland, K; Olsen-Rasmussen, M; Fouchier, R; Gunther, S; Osterhaus, ADME; Drosten, C; Pallansch, MA; Anderson, LJ; Bellini, WJ Rota, PA; Oberste, MS; Monroe, SS; Nix, WA; Campagnoli, R; Icenogle, JP; Penaranda, S; Bankamp, B; Maher, K; Chen, MH; Tong, SX; Tamin, A; Lowe, L; Frace, M; DeRisi, JL; Chen, Q; Wang, D; Erdman, DD; Peret, TCT; Burns, C; Ksiazek, TG; Rollin, PE; Sanchez, A; Liffick, S; Holloway, B; Limor, J; McCaustland, K; Olsen-Rasmussen, M; Fouchier, R; Gunther, S; Osterhaus, ADME; Drosten, C; Pallansch, MA; Anderson, LJ; Bellini, WJ Characterization of a novel coronavirus associated with severe acute respiratory syndrome SCIENCE English Article TRANSMISSIBLE GASTROENTERITIS CORONAVIRUS; TARGETED RECOMBINATION; SPIKE GENE; VIRUS; DETERMINANT; ENTRY In March 2003, a novel coronavirus (SARS-CoV) was discovered in association with cases of severe acute respiratory syndrome (SARS). The sequence of the complete genome of SARS-CoV was determined, and the initial characterization of the viral genome is presented in this report. The genome of SARS-CoV is 29,727 nucleotides in length and has 11 open reading frames, and its genome organization is similar to that of other coronaviruses. Phylogenetic analyses and sequence comparisons showed that SARS-CoV is not closely related to any of the previously characterized coronaviruses. Ctr Dis Control, Natl Ctr Infect Dis, Atlanta, GA 30333 USA; Univ Calif San Francisco, Dept Biochem, San Francisco, CA 94143 USA; Univ Calif San Francisco, Dept Biophys, San Francisco, CA 94143 USA; Erasmus Univ, Dept Virol, NL-3000 DR Rotterdam, Netherlands; Bernhard Nocht Inst Trop Med, Dept Virol, D-20359 Hamburg, Germany Rota, PA (reprint author), Ctr Dis Control, Natl Ctr Infect Dis, Atlanta, GA 30333 USA. prota@cdc.gov Fouchier, Ron/Y-3755-2019; Fouchier, Ron A/A-1911-2014 Fouchier, Ron/0000-0001-8095-2869; Fouchier, Ron A/0000-0001-8095-2869; Monroe, Stephan/0000-0002-5424-716X; Campagnoli, Ray/0000-0003-0531-3893; Guan, Yi/0000-0001-6057-9243; Osterhaus, Albert/0000-0002-6074-1172; Gunther, Stephan/0000-0002-6562-0230 Centers for Disease Control and Prevention (CDC), 2003, MMWR-MORBID MORTAL W, V52, P357; de Haan CAM, 2002, VIRUS RES, V82, P77; de Haan CAM, 1998, J VIROL, V72, P6838, DOI 10.1128/JVI.72.8.6838-6850.1998; DROSTEN C, 2003, N ENGL J MED 0417; Escors D, 2001, J VIROL, V75, P1312, DOI 10.1128/JVI.75.3.1312-1324.2001; Garoff H, 1998, MICROBIOL MOL BIOL R, V62, P1171, DOI 10.1128/MMBR.62.4.1171-1190.1998; HOLMES KV, 2001, FIELDS VIROLOGY, pCH36; Ksiazek TG, 2003, NEW ENGL J MED, V348, P1953, DOI 10.1056/NEJMoa030781; LAI MMC, 2001, FIELDS VIROLOGY, pCH35; LEE N, 2003, N ENGL J MED 0417; Leparc-Goffart I, 1998, J VIROL, V72, P9628, DOI 10.1128/JVI.72.12.9628-9636.1998; LIU DX, 1992, J VIROL, V66, P6143, DOI 10.1128/JVI.66.10.6143-6154.1992; Lole KS, 1999, J VIROL, V73, P152, DOI 10.1128/JVI.73.1.152-160.1999; Marra MA, 2003, SCIENCE, V300, P1399, DOI 10.1126/science.1085953; Peiris JSM, 2003, LANCET, V361, P1319, DOI 10.1016/S0140-6736(03)13077-2; POUTANEN SM, 2003, N ENGL J MED 0417; Sanchez CM, 1999, J VIROL, V73, P7607; Sawicki SG, 1998, ADV EXP MED BIOL, V440, P215; SIDDELL SG, 1995, CORONAVIRIDAE; THIEL V, 1994, J GEN VIROL, V75, P3041, DOI 10.1099/0022-1317-75-11-3041; TSANG KW, 2003, N ENGL J MED 0417; van Regenmortel MHV, 2000, VIRUS TAXONOMY CLASS, P835; Ziebuhr J, 2000, J GEN VIROL, V81, P853, DOI 10.1099/0022-1317-81-4-853 23 1493 1752 47 149 AMER ASSOC ADVANCEMENT SCIENCE WASHINGTON 1200 NEW YORK AVE, NW, WASHINGTON, DC 20005 USA 0036-8075 1095-9203 SCIENCE Science MAY 30 2003 300 5624 1394 1399 10.1126/science.1085952 6 Multidisciplinary Sciences Science & Technology - Other Topics 683ZW WOS:000183181800035 12730500 Bronze 2020-04-01 J Peiris, JSM; Lai, ST; Poon, LLM; Guan, Y; Yam, LYC; Lim, W; Nicholls, J; Yee, WKS; Yan, WW; Cheung, MT; Cheng, VCC; Chan, KH; Tsang, DNC; Yung, RWH; Ng, TK; Yuen, KY Peiris, JSM; Lai, ST; Poon, LLM; Guan, Y; Yam, LYC; Lim, W; Nicholls, J; Yee, WKS; Yan, WW; Cheung, MT; Cheng, VCC; Chan, KH; Tsang, DNC; Yung, RWH; Ng, TK; Yuen, KY SARS Study Grp Coronavirus as a possible cause of severe acute respiratory syndrome LANCET English Article HUMAN-DISEASE; VIRUS; INFECTIONS; DIAGNOSIS Background An outbreak of severe acute respiratory syndrome (SARS) has been reported in Hong Kong. We investigated the viral cause and clinical presentation among 50 patients. Methods We analysed case notes and microbiological findings for 50 patients with SARS, representing more than five separate epidemiologically linked transmission clusters. We defined the clinical presentation and risk factors associated with severe disease and investigated the causal agents by chest radiography and laboratory testing of nasopharyngeal aspirates and sera samples. We compared the laboratory findings with those submitted for microbiological investigation of other diseases from patients whose identity was masked. Findings Patients, age ranged from 23 to 74 years. Fever, chills, myalgia, and cough were the most frequent complaints. When compared with chest radiographic changes, respiratory symptoms and auscultatory findings were disproportionally mild. Patients who were household contacts of other infected people and had older age, lymphopenia, and liver dysfunction were associated with severe disease. A virus belonging to the family Coronaviridae was isolated from two patients. By use of serological and reverse-transcriptase PCR specific for this virus, 45 of 50 patients with SARS, but no controls, had evidence of infection with this virus. Interpretation A coronavirus was isolated from patients with SARS that might be the primary agent associated with this disease. Serological and molecular tests specific for the virus permitted a definitive laboratory diagnosis to be made and allowed further investigation to define whether other cofactors play a part in disease progression. Univ Hong Kong, Queen Mary Hosp, Dept Pathol & Microbiol, Hong Kong, Hong Kong, Peoples R China; Princess Margaret Hosp, Dept Med Intens Care & Pathol, Hong Kong, Hong Kong, Peoples R China; Dept Hlth, Govt Virus Unit, Hong Kong, Hong Kong, Peoples R China; Pamela Youde Nethersole Eastern Hosp, Dept Pathol & Med, Hong Kong, Hong Kong, Peoples R China; Kwong Wah Hosp, Dept Med, Hong Kong, Hong Kong, Peoples R China; Queen Elizabeth Hosp, Dept Pathol, Kowloon, Hong Kong, Peoples R China Peiris, JSM (reprint author), Univ Hong Kong, Queen Mary Hosp, Dept Microbiol, Pokfulam Rd, Hong Kong, Hong Kong, Peoples R China. Poon, Leo/C-4382-2009; Yuen, Kwok Yung/C-4465-2009; Nicholls, John Malcolm/C-4375-2009; Peiris, Joseph Sriyal Malik/C-4380-2009 Poon, Leo/0000-0002-9101-7953; Yuen, Kwok-yung/0000-0002-2083-1552; Nicholls, John Malcolm/0000-0001-7217-7444; Peiris, Joseph Sriyal Malik/0000-0001-8217-5995 PHS HHSUnited States Public Health Service [A195357] CAUL EO, 1977, ARCH VIROL, V54, P107, DOI 10.1007/BF01314383; Chan KH, 2002, J CLIN MICROBIOL, V40, P1675, DOI 10.1128/JCM.40.5.1675-1680.2002; Cheung CY, 2002, LANCET, V360, P1831, DOI 10.1016/S0140-6736(02)11772-7; El-Sahly HM, 2000, CLIN INFECT DIS, V31, P96, DOI 10.1086/313937; FOTZ RJ, 1999, CHEST, V115, P901; Fouchier RAM, 2000, J CLIN MICROBIOL, V38, P4096, DOI 10.1128/JCM.38.11.4096-4101.2000; HOLMES KV, 2001, FIELDS VIROLOGY, P1187; McIntosh K., 1974, Current Topics in Microbiology and Immunology, V63, P85; MCINTOSH K, 1970, AM J EPIDEMIOL, V91, P585, DOI 10.1093/oxfordjournals.aje.a121171; TALBOT PJ, IN PRESS ADV EXP MED; WENZEL RP, 1974, AM REV RESPIR DIS, V109, P621; *WHO, 2003, WKLY EPIDEMIOL REC, V78, P81; Wiedbrauk DL, 1993, MANUAL CLIN VIROLOGY; World Health Organization, 2003, WKLY EPIDEMIOL REC, V78, P86; Yuen KY, 1998, LANCET, V351, P467, DOI 10.1016/S0140-6736(98)01182-9 15 1454 1682 87 270 LANCET LTD LONDON 84 THEOBALDS RD, LONDON WC1X 8RR, ENGLAND 0140-6736 LANCET Lancet APR 19 2003 361 9366 1319 1325 10.1016/S0140-6736(03)13077-2 7 Medicine, General & Internal General & Internal Medicine 669HP WOS:000182346100007 12711465 Bronze 2020-04-01 J JOHNSTON, SL; PATTEMORE, PK; SANDERSON, G; SMITH, S; LAMPE, F; JOSEPHS, L; SYMINGTON, P; OTOOLE, S; MYINT, SH; TYRRELL, DAJ; HOLGATE, ST JOHNSTON, SL; PATTEMORE, PK; SANDERSON, G; SMITH, S; LAMPE, F; JOSEPHS, L; SYMINGTON, P; OTOOLE, S; MYINT, SH; TYRRELL, DAJ; HOLGATE, ST COMMUNITY STUDY OF ROLE OF VIRAL-INFECTIONS IN EXACERBATIONS OF ASTHMA IN 9-11 YEAR-OLD CHILDREN BRITISH MEDICAL JOURNAL English Article WHEEZY BRONCHITIS; RESPIRATORY-INFECTIONS; VIRUSES; SYMPTOMS; ADULTS; PRECIPITANTS; ASSOCIATION; CORONAVIRUS; CHILDHOOD Objective-To study the association between upper and lower respiratory viral infections and acute exacerbations of asthma in schoolchildren in the community. Design-Community based 13 month longitudinal study using diary card respiratory symptom and peak expiratory flow monitoring to allow early sampling for viruses. Subjects-1O8 Children aged 9-11 years who had reported wheeze or cough, or both, in a questionnaire. Setting-Southampton and surrounding community. Main outcome measures-Upper and lower respiratory viral infections detected by polymerase chain reaction or conventional methods, reported exacerbations of asthma, computer identified episodes of respiratory tract symptoms or peak flow reductions. Results-Viruses were detected in 80% of reported episodes of reduced peak expiratory flow, 80% of reported episodes of wheeze, and in 85% of reported episodes of upper respiratory symptoms, cough, wheeze, and a fall in peak expiratory flow. The median duration of reported falls in peak expiratory flow was 14 days, and the median maximum fall in peak expiratory flow was 81 1/min. The most commonly identified virus type was rhinovirus. Conclusions-This study supports the hypothesis that upper respiratory viral infections are associated with 80-85% of asthma exacerbations in school age children. UNIV SOUTHAMPTON,DEPT MED STAT & COMP,SOUTHAMPTON SO9 4XY,HANTS,ENGLAND; UNIV LEICESTER,DEPT MICROBIOL,LEICESTER LE1 9HN,LEICS,ENGLAND; MRC,COMMON COLD UNIT,SALISBURY,WILTS,ENGLAND JOHNSTON, SL (reprint author), UNIV MED SOUTHAMPTON,SOUTHAMPTON GEN HOSP,SOUTHAMPTON SO9 4XY,HANTS,ENGLAND. 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NOV 8 2012 367 19 1814 1820 10.1056/NEJMoa1211721 7 Medicine, General & Internal General & Internal Medicine 033DG WOS:000310773200008 23075143 Bronze Y N 2020-04-01 J Marra, MA; Jones, SJM; Astell, CR; Holt, RA; Brooks-Wilson, A; Butterfield, YSN; Khattra, J; Asano, JK; Barber, SA; Chan, SY; Cloutier, A; Coughlin, SM; Freeman, D; Girn, N; Griffith, OL; Leach, SR; Mayo, M; McDonald, H; Montgomery, SB; Pandoh, PK; Petrescu, AS; Robertson, AG; Schein, JE; Siddiqui, A; Smailus, DE; Stott, JE; Yang, GS; Plummer, F; Andonov, A; Artsob, H; Bastien, N; Bernard, K; Booth, TF; Bowness, D; Czub, M; Drebot, M; Fernando, L; Flick, R; Garbutt, M; Gray, M; Grolla, A; Jones, S; Feldmann, H; Meyers, A; Kabani, A; Li, Y; Normand, S; Stroher, U; Tipples, GA; Tyler, S; Vogrig, R; Ward, D; Watson, B; Brunham, RC; Krajden, M; Petric, M; Skowronski, DM; Upton, C; Roper, RL Marra, MA; Jones, SJM; Astell, CR; Holt, RA; Brooks-Wilson, A; Butterfield, YSN; Khattra, J; Asano, JK; Barber, SA; Chan, SY; Cloutier, A; Coughlin, SM; Freeman, D; Girn, N; Griffith, OL; Leach, SR; Mayo, M; McDonald, H; Montgomery, SB; Pandoh, PK; Petrescu, AS; Robertson, AG; Schein, JE; Siddiqui, A; Smailus, DE; Stott, JE; Yang, GS; Plummer, F; Andonov, A; Artsob, H; Bastien, N; Bernard, K; Booth, TF; Bowness, D; Czub, M; Drebot, M; Fernando, L; Flick, R; Garbutt, M; Gray, M; Grolla, A; Jones, S; Feldmann, H; Meyers, A; Kabani, A; Li, Y; Normand, S; Stroher, U; Tipples, GA; Tyler, S; Vogrig, R; Ward, D; Watson, B; Brunham, RC; Krajden, M; Petric, M; Skowronski, DM; Upton, C; Roper, RL The genome sequence of the SARS-associated coronavirus SCIENCE English Article PROTEIN FAMILIES; RNA-SYNTHESIS; VIRUS; TRANSCRIPTION; DATABASE; GENERATION; INTERPRO; SITES We sequenced the 29,751-base genome of the severe acute respiratory syndrome (SARS)-associated coronavirus known as the Tor2 isolate. The genome sequence reveals that this coronavirus is only moderately related to other known coronaviruses, including two human coronaviruses, HCoV-OC43 and HCoV-229E. Phylogenetic analysis of the predicted viral proteins indicates that the virus does not closely resemble any of the three previously known groups of coronaviruses. The genome sequence will aid in the diagnosis of SARS virus infection in humans and potential animal hosts (using polymerase chain reaction and immunological tests), in the development of antivirals (including neutralizing antibodies), and in the identification of putative epitopes for vaccine development. British Columbia Canc Agcy, Genome Sci Ctr, Vancouver, BC V5Z 4E6, Canada; Natl Microbiol Lab, Winnipeg, MB R3E 3R2, Canada; British Columbia Ctr Dis Control, Vancouver, BC V5Z 4R4, Canada; Univ British Columbia, Ctr Dis Control, Vancouver, BC V5Z 4R4, Canada; Univ Victoria, Dept Biochem & Microbiol, Victoria, BC V8W 3P6, Canada Marra, MA (reprint author), British Columbia Canc Agcy, Genome Sci Ctr, 600 W 10th Ave, Vancouver, BC V5Z 4E6, Canada. mmarra@bccgsc.ca Upton, Chris/A-4670-2008; Holt, Robert A/C-3303-2009; Schein, Jacquie E/G-3674-2015; Marra, Marco A/B-5987-2008; Jones, Steven J/C-3621-2009; Brooks-Wilson, Angela/E-9399-2012; Roper, Rachel/A-7935-2013; Griffith, Obi/P-1286-2014 Holt, Robert A/0000-0002-7259-1247; Marra, Marco A/0000-0001-7146-7175; Jones, Steven J/0000-0003-3394-2208; Brooks-Wilson, Angela/0000-0003-1009-6408; Roper, Rachel/0000-0001-6971-7745; Griffith, Obi/0000-0002-0843-4271; Upton, Chris/0000-0002-9019-8967 Altschul SF, 1997, NUCLEIC ACIDS RES, V25, P3389, DOI 10.1093/nar/25.17.3389; Apweiler R, 2001, NUCLEIC ACIDS RES, V29, P37, DOI 10.1093/nar/29.1.37; Bateman A, 2002, NUCLEIC ACIDS RES, V30, P276, DOI 10.1093/nar/30.1.276; DONNELLY CA, 2003, LANCET 0507; FELSENSTEIN J, 1993, PHYLIP PHYLOGENY INF; FIELDS BN, 2001, FIELDS VIROLOGY; HOFMANN K, 1993, BIOL CHEM HOPPESEYLE, V347, P166; Jonassen CM, 1998, J GEN VIROL, V79, P715, DOI 10.1099/0022-1317-79-4-715; Krishnan R, 1996, VIROLOGY, V218, P400, DOI 10.1006/viro.1996.0210; KSIAZEK TG, 2003, N ENGL J MED 0410; KUO L, 2002, ANN M AM SOC VIR LEX; Lai MMC, 1997, ADV VIRUS RES, V48, P1, DOI 10.1016/S0065-3527(08)60286-9; LAPPS W, 1987, VIROLOGY, V157, P47, DOI 10.1016/0042-6822(87)90312-6; Munch R, 2003, MICROBES INFECT, V5, P69, DOI 10.1016/S1286-4579(02)00053-9; MYINT SH, 1995, CORONAVIRIDAE, P389; Nielsen H, 1997, PROTEIN ENG, V10, P1, DOI 10.1093/protein/10.1.1; Ortego J, 2002, J VIROL, V76, P11518, DOI 10.1128/JVI.76.22.11518-11529.2002; PEARSON WR, 1988, P NATL ACAD SCI USA, V85, P2444, DOI 10.1073/pnas.85.8.2444; PEIRIS JSM, 2003, LANCET 0408; POUTANEN SM, 2003, N ENGL J MED 0331; Rota PA, 2003, SCIENCE, V300, P1394, DOI 10.1126/science.1085952; SAWICKI DL, 2001, J GEN VIROL, V82, P386; Sawicki SG, 1998, ADV EXP MED BIOL, V440, P215; SAWICKI SG, 1990, J VIROL, V64, P1050, DOI 10.1128/JVI.64.3.1050-1056.1990; SCHAAD MC, 1994, J VIROL, V68, P8169, DOI 10.1128/JVI.68.12.8169-8179.1994; SETHNA PB, 1989, P NATL ACAD SCI USA, V86, P5626, DOI 10.1073/pnas.86.14.5626; Sonnhammer E L, 1998, Proc Int Conf Intell Syst Mol Biol, V6, P175; THOMPSON JD, 1994, NUCLEIC ACIDS RES, V22, P4673, DOI 10.1093/nar/22.22.4673; Tsai JC, 2003, J VIROL, V77, P841, DOI 10.1128/JVI.77.2.841-850.2003; van Regenmortel MHV, 2000, VIRUS TAXONOMY CLASS, P835; Zdobnov EM, 2001, BIOINFORMATICS, V17, P847, DOI 10.1093/bioinformatics/17.9.847; Ziebuhr J, 2000, J GEN VIROL, V81, P853, DOI 10.1099/0022-1317-81-4-853 32 1277 1539 46 141 AMER ASSOC ADVANCEMENT SCIENCE WASHINGTON 1200 NEW YORK AVE, NW, WASHINGTON, DC 20005 USA 0036-8075 SCIENCE Science MAY 30 2003 300 5624 1399 1404 10.1126/science.1085953 7 Multidisciplinary Sciences Science & Technology - Other Topics 683ZW WOS:000183181800036 12730501 Bronze 2020-04-01 J Allander, T; Tammi, MT; Eriksson, M; Bjerkner, A; Tiveljung-Lindell, A; Andersson, B Allander, T; Tammi, MT; Eriksson, M; Bjerkner, A; Tiveljung-Lindell, A; Andersson, B Cloning of a human parvovirus by molecular screening of respiratory tract samples PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA English Article bioinformatics; nucleotide sequencing; respiratory tract infection; virus MINUTE VIRUS; BOVINE PARVOVIRUS; SYNCYTIAL VIRUS; CANINES MVC; SEQUENCE; IDENTIFICATION; CHILDREN; CORONAVIRUS; HOSPITALIZATIONS; PATHOGENICITY The identification of new virus species is a key issue for the study of infectious disease but is technically very difficult. We developed a system for large-scale molecular virus screening of clinical samples based on host DNA depletion, random PCR amplification, large-scale sequencing, and bioinformatics. The technology was applied to pooled human respiratory tract samples. The first experiments detected seven human virus species without the use of any specific reagent. Among the detected viruses were one coronavirus and one parvovirus, both of which were at that time uncharacterized. The parvovirus, provisionally named human bocavirus, was in a retrospective clinical study detected in 17 additional patients and associated with lower respiratory tract infections in children. The molecular virus screening procedure provides a general culture-independent solution to the problem of detecting unknown virus species in single or pooled samples. We suggest that a systematic exploration of the viruses that infect humans, "the human virome," can be initiated. Karolinska Univ Hosp, Dept Clin Microbiol, SE-17176 Stockholm, Sweden; Karolinska Univ Hosp, Ctr Mol Med, SE-17176 Stockholm, Sweden; Karolinska Inst, Dept Woman & Child Hlth, Astrid Lindgren Childrens Hosp, SE-17177 Stockholm, Sweden; Karolinska Inst, Ctr Genom & Bioinformat, SE-17177 Stockholm, Sweden; Natl Univ Singapore, Dept Biol Sci, Singapore 117543, Singapore; Natl Univ Singapore, Dept Biochem, Singapore 117543, Singapore Allander, T (reprint author), Karolinska Univ Hosp, Dept Clin Microbiol, L2-02, SE-17176 Stockholm, Sweden. tobias.allander@karolinska.se Andersson, Bjorn/G-9832-2013; Tammi, Martti/C-1115-2008 Andersson, Bjorn/0000-0002-4624-0259; Allander T, 2001, P NATL ACAD SCI USA, V98, P11609, DOI 10.1073/pnas.211424698; Altschul SF, 1997, NUCLEIC ACIDS RES, V25, P3389, DOI 10.1093/nar/25.17.3389; Bloom M. 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Natl. Acad. Sci. U. S. A. SEP 6 2005 102 36 12891 12896 10.1073/pnas.0504666102 6 Multidisciplinary Sciences Science & Technology - Other Topics 962FP WOS:000231716700045 16118271 Bronze, Green Published 2020-04-01 J COHEN, S; TYRRELL, DAJ; SMITH, AP COHEN, S; TYRRELL, DAJ; SMITH, AP PSYCHOLOGICAL STRESS AND SUSCEPTIBILITY TO THE COMMON COLD NEW ENGLAND JOURNAL OF MEDICINE English Article VOLUNTEERS; INFECTION Background. It is not known whether psychological stress suppresses host resistance to infection. To investigate this issue, we prospectively studied the relation between psychological stress and the frequency of documented clinical colds among subjects intentionally exposed to respiratory viruses. Methods. After completing questionnaires assessing degrees of psychological stress, 394 healthy subjects were given nasal drops containing one of five respiratory viruses (rhinovirus type 2, 9, or 14, respiratory syncytial virus, or coronavirus type 229E), and an additional 26 were given saline nasal drops. The subjects were then quarantined and monitored for the development of evidence of infection and symptoms. Clinical colds were defined as clinical symptoms in the presence of an infection verified by the isolation of virus or by an increase in the virus-specific antibody titer. Results. The rates of both respiratory infection (P < 0.005) and clinical colds (P < 0.02) increased in a dose-response manner with increases in the degree of psychological stress. Infection rates ranged from approximately 74 percent to approximately 90 percent, according to levels of psychological stress, and the incidence of clinical colds ranged from approximately 27 percent to 47 percent. These effects were not altered when we controlled for age, sex, education, allergic status, weight, the season, the number of subjects housed together, the infectious status of subjects sharing the same housing, and virus-specific antibody status at base line (before challenge). Moreover, the associations observed were similar for all five challenge viruses. Several potential stress-illness mediators, including smoking, alcohol consumption, exercise, diet, quality of sleep, white-cell counts, and total immunoglobulin levels, did not explain the association between stress and illness. Similarly, controls for personality variables (self-esteem, personal control, and introversion-extraversion) failed to alter our findings. Conclusions. Psychological stress was associated in a dose-response manner with an increased risk of acute infectious respiratory illness, and this risk was attributable to increased rates of infection rather than to an increased frequency of symptoms after infection. 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Here we identify a metallopeptidase, angiotensin-converting enzyme 2 (ACE2)(3,4), isolated from SARS coronavirus (SARS-CoV)permissive Vero E6 cells, that efficiently binds the S1 domain of the SARS-CoV S protein. We found that a soluble form of ACE2, but not of the related enzyme ACE1, blocked association of the S1 domain with Vero E6 cells. 293T cells transfected with ACE2, but not those transfected with human immunodeficiency virus-1 receptors, formed multinucleated syncytia with cells expressing S protein. Furthermore, SARS-CoV replicated efficiently on ACE2-transfected but not mock-transfected 293T cells. Finally, anti-ACE2 but not anti-ACE1 antibody blocked viral replication on Vero E6 cells. Together our data indicate that ACE2 is a functional receptor for SARS-CoV. 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SCoV-like viruses were isolated from Himalayan palm civets found in a live-animal market in Guangdong, China. Evidence of virus infection was also detected in other animals ( including a raccoon dog, Nyctereutes procyonoides) and in humans working at the same market. All the animal isolates retain a 29-nucleotide sequence that is not found in most human isolates. The detection of SCoV-like viruses in small, live wild mammals in a retail market indicates a route of interspecies transmission, although the natural reservoir is not known. Univ Hong Kong, Dept Microbiol, Queen Mary Hosp, Hong Kong, Hong Kong, Peoples R China; Ctr Dis Control & Prevent, Shenzhen, Guangdong Prov, Peoples R China; Univ Hong Kong, Dept Pathol, Queen Mary Hosp, Hong Kong, Hong Kong, Peoples R China; Dept Hlth, Govt Virus Unit, Hong Kong, Hong Kong, Peoples R China Guan, Y (reprint author), Univ Hong Kong, Dept Microbiol, Queen Mary Hosp, Univ Pathol Bldg, Hong Kong, Hong Kong, Peoples R China. Poon, Leo/C-4382-2009; Yuen, Kwok Yung/C-4465-2009 Poon, Leo/0000-0002-9101-7953; Fouchier RAM, 2003, NATURE, V423, P240, DOI 10.1038/423240a; HOLMES KR, UNPUB; KIMURA M, 1980, J MOL EVOL, V16, P111, DOI 10.1007/BF01731581; Ksiazek TG, 2003, NEW ENGL J MED, V348, P1953, DOI 10.1056/NEJMoa030781; Kumar S, 2001, BIOINFORMATICS, V17, P1244, DOI 10.1093/bioinformatics/17.12.1244; Marra MA, 2003, SCIENCE, V300, P1399, DOI 10.1126/science.1085953; Peiris JSM, 2003, LANCET, V361, P1319, DOI 10.1016/S0140-6736(03)13077-2; ZHONG NS, IN PRESS LANCET 8 904 1004 43 204 AMER ASSOC ADVANCEMENT SCIENCE WASHINGTON 1200 NEW YORK AVE, NW, WASHINGTON, DC 20005 USA 0036-8075 SCIENCE Science OCT 10 2003 302 5643 276 278 10.1126/science.1087139 3 Multidisciplinary Sciences Science & Technology - Other Topics 730HT WOS:000185825900039 12958366 Bronze 2020-04-01 J Li, WD; Shi, ZL; Yu, M; Ren, WZ; Smith, C; Epstein, JH; Wang, HZ; Crameri, G; Hu, ZH; Zhang, HJ; Zhang, JH; McEachern, J; Field, H; Daszak, P; Eaton, BT; Zhang, SY; Wang, LF Li, WD; Shi, ZL; Yu, M; Ren, WZ; Smith, C; Epstein, JH; Wang, HZ; Crameri, G; Hu, ZH; Zhang, HJ; Zhang, JH; McEachern, J; Field, H; Daszak, P; Eaton, BT; Zhang, SY; Wang, LF Bats are natural reservoirs of SARS-like coronaviruses SCIENCE English Article ACUTE RESPIRATORY SYNDROME; NIPAH VIRUS; ANTIBODIES; IDENTIFICATION; BANGLADESH; EVOLUTION; PROTEIN; CIVETS; CHINA; COV Severe acute respiratory syndrome (SARS) emerged in 2002 to 2003 in southern China. The origin of its etiological agent, the SARS coronavirus (SARS-CoV), remains elusive. Here we report that species of bats are a natural host of coronaviruses closely related to those responsible for the SARS, outbreak. These viruses, termed SARS-like coronaviruses (SL-CoVs), display greater genetic variation than SARS-CoV isolated from humans or from civets. The human and civet isolates of SARS-CoV nestle phylogenetically within the spectrum of SL-CoVs, indicating that the virus responsible for the SARS outbreak Was a member of this coronavirus group. CAS, Wuhan Inst Virol, State Key Lab Virol, Wuhan, Peoples R China; Chinese Acad Sci, Inst Zool, Beijing, Peoples R China; CSIRO Livestock Ind, Australian Anim Hlth Lab, Geelong, Vic, Australia; Dept Primary Ind & Fisheries, Moorooka, Qld, Australia; Consortium Conservat Med, New York, NY USA; Guangzhou Inst Biomed & Hlth, Guangzhou, Peoples R China Shi, ZL (reprint author), CAS, Wuhan Inst Virol, State Key Lab Virol, Wuhan, Peoples R China. zlshi@wh.iov.cn; zhangsy@ioz.ac.cn; linfa.wang@csiro.au Barr, Jennifer/H-9254-2013; daszak, peter/U-4588-2017; Ren, Wuze/D-2926-2011; Shi, Zhengli/A-1013-2013; Crameri, Gary/H-8441-2013; Zhang, Shuyi/B-5117-2011 daszak, peter/0000-0002-2046-5695; Shi, Zhengli/0000-0001-8089-163X; Hu, Zhihong/0000-0002-1560-0928; Barr, Jennifer/0000-0001-5266-9142 FIC NIH HHSUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USANIH Fogarty International Center (FIC) [R01-TW05869] AbuBakar S, 2004, EMERG INFECT DIS, V10, P2228, DOI 10.3201/eid1012.040452; Brian DA, 2005, CURR TOP MICROBIOL, V287, P1, DOI 10.1007/3-540-26765-4_1; Chua KB, 2000, SCIENCE, V288, P1432, DOI 10.1126/science.288.5470.1432; Fenton M. 