Serveur d'exploration SRAS

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Date of origin of the SARS coronavirus strains.

Identifieur interne : 002F13 ( PubMed/Curation ); précédent : 002F12; suivant : 002F14

Date of origin of the SARS coronavirus strains.

Auteurs : Hongchao Lu [République populaire de Chine] ; Yi Zhao ; Jingfen Zhang ; Yuelan Wang ; Wei Li ; Xiaopeng Zhu ; Shiwei Sun ; Jingyi Xu ; Lunjiang Ling ; Lun Cai ; Dongbo Bu ; Runsheng Chen

Source :

RBID : pubmed:15028113

Descripteurs français

English descriptors

Abstract

A new respiratory infectious epidemic, severe acute respiratory syndrome (SARS), broke out and spread throughout the world. By now the putative pathogen of SARS has been identified as a new coronavirus, a single positive-strand RNA virus. RNA viruses commonly have a high rate of genetic mutation. It is therefore important to know the mutation rate of the SARS coronavirus as it spreads through the population. Moreover, finding a date for the last common ancestor of SARS coronavirus strains would be useful for understanding the circumstances surrounding the emergence of the SARS pandemic and the rate at which SARS coronavirus diverge.

DOI: 10.1186/1471-2334-4-3
PubMed: 15028113

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pubmed:15028113

Le document en format XML

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<name sortKey="Lu, Hongchao" sort="Lu, Hongchao" uniqKey="Lu H" first="Hongchao" last="Lu">Hongchao Lu</name>
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<nlm:affiliation>Bioinformatics Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P R China. lhc@ict.ac.cn</nlm:affiliation>
<country xml:lang="fr" wicri:curation="lc">République populaire de Chine</country>
<wicri:regionArea>Bioinformatics Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing</wicri:regionArea>
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<name sortKey="Zhao, Yi" sort="Zhao, Yi" uniqKey="Zhao Y" first="Yi" last="Zhao">Yi Zhao</name>
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<name sortKey="Zhang, Jingfen" sort="Zhang, Jingfen" uniqKey="Zhang J" first="Jingfen" last="Zhang">Jingfen Zhang</name>
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<name sortKey="Wang, Yuelan" sort="Wang, Yuelan" uniqKey="Wang Y" first="Yuelan" last="Wang">Yuelan Wang</name>
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<name sortKey="Li, Wei" sort="Li, Wei" uniqKey="Li W" first="Wei" last="Li">Wei Li</name>
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<name sortKey="Zhu, Xiaopeng" sort="Zhu, Xiaopeng" uniqKey="Zhu X" first="Xiaopeng" last="Zhu">Xiaopeng Zhu</name>
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<name sortKey="Sun, Shiwei" sort="Sun, Shiwei" uniqKey="Sun S" first="Shiwei" last="Sun">Shiwei Sun</name>
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<name sortKey="Xu, Jingyi" sort="Xu, Jingyi" uniqKey="Xu J" first="Jingyi" last="Xu">Jingyi Xu</name>
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<name sortKey="Ling, Lunjiang" sort="Ling, Lunjiang" uniqKey="Ling L" first="Lunjiang" last="Ling">Lunjiang Ling</name>
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<name sortKey="Cai, Lun" sort="Cai, Lun" uniqKey="Cai L" first="Lun" last="Cai">Lun Cai</name>
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<name sortKey="Bu, Dongbo" sort="Bu, Dongbo" uniqKey="Bu D" first="Dongbo" last="Bu">Dongbo Bu</name>
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<name sortKey="Chen, Runsheng" sort="Chen, Runsheng" uniqKey="Chen R" first="Runsheng" last="Chen">Runsheng Chen</name>
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<name sortKey="Zhao, Yi" sort="Zhao, Yi" uniqKey="Zhao Y" first="Yi" last="Zhao">Yi Zhao</name>
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<name sortKey="Zhang, Jingfen" sort="Zhang, Jingfen" uniqKey="Zhang J" first="Jingfen" last="Zhang">Jingfen Zhang</name>
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<name sortKey="Wang, Yuelan" sort="Wang, Yuelan" uniqKey="Wang Y" first="Yuelan" last="Wang">Yuelan Wang</name>
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<name sortKey="Li, Wei" sort="Li, Wei" uniqKey="Li W" first="Wei" last="Li">Wei Li</name>
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<name sortKey="Zhu, Xiaopeng" sort="Zhu, Xiaopeng" uniqKey="Zhu X" first="Xiaopeng" last="Zhu">Xiaopeng Zhu</name>
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<name sortKey="Sun, Shiwei" sort="Sun, Shiwei" uniqKey="Sun S" first="Shiwei" last="Sun">Shiwei Sun</name>
