Characterization of severe acute respiratory syndrome coronavirus genomes in Taiwan: Molecular epidemiology and genome evolution
Identifieur interne : 000742 ( Pmc/Corpus ); précédent : 000741; suivant : 000743Characterization of severe acute respiratory syndrome coronavirus genomes in Taiwan: Molecular epidemiology and genome evolution
Auteurs : Shiou-Hwei Yeh ; Hurng-Yi Wang ; Ching-Yi Tsai ; Chuan-Liang Kao ; Jyh-Yuan Yang ; Hwan-Wun Liu ; Ih-Jen Su ; Shih-Feng Tsai ; Ding-Shinn Chen ; Pei-Jer ChenSource :
- Proceedings of the National Academy of Sciences of the United States of America [ 0027-8424 ] ; 2004.
Abstract
Since early March 2003, the severe acute respiratory syndrome (SARS) coronavirus (CoV) infection has claimed 346 cases and 37 deaths in Taiwan. The epidemic occurred in two stages. The first stage caused limited familial or hospital infections and lasted from early March to mid-April. All cases had clear contact histories, primarily from Guangdong or Hong Kong. The second stage resulted in a large outbreak in a municipal hospital, and quickly spread to northern and southern Taiwan from late April to mid-June. During this stage, there were some sporadic cases with untraceable contact histories. To investigate the origin and transmission route of SARS-CoV in Taiwan's epidemic, we conducted a systematic viral lineage study by sequencing the entire viral genome from ten SARS patients. SARS-CoV viruses isolated from Taiwan were found closely related to those from Guangdong and Hong Kong. In addition, all cases from the second stage belonged to the same lineage after the municipal hospital outbreak, including the patients without an apparent contact history. Analyses of these full-length sequences showed a positive selection occurring during SARS-CoV virus evolution. The mismatch distribution indicated that SARS viral genomes did not reach equilibrium and suggested a recent introduction of the viruses into human populations. The estimated genome mutation rate was ≈0.1 per genome, demonstrating possibly one of the lowest rates among known RNA viruses.
Url:
DOI: 10.1073/pnas.0307904100
PubMed: 14983045
PubMed Central: 356986
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Characterization of severe acute respiratory syndrome coronavirus genomes in Taiwan: Molecular epidemiology and genome evolution</title><author><name sortKey="Yeh, Shiou Hwei" sort="Yeh, Shiou Hwei" uniqKey="Yeh S" first="Shiou-Hwei" last="Yeh">Shiou-Hwei Yeh</name><affiliation><nlm:aff id="N0x9b670c8.0xa22b5a0">Division of Molecular and Genomic Medicine, National Health Research Institutes, Taipei 115, Taiwan;</nlm:aff></affiliation><affiliation><nlm:aff wicri:cut=" and" id="N0x9b670c8.0xa22b5a0">Hepatitis Research Center</nlm:aff></affiliation></author><author><name sortKey="Wang, Hurng Yi" sort="Wang, Hurng Yi" uniqKey="Wang H" first="Hurng-Yi" last="Wang">Hurng-Yi Wang</name><affiliation><nlm:aff id="N0x9b670c8.0xa22b5a0">Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan;</nlm:aff></affiliation></author><author><name sortKey="Tsai, Ching Yi" sort="Tsai, Ching Yi" uniqKey="Tsai C" first="Ching-Yi" last="Tsai">Ching-Yi Tsai</name><affiliation><nlm:aff wicri:cut=" and" id="N0x9b670c8.0xa22b5a0">Hepatitis Research Center</nlm:aff></affiliation></author><author><name sortKey="Kao, Chuan Liang" sort="Kao, Chuan Liang" uniqKey="Kao C" first="Chuan-Liang" last="Kao">Chuan-Liang Kao</name><affiliation><nlm:aff id="N0x9b670c8.0xa22b5a0">Department of Medical Technology, National Taiwan University, Taipei 100, Taiwan;</nlm:aff></affiliation></author><author><name sortKey="Yang, Jyh Yuan" sort="Yang, Jyh Yuan" uniqKey="Yang J" first="Jyh-Yuan" last="Yang">Jyh-Yuan Yang</name><affiliation><nlm:aff id="N0x9b670c8.0xa22b5a0">Center for Disease Control, Taipei 115, Taiwan;</nlm:aff></affiliation></author><author><name