Comparative full-length genome sequence analysis of 14 sars coronavirus isolates and common mutations associated with putative origins of infection. Commentary
Identifieur interne : 006413 ( Main/Exploration ); précédent : 006412; suivant : 006414Comparative full-length genome sequence analysis of 14 sars coronavirus isolates and common mutations associated with putative origins of infection. Commentary
Auteurs : YIJUN RUAN [Singapour] ; CHIA LIN WEI [Singapour] ; LING AI EE [Singapour] ; Vinsensius B. Vega [Singapour] ; Herve Thoreau [Singapour] ; SE THOE SU YUN [Singapour] ; Jer-Ming Chia [Singapour] ; Patrick Ng [Singapour] ; KUO PING CHIU [Singapour] ; LANDRI LIM [Singapour] ; ZHANG TAO [Singapour] ; CHAN KWAI PENG [Singapour] ; Lynette Oon Lin Ean [Singapour] ; NG MAH LEE [Singapour] ; LEO YEE SIN [Singapour] ; Lisa F. P. Ng [Singapour] ; REN EE CHEE [Singapour] ; Lawrence W. Stanton [Singapour] ; Philip M. Long [Singapour] ; Edison T. Liu [Singapour] ; Earl G. Brown [Canada] ; Jason A. Tetro [Canada]Source :
- Lancet : (British edition) [ 0140-6736 ] ; 2003.
Descripteurs français
- Pascal (Inist)
- Wicri :
- topic : Homme.
English descriptors
- KwdEn :
Abstract
Background The cause of severe acute respiratory syndrome (SARS) has been identified as a new coronavirus. Whole genome sequence analysis of various isolates might provide an indication of potential strain differences of this new virus. Moreover, mutation analysis will help to develop effective vaccines. Methods We sequenced the entire SARS viral genome of cultured isolates from the index case (SIN2500) presenting in Singapore, from three primary contacts (SIN2774, SIN2748, and SIN2677), and one secondary contact (SIN2679). These sequences were compared with the isolates from Canada (TOR2), Hong Kong (CUHK-W1 and HKU39849), Hanoi (URBANI), Guangzhou (GZ01), and Beijing (BJ01, BJ02, BJ03, BJ04). Findings We identified 129 sequence variations among the 14 isolates, with 16 recurrent variant sequences. Common variant sequences at four loci define two distinct genotypes of the SARS virus. One genotype was linked with infections originating in Hotel M in Hong Kong, the second contained isolates from Hong Kong, Guangzhou, and Beijing with no association with Hotel M (p<0.0001). Moreover, other common sequence variants further distinguished the geographical origins of the isolates, especially between Singapore and Beijing. Interpretation Despite the recent onset of the SARS epidemic, genetic signatures are emerging that partition the worldwide SARS viral isolates into groups on the basis of contact source history and geography. These signatures can be used to trace sources of infection. In addition, a common variant associated with a non-conservative aminoacid change in the S1 region of the spike protein, suggests that immunological pressures might be starting to influence the evolution of the SARS virus in human populations.
Affiliations:
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Liu</name><affiliation wicri:level="1"><inist:fA14 i1="01"><s1>Genome Institute of Singapore</s1><s3>SGP</s3><sZ>1 aut.</sZ><sZ>2 aut.</sZ><sZ>4 aut.</sZ><sZ>5 aut.</sZ><sZ>7 aut.</sZ><sZ>8 aut.</sZ><sZ>9 aut.</sZ><sZ>10 aut.</sZ><sZ>11 aut.</sZ><sZ>16 aut.</sZ><sZ>17 aut.</sZ><sZ>18 aut.</sZ><sZ>19 aut.</sZ><sZ>20 aut.</sZ></inist:fA14><country>Singapour</country><wicri:noRegion>Genome Institute of Singapore</wicri:noRegion></affiliation></author><author><name sortKey="Brown, Earl G" sort="Brown, Earl G" uniqKey="Brown E" first="Earl G." last="Brown">Earl G. Brown</name><affiliation wicri:level="1"><inist:fA14 i1="05"><s1>Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa</s1><s2>Ottawa, Ontario, K1H 8M5</s2><s3>CAN</s3><sZ>21 aut.</sZ><sZ>22 aut.</sZ></inist:fA14><country>Canada</country><wicri:noRegion>Ottawa, Ontario, K1H 8M5</wicri:noRegion></affiliation></author><author><name sortKey="Tetro, Jason A" sort="Tetro, Jason A" uniqKey="Tetro J" first="Jason A." last="Tetro">Jason A. Tetro</name><affiliation wicri:level="1"><inist:fA14 i1="05"><s1>Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa</s1><s2>Ottawa, Ontario, K1H 8M5</s2><s3>CAN</s3><sZ>21 aut.</sZ><sZ>22 aut.</sZ></inist:fA14><country>Canada</country><wicri:noRegion>Ottawa, Ontario, K1H 8M5</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">INIST</idno><idno type="inist">03-0368219</idno><date when="2003">2003</date><idno type="stanalyst">PASCAL 03-0368219 INIST</idno><idno type="RBID">Pascal:03-0368219</idno><idno type="wicri:Area/PascalFrancis/Corpus">000975</idno><idno type="wicri:Area/PascalFrancis/Curation">000016</idno><idno type="wicri:Area/PascalFrancis/Checkpoint">000976</idno><idno type="wicri:explorRef" wicri:stream="PascalFrancis" wicri:step="Checkpoint">000976</idno><idno type="wicri:doubleKey">0140-6736:2003:Yijun Ruan:comparative:full:length</idno><idno type="wicri:Area/Main/Merge">006925</idno><idno type="wicri:Area/Main/Curation">006413</idno><idno type="wicri:Area/Main/Exploration">006413</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a">Comparative full-length genome sequence analysis of 14 sars coronavirus isolates and common mutations associated with putative origins of infection. Commentary</title><author><name sortKey="Yijun Ruan" sort="Yijun Ruan" uniqKey="Yijun Ruan" last="Yijun Ruan">YIJUN RUAN</name><affiliation wicri:level="1"><inist:fA14 i1="01"><s1>Genome Institute of Singapore</s1><s3>SGP</s3><sZ>1 aut.</sZ><sZ>2 aut.</sZ><sZ>4 aut.</sZ><sZ>5 aut.</sZ><sZ>7 aut.</sZ><sZ>8 aut.</sZ><sZ>9 aut.</sZ><sZ>10 aut.</sZ><sZ>11 aut.</sZ><sZ>16 aut.</sZ><sZ>17 aut.</sZ><sZ>18 aut.</sZ><sZ>19 aut.</sZ><sZ>20 aut.</sZ></inist:fA14><country>Singapour</country><wicri:noRegion>Genome Institute of Singapore</wicri:noRegion></affiliation></author><author><name sortKey="Chia Lin Wei" sort="Chia Lin Wei" uniqKey="Chia Lin Wei" last="Chia Lin Wei">CHIA LIN WEI</name><affiliation wicri:level="1"><inist:fA14 i1="01"><s1>Genome Institute of Singapore</s1><s3>SGP</s3><sZ>1 aut.</sZ><sZ>2 aut.</sZ><sZ>4 aut.</sZ><sZ>5 aut.</sZ><sZ>7 aut.</sZ><sZ>8 aut.</sZ><sZ>9 aut.</sZ><sZ>10 aut.</sZ><sZ>11 aut.</sZ><sZ>16 aut.</sZ><sZ>17 aut.</sZ><sZ>18 aut.</sZ><sZ>19 aut.</sZ><sZ>20 aut.</sZ></inist:fA14><country>Singapour</country><wicri:noRegion>Genome Institute of Singapore</wicri:noRegion></affiliation></author><author><name sortKey="Ling Ai Ee" sort="Ling Ai Ee" uniqKey="Ling Ai Ee" last="Ling Ai Ee">LING AI EE</name><affiliation wicri:level="1"><inist:fA14 i1="02"><s1>Virology Section, Department of Pathology, Singapore General Hospital</s1><s3>SGP</s3><sZ>3 aut.