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Methods We followed up 75 patients for 3 weeks managed with a standard treatment protocol of ribavirin and corticosteroids, and assessed the, pattern of clinical disease, viral load, risk factors for poor clinical outcome, and the usefulness of virological diagnostic methods. Findings Fever and pneumonia initially improved but 64 (85%) patients developed recurrent fever after a mean of 8-9 (SD 3.1) days, 55 (73%) had watery diarrhoea after 7.5 (2.3) days, 60 (80%) had radiological worsening after 7.4 (2.2) days, and respiratory symptoms worsened in 34 (45%) after 8.6 (3.0) days. In 34 (45%) patients, improvement of initial pulmonary lesions was associated with appearance of new radiological lesions at other sites. Nine (12%) patients developed spontaneous pneumomediastinum and 15 (20%) developed acute respiratory distress syndrome (ARDS) in week 3. Quantitative reverse-transcriptase (RT) PCR of nasopharyngeal aspirates in 14 patients (four with ARDS) showed peak viral load at day 10, and at day 15 a load lower than at admission. Age and chronic hepatitis B virus infection treated with lamivudine were independent significant risk factors for progression to ARDS (p=0.001). SARS-associated coronavirus in faeces was seen on RT-PCR in 65 (97%) of 67 patients at day 14. The mean time to seroconversion was 20 days. Interpretation The consistent clinical progression, shifting radiological infiltrates, and an inverted V viral-load profile suggest that worsening in week 2 is unrelated to uncontrolled viral replication but may be related to immunopathological damage. Univ Hong Kong, Queen Mary Hosp, Dept Microbiol, Hong Kong, Hong Kong, Peoples R China; Univ Hong Kong, Queen Mary Hosp, Dept Med, Hong Kong, Hong Kong, Peoples R China; United Christian Hosp, Dept Med Intens Care Radiol & Pathol, Hong Kong, Hong Kong, Peoples R China Yuen, KY (reprint author), Univ Hong Kong, Queen Mary Hosp, Dept Microbiol, Pokfulam Rd, Hong Kong, Hong Kong, Peoples R China. Poon, Leo/C-4382-2009; Yuen, Kwok Yung/C-4465-2009; Chan, Chung Sing/C-4577-2009; Peiris, Joseph Sriyal Malik/C-4380-2009 Poon, Leo/0000-0002-9101-7953; Yuen, Kwok-yung/0000-0002-2083-1552; Chu, Chung Ming/0000-0002-9959-1271; Peiris, Joseph Sriyal Malik/0000-0001-8217-5995; Hung, Ivan Fan Ngai/0000-0002-1556-2538 PHS HHSUnited States Public Health Service [A195357] BERNARD GR, 1994, AM J RESP CRIT CARE, V149, P818, DOI 10.1164/ajrccm.149.3.7509706; *CDCP, SARS COR SEQ; *HA, HA GUID SEV AC RESP; Ho W, 2003, LANCET, V361, P1313, DOI 10.1016/S0140-6736(03)13085-1; KNAUS WA, 1985, CRIT CARE MED, V13, P818, DOI 10.1097/00003246-198510000-00009; KSIAZEK TG, NOVEL CORONAVIRUS AS; LEE N, MAJOR OUTBREAK SEVER; Majeski EI, 2003, AM J RESP CELL MOL, V28, P208, DOI 10.1165/rcmb.4891; Ning Q, 1998, J IMMUNOL, V160, P3487; OLLIFF JFC, 1989, CLIN RADIOL, V40, P463, DOI 10.1016/S0009-9260(89)80245-4; Peiris JSM, 2003, LANCET, V361, P1319, DOI 10.1016/S0140-6736(03)13077-2; POON LLM, RAPID DIAGNOSIS CORO; POUTANEN SM, IDENTIFICATION SEVER; *SEV AC RESP SYNDR, MULT COUNTR OUTBR; TSANG KW, CLUSTER CASES SEVERE; TURNER RB, 1986, J INFECT DIS, V154, P443, DOI 10.1093/infdis/154.3.443; TUTOR JD, 1995, PEDIATR PULM, V19, P393, DOI 10.1002/ppul.1950190614; ATYPICAL PNEUMONIA 18 833 916 52 147 LANCET LTD LONDON 84 THEOBALDS RD, LONDON WC1X 8RR, ENGLAND 0140-6736 LANCET Lancet MAY 24 2003 361 9371 1767 1772 10.1016/S0140-6736(03)13412-5 6 Medicine, General & Internal General & Internal Medicine 682CY WOS:000183074800008 12781535 Bronze 2020-04-01 J NICHOLSON, KG; KENT, J; IRELAND, DC NICHOLSON, KG; KENT, J; IRELAND, DC RESPIRATORY VIRUSES AND EXACERBATIONS OF ASTHMA IN ADULTS BRITISH MEDICAL JOURNAL English Article RHINOVIRUS INFECTION; PULMONARY-FUNCTION; WHEEZY BRONCHITIS; CHILDREN; TRACT; PRECIPITANTS; VOLUNTEERS; AIRWAYS Objective-To study the role of respiratory viruses in exacerbations of asthma in adults. Design-Longitudinal study of 138 adults with asthma. Setting-Leicestershire Health Authority. Subjects-48 men and 90 women 19-46 years of age with a mean duration of wheeze of 19.6 years. 75% received regular treatment with bronchodilators; 89% gave a history of eczema, hay fever, allergic rhinitis, nasal polyps, or allergies; 38% had been admitted to hospital with asthma. Main outcome measures-Symptomatic colds and asthma exacerbations; objective exacerbations of asthma with greater-than-or-equal-to 50 l/min reduction in mean peak expiratory flow rate when morning and night time readings on days 1-7 after onset of symptoms were compared with rates during an asymptomatic control period; laboratory confirmed respiratory tract infections. Results-Colds were reported in 80% (223/280) of episodes with symptoms of wheeze, chest tightness, or breathlessness, and 89% (223/250) of colds were associated with asthma symptoms. 24% of 115 laboratory confirmed non-bacterial infections were associated with reductions in mean peak expiratory flow rate greater-than-or-equal-to 50 l/min through days 1-7 and 48% had mean decreases greater-than-or-equal-to 25 l/min. 44% of episodes with mean decreases in flow rate greater-than-or-equal-to 50 l/min were associated with laboratory confirmed infections. Infections with rhinoviruses, coronaviruses OC43 and 229E, influenza B, respiratory syncytial virus, parainfluenza virus, and chlamydia were all associated with objective evidence of an exacerbation of asthma. 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Med. J. OCT 16 1993 307 6910 982 986 10.1136/bmj.307.6910.982 5 Medicine, General & Internal General & Internal Medicine MC441 WOS:A1993MC44100020 8241910 Bronze, Green Published 2020-04-01 J Reyes-Turcu, FE; Ventii, KH; Wilkinson, KD Reyes-Turcu, Francisca E.; Ventii, Karen H.; Wilkinson, Keith D. Regulation and Cellular Roles of Ubiquitin-Specific Deubiquitinating Enzymes ANNUAL REVIEW OF BIOCHEMISTRY Annual Review of Biochemistry English Review; Book Chapter cell cycle; DNA damage; endocytosis; histone; proteasome; signal transduction NF-KAPPA-B; TUMOR-SUPPRESSOR CYLD; RESPIRATORY SYNDROME CORONAVIRUS; POLYGLUTAMINE DISEASE PROTEIN; HISTONE H2B UBIQUITYLATION; FREE POLYUBIQUITIN CHAINS; FANCONI-ANEMIA PATHWAY; C-TERMINAL HYDROLASES; MESSENGER-RNA EXPORT; PAPAIN-LIKE PROTEASE Deubiquitinating enzymes (DUBs) are proteases that process ubiquitin or ubiquitin-like gene products, reverse the modification of proteins by a single ubiquitin(-like) protein, and remodel polyubiquitin(-like) chains on target proteins. The human genome encodes nearly 100 DUBs with specificity for ubiquitin in five gene families. Most DUB activity is cryptic, and conformational rearrangements often occur during the binding of ubiquitin and/or scaffold proteins. DUBs with specificity for ubiquitin contain insertions and extensions modulating DUB substrate specificity, protein-protein interactions, and Cellular localization. Binding partners and multiprotein complexes with which DUBs associate Modulate DUB activity and substrate specificity. Quantitative studies of activity and protein-protein interactions, together with genetic studies and the advent of RNAi, have led to new insights into the function of yeast and human DUBs. This review discusses ubiquitin-specific DUBs, some of the generalizations emerging from recent studies of the regulation of DUB activity, and their roles in various cellular processes. 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Fourteen putative open reading frames were identified, 12 of which were predicted to be expressed from a nested set of eight subgenomic mRNAs. The synthesis of these mRNAs in SARS-CoV-infected cells was confirmed experimentally. The 4382- and 7073 amino acid residue SARS-CoV replicase poly-proteins are predicted to be cleaved into 16 subunits by two viral proteinases (bringing the total number of SARS-CoV proteins to 28). A phylogenetic analysis of the replicase gene, using a distantly related torovirus as an outgroup, demonstrated that, despite a number of unique features, SARS-CoV is most closely related to group 2 coronaviruses. Distant homologs of cellular RNA processing enzymes were identified in group 2 coronaviruses, with four of them being conserved in SARS-CoV. These newly recognized viral enzymes place the mechanism of coronavirus RNA synthesis in a completely new perspective. 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Mol. Biol. AUG 29 2003 331 5 991 1004 10.1016/S0022-2836(03)00865-9 14 Biochemistry & Molecular Biology Biochemistry & Molecular Biology 716NZ WOS:000185036400004 12927536 Bronze 2020-04-01 J Calisher, CH; Childs, JE; Field, HE; Holmes, KV; Schountz, T Calisher, Charles H.; Childs, James E.; Field, Hume E.; Holmes, Kathryn V.; Schountz, Tony Bats: Important reservoir hosts of emerging viruses CLINICAL MICROBIOLOGY REVIEWS English Review RESPIRATORY SYNDROME CORONAVIRUS; SOUTHWESTERN UNITED-STATES; NIPAH-VIRUS; RABIES VIRUS; FRUIT BATS; EQUINE MORBILLIVIRUS; HUMAN INFECTION; HENDRA-VIRUS; LYSSAVIRUS INFECTION; FATAL ENCEPHALITIS Bats (order Chiroptera, suborders Megachiroptera and Microchiroptera) are abundant, diverse, and geographically widespread. These mammals provide us with resources, but their importance is minimized and many of their populations and species are at risk, even threatened or endangered. Some of their characteristics (food choices, colonial or solitary nature, population structure, ability to fly, seasonal migration and daily movement patterns, torpor and hibernation, life span, roosting behaviors, ability to echolocate, virus susceptibility) make them exquisitely suitable hosts of viruses and other disease agents. Bats of certain species are well recognized as being capable of transmitting rabies virus, but recent observations of outbreaks and epidemics of newly recognized human and livestock diseases caused by viruses transmitted by various megachiropteran and microchiropteran bats have drawn attention anew to these remarkable mammals. This paper summarizes information regarding chiropteran characteristics and information regarding 66 viruses that have been isolated from bats. From these summaries, it is clear that we do not know enough about bat biology, that we are doing too little in terms of bat conservation, and that there remain a multitude of questions regarding the role of bats in disease emergence. 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JUL 2006 19 3 531 + 10.1128/CMR.00017-06 16 Microbiology Microbiology 069BL WOS:000239419600004 16847084 Green Published, Bronze 2020-04-01 J Poutanen, SM; Low, DE; Henry, B; Finkelstein, S; Rose, D; Green, K; Tellier, R; Draker, R; Adachi, D; Ayers, M; Chan, AK; Skowronski, DM; Salit, I; Simor, AE; Slutsky, AS; Doyle, PW; Krajden, M; Petric, M; Brunham, RC; McGeer, AJ Poutanen, SM; Low, DE; Henry, B; Finkelstein, S; Rose, D; Green, K; Tellier, R; Draker, R; Adachi, D; Ayers, M; Chan, AK; Skowronski, DM; Salit, I; Simor, AE; Slutsky, AS; Doyle, PW; Krajden, M; Petric, M; Brunham, RC; McGeer, AJ Natl Microbiology Lab Canada; Canadian Severe Acute Respiratory Identification of severe acute respiratory syndrome in Canada NEW ENGLAND JOURNAL OF MEDICINE English Article HUMAN METAPNEUMOVIRUS; MECHANICAL VENTILATION; CORONAVIRUS; INFECTIONS; RIBAVIRIN; CHILDREN; TRIAL BACKGROUND Severe acute respiratory syndrome (SARS) is a condition of unknown cause that has recently been recognized in patients in Asia, North America, and Europe. This report summarizes the initial epidemiologic findings, clinical description, and diagnostic findings that followed the identification of SARS in Canada. METHODS SARS was first identified in Canada in early March 2003. We collected epidemiologic, clinical, and diagnostic data from each of the first 10 cases prospectively as they were identified. Specimens from all cases were sent to local, provincial, national, and international laboratories for studies to identify an etiologic agent. RESULTS The patients ranged from 24 to 78 years old; 60 percent were men. Transmission occurred only after close contact. The most common presenting symptoms were fever (in 100 percent of cases) and malaise (in 70 percent), followed by nonproductive cough (in 100 percent) and dyspnea (in 80 percent) associated with infiltrates on chest radiography (in 100 percent). Lymphopenia (in 89 percent of those for whom data were available), elevated lactate dehydrogenase levels (in 80 percent), elevated aspartate aminotransferase levels (in 78 percent), and elevated creatinine kinase levels (in 56 percent) were common. Empirical therapy most commonly included antibiotics, oseltamivir, and intravenous ribavirin. Mechanical ventilation was required in five patients. Three patients died, and five have had clinical improvement. The results of laboratory investigations were negative or not clinically significant except for the amplification of human metapneumovirus from respiratory specimens from five of nine patients and the isolation and amplification of a novel coronavirus from five of nine patients. In four cases both pathogens were isolated. CONCLUSIONS SARS is a condition associated with substantial morbidity and mortality. It appears to be of viral origin, with patterns suggesting droplet or contact transmission. The role of human metapneumovirus, a novel coronavirus, or both requires further investigation. Toronto Med Labs, Toronto, ON M5G 1X5, Canada; Mt Sinai Hosp, Dept Microbiol, Toronto, ON M5G 1X5, Canada; Univ Toronto, Dept Lab Med & Pathobiol, Toronto, ON, Canada; Univ Toronto, Dept Med, Div Infect Dis, Toronto, ON, Canada; Univ Toronto, Interdept Div Crit Care, Toronto, ON, Canada; City Toronto Publ Hlth Dept, Toronto, ON, Canada; Scarborough Gen Hosp, Toronto, ON, Canada; Hosp Sick Children, Toronto, ON M5G 1X8, Canada; British Columbia Ctr Dis Control, Epidemiol Serv, Vancouver, BC, Canada; British Columbia Ctr Dis Control, Lab Serv, Vancouver, BC, Canada; Univ Hlth Network, Toronto, ON, Canada; Sunnybrook & Womens Coll, Hlth Sci Ctr, Toronto, ON, Canada; St Michaels Hosp, Toronto, ON M5B 1W8, Canada; Vancouver Hosp & Hlth Sci Ctr, Dept Pathol & Lab Med, Vancouver, BC V5Z 1M9, Canada; Univ British Columbia, Ctr Dis Control, Vancouver, BC V5Z 1M9, Canada McGeer, AJ (reprint author), Toronto Med Labs, 600 Univ Ave,Rm 1460, Toronto, ON M5G 1X5, Canada. mcgeer, allison/H-7747-2014; McGeer, Allison/AAB-6885-2020; Low, Donald/B-1726-2012; Poutanen, Susan M/F-9640-2012; Poutanen, Susan M./N-8066-2019; Slutsky, Arthur S/A-6013-2008; Slutsky, Arthur/M-3325-2019 mcgeer, allison/0000-0001-5647-6137; McGeer, Allison/0000-0001-5647-6137; Poutanen, Susan M/0000-0003-4747-2550; Poutanen, Susan M./0000-0003-4747-2550; Slutsky, Arthur S/0000-0002-6063-3876; BERNARD GR, 1994, AM J RESP CRIT CARE, V149, P818, DOI 10.1164/ajrccm.149.3.7509706; Boivin G, 2002, J INFECT DIS, V186, P1330, DOI 10.1086/344319; Borio L, 2002, JAMA-J AM MED ASSOC, V287, P2391, DOI 10.1001/jama.287.18.2391; Brower RG, 2000, NEW ENGL J MED, V342, P1301, DOI 10.1056/nejm200005043421801; Crotty S, 2001, NAT MED, V7, P255; Falsey AR, 1997, J AM GERIATR SOC, V45, P706, DOI 10.1111/j.1532-5415.1997.tb01474.x; Farr BM, 2000, RESP MED, V94, P954, DOI 10.1053/rmed.2000.0865; Greensill J, 2003, EMERG INFECT DIS, V9, P372, DOI 10.3201/eid0903.020289; Heymann D L, 2001, Lancet Infect Dis, V1, P345, DOI 10.1016/S1473-3099(01)00148-7; Imai Y, 2003, JAMA-J AM MED ASSOC, V289, P2104, DOI 10.1001/jama.289.16.2104; Nissen MD, 2002, MED J AUSTRALIA, V176, P188, DOI 10.5694/j.1326-5377.2002.tb04354.x; Peret TCT, 2002, J INFECT DIS, V185, P1660, DOI 10.1086/340518; SIDWELL RW, 1987, ANTIMICROB AGENTS CH, V31, P1130, DOI 10.1128/AAC.31.7.1130; Slutsky AS, 1998, AM J RESP CRIT CARE, V157, P1721, DOI 10.1164/ajrccm.157.6.9709092; SMITH DW, 1991, NEW ENGL J MED, V325, P24, DOI 10.1056/NEJM199107043250105; Stockton J, 2002, EMERG INFECT DIS, V8, P897, DOI 10.3201/eid0809.020084; TRUYEN U, 1995, VET MICROBIOL, V43, P103, DOI 10.1016/0378-1135(95)92531-F; Vabret A, 1998, PRESSE MED, V27, P1813; van den Hoogen BG, 2001, NAT MED, V7, P719, DOI 10.1038/89098; Ware LB, 2000, NEW ENGL J MED, V342, P1334, DOI 10.1056/NEJM200005043421806; WEISS RC, 1989, VET MICROBIOL, V20, P255, DOI 10.1016/0378-1135(89)90049-7; 2003, WKLY EPIDEMIOL REC, V78, P81; 2003, MMWR MORB MORTAL WKL, V52, P241 23 658 776 11 34 MASSACHUSETTS MEDICAL SOC/NEJM WALTHAM WALTHAM WOODS CENTER, 860 WINTER ST,, WALTHAM, MA 02451-1413 USA 0028-4793 NEW ENGL J MED N. Engl. J. Med. MAY 15 2003 348 20 1995 2005 10.1056/NEJMoa030634 11 Medicine, General & Internal General & Internal Medicine 677TJ WOS:000182823400008 12671061 Bronze, Green Published 2020-04-01 J Lau, SKP; Woo, PCY; Li, KSM; Huang, Y; Tsoi, HW; Wong, BHL; Wong, SSY; Leung, SY; Chan, KH; Yuen, KY Lau, SKP; Woo, PCY; Li, KSM; Huang, Y; Tsoi, HW; Wong, BHL; Wong, SSY; Leung, SY; Chan, KH; Yuen, KY Severe acute respiratory syndrome coronavirus-like virus in Chinese horseshoe bats PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA English Article SARS-CORONAVIRUS; PROTEIN FAMILIES; GENOME SEQUENCE; IDENTIFICATION; RECEPTOR Although the finding of severe acute respiratory syndrome coronavirus (SARS-CoV) in caged palm civets from live animal markets in China has provided evidence for interspecies transmission in the genesis of the SARS epidemic, subsequent studies suggested that the civet may have served only as an amplification host for SARS-CoV. In a surveillance study for CoV in noncaged animals from the wild areas of the Hong Kong Special Administration Region, we identified a CoV closely related to SARS-CoV (bat-SARS-CoV) from 23 (39%) of 59 anal swabs of wild Chinese horseshoe bats (Rhinolophus sinicus) by using RT-PCR. Sequencing and analysis of three bat-SARS-CoV genomes from samples collected at different dates showed that bat-SARS-CoV is closely related to SARS-CoV from humans and civets. Phylogenetic analysis showed that bat-SARS-CoV formed a distinct cluster with SARS-CoV as group 2b CoV, distantly related to known group 2 CoV. Most differences between the bat-SARS-CoV and SARS-CoV genomes were observed in the spike genes, ORF 3 and ORF 8, which are the regions where most variations also were observed between human and civet SARS-CoV genomes. In addition, the presence of a 29-bp insertion in ORF 8 of bat-SARS-CoV genome, not in most human SARS-CoV genomes, suggests that it has a common ancestor with civet SARS-CoV. Antibody against recombinant bat-SARSCoV nucleocapsid protein was detected in 84% of Chinese horseshoe bats by using an enzyme immunoassay. Neutralizing antibody to human SARS-CoV also was detected in bats with lower viral loads. Precautions should be exercised in the handling of these animals. 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SEP 27 2005 102 39 14040 14045 10.1073/pnas.0506735102 6 Multidisciplinary Sciences Science & Technology - Other Topics 969KB WOS:000232231900059 16169905 Green Published, Bronze 2020-04-01 J Woo, PCY; Lau, SKP; Chu, CM; Chan, KH; Tsoi, HW; Huang, Y; Wong, BHL; Wong, HL; Poon, RWS; Cai, JJ; Luk, WK; Poon, LLM; Wong, SSY; Guan, Y; Peiris, JSM; Yuen, KY Woo, PCY; Lau, SKP; Chu, CM; Chan, KH; Tsoi, HW; Huang, Y; Wong, BHL; Wong, HL; Poon, RWS; Cai, JJ; Luk, WK; Poon, LLM; Wong, SSY; Guan, Y; Peiris, JSM; Yuen, KY Characterization and complete genome sequence of a novel coronavirus, coronavirus HKU1, from patients with pneumonia JOURNAL OF VIROLOGY English Article ACUTE RESPIRATORY SYNDROME; MOUSE HEPATITIS-VIRUS; INTERNAL RIBOSOME ENTRY; SARS-CORONAVIRUS; HEMAGGLUTININ-ESTERASE; BOVINE CORONAVIRUS; PROTEIN FAMILIES; TRACT INFECTIONS; MESSENGER-RNAS; LEADER RNA Despite extensive laboratory investigations in patients with respiratory tract infections, no microbiological cause can be identified in a significant proportion of patients. In the past 3 years, several novel respiratory viruses, including human metapneumovirus, severe acute respiratory syndrome (SARS) coronavirus (SARSCoV), and human coronavirus NL63, were discovered. Here we report the discovery of another novel coronavirus, coronavirus HKU1 (CoV-HKU1), from a 71-year-old man with pneumonia who had just returned from Shenzhen, China. Quantitative reverse transcription-PCR showed that the amount of CoV-HKU1 RNA was 8.5 to 9.6 X 10(6) copies per ml in his nasopharyngeal aspirates (NPAs) during the first week of the illness and dropped progressively to undetectable levels in subsequent weeks. He developed increasing serum levels of specific antibodies against the recombinant nucleocapsid protein of CoV-HKU1, with immunoglobulin M (IgM) titers of 1:20, 1:40, and 1:80 and IgG titers of <1:1,000, 1:2,000, and 1:8,000 in the first, second and fourth weeks of the illness, respectively. Isolation of the virus by using various cell lines, mixed neuron-glia culture, and intracerebral inoculation of suckling mice was unsuccessful. The complete genome sequence of CoV-HKUI is a 29,926-nucleotide, polyadenylated RNA, with G+C content of 32%, the lowest among all known coronaviruses with available genome sequence. Phylogenetic analysis reveals that CoV-HKU1 is a new group 2 coronavirus. Screening of 400 NPAs, negative for SARS-CoV, from patients with respiratory illness during the SARS period identified the presence of CoV-HKUI RNA in an additional specimen, with a viral load of 1.13 X 10(6) copies per ml, from a 35-year-old woman with pneumonia. Our data support the existence of a novel group 2 coronavirus associated with pneumonia in humans. Univ Hong Kong, Dept Microbiol, Hong Kong, Peoples R China; Univ Hong Kong, State Key Lab Emerging Infect Dis, Hong Kong, Peoples R China; United Christian Hosp, Dept Med, Div Resp Med, Hong Kong, Peoples R China; Tseung Kwan O Hosp, Dept Microbiol, Hong Kong, Hong Kong, Peoples R China Yuen, KY (reprint author), Univ Hong Kong, Dept Microbiol, Univ Pathol Bldg,, Hong Kong, Peoples R China. hkumicro@hkucc.hku.hk Tsoi, Hoi Wah/C-4428-2009; Woo, Patrick/C-4449-2009; Yuen, Kwok Yung/C-4465-2009; Wong, Samson/C-4446-2009; Poon, Leo/C-4382-2009; Lau, Susanna/C-4321-2009; Peiris, Joseph Sriyal Malik/C-4380-2009; Cai, James/C-4928-2008 Poon, Leo/0000-0002-9101-7953; Yuen, Kwok-yung/0000-0002-2083-1552; Chu, Chung Ming/0000-0002-9959-1271; Peiris, Joseph Sriyal Malik/0000-0001-8217-5995; Cai, James/0000-0002-8081-6725 NIAID NIH HHSUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USANIH National Institute of Allergy & Infectious Diseases (NIAID) [N01AI95357] Apweiler R, 2001, NUCLEIC ACIDS RES, V29, P37, DOI 10.1093/nar/29.1.37; Bateman A, 2002, NUCLEIC ACIDS RES, V30, P276, DOI 10.1093/nar/30.1.276; Combet C, 2000, TRENDS BIOCHEM SCI, V25, P147, DOI 10.1016/S0968-0004(99)01540-6; Eickmann M, 2003, SCIENCE, V302, P1504; Fischer F, 1997, J VIROL, V71, P996, DOI 10.1128/JVI.71.2.996-1003.1997; Fouchier RAM, 2004, P NATL ACAD SCI USA, V101, P6212, DOI 10.1073/pnas.0400762101; Gattiker Alexandre, 2002, Appl Bioinformatics, V1, P107; Goebel SJ, 2004, J VIROL, V78, P669, DOI 10.1128/JVI.78.2.669-682.2004; GUAN Y, 2003, CHINA SCIENCE, V302, P276; Herold J, 1999, J BIOL CHEM, V274, P14918, DOI 10.1074/jbc.274.21.14918; HOFMANN K, 1993, BIOL CHEM HOPPESEYLE, V347, P166; Jendrach M, 1999, ARCH VIROL, V144, P921, DOI 10.1007/s007050050556; Kanjanahaluethai A, 2003, J VIROL, V77, P7376, DOI 10.1128/JVI.77.13.7376-7382.2003; Klausegger A, 1999, J VIROL, V73, P3737, DOI 10.1128/JVI.73.5.3737-3743.1999; Krempl C, 1995, Adv Exp Med Biol, V380, P371; LAI MMC, 1984, P NATL ACAD SCI-BIOL, V81, P3626, DOI 10.1073/pnas.81.12.3626; Lai MMC, 1997, ADV VIRUS RES, V48, P1, DOI 10.1016/S0065-3527(08)60286-9; MACFARLANE JT, 1993, LANCET, V341, P511, DOI 10.1016/0140-6736(93)90275-L; MAKINO S, 1986, P NATL ACAD SCI USA, V83, P4204, DOI 10.1073/pnas.83.12.4204; Marra MA, 2003, SCIENCE, V300, P1399, DOI 10.1126/science.1085953; Nielsen H, 1997, PROTEIN ENG, V10, P1, DOI 10.1093/protein/10.1.1; NUSSENZWEIG V, 1985, CELL, V42, P401, DOI 10.1016/0092-8674(85)90093-5; Peiris JSM, 2003, NEW ENGL J MED, V349, P2431, DOI 10.1056/NEJMra032498; Peiris JSM, 2003, LANCET, V361, P1319, DOI 10.1016/S0140-6736(03)13077-2; Peiris JSM, 2003, LANCET, V361, P1767, DOI 10.1016/S0140-6736(03)13412-5; Popova R, 2002, VIROLOGY, V294, P222, DOI 10.1006/viro.2001.1307; RISKI H, 1980, J MED VIROL, V6, P259, DOI 10.1002/jmv.1890060309; Rota PA, 2003, SCIENCE, V300, P1394, DOI 10.1126/science.1085952; Ruiz M, 1999, AM J RESP CRIT CARE, V160, P397, DOI 10.1164/ajrccm.160.2.9808045; SCHWARZ B, 1990, J VIROL, V64, P4784, DOI 10.1128/JVI.64.10.4784-4791.1990; Snijder EJ, 2003, J MOL BIOL, V331, P991, DOI 10.1016/S0022-2836(03)00865-9; Sonnhammer E L, 1998, Proc Int Conf Intell Syst Mol Biol, V6, P175; Suzuki H, 1996, J VIROL, V70, P2632, DOI 10.1128/JVI.70.4.2632-2636.1996; THIEL V, 1994, J GEN VIROL, V75, P3041, DOI 10.1099/0022-1317-75-11-3041; Vabret A, 2003, CLIN INFECT DIS, V36, P985, DOI 10.1086/374222; van den Hoogen BG, 2001, NAT MED, V7, P719, DOI 10.1038/89098; van der Hoek L, 2004, NAT MED, V10, P368, DOI 10.1038/nm1024; VLASAK R, 1988, P NATL ACAD SCI USA, V85, P4526, DOI 10.1073/pnas.85.12.4526; VLASAK R, 1988, J VIROL, V62, P4686, DOI 10.1128/JVI.62.12.4686-4690.1988; WENZEL RP, 1974, AM REV RESPIR DIS, V109, P621; Wessner DR, 1998, J VIROL, V72, P1941, DOI 10.1128/JVI.72.3.1941-1948.1998; Williams GD, 1999, J VIROL, V73, P8349, DOI 10.1128/JVI.73.10.8349-8355.1999; WILLIAMS RK, 1991, P NATL ACAD SCI USA, V88, P5533, DOI 10.1073/pnas.88.13.5533; Woo PCY, 2004, J CLIN MICROBIOL, V42, P2306, DOI 10.1128/JCM.42.5.2306-2309.2004; Woo PCY, 2004, LANCET, V363, P841, DOI 10.1016/S0140-6736(04)15729-2; Woo PCY, 1997, J CLIN MICROBIOL, V35, P1579, DOI 10.1128/JCM.35.6.1579-1581.1997; Yang HJ, 2000, MOL BIOCHEM PARASIT, V111, P213, DOI 10.1016/S0166-6851(00)00298-X; Yeh SH, 2004, P NATL ACAD SCI USA, V101, P2542, DOI 10.1073/pnas.0307904100; Yokomori K, 1995, J NEUROVIROL, V1, P330, DOI 10.3109/13550289509111022; YOKOMORI K, 1991, VIROLOGY, V183, P647, DOI 10.1016/0042-6822(91)90994-M; Zhong NS, 2003, LANCET, V362, P1353, DOI 10.1016/S0140-6736(03)14630-2 51 654 735 20 99 AMER SOC MICROBIOLOGY WASHINGTON 1752 N ST NW, WASHINGTON, DC 20036-2904 USA 0022-538X 1098-5514 J VIROL J. Virol. JAN 2005 79 2 884 895 10.1128/JVI.79.2.884-895.2005 12 Virology Virology 885IG WOS:000226149700024 15613317 Green Published, Bronze 2020-04-01 J Chou, KC Chou, KC Structural bioinformatics and its impact to biomedical science CURRENT MEDICINAL CHEMISTRY English Review bovine somatotropin; antifreeze protein; adhesion proteins; complement control protein; caspase; beta-secretase & zymogen; neuronal kinase; alpha 7 nAChR; ion-channels; GFAT; GABA(A) receptors; SARS PROTEIN SUBCELLULAR LOCATION; BENZODIAZEPINE BINDING-SITE; CORONAVIRUS MAIN PROTEINASE; AMYLOID PRECURSOR PROTEIN; LOW-FREQUENCY VIBRATIONS; NEURONAL CDK5 ACTIVATOR; LOOP-HELIX INTERACTIONS; AMINO-ACID-COMPOSITION; BOVINE GROWTH-HORMONE; GABA-A RECEPTORS During the last two decades, the number of sequence-known proteins has increased rapidly. In contrast, the corresponding increment for structure-known proteins is much slower. The unbalanced Situation has critically limited our ability to understand the molecular mechanism of proteins and conduct structure-based drug design by timely using the updated information of newly found sequences. Therefore, it is highly desired to develop an automated method for fast deriving the 3D (3-dimensional) structure of a protein from its sequence. Under such a circumstance, the structural bioinformatics was emerging naturally as the time required. In this review, three main strategies developed in structural bioinformatics, i.e., pure energetic approach, heuristic approach, and homology modeling approach, as well as their underlying principles, are briefly introduced. Meanwhile, a series of demonstrations are presented to show how the Structural bioinformatics has been applied to timely derive the 3D structures of some functionally important proteins, helping to understand their action mechanisms and stimulating the course of drug discovery. Also, the limitation of these approaches and the future challenges of structural bioinformatics are briefly addressed. 