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<name sortKey="Xu, Jingyi" sort="Xu, Jingyi" uniqKey="Xu J" first="Jingyi" last="Xu">Jingyi Xu</name>
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<name sortKey="Ling, Lunjiang" sort="Ling, Lunjiang" uniqKey="Ling L" first="Lunjiang" last="Ling">Lunjiang Ling</name>
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<name sortKey="Cai, Lun" sort="Cai, Lun" uniqKey="Cai L" first="Lun" last="Cai">Lun Cai</name>
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<name sortKey="Bu, Dongbo" sort="Bu, Dongbo" uniqKey="Bu D" first="Dongbo" last="Bu">Dongbo Bu</name>
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<name sortKey="Chen, Runsheng" sort="Chen, Runsheng" uniqKey="Chen R" first="Runsheng" last="Chen">Runsheng Chen</name>
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<title level="j">BMC infectious diseases</title>
<idno type="eISSN">1471-2334</idno>
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<date when="2004" type="published">2004</date>
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<term>China (epidemiology)</term>
<term>Chronology as Topic</term>
<term>Disease Outbreaks</term>
<term>Evolution, Molecular</term>
<term>HIV-1 (genetics)</term>
<term>Humans</term>
<term>Models, Biological</term>
<term>SARS Virus (genetics)</term>
<term>Severe Acute Respiratory Syndrome (epidemiology)</term>
<term>Severe Acute Respiratory Syndrome (virology)</term>
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<term>Chine (épidémiologie)</term>
<term>Chronologie comme sujet</term>
<term>Flambées de maladies</term>
<term>Humains</term>
<term>Modèles biologiques</term>
<term>Syndrome respiratoire aigu sévère (virologie)</term>
<term>Syndrome respiratoire aigu sévère (épidémiologie)</term>
<term>VIH-1 (Virus de l'Immunodéficience Humaine de type 1) (génétique)</term>
<term>Virus du SRAS (génétique)</term>
<term>Évolution moléculaire</term>
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<term>China</term>
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<term>Severe Acute Respiratory Syndrome</term>
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<keywords scheme="MESH" qualifier="genetics" xml:lang="en">
<term>HIV-1</term>
<term>SARS Virus</term>
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<term>VIH-1 (Virus de l'Immunodéficience Humaine de type 1)</term>
<term>Virus du SRAS</term>
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<keywords scheme="MESH" qualifier="virologie" xml:lang="fr">
<term>Syndrome respiratoire aigu sévère</term>
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<keywords scheme="MESH" qualifier="virology" xml:lang="en">
<term>Severe Acute Respiratory Syndrome</term>
</keywords>
<keywords scheme="MESH" qualifier="épidémiologie" xml:lang="fr">
<term>Chine</term>
<term>Syndrome respiratoire aigu sévère</term>
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<term>Chronology as Topic</term>
<term>Disease Outbreaks</term>
<term>Evolution, Molecular</term>
<term>Humans</term>
<term>Models, Biological</term>
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<term>Flambées de maladies</term>
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<term>Évolution moléculaire</term>
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<front>
<div type="abstract" xml:lang="en">A new respiratory infectious epidemic, severe acute respiratory syndrome (SARS), broke out and spread throughout the world. By now the putative pathogen of SARS has been identified as a new coronavirus, a single positive-strand RNA virus. RNA viruses commonly have a high rate of genetic mutation. It is therefore important to know the mutation rate of the SARS coronavirus as it spreads through the population. Moreover, finding a date for the last common ancestor of SARS coronavirus strains would be useful for understanding the circumstances surrounding the emergence of the SARS pandemic and the rate at which SARS coronavirus diverge.</div>
</front>
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<PMID Version="1">15028113</PMID>
<DateCompleted>
<Year>2004</Year>
<Month>06</Month>
<Day>16</Day>
</DateCompleted>
<DateRevised>
<Year>2018</Year>
<Month>11</Month>
<Day>13</Day>
</DateRevised>
<Article PubModel="Electronic">
<Journal>
<ISSN IssnType="Electronic">1471-2334</ISSN>
<JournalIssue CitedMedium="Internet">
<Volume>4</Volume>
<PubDate>
<Year>2004</Year>
<Month>Feb</Month>
<Day>06</Day>
</PubDate>
</JournalIssue>
<Title>BMC infectious diseases</Title>
<ISOAbbreviation>BMC Infect. Dis.</ISOAbbreviation>
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<ArticleTitle>Date of origin of the SARS coronavirus strains.</ArticleTitle>