</sZ><sZ>6 aut.</sZ><sZ>12 aut.</sZ><sZ>13 aut.</sZ></inist:fA14><country>Singapour</country><wicri:noRegion>Virology Section, Department of Pathology, Singapore General Hospital</wicri:noRegion></affiliation></author><author><name sortKey="Vega, Vinsensius B" sort="Vega, Vinsensius B" uniqKey="Vega V" first="Vinsensius B." last="Vega">Vinsensius B. Vega</name><affiliation wicri:level="1"><inist:fA14 i1="01"><s1>Genome Institute of Singapore</s1><s3>SGP</s3><sZ>1 aut.</sZ><sZ>2 aut.</sZ><sZ>4 aut.</sZ><sZ>5 aut.</sZ><sZ>7 aut.</sZ><sZ>8 aut.</sZ><sZ>9 aut.</sZ><sZ>10 aut.</sZ><sZ>11 aut.</sZ><sZ>16 aut.</sZ><sZ>17 aut.</sZ><sZ>18 aut.</sZ><sZ>19 aut.</sZ><sZ>20 aut.</sZ></inist:fA14><country>Singapour</country><wicri:noRegion>Genome Institute of Singapore</wicri:noRegion></affiliation></author><author><name sortKey="Thoreau, Herve" sort="Thoreau, Herve" uniqKey="Thoreau H" first="Herve" last="Thoreau">Herve Thoreau</name><affiliation wicri:level="1"><inist:fA14 i1="01"><s1>Genome Institute of Singapore</s1><s3>SGP</s3><sZ>1 aut.</sZ><sZ>2 aut.</sZ><sZ>4 aut.</sZ><sZ>5 aut.</sZ><sZ>7 aut.</sZ><sZ>8 aut.</sZ><sZ>9 aut.</sZ><sZ>10 aut.</sZ><sZ>11 aut.</sZ><sZ>16 aut.</sZ><sZ>17 aut.</sZ><sZ>18 aut.</sZ><sZ>19 aut.</sZ><sZ>20 aut.</sZ></inist:fA14><country>Singapour</country><wicri:noRegion>Genome Institute of Singapore</wicri:noRegion></affiliation></author><author><name sortKey="Se Thoe Su Yun" sort="Se Thoe Su Yun" uniqKey="Se Thoe Su Yun" last="Se Thoe Su Yun">SE THOE SU YUN</name><affiliation wicri:level="1"><inist:fA14 i1="02"><s1>Virology Section, Department of Pathology, Singapore General Hospital</s1><s3>SGP</s3><sZ>3 aut.</sZ><sZ>6 aut.</sZ><sZ>12 aut.</sZ><sZ>13 aut.</sZ></inist:fA14><country>Singapour</country><wicri:noRegion>Virology Section, Department of Pathology, Singapore General Hospital</wicri:noRegion></affiliation></author><author><name sortKey="Chia, Jer Ming" sort="Chia, Jer Ming" uniqKey="Chia J" first="Jer-Ming" last="Chia">Jer-Ming Chia</name><affiliation wicri:level="1"><inist:fA14 i1="01"><s1>Genome Institute of Singapore</s1><s3>SGP</s3><sZ>1 aut.</sZ><sZ>2 aut.</sZ><sZ>4 aut.</sZ><sZ>5 aut.</sZ><sZ>7 aut.</sZ><sZ>8 aut.</sZ><sZ>9 aut.</sZ><sZ>10 aut.</sZ><sZ>11 aut.</sZ><sZ>16 aut.</sZ><sZ>17 aut.</sZ><sZ>18 aut.</sZ><sZ>19 aut.</sZ><sZ>20 aut.</sZ></inist:fA14><country>Singapour</country><wicri:noRegion>Genome Institute of Singapore</wicri:noRegion></affiliation></author><author><name sortKey="Ng, Patrick" sort="Ng, Patrick" uniqKey="Ng P" first="Patrick" last="Ng">Patrick Ng</name><affiliation wicri:level="1"><inist:fA14 i1="01"><s1>Genome Institute of Singapore</s1><s3>SGP</s3><sZ>1 aut.</sZ><sZ>2 aut.</sZ><sZ>4 aut.</sZ><sZ>5 aut.</sZ><sZ>7 aut.</sZ><sZ>8 aut.</sZ><sZ>9 aut.</sZ><sZ>10 aut.</sZ><sZ>11 aut.</sZ><sZ>16 aut.</sZ><sZ>17 aut.</sZ><sZ>18 aut.</sZ><sZ>19 aut.</sZ><sZ>20 aut.</sZ></inist:fA14><country>Singapour</country><wicri:noRegion>Genome Institute of Singapore</wicri:noRegion></affiliation></author><author><name sortKey="Kuo Ping Chiu" sort="Kuo Ping Chiu" uniqKey="Kuo Ping Chiu" last="Kuo Ping Chiu">KUO PING CHIU</name><affiliation wicri:level="1"><inist:fA14 i1="01"><s1>Genome Institute of Singapore</s1><s3>SGP</s3><sZ>1 aut.