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T.; Alabdullatif, Zaki N.; Assad, Maher; Almulhim, Abdulmohsen; Makhdoom, Hatem; Madani, Hossam; Alhakeem, Rafat; Al-Tawfiq, Jaffar A.; Cotten, Matthew; Watson, Simon J.; Kellam, Paul; Zumla, Alimuddin I.; Memish, Ziad A. KSA MERS-CoV Invest Team Hospital Outbreak of Middle East Respiratory Syndrome Coronavirus NEW ENGLAND JOURNAL OF MEDICINE English Article INFECTIONS; SARS Background In September 2012, the World Health Organization reported the first cases of pneumonia caused by the novel Middle East respiratory syndrome coronavirus (MERS-CoV). We describe a cluster of health care-acquired MERS-CoV infections. Methods Medical records were reviewed for clinical and demographic information and determination of potential contacts and exposures. Case patients and contacts were interviewed. The incubation period and serial interval (the time between the successive onset of symptoms in a chain of transmission) were estimated. Viral RNA was sequenced. Results Between April 1 and May 23, 2013, a total of 23 cases of MERS-CoV infection were reported in the eastern province of Saudi Arabia. Symptoms included fever in 20 patients (87%), cough in 20 (87%), shortness of breath in 11 (48%), and gastrointestinal symptoms in 8 (35%); 20 patients (87%) presented with abnormal chest radiographs. As of June 12, a total of 15 patients (65%) had died, 6 (26%) had recovered, and 2 (9%) remained hospitalized. The median incubation period was 5.2 days (95% confidence interval [CI], 1.9 to 14.7), and the serial interval was 7.6 days (95% CI, 2.5 to 23.1). A total of 21 of the 23 cases were acquired by person-to-person transmission in hemodialysis units, intensive care units, or in-patient units in three different health care facilities. Sequencing data from four isolates revealed a single monophyletic clade. Among 217 household contacts and more than 200 health care worker contacts whom we identified, MERS-CoV infection developed in 5 family members (3 with laboratory-confirmed cases) and in 2 health care workers (both with laboratory-confirmed cases). Conclusions Person-to-person transmission of MERS-CoV can occur in health care settings and may be associated with considerable morbidity. Surveillance and infection-control measures are critical to a global public health response. [Assiri, Abdullah; Al Rabeeah, Abdullah A.; Alabdullatif, Zaki N.; Assad, Maher; Almulhim, Abdulmohsen; Makhdoom, Hatem; Madani, Hossam; Alhakeem, Rafat; Zumla, Alimuddin I.; Memish, Ziad A.] Minist Hlth, Global Ctr Mass Gatherings Med, Riyadh 11176, Saudi Arabia; [Memish, Ziad A.] Al Faisal Univ, Riyadh, Saudi Arabia; [Al-Tawfiq, Jaffar A.] Saudi Aramco Med Serv Org, Dhahran, Saudi Arabia; [McGeer, Allison] Univ Toronto, Mt Sinai Hosp, Toronto, ON M5G 1X5, Canada; [McGeer, Allison] Univ Toronto, Dept Lab Med & Pathobiol, Toronto, ON, Canada; [Perl, Trish M.] Johns Hopkins Univ, Dept Med, Baltimore, MD USA; [Perl, Trish M.] Johns Hopkins Univ, Dept Pathol, Baltimore, MD USA; [Perl, Trish M.; Cummings, Derek A. 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We report the clinical and microbiological features of patients infected with influenza A H7N9 virus and compare genomic features of the human virus with those of the virus in market poultry in Zhejiang, China. Methods Between March 7 and April 8, 2013, we included hospital inpatients if they had new-onset respiratory symptoms, unexplained radiographic infiltrate, and laboratory-confirmed H7N9 virus infection. We recorded histories and results of haematological, biochemical, radiological, and microbiological investigations. We took throat and sputum samples, used RT-PCR to detect M, H7, and N9 genes, and cultured samples in Madin-Darby canine kidney cells. We tested for co-infections and monitored serum concentrations of six cytokines and chemokines. We collected cloacal swabs from 86 birds from epidemiologically linked wet markets and inoculated embryonated chicken eggs with the samples. We identified and subtyped isolates by RT-PCR sequencing. RNA extraction, complementary DNA synthesis, and PCR sequencing were done for one human and one chicken isolate. We characterised and phylogenetically analysed the eight gene segments of the viruses in the patient's and the chicken's isolates, and constructed phylogenetic trees of H, N, PB2, and NS genes. Findings We identified four patients (mean age 56 years), all of whom had contact with poultry 3-8 days before disease onset. They presented with fever and rapidly progressive pneumonia that did not respond to antibiotics. Patients were leucopenic and lymphopenic, and had impaired liver or renal function, substantially increased serum cytokine or chemokine concentrations, and disseminated intravascular coagulation with disease progression. Two patients died. Sputum specimens were more likely to test positive for the H7N9 virus than were samples from throat swabs. The viral isolate from the patient was closely similar to that from an epidemiologically linked market chicken. All viral gene segments were of avian origin. The H7 of the isolated viruses was closest to that of the H7N3 virus from domestic ducks in Zhejiang, whereas the N9 was closest to that of the wild bird H7N9 virus in South Korea. We noted Gln226Leu and Gly186Val substitutions in human virus H7 (associated with increased affinity for alpha-2,6-linked sialic acid receptors) and the PB2 Asp701Asn mutation (associated with mammalian adaptation). Ser31Asn mutation, which is associated with adamantane resistance, was noted in viral M2. Interpretation Cross species poultry-to-person transmission of this new reassortant H7N9 virus is associated with severe pneumonia and multiorgan dysfunction in human beings. Monitoring of the viral evolution and further study of disease pathogenesis will improve disease management, epidemic control, and pandemic preparedness. [Chen, Yu; Liang, Weifeng; Yang, Shigui; Wu, Nanping; Gao, Hainv; Sheng, Jifang; Yao, Hangping; Wo, Jianer; Fang, Qiang; Cui, Dawei; Zhang, Yuntao; Wu, Haibo; Zheng, Shufa; Diao, Hongyan; Li, Lanjuan] Zhejiang Univ, Coll Med, Affiliated Hosp 1, State Key Lab Diag & Treatment Infect Dis, Hangzhou 310003, Zhejiang, Peoples R China; [Chen, Yu; Liang, Weifeng; Yang, Shigui; Wu, Nanping; Gao, Hainv; Sheng, Jifang; Yao, Hangping; Wo, Jianer; Wu, Haibo; Diao, Hongyan; Chen, Honglin; Li, Lanjuan; Yuen, Kwok-Yung] Collaborat Innovat Ctr Diag & Treatment Infect Di, Hangzhou, Zhejiang, Peoples R China; [Li, Yongcheng] Xiaoshan Peoples Hosp, Hangzhou, Zhejiang, Peoples R China; [Yao, Xing] Huzhou Cent Hosp, Huzhou, Peoples R China; [Xia, Shichang; Zhang, Yanjun] Zhejiang Prov Ctr Dis Control & Prevent, Hangzhou, Zhejiang, Peoples R China; [Chan, Kwok-Hung; Tsoi, Hoi-Wah; Teng, Jade Lee-Lee; Song, Wenjun; Wang, Pui; Lau, Siu-Ying; Zheng, Min; Chan, Jasper Fuk-Woo; To, Kelvin Kai-Wang; Chen, Honglin; Yuen, Kwok-Yung] Univ Hong Kong, Dept Microbiol, State Key Lab Emerging Infect Dis, Hong Kong, Hong Kong, Peoples R China Li, LJ (reprint author), Zhejiang Univ, Coll Med, Affiliated Hosp 1, State Key Lab Diag & Treatment Infect Dis, 79 Qingchun Rd, Hangzhou 310003, Zhejiang, Peoples R China. ljli@zju.edu.cn Chan, Jasper F. W./D-8007-2013; Chen, Yu/Y-3292-2019; Chen, Honglin/C-4224-2009 Chan, Jasper F. W./0000-0001-6336-6657; Chen, Honglin/0000-0001-5108-8338; To, Kelvin/0000-0002-1921-5824; Yuen, Kwok-yung/0000-0002-2083-1552; gao, hainv/0000-0003-4590-9181 National Key Program for Infectious Diseases of China Larry Chi-Kin Yung, National Key Program for Infectious Diseases of China. 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Most cells from normal CNS, in contrast, lay within this latter, CD45low population. From previous in situ immunohistochemical studies, the fortuitously isolated CD45low cells were probably resident (ramified) microglia. Using irradiation chimeras, we show that resident microglia respond to inflammation by upregulating CD45, CD4, and MHC class I molecules with a minority of these cells increasing their expression of MHC class II molecules. A 3- to 4-fold increase in the number of microglia isolated from inflamed CNS provided indirect evidence that the cells had proliferated. In normal CNS, a very small population of blood-derived CD45high-expressing cells are present; most MHC class II expression is associated with these few cells and not with the resident microglia. INST ANIM PHYSIOL & GENET RES,DEPT IMMUNOL,CAMBRIDGE RES STN,CAMBRIDGE CB2 4AT,ENGLAND SEDGWICK, JD (reprint author), UNIV WURZBURG,INST VIROL & IMMUNOBIOL,VERSBACHER STR 7,W-8700 WURZBURG,GERMANY. 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Natl. Acad. Sci. U. S. A. AUG 1991 88 16 7438 7442 10.1073/pnas.88.16.7438 5 Multidisciplinary Sciences Science & Technology - Other Topics GB701 WOS:A1991GB70100111 1651506 Bronze, Green Published 2020-04-01 J LAI, MMC LAI, MMC RNA RECOMBINATION IN ANIMAL AND PLANT-VIRUSES MICROBIOLOGICAL REVIEWS English Review MOUTH-DISEASE VIRUS; MOUSE HEPATITIS-VIRUS; INTERTYPIC POLIOVIRUS RECOMBINANTS; DEFECTIVE INTERFERING PARTICLES; VESICULAR STOMATITIS-VIRUS; AVIAN CORONAVIRUS-IBV; TURNIP CRINKLE VIRUS; GENETIC-RECOMBINATION; MURINE CORONAVIRUS; CROSSOVER REGIONS An increasing number of animal and plant viruses have been shown to undergo RNA-RNA recombination, which is defined as the exchange of genetic information between nonsegmented RNAs. Only some of these viruses have been shown to undergo recombination in experimental infection of tissue culture, animals, and plants. However, a survey of viral RNA structure and sequences suggests that many RNA viruses were derived form homologous or nonhomogolous recombination between viruses or between viruses and cellular genes during natural viral evolution. The high frequency and widespread nature of RNA recombination indicate that this phenomenon plays a more significant role in the biology of RNA viruses than was previously recognized. Three types of RNA recombination are defined: homologous recombination; aberrant homologous recombination, which results in sequence duplication, insertion, or deletion during recombination; and nonhomologous (illegitimate) recombination, which does not involve sequence homology. RNA recombination has been shown to occur by a copy choice mechanism in some viruses. A model for this recombination mechanism is presented. 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Rev. MAR 1992 56 1 61 79 10.1128/MMBR.56.1.61-79.1992 19 Microbiology Microbiology HH375 WOS:A1992HH37500004 1579113 Bronze 2020-04-01 J Gaynor, AM; Nissen, MD; Whiley, DM; Mackay, IM; Lambert, SB; Wu, G; Brennan, DC; Storch, GA; Sloots, TP; Wang, D Gaynor, Anne M.; Nissen, Michael D.; Whiley, David M.; Mackay, Ian M.; Lambert, Stephen B.; Wu, Guang; Brennan, Daniel C.; Storch, Gregory A.; Sloots, Theo P.; Wang, David Identification of a novel polyomavirus from patients with acute respiratory tract infections PLOS PATHOGENS English Article POLYMERASE-CHAIN-REACTION; BK-VIRUS; HUMAN CORONAVIRUS; CHILDREN; SV40; DISEASE; DNA; SIMIAN-VIRUS-40; ASSOCIATION; ANTIBODIES We report the identification of a novel polyomavirus present in respiratory secretions from human patients with symptoms of acute respiratory tract infection. The virus was initially detected in a nasopharyngeal aspirate from a 3-year-old child from Australia diagnosed with pneumonia. A random library was generated from nucleic acids extracted from the nasopharyngeal aspirate and analyzed by high throughput DNA sequencing. Multiple DNA fragments were cloned that possessed limited homology to known polyomaviruses. We subsequently sequenced the entire virus genome of 5,229 bp, henceforth referred to as WU virus, and found it to have genomic features characteristic of the family Polyomaviridae. The genome was predicted to encode small T antigen, large T antigen, and three capsid proteins: VP1, VP2, and VP3. Phylogenetic analysis clearly revealed that the WU virus was divergent from all known polyomaviruses. Screening of 2,135 patients with acute respiratory tract infections in Brisbane, Queensland, Australia, and St. Louis, Missouri, United States, using WU virus-specific PCR primers resulted in the detection of 43 additional specimens that contained WU virus. The presence of multiple instances of the virus in two continents suggests that this virus is geographically widespread in the human population and raises the possibility that the WU virus may be a human pathogen. Washington Univ, Sch Med, Dept Mol Microbiol, St Louis, MO 63110 USA; Washington Univ, Sch Med, Dept Internal Med, St Louis, MO 63110 USA; Washington Univ, Sch Med, Dept Pediat, St Louis, MO 63110 USA; Washington Univ, Sch Med, Dept Pathol & Immunol, St Louis, MO 63110 USA; Royal Childrens Hosp, Queensland Paediat Infect Dis Lab, Sir Albert Sakzewski Virus Res Ctr, Brisbane, Qld, Australia Wang, D (reprint author), Washington Univ, Sch Med, Dept Mol Microbiol, St Louis, MO 63110 USA. davewang@borcim.wustl.edu Nissen, Michael D/M-6823-2013; Lambert, Stephen/N-7819-2019; Whiley, David/E-8955-2011; Lambert, Stephen B/B-8348-2008; Sloots, Theo P/E-6118-2011; Mackay, Ian M./B-2537-2010 Nissen, Michael D/0000-0003-1686-3313; Lambert, Stephen/0000-0002-2709-193X; Whiley, David/0000-0001-5969-3161; Lambert, Stephen B/0000-0002-2709-193X; Mackay, Ian M./0000-0003-3598-2350 NIAID NIH HHSUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USANIH National Institute of Allergy & Infectious Diseases (NIAID) [U54 AI057160]; NIDDK NIH HHSUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USANIH National Institute of Diabetes & Digestive & Kidney Diseases (NIDDK) [K24 DK002886, K24 DK02886] Agostini HT, 1997, ARCH VIROL, V142, P637, DOI 10.1007/s007050050108; Allander T, 2005, P NATL ACAD SCI USA, V102, P12891, DOI 10.1073/pnas.0504666102; Allander T, 2007, J VIROL, V81, P4130, DOI 10.1128/JVI.00028-07; ALTSCHUL SF, 1997, NUCLEIC ACIDS RES, V25, P3402; Arden KE, 2006, J MED VIROL, V78, P1232, DOI 10.1002/jmv.20689; ARTHUR RR, 1986, NEW ENGL J MED, V315, P230, DOI 10.1056/NEJM198607243150405; Behzad-Behbahani A, 2004, J CLIN VIROL, V29, P224, DOI 10.1016/S1386-6532(03)00155-0; BIKEL I, 1987, CELL, V48, P321, DOI 10.1016/0092-8674(87)90435-1; Brennan DC, 2005, AM J TRANSPLANT, V5, P582, DOI 10.1111/j.1600-6143.2005.00742.x; Cantalupo P, 2005, J VIROL, V79, P13094, DOI 10.1128/JVI.79.20.13094-13104.2005; Choi EH, 2006, CLIN INFECT DIS, V43, P585, DOI 10.1086/506350; Ewing B, 1998, GENOME RES, V8, P175, DOI 10.1101/gr.8.3.175; GARDNER SD, 1971, LANCET, V1, P1253; GOUDSMIT J, 1982, J MED VIROL, V10, P91, DOI 10.1002/jmv.1890100203; GREENLEE JE, 1981, INFECT IMMUN, V33, P297, DOI 10.1128/IAI.33.1.297-303.1981; Hahn WC, 1999, NATURE, V400, P464; Heikkinen T, 2003, LANCET, V361, P51, DOI 10.1016/S0140-6736(03)12162-9; Jafar S, 1998, J MED VIROL, V54, P276, DOI 10.1002/(SICI)1096-9071(199804)54:4<276::AID-JMV7>3.0.CO;2-1; Ksiazek TG, 2003, NEW ENGL J MED, V348, P1953, DOI 10.1056/NEJMoa030781; Lundstig A, 2005, J GEN VIROL, V86, P1703, DOI 10.1099/vir.0.80783-0; MARKOWITZ RB, 1993, J INFECT DIS, V167, P13, DOI 10.1093/infdis/167.1.13; Minor P, 2003, J MED VIROL, V70, P490, DOI 10.1002/jmv.10422; Mulholland K, 2003, PEDIATR PULM, V36, P469, DOI 10.1002/ppul.10344; PADGETT BL, 1971, LANCET, V1, P1257; PIPAS JM, 1992, J VIROL, V66, P3979, DOI 10.1128/JVI.66.7.3979-3985.1992; Poulin DL, 2006, J CLIN ONCOL, V24, P4356, DOI 10.1200/JCO.2005.03.7101; Shah KV, 2004, J INFECT DIS, V190, P2061, DOI 10.1086/425999; Sloots TP, 2006, J CLIN VIROL, V35, P99, DOI 10.1016/j.jcv.2005.09.008; Stolt A, 2003, J GEN VIROL, V84, P1499, DOI 10.1099/vir.0.18842-0; Sumino KC, 2005, J INFECT DIS, V192, P1052, DOI 10.1086/432728; SUNDSFJORD A, 1994, J CLIN MICROBIOL, V32, P1390, DOI 10.1128/JCM.32.5.1390-1394.1994; van den Hoogen BG, 2001, NAT MED, V7, P719, DOI 10.1038/89098; van der Hoek L, 2004, NAT MED, V10, P368, DOI 10.1038/nm1024; Wang D, 2003, PLOS BIOL, V1, P257, DOI 10.1371/journal.pbio.0000002; Woo PCY, 2005, J VIROL, V79, P884, DOI 10.1128/JVI.79.2.884-895.2005 35 493 531 6 20 PUBLIC LIBRARY SCIENCE SAN FRANCISCO 185 BERRY ST, STE 1300, SAN FRANCISCO, CA 94107 USA 1553-7366 PLOS PATHOG PLoS Pathog. MAY 2007 3 5 595 604 e64 10.1371/journal.ppat.0030064 10 Microbiology; Parasitology; Virology Microbiology; Parasitology; Virology 196VU WOS:000248511100004 17480120 DOAJ Gold, Green Published 2020-04-01 J Kuiken, T; Fouchier, RAM; Schutten, M; Rimmelzwaan, GF; van Amerongen, G; van Riel, D; Laman, JD; de Jong, T; van Doornum, G; Lim, W; Ling, AE; Chan, PKS; Tam, JS; Zambon, MC; Gopal, R; Drosten, C; van der Werf, S; Escriou, N; Manuguerra, JC; Stohr, K; Peiris, JSM; Osterhaus, ADME Kuiken, T; Fouchier, RAM; Schutten, M; Rimmelzwaan, GF; van Amerongen, G; van Riel, D; Laman, JD; de Jong, T; van Doornum, G; Lim, W; Ling, AE; Chan, PKS; Tam, JS; Zambon, MC; Gopal, R; Drosten, C; van der Werf, S; Escriou, N; Manuguerra, JC; Stohr, K; Peiris, JSM; Osterhaus, ADME Newly discovered coronavirus as the primary cause of severe acute respiratory syndrome LANCET English Article POLYMERASE-CHAIN-REACTION; HONG-KONG; EXPERIMENTAL-INFECTION; IDENTIFICATION; PATHOGENICITY; CHILDREN; OUTBREAK; DISEASE; GENE; PCR Background The worldwide outbreak. of severe acute respiratory syndrome (SARS) is associated with a newly discovered coronavirus, SARS-associated coronavirus (SARS-CoV). We did clinical and experimental studies to assess the role of this virus in the cause of SARS. Methods We tested clinical and postmortem samples from 436 SARS patients in six countries for infection with SARS-CoV, human metapneumovirus, and other respiratory pathogens. We infected four cynomolgus macaques (Macaca fascicularis) with SARS-CoV in an attempt to replicate SARS and did necropsies on day 6 after infection. Findings SARS-CoV infection was diagnosed in 329 (75%) of 436 patients fitting the case definition of SARS; human metapneumovirus was diagnosed in 41 (12%) of 335, and other respiratory pathogens were diagnosed only sporadically. SARS-CoV was, therefore, the most likely causal agent of SARS. The four SARS-CoV-infected macaques excreted SARS-CoV from nose, mouth, and pharynx from 2 days after infection. Three of four macaques developed diffuse alveolar damage, similar to that in SARS patients, and characterised by epithelial necrosis, serosanguineous exudate, formation of hyaline membranes, type 2 pneumocyte hyperplasia, and the presence of syncytia. SARS-CoV was detected in pneumonic areas by virus isolation and RT-PCR, and was localised to alveolar epithelial cells and syncytia by immunohistochemistry and transmission electron microscopy. Interpretation Replication in SARS-CoV-infected macaques of pneumonia similar to that in human beings with SARS, combined with the high prevalence of SARS-CoV infection in SARS patients, fulfill the criteria required to prove that SARS-CoV is the primary cause of SARS. Erasmus Med Ctr, Dept Virol, NL-3000 DR Rotterdam, Netherlands; Erasmus Med Ctr, Dept Immunol, NL-3000 DR Rotterdam, Netherlands; Erasmus Med Ctr, Dept Pathol, NL-3000 DR Rotterdam, Netherlands; Publ Hlth Lab Ctr, Govt Virus Unit, Kowloon, Hong Kong, Peoples R China; Singapore Gen Hosp, Dept Pathol, Singapore 0316, Singapore; Chinese Univ Hong Kong, Prince Wales Hosp, Dept Microbiol, Hong Kong, Hong Kong, Peoples R China; Hlth Protect Agcy, Enter Resp & Neurol Virus Lab, London, England; Bernhard Nocht Inst Trop Med, Dept Virol, Hamburg, Germany; Inst Pasteur, Unite Genet Mol Virus Resp, Paris, France; WHO, SARS Aetiol Study Grp, CH-1211 Geneva, Switzerland; Univ Hong Kong, Queen Mary Hosp, Dept Microbiol & Med, Hong Kong, Hong Kong, Peoples R China Kuiken, T (reprint author), Erasmus Med Ctr, Dept Virol, POB 1738, NL-3000 DR Rotterdam, Netherlands. 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Comparative sequence analysis of 3'-terminal structural genes of the single-stranded RNA viral genome revealed the presence of two genotypic classes of PRRSV, represented by the prototype North American and European strains, VR-2332 and Lelystad virus (LV), respectively. To better understand the evolution and pathogenicity of PRRSV, we obtained the 12,066-base 5'-terminal nucleotide sequence of VR-2332, encoding the viral replication activities, and compared it to those of LV and other arteriviruses. VR-2332 and LV differ markedly in the 5' leader and sections of the open reading frame (ORF) 1a region. The ORF 1b sequence was nearly colinear but varied in similarity of proteins encoded in identified regions. Furthermore, molecular and biochemical analysis of subgenomic mRNA (sgmRNA) processing revealed extensive variation in the number of sgmRNAs which may be generated during infection and in the lengths of noncoding sequence between leader-body junctions and the translation-initiating codon AUG. In addition, VR-2332 and LV select different leader-body junction sites from a pool of similar candidate sites to produce sgmRNA 7, encoding the viral nucleocapsid protein. The presence of substantial variations across the entire genome and in sgmRNA processing indicates that PRRSV has evolved independently on separate continents. The near-simultaneous global emergence of a new swine disease caused by divergently evolved viruses suggests that changes in swine husbandry and management may have contributed to the emergence of PRRS. 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Virol. 1978 58 3 243 247 10.1007/BF01317606 5 Virology Virology FW408 WOS:A1978FW40800007 83132 Bronze 2020-04-01 J Ernst, B; Magnani, JL Ernst, Beat; Magnani, John L. From carbohydrate leads to glycomimetic drugs NATURE REVIEWS DRUG DISCOVERY English Review MYELIN-ASSOCIATED GLYCOPROTEIN; TRANSFER DIFFERENCE NMR; FIMBRIATED ESCHERICHIA-COLI; ALPHA-SERIES GANGLIOSIDES; URINARY-TRACT-INFECTION; LECTIN PA-IIL; RESPIRATORY SYNDROME CORONAVIRUS; ANTIBODY-DEFINED ANTIGEN; HUMAN DENDRITIC CELLS; HIGH-AFFINITY BINDING Carbohydrates are the most abundant natural products. Besides their role in metabolism and as structural building blocks, they are fundamental constituents of every cell surface, where they are involved in vital cellular recognition processes. Carbohydrates are a relatively untapped source of new drugs and therefore offer exciting new therapeutic opportunities. Advances in the functional understanding of carbohydrate-protein interactions have enabled the development of a new class of small-molecule drugs, known as glycomimetics. These compounds mimic the bioactive function of carbohydrates and address the drawbacks of carbohydrate leads, namely their low activity and insufficient drug-like properties. Here, we examine examples of approved carbohydrate-derived drugs, discuss the potential of carbohydrate-binding proteins as new drug targets ( focusing on the lectin families) and consider ways to overcome the challenges of developing this unique class of novel therapeutics. 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Rev. Drug Discov. AUG 2009 8 8 661 677 10.1038/nrd2852 17 Biotechnology & Applied Microbiology; Pharmacology & Pharmacy Biotechnology & Applied Microbiology; Pharmacology & Pharmacy 477KI WOS:000268517600022 19629075 Y N 2020-04-01 J Raj, VS; Mou, HH; Smits, SL; Dekkers, DHW; Muller, MA; Dijkman, R; Muth, D; Demmers, JAA; Zaki, A; Fouchier, RAM; Thiel, V; Drosten, C; Rottier, PJM; Osterhaus, ADME; Bosch, BJ; Haagmans, BL Raj, V. Stalin; Mou, Huihui; Smits, Saskia L.; Dekkers, Dick H. W.; Mueller, Marcel A.; Dijkman, Ronald; Muth, Doreen; Demmers, Jeroen A. A.; Zaki, Ali; Fouchier, Ron A. M.; Thiel, Volker; Drosten, Christian; Rottier, Peter J. M.; Osterhaus, Albert D. M. E.; Bosch, Berend Jan; Haagmans, Bart L. Dipeptidyl peptidase 4 is a functional receptor for the emerging human coronavirus-EMC NATURE English Article ACUTE-RESPIRATORY-SYNDROME; ANGIOTENSIN-CONVERTING ENZYME-2; SARS CORONAVIRUS; AMINOPEPTIDASE-N; PATHOGENESIS; MECHANISMS; RESERVOIRS; BATS Most human coronaviruses cause mild upper respiratory tract disease but may be associated with more severe pulmonary disease in immunocompromised individuals'. However, SARS coronavirus caused severe lower respiratory disease with nearly 10% mortality and evidence of systemic spread(2). Recently, another coronavirus (human coronavirus-Erasmus Medical Center (hCoV-EMC)) was identified in patients with severe and sometimes lethal lower respiratory tract infection(3,4). Viral genome analysis revealed close relatedness to coronaviruses found in bats'. Here we identify dipeptidyl peptidase 4 (DPP4; also known as CD26) as a functional receptor for hCoV-EMC. DPP4 specifically co-purified with the receptor-binding Si domain of the hCoV-EMC spike protein from lysates of susceptible Huh-7 cells. Antibodies directed against DPP4 inhibited hCoV-EMC infection of primary human bronchial epithelial cells and Huh-7 cells. Expression of human and bat (Pipistrellus pipistrellus) DPP4 in non-susceptible COS-7 cells enabled infection by hCoV-EMC. The use of the evolutionarily conserved DPP4 protein from different species as a functional receptor provides clues about the host range potential of hCoV-EMC. In addition, it will contribute critically to our understanding of the pathogenesis and epidemiology of this emerging human coronavirus, and may facilitate the development of intervention strategies. [Raj, V. Stalin; Smits, Saskia L.; Fouchier, Ron A. M.; Osterhaus, Albert D. M. E.; Haagmans, Bart L.] Erasmus MC, Dept Virosci, NL-3000 CA Rotterdam, Netherlands; [Mou, Huihui; Rottier, Peter J. M.; Bosch, Berend Jan] Univ Utrecht, Fac Vet Med, Dept Infect Dis & Immunol, Div Virol, NL-3508 TD Utrecht, Netherlands; [Smits, Saskia L.] Viroclin Biosci BV, NL-3029 AK Rotterdam, Netherlands; [Dekkers, Dick H. W.; Demmers, Jeroen A. A.] Erasmus MC, Prote Dept, NL-3000 CA Rotterdam, Netherlands; [Mueller, Marcel A.; Muth, Doreen; Drosten, Christian] Univ Bonn, Med Ctr, Inst Virol, D-53105 Bonn, Germany; [Dijkman, Ronald; Thiel, Volker] Kantonal Hosp St Gallen, Inst Immunobiol, CH-9007 St Gallen, Switzerland; [Zaki, Ali] Dr Soliman Fakeeh Hosp, Virol Lab, Jeddah, Saudi Arabia; [Thiel, Volker] Univ Zurich, Vetsuisse Fac, CH-8057 Zurich, Switzerland Bosch, BJ (reprint author), Univ Utrecht, Fac Vet Med, Dept Infect Dis & Immunol, Div Virol, NL-3508 TD Utrecht, Netherlands. b.j.bosch@uu.nl; b.haagmans@erasmusmc.nl Smits, Saskia/A-2953-2014; Fouchier, Ron A/A-1911-2014; Fouchier, Ron/Y-3755-2019; Demmers, Jeroen AA/F-4046-2016; Thiel, Volker/AAI-2391-2019; Mueller, Marcel/O-2425-2019; Victor, Stalin Raj/E-9670-2016 Fouchier, Ron A/0000-0001-8095-2869; Fouchier, Ron/0000-0001-8095-2869; Demmers, Jeroen AA/0000-0002-8757-9611; Mueller, Marcel/0000-0003-2242-5117; Thiel, Volker/0000-0002-5783-0887; Osterhaus, Albert/0000-0002-6074-1172; Victor, Stalin Raj/0000-0003-2250-8481; Haagmans, Bart/0000-0001-6221-2015; Dijkman, Ronald/0000-0003-0320-2743 European Union FP7European Union (EU) [223498]; ANTIGONE [278976]; Swiss National Science FoundationSwiss National Science Foundation (SNSF) [31003A_132898]; 3R Research Foundation Switzerland [128-11]; German Research Foundation (DFG)German Research Foundation (DFG) [DR 772/3-1, KAl241/18-1]; German Ministry of Education and Research (BMBF SARS II)Federal Ministry of Education & Research (BMBF) We thank E. Snijder for peoviding the anti-SARS-CoV NSP4 antibody, and E. Kindler, H. Jonsdottir, R. Rodriguez, T. Bestebroer, S. Pas, G. Arron, M. van Velzen and W. Ouwendijk for techn ical assistance. This work was supported by a fellowship from China Scholarship Council to H.M. The study was financed by the European Union FP7 project EMPERIE (contract number 223498), ANTIGONE (contract number 278976), the Swiss National Science Foundation (31003A_132898) and the 3R Research Foundation Switzerland (Project 128-11). C.D. was supported by the German Research Foundation (DFG grant DR 772/3-1, KAl241/18-1) and the German Ministry of Education and Research (BMBF SARS II). 