sortKey="Liu, Hwan Wun" sort="Liu, Hwan Wun" uniqKey="Liu H" first="Hwan-Wun" last="Liu">Hwan-Wun Liu</name><affiliation><nlm:aff wicri:cut="; and" id="N0x9b670c8.0xa22b5a0">Institute of Preventive Medicine, National Defense Medical College, Taipei 237, Taiwan</nlm:aff></affiliation></author><author><name sortKey="Su, Ih Jen" sort="Su, Ih Jen" uniqKey="Su I" first="Ih-Jen" last="Su">Ih-Jen Su</name><affiliation><nlm:aff id="N0x9b670c8.0xa22b5a0">Center for Disease Control, Taipei 115, Taiwan;</nlm:aff></affiliation></author><author><name sortKey="Tsai, Shih Feng" sort="Tsai, Shih Feng" uniqKey="Tsai S" first="Shih-Feng" last="Tsai">Shih-Feng Tsai</name><affiliation><nlm:aff id="N0x9b670c8.0xa22b5a0">Division of Molecular and Genomic Medicine, National Health Research Institutes, Taipei 115, Taiwan;</nlm:aff></affiliation></author><author><name sortKey="Chen, Ding Shinn" sort="Chen, Ding Shinn" uniqKey="Chen D" first="Ding-Shinn" last="Chen">Ding-Shinn Chen</name><affiliation><nlm:aff wicri:cut=" and" id="N0x9b670c8.0xa22b5a0">Hepatitis Research Center</nlm:aff></affiliation><affiliation><nlm:aff id="N0x9b670c8.0xa22b5a0">Department of Internal Medicine, National Taiwan University Hospital, Taipei 100, Taiwan;</nlm:aff></affiliation><affiliation><nlm:aff id="N0x9b670c8.0xa22b5a0">Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei 100, Taiwan</nlm:aff></affiliation></author><author><name sortKey="Chen, Pei Jer" sort="Chen, Pei Jer" uniqKey="Chen P" first="Pei-Jer" last="Chen">Pei-Jer Chen</name><affiliation><nlm:aff wicri:cut=" and" id="N0x9b670c8.0xa22b5a0">Hepatitis Research Center</nlm:aff></affiliation><affiliation><nlm:aff id="N0x9b670c8.0xa22b5a0">Department of Internal Medicine, National Taiwan University Hospital, Taipei 100, Taiwan;</nlm:aff></affiliation><affiliation><nlm:aff id="N0x9b670c8.0xa22b5a0">Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei 100, Taiwan</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">14983045</idno><idno type="pmc">356986</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC356986</idno><idno type="RBID">PMC:356986</idno><idno type="doi">10.1073/pnas.0307904100</idno><date when="2004">2004</date><idno type="wicri:Area/Pmc/Corpus">000742</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000742</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Characterization of severe acute respiratory syndrome coronavirus genomes in Taiwan: Molecular epidemiology and genome evolution</title><author><name sortKey="Yeh, Shiou Hwei" sort="Yeh, Shiou Hwei" uniqKey="Yeh S" first="Shiou-Hwei" last="Yeh">Shiou-Hwei Yeh</name><affiliation><nlm:aff id="N0x9b670c8.0xa22b5a0">Division of Molecular and Genomic Medicine, National Health Research Institutes, Taipei 115, Taiwan;</nlm:aff></affiliation><affiliation><nlm:aff wicri:cut=" and" id="N0x9b670c8.0xa22b5a0">Hepatitis Research Center</nlm:aff></affiliation></author><author><name sortKey="Wang, Hurng Yi" sort="Wang, Hurng Yi" uniqKey="Wang H" first="Hurng-Yi" last="Wang">Hurng-Yi Wang</name><affiliation><nlm:aff id="N0x9b670c8.0xa22b5a0">Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan;</nlm:aff></affiliation></author><author><name sortKey="Tsai, Ching Yi" sort="Tsai, Ching Yi" uniqKey="Tsai C" first="Ching-Yi" last="Tsai">Ching-Yi Tsai</name><affiliation><nlm:aff wicri:cut=" and" id="N0x9b670c8.0xa22b5a0">Hepatitis Research Center</nlm:aff></affiliation></author><author><name sortKey="Kao, Chuan Liang" sort="Kao, Chuan Liang" uniqKey="Kao C" first="Chuan-Liang" last="Kao">Chuan-Liang Kao</name><affiliation><nlm:aff id="N0x9b670c8.0xa22b5a0">Department of Medical Technology, National Taiwan University, Taipei 100, Taiwan;</nlm:aff></affiliation></author><author><name sortKey="Yang, Jyh Yuan" sort="Yang, Jyh Yuan" uniqKey="Yang J" first="Jyh-Yuan" last="Yang">Jyh-Yuan Yang</name><affiliation><nlm:aff