</sZ><sZ>2 aut.</sZ><sZ>4 aut.</sZ><sZ>5 aut.</sZ><sZ>7 aut.</sZ><sZ>8 aut.</sZ><sZ>9 aut.</sZ><sZ>10 aut.</sZ><sZ>11 aut.</sZ><sZ>16 aut.</sZ><sZ>17 aut.</sZ><sZ>18 aut.</sZ><sZ>19 aut.</sZ><sZ>20 aut.</sZ></inist:fA14><country>Singapour</country><wicri:noRegion>Genome Institute of Singapore</wicri:noRegion></affiliation></author><author><name sortKey="Landri Lim" sort="Landri Lim" uniqKey="Landri Lim" last="Landri Lim">LANDRI LIM</name><affiliation wicri:level="1"><inist:fA14 i1="01"><s1>Genome Institute of Singapore</s1><s3>SGP</s3><sZ>1 aut.</sZ><sZ>2 aut.</sZ><sZ>4 aut.</sZ><sZ>5 aut.</sZ><sZ>7 aut.</sZ><sZ>8 aut.</sZ><sZ>9 aut.</sZ><sZ>10 aut.</sZ><sZ>11 aut.</sZ><sZ>16 aut.</sZ><sZ>17 aut.</sZ><sZ>18 aut.</sZ><sZ>19 aut.</sZ><sZ>20 aut.</sZ></inist:fA14><country>Singapour</country><wicri:noRegion>Genome Institute of Singapore</wicri:noRegion></affiliation></author><author><name sortKey="Zhang Tao" sort="Zhang Tao" uniqKey="Zhang Tao" last="Zhang Tao">ZHANG TAO</name><affiliation wicri:level="1"><inist:fA14 i1="01"><s1>Genome Institute of Singapore</s1><s3>SGP</s3><sZ>1 aut.</sZ><sZ>2 aut.</sZ><sZ>4 aut.</sZ><sZ>5 aut.</sZ><sZ>7 aut.</sZ><sZ>8 aut.</sZ><sZ>9 aut.</sZ><sZ>10 aut.</sZ><sZ>11 aut.</sZ><sZ>16 aut.</sZ><sZ>17 aut.</sZ><sZ>18 aut.</sZ><sZ>19 aut.</sZ><sZ>20 aut.</sZ></inist:fA14><country>Singapour</country><wicri:noRegion>Genome Institute of Singapore</wicri:noRegion></affiliation></author><author><name sortKey="Chan Kwai Peng" sort="Chan Kwai Peng" uniqKey="Chan Kwai Peng" last="Chan Kwai Peng">CHAN KWAI PENG</name><affiliation wicri:level="1"><inist:fA14 i1="02"><s1>Virology Section, Department of Pathology, Singapore General Hospital</s1><s3>SGP</s3><sZ>3 aut.</sZ><sZ>6 aut.</sZ><sZ>12 aut.</sZ><sZ>13 aut.</sZ></inist:fA14><country>Singapour</country><wicri:noRegion>Virology Section, Department of Pathology, Singapore General Hospital</wicri:noRegion></affiliation></author><author><name sortKey="Oon Lin Ean, Lynette" sort="Oon Lin Ean, Lynette" uniqKey="Oon Lin Ean L" first="Lynette" last="Oon Lin Ean">Lynette Oon Lin Ean</name><affiliation wicri:level="1"><inist:fA14 i1="02"><s1>Virology Section, Department of Pathology, Singapore General Hospital</s1><s3>SGP</s3><sZ>3 aut.</sZ><sZ>6 aut.</sZ><sZ>12 aut.</sZ><sZ>13 aut.</sZ></inist:fA14><country>Singapour</country><wicri:noRegion>Virology Section, Department of Pathology, Singapore General Hospital</wicri:noRegion></affiliation></author><author><name sortKey="Ng Mah Lee" sort="Ng Mah Lee" uniqKey="Ng Mah Lee" last="Ng Mah Lee">NG MAH LEE</name><affiliation wicri:level="4"><inist:fA14 i1="03"><s1>Department of Microbiology and Electron Microscopy Unit, National University of Singapore</s1><s3>SGP</s3><sZ>14 aut.</sZ></inist:fA14><country>Singapour</country><orgName type="university">Université nationale de Singapour</orgName></affiliation></author><author><name sortKey="Leo Yee Sin" sort="Leo Yee Sin" uniqKey="Leo Yee Sin" last="Leo Yee Sin">LEO YEE SIN</name><affiliation wicri:level="1"><inist:fA14 i1="04"><s1>Tan Tock Seng Hospital</s1><s3>SGP</s3><sZ>15 aut.