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Gen. Virol. APR 2000 81 4 853 879 10.1099/0022-1317-81-4-853 27 Biotechnology & Applied Microbiology; Virology Biotechnology & Applied Microbiology; Virology 301ZX WOS:000086341400001 10725411 Bronze 2020-04-01 J Ruuskanen, O; Lahti, E; Jennings, LC; Murdoch, DR Ruuskanen, Olli; Lahti, Elina; Jennings, Lance C.; Murdoch, David R. Viral pneumonia LANCET English Article COMMUNITY-ACQUIRED PNEUMONIA; RESPIRATORY-TRACT INFECTIONS; HUMAN METAPNEUMOVIRUS INFECTION; INFLUENZA A(H1N1) INFECTION; POLYMERASE-CHAIN-REACTION; SYNCYTIAL VIRUS; PANDEMIC INFLUENZA; REQUIRING HOSPITALIZATION; STAPHYLOCOCCUS-AUREUS; ETIOLOGIC DIAGNOSIS About 200 million cases of viral community-acquired pneumonia occur every year-100 million in children and 100 million in adults. Molecular diagnostic tests have greatly increased our uwnderstanding of the role of viruses in pneumonia, and findings indicate that the incidence of viral pneumonia has been underestimated. In children, respiratory syncytial virus, rhinovirus, human metapneumovirus, human bocavirus, and parainfluenza viruses are the agents identified most frequently in both developed and developing countries. Dual viral infections are common, and a third of children have evidence of viral-bacterial co-infection. In adults, viruses are the putative causative agents in a third of cases of community-acquired pneumonia, in particular influenza viruses, rhinoviruses, and coronaviruses. Bacteria continue to have a predominant role in adults with pneumonia. Presence of viral epidemics in the community, patient's age, speed of onset of illness, symptoms, biomarkers, radiographic changes, and response to treatment can help differentiate viral from bacterial pneumonia. However, no clinical algorithm exists that will distinguish clearly the cause of pneumonia. No clear consensus has been reached about whether patients with obvious viral community-acquired pneumonia need to be treated with antibiotics. Apart from neuraminidase inhibitors for pneumonia caused by influenza viruses, there is no clear role for use of specific antivirals to treat viral community-acquired pneumonia. Influenza vaccines are the only available specific preventive measures. Further studies are needed to better understand the cause and pathogenesis of community-acquired pneumonia. Furthermore, regional differences in cause of pneumonia should be investigated, in particular to obtain more data from developing countries. [Ruuskanen, Olli; Lahti, Elina] Turku Univ Hosp, Dept Paediat, Turku 20521, Finland; [Jennings, Lance C.; Murdoch, David R.] Univ Otago, Microbiol Unit, Canterbury Hlth Labs, Christchurch, New Zealand; [Jennings, Lance C.; Murdoch, David R.] Univ Otago, Dept Pathol, Christchurch, New Zealand Ruuskanen, O (reprint author), Turku Univ Hosp, Dept Paediat, PL 52, Turku 20521, Finland. olli.ruuskanen@tyks.fi Murdoch, David/A-2012-2009 Hoffmann La-RocheHoffmann-La Roche EL and DRM declare that they have no conflicts of interest. OR has been a consultant to Novartis Vaccines and Abbot. LCJ has received grant support from Hoffmann La-Roche and honoraria or travel assistance from Hoffmann La-Roche, GlaxoSmithKline, Sanofi Pasteur, Baxter, Novartis, Wyeth, and CSL for participation in advisory groups and scientific meetings. 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ASHMUN, RA; WILLIAMS, RK; CARDELLICHIO, CB; SHAPIRO, LH; LOOK, AT; HOLMES, KV YEAGER, CL; ASHMUN, RA; WILLIAMS, RK; CARDELLICHIO, CB; SHAPIRO, LH; LOOK, AT; HOLMES, KV HUMAN AMINOPEPTIDASE-N IS A RECEPTOR FOR HUMAN CORONAVIRUS-229E NATURE English Article AMINO-ACID SEQUENCE; ENDOPEPTIDASE 24.11 ENKEPHALINASE; MEMBRANE ANTIGEN GP150; NEUTRAL ENDOPEPTIDASE; MOLECULAR-CLONING; LEUKEMIA ANTIGEN; GENE; KIDNEY; IDENTIFICATION; EXPRESSION HUMAN coronaviruses (HCV) in two serogroups represented by HCV-229E and HCV-OC43 are an important cause of upper respiratory tract infections 1. Here we report that human aminopeptidase N, a cell-surface metalloprotease on intestinal, lung and kidney epithelial cells 2-5, is a receptor for human coronavirus strain HCV-229E, but not for HCV-OC43. A monoclonal antibody, RBS, blocked HCV-229E virus infection of human lung fibroblasts, immunoprecipitated aminopeptidase N and inhibited its enzymatic activity. HCV-229E-resistant murine fibroblasts became susceptible after transfection with complementary DNA encoding human aminopeptidase N. By contrast, infection of human cells with HCV-OC43 was not inhibited by antibody RBS and expression of aminopeptidase N did not enhance HCV-OC43 replication in mouse cells. A mutant aminopeptidase lacking the catalytic site of the enzyme did not bind HCV-229E or RBS and did not render murine cells susceptible to HCV-229E infection, suggesting that the virus-binding site may lie at or near the active site of the human aminopeptidase molecule. UNIFORMED SERV UNIV HLTH SCI, DEPT PATHOL, 4301 JONES BRIDGE RD, BETHESDA, MD 20814 USA; ST JUDE CHILDRENS RES HOSP, DEPT HEMATOL ONCOL, MEMPHIS, TN 38105 USA; ST JUDE CHILDRENS RES HOSP, DEPT TUMOR CELL BIOL, MEMPHIS, TN 38105 USA; UNIV TENNESSEE, CTR HLTH SCI, COLL MED, DEPT PEDIAT, MEMPHIS, TN 38163 USA ASHMUN RA, 1990, BLOOD, V75, P462; ASHMUN RA, IN PRESS BLOOD; DELMAS B, 1992, NATURE, V357, P417, DOI 10.1038/357417a0; DEVAULT A, 1987, EMBO J, V6, P1317, DOI 10.1002/j.1460-2075.1987.tb02370.x; DVEKSLER GS, 1991, J VIROL, V65, P6881, DOI 10.1128/JVI.65.12.6881-6891.1991; KENNY AJ, 1982, PHYSIOL REV, V62, P91; LETARTE M, 1988, J EXP MED, V168, P1247, DOI 10.1084/jem.168.4.1247; LOOK AT, 1985, J CLIN INVEST, V75, P569, DOI 10.1172/JCI111733; LOOK AT, 1986, J CLIN INVEST, V78, P914, DOI 10.1172/JCI112680; LOOK AT, 1989, J CLIN INVEST, V83, P1299, DOI 10.1172/JCI114015; LOOK AT, 1989, LEUCOCYTE TYPING, V4, P784; MALFROY B, 1988, FEBS LETT, V229, P206, DOI 10.1016/0014-5793(88)80828-7; MATSAS R, 1985, BIOCHEM J, V231, P445, DOI 10.1042/bj2310445; MCINTOSH K, 1990, VIROLOGY, P857; NOREN O, 1989, FEBS LETT, V259, P107, DOI 10.1016/0014-5793(89)81506-6; Noren O, 1986, MOL CELLULAR BASIS D, P335; OLSEN J, 1989, FEBS LETT, V251, P275, DOI 10.1016/0014-5793(89)81470-X; RICH DH, 1984, J MED CHEM, V27, P417, DOI 10.1021/jm00370a001; SAKAGUCHI AY, 1982, SOMAT CELL GENET, V8, P83, DOI 10.1007/BF01538652; SEMENZA G, 1986, ANNU REV CELL BIOL, V2, P255, DOI 10.1146/annurev.cellbio.2.1.255; SHIPP MA, 1989, P NATL ACAD SCI USA, V86, P297, DOI 10.1073/pnas.86.1.297; TURNER AJ, 1987, MAMMALIAN ECTOENZYME, P211; UMEZAWA H, 1985, J ANTIBIOT, V38, P1629, DOI 10.7164/antibiotics.38.1629; VALLEE BL, 1990, BIOCHEMISTRY-US, V29, P5647, DOI 10.1021/bi00476a001; WATT VM, 1989, J BIOL CHEM, V264, P5480; WILKES SH, 1985, J BIOL CHEM, V260, P3154; WILLIAMS RK, 1990, J VIROL, V64, P3817, DOI 10.1128/JVI.64.8.3817-3823.1990; WILLIAMS RK, 1991, P NATL ACAD SCI USA, V88, P5533, DOI 10.1073/pnas.88.13.5533; WU Q, 1991, P NATL ACAD SCI USA, V88, P676, DOI 10.1073/pnas.88.2.676; WU Q, 1990, P NATL ACAD SCI USA, V87, P993, DOI 10.1073/pnas.87.3.993 30 455 493 4 15 NATURE PUBLISHING GROUP LONDON MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND 0028-0836 NATURE Nature JUN 4 1992 357 6377 420 422 10.1038/357420a0 3 Multidisciplinary Sciences Science & Technology - Other Topics HX172 WOS:A1992HX17200069 1350662 Bronze 2020-04-01 J White, JM; Delos, SE; Brecher, M; Schornberg, K White, Judith M.; Delos, Sue E.; Brecher, Matthew; Schornberg, Kathryn Structures and mechanisms of viral membrane fusion proteins: Multiple variations on a common theme CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY English Review trimer-of-hairpins; hemifusion; fusion pore; Class I fusion proteins; Class II fusion proteins; Class III fusion proteins HUMAN-IMMUNODEFICIENCY-VIRUS; HERPES-SIMPLEX-VIRUS; MURINE LEUKEMIA-VIRUS; SEMLIKI-FOREST-VIRUS; CELL-CELL FUSION; TYPE-1 ENVELOPE GLYCOPROTEIN; TICK-BORNE ENCEPHALITIS; CORONAVIRUS SPIKE GLYCOPROTEIN; INDUCED CONFORMATIONAL-CHANGES; ENV-MEDIATED FUSION Recent work has identified three distinct classes of viral membrane fusion proteins based on structural criteria. In addition, there are at least four distinct mechanisms by which viral fusion proteins can be triggered to undergo fusion-inducing conformational changes. Viral fusion proteins also contain different types of fusion peptides and vary in their reliance on accessory proteins. These differing features combine to yield a rich diversity of fusion proteins. Yet despite this staggering diversity, all characterized viral fusion proteins convert from a fusion-competent state (dimers or trimers, depending on the class) to a membrane-embedded homotrimeric prehairpin, and then to a trimer-of-hairpins that brings the fusion peptide, attached to the target membrane, and the transmembrane domain, attached to the viral membrane, into close proximity thereby facilitating the union of viral and target membranes. 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To investigate the molecular determinants of the infection, we characterized the surface molecule used by the virus for binding and entry into host cells. Here we report that aminopeptidase N, an ectoenzyme abundantly expressed at the apical membrane of the enterocytes, serves as a receptor for TGEV. Monoclonal antibodies were selected for their ability to block infection by TGEV of porcine cell lines. They recognized a brush-border membrane protein of M(r) 150K, which was identified as aminopeptidase N by amino-terminal sequencing. Two lines of evidence supported the view that the peptidase itself acts as a receptor. First, virions bound specifically to aminopeptidase N that was purified to homogeneity. Second, recombinant expression of aminopeptidase N conferred infectivity by TGEV to an otherwise non-permissive cell line. 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Clin. Microbiol. FEB 1998 36 2 539 542 4 Microbiology Microbiology YR636 WOS:000071515100037 9466772 2020-04-01 J Nicholls, JM; Poon, LLM; Lee, KC; Ng, WF; Lai, ST; Leung, CY; Chu, CM; Hui, PK; Mak, KL; Lim, W; Yan, KW; Chan, KH; Tsang, NC; Guan, Y; Yuen, KY; Peiris, JSM Nicholls, JM; Poon, LLM; Lee, KC; Ng, WF; Lai, ST; Leung, CY; Chu, CM; Hui, PK; Mak, KL; Lim, W; Yan, KW; Chan, KH; Tsang, NC; Guan, Y; Yuen, KY; Peiris, JSM Lung pathology of fatal severe acute respiratory syndrome LANCET English Article A H5N1 VIRUS; CLINICAL-FEATURES; HUMAN MACROPHAGES; HUMAN-DISEASE; INFLUENZA; PNEUMONIA Background Severe acute respiratory syndrome (SARS) is a novel infectious disease with global impact. A virus from the family Coronaviridae has been identified as the cause, but the pathogenesis is still unclear. Methods Post-mortem tissue samples from six patients who died from SARS in February and March, 2003, and an open lung biopsy from one of these patients were studied by histology and virology. Only one full autopsy was done. Evidence of infection with the SARS-associated coronavirus (SARS-CoV) and human metapneumovirus was sought by reverse-transcriptase PCR and serology. Pathological samples were examined by light and electron microscopy and immunohistochemistry. Findings All six patients had serological evidence of recent infection with SARS-CoV. Diffuse alveolar damage was common but not universal. Morphological changes identified were bronchial epithelial denudation, loss of cilia, and squamous metaplasia. Secondary bacterial pneumonia was present in one case. A giant-cell infiltrate was seen in four patients, with a pronounced increase in macrophages in the alveoli and the interstitium of the lung. Haemophagocytosis was present in two patients. The alveolar pneumocytes also showed cytomegaly with granular amphophilic cytoplasm. The patient for whom full autopsy was done had atrophy of the white pulp of the spleen. Electron microscopy revealed viral particles in the cytoplasm of epithelial cells corresponding to coronavirus. Interpretation SARS is associated with epithelial-cell proliferation and an increase in macrophages in the lung. The presence of haemophagocytosis supports the contention that cytokine dysregulation may account, at least partly, for the severity of the clinical disease. The case definition of SARS should acknowledge the range of lung pathology associated with this disease. 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DEC 1988 69 12 2939 2952 10.1099/0022-1317-69-12-2939 14 Biotechnology & Applied Microbiology; Virology Biotechnology & Applied Microbiology; Virology R6136 WOS:A1988R613600001 3058868 Bronze 2020-04-01 J Storch, MK; Stefferl, A; Brehm, U; Weissert, R; Wallstrom, E; Kerschensteiner, M; Olsson, T; Linington, C; Lassmann, H Storch, MK; Stefferl, A; Brehm, U; Weissert, R; Wallstrom, E; Kerschensteiner, M; Olsson, T; Linington, C; Lassmann, H Autoimmunity to myelin oligodendrocyte glycoprotein in rats mimics the spectrum of multiple sclerosis pathology BRAIN PATHOLOGY English Article EXPERIMENTAL ALLERGIC ENCEPHALOMYELITIS; DEMYELINATING ENCEPHALOMYELITIS; CELL-DEATH; LEWIS RAT; PATHOGENESIS; PATTERNS; ANTIBODY; CORONAVIRUS; EXPRESSION; ANTIGEN Multiple sclerosis is a chronic inflammatory disease characterized by perivenous inflammation and focal destruction of myelin, Many attempts have been undertaken previously to create animal models of chronic inflammatory demyelinating diseases through autoimmunity or virus infection. Recently, however, a new model of myelin oligodendrocyte glycoprotein (MOG) induced autoimmune encephalomyelitis became available, which, in a very standardized and predictable way, leads to chronic (relapsing or progressive) disease and widespread CNS demyelination. In the present study we actively induced MOG-experimental autoimmune encephalomyelitis (EAE) in different inbred rat strains using different immunization protocols, The pathology found in our models closely reflects the spectrum of multiple sclerosis (MS) pathology: Classical MS as well as variants such as optic neuritis, Devic's disease and Marburg's type of acute MS are mimicked in rats immunized with MOG antigen. Furthermore we demonstrate, that by using the proper strain/sensitization regime, subforms of MS such as for instance neuromyelitis optica can be reproducibly induced, Our study further supports the notion, that incidence and expression of the disease in this model, alike the situation in multiple sclerosis, is determined by genetic and environmental factors. Univ Vienna, Inst Neurol, A-1090 Vienna, Austria; Max Planck Inst Neurobiol, D-82152 Martinsried, Germany; Karolinska Hosp, Ctr Mol Med, Neuroimmunol Unit, S-17176 Stockholm, Sweden Lassmann, H (reprint author), Univ Vienna, Inst Neurol, Schwarzspanierstr 17, A-1090 Vienna, Austria. 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OCT 1998 8 4 681 694 10.1111/j.1750-3639.1998.tb00194.x 14 Clinical Neurology; Neurosciences; Pathology Neurosciences & Neurology; Pathology 126MP WOS:000076297500009 9804377 2020-04-01 J Allander, T; Jartti, T; Gupta, S; Niesters, HGM; Lehtinen, P; Osterback, R; Vuorinen, T; Waris, M; Bjerkner, A; Tiveljung-Lindell, A; van den Hoogen, BG; Hyypia, T; Ruuskanen, O Allander, Tobias; Jartti, Tuomas; Gupta, Shawon; Niesters, Hubert G. M.; Lehtinen, Pasi; Osterback, Riikka; Vuorinen, Tytti; Waris, Matti; Bjerkner, Annelie; Tiveljung-Lindell, Annika; van den Hoogen, Bernadette G.; Hyypia, Timo; Ruuskanen, Olli Human bocavirus and acute wheezing in children CLINICAL INFECTIOUS DISEASES English Article RESPIRATORY SYNCYTIAL VIRUS; HUMAN METAPNEUMOVIRUS; FREQUENT DETECTION; CORONAVIRUS HKU1; HUMAN PARVOVIRUS; YOUNG-CHILDREN; INFECTION; RHINOVIRUS; DISEASE; IDENTIFICATION Background. Human bocavirus is a newly discovered parvovirus. It has been detected primarily in children with acute lower respiratory tract infection, but its occurrence, clinical profile, and role as a causative agent of respiratory tract disease are not clear. Methods. We investigated the presence of human bocavirus by quantitative polymerase chain reaction of nasopharyngeal aspirate specimens and selected serum samples obtained from 259 children (median age, 1.6 years) who had been hospitalized for acute expiratory wheezing. The samples were analyzed for 16 respiratory viruses by polymerase chain reaction, virus culture, antigen detection, and serological assays. Results. At least 1 potential etiologic agent was detected in 95% of children, and 11 agent was detected in 34% of children. Human bocavirus was detected in 49 children (19%). A large proportion of the cases were mixed infections with other viruses, but human bocavirus was the only virus detected in 12 children (5%). High viral loads of human bocavirus were noted mainly in the absence of other viral agents, suggesting a causative role for acute wheezing. In addition, infections that had uncertain clinical relevance and low viral loads were prevalent. Human bocavirus DNA was frequently detected in serum specimens obtained from patients with acute wheezing, suggesting systemic infection. Conclusions. Human bocavirus is prevalent among children with acute wheezing and can cause systemic infection. Results suggest a model for bocavirus infection in which high viral loads are potentially associated with respiratory symptoms and low viral loads indicate asymptomatic shedding. Therefore, quantitative polymerase chain reaction analysis may be important for additional studies of human bocavirus. 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Coronaviruses are exceptionally large RNA viruses and employ complex regulatory mechanisms to express their genomes. Here, we determined the sequence of SARS coronavinus (SARS-CoV), isolate Frankfurt 1, and characterized key RNA elements and protein functions involved in viral genome expression. Important regulatory mechanisms, such as the (discontinuous) synthesis of eight subgenomic mRNAs, ribosomal frameshifting and post-translational proteolytic processing, were addressed. Activities of three SARS coronavirus enzymes, the helicase and two cysteine proteinases, which are known to be critically involved in replication, transcription and/or post-translational polyprotein processing, were characterized. The availability of recombinant forms of key replicative enzymes of SARS coronavirus should pave the way for high-throughput screening approaches to identify candidate inhibitors in compound libraries. 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We have developed an improved method for Epstein-Barr virus transformation of human B cells. We used this method to analyze the memory repertoire of a patient who recovered from severe acute respiratory syndrome coronavirus (SARS-CoV) infection and to isolate monoclonal antibodies specific for different viral proteins, including 35 antibodies with in vitro neutralizing activity ranging from 10(-8)M to 10(-11)M. One such antibody confers protection in vivo in a mouse model of SARS-CoV infection. These results show that it is possible to interrogate the memory repertoire of immune donors to rapidly and efficiently isolate neutralizing antibodies that have been selected in the course of natural infection. 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Med. AUG 2004 10 8 871 875 10.1038/nm1080 5 Biochemistry & Molecular Biology; Cell Biology; Medicine, Research & Experimental Biochemistry & Molecular Biology; Cell Biology; Research & Experimental Medicine 843DK WOS:000223055700043 15247913 Bronze 2020-04-01 J Imai, Y; Kuba, K; Rao, S; Huan, Y; Guo, F; Guan, B; Yang, P; Sarao, R; Wada, T; Leong-Poi, H; Crackower, MA; Fukamizu, A; Hui, CC; Hein, L; Uhlig, S; Slutsky, AS; Jiang, CY; Penninger, JM Imai, Y; Kuba, K; Rao, S; Huan, Y; Guo, F; Guan, B; Yang, P; Sarao, R; Wada, T; Leong-Poi, H; Crackower, MA; Fukamizu, A; Hui, CC; Hein, L; Uhlig, S; Slutsky, AS; Jiang, CY; Penninger, JM Angiotensin-converting enzyme 2 protects from severe acute lung failure NATURE English Article ACUTE RESPIRATORY SYNDROME; DISTRESS-SYNDROME; FUNCTIONAL RECEPTOR; SARS CORONAVIRUS; DEFICIENT MICE; HONG-KONG; EXPRESSION; IDENTIFICATION; REGULATOR; CLONING Acute respiratory distress syndrome (ARDS), the most severe form of acute lung injury, is a devastating clinical syndrome with a high mortality rate (30-60%) (refs 1-3). Predisposing factors for ARDS are diverse(1,3) and include sepsis, aspiration, pneumonias and infections with the severe acute respiratory syndrome (SARS) corona-virus(4,5). At present, there are no effective drugs for improving the clinical outcome of ARDS(1-3). Angiotensin-converting enzyme (ACE) and ACE2 are homologues with different key functions in the renin-angiotensin system(6-8). ACE cleaves angiotensin I to generate angiotensin II, whereas ACE2 inactivates angiotensin II and is a negative regulator of the system. ACE2 has also recently been identified as a potential SARS virus receptor and is expressed in lungs(9,10). Here we report that ACE2 and the angiotensin II type 2 receptor (AT(2)) protect mice from severe acute lung injury induced by acid aspiration or sepsis. However, other components of the renin-angiotensin system, including ACE, angiotensin II and the angiotensin II type 1a receptor (AT(1)a), promote disease pathogenesis, induce lung oedemas and impair lung function. We show that mice deficient for Ace show markedly improved disease, and also that recombinant ACE2 can protect mice from severe acute lung injury. Our data identify a critical function for ACE2 in acute lung injury, pointing to a possible therapy for a syndrome affecting millions of people worldwide every year. Austrian Acad Sci, IMBA, Inst Mol Biotechnol, A-1030 Vienna, Austria; Chinese Acad Med Sci, Inst Basic Med Sci, Natl Lab Med Mol Biol, Beijing 100005, Peoples R China; Peking Union Med Coll, Beijing 100005, Peoples R China; St Michaels Hosp, Dept Cardiol, Toronto, ON M5B 1W8, Canada; Merck Frosst Ctr Therapeut Res, Dept Biochem & Mol Biol, Montreal, PQ H3R 4P8, Canada; Univ Tsukuba, Ctr Tsukuba Adv Res Alliance, Tsukuba, Ibaraki 3058577, Japan; Hosp Sick Children, Program Dev Biol, Toronto, ON M5G 1X8, Canada; Univ Toronto, Dept Mol & Med Genet, Toronto, ON M5G 1X8, Canada; Univ Freiburg, Dept Pharmacol, D-79104 Freiburg, Germany; Res Ctr Borstel, Div Pulm Pharmacol, D-23845 Borstel, Germany; Univ Toronto, St Michaels Hosp, Dept Med, Toronto, ON M5B 1W8, Canada; Univ Toronto, St Michaels Hosp, Interdepartmental Div Crit Care, Toronto, ON M5B 1W8, Canada Penninger, JM (reprint author), Austrian Acad Sci, IMBA, Inst Mol Biotechnol, A-1030 Vienna, Austria. 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Meanwhile, because of the rapid penetrations from these disciplines, medicinal chemistry is currently undergoing an unprecedented revolution. In this minireview, we are to summarize the progresses by focusing on the following six aspects. (1) Use the pseudo amino acid composition or PseAAC to predict various attributes of protein/peptide sequences that are useful for drug development. (2) Use pseudo oligonucleotide composition or PseKNC to do the same for DNA/RNA sequences. (3) Introduce the multi-label approach to study those systems where the constituent elements bear multiple characters and functions. (4) Utilize the graphical rules and "wenxiang" diagrams to analyze complicated biomedical systems. (5) Recent development in identifying the interactions of drugs with its various types of target proteins in cellular networking. (6) Distorted key theory and its application in developing peptide drugs. 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Chem. 2015 11 3 218 234 10.2174/1573406411666141229162834 17 Chemistry, Medicinal Pharmacology & Pharmacy CF1RM WOS:000352325300002 25548930 Y N 2020-04-01 J Bosch, BJ; van der Zee, R; de Haan, CAM; Rottier, PJM Bosch, BJ; van der Zee, R; de Haan, CAM; Rottier, PJM The coronavirus spike protein is a class I virus fusion protein: Structural and functional characterization of the fusion core complex JOURNAL OF VIROLOGY English Article ACUTE RESPIRATORY SYNDROME; MOUSE HEPATITIS-VIRUS; TO-CELL FUSION; HIV-1 TRANSMEMBRANE GLYCOPROTEIN; INDUCED CONFORMATIONAL-CHANGES; VIRAL MEMBRANE-FUSION; STRANDED COILED-COIL; ENVELOPE GLYCOPROTEIN; POTENT INHIBITORS; INFLUENZA-VIRUS Coronavirus entry is mediated by the viral spike (S) glycoprotein. The 180-kDa oligomeric S protein of the murine coronavirus mouse hepatitis virus strain A59 is posttranslationally cleaved into an S1 receptor binding unit and an S2 membrane fusion unit. The latter is thought to contain an internal fusion peptide and has two 4,3 hydrophobic (heptad) repeat regions designated HR1 and HR2. HR2 is located close to the membrane anchor, and HR1 is some 170 amino acids (aa) upstream of it. Heptad repeat (HR) regions are found in fusion proteins of many different viruses and form an important characteristic of class I viral fusion proteins. We investigated the role of these regions in coronavirus membrane fusion. Peptides HR1 (96 aa) and HR2 (39 aa), corresponding to the HR1 and HR2 regions, were produced in Escherichia coli. When mixed together, the two peptides were found to assemble into an extremely stable oligomeric complex. Both on their own and within the complex, the peptides were highly alpha helical. Electron microscopic analysis of the complex revealed a rod-like structure similar to14.5 nm in length. Limited proteolysis in combination with mass spectrometry indicated that HR1 and HR2 occur in the complex in an antiparallel fashion. In the native protein, such a conformation would bring the proposed fusion peptide, located in the N-terminal domain of HR1, and the transmembrane anchor into close proximity. Using biological assays, the HR2 peptide was shown to be a potent inhibitor of virus entry into the cell, as well as of cell-cell fusion. Both biochemical and functional data show that the coronavirus spike protein is a class I viral fusion protein. 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Virol. AUG 2003 77 16 8801 8811 10.1128/JVI.77.16.8801-8811.2003 11 Virology Virology 706PU WOS:000184462800022 12885899 Bronze, Green Published 2020-04-01 J Daffis, S; Szretter, KJ; Schriewer, J; Li, JQ; Youn, S; Errett, J; Lin, TY; Schneller, S; Zust, R; Dong, HP; Thiel, V; Sen, GC; Fensterl, V; Klimstra, WB; Pierson, TC; Buller, RM; Gale, M; Shi, PY; Diamond, MS Daffis, Stephane; Szretter, Kristy J.; Schriewer, Jill; Li, Jianqing; Youn, Soonjeon; Errett, John; Lin, Tsai-Yu; Schneller, Stewart; Zust, Roland; Dong, Hongping; Thiel, Volker; Sen, Ganes C.; Fensterl, Volker; Klimstra, William B.; Pierson, Theodore C.; Buller, R. Mark; Gale, Michael, Jr.; Shi, Pei-Yong; Diamond, Michael S. 2 '-O methylation of the viral mRNA cap evades host restriction by IFIT family members NATURE English Article NILE-VIRUS-INFECTION; PROTEINS; GENES; METHYLTRANSFERASE; TRANSLATION; IDENTIFICATION; INITIATION; INDUCTION; PROTECTS; ALPHA Cellular messenger RNA (mRNA) of higher eukaryotes and many viral RNAs are methylated at the N-7 and 2'-O positions of the 5' guanosine cap by specific nuclear and cytoplasmic methyltransferases (MTases), respectively. Whereas N-7 methylation is essential for RNA translation and stability(1), the function of 2'-O methylation has remained uncertain since its discovery 35 years ago(2-4). Here we show that a West Nile virus (WNV) mutant (E218A) that lacks 2'-O MTase activity was attenuated in wild-type primary cells and mice but was pathogenic in the absence of type I interferon (IFN) signalling. 