id="N0x9b670c8.0xa22b5a0">Center for Disease Control, Taipei 115, Taiwan;</nlm:aff></affiliation></author><author><name sortKey="Liu, Hwan Wun" sort="Liu, Hwan Wun" uniqKey="Liu H" first="Hwan-Wun" last="Liu">Hwan-Wun Liu</name><affiliation><nlm:aff wicri:cut="; and" id="N0x9b670c8.0xa22b5a0">Institute of Preventive Medicine, National Defense Medical College, Taipei 237, Taiwan</nlm:aff></affiliation></author><author><name sortKey="Su, Ih Jen" sort="Su, Ih Jen" uniqKey="Su I" first="Ih-Jen" last="Su">Ih-Jen Su</name><affiliation><nlm:aff id="N0x9b670c8.0xa22b5a0">Center for Disease Control, Taipei 115, Taiwan;</nlm:aff></affiliation></author><author><name sortKey="Tsai, Shih Feng" sort="Tsai, Shih Feng" uniqKey="Tsai S" first="Shih-Feng" last="Tsai">Shih-Feng Tsai</name><affiliation><nlm:aff id="N0x9b670c8.0xa22b5a0">Division of Molecular and Genomic Medicine, National Health Research Institutes, Taipei 115, Taiwan;</nlm:aff></affiliation></author><author><name sortKey="Chen, Ding Shinn" sort="Chen, Ding Shinn" uniqKey="Chen D" first="Ding-Shinn" last="Chen">Ding-Shinn Chen</name><affiliation><nlm:aff wicri:cut=" and" id="N0x9b670c8.0xa22b5a0">Hepatitis Research Center</nlm:aff></affiliation><affiliation><nlm:aff id="N0x9b670c8.0xa22b5a0">Department of Internal Medicine, National Taiwan University Hospital, Taipei 100, Taiwan;</nlm:aff></affiliation><affiliation><nlm:aff id="N0x9b670c8.0xa22b5a0">Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei 100, Taiwan</nlm:aff></affiliation></author><author><name sortKey="Chen, Pei Jer" sort="Chen, Pei Jer" uniqKey="Chen P" first="Pei-Jer" last="Chen">Pei-Jer Chen</name><affiliation><nlm:aff wicri:cut=" and" id="N0x9b670c8.0xa22b5a0">Hepatitis Research Center</nlm:aff></affiliation><affiliation><nlm:aff id="N0x9b670c8.0xa22b5a0">Department of Internal Medicine, National Taiwan University Hospital, Taipei 100, Taiwan;</nlm:aff></affiliation><affiliation><nlm:aff id="N0x9b670c8.0xa22b5a0">Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei 100, Taiwan</nlm:aff></affiliation></author></analytic><series><title level="j">Proceedings of the National Academy of Sciences of the United States of America</title><idno type="ISSN">0027-8424</idno><idno type="eISSN">1091-6490</idno><imprint><date when="2004">2004</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Since early March 2003, the severe acute respiratory syndrome (SARS) coronavirus (CoV) infection has claimed 346 cases and 37 deaths in Taiwan. The epidemic occurred in two stages. The first stage caused limited familial or hospital infections and lasted from early March to mid-April. All cases had clear contact histories, primarily from Guangdong or Hong Kong. The second stage resulted in a large outbreak in a municipal hospital, and quickly spread to northern and southern Taiwan from late April to mid-June. During this stage, there were some sporadic cases with untraceable contact histories. To investigate the origin and transmission route of SARS-CoV in Taiwan's epidemic, we conducted a systematic viral lineage study by sequencing the entire viral genome from ten SARS patients. SARS-CoV viruses isolated from Taiwan were found closely related to those from Guangdong and Hong Kong. In addition, all cases from the second stage belonged to the same lineage after the municipal hospital outbreak, including the patients without an apparent contact history. Analyses of these full-length sequences showed a positive selection occurring during SARS-CoV virus evolution. The mismatch distribution indicated that SARS viral genomes did not reach equilibrium and suggested a recent introduction of the viruses into human populations. The estimated genome mutation rate was ≈0.1 per genome, demonstrating possibly one of the lowest rates among known RNA viruses.