<Pagination>
<MedlinePgn>3</MedlinePgn>
</Pagination>
<Abstract>
<AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">A new respiratory infectious epidemic, severe acute respiratory syndrome (SARS), broke out and spread throughout the world. By now the putative pathogen of SARS has been identified as a new coronavirus, a single positive-strand RNA virus. RNA viruses commonly have a high rate of genetic mutation. It is therefore important to know the mutation rate of the SARS coronavirus as it spreads through the population. Moreover, finding a date for the last common ancestor of SARS coronavirus strains would be useful for understanding the circumstances surrounding the emergence of the SARS pandemic and the rate at which SARS coronavirus diverge.</AbstractText>
<AbstractText Label="METHODS" NlmCategory="METHODS">We propose a mathematical model to estimate the evolution rate of the SARS coronavirus genome and the time of the last common ancestor of the sequenced SARS strains. Under some common assumptions and justifiable simplifications, a few simple equations incorporating the evolution rate (K) and time of the last common ancestor of the strains (T0) can be deduced. We then implemented the least square method to estimate K and T0 from the dataset of sequences and corresponding times. Monte Carlo stimulation was employed to discuss the results.</AbstractText>
<AbstractText Label="RESULTS" NlmCategory="RESULTS">Based on 6 strains with accurate dates of host death, we estimated the time of the last common ancestor to be about August or September 2002, and the evolution rate to be about 0.16 base/day, that is, the SARS coronavirus would on average change a base every seven days. We validated our method by dividing the strains into two groups, which coincided with the results from comparative genomics.</AbstractText>
<AbstractText Label="CONCLUSION" NlmCategory="CONCLUSIONS">The applied method is simple to implement and avoid the difficulty and subjectivity of choosing the root of phylogenetic tree. Based on 6 strains with accurate date of host death, we estimated a time of the last common ancestor, which is coincident with epidemic investigations, and an evolution rate in the same range as that reported for the HIV-1 virus.</AbstractText>
</Abstract>
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<LastName>Lu</LastName>
<ForeName>Hongchao</ForeName>
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<Affiliation>Bioinformatics Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P R China. lhc@ict.ac.cn</Affiliation>
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<LastName>Zhao</LastName>
<ForeName>Yi</ForeName>
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<LastName>Zhang</LastName>
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<LastName>Zhu</LastName>
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<LastName>Sun</LastName>
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<LastName>Xu</LastName>
<ForeName>Jingyi</ForeName>
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<LastName>Ling</LastName>
<ForeName>Lunjiang</ForeName>
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<DescriptorName UI="D008954" MajorTopicYN="N">Models, Biological</DescriptorName>
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<Citation>Science. 2000 Jun 9;288(5472):1789-96</Citation>
<ArticleIdList>
<ArticleId IdType="pubmed">10846155</ArticleId>
</ArticleIdList>
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<Citation>Lancet. 2003 Apr 19;361(9366):1319-25</Citation>
<ArticleIdList>
<ArticleId IdType="pubmed">12711465</ArticleId>
</ArticleIdList>
</Reference>
<Reference>
<Citation>N Engl J Med. 2003 May 15;348(20):1977-85</Citation>
<ArticleIdList>
<ArticleId IdType="pubmed">12671062</ArticleId>
</ArticleIdList>
</Reference>
<Reference>
<Citation>Lancet. 2003 May 24;361(9371):1779-85</Citation>
<ArticleIdList>
<ArticleId IdType="pubmed">12781537</ArticleId>
</ArticleIdList>
</Reference>
<Reference>
<Citation>N Engl J Med. 2003 May 15;348(20):1953-66</Citation>
<ArticleIdList>
<ArticleId IdType="pubmed">12690092</ArticleId>
</ArticleIdList>
</Reference>
<Reference>
<Citation>Science. 2003 May 30;300(5624):1394-9</Citation>
<ArticleIdList>
<ArticleId IdType="pubmed">12730500</ArticleId>
</ArticleIdList>
</Reference>
<Reference>
<Citation>Science. 2003 May 30;300(5624):1399-404</Citation>
<ArticleIdList>
<ArticleId IdType="pubmed">12730501</ArticleId>
</ArticleIdList>
</Reference>
<Reference>
<Citation>N Engl J Med. 2003 May 15;348(20):1967-76</Citation>
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