2'-O methylation of viral RNA did not affect IFN induction in WNV-infected fibroblasts but instead modulated the antiviral effects of IFN-induced proteins with tetratricopeptide repeats (IFIT), which are interferon-stimulated genes (ISGs) implicated in regulation of protein translation. Poxvirus and coronavirus mutants that lacked 2'-O MTase activity similarly showed enhanced sensitivity to the antiviral actions of IFN and, specifically, IFIT proteins. Our results demonstrate that the 2'-O methylation of the 5' cap of viral RNA functions to subvert innate host antiviral responses through escape of IFIT-mediated suppression, and suggest an evolutionary explanation for 2'-O methylation of cellular mRNA: to distinguish self from non-self RNA. Differential methylation of cytoplasmic RNA probably serves as an example for pattern recognition and restriction of propagation of foreign viral RNA in host cells. [Daffis, Stephane; Szretter, Kristy J.; Youn, Soonjeon; Diamond, Michael S.] Washington Univ, Sch Med, Dept Med, St Louis, MO 63110 USA; [Li, Jianqing; Diamond, Michael S.] Washington Univ, Sch Med, Dept Mol Microbiol, St Louis, MO 63110 USA; [Diamond, Michael S.] Washington Univ, Sch Med, Dept Pathol & Immunol, St Louis, MO 63110 USA; [Buller, R. Mark; Gale, Michael, Jr.; Shi, Pei-Yong; Diamond, Michael S.] Midw Reg Ctr Biodef & Emerging Infect Dis Res, St Louis, MO 63104 USA; [Schriewer, Jill; Buller, R. Mark] St Louis Univ, Sch Med, Dept Mol Microbiol & Immunol, St Louis, MO 63104 USA; [Errett, John; Gale, Michael, Jr.] Univ Washington, Sch Med, Dept Immunol, Seattle, WA 98195 USA; [Lin, Tsai-Yu; Pierson, Theodore C.] NIH, Viral Pathogenesis Sect, Viral Dis Lab, Bethesda, MD 20892 USA; [Schneller, Stewart] Auburn Univ, Dept Chem & Biochem, Auburn, AL 36849 USA; [Zust, Roland; Thiel, Volker] Kantonal Hosp St Gallen, Inst Immunobiol, CH-9007 St Gallen, Switzerland; [Thiel, Volker] Univ Zurich, Vetsuisse Fac, CH-8006 Zurich, Switzerland; [Dong, Hongping; Shi, Pei-Yong] New York State Dept Hlth, Wadsworth Ctr, Albany, NY 12208 USA; [Sen, Ganes C.; Fensterl, Volker] Cleveland Clin, Lerner Res Inst, Cleveland, OH 44195 USA; [Klimstra, William B.] Univ Pittsburgh, Sch Med, Dept Microbiol & Mol Genet, Pittsburgh, PA 15261 USA; [Buller, R. Mark; Gale, Michael, Jr.; Shi, Pei-Yong; Diamond, Michael S.] Pacific NW Reg Ctr Biodef & Emerging Infect Dis R, St Louis, MO 63104 USA; [Buller, R. Mark; Gale, Michael, Jr.; Shi, Pei-Yong; Diamond, Michael S.] NE Reg Ctr Biodef & Emerging Infect Dis Res, St Louis, MO 63104 USA Diamond, MS (reprint author), Washington Univ, Sch Med, Dept Med, St Louis, MO 63110 USA. diamond@borcim.wustl.edu Lin, Tsai-Yu/B-8873-2016; Jha, Babal/AAC-8337-2020; Diamond, Michael/AAH-1733-2019; Thiel, Volker/AAI-2391-2019 Lin, Tsai-Yu/0000-0002-8076-1584; Jha, Babal/0000-0002-7660-5255; Diamond, Michael/0000-0002-8791-3165; Szretter, Kristy/0000-0003-0391-2307; Gale, Michael/0000-0002-6332-7436; Thiel, Volker/0000-0002-5783-0887 National Institutes of HealthUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USA [U54 AI081680, U19 AI083019, R01 AI074973, R01 AI56540, U54 AI057160, U54 AI057158, R01 CA068782]; Swiss National Science FoundationSwiss National Science Foundation (SNSF) [3100A0-118425/1]; Novartis FoundationNovartis This work was supported by National Institutes of Health grants U54 AI081680, U19 AI083019 and R01 AI074973 (to M.G. and M.S.D.), R01 AI56540 (to S.S.), U54 AI057160 (to R.M.B.) and U54 AI057158 (to P.Y.S.), R01 CA068782 (to G.C.S.) the Swiss National Science Foundation, 3100A0-118425/1, and the Novartis Foundation (to V.T. and R.Z.). We thank H. Virgin and B. Moss for reading the manuscript. 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Direct estimation of the proportion of asymptomatic and presymptomatic infections is achievable by contact tracing and should be a priority during an outbreak of a novel infectious agent. 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Natl. Acad. Sci. U. S. A. APR 20 2004 101 16 6146 6151 10.1073/pnas.0307506101 6 Multidisciplinary Sciences Science & Technology - Other Topics 814ME WOS:000220978000084 15071187 Bronze, Green Published 2020-04-01 J Assiri, A; Al-Tawfiq, JA; Al-Rabeeah, AA; Al-Rabiah, FA; Al-Hajjar, S; Al-Barrak, A; Flemban, H; Al-Nassir, WN; Balkhy, HH; Al-Hakeem, RF; Makhdoom, HQ; Zumla, AI; Memish, ZA Assiri, Abdullah; Al-Tawfiq, Jaffar A.; Al-Rabeeah, Abdullah A.; Al-Rabiah, Fahad A.; Al-Hajjar, Sami; Al-Barrak, Ali; Flemban, Hesham; Al-Nassir, Wafa N.; Balkhy, Hanan H.; Al-Hakeem, Rafat F.; Makhdoom, Hatem Q.; Zumla, Alimuddin I.; Memish, Ziad A. Epidemiological, demographic, and clinical characteristics of 47 cases of Middle East respiratory syndrome coronavirus disease from Saudi Arabia: a descriptive study LANCET INFECTIOUS DISEASES English Article FEATURES; SARS; CONFIRMATION Background Middle East respiratory syndrome (MERS) is a new human disease caused by a novel coronavirus (CoV). Clinical data on MERS-CoV infections are scarce. We report epidemiological, demographic, clinical, and laboratory characteristics of 47 cases of MERS-CoV infections, identify knowledge gaps, and define research priorities. Methods We abstracted and analysed epidemiological, demographic, clinical, and laboratory data from confirmed cases of sporadic, household, community, and health-care-associated MERS-CoV infections reported from Saudi Arabia between Sept 1, 2012, and June 15, 2013. Cases were confirmed as having MERS-CoV by real-time RT-PCR. Findings 47 individuals (46 adults, one child) with laboratory-confirmed MERS-CoV disease were identified; 36 (77%) were male (male:female ratio 3.3:1). 28 patients died, a 60% case-fatality rate. The case-fatality rate rose with increasing age. Only two of the 47 cases were previously healthy; most patients (45 [96%]) had underlying comorbid medical disorders, including diabetes (32 [68%]), hypertension (16 [34%]), chronic cardiac disease (13 [28%]), and chronic renal disease (23 [49%]). Common symptoms at presentation were fever (46 [98%]), fever with chills or rigors (41 [87%]), cough (39 [83%]), shortness of breath (34 [72%]), and myalgia (15 [32%]). Gastrointestinal symptoms were also frequent, including diarrhoea (12 [26%]), vomiting (ten [21%]), and abdominal pain (eight [17%]). All patients had abnormal findings on chest radiography, ranging from subtle to extensive unilateral and bilateral abnormalities. Laboratory analyses showed raised concentrations of lactate dehydrogenase (23 [49%]) and aspartate aminotransferase (seven [15%]) and thrombocytopenia (17 [36%]) and lymphopenia (16 [34%]). Interpretation Disease caused by MERS-CoV presents with a wide range of clinical manifestations and is associated with substantial mortality in admitted patients who have medical comorbidities. Major gaps in our knowledge of the epidemiology, community prevalence, and clinical spectrum of infection and disease need urgent definition. [Assiri, Abdullah; Al-Rabeeah, Abdullah A.; Al-Hakeem, Rafat F.; Zumla, Alimuddin I.; Memish, Ziad A.] Minist Hlth, Global Ctr Mass Gatherings Med, Riyadh 11176, Saudi Arabia; [Assiri, Abdullah] Minist Hlth, Infect Prevent & Control Program, Publ Hlth Directorate, Riyadh 11176, Saudi Arabia; [Al-Tawfiq, Jaffar A.] Saudi ARAMCO Med Serv Org, Dhahran, Saudi Arabia; [Al-Rabiah, Fahad A.; Al-Hajjar, Sami] King Faisal Specialist Hosp & Res Ctr, Riyadh, Saudi Arabia; [Al-Barrak, Ali] Prince Sultan Mil Med City, Riyadh, Saudi Arabia; [Flemban, Hesham] Alhada Mil Hosp, Riyadh, Saudi Arabia; [Al-Nassir, Wafa N.] Imam Abdulrahman Bin Mohamed Hosp, Natl Guard Hlth Affairs, Dammam, Saudi Arabia; [Balkhy, Hanan H.] King Abdul Aziz Med City, Riyadh, Saudi Arabia; [Al-Hakeem, Rafat F.] Minist Hlth, Communicable Dis Program, Riyadh 11176, Saudi Arabia; [Makhdoom, Hatem Q.] Minist Hlth, Jeddah Reg Lab, Jeddah, Saudi Arabia; [Zumla, Alimuddin I.] UCL, Div Infect & Immun, London, England; [Zumla, Alimuddin I.] Univ Coll London Hosp NHS Fdn Trust, London, England; [Memish, Ziad A.] Minist Hlth, Publ Hlth Directorate, Riyadh 11176, Saudi Arabia; [Memish, Ziad A.] Al Faisal Univ, Riyadh, Saudi Arabia Memish, ZA (reprint author), Minist Hlth, Riyadh 11176, Saudi Arabia. zmemish@yahoo.com Jha, Babal/AAC-8337-2020 Jha, Babal/0000-0002-7660-5255; Zumla, Alimuddin/0000-0002-5111-5735; Assiri, Abdullah/0000-0002-5605-2876 National Institute of Health Research, Biomedical Research Centre, UCL Hospital, London, UK; European and Developing Countries Clinical Trials Partnership; Hague, NetherlandsNetherlands Government; EC-FW7 (European Commission's seventh framework programme for research), Brussels, Belgium We thank staff of the Ministry of Health, Riyadh, Saudi Arabia, and Adam Zumla (UCL School of Pharmacy, London, UK) and Matthew Bates (UNZA-UCLMS Project, Lusaka, Zambia) for technical and administrative support. AIZ acknowledges support from. the National Institute of Health Research, Biomedical Research Centre, UCL Hospital, London, UK; the European and Developing Countries Clinical Trials Partnership, The Hague, Netherlands; and EC-FW7 (European Commission's seventh framework programme for research), Brussels, Belgium. 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Dis. SEP 2013 13 9 752 761 10.1016/S1473-3099(13)70204-4 10 Infectious Diseases Infectious Diseases 205SU WOS:000323465900020 23891402 Bronze Y N 2020-04-01 J Chou, KC Chou, Kuo-Chen Pseudo Amino Acid Composition and its Applications in Bioinformatics, Proteomics and System Biology CURRENT PROTEOMICS English Review Protein attributes; sequential model; discrete model; PseAAC; functional domain; gene ontology; sequential evolution; optimal PseAAC PROTEIN SUBCELLULAR LOCATION; FUNCTIONAL DOMAIN COMPOSITION; SUPPORT VECTOR MACHINE; STRUCTURAL CLASS PREDICTION; MODIFIED MAHALANOBIS DISCRIMINANT; LOW-FREQUENCY VIBRATIONS; SEQUENTIAL EVOLUTION INFORMATION; CORONAVIRUS MAIN PROTEINASE; SECONDARY STRUCTURE-CONTENT; COMPLEXITY MEASURE FACTOR With the avalanche of protein sequences generated in the post-genomic age, it is highly desired to develop automated methods for efficiently identifying various attributes of uncharacterized proteins. This is one of the most important tasks facing us today in bioinformatics, and the information thus obtained will have important impacts on the development of proteomics and system biology. To realize that, one of the keys is to find an effective model to represent the sample of a protein. The most straightforward model in this regard is its entire amino acid sequence; however, the entire sequence model would fail to work when the query protein did not have significant homology to proteins of known characteristics. Thus, various non-sequential models or discrete models were proposed. The simplest discrete model is the amino acid ( AA) composition. Using it to represent a protein, however, all the sequence-order information would be completely lost. To cope with such a dilemma, the concept of pseudo amino acid (PseAA) composition was introduced. Its essence is to keep using a discrete model to represent a protein yet without completely losing its sequence-order information. Therefore, in a broad sense, the PseAA composition of a protein is actually a set of discrete numbers that is derived from its amino acid sequence and that is different from the classical AA composition and able to harbour some sort of sequence order or pattern information. Ever since the first PseAA composition was formulated to predict protein subcellular localization and membrane protein types, it has stimulated many different modes of PseAA composition for studying various kinds of problems in proteins and proteins-related systems. In this review, we shall give a brief and systematic introduction of various modes of PseAA composition and their applications. Meanwhile, the challenges for finding the optimal PseAA composition are also briefly discussed. 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Proteomics DEC 2009 6 4 262 274 10.2174/157016409789973707 13 Biochemical Research Methods; Biochemistry & Molecular Biology Biochemistry & Molecular Biology 532VI WOS:000272777800007 Y N 2020-04-01 J Cavanagh, D Cavanagh, Dave Coronavirus avian infectious bronchitis virus VETERINARY RESEARCH English Review vaccines; tropism; host range; in ovo TRANSMISSIBLE GASTROENTERITIS CORONAVIRUS; CYTOTOXIC T-LYMPHOCYTES; OPEN READING FRAME; SPIKE PROTEIN; S1 GENE; CROSS-PROTECTION; SIALIC-ACID; MONOCLONAL-ANTIBODIES; SEQUENCE-ANALYSIS; VACCINE STRAINS Infectious bronchitis virus (IBV), the coronavirus of the chicken (Gallus gallus), is one of the foremost causes of economic loss within the poultry industry, affecting the performance of both meat-type and egg-laying birds. The virus replicates not only in the epithelium of upper and lower respiratory tract tissues, but also in many tissues along the alimentary tract and elsewhere e. g. kidney, oviduct and testes. It can be detected in both respiratory and faecal material. There is increasing evidence that IBV can infect species of bird other than the chicken. Interestingly breeds of chicken vary with respect to the severity of infection with IBV, which may be related to the immune response. Probably the major reason for the high profile of IBV is the existence of a very large number of serotypes. Both live and inactivated IB vaccines are used extensively, the latter requiring priming by the former. Their effectiveness is diminished by poor cross-protection. The nature of the protective immune response to IBV is poorly understood. What is known is that the surface spike protein, indeed the amino-terminal S1 half, is sufficient to induce good protective immunity. There is increasing evidence that only a few amino acid differences amongst S proteins are sufficient to have a detrimental impact on cross-protection. Experimental vector IB vaccines and genetically manipulated IBVs-with heterologous spike protein genes-have produced promising results, including in the context of in ovo vaccination. 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Res. FEB-MAR 2007 38 2 281 297 10.1051/vetres:2006055 17 Veterinary Sciences Veterinary Sciences 136GA WOS:000244209400008 17296157 Bronze 2020-04-01 J van Boheemen, S; de Graaf, M; Lauber, C; Bestebroer, TM; Raj, VS; Zaki, AM; Osterhaus, ADME; Haagmans, BL; Gorbalenya, AE; Snijder, EJ; Fouchier, RAM van Boheemen, Sander; de Graaf, Miranda; Lauber, Chris; Bestebroer, Theo M.; Raj, V. Stalin; Zaki, Ali Moh; Osterhaus, Albert D. M. E.; Haagmans, Bart L.; Gorbalenya, Alexander E.; Snijder, Eric J.; Fouchier, Ron A. M. Genomic Characterization of a Newly Discovered Coronavirus Associated with Acute Respiratory Distress Syndrome in Humans MBIO English Article MURINE CORONAVIRUS; VIRUS; RNA; TRANSCRIPTION; REPLICATION; SEQUENCE; BATS; IDENTIFICATION; NIDOVIRALES; EVOLUTION A novel human coronavirus (HCoV-EMC/2012) was isolated from a man with acute pneumonia and renal failure in June 2012. This report describes the complete genome sequence, genome organization, and expression strategy of HCoV-EMC/2012 and its relation with known coronaviruses. The genome contains 30,119 nucleotides and contains at least 10 predicted open reading frames, 9 of which are predicted to be expressed from a nested set of seven subgenomic mRNAs. Phylogenetic analysis of the replicase gene of coronaviruses with completely sequenced genomes showed that HCoV-EMC/2012 is most closely related to Tylonycteris bat coronavirus HKU4 (BtCoV-HKU4) and Pipistrellus bat coronavirus HKU5 (BtCoV-HKU5), which prototype two species in lineage C of the genus Betacoronavirus. In accordance with the guidelines of the International Committee on Taxonomy of Viruses, and in view of the 75% and 77% amino acid sequence identity in 7 conserved replicase domains with BtCoV-HKU4 and BtCoV-HKU5, respectively, we propose that HCoV-EMC/2012 prototypes a novel species in the genus Betacoronavirus. HCoV-EMC/2012 may be most closely related to a coronavirus detected in Pipistrellus pipistrellus in The Netherlands, but because only a short sequence from the most conserved part of the RNA-dependent RNA polymerase-encoding region of the genome was reported for this bat virus, its genetic distance from HCoV-EMC remains uncertain. HCoV-EMC/2012 is the sixth coronavirus known to infect humans and the first human virus within betacoronavirus lineage C. IMPORTANCE Coronaviruses are capable of infecting humans and many animal species. Most infections caused by human coronaviruses are relatively mild. However, the outbreak of severe acute respiratory syndrome (SARS) caused by SARS-CoV in 2002 to 2003 and the fatal infection of a human by HCoV-EMC/2012 in 2012 show that coronaviruses are able to cause severe, sometimes fatal disease in humans. We have determined the complete genome of HCoV-EMC/2012 using an unbiased virus discovery approach involving next-generation sequencing techniques, which enabled subsequent state-of-the-art bioinformatics, phylogenetics, and taxonomic analyses. By establishing its complete genome sequence, HCoV-EMC/2012 was characterized as a new genotype which is closely related to bat coronaviruses that are distant from SARS-CoV. We expect that this information will be vital to rapid advancement of both clinical and vital research on this emerging pathogen. [van Boheemen, Sander; de Graaf, Miranda; Bestebroer, Theo M.; Raj, V. Stalin; Osterhaus, Albert D. M. E.; Haagmans, Bart L.; Fouchier, Ron A. M.] Erasmus MC, Virosci Lab, Rotterdam, Netherlands; [Lauber, Chris; Gorbalenya, Alexander E.; Snijder, Eric J.] Leiden Univ, Med Ctr, Ctr Infect Dis, Mol Virol Lab,Dept Med Microbiol, Leiden, Netherlands; [Zaki, Ali Moh] Dr Soliman Fakeeh Hosp, Jeddah, Saudi Arabia; [Gorbalenya, Alexander E.] Moscow MV Lomonosov State Univ, Fac Bioengn & Bioinformat, Moscow, Russia Fouchier, RAM (reprint author), Erasmus MC, Virosci Lab, Rotterdam, Netherlands. r.fouchier@erasmusmc.nl Fouchier, Ron/Y-3755-2019; Snijder, Eric J./E-6073-2018; Fouchier, Ron A/A-1911-2014; de Graaf, Miranda/K-1262-2018; Gorbalenya, Alexander E/J-4818-2012; Victor, Stalin Raj/E-9670-2016 Fouchier, Ron/0000-0001-8095-2869; Snijder, Eric J./0000-0003-3297-2309; Fouchier, Ron A/0000-0001-8095-2869; de Graaf, Miranda/0000-0002-7831-0098; Gorbalenya, Alexander E/0000-0002-4967-7341; Victor, Stalin Raj/0000-0003-2250-8481; Osterhaus, Albert/0000-0002-6074-1172; Haagmans, Bart/0000-0001-6221-2015 European Union under EMPERIE [223498]; European Union under SILVER [260644] The research leading to these results has received funding from the European Union Seventh Framework Programme (FP7) under EMPERIE grant agreement no. 223498 and SILVER grant agreement no. 260644. 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At present, no specific treatment has been identified for SARS-associated coronavirus Infection. We assessed the antiviral potential of ribavirin, 6-azauridine, pyrazofurin, mycophenolic acid, and glycyrrhizin against two clinical Isolates of coronavirus (FFM-1 and FFM-2) from patients with SARS admitted to the clinical centre of Frankfurt University, Germany. Of all the compounds, glycyrrhizin was the most active in inhibiting replication of the SARS-associated virus. Our findings suggest that glycyrrhizin should be assessed for treatment of SARS. Univ Frankfurt, Sch Med, Inst Med Virol, D-60596 Frankfurt, Germany Cinatl, J (reprint author), Univ Frankfurt, Sch Med, Inst Med Virol, Paul Ehrlich Str 40, D-60596 Frankfurt, Germany. 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The order includes the distantly related coronaviruses, toroviruses, and roniviruses, which possess the largest known RNA genomes from 26 to 32 kb) and will therefore be called 'large' nidoviruses in this review. They are compared with their arterivirus cousins, which also belong to the Nidovirales despite having a Much smaller genome ( 13-16 kb). Common and unique features that have been identified for either large or all nidoviruses are outlined. These include the nidovirus genetic plan and genome diversity, the composition of the replicase machinery and virus particles, virus-specific accessory genes, the mechanisms of RNA and protein synthesis, and the origin and evolution of nidoviruses with small and large genomes. Nidoviruses employ single-stranded, polycistronic RNA genomes of positive polarity that direct the synthesis of the subunits of the replicative complex, including the RNA-dependent RNA polymerase and helicase. Replicase gene expression is under the principal control of a ribosomal frameshifting signal and a chymotrypsin-like protease, which is assisted by one or more papain-like proteases. A nested set of subgenomic RNAs is synthesized to express the 3'-proximal ORFs that encode most conserved structural proteins and, in some large nidoviruses, also diverse accessory proteins that may promote Virus adaptation to specific hosts. The replicase machinery includes a set of RNA-processing enzymes some of which are unique for either all or large nidoviruses. The acquisition of these enzymes may have improved the low fidelity of RNA replication to allow genome expansion and give rise to the ancestors of small and, Subsequently, large nidoviruses. (c) 2006 Elsevier B.V. All rights reserved. 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APR 2006 117 1 17 37 10.1016/j.virusres.2006.01.017 21 Virology Virology 032AJ WOS:000236746000003 16503362 2020-04-01 J Meyers, LA; Pourbohloul, B; Newman, MEJ; Skowronski, DM; Brunham, RC Meyers, LA; Pourbohloul, B; Newman, MEJ; Skowronski, DM; Brunham, RC Network theory and SARS: predicting outbreak diversity JOURNAL OF THEORETICAL BIOLOGY English Article SARS; epidemiology; intervention; contact network; mathematical model ACUTE RESPIRATORY SYNDROME; INFECTIOUS-DISEASES; MODEL; TRANSMISSION; SPREAD; CORONAVIRUS; EPIDEMICS Many infectious diseases spread through populations via the networks formed by physical contacts among individuals. The patterns of these contacts tend to be highly heterogeneous. Traditional "compartmental" modeling in epidemiology, however, assumes that population groups are fully mixed, that is, every individual has an equal chance of spreading the disease to every other. 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Med. DEC 2004 10 12 S S88 S97 10.1038/nm1143 10 Biochemistry & Molecular Biology; Cell Biology; Medicine, Research & Experimental Biochemistry & Molecular Biology; Cell Biology; Research & Experimental Medicine 879RC WOS:000225733900005 15577937 Green Published, Bronze 2020-04-01 J Reusken, CBEM; Haagmans, BL; Muller, MA; Gutierrez, C; Godeke, GJ; Meyer, B; Muth, D; Raj, VS; Smits-De Vries, L; Corman, VM; Drexler, JF; Smits, SL; El Tahir, YE; De Sousa, R; van Beek, J; Nowotny, N; van Maanen, K; Hidalgo-Hermoso, E; Bosch, BJ; Rottier, P; Osterhaus, A; Gortazar, C; Drosten, C; Koopmans, MPG Reusken, Chantal B. E. M.; Haagmans, Bart L.; Mueller, Marcel A.; Gutierrez, Carlos; Godeke, Gert-Jan; Meyer, Benjamin; Muth, Doreen; Raj, V. Stalin; Smits-De Vries, Laura; Corman, Victor M.; Drexler, Jan-Felix; Smits, Saskia L.; El Tahir, Yasmin E.; De Sousa, Rita; van Beek, Janko; Nowotny, Norbert; van Maanen, Kees; Hidalgo-Hermoso, Ezequiel; Bosch, Berend-Jan; Rottier, Peter; Osterhaus, Albert; Gortazar, Christian; Drosten, Christian; Koopmans, Marion P. G. Middle East respiratory syndrome coronavirus neutralising serum antibodies in dromedary camels: a comparative serological study LANCET INFECTIOUS DISEASES English Article BOVINE CORONAVIRUS; BAT CORONAVIRUS; INFECTION; VIRUS; SEQUENCE; PROTEIN; RISK; 2C Background A new betacoronavirus Middle East respiratory syndrome coronavirus (MERS-CoV) has been identified in patients with severe acute respiratory infection. Although related viruses infect bats, molecular clock analyses have been unable to identify direct ancestors of MERS-CoV. Anecdotal exposure histories suggest that patients had been in contact with dromedary camels or goats. We investigated possible animal reservoirs of MERSCoV by assessing specific serum antibodies in livestock. Methods We took sera from animals in the Middle East (Oman) and from elsewhere (Spain, Netherlands, Chile). Cattle (n=80), sheep (n=40), goats (n=40), dromedary camels (n=155), and various other camelid species (n=34) were tested for specific serum IgG by protein microarray using the receptor-binding Si subunits of spike proteins of MERS-CoV, severe acute respiratory syndrome coronavirus, and human coronavirus 0C43. Results were confirmed by virus neutralisation tests for MERS-CoV and bovine coronavirus. Findings 50 of 50 (100%) sera from Omani camels and 15 of 105 (14%) from Spanish camels had protein-specific antibodies against MERS-CoV spike. Sera from European sheep, goats, cattle, and other camelids had no such antibodies. MERS-CoV neutralising antibody titres varied between 1/320 and 1/2560 for the Omani camel sera and between 1/20 and 1/320 for the Spanish camel sera. There was no evidence for cross-neutralisation by bovine coronavirus antibodies. Interpretation MERS-CoV or a related virus has infected camel populations. Both titres and seroprevalences in sera from different locations in Oman suggest widespread infection. [Reusken, Chantal B. E. M.; Godeke, Gert-Jan; De Sousa, Rita; van Beek, Janko; Koopmans, Marion P. G.] Natl Inst Publ Hlth & Environm, Ctr Infect Dis Res Diagnost & Screening, Div Virol, POB 1, NL-3720 BA Bilthoven, Netherlands; [Haagmans, Bart L.; Raj, V. Stalin; Smits, Saskia L.; Osterhaus, Albert; Koopmans, Marion P. G.] Erasmus MC, Dept Virosci, Rotterdam, Netherlands; [Mueller, Marcel A.; Meyer, Benjamin; Muth, Doreen; Corman, Victor M.; Drexler, Jan-Felix; Drosten, Christian] Univ Bonn, Med Ctr, Inst Virol, Bonn, Germany; [Gutierrez, Carlos] Univ Las Palmas Gran Canaria, Fac Vet, Dept Anim Med & Surg, Las Palmas Gran Canaria, Canary Islands, Spain; [Smits-De Vries, Laura; Bosch, Berend-Jan; Rottier, Peter] Univ Utrecht, Fac Vet Med, Dept Infect Dis & Immunol, Utrecht, Netherlands; [El Tahir, Yasmin E.] Sultan Qaboos Univ, Coll Agr & Marine Sci, Dept Anim & Vet Sci, Muscat, Oman; [Nowotny, Norbert] Sultan Qaboos Univ, Coll Med & Hlth Sci, Dept Microbiol & Immunol, Muscat, Oman; [De Sousa, Rita] European Ctr Dis Control, European Programme Publ Hlth Microbiol Training, Stockholm, Sweden; [Nowotny, Norbert] Univ Vet Med Vienna, Inst Virol, Viral Zoonoses Emerging & Vector Borne Infect Grp, Vienna, Austria; [van Maanen, Kees] Anim Hlth Serv, Deventer, Netherlands; [Hidalgo-Hermoso, Ezequiel] Parque Zool Buin Zoo, Dept Conservat & Res, Buin, Chile; [Gortazar, Christian] SaBio IREC CSIC UCLM JCCM, Ciudad Real, Spain; [Smits, Saskia L.; Osterhaus, Albert] Viroclin Biosci BV, Rotterdam, Netherlands Reusken, CBEM (reprint author), Natl Inst Publ Hlth & Environm, Ctr Infect Dis Res Diagnost & Screening, Div Virol, POB 1, NL-3720 BA Bilthoven, Netherlands. Chantal.Reusken@RIVM.nl Nowotny, Norbert/A-5474-2019; Meyer, Bernhard/Q-9413-2016; Raj, V Stalin/E-9670-2016; Koopmans, Marion/Y-9170-2019; Gutierrez, Carlos/E-2989-2012; Meyer, Benjamin/F-3285-2018; Drexler, Jan Felix/C-1004-2014; Corman, Victor Max/K-1319-2019; Mueller, Marcel/O-2425-2019; Smits, Saskia/A-2953-2014; Gortazar, Christian/E-7918-2012 Nowotny, Norbert/0000-0002-3548-571X; Raj, V Stalin/0000-0003-2250-8481; Koopmans, Marion/0000-0002-5204-2312; Gutierrez, Carlos/0000-0003-0764-7408; Meyer, Benjamin/0000-0003-0601-3550; Corman, Victor Max/0000-0002-3605-0136; Mueller, Marcel/0000-0003-2242-5117; Haagmans, Bart/0000-0001-6221-2015; Osterhaus, Albert/0000-0002-6074-1172; Gortazar, Christian/0000-0003-0012-4006; Drexler, Jan Felix/0000-0002-3509-0232; De Sousa, Rita/0000-0001-6134-6003 European Public Health Training Program (Euphem), ECDC, Stockholm, Sweden; European UnionEuropean Union (EU) [223498]; ANTIGONE [278976]; Deutsche Forschungsgemeinschaft (DFG)German Research Foundation (DFG) [DR772/3-1] We thank Prof MC Horzinek for helpful suggestions. RDS was funded by the European Public Health Training Program (Euphem), ECDC, Stockholm, Sweden. Contributions to the study were funded through the European Union FP7 projects EMPERIE (contract number 223498; to BLH, SLS, AO, CD) and ANTIGONE (contract number 278976; to CG, CD, MPGK, AO). Work in Bonn was also funded by Deutsche Forschungsgemeinschaft (DFG grant DR772/3-1 to CD). 