</p></div></front></TEI><pmc article-type="research-article"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Proc Natl Acad Sci U S A</journal-id><journal-id journal-id-type="publisher-id">pnas</journal-id><journal-title>Proceedings of the National Academy of Sciences of the United States of America</journal-title><issn pub-type="ppub">0027-8424</issn><issn pub-type="epub">1091-6490</issn><publisher><publisher-name>National Academy of Sciences</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">14983045</article-id><article-id pub-id-type="pmc">356986</article-id><article-id pub-id-type="publisher-id">1012542</article-id><article-id pub-id-type="doi">10.1073/pnas.0307904100</article-id><article-categories><subj-group subj-group-type="heading"><subject>Biological Sciences</subject><subj-group><subject>Microbiology</subject></subj-group></subj-group></article-categories><title-group><article-title>Characterization of severe acute respiratory syndrome coronavirus genomes in Taiwan: Molecular epidemiology and genome evolution</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Yeh</surname><given-names>Shiou-Hwei</given-names></name><xref ref-type="aff" rid="N0x9b670c8.0xa22b5a0">*</xref><xref ref-type="aff" rid="N0x9b670c8.0xa22b5a0">†</xref></contrib><contrib contrib-type="author"><name><surname>Wang</surname><given-names>Hurng-Yi</given-names></name><xref ref-type="aff" rid="N0x9b670c8.0xa22b5a0">‡</xref></contrib><contrib contrib-type="author"><name><surname>Tsai</surname><given-names>Ching-Yi</given-names></name><xref ref-type="aff" rid="N0x9b670c8.0xa22b5a0">†</xref></contrib><contrib contrib-type="author"><name><surname>Kao</surname><given-names>Chuan-Liang</given-names></name><xref ref-type="aff" rid="N0x9b670c8.0xa22b5a0">§</xref></contrib><contrib contrib-type="author"><name><surname>Yang</surname><given-names>Jyh-Yuan</given-names></name><xref ref-type="aff" rid="N0x9b670c8.0xa22b5a0">¶</xref></contrib><contrib contrib-type="author"><name><surname>Liu</surname><given-names>Hwan-Wun</given-names></name><xref ref-type="aff" rid="N0x9b670c8.0xa22b5a0">∥</xref></contrib><contrib contrib-type="author"><name><surname>Su</surname><given-names>Ih-Jen</given-names></name><xref ref-type="aff" rid="N0x9b670c8.0xa22b5a0">¶</xref></contrib><contrib contrib-type="author"><name><surname>Tsai</surname><given-names>Shih-Feng</given-names></name><xref ref-type="aff" rid="N0x9b670c8.0xa22b5a0">*</xref></contrib><contrib contrib-type="author"><name><surname>Chen</surname><given-names>Ding-Shinn</given-names></name><xref ref-type="aff" rid="N0x9b670c8.0xa22b5a0">†</xref><xref ref-type="aff" rid="N0x9b670c8.0xa22b5a0">**</xref><xref ref-type="aff" rid="N0x9b670c8.0xa22b5a0">††</xref><xref ref-type="corresp" rid="cor1">‡‡</xref></contrib><contrib contrib-type="author"><name><surname>Chen</surname><given-names>Pei-Jer</given-names></name><xref ref-type="aff" rid="N0x9b670c8.0xa22b5a0">†</xref><xref ref-type="aff" rid="N0x9b670c8.0xa22b5a0">**</xref><xref ref-type="aff" rid="N0x9b670c8.0xa22b5a0">††</xref><xref ref-type="corresp" rid="cor1">‡‡</xref></contrib><contrib contrib-type="author"><collab>the National Taiwan University SARS Research Team<xref ref-type="fn" rid="fn1">§§</xref></collab></contrib></contrib-group><aff id="N0x9b670c8.0xa22b5a0"><label>*</label>Division of Molecular and Genomic Medicine, National Health Research Institutes, Taipei 115, Taiwan;<label>†</label>Hepatitis Research Center and<label>**</label>Department of Internal Medicine, National Taiwan University Hospital, Taipei 100, Taiwan;<label>‡</label>Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan;<label>§</label>Department of Medical Technology, National Taiwan University, Taipei 100, Taiwan;<label>¶</label>Center for Disease Control, Taipei 115, Taiwan;<label>∥</label>Institute of Preventive Medicine, National Defense Medical College, Taipei 