</sZ></inist:fA14><country>Singapour</country><wicri:noRegion>Tan Tock Seng Hospital</wicri:noRegion></affiliation></author><author><name sortKey="Ng, Lisa F P" sort="Ng, Lisa F P" uniqKey="Ng L" first="Lisa F. P." last="Ng">Lisa F. P. Ng</name><affiliation wicri:level="1"><inist:fA14 i1="01"><s1>Genome Institute of Singapore</s1><s3>SGP</s3><sZ>1 aut.</sZ><sZ>2 aut.</sZ><sZ>4 aut.</sZ><sZ>5 aut.</sZ><sZ>7 aut.</sZ><sZ>8 aut.</sZ><sZ>9 aut.</sZ><sZ>10 aut.</sZ><sZ>11 aut.</sZ><sZ>16 aut.</sZ><sZ>17 aut.</sZ><sZ>18 aut.</sZ><sZ>19 aut.</sZ><sZ>20 aut.</sZ></inist:fA14><country>Singapour</country><wicri:noRegion>Genome Institute of Singapore</wicri:noRegion></affiliation></author><author><name sortKey="Ren Ee Chee" sort="Ren Ee Chee" uniqKey="Ren Ee Chee" last="Ren Ee Chee">REN EE CHEE</name><affiliation wicri:level="1"><inist:fA14 i1="01"><s1>Genome Institute of Singapore</s1><s3>SGP</s3><sZ>1 aut.</sZ><sZ>2 aut.</sZ><sZ>4 aut.</sZ><sZ>5 aut.</sZ><sZ>7 aut.</sZ><sZ>8 aut.</sZ><sZ>9 aut.</sZ><sZ>10 aut.</sZ><sZ>11 aut.</sZ><sZ>16 aut.</sZ><sZ>17 aut.</sZ><sZ>18 aut.</sZ><sZ>19 aut.</sZ><sZ>20 aut.</sZ></inist:fA14><country>Singapour</country><wicri:noRegion>Genome Institute of Singapore</wicri:noRegion></affiliation></author><author><name sortKey="Stanton, Lawrence W" sort="Stanton, Lawrence W" uniqKey="Stanton L" first="Lawrence W." last="Stanton">Lawrence W. Stanton</name><affiliation wicri:level="1"><inist:fA14 i1="01"><s1>Genome Institute of Singapore</s1><s3>SGP</s3><sZ>1 aut.</sZ><sZ>2 aut.</sZ><sZ>4 aut.</sZ><sZ>5 aut.</sZ><sZ>7 aut.</sZ><sZ>8 aut.</sZ><sZ>9 aut.</sZ><sZ>10 aut.</sZ><sZ>11 aut.</sZ><sZ>16 aut.</sZ><sZ>17 aut.</sZ><sZ>18 aut.</sZ><sZ>19 aut.</sZ><sZ>20 aut.</sZ></inist:fA14><country>Singapour</country><wicri:noRegion>Genome Institute of Singapore</wicri:noRegion></affiliation></author><author><name sortKey="Long, Philip M" sort="Long, Philip M" uniqKey="Long P" first="Philip M." last="Long">Philip M. Long</name><affiliation wicri:level="1"><inist:fA14 i1="01"><s1>Genome Institute of Singapore</s1><s3>SGP</s3><sZ>1 aut.</sZ><sZ>2 aut.</sZ><sZ>4 aut.</sZ><sZ>5 aut.</sZ><sZ>7 aut.</sZ><sZ>8 aut.</sZ><sZ>9 aut.</sZ><sZ>10 aut.</sZ><sZ>11 aut.</sZ><sZ>16 aut.</sZ><sZ>17 aut.</sZ><sZ>18 aut.</sZ><sZ>19 aut.</sZ><sZ>20 aut.</sZ></inist:fA14><country>Singapour</country><wicri:noRegion>Genome Institute of Singapore</wicri:noRegion></affiliation></author><author><name sortKey="Liu, Edison T" sort="Liu, Edison T" uniqKey="Liu E" first="Edison T." last="Liu">Edison T. Liu</name><affiliation wicri:level="1"><inist:fA14 i1="01"><s1>Genome Institute of Singapore</s1><s3>SGP</s3><sZ>1 aut.</sZ><sZ>2 aut.</sZ><sZ>4 aut.</sZ><sZ>5 aut.</sZ><sZ>7 aut.</sZ><sZ>8 aut.</sZ><sZ>9 aut.</sZ><sZ>10 aut.</sZ><sZ>11 aut.</sZ><sZ>16 aut.</sZ><sZ>17 aut.</sZ><sZ>18 aut.</sZ><sZ>19 aut.</sZ><sZ>20 aut.</sZ></inist:fA14><country>Singapour</country><wicri:noRegion>Genome Institute of Singapore</wicri:noRegion></affiliation></author><author><name sortKey="Brown, Earl G" sort="Brown, Earl G" uniqKey="Brown E" first="Earl G." last="Brown">Earl G. Brown</name><affiliation wicri:level="1"><inist:fA14 i1="05"><s1>Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa</s1><s2>Ottawa, Ontario, K1H 8M5</s2><s3>CAN</s3><sZ>21 aut.</sZ><sZ>22 aut.