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Dis. OCT 2013 13 10 859 866 10.1016/S1473-3099(13)70164-6 8 Infectious Diseases Infectious Diseases 224PD WOS:000324899700020 23933067 Bronze Y N 2020-04-01 J Hota, B Hota, B Contamination, disinfection, and cross-colonization: Are hospital surfaces reservoirs for nosocomial infection? CLINICAL INFECTIOUS DISEASES English Article RESISTANT STAPHYLOCOCCUS-AUREUS; INTENSIVE-CARE-UNIT; ENVIRONMENTAL CONTAMINATION; ACINETOBACTER-BAUMANNII; CLOSTRIDIUM-DIFFICILE; ENTEROCOCCUS-FAECIUM; PSEUDOMONAS-AERUGINOSA; MOLECULAR EPIDEMIOLOGY; AIRBORNE TRANSMISSION; RISK-FACTORS Despite documentation that the inanimate hospital environment (e. g., surfaces and medical equipment) becomes contaminated with nosocomial pathogens, the data that suggest that contaminated fomites lead to nosocomial infections do so indirectly. Pathogens for which there is more-compelling evidence of survival in environmental reservoirs include Clostridium difficile, vancomycin-resistant enterococci, and methicillin-resistant Staphylococcus aureus, and pathogens for which there is evidence of probable survival in environmental reservoirs include norovirus, influenza virus, severe acute respiratory syndrome associated coronavirus, and Candida species. Strategies to reduce the rates of nosocomial infection with these pathogens should conform to established guidelines, with an emphasis on thorough environmental cleaning and use of Environmental Protection Agency-approved detergent-disinfectants. 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A number of these ORFs are predicted to encode structural EAV proteins. The organization and expression of the 3' part of the EAV genome are remarkably similar to those of coronaviruses and toroviruses. The 5'-terminal three-quarters of the genome contain the putative EAV polymerase gene, which also shares a number of features with the corresponding gene of corona- and toroviruses. The gene contains two large ORFs, ORF1a and ORF1b, with an overlap region of 19 nucleotides. The presence of a "shifty" heptanucleotide sequence in this region and a downstream RNA pseudoknot structure indicate that ORF1b is probably expressed by ribosomal frameshifting. The frameshift-directing potential of the ORF1a/ORF1b overlap region was demonstrated by using a reporter gene. Moreover, the predicted ORF1b product was found to contain four domains which have been identified in the same relative positions in coronavirus and torovirus ORF1b products. The sequences of the EAV and coronavirus ORF1a proteins were found to be much more diverged. The EAV ORF1a product contains a putative trypsinlike serine protease motif. Our data indicate that EAV, presently considered a togavirus, is evolutionarily related to viruses from the coronaviruslike superfamily. 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Virol. JUN 1991 65 6 2910 2920 10.1128/JVI.65.6.2910-2920.1991 11 Virology Virology FM165 WOS:A1991FM16500018 1851863 Bronze, Green Published 2020-04-01 J Fouchier, RAM; Hartwig, NG; Bestebroer, TM; Niemeyer, B; de Jong, JC; Simon, JH; Osterhaus, ADME Fouchier, RAM; Hartwig, NG; Bestebroer, TM; Niemeyer, B; de Jong, JC; Simon, JH; Osterhaus, ADME A previously undescribed coronavirus associated with respiratory disease in humans PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA English Article HOSPITALIZED-PATIENTS; VIRUS-INFECTIONS; IDENTIFICATION; COMMUNITY; SEQUENCE; ETIOLOGY; CHILDREN; ILLNESS; GENOME; PCR The etiology of acute respiratory tract illnesses is sometimes unclear due to limitations of diagnostic tests or the existence of as-yet-unidentified pathogens. Here we describe the identification and characterization of a not previously recognized coronavirus obtained from an 8-mo-old boy suffering from pneumonia. This coronavirus replicated efficiently in tertiary monkey kidney cells and Vero cells, in contrast to human coronaviruses (HCoV) 229E and OC43. The entire cDNA genome sequence of the previously undescribed coronavirus was determined, revealing that it is most closely related to porcine epidemic diarrhea virus and HCoV 229E. The maximum amino acid sequence identity between ORFs of the newly discovered coronavirus and related group 1 coronaviruses ranged from 43% to 67%. Real-time RT-PCR assays were designed to test for the prevalence of the previously undescribed coronavirus in humans. Using these tests, the virus was detected in four of 139 individuals (3%) who were suffering from respiratory illness with unknown etiology. All four patients suffered from fever, runny nose, and dry cough, and all four had underlying or additional morbidity. Our data will enable the development of diagnostic tests to study the prevalence and clinical impact of this virus in humans in more detail. Moreover, it will be important to discriminate this previously undescribed coronavirus from HCoV 229E and OC43 and the severe acute respiratory syndrome coronavirus. 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Natl. Acad. Sci. U. S. A. APR 20 2004 101 16 6212 6216 10.1073/pnas.0400762101 5 Multidisciplinary Sciences Science & Technology - Other Topics 814ME WOS:000220978000095 15073334 Green Published, Bronze 2020-04-01 J de Groot, RJ; Baker, SC; Baric, RS; Brown, CS; Drosten, C; Enjuanes, L; Fouchier, RAM; Galiano, M; Gorbalenya, AE; Memish, ZA; Perlman, S; Poon, LLM; Snijder, EJ; Stephens, GM; Woo, PCY; Zaki, AM; Zambon, M; Ziebuhr, J de Groot, Raoul J.; Baker, Susan C.; Baric, Ralph S.; Brown, Caroline S.; Drosten, Christian; Enjuanes, Luis; Fouchier, Ron A. M.; Galiano, Monica; Gorbalenya, Alexander E.; Memish, Ziad A.; Perlman, Stanley; Poon, Leo L. M.; Snijder, Eric J.; Stephens, Gwen M.; Woo, Patrick C. Y.; Zaki, Ali M.; Zambon, Maria; Ziebuhr, John Middle East Respiratory Syndrome Coronavirus (MERS-CoV): Announcement of the Coronavirus Study Group JOURNAL OF VIROLOGY English Editorial Material [de Groot, Raoul J.] Univ Utrecht, Fac Vet Med, Dept Infect Dis & Immunol, Div Virol, Utrecht, Netherlands; [Baker, Susan C.] Loyola Univ, Med Ctr, Dept Microbiol & Immunol, Maywood, IL 60153 USA; [Baric, Ralph S.] Univ N Carolina, Dept Epidemiol, Chapel Hill, NC USA; [Brown, Caroline S.] WHO, WHO Reg Off Europe, Copenhagen, Denmark; [Drosten, Christian] Univ Bonn, Med Ctr, Inst Virol, Bonn, Germany; [Enjuanes, Luis] Campus Univ Autonoma Madrid, Natl Ctr Biotechnol CNB CSIC, Dept Mol & Cell Biol, Madrid, Spain; [Fouchier, Ron A. M.] Erasmus MC, Virosci Lab, Rotterdam, Netherlands; [Galiano, Monica; Zambon, Maria] Publ Hlth England, Hlth Protect Agcy, London, England; [Gorbalenya, Alexander E.; Snijder, Eric J.] Leiden Univ, Med Ctr, Dept Med Microbiol, Leiden, Netherlands; [Memish, Ziad A.; Stephens, Gwen M.] Minist Hlth, Publ Hlth Directorate, Riyadh, Saudi Arabia; [Perlman, Stanley] Univ Iowa, Dept Microbiol, Iowa City, IA 52242 USA; [Poon, Leo L. M.] Univ Hong Kong, Influenza Res Ctr, Hong Kong, Hong Kong, Peoples R China; [Poon, Leo L. M.] Univ Hong Kong, Sch Publ Hlth, Hong Kong, Hong Kong, Peoples R China; [Woo, Patrick C. Y.] Univ Hong Kong, Dept Microbiol, Hong Kong, Hong Kong, Peoples R China; [Zaki, Ali M.] Ain Shams Univ, Fac Med, Cairo, Egypt; [Ziebuhr, John] Univ Giessen, Inst Med Virol, D-35390 Giessen, Germany de Groot, RJ (reprint author), Univ Utrecht, Fac Vet Med, Dept Infect Dis & Immunol, Div Virol, Utrecht, Netherlands. r.j.degroot@uu.nl Jha, Babal/AAC-8337-2020; Gorbalenya, Alexander E/J-4818-2012; Fouchier, Ron A/A-1911-2014; Enjuanes, Luis/F-7845-2016; Fouchier, Ron/Y-3755-2019; Woo, Patrick Chiu Yat/AAJ-6112-2020; Snijder, Eric J./E-6073-2018; Poon, Leo/C-4382-2009; Ziebuhr, John/G-7669-2015 Jha, Babal/0000-0002-7660-5255; Gorbalenya, Alexander E/0000-0002-4967-7341; Fouchier, Ron A/0000-0001-8095-2869; Fouchier, Ron/0000-0001-8095-2869; Woo, Patrick Chiu Yat/0000-0001-9401-1832; Snijder, Eric J./0000-0003-3297-2309; Poon, Leo/0000-0002-9101-7953; Enjuanes, Luis/0000-0002-0854-0226; Perlman, Stanley/0000-0003-4213-2354; Ziebuhr, John/0000-0002-5741-8825 NIAID NIH HHSUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USANIH National Institute of Allergy & Infectious Diseases (NIAID) [R01 AI085089, P01 AI060699] Annan A, 2013, EMERG INFECT DIS, V19, P456, DOI 10.3201/eid1903.121503; Bermingham A, 2012, EUROSURVEILLANCE, V17, P6; Cotten M, 2013, EMERG INFECT DIS, V19, P736, DOI 10.3201/eid1905.130057; deGroot R.J., 2012, VIRUS TAXONOMY, P806; European Centre for Disease Prevention and Control (ECDC), 2012, COMM DIS THREATS REP, P2; Falcon A, 2011, ARCH VIROL, V156, P1883, DOI 10.1007/s00705-011-1057-1; Reusken CBEM, 2010, VECTOR-BORNE ZOONOT, V10, P785, DOI 10.1089/vbz.2009.0173; Tahir M, 2013, EUROSURVEILLANCE, V18, P4; van Boheemen S, 2012, MBIO, V3, DOI 10.1128/mBio.00473-12; Woo PCY, 2009, EXP BIOL MED, V234, P1117, DOI 10.3181/0903-MR-94; World Health Organization, COR INF; World Health Organization, 2012, BACKGR SUMM NOV COR; Zaki A., 2012, INT SOC INFECT DIS; Zaki AM, 2012, NEW ENGL J MED, V367, P1814, DOI 10.1056/NEJMoa1211721 14 335 343 13 94 AMER SOC MICROBIOLOGY WASHINGTON 1752 N ST NW, WASHINGTON, DC 20036-2904 USA 0022-538X 1098-5514 J VIROL J. Virol. JUL 2013 87 14 7790 7792 10.1128/JVI.01244-13 3 Virology Virology 172PX WOS:000321017700001 23678167 Bronze, Green Published 2020-04-01 J Yang, HT; Yang, MJ; Ding, Y; Liu, YW; Lou, ZY; Zhou, Z; Sun, L; Mo, LJ; Ye, S; Pang, H; Gao, GF; Anand, K; Bartlam, M; Hilgenfeld, R; Rao, ZH Yang, HT; Yang, MJ; Ding, Y; Liu, YW; Lou, ZY; Zhou, Z; Sun, L; Mo, LJ; Ye, S; Pang, H; Gao, GF; Anand, K; Bartlam, M; Hilgenfeld, R; Rao, ZH The crystal structures of severe acute respiratory syndrome virus main protease and its complex with an inhibitor PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA English Article GENOME SEQUENCE; CORONAVIRUS; PROTEINASE A newly identified severe acute respiratory syndrome coronavirus (SARS-CoV), is the etiological agent responsible for the outbreak of SARS. The SARS-CoV main protease, which is a 33.8-kDa protease (also called the 3C-like protease), plays a pivotal role in mediating viral replication and transcription functions through extensive proteolytic processing of two replicase polyproteins, pp1a (486 kDa) and pp1ab (790 kDa). Here, we report the crystal structures of the SARS-CoV main protease at different pH values and in complex with a specific inhibitor. The protease structure has a fold that can be described as an augmented serine-protease, but with a Cys-His at the active site. This series of crystal structures, which is the first, to our knowledge, of any protein from the SARS virus, reveal substantial pH-dependent conformational changes, and an unexpected mode of inhibitor binding, providing a structural basis for rational drug design. Tsing Hua Univ, Struct Biol Lab, Beijing 100084, Peoples R China; Chinese Acad Sci, Inst Biophys, Natl Lab Biomacromol, Beijing 100084, Peoples R China; Med Univ Lubeck, Inst Biochem, D-23538 Lubeck, Germany Rao, ZH (reprint author), Tsing Hua Univ, Struct Biol Lab, Beijing 100084, Peoples R China. 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Natl. Acad. Sci. U. S. A. NOV 11 2003 100 23 13190 13195 10.1073/pnas.1835675100 6 Multidisciplinary Sciences Science & Technology - Other Topics 743LR WOS:000186573700016 14585926 Green Published, Bronze 2020-04-01 J Stevenson, GW; Hoang, H; Schwartz, KJ; Burrough, ER; Sun, D; Madson, D; Cooper, VL; Pillatzki, A; Gauger, P; Schmitt, BJ; Koster, LG; Killian, ML; Yoon, KJ Stevenson, Gregory W.; Hoang, Hai; Schwartz, Kent J.; Burrough, Eric R.; Sun, Dong; Madson, Darin; Cooper, Vickie L.; Pillatzki, Angela; Gauger, Philip; Schmitt, Beverly J.; Koster, Leo G.; Killian, Mary L.; Yoon, Kyoungjin J. Emergence of Porcine epidemic diarrhea virus in the United States: clinical signs, lesions, and viral genomic sequences JOURNAL OF VETERINARY DIAGNOSTIC INVESTIGATION English Article Diarrhea; enteric disease; porcine; Porcine epidemic diarrhea virus TISSUES During the 10 days commencing April 29, 2013, the Iowa State University Veterinary Diagnostic Laboratory received the first 4 of many submissions from swine farms experiencing explosive epidemics of diarrhea and vomiting affecting all ages, with 90-95% mortality in suckling pigs. Histology revealed severe atrophy of villi in all segments of the small intestines with occasional villus-epithelial syncytial cells, but testing for rotaviruses and Transmissible gastroenteritis virus (Alphacoronavirus 1) were negative. Negative-staining electron microscopy of feces revealed coronavirus-like particles and a pan-coronavirus polymerase chain reaction (PCR) designed to amplify a conserved region of the polymerase gene for all members in the family Coronaviridae produced expected 251-bp amplicons. Subsequent sequencing and analysis revealed 99.6-100% identity among the PCR amplicons from the 4 farms and 97-99% identity to the corresponding portion of the polymerase gene of Porcine epidemic diarrhea virus (PEDV) strains, with the highest identity (99%) to strains from China in 2012. Findings were corroborated at National Veterinary Services Laboratories using 2 nested S-gene and 1 nested N-gene PCR tests where the sequenced amplicons also had the highest identity with 2012 China strains. Whole genome sequence for the virus from 2 farms in 2 different states using next-generation sequencing technique was compared to PEDV sequences available in GenBank. The 2013 U.S. PEDV had 96.6-99.5% identity with all known PEDV strains and the highest identity (>99.0%) to some of the 2011-2012 Chinese strains. The nearly simultaneous outbreaks of disease, and high degree of homology (99.6-100%) between the PEDV strains from the 4 unrelated farms, suggests a common source of virus. [Stevenson, Gregory W.; Schwartz, Kent J.; Burrough, Eric R.; Madson, Darin; Cooper, Vickie L.; Pillatzki, Angela; Gauger, Philip; Yoon, Kyoungjin J.] Iowa State Univ, Dept Vet Diagnost & Prod Anim Med, Ames, IA 50011 USA; [Hoang, Hai; Sun, Dong] Iowa State Univ, Dept Vet Microbiol & Prevent Med, Ames, IA 50011 USA; [Schmitt, Beverly J.; Koster, Leo G.; Killian, Mary L.] US Anim & Plant Hlth Inspect Serv, Diagnost Virol Lab, Natl Vet Serv Labs, USDA,Vet Serv, Ames, IA USA Stevenson, GW (reprint author), Iowa State Univ, Vet Diagnost Lab, 1600 South 16th St, Ames, IA 50011 USA. stevengw@iastate.edu; kyoon@iastate.edu Pillatzki, Angela/W-9005-2019 Pillatzki, Angela/0000-0002-1888-396X Hermann JR, 2008, CAN J VET RES, V72, P367; Kim O, 1999, J VET DIAGN INVEST, V11, P458, DOI 10.1177/104063879901100512; Marthaler D, 2012, VIROLOGY, V433, P85, DOI 10.1016/j.virol.2012.07.006; Moes E, 2005, BMC INFECT DIS, V5, DOI 10.1186/1471-2334-5-6; Shoup DI, 1996, J VET DIAGN INVEST, V8, P161, DOI 10.1177/104063879600800204; Song D, 2012, VIRUS GENES, V44, P167, DOI 10.1007/s11262-012-0713-1 6 332 368 2 104 SAGE PUBLICATIONS INC THOUSAND OAKS 2455 TELLER RD, THOUSAND OAKS, CA 91320 USA 1040-6387 1943-4936 J VET DIAGN INVEST J. Vet. Diagn. Invest. SEP 2013 25 5 649 654 10.1177/1040638713501675 6 Veterinary Sciences Veterinary Sciences 289CX WOS:000329660100018 23963154 Bronze Y N 2020-04-01 J Song, D; Park, B Song, Daesub; Park, Bongkyun Porcine epidemic diarrhoea virus: a comprehensive review of molecular epidemiology, diagnosis, and vaccines VIRUS GENES English Article Porcine epidemic diarrhoea virus; Review; Molecular epidemiology; Diagnosis; Vaccine TRANSMISSIBLE GASTROENTERITIS VIRUS; CORONAVIRUS SPIKE PROTEIN; POLYMERASE-CHAIN-REACTION; SEQUENCE-ANALYSIS; RT-PCR; PROTECTIVE IMMUNITY; ANTIBODY-RESPONSES; LYMPHOPROLIFERATIVE RESPONSES; DIFFERENTIAL DETECTION; ALPHA-INTERFERON The porcine epidemic diarrhoea virus (PEDV), a member of the Coronaviridae family, causes acute diarrhoea and dehydration in pigs. Although it was first identified in Europe, it has become increasingly problematic in many Asian countries, including Korea, China, Japan, the Philippines, and Thailand. The economic impacts of the PEDV are substantial, given that it results in significant morbidity and mortality in neonatal piglets and is associated with increased costs related to vaccination and disinfection. Recently, progress has been made in understanding the molecular epidemiology of PEDV, thereby leading to the development of new vaccines. In the current review, we first describe the molecular and genetic characteristics of the PEDV. Then we discuss its molecular epidemiology and diagnosis, what vaccines are available, and how PEDV can be treated. 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Virology Genetics & Heredity; Virology 900RB WOS:000300905100002 22270324 2020-04-01 J Woo, PCY; Lau, SKP; Lam, CSF; Lau, CCY; Tsang, AKL; Lau, JHN; Bai, R; Teng, JLL; Tsang, CCC; Wang, M; Zheng, BJ; Chan, KH; Yuen, KY Woo, Patrick C. Y.; Lau, Susanna K. P.; Lam, Carol S. F.; Lau, Candy C. Y.; Tsang, Alan K. L.; Lau, John H. N.; Bai, Ru; Teng, Jade L. L.; Tsang, Chris C. C.; Wang, Ming; Zheng, Bo-Jian; Chan, Kwok-Hung; Yuen, Kwok-Yung Discovery of Seven Novel Mammalian and Avian Coronaviruses in the Genus Deltacoronavirus Supports Bat Coronaviruses as the Gene Source of Alphacoronavirus and Betacoronavirus and Avian Coronaviruses as the Gene Source of Gammacoronavirus and Deltacoronavirus JOURNAL OF VIROLOGY English Article ACUTE RESPIRATORY SYNDROME; CHINESE HORSESHOE BATS; COMPLETE GENOME; SARS-CORONAVIRUS; NATURAL RECOMBINATION; DIFFERENT GENOTYPES; TURKEY CORONAVIRUS; MOLECULAR-BIOLOGY; PROTEIN FAMILIES; SOUTHERN CHINA Recently, we reported the discovery of three novel coronaviruses, bulbul coronavirus HKU11, thrush coronavirus HKU12, and munia coronavirus HKU13, which were identified as representatives of a novel genus, Deltacoronavirus, in the subfamily Coronavirinae. In this territory-wide molecular epidemiology study involving 3,137 mammals and 3,298 birds, we discovered seven additional novel deltacoronaviruses in pigs and birds, which we named porcine coronavirus HKU15, white-eye coronavirus HKU16, sparrow coronavirus HKU17, magpie robin coronavirus HKU18, night heron coronavirus HKU19, wigeon coronavirus HKU20, and common moorhen coronavirus HKU21. Complete genome sequencing and comparative genome analysis showed that the avian and mammalian deltacoronaviruses have similar genome characteristics and structures. They all have relatively small genomes (25.421 to 26.674 kb), the smallest among all coronaviruses. They all have a single papain-like protease domain in the nsp3 gene; an accessory gene, NS6 open reading frame (ORF), located between the M and N genes; and a variable number of accessory genes (up to four) downstream of the N gene. Moreover, they all have the same putative transcription regulatory sequence of ACACCA. Molecular clock analysis showed that the most recent common ancestor of all coronaviruses was estimated at approximately 8100 BC, and those of Alphacoronavirus, Betacoronavirus, Gammacoronavirus, and Deltacoronavirus were at approximately 2400 BC, 3300 BC, 2800 BC, and 3000 BC, respectively. From our studies, it appears that bats and birds, the warm blooded flying vertebrates, are ideal hosts for the coronavirus gene source, bats for Alphacoronavirus and Betacoronavirus and birds for Gammacoronavirus and Deltacoronavirus, to fuel coronavirus evolution and dissemination. [Woo, Patrick C. Y.; Lau, Susanna K. P.; Lam, Carol S. F.; Lau, Candy C. Y.; Tsang, Alan K. L.; Lau, John H. N.; Bai, Ru; Teng, Jade L. L.; Tsang, Chris C. C.; Zheng, Bo-Jian; Chan, Kwok-Hung; Yuen, Kwok-Yung] Univ Hong Kong, Dept Microbiol, Hong Kong, Hong Kong, Peoples R China; [Woo, Patrick C. Y.; Lau, Susanna K. 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This work is partly supported by Research Grant Council grant HKU 780709 M; University Development Fund and Outstanding Young Researcher Award, The University of Hong Kong; The Tung Wah Group of Hospitals Fund for Research in Infectious Diseases; the HKSAR Research Fund for the Control of Infectious Diseases of the Health, Welfare and Food Bureau; and the Shaw Foundation. 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Virol. APR 2012 86 7 3995 4008 10.1128/JVI.06540-11 14 Virology Virology 906TV WOS:000301371500055 22278237 Green Published, Bronze Y N 2020-04-01 J Chou, KC; Wei, DQ; Zhong, WZ Chou, KC; Wei, DQ; Zhong, WZ Binding mechanism of coronavirus main proteinase with ligands and its implication to drug design against SARS BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS English Article SARS; coronavirus proteinase; KZ7088; AG7088; binding pocket; octapeptide substrate; "distorted key" mechanism PROTEASE CLEAVAGE SITES; TERTIARY STRUCTURE; PREDICTION; COMPLEX; MODEL; CDK5 In order to stimulate the development of drugs against severe acute respiratory syndrome (SARS), based on the atomic coordinates of the SARS coronavirus main proteinase determined recently [Science 13 (May) (2003) (online)], studies of docking KZ7088 (a derivative of AG7088) and the AVLQSGFR octapeptide to the enzyme were conducted. It has been observed that both the above compounds interact with the active site of the SARS enzyme through six hydrogen bonds. Also, a clear definition of the binding pocket for KZ7088 has been presented. These findings may provide a solid basis for subsite analysis and mutagenesis relative to rational design of highly selective inhibitors for therapeutic application. Meanwhile, the idea of how to develop inhibitors of the SARS enzyme based on the knowledge of its own peptide substrates (the so-called "distorted key" approach) was also briefly elucidated. (C) 2003 Elsevier Inc. All rights reserved. Gordon Life Sci Inst, Kalamazoo, MI 49009 USA; Tianjin Normal Univ, TIBDD, Tianjin, Peoples R China Chou, KC (reprint author), Gordon Life Sci Inst, 7088 Arbor Valley, Kalamazoo, MI 49009 USA. 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AUG 15 2003 308 1 148 151 10.1016/S0006-291X(03)01342-1 4 Biochemistry & Molecular Biology; Biophysics Biochemistry & Molecular Biology; Biophysics 709AG WOS:000184602100023 12890493 Bronze 2020-04-01 J Rakes, CP; Arruda, E; Ingram, JM; Hoover, GE; Zambrano, JC; Hayden, FG; Platts-Mills, TAE; Heymann, PW Rakes, CP; Arruda, E; Ingram, JM; Hoover, GE; Zambrano, JC; Hayden, FG; Platts-Mills, TAE; Heymann, PW Rhinovirus and respiratory syncytial virus in wheezing children requiring emergency care - IgE and eosinophil analyses AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE English Article ASTHMATIC SUBJECTS; CATIONIC PROTEIN; INFECTION; EXACERBATIONS; INFANTS; LYMPHOCYTES; COMMUNITY; ADULTS; RNA; PCR This cross-sectional emergency department study of 70 wheezing children and 59 control subjects (2 mo to 16 yr of age) examined the prevalence of respiratory viruses and their relationship to age, atopic status, and eosinophil markers. Nasal washes were cultured for respiratory viruses, assayed for respiratory syncytial virus (RSV) antigen, and tested for coronavirus and rhinovirus RNA using reverse transcription-PCR (RT-PCR). Also evaluated were eosinophil numbers and eosinophil cationic protein (ECP) in both nasal washes and serum, along with total IgE and specific IgE antibody in serum. Respiratory viruses were detected in 82% (18 of 22) of wheezing infants younger than 2 yr of age and in 83% (40 of 48) of older wheezing children. The predominant pathogens were RSV in infants (detected in 68% of wheezing subjects) and rhinovirus in older wheezing children (71%), and both were strongly associated with wheezing (p < 0.005). RSV was largely limited to wheezing children younger than 24 mo of age, but rhinovirus was detected by KT-PCR in 41% of all infants and in 35% of nonwheezing control subjects older than 2 yr of age. After 2 yr of age the strongest odds for wheezing were observed among those who had a positive RT-PCR test for rhinovirus together with a positive serum radioallergosorbent testing (RAST), nasal eosinophilia, or elevated nasal ECP (odds ratios = 17, 21, and 25, respectively). Results from this study demonstrate that a large majority of emergent wheezing illnesses during childhood (2 to 16 yr of age) can be linked to infection with rhinovirus, and that these wheezing attacks are most likely in those who have rhinovirus together with evidence of atopy or eosinophilic airway inflammation. Univ Virginia, Hlth Sci Ctr, Dept Pediat, Charlottesville, VA 22908 USA; Univ Virginia, Hlth Sci Ctr, Dept Internal Med, Charlottesville, VA 22908 USA; Univ Virginia, Hlth Sci Ctr, Dept Pathol, Charlottesville, VA 22908 USA Rakes, CP (reprint author), Univ Virginia, Hlth Sci Ctr, Dept Pediat, MR-4 Bldg,Box 29,Room 5061, Charlottesville, VA 22908 USA. 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MAR 1999 159 3 785 790 10.1164/ajrccm.159.3.9801052 6 Critical Care Medicine; Respiratory System General & Internal Medicine; Respiratory System 175QQ WOS:000079106600014 10051251 2020-04-01 J Zust, R; Cervantes-Barragan, L; Habjan, M; Maier, R; Neuman, BW; Ziebuhr, J; Szretter, KJ; Baker, SC; Barchet, W; Diamond, MS; Siddell, SG; Ludewig, B; Thiel, V Zuest, Roland; Cervantes-Barragan, Luisa; Habjan, Matthias; Maier, Reinhard; Neuman, Benjamin W.; Ziebuhr, John; Szretter, Kristy J.; Baker, Susan C.; Barchet, Winfried; Diamond, Michael S.; Siddell, Stuart G.; Ludewig, Burkhard; Thiel, Volker Ribose 2 '-O-methylation provides a molecular signature for the distinction of self and non-self mRNA dependent on the RNA sensor Mda5 NATURE IMMUNOLOGY English Article MOUSE HEPATITIS-VIRUS; RIG-I; SARS-CORONAVIRUS; INNATE IMMUNITY; STRANDED-RNA; VACCINIA VIRUS; INTERFERON; PROTEIN; RECOGNITION; INFECTION The 5' cap structures of higher eukaryote mRNAs have ribose 2'-O-methylation. Likewise, many viruses that replicate in the cytoplasm of eukaryotes have evolved 2'-O-methyltransferases to autonomously modify their mRNAs. However, a defined biological role for 2'-O-methylation of mRNA remains elusive. Here we show that 2'-O-methylation of viral mRNA was critically involved in subverting the induction of type I interferon. We demonstrate that human and mouse coronavirus mutants lacking 2'-O-methyltransferase activity induced higher expression of type I interferon and were highly sensitive to type I interferon. Notably, the induction of type I interferon by viruses deficient in 2'-O-methyltransferase was dependent on the cytoplasmic RNA sensor Mda5. This link between Mda5-mediated sensing of viral RNA and 2'-O-methylation of mRNA suggests that RNA modifications such as 2'-O-methylation provide a molecular signature for the discrimination of self and non-self mRNA. [Zuest, Roland; Cervantes-Barragan, Luisa; Habjan, Matthias; Maier, Reinhard; Ludewig, Burkhard; Thiel, Volker] Kantonal Hosp St Gallen, Inst Immunobiol, St Gallen, Switzerland; [Neuman, Benjamin W.] Univ Reading, Sch Biol Sci, Reading, Berks, England; [Ziebuhr, John] Queens Univ Belfast, Ctr Infect & Immun, Belfast, Antrim, North Ireland; [Ziebuhr, John] Univ Giessen, Inst Med Virol, Giessen, Germany; [Szretter, Kristy J.; Diamond, Michael S.] Washington Univ, Sch Med, Dept Mol Microbiol, Dept Med, St Louis, MO 63110 USA; [Szretter, Kristy J.; Diamond, Michael S.] Washington Univ, Sch Med, Dept Pathol & Immunol, St Louis, MO USA; [Baker, Susan C.] Loyola Univ, Stritch Sch Med, Dept Microbiol & Immunol, Maywood, IL 60153 USA; [Barchet, Winfried] Univ Bonn, Univ Hosp, Inst Clin Chem & Pharmacol, D-5300 Bonn, Germany; [Siddell, Stuart G.] Univ Bristol, Sch Med & Vet Sci, Dept Cellular & Mol Med, Bristol, Avon, England; [Ludewig, Burkhard; Thiel, Volker] Univ Zurich, Vetsuisse Fac, Zurich, Switzerland Thiel, V (reprint author), Kantonal Hosp St Gallen, Inst Immunobiol, St Gallen, Switzerland. volker.thiel@kssg.ch Jha, Babal/AAC-8337-2020; Thiel, Volker/AAI-2391-2019; Maier, Reinhard/AAH-5159-2020; Diamond, Michael/AAH-1733-2019; Ziebuhr, John/G-7669-2015 Jha, Babal/0000-0002-7660-5255; Diamond, Michael/0000-0002-8791-3165; Barchet, Winfried/0000-0002-6745-6606; Habjan, Matthias/0000-0002-3623-4496; Ziebuhr, John/0000-0002-5741-8825; Thiel, Volker/0000-0002-5783-0887; Siddell, Stuart/0000-0002-8702-7868; Neuman, Benjamin/0000-0003-1240-8954; Szretter, Kristy/0000-0003-0391-2307 Swiss National Science FoundationSwiss National Science Foundation (SNSF); European Commission (TOLERAGE)European Commission Joint Research Centre; Novartis Foundation for Biomedical Research, Switzerland; German Ministry of Education and ResearchFederal Ministry of Education & Research (BMBF); Austrian Science FundAustrian Science Fund (FWF) [FWF J3044]; Deutsche ForschungsgemeinschaftGerman Research Foundation (DFG); National Institutes of HealthUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USA [AI060915, AI085089, U54 AI081680]; Medical Research CouncilMedical Research Council UK (MRC); Wellcome TrustWellcome Trust; Biotechnology and Biological Sciences Research CouncilBiotechnology and Biological Sciences Research Council (BBSRC) [BB/G012067/1] We thank V. Lohmann (University of Heidelberg) for Huh-7 cells; G. L. Smith (Imperial College, London) for D980R cells; S. G. Sawicki (Medical University of Ohio) for 17Cl1 cells; M. Pelegrin (Institut de Genetique Moleculaire de Montpellier) for LL171 cells; L. Onder for assistance with fluorescence microscopy; and R. de Giuli, B. Schelle and N. Karl for technical assistance. This study was supported by the Swiss National Science Foundation, the European Commission (TOLERAGE), the Novartis Foundation for Biomedical Research, Switzerland, the German Ministry of Education and Research (V. T.), the Austrian Science Fund (FWF J3044 to M. H.), Deutsche Forschungsgemeinschaft (J.Z.), the National Institutes of Health (AI060915 and AI085089 to S. C. B.; U54 AI081680 (Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research to M. S. D), the Medical Research Council (B. W. N.) and the Wellcome Trust (S.G.S.). 