237, Taiwan; and<label>††</label>Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei 100, Taiwan</aff><author-notes><fn id="cor1"><label>‡‡</label><p> To whom correspondence should be addressed at: Hepatitis Research Center, National Taiwan University Hospital, 7 Chung-Shan South Road, Taipei 100, Taiwan. E-mail: <email>dschen@ha.mc.ntu.edu.tw</email> or <email>peijer@ha.mc.ntu.edu.tw</email>. </p></fn><fn id="fn1"><label>§§</label><p>The National Taiwan University SARS Research Team: Ding-Shinn Chen<sup>a,b</sup>, Yuan-Teh Lee<sup>c,d</sup>, Che-Ming Teng<sup>e</sup>, Pan-Chyr Yang<sup>b</sup>, Hong-Nerng Ho<sup>f</sup>, Pei-Jer Chen<sup>g</sup>, Ming-Fu Chang<sup>h</sup>, Jin-Town Wang<sup>i</sup>, Shan-Chwen Chang<sup>b</sup>, Chuan-Liang Kao<sup>j</sup>, Wei-Kung Wang<sup>i</sup>, Cheng-Hsiang Hsiao<sup>k</sup>, and Po-Ren Hsueh<sup>l</sup>.</p></fn><fn><p>Communicated by Robert H. Purcell, Bethesda, MD, November 27, 2003</p></fn></author-notes><pub-date pub-type="ppub"><day>24</day><month>2</month><year>2004</year></pub-date><pub-date pub-type="epub"><day>11</day><month>2</month><year>2004</year></pub-date><volume>101</volume><issue>8</issue><fpage>2542</fpage><lpage>2547</lpage><history><date date-type="received"><day>28</day><month>6</month><year>2003</year></date></history><copyright-statement>Copyright © 2004, The National Academy of Sciences</copyright-statement><copyright-year>2004</copyright-year><abstract><p>Since early March 2003, the severe acute respiratory syndrome (SARS) coronavirus (CoV) infection has claimed 346 cases and 37 deaths in Taiwan. The epidemic occurred in two stages. The first stage caused limited familial or hospital infections and lasted from early March to mid-April. All cases had clear contact histories, primarily from Guangdong or Hong Kong. The second stage resulted in a large outbreak in a municipal hospital, and quickly spread to northern and southern Taiwan from late April to mid-June. During this stage, there were some sporadic cases with untraceable contact histories. To investigate the origin and transmission route of SARS-CoV in Taiwan's epidemic, we conducted a systematic viral lineage study by sequencing the entire viral genome from ten SARS patients. SARS-CoV viruses isolated from Taiwan were found closely related to those from Guangdong and Hong Kong. In addition, all cases from the second stage belonged to the same lineage after the municipal hospital outbreak, including the patients without an apparent contact history. Analyses of these full-length sequences showed a positive selection occurring during SARS-CoV virus evolution. The mismatch distribution indicated that SARS viral genomes did not reach equilibrium and suggested a recent introduction of the viruses into human populations. The estimated genome mutation rate was ≈0.1 per genome, demonstrating possibly one of the lowest rates among known RNA viruses.</p></abstract></article-meta><notes><fn-group><fn><p>Abbreviations: SARS, severe acute respiratory syndrome; CoV, coronavirus.</p></fn><fn><p>Data deposition: The sequences reported in this paper have been deposited in the GenBank database (accession nos. AY291451 and AY502923–AY502932). Offices of <sup>a</sup>the Dean and <sup>e</sup>Research and Development, and Departments of <sup>b</sup>Internal Medicine, <sup>h</sup>Biochemistry and Molecular Biology, <sup>i</sup>Microbiology, <sup>j</sup>Medical Technology, <sup>k</sup>Pathology, <sup>l</sup>Laboratory Medicine, and <sup>g</sup>Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei 100, Taiwan; and <sup>c</sup>Office of the Superintendent and Departments of <sup>d</sup>Internal Medicine and <sup>f</sup>Medical Research, National Taiwan University Hospital, Taipei 100, Taiwan.</p></fn></fn-group></notes></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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