</sZ></inist:fA14><country>Canada</country><wicri:noRegion>Ottawa, Ontario, K1H 8M5</wicri:noRegion></affiliation></author><author><name sortKey="Tetro, Jason A" sort="Tetro, Jason A" uniqKey="Tetro J" first="Jason A." last="Tetro">Jason A. Tetro</name><affiliation wicri:level="1"><inist:fA14 i1="05"><s1>Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa</s1><s2>Ottawa, Ontario, K1H 8M5</s2><s3>CAN</s3><sZ>21 aut.</sZ><sZ>22 aut.</sZ></inist:fA14><country>Canada</country><wicri:noRegion>Ottawa, Ontario, K1H 8M5</wicri:noRegion></affiliation></author></analytic><series><title level="j" type="main">Lancet : (British edition)</title><title level="j" type="abbreviated">Lancet : (Br. ed.)</title><idno type="ISSN">0140-6736</idno><imprint><date when="2003">2003</date></imprint></series></biblStruct></sourceDesc><seriesStmt><title level="j" type="main">Lancet : (British edition)</title><title level="j" type="abbreviated">Lancet : (Br. ed.)</title><idno type="ISSN">0140-6736</idno></seriesStmt></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Acute</term><term>Coronavirus</term><term>Etiology</term><term>Genome</term><term>Human</term><term>Mutation</term><term>Pathogen strain</term><term>Pneumopathy</term><term>Sequential analysis</term><term>Syndrome</term></keywords><keywords scheme="Pascal" xml:lang="fr"><term>Pneumopathie</term><term>Aigu</term><term>Syndrome</term><term>Homme</term><term>Etiologie</term><term>Souche pathogène</term><term>Coronavirus</term><term>Analyse séquentielle</term><term>Génome</term><term>Mutation</term></keywords><keywords scheme="Wicri" type="topic" xml:lang="fr"><term>Homme</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Background The cause of severe acute respiratory syndrome (SARS) has been identified as a new coronavirus. Whole genome sequence analysis of various isolates might provide an indication of potential strain differences of this new virus. Moreover, mutation analysis will help to develop effective vaccines. Methods We sequenced the entire SARS viral genome of cultured isolates from the index case (SIN2500) presenting in Singapore, from three primary contacts (SIN2774, SIN2748, and SIN2677), and one secondary contact (SIN2679). These sequences were compared with the isolates from Canada (TOR2), Hong Kong (CUHK-W1 and HKU39849), Hanoi (URBANI), Guangzhou (GZ01), and Beijing (BJ01, BJ02, BJ03, BJ04). Findings We identified 129 sequence variations among the 14 isolates, with 16 recurrent variant sequences. Common variant sequences at four loci define two distinct genotypes of the SARS virus. One genotype was linked with infections originating in Hotel M in Hong Kong, the second contained isolates from Hong Kong, Guangzhou, and Beijing with no association with Hotel M (p<0.0001). Moreover, other common sequence variants further distinguished the geographical origins of the isolates, especially between Singapore and Beijing. Interpretation Despite the recent onset of the SARS epidemic, genetic signatures are emerging that partition the worldwide SARS viral isolates into groups on the basis of contact source history and geography. These signatures can be used to trace sources of infection. In addition, a common variant associated with a non-conservative aminoacid change in the S1 region of the spike protein, suggests that immunological pressures might be starting to influence the evolution of the SARS virus in human populations.