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Immunol. FEB 2011 12 2 137 U46 10.1038/ni.1979 8 Immunology Immunology 708QF WOS:000286378400007 21217758 Green Accepted, Green Published Y N 2020-04-01 J Yang, ZY; Kong, WP; Huang, Y; Roberts, A; Murphy, BR; Subbarao, K; Nabel, GJ Yang, ZY; Kong, WP; Huang, Y; Roberts, A; Murphy, BR; Subbarao, K; Nabel, GJ A DNA vaccine induces SARS coronavirus neutralization and protective immunity in mice NATURE English Article ACUTE RESPIRATORY SYNDROME; HONG-KONG; VIRUS; IDENTIFICATION; CHALLENGE; INFECTION; PROTEINS; GENOME; PIGS Public health measures have successfully identified and contained outbreaks of the severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV)(1-5), but concerns remain over the possibility of future recurrences. Finding a vaccine for this virus therefore remains a high priority. Here, we show that a DNA vaccine encoding the spike (S) glycoprotein of the SARS-CoV induces T cell and neutralizing antibody responses, as well as protective immunity, in a mouse model. Alternative forms of S were analysed by DNA immunization. These expression vectors induced robust immune responses mediated by CD4 and CD8 cells, as well as significant antibody titres, measured by enzyme-linked immunosorbent assay. Moreover, antibody responses in mice vaccinated with an expression vector encoding a form of S that includes its transmembrane domain elicited neutralizing antibodies. Viral replication was reduced by more than six orders of magnitude in the lungs of mice vaccinated with these S plasmid DNA expression vectors, and protection was mediated by a humoral but not a T-cell-dependent immune mechanism. Gene-based vaccination for the SARS-CoV elicits effective immune responses that generate protective immunity in an animal model. 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The discovery of new cathepsins, such as cathepsins K, V, X, F and 0, and their tissue distribution suggested that at least some of them are involved in very specific cellular processes. Moreover, gene ablation experiments revealed that cathepsins play a vital role in numerous physiological processes, such as antigen processing and presentation, bone remodelling, prohorinone processing and wound healing. Their involvement in several pathologies, including osteoporosis, rheurnatoid arthritis, osteoarthritis, bronchial asthma and cancer have also been confirmed and today several of them have been validated as relevant targets for therapies. Compounds targeting cathepsins S and K are already in clinical evaluation, whereas others are in experimental phases. The cathepsin K inhibitor AAE-581 (balicatib) as the most advanced of them passed Phase 11 clinical trials in 2005. In this review, we discuss the current view on cathepsins as an emerging group of targets for several diseases and the development of cathepsin K and S inhibitors for treatment ofosteoporosis and various immune disorders. 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Pharm. Design 2007 13 4 387 403 10.2174/138161207780162962 17 Pharmacology & Pharmacy Pharmacology & Pharmacy 150FL WOS:000245200900004 17311556 2020-04-01 S Masters, PS Maramorosch, K; Shatkin, AJ Masters, Paul S. The molecular biology of coronaviruses ADVANCES IN VIRUS RESEARCH, VOL 66 Advances in Virus Research English Review; Book Chapter MOUSE HEPATITIS-VIRUS; ACUTE-RESPIRATORY-SYNDROME; INFECTIOUS-BRONCHITIS-VIRUS; TRANSMISSIBLE GASTROENTERITIS VIRUS; DEFECTIVE INTERFERING RNA; NUCLEAR RIBONUCLEOPROTEIN A1; 3' UNTRANSLATED REGION; OPEN READING FRAME; TEMPERATURE-SENSITIVE MUTANTS; ANGIOTENSIN-CONVERTING ENZYME-2 Coronaviruses are large, enveloped RNA viruses of both medical and veterinary importance. Interest in this viral family has intensified in the past few years as a result of the identification of a newly emerged coronavirus as the causative agent of severe acute respiratory syndrome (SARS). At the molecular level, coronaviruses employ a variety of unusual strategies to accomplish a complex program of gene expression. Coronavirus replication entails ribosome frameshifting during genome translation, the synthesis of both genomic and multiple sub-genomic RNA species, and the assembly of progeny virions by a pathway that is unique among enveloped RNA viruses. Progress in the investigation of these processes has been enhanced by the development of reverse genetic systems, an advance that was heretofore obstructed by the enormous size of the coronavirus genome. This review summarizes both classical and contemporary discoveries in the study of the molecular biology of these infectious agents, with particular emphasis on the nature and recognition of viral receptors, viral RNA synthesis, and the molecular interactions governing virion assembly. 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PETERSENDENBESTEN, A; DEKLUYVER, EP; MOORMANN, RJM; SCHAAPER, WMM; WENSVOORT, G MEULENBERG, JJM; PETERSENDENBESTEN, A; DEKLUYVER, EP; MOORMANN, RJM; SCHAAPER, WMM; WENSVOORT, G CHARACTERIZATION OF PROTEINS ENCODED BY ORF-2 TO ORF-7 OF LELYSTAD-VIRUS VIROLOGY English Article DEHYDROGENASE-ELEVATING VIRUS; RESPIRATORY SYNDROME VIRUS; EQUINE ARTERITIS VIRUS; PORCINE EPIDEMIC ABORTION; STRUCTURAL PROTEINS; SWINE INFERTILITY; MEMBRANE-PROTEIN; CORONAVIRUS IBV; SEQUENCE; SITES The genome of Lelystad virus (LV), a positive-strand RNA virus, is 15 kb in length and contains 8 open reading frames (ORFs) that encode putative viral proteins. ORFs 2 to 7 were cloned in plasmids downstream of the Sp6 RNA polymerase promoter, and the translation of transcripts generated in vitro yielded proteins that could be immunoprecipitated with porcine anti-LV serum. Synthetic polypeptides of 15 to 17 amino acids were selected from the amino acid sequences of ORFs 2 to 7 and antipeptide sera were raised in rabbits. Antisera that immunoprecipitated the in vitro translation products of ORFs 2 to 5 and 7 were obtained. Sera containing antibodies directed against peptides from ORFs 3 to 7 reacted positively with LV-infected alveolar lung macrophages in the immunoperoxidase monolayer assay. Using these antipeptide sera and porcine anti-LV serum, we identified three structural proteins and assigned their corresponding genes. Virions were found to contain a nucleocapsid protein of 15 kDa (N), an unglycosylated membrane protein of 18 kDa (M), and a glycosylated membrane protein of 25 kDa (E). The N protein is encoded by ORF7, the M protein is encoded by ORF6, and the E protein is encoded by ORF5. The E protein in virus particles contains one or two N-glycans that are resistant to endo-beta-N-acetyl-D-glucosaminidase H. This finding indicates that the high-mannose glycans are processed into complex glycans in the Golgi compartment. The protein composition of the LV virions further confirms that LV is evolutionarily related to equine arteritis virus, simian hemorrhagic fever virus, and lactate dehydrogenase-elevating virus. (C) 1995 academic Press, Inc. DLO,INST ANIM SCI & HLTH,MOLEC IMMUNOL LAB,8200 AB LELYSTAD,NETHERLANDS MEULENBERG, JJM (reprint author), DLO,INST ANIM SCI & HLTH,DEPT VIROL,HOUTRIBWEG 39,8200 AJ LELYSTAD,NETHERLANDS. 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The available rapid detection methods either lack sensitivity or require complex laboratory manipulation. This study describes a rapid, sensitive detection method that can be easily applied to routine diagnosis. This method simultaneously detects influenza viruses A and B in specimens of patients with respiratory infections using a TaqMan-based real-time PCR assay. Primers and probes were selected from highly conserved regions of the matrix protein gene of influenza virus A and the hemagglutinin gene segment of influenza virus B. The applicability of this multiplex PCR was evaluated with 27 influenza virus A and 9 influenza virus B reference strains and isolates. In addition, the specificity of the assay was assessed using eight reference strains of other respiratory viruses (parainfluenza viruses 1 to 3, respiratory syncytial virus Long strain, rhinoviruses 1A and 14, and coronaviruses OC43 and 229E) and 30 combined nose and throat swabs from asymptomatic subjects. Electron microscopy-counted stocks of influenza viruses A and B were used to develop a quantitative PCR format. Thirteen copies of viral RNA were detected for influenza virus A, and 11 copies were detected for influenza virus B, equaling 0.02 and 0.006 50% tissue culture infective doses, respectively. The diagnostic efficacy of the multiplex TaqMan-based PCR was determined by testing 98 clinical samples. This real-time PCR technique was found to be more sensitive than the combination of conventional viral culturing and shell vial culturing. Univ Med Ctr Utrecht, Dept Virol, Eijkman Winkler Inst Microbiol Infect Dis & Inflam, NL-3508 GA Utrecht, Netherlands van Elden, LJR (reprint author), Univ Med Ctr Utrecht, Dept Virol, Eijkman Winkler Inst Microbiol Infect Dis & Inflam, POB 85500, NL-3508 GA Utrecht, Netherlands. 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Clin. Microbiol. JAN 2001 39 1 196 200 10.1128/JCM.39.1.196-200.2001 5 Microbiology Microbiology 393KZ WOS:000166468900032 11136770 Bronze, Green Published 2020-04-01 J Parrish, CR; Holmes, EC; Morens, DM; Park, EC; Burke, DS; Calisher, CH; Laughlin, CA; Saif, LJ; Daszak, P Parrish, Colin R.; Holmes, Edward C.; Morens, David M.; Park, Eun-Chung; Burke, Donald S.; Calisher, Charles H.; Laughlin, Catherine A.; Saif, Linda J.; Daszak, Peter Cross-species virus transmission and the emergence of new epidemic diseases MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS English Review INFLUENZA-A VIRUS; RESPIRATORY SYNDROME CORONAVIRUS; EMERGING INFECTIOUS-DISEASES; CANINE TRANSFERRIN RECEPTOR; HOST-RANGE; AVIAN INFLUENZA; SARS CORONAVIRUS; PUBLIC-HEALTH; RNA VIRUSES; FELINE PARVOVIRUSES Host range is a viral property reflecting natural hosts that are infected either as part of a principal transmission cycle or, less commonly, as "spillover" infections into alternative hosts. Rarely, viruses gain the ability to spread efficiently within a new host that was not previously exposed or susceptible. These transfers involve either increased exposure or the acquisition of variations that allow them to overcome barriers to infection of the new hosts. In these cases, devastating outbreaks can result. Steps involved in transfers of viruses to new hosts include contact between the virus and the host, infection of an initial individual leading to amplification and an outbreak, and the generation within the original or new host of viral variants that have the ability to spread efficiently between individuals in populations of the new host. Here we review what is known about host switching leading to viral emergence from known examples, considering the evolutionary mechanisms, virus-host interactions, host range barriers to infection, and processes that allow efficient host-to-host transmission in the new host population. [Parrish, Colin R.] Cornell Univ, Coll Vet Med, James A Baker Inst Anim Hlth, Ithaca, NY 14853 USA; [Holmes, Edward C.] Penn State Univ, Dept Biol, Ctr Infect Dis Dynam, University Pk, PA 16802 USA; [Park, Eun-Chung; Laughlin, Catherine A.] NIAID, NIH, Virol Branch, Bethesda, MD 20892 USA; [Burke, Donald S.] Univ Pittsburgh, Grad Sch Publ Hlth, Pittsburgh, PA 15261 USA; [Calisher, Charles H.] Colorado State Univ, Coll Vet Med & Biomed Sci, Dept Microbiol Immunol & Pathol, Arthropod Borne & Infect Dis Lab, Ft Collins, CO 80523 USA; [Saif, Linda J.] Ohio State Univ, Ohio Agr Res & Dev Ctr, Food Anim Hlth Res Program, Wooster, OH 44691 USA; [Daszak, Peter] Consortium Conservat Med, New York, NY 10001 USA Parrish, CR (reprint author), Cornell Univ, Coll Vet Med, James A Baker Inst Anim Hlth, Ithaca, NY 14853 USA. crp3@cornell.edu daszak, peter/U-4588-2017; Holmes, Edward/Y-2789-2019 daszak, peter/0000-0002-2046-5695; Holmes, Edward/0000-0001-9596-3552; /0000-0002-5704-8094 National Institutes of Allergy and Infectious DiseasesUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USANIH National Institute of Allergy & Infectious Diseases (NIAID); U. S. National Institutes of HealthUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USA This review in part summarizes a meeting (Emergence of new epidemic viruses through host switching, 6 to 8 September 2005, Washington, DC) sponsored by the National Institutes of Allergy and Infectious Diseases and the Office of Rare Diseases of the U. S. National Institutes of Health. 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Central to this approach was a DNA microarray designed to detect a wide range of known viruses as well as novel members of existing viral families; this microarray contained the most highly conserved 70mer sequences from every fully sequenced reference viral genome in GenBank. During an outbreak of severe acute respiratory syndrome (SARS) in March 2003, hybridization to this microarray revealed the presence of a previously uncharacterized coronavirus in a viral isolate cultivated from a SARS patient. To further characterize this new virus, approximately 1 kb of the unknown virus genome was cloned by physically recovering viral sequences hybridized to individual array elements. Sequencing of these fragments confirmed that the virus was indeed a new member of the coronavirus family. This combination of array hybridization followed by direct viral sequence recovery should prove to be a general strategy for the rapid identification and characterization of novel viruses and emerging infectious disease. 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E.; Zevenhoven-Dobbe, Jessika C.; van der Meer, Yvonne; Koster, Abraham J.; Mommaas, A. Mieke; Snijder, Eric J. SARS-coronavirus replication is supported by a reticulovesicular network of modified endoplasmic reticulum PLOS BIOLOGY English Article MOUSE HEPATITIS-VIRUS; ACUTE RESPIRATORY SYNDROME; DOUBLE-STRANDED-RNA; DOUBLE-MEMBRANE-VESICLES; VIRAL REPLICATION; NONSTRUCTURAL PROTEIN-3; INFECTED CELLS; ELECTRON TOMOGRAPHY; INTERFERON RESPONSE; CELLULAR AUTOPHAGY Positive-strand RNA viruses, a large group including human pathogens such as SARS-coronavirus (SARS-CoV), replicate in the cytoplasm of infected host cells. Their replication complexes are commonly associated with modified host cell membranes. Membrane structures supporting viral RNA synthesis range from distinct spherular membrane invaginations to more elaborate webs of packed membranes and vesicles. Generally, their ultrastructure, morphogenesis, and exact role in viral replication remain to be defined. Poorly characterized double-membrane vesicles (DMVs) were previously implicated in SARS-CoV RNA synthesis. We have now applied electron tomography of cryofixed infected cells for the three-dimensional imaging of coronavirus-induced membrane alterations at high resolution. Our analysis defines a unique reticulovesicular network of modified endoplasmic reticulum that integrates convoluted membranes, numerous interconnected DMVs ( diameter 200-300 nm), and "vesicle packets'' apparently arising from DMV merger. The convoluted membranes were most abundantly immunolabeled for viral replicase subunits. However, double-stranded RNA, presumably revealing the site of viral RNA synthesis, mainly localized to the DMV interior. Since we could not discern a connection between DMV interior and cytosol, our analysis raises several questions about the mechanism of DMV formation and the actual site of SARS-CoV RNA synthesis. Our data document the extensive virus-induced reorganization of host cell membranes into a network that is used to organize viral replication and possibly hide replicating RNA from antiviral defense mechanisms. Together with biochemical studies of the viral enzyme complex, our ultrastructural description of this "replication network'' will aid to further dissect the early stages of the coronavirus life cycle and its virus-host interactions. [Knoops, Kevin; Kikkert, Marjolein; van den Worm, Sjoerd H. E.; Zevenhoven-Dobbe, Jessika C.; van der Meer, Yvonne; Snijder, Eric J.] Leiden Univ, Med Ctr, Dept Med Microbiol, Mol Virol Lab, Leiden, Netherlands; [Knoops, Kevin; Koster, Abraham J.; Mommaas, A. Mieke] Leiden Univ, Med Ctr, Dept Mol Cell Biol, Sect Electron Microscopy, Leiden, Netherlands Snijder, EJ (reprint author), Leiden Univ, Med Ctr, Dept Med Microbiol, Mol Virol Lab, Leiden, Netherlands. e.j.snijder@lumc.nl Jha, Babal/AAC-8337-2020; Koster, Abraham/I-7665-2017; Snijder, Eric J./E-6073-2018; Knoops, Kevin/F-6247-2012 Jha, Babal/0000-0002-7660-5255; Koster, Abraham/0000-0003-1717-2549; Snijder, Eric J./0000-0003-3297-2309; Euro-Asian SARS-DTV Network [SP22-CT-2004-511064]; Netherlands Organization for Scientific Research NWO-CWNetherlands Organization for Scientific Research (NWO) [700.52.306, 700.55.002] This work was supported (in part) by the European Commission under the context Euro-Asian SARS-DTV Network (SP22-CT-2004-511064) and by grants from the Council for Chemical Sciences of the Netherlands Organization for Scientific Research (NWO-CW grants 700.52.306 and 700.55.002). 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The crystal structure at 2.9 angstrom resolution of the RBD bound with the peptidase domain of human ACE2 shows that the RBD presents a gently concave surface, which cradles the N-terminal lobe of the peptidase. The atomic details at the interface between the two proteins clarify the importance of residue changes that facilitate efficient cross-species infection and human-to-human transmission. The structure of the RBD suggests ways to make truncated disulfide-stabilized RBD variants for use in the design of coronavirus vaccines. 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Gen. Virol. JAN 1987 68 1 57 77 10.1099/0022-1317-68-1-57 21 Biotechnology & Applied Microbiology; Virology Biotechnology & Applied Microbiology; Virology F6814 WOS:A1987F681400005 3027249 Bronze 2020-04-01 J Simmons, G; Gosalia, DN; Rennekamp, AJ; Reeves, JD; Diamond, SL; Bates, P Simmons, G; Gosalia, DN; Rennekamp, AJ; Reeves, JD; Diamond, SL; Bates, P Inhibitors of cathepsin L prevent severe acute respiratory syndrome coronavirus entry PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA English Article SARS; viral entry; proteolysis; membrane fusion; viral envelope IMMUNODEFICIENCY-VIRUS TYPE-1; ENVELOPE GLYCOPROTEIN; SPIKE GLYCOPROTEIN; SARS CORONAVIRUS; MEMBRANE-FUSION; AVIAN-SARCOMA; SUBGROUP-A; LOW PH; RECEPTOR; INFECTION Severe acute respiratory syndrome (SARS) is caused by an emergent coronavirus (SARS-CoV), for which there is currently no effective treatment. SARS-CoV mediates receptor binding and entry by its spike (S) glycoprotein, and infection is sensitive to lysosomotropic agents that perturb endosomal pH. We demonstrate here that the lysosomotropic-agent-mediated block to SARS-CoV infection is overcome by protease treatment of target-cell-associated virus. In addition, SARS-CoV infection was blocked by specific inhibitors of the pH-sensitive endosomal protease cathepsin L. A cell-free membrane-fusion system demonstrates that engagement of receptor followed by proteolysis is required for SARS-CoV membrane fusion and indicates that cathepsin L is sufficient to activate membrane fusion by SARS-CoV S. These results suggest that SARS-CoV infection results from a unique, three-step process: receptor binding and induced conformational changes in S glycoprotein followed by cathepsin L proteolysis within endosomes. The requirement for cathepsin L proteolysis identifies a previously uncharacterized class of inhibitor for SARS-CoV infection. 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Natl. Acad. Sci. U. S. A. AUG 16 2005 102 33 11876 11881 10.1073/pnas.0505577102 6 Multidisciplinary Sciences Science & Technology - Other Topics 956RH WOS:000231317000055 16081529 Green Published, Bronze 2020-04-01 J Azhar, EI; El-Kafrawy, SA; Farraj, SA; Hassan, AM; Al-Saeed, MS; Hashem, AM; Madani, TA Azhar, Esam I.; El-Kafrawy, Sherif A.; Farraj, Suha A.; Hassan, Ahmed M.; Al-Saeed, Muneera S.; Hashem, Anwar M.; Madani, Tariq A. Evidence for Camel-to-Human Transmission of MERS Coronavirus NEW ENGLAND JOURNAL OF MEDICINE English Article RESPIRATORY SYNDROME CORONAVIRUS; MIDDLE-EAST; DROMEDARY CAMELS We describe the isolation and sequencing of Middle East respiratory syndrome coronavirus (MERS-CoV) obtained from a dromedary camel and from a patient who died of laboratory-confirmed MERS-CoV infection after close contact with camels that had rhinorrhea. Nasal swabs collected from the patient and from one of his nine camels were positive for MERS-CoV RNA. In addition, MERS-CoV was isolated from the patient and the camel. The full genome sequences of the two isolates were identical. Serologic data indicated that MERS-CoV was circulating in the camels but not in the patient before the human infection occurred. These data suggest that this fatal case of human MERS-CoV infection was transmitted through close contact with an infected camel. [Azhar, Esam I.] King Abdulaziz Univ, Dept Med Lab Technol, Fac Appl Med Sci, Jeddah 21589, Saudi Arabia; [Azhar, Esam I.; El-Kafrawy, Sherif A.; Farraj, Suha A.; Hassan, Ahmed M.; Al-Saeed, Muneera S.; Hashem, Anwar M.] King Abdulaziz Univ, Special Infect Agents Unit, King Fahd Med Res Ctr, Jeddah 21589, Saudi Arabia; [Hashem, Anwar M.] King Abdulaziz Univ, Fac Med, Dept Med Microbiol & Parasitol, Jeddah 21589, Saudi Arabia; [Madani, Tariq A.] King Abdulaziz Univ, Fac Med, Dept Med, Jeddah 21589, Saudi Arabia Madani, TA (reprint author), King Abdulaziz Univ, Dept Med, POB 80215, Jeddah 21589, Saudi Arabia. tmadani@kau.edu.sa Hashem, Anwar/E-9411-2011; El-Kafrawy, Sherif A/C-8699-2012; Hassan, Ahmed/AAB-7241-2019 El-Kafrawy, Sherif A/0000-0002-3667-7529; Assiri A, 2013, NEW ENGL J MED, V369, P407, DOI 10.1056/NEJMoa1306742; Bermingham A, 2012, EUROSURVEILLANCE, V17, P6; Corman VM, 2012, EUROSURVEILLANCE, V17, P2; Cotten M, 2013, LANCET, V382, P1993, DOI 10.1016/S0140-6736(13)61887-5; Guery B, 2013, LANCET, V381, P2254; Guery B, 2013, LANCET, V381, P2265, DOI 10.1016/S0140-6736(13)60982-4; Haagmans BL, 2014, LANCET INFECT DIS, V14, P140, DOI 10.1016/S1473-3099(13)70690-X; Ithete NL, 2013, EMERG INFECT DIS, V19, P1697, DOI 10.3201/eid1910.130946; Memish ZA, 2013, EMERG INFECT DIS, V19, P1819, DOI 10.3201/eid1911.131172; Memish ZA, 2013, NEW ENGL J MED, V368, P2487, DOI 10.1056/NEJMoa1303729; Perera RA, 2013, EUROSURVEILLANCE, V18, P8, DOI 10.2807/1560-7917.ES2013.18.36.20574; Reusken CBEM, 2013, LANCET INFECT DIS, V13, P859, DOI 10.1016/S1473-3099(13)70164-6; van Boheemen S, 2012, MBIO, V3, DOI 10.1128/mBio.00473-12; WHO, 2013, LAB TEST MIDDL E RES; Zaki AM, 2013, NEW ENGL J MED, V369, P394; Zaki AM, 2012, NEW ENGL J MED, V367, P1814, DOI 10.1056/NEJMoa1211721 16 298 311 17 85 MASSACHUSETTS MEDICAL SOC WALTHAM WALTHAM WOODS CENTER, 860 WINTER ST,, WALTHAM, MA 02451-1413 USA 0028-4793 1533-4406 NEW ENGL J MED N. Engl. J. Med. JUN 26 2014 370 26 2499 2505 10.1056/NEJMoa1401505 7 Medicine, General & Internal General & Internal Medicine AJ6KY WOS:000337804400007 24896817 Bronze Y N 2020-04-01 J Lloyd-Smith, JO; George, D; Pepin, KM; Pitzer, VE; Pulliam, JRC; Dobson, AP; Hudson, PJ; Grenfell, BT Lloyd-Smith, James O.; George, Dylan; Pepin, Kim M.; Pitzer, Virginia E.; Pulliam, Juliet R. C.; Dobson, Andrew P.; Hudson, Peter J.; Grenfell, Bryan T. Epidemic Dynamics at the Human-Animal Interface SCIENCE English Review ACUTE RESPIRATORY SYNDROME; TRANSMISSION DYNAMICS; INFECTIOUS-DISEASES; SYNDROME CORONAVIRUS; RISK-FACTORS; HOST-RANGE; HONG-KONG; EMERGENCE; INFLUENZA; PATHOGENS Few infectious diseases are entirely human-specific: Most human pathogens also circulate in animals or else originated in nonhuman hosts. Influenza, plague, and trypanosomiasis are classic examples of zoonotic infections that transmit from animals to humans. The multihost ecology of zoonoses leads to complex dynamics, and analytical tools, such as mathematical modeling, are vital to the development of effective control policies and research agendas. Much attention has focused on modeling pathogens with simpler life cycles and immediate global urgency, such as influenza and severe acute respiratory syndrome. Meanwhile, vector-transmitted, chronic, and protozoan infections have been neglected, as have crucial processes such as cross-species transmission. Progress in understanding and combating zoonoses requires a new generation of models that addresses a broader set of pathogen life histories and integrates across host species and scientific disciplines. [Lloyd-Smith, James O.] Univ Calif Los Angeles, Dept Ecol & Evolutionary Biol, Los Angeles, CA 90095 USA; [Lloyd-Smith, James O.; George, Dylan; Pitzer, Virginia E.; Pulliam, Juliet R. C.; Hudson, Peter J.; Grenfell, Bryan T.] NIH, Fogarty Int Ctr, Bethesda, MD 20892 USA; [George, Dylan] Colorado State Univ, Dept Biol, Ft Collins, CO 80523 USA; [Pepin, Kim M.; Pitzer, Virginia E.; Hudson, Peter J.; Grenfell, Bryan T.] Penn State Univ, Ctr Infect Dis Dynam, University Pk, PA 16802 USA; [Dobson, Andrew P.; Grenfell, Bryan T.] Princeton Univ, Dept Ecol & Evolutionary Biol, Princeton, NJ 08544 USA; [Dobson, Andrew P.; Grenfell, Bryan T.] Princeton Univ, Woodrow Wilson Sch, Princeton, NJ 08544 USA Lloyd-Smith, JO (reprint author), Univ Calif Los Angeles, Dept Ecol & Evolutionary Biol, Los Angeles, CA 90095 USA. jlloydsmith@ucla.edu Hudson, Peter/AAB-8080-2020; /K-4080-2012; Pulliam, Juliet/L-3503-2019; Pulliam, Juliet/A-6516-2008 Hudson, Peter/0000-0003-0468-3403; /0000-0001-7941-502X; Pulliam, Juliet/0000-0003-3314-8223; Pulliam, Juliet/0000-0003-3314-8223; Pitzer, Virginia/0000-0003-1015-2289 Science and Technology Directorate, U. S. Department of Homeland SecurityUnited States Department of Homeland Security (DHS); Fogarty International Center, NIHUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USANIH Fogarty International Center (FIC) This work was supported by the Research and Policy for Infectious Disease Dynamics (RAPIDD) program of the Science and Technology Directorate, U. S. Department of Homeland Security, and the Fogarty International Center, NIH. We are grateful to O. Bjornstad, E. McKenzie, M. Poss, A. Read, and L. Simonsen for valuable comments and to B. Gee for assistance with figure preparation. J. L.