</div></front></TEI><affiliations><list><country><li>Canada</li><li>Singapour</li></country><orgName><li>Université nationale de Singapour</li></orgName></list><tree><country name="Singapour"><noRegion><name sortKey="Yijun Ruan" sort="Yijun Ruan" uniqKey="Yijun Ruan" last="Yijun Ruan">YIJUN RUAN</name></noRegion><name sortKey="Chan Kwai Peng" sort="Chan Kwai Peng" uniqKey="Chan Kwai Peng" last="Chan Kwai Peng">CHAN KWAI PENG</name><name sortKey="Chia Lin Wei" sort="Chia Lin Wei" uniqKey="Chia Lin Wei" last="Chia Lin Wei">CHIA LIN WEI</name><name sortKey="Chia, Jer Ming" sort="Chia, Jer Ming" uniqKey="Chia J" first="Jer-Ming" last="Chia">Jer-Ming Chia</name><name sortKey="Kuo Ping Chiu" sort="Kuo Ping Chiu" uniqKey="Kuo Ping Chiu" last="Kuo Ping Chiu">KUO PING CHIU</name><name sortKey="Landri Lim" sort="Landri Lim" uniqKey="Landri Lim" last="Landri Lim">LANDRI LIM</name><name sortKey="Leo Yee Sin" sort="Leo Yee Sin" uniqKey="Leo Yee Sin" last="Leo Yee Sin">LEO YEE SIN</name><name sortKey="Ling Ai Ee" sort="Ling Ai Ee" uniqKey="Ling Ai Ee" last="Ling Ai Ee">LING AI EE</name><name sortKey="Liu, Edison T" sort="Liu, Edison T" uniqKey="Liu E" first="Edison T." last="Liu">Edison T. Liu</name><name sortKey="Long, Philip M" sort="Long, Philip M" uniqKey="Long P" first="Philip M." last="Long">Philip M. Long</name><name sortKey="Ng Mah Lee" sort="Ng Mah Lee" uniqKey="Ng Mah Lee" last="Ng Mah Lee">NG MAH LEE</name><name sortKey="Ng, Lisa F P" sort="Ng, Lisa F P" uniqKey="Ng L" first="Lisa F. P." last="Ng">Lisa F. P. Ng</name><name sortKey="Ng, Patrick" sort="Ng, Patrick" uniqKey="Ng P" first="Patrick" last="Ng">Patrick Ng</name><name sortKey="Oon Lin Ean, Lynette" sort="Oon Lin Ean, Lynette" uniqKey="Oon Lin Ean L" first="Lynette" last="Oon Lin Ean">Lynette Oon Lin Ean</name><name sortKey="Ren Ee Chee" sort="Ren Ee Chee" uniqKey="Ren Ee Chee" last="Ren Ee Chee">REN EE CHEE</name><name sortKey="Se Thoe Su Yun" sort="Se Thoe Su Yun" uniqKey="Se Thoe Su Yun" last="Se Thoe Su Yun">SE THOE SU YUN</name><name sortKey="Stanton, Lawrence W" sort="Stanton, Lawrence W" uniqKey="Stanton L" first="Lawrence W." last="Stanton">Lawrence W. Stanton</name><name sortKey="Thoreau, Herve" sort="Thoreau, Herve" uniqKey="Thoreau H" first="Herve" last="Thoreau">Herve Thoreau</name><name sortKey="Vega, Vinsensius B" sort="Vega, Vinsensius B" uniqKey="Vega V" first="Vinsensius B." last="Vega">Vinsensius B. Vega</name><name sortKey="Zhang Tao" sort="Zhang Tao" uniqKey="Zhang Tao" last="Zhang Tao">ZHANG TAO</name></country><country name="Canada"><noRegion><name sortKey="Brown, Earl G" sort="Brown, Earl G" uniqKey="Brown E" first="Earl G." last="Brown">Earl G. Brown</name></noRegion><name sortKey="Tetro, Jason A" sort="Tetro, Jason A" uniqKey="Tetro J" first="Jason A." last="Tetro">Jason A. Tetro</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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|texte= Comparative full-length genome sequence analysis of 14 sars coronavirus isolates and common mutations associated with putative origins of infection. Commentary
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