-S. is grateful for the support of the De Logi Chair in Biological Sciences. 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An ongoing outbreak of Middle East respiratory syndrome coronavirus(2) suggests that this group of viruses remains a key threat and that their distribution is wider than previously recognized. Although bats have been suggested to be the natural reservoirs of both viruses(3-5), attempts to isolate the progenitor virus of SARS-CoV from bats have been unsuccessful. Diverse SARS-like coronaviruses (SL-CoVs) have now been reported from bats in China, Europe and Africa(5-8), but none is considered a direct progenitor of SARS-CoV because of their phylogenetic disparity from this virus and the inability of their spike proteins to use the SARS-CoV cellular receptor molecule, the human angiotensin converting enzyme II (ACE2)(9,10). Here we report whole-genome sequences of two novel bat coronaviruses from Chinese horseshoe bats (family: Rhinolophidae) in Yunnan, China: RsSHC014 and Rs3367. These viruses are far more closely related to SARS-CoV than any previously identified bat coronaviruses, particularly in the receptor binding domain of the spike protein. Most importantly, we report the first recorded isolation of a live SL-CoV (bat SL-CoV-WIV1) from bat faecal samples in Vero E6 cells, which has typical coronavirus morphology, 99.9% sequence identity to Rs3367 and uses ACE2 from humans, civets and Chinese horseshoe bats for cell entry. Preliminary in vitro testing indicates that WIV1 also has a broad species tropism. Our results provide the strongest evidence to date that Chinese horseshoe bats are natural reservoirs of SARS-CoV, and that intermediate hosts may not be necessary for direct human infection by some bat SL-CoVs. They also highlight the importance of pathogen-discovery programs targeting high-risk wildlife groups in emerging disease hotspots as a strategy for pandemic preparedness. [Ge, Xing-Yi; Li, Jia-Lu; Yang, Xing-Lou; Hu, Ben; Zhang, Wei; Peng, Cheng; Zhang, Yu-Ji; Luo, Chu-Ming; Tan, Bing; Wang, Ning; Zhu, Yan; Shi, Zheng-Li] Chinese Acad Sci, Wuhan Inst Virol, State Key Lab Virol, Ctr Emerging Infect Dis, Wuhan 430071, Peoples R China; [Chmura, Aleksei A.; Zhu, Guangjian; Epstein, Jonathan H.; Daszak, Peter] EcoHlth Alliance, New York, NY 10001 USA; [Mazet, Jonna K.] Univ Calif Davis, Sch Vet Med, Hlth Inst 1, Davis, CA 95616 USA; [Crameri, Gary; Wang, Lin-Fa] CSIRO Australian Anim Hlth Lab, Geelong, Vic 3220, Australia; [Zhang, Shu-Yi] E China Normal Univ, Coll Life Sci, Shanghai 200062, Peoples R China; [Wang, Lin-Fa] Duke NUS Grad Med Sch, Emerging Infect Dis Program, Singapore 169857, Singapore Daszak, P (reprint author), EcoHlth Alliance, New York, NY 10001 USA. daszak@ecohealthalliance.org; zlshi@wh.iov.cn Crameri, Gary/H-8441-2013; Shi, Zhengli/A-1013-2013; daszak, peter/U-4588-2017; Chmura, Aleksei/K-9971-2018 Shi, Zhengli/0000-0001-8089-163X; daszak, peter/0000-0002-2046-5695; Chmura, Aleksei/0000-0001-5544-0431; Li, Jialu/0000-0001-9772-3886; Wang, Lin-Fa/0000-0003-2752-0535; Yang, Xing-Lou/0000-0002-5317-8983 State Key Program for Basic ResearchState Key Development Program for Basic Research of China [2011CB504701, 2010CB530100]; National Natural Science Foundation of ChinaNational Natural Science Foundation of China [81290341, 31321001]; Scientific and technological basis special project [2013FY113500]; CSIRO OCE Science Leaders Award; National Institute of Allergy and Infectious Diseases (NIAID)United States Department of Health & Human ServicesNational Institutes of Health (NIH) - USANIH National Institute of Allergy & Infectious Diseases (NIAID) [R01AI079231]; National Institutes of Health (NIH)/National Science Foundation (NSF) 'Ecology and Evolution of Infectious Diseases' award from the NIH Fogarty International Center [R01TW005869]; NIH Fogarty International CenterUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USANIH Fogarty International Center (FIC); Office of the Secretary of the Department of Health and Human Services [R56TW009502]; United States Agency for International Development (USAID) Emerging Pandemic Threats PREDICTUnited States Agency for International Development (USAID) We acknowledge financial support from the State Key Program for Basic Research (2011CB504701 and 2010CB530100), National Natural Science Foundation of China (81290341 and 31321001), Scientific and technological basis special project (2013FY113500), CSIRO OCE Science Leaders Award, National Institute of Allergy and Infectious Diseases (NIAID) award number R01AI079231, a National Institutes of Health (NIH)/National Science Foundation (NSF) 'Ecology and Evolution of Infectious Diseases' award from the NIH Fogarty International Center (R01TW005869), an award from the NIH Fogarty International Center supported by International Influenza Funds from the Office of the Secretary of the Department of Health and Human Services (R56TW009502), and United States Agency for International Development (USAID) Emerging Pandemic Threats PREDICT. The contents are the responsibility of the authors and do not necessarily reflect the views of NIAID, NIH, NSF, USAID or the United States Government. We thank X. Che from Zhujiang Hospital, Southern Medical University, for providing human SARS patient sera. 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JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY English Article; Proceedings Paper 19th Annual Meeting of the European-Society-for-Paediatric-Infectious-Diseases MAR 26-28, 2001 ISTANBUL, TURKEY European Soc Paediat Infect Dis asthma; atopy; coronavirus; polymerase chain reaction; enterovirus; rhinovirus; wheezing RESPIRATORY SYNCYTIAL VIRUS; HOSPITALIZED CHILDREN; VIRAL-INFECTIONS; EASTERN FINLAND; RISK-FACTORS; DIAGNOSIS; PCR; BRONCHIOLITIS; EPIDEMIOLOGY; PREVALENCE Background: Although known as common causes of upper respiratory infections, rhinoviruses, enteroviruses, and coronaviruses are poorly studied as inducers of wheezing in infants, and their possible role in the development of childhood asthma has not been investigated. Objective: The purposes of this study were to assess the occurrence of RV, enterovirus, and coronavirus infections in wheezing infants and to evaluate the association of these viral findings with early school-age asthma. Methods: In 1999, outcome in relation to asthma was studied in 82 of 100 initially recruited children who had been hospitalized for wheezing in infancy during the period 1992-1993. In 2000, etiologic viral studies regarding the index episode of wheezing were supplemented by rhinovirus, enterovirus, and coronavirus detection by RT-PCR from frozen nasopharyngeal aspirates in 81 of the children for whom adequate samples were available. Of these children, 66 had participated in the follow-up in 1999. Results: Rhinoviruses were identified in 27 (33%) of the 81 children, enteroviruses in 10 (12%), and coronaviruses in none. Rhinoviruses were present as single viral findings in 22 (81%) of the 27 rhinovirus-positive cases, and rhinovirus infections were associated with the presence of atopic dermatitis in infancy. Enteroviruses were commonly encountered in mixed infections and had no association with atopy. As single viral findings, rhinoviruses were associated with the development of asthma (P =.047; odds ratio, 4.14; 95% Cl, 1.02-16.77 versus rhinovirus-negative cases [by logistic regression adjusted for age, sex, and atopic dermatitis on entry)]. Conclusion: Our results present rhinoviruses as important inducers of wheezing even in infancy. The association with atopy and subsequent asthma calls for reevaluation of the role of rhinoviruses in the development of asthma. Kuopio Univ Hosp, Dept Pediat, FIN-70211 Kuopio, Finland; Univ Kuopio, Dept Pediat, FIN-70211 Kuopio, Finland; Univ Turku, Dept Virol, Turku, Finland Kotaniemi-Syrjanen, A (reprint author), Kuopio Univ Hosp, Dept Pediat, POB 1777, FIN-70211 Kuopio, Finland. 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Therefore, computational tools for reliably predicting linear B-cell epitopes are highly desirable. We evaluated Support Vector Machine (SVM) classifiers trained utilizing five different kernel methods using fivefold cross-validation on a homology-reduced data set of 701 linear B-cell epitopes, extracted from Bcipep database, and 701 non-epitopes, randomly extracted from SwissProt sequences. Based on the results of our computational experiments, we propose BCPred, a novel method for predicting linear B-cell epitopes using the subsequence kernel. We show that the predictive performance of BCPred (AUC = 0.758) outperforms 11 SVM-based classifiers developed and evaluated in our experiments as well as our implementation of AAP (AUC = 0.7), a recently proposed method for predicting linear B-cell epitopes using amino acid pair antigenicity. Furthermore, we compared BCPred with AAP and ABCPred, a method that uses recurrent neural networks, using two data sets of unique B-cell epitopes that had been previously used to evaluate ABCPred. Analysis of the data sets used and the results of this comparison show that conclusions about the relative performance of different B-cell epitope prediction methods drawn on the basis of experiments using data sets of unique B-cell epitopes are likely to yield overly optimistic estimates of performance of evaluated methods. This argues for the use of carefully homology-reduced data sets in comparing B-cell epitope prediction methods to avoid misleading conclusions about how different methods compare to each other. Our homology-reduced data set and implementations of BCPred as well as the APP method are publicly available through our web-based server, BCPREDS, at: http://ailab.cs.iastate.edu/bcpreds/. Copyright (C) 2008 John Wiley & Sons, Ltd. [El-Manzalawy, Yasser; Honavar, Vasant] Iowa State Univ, Artificial Intelligence Lab, Ames, IA 50010 USA; [El-Manzalawy, Yasser; Honavar, Vasant] Iowa State Univ, Dept Comp Sci, Ames, IA 50010 USA; [Dobbs, Drena] Iowa State Univ, Dept Genet Dev & Cell Biol, Ames, IA 50010 USA; [El-Manzalawy, Yasser; Dobbs, Drena; Honavar, Vasant] Iowa State Univ, Bioinformat & Computat Biol Grad Program, Ames, IA 50010 USA; [El-Manzalawy, Yasser; Dobbs, Drena; Honavar, Vasant] Iowa State Univ, Ctr Computat Intelligence, Ames, IA 50010 USA El-Manzalawy, Y (reprint author), Iowa State Univ, Artificial Intelligence Lab, 226 Atanasoff Hall, Ames, IA 50010 USA. yasser@iastate.edu Honavar, Vasant G/K-9835-2015 Honavar, Vasant G/0000-0001-5399-3489; Dobbs, Drena/0000-0003-4404-9554 NIGMS NIH HHSUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USANIH National Institute of General Medical Sciences (NIGMS) [R33 GM066387, R33 GM066387-03, R21 GM066387, GM066387, R33 GM066387-04] Alix AJP, 1999, VACCINE, V18, P311, DOI 10.1016/S0264-410X(99)00329-1; Bairoch A, 2000, NUCLEIC ACIDS RES, V28, P45, DOI 10.1093/nar/28.1.45; Baldi P, 2000, BIOINFORMATICS, V16, P412, DOI 10.1093/bioinformatics/16.5.412; BARLOW DJ, 1986, NATURE, V322, P747, DOI 10.1038/322747a0; Beniac DR, 2006, NAT STRUCT MOL BIOL, V13, P751, DOI 10.1038/nsmb1123; Bjorklund AK, 2005, BIOINFORMATICS, V21, P39, DOI 10.1093/bioinformatics/bth477; Blythe MJ, 2005, PROTEIN SCI, V14, P246, DOI 10.1110/ps.041059505; Bulashevska A, 2006, BMC BIOINFORMATICS, V7, DOI 10.1186/1471-2105-7-298; Chen J, 2007, AMINO ACIDS, V33, P423, DOI 10.1007/s00726-006-0485-9; CLARK A, 2006, INT C GRAMM INF ICGI; Cui J, 2006, IMMUNOGENETICS, V58, P607, DOI 10.1007/s00251-006-0117-2; Demsar J, 2006, J MACH LEARN RES, V7, P1; Dimitrov DS, 2003, CELL, V115, P652, DOI 10.1016/S0092-8674(03)00976-0; Drosten C, 2003, NEW ENGL J MED, V348, P1967, DOI 10.1056/NEJMoa030747; EMINI EA, 1985, J VIROL, V55, P836, DOI 10.1128/JVI.55.3.836-839.1985; Fisher R A., 1973, STAT METHODS SCI INF; Flower D.R., 2007, IMMUNOINFORMATICS PR; Fouchier RAM, 2003, NATURE, V423, P240, DOI 10.1038/423240a; Friedman M, 1940, ANN MATH STAT, V11, P86, DOI 10.1214/aoms/1177731944; Greenbaum JA, 2007, J MOL RECOGNIT, V20, P75, DOI 10.1002/jmr.815; Haussler D., 1999, UCSCRL9910; KARPLUS PA, 1985, NATURWISSENSCHAFTEN, V72, P213; Ksiazek TG, 2003, NEW ENGL J MED, V348, P1953, DOI 10.1056/NEJMoa030781; Langeveld JPM, 2001, VACCINE, V19, P2352, DOI 10.1016/S0264-410X(00)00526-0; Larsen Jens Erik Pontoppidan, 2006, Immunome Res, V2, P2, DOI 10.1186/1745-7580-2-2; Leslie C., 2002, P PSB, V7, P566; Leslie CS, 2004, BIOINFORMATICS, V20, P467, DOI 10.1093/bioinformatics/btg431; Li WH, 2003, NATURE, V426, P450, DOI 10.1038/nature02145; Li WZ, 2002, BIOINFORMATICS, V18, P77, DOI 10.1093/bioinformatics/18.1.77; Lien SP, 2007, BIOCHEM BIOPH RES CO, V358, P716, DOI 10.1016/j.bbrc.2007.04.164; Lodhi H, 2002, J MACH LEARN RES, V2, P419, DOI 10.1162/153244302760200687; Neter J., 1985, APPL LINEAR STAT MOD; Odorico M, 2003, J MOL RECOGNIT, V16, P20, DOI 10.1002/jmr.602; PARKER JMR, 1986, BIOCHEMISTRY-US, V25, P5425, DOI 10.1021/bi00367a013; Peiris JSM, 2003, LANCET, V361, P1319, DOI 10.1016/S0140-6736(03)13077-2; PELLEQUER JL, 1993, IMMUNOL LETT, V36, P83, DOI 10.1016/0165-2478(93)90072-A; PELLEQUER JL, 1991, METHOD ENZYMOL, V203, P176; PELLEQUER JL, 1993, J MOL GRAPH MODEL, V11, P204, DOI 10.1016/0263-7855(93)80074-2; Pier G.B., 2004, IMMUNOLOGY INFECT IM; Platt J, 1998, FAST TRAINING SUPPOR; Prabakaran P, 2006, J BIOL CHEM, V281, P15829, DOI 10.1074/jbc.M600697200; RANGWALA H, 2006, PROTEIN STRUCTURE PR; Saha S, 2005, BMC GENOMICS, V6, DOI 10.1186/1471-2164-6-79; Saha S, 2004, LECT NOTES COMPUT SC, V3239, P197; SAHA S, 2006, ABCPRED BENCHMARKING; Saha S, 2006, PROTEINS, V65, P40, DOI 10.1002/prot.21078; Saigo H, 2004, BIOINFORMATICS, V20, P1682, DOI 10.1093/bioinformatics/bth141; Sainz B, 2005, J VIROL, V79, P7195, DOI 10.1128/JVI.79.11.7195-7206.2005; Salomon J, 2006, BMC BIOINFORMATICS, V7, DOI 10.1186/1471-2105-7-501; SEEWALD A, 2005, TR200513; Sollner J, 2006, J MOL RECOGNIT, V19, P200, DOI 10.1002/jmr.771; Sui JH, 2004, P NATL ACAD SCI USA, V101, P2536, DOI 10.1073/pnas.0307140101; Vapnik V, 2000, NATURE STAT LEARNING; WALTER G, 1986, J IMMUNOL METHODS, V88, P149, DOI 10.1016/0022-1759(86)90001-3; Witten I. 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JUL-AUG 2008 21 4 243 255 10.1002/jmr.893 13 Biochemistry & Molecular Biology; Biophysics Biochemistry & Molecular Biology; Biophysics 331IR WOS:000258006400006 18496882 Green Accepted, Green Published 2020-04-01 J Li, BJ; Tang, QQ; Cheng, D; Qin, C; Xie, FY; Wei, Q; Xu, J; Liu, YJ; Zheng, BJ; Woodle, MC; Zhong, NS; Lu, PY Li, BJ; Tang, QQ; Cheng, D; Qin, C; Xie, FY; Wei, Q; Xu, J; Liu, YJ; Zheng, BJ; Woodle, MC; Zhong, NS; Lu, PY Using siRNA in prophylactic and therapeutic regimens against SARS coronavirus in rhesus macaque NATURE MEDICINE English Article ACUTE RESPIRATORY SYNDROME; SMALL INTERFERING RNAS; SPIKE PROTEIN; GENE-TRANSFER; VIRUS; MICE; REPLICATION; INFECTION; SEQUENCE; EXPRESSION Development of therapeutic agents for severe acute respiratory syndrome ( SARS) viral infection using short interfering RNA ( siRNA) inhibitors exemplifies a powerful new means to combat emerging infectious diseases. Potent siRNA inhibitors of SARS coronavirus ( SCV) in vitro were further evaluated for efficacy and safety in a rhesus macaque ( Macaca mulatta) SARS model using clinically viable delivery while comparing three dosing regimens. Observations of SARS- like symptoms, measurements of SCV RNA presence and lung histopathology and immunohistochemistry consistently showed siRNA- mediated anti- SARS efficacy by either prophylactic or therapeutic regimens. The siRNAs used provided relief from SCV infection - induced fever, diminished SCV viral levels and reduced acute diffuse alveoli damage. The 10 - 40 mg/ kg accumulated dosages of siRNA did not show any sign of siRNA- induced toxicity. These results suggest that a clinical investigation is warranted and illustrate the prospects for siRNA to enable a massive reduction in development time for new targeted therapeutic agents. 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Med. SEP 2005 11 9 944 951 10.1038/nm1280 8 Biochemistry & Molecular Biology; Cell Biology; Medicine, Research & Experimental Biochemistry & Molecular Biology; Cell Biology; Research & Experimental Medicine 962IL WOS:000231724700021 16116432 Bronze 2020-04-01 J Haagmans, BL; Al Dhahiry, SHS; Reusken, CBEM; Raj, VS; Galiano, M; Myers, R; Godeke, GJ; Jonges, M; Farag, E; Diab, A; Ghobashy, H; Alhajri, F; Al-Thani, M; Al-Marri, SA; Al Romaihi, HE; Al Khal, A; Bermingham, A; Osterhaus, ADME; AlHajri, MM; Koopmans, MPG Haagmans, Bart L.; Al Dhahiry, Said H. S.; Reusken, Chantal B. E. M.; Raj, V. Stalin; Galiano, Monica; Myers, Richard; Godeke, Gert-Jan; Jonges, Marcel; Farag, Elmoubasher; Diab, Ayman; Ghobashy, Hazem; Alhajri, Farhoud; Al-Thani, Mohamed; Al-Marri, Salih A.; Al Romaihi, Hamad E.; Al Khal, Abdullatif; Bermingham, Alison; Osterhaus, Albert D. M. E.; AlHajri, Mohd M.; Koopmans, Marion P. G. Middle East respiratory syndrome coronavirus in dromedary camels: an outbreak investigation LANCET INFECTIOUS DISEASES English Article PROTEIN; BAT Background Middle East respiratory syndrome coronavirus (MERS-CoV) causes severe lower respiratory tract infection in people. Previous studies suggested dromedary camels were a reservoir for this virus. We tested for the presence of MERS-CoV in dromedary camels from a farm in Qatar linked to two human cases of the infection in October, 2013. Methods We took nose swabs, rectal swabs, and blood samples from all camels on the Qatari farm. We tested swabs with RT-PCR, with amplification targeting the E gene (upE), nudeocapsid (N) gene, and open reading frame (ORF) la. PCR positive samples were tested by different MERS-CoV specific PCRs and obtained sequences were used for phylogentic analysis together with sequences from the linked human cases and other human cases. We tested serum samples from the camels for IgG immunofluorescence assay, protein microarray, and virus neutralisation assay. Findings We obtained samples from 14 camels on Oct 17, 2013. We detected MERS-CoV in nose swabs from three camels by three independent RT-PCRs and sequencing. The nudeotide sequence of an ORFla fragment (940 nucleotides) and a 4.2 kb concatenated fragment were very similar to the MERS-CoV from two human cases on the same farm and a MERS-CoV isolate from Hafr-Al-Batin. Eight additional camel nose swabs were positive on one or more RT-PCRs, but could not be confirmed by sequencing. All camels had MERS-CoV spike-binding antibodies that correlated well with the presence of neutralising antibodies to MERS-CoV. Interpretation Our study provides virological confirmation of MERS-CoV in camels and suggests a recent outbreak affecting both human beings and camels. We cannot condude whether the people on the farm were infected by the camels or vice versa, or if a third source was responsible. [Haagmans, Bart L.; Raj, V. Stalin; Osterhaus, Albert D. M. E.; Koopmans, Marion P. G.] Erasmus MC, Dept Virosci, Rotterdam, Netherlands; [Al Dhahiry, Said H. S.] Hamad Med Corp, Dept Lab Med & Pathol, Doha, Qatar; [Reusken, Chantal B. E. M.; Godeke, Gert-Jan; Jonges, Marcel; Koopmans, Marion P. G.] Natl Inst Publ Hlth & Environm, Ctr Infect Dis Res Diagnost & Screening, Div Virol, NL-3720 BA Bilthoven, Netherlands; [Galiano, Monica; Myers, Richard; Bermingham, Alison] Publ Hlth England, Virus Reference Dept, London, England; [Farag, Elmoubasher; Diab, Ayman; Ghobashy, Hazem; Alhajri, Farhoud; Al-Thani, Mohamed; Al-Marri, Salih A.; Al Romaihi, Hamad E.; Al Khal, Abdullatif; AlHajri, Mohd M.] Supreme Council Hlth, Doha, Qatar AlHajri, MM (reprint author), Supreme Council Hlth, POB 42, Doha, Qatar. malhajri1@sch.gov.qa; m.koopmans@erasmusmc.nl Raj, V Stalin/E-9670-2016; Koopmans, Marion/Y-9170-2019 Raj, V Stalin/0000-0003-2250-8481; Koopmans, Marion/0000-0002-5204-2312; Haagmans, Bart/0000-0001-6221-2015 European Union FP7 project EMPERIE [223498]; European Union FP7 project ANTIGONE [278976] We thank WHO and the Food and Agriculture Organization of the United Nations for their generous help in organisation of the study, Theo Bestebroer for providing Middle East respiratory syndrome coronavirus specific primer sets, Berend Jan Bosch for providing antigens for the microarray, and Jeroen Cremer for technical support. Contributions to the study were funded through the European Union FP7 projects EMPERIE (contract number 223498; to BLH and ADMEO) and ANTIGONE (contract number 278976; to MPGK and ADMEO). 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Virus from 1 bat showed 100% nucleotide identity to virus from the human index case-patient. Bats might play a role in human infection. [Memish, Ziad A.; Fagbo, Shamsudeen F.; AlHakeem, Rafat; Al Rabeeah, Abdullah A.] Minist Hlth, Riyadh, Saudi Arabia; [Mishra, Nischay; Kapoor, Vishal; Kapoor, Amit; Briese, Thomas; Lipkin, W. Ian] Columbia Univ, New York, NY USA; [Olival, Kevin J.; Epstein, Jonathan H.; Daszak, Peter] EcoHlth Alliance, New York, NY USA; [Al Asmari, Mushabab] Minist Hlth, Bisha, Saudi Arabia; [Islam, Ariful] EcoHlth Alliance, Dhaka, Bangladesh Lipkin, WI (reprint author), Columbia Univ, Ctr Infect & Immun, 722 West 168th St, New York, NY 10032 USA. wil2001@columbia.edu daszak, peter/U-4588-2017; islam, ariful/V-8200-2019 daszak, peter/0000-0002-2046-5695; Olival, Kevin/0000-0003-3211-1875; Lipkin, W. Ian/0000-0002-8768-9386; Fagbo, Shamsudeen/0000-0003-3448-6136 National Institute of Allergy and Infectious DiseasesUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USANIH National Institute of Allergy & Infectious Diseases (NIAID); US Agency for International Development (PREDICT)United States Agency for International Development (USAID); Defense Threat Reduction AgencyUnited States Department of DefenseDefense Threat Reduction Agency Work in the Center for Infection and Immunity and EcoHealth Alliance was supported by the National Institute of Allergy and Infectious Diseases, the US Agency for International Development (PREDICT), and the Defense Threat Reduction Agency. 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Frequent detection of human rhinoviruses, paramyxoviruses, coronaviruses, and bocavirus during acute respiratory tract infections JOURNAL OF MEDICAL VIROLOGY English Article virus; respiratory infection; epidemiology; RT-PCR; diagnostics POLYMERASE-CHAIN-REACTION; TRANSCRIPTASE-PCR ASSAY; REAL-TIME PCR; CLINICAL SPECIMENS; SEQUENCE-ANALYSIS; SYNCYTIAL-VIRUS; RT-PCR; DIAGNOSIS; CHILDREN; SAMPLES Viruses are the major cause of pediatric acute respiratory tract infection (ARTI) and yet many suspected cases of infection remain uncharacterized. We employed 17 PCR assays and retrospectively screened 315 specimens selected by season from a predominantly pediatric hospital-based population. Before the Brisbane respiratory virus research study commenced, one or more predominantly viral pathogens had been detected in 15.2% (n = 48) of all specimens. The Brisbane study made an additional 206 viral detections, resulting in the identification of a microbe in 67.0% of specimens. After our study, the majority of microbes detected were RNA viruses (89.9%). Overall, human rhinoviruses (HRVs) were the most frequently identified target (n=140) followed by human adenoviruses (HAdVs; n = 25), human metapneumovirus (HMPV; n=18), human bocavirus (HBoV; n = 15), human respiratory syncytial virus (HRSV; n = 12), human coronaviruses (HCoVs; n = 11), and human herpesvirus-6 (n = 11). HRVs were the sole microbe detected in 37.8% (n = 31) of patients with suspected lower respiratory tract infection (LRTI). Genotyping of the HRV VP4/VP2 region resulted in a proposed subdivision of HRV type A into sublineages A1 and A2. Most of the genotyped HAdV strains were found to be type C. This study describes the high microbial burden imposed by HRVs, HMPV, HRSV, HCoVs, and the newly identified virus, HBoV on a predominantly paediatric hospital population with suspected acute respiratory tract infections and proposes a new formulation of viral targets for future diagnostic research studies. 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Med. Virol. SEP 2006 78 9 1232 1240 10.1002/jmv.20689 9 Virology Virology 068WE WOS:000239404400013 16847968 Bronze 2020-04-01 J Wong, SK; Li, WH; Moore, MJ; Choe, H; Farzan, M Wong, SK; Li, WH; Moore, MJ; Choe, H; Farzan, M A 193-amino acid fragment of the SARS coronavirus S protein efficiently binds angiotensin-converting enzyme 2 JOURNAL OF BIOLOGICAL CHEMISTRY English Article ACUTE RESPIRATORY SYNDROME; SPIKE GLYCOPROTEIN; RECEPTOR; VIRUS; IDENTIFICATION; EXPRESSION; DOMAIN; ENTRY; SITE The coronavirus spike (S) protein mediates infection of receptor-expressing host cells and is a critical target for antiviral neutralizing antibodies. Angiotensin-converting enzyme 2 (ACE2) is a functional receptor for the coronavirus (severe acute respiratory syndrome (SARS)-CoV) that causes SARS. Here we demonstrate that a 193-amino acid fragment of the S protein (residues 318-510) bound ACE2 more efficiently than did the full S1 domain (residues 12-672). Smaller S protein fragments, expressing residues 327-510 or 318-490, did not detectably bind ACE2. A point mutation at aspartic acid 454 abolished association of the full S1 domain and of the 193-residue fragment with ACE2. The 193-residue fragment blocked S protein-mediated infection with an IC50 of less than 10 nM, whereas the IC50 of the S1 domain was similar to50 nM. These data identify an independently folded receptor-binding domain of the SARS-CoV S protein. 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The N-terminal 25-amino acid sequence of immunoaffinity-purified MHV receptor was identical to the predicted mature N termini of two mouse genes related to human carcinoembryonic antigen (CEA) and was strongly homologous to the N termini of members of the CEA family in humans and rats. Polyclonal antibodies to human CEA recognized the immunoaffinity-purified MHV receptor and the MHV receptor in liver membranes and intestinal brush border membranes from MHV-susceptible mouse strains. In membranes from MHV-resistant SJL/J mice, the anti-CEA antibodies recognized a homologous glycoprotein that failed to bind MHV. The MHV receptor glycoprotein was detected in membranes of BALB/c colon, small intestine, and liver, which are the principal targets for MHV replication in vivo. The MHV receptor glycoprotein resembled members of the human CEA family in molecular weight, acidic pI, extensive glycosylation, solubility in perchloric acid, and tissue distribution. Thus, the MHV receptor is, to our knowledge, the first member of the CEA family of glycoproteins to be identified as a virus receptor. 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