Date of origin of the SARS coronavirus strains.
Identifieur interne : 002F13 ( PubMed/Corpus ); précédent : 002F12; suivant : 002F14Date of origin of the SARS coronavirus strains.
Auteurs : Hongchao Lu ; Yi Zhao ; Jingfen Zhang ; Yuelan Wang ; Wei Li ; Xiaopeng Zhu ; Shiwei Sun ; Jingyi Xu ; Lunjiang Ling ; Lun Cai ; Dongbo Bu ; Runsheng ChenSource :
- BMC infectious diseases [ 1471-2334 ] ; 2004.
English descriptors
- KwdEn :
- MESH :
- geographic , epidemiology : China.
- epidemiology : Severe Acute Respiratory Syndrome.
- genetics : HIV-1, SARS Virus.
- virology : Severe Acute Respiratory Syndrome.
- Chronology as Topic, Disease Outbreaks, Evolution, Molecular, Humans, Models, Biological.
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
Links to Exploration step
pubmed:15028113Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Date of origin of the SARS coronavirus strains.</title>
<author><name sortKey="Lu, Hongchao" sort="Lu, Hongchao" uniqKey="Lu H" first="Hongchao" last="Lu">Hongchao Lu</name>
<affiliation><nlm:affiliation>Bioinformatics Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P R China. lhc@ict.ac.cn</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Zhao, Yi" sort="Zhao, Yi" uniqKey="Zhao Y" first="Yi" last="Zhao">Yi Zhao</name>
</author>
<author><name sortKey="Zhang, Jingfen" sort="Zhang, Jingfen" uniqKey="Zhang J" first="Jingfen" last="Zhang">Jingfen Zhang</name>
</author>
<author><name sortKey="Wang, Yuelan" sort="Wang, Yuelan" uniqKey="Wang Y" first="Yuelan" last="Wang">Yuelan Wang</name>
</author>
<author><name sortKey="Li, Wei" sort="Li, Wei" uniqKey="Li W" first="Wei" last="Li">Wei Li</name>
</author>
<author><name sortKey="Zhu, Xiaopeng" sort="Zhu, Xiaopeng" uniqKey="Zhu X" first="Xiaopeng" last="Zhu">Xiaopeng Zhu</name>
</author>
<author><name sortKey="Sun, Shiwei" sort="Sun, Shiwei" uniqKey="Sun S" first="Shiwei" last="Sun">Shiwei Sun</name>
</author>
<author><name sortKey="Xu, Jingyi" sort="Xu, Jingyi" uniqKey="Xu J" first="Jingyi" last="Xu">Jingyi Xu</name>
</author>
<author><name sortKey="Ling, Lunjiang" sort="Ling, Lunjiang" uniqKey="Ling L" first="Lunjiang" last="Ling">Lunjiang Ling</name>
</author>
<author><name sortKey="Cai, Lun" sort="Cai, Lun" uniqKey="Cai L" first="Lun" last="Cai">Lun Cai</name>
</author>
<author><name sortKey="Bu, Dongbo" sort="Bu, Dongbo" uniqKey="Bu D" first="Dongbo" last="Bu">Dongbo Bu</name>
</author>
<author><name sortKey="Chen, Runsheng" sort="Chen, Runsheng" uniqKey="Chen R" first="Runsheng" last="Chen">Runsheng Chen</name>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PubMed</idno>
<date when="2004">2004</date>
<idno type="RBID">pubmed:15028113</idno>
<idno type="pmid">15028113</idno>
<idno type="doi">10.1186/1471-2334-4-3</idno>
<idno type="wicri:Area/PubMed/Corpus">002F13</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002F13</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en">Date of origin of the SARS coronavirus strains.</title>
<author><name sortKey="Lu, Hongchao" sort="Lu, Hongchao" uniqKey="Lu H" first="Hongchao" last="Lu">Hongchao Lu</name>
<affiliation><nlm:affiliation>Bioinformatics Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P R China. lhc@ict.ac.cn</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Zhao, Yi" sort="Zhao, Yi" uniqKey="Zhao Y" first="Yi" last="Zhao">Yi Zhao</name>
</author>
<author><name sortKey="Zhang, Jingfen" sort="Zhang, Jingfen" uniqKey="Zhang J" first="Jingfen" last="Zhang">Jingfen Zhang</name>
</author>
<author><name sortKey="Wang, Yuelan" sort="Wang, Yuelan" uniqKey="Wang Y" first="Yuelan" last="Wang">Yuelan Wang</name>
</author>
<author><name sortKey="Li, Wei" sort="Li, Wei" uniqKey="Li W" first="Wei" last="Li">Wei Li</name>
</author>
<author><name sortKey="Zhu, Xiaopeng" sort="Zhu, Xiaopeng" uniqKey="Zhu X" first="Xiaopeng" last="Zhu">Xiaopeng Zhu</name>
</author>
<author><name sortKey="Sun, Shiwei" sort="Sun, Shiwei" uniqKey="Sun S" first="Shiwei" last="Sun">Shiwei Sun</name>
</author>
<author><name sortKey="Xu, Jingyi" sort="Xu, Jingyi" uniqKey="Xu J" first="Jingyi" last="Xu">Jingyi Xu</name>
</author>
<author><name sortKey="Ling, Lunjiang" sort="Ling, Lunjiang" uniqKey="Ling L" first="Lunjiang" last="Ling">Lunjiang Ling</name>
</author>
<author><name sortKey="Cai, Lun" sort="Cai, Lun" uniqKey="Cai L" first="Lun" last="Cai">Lun Cai</name>
</author>
<author><name sortKey="Bu, Dongbo" sort="Bu, Dongbo" uniqKey="Bu D" first="Dongbo" last="Bu">Dongbo Bu</name>
</author>
<author><name sortKey="Chen, Runsheng" sort="Chen, Runsheng" uniqKey="Chen R" first="Runsheng" last="Chen">Runsheng Chen</name>
</author>
</analytic>
<series><title level="j">BMC infectious diseases</title>
<idno type="eISSN">1471-2334</idno>
<imprint><date when="2004" type="published">2004</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><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>
</keywords>
<keywords scheme="MESH" type="geographic" qualifier="epidemiology" xml:lang="en"><term>China</term>
</keywords>
<keywords scheme="MESH" qualifier="epidemiology" xml:lang="en"><term>Severe Acute Respiratory Syndrome</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>HIV-1</term>
<term>SARS Virus</term>
</keywords>
<keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Severe Acute Respiratory Syndrome</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Chronology as Topic</term>
<term>Disease Outbreaks</term>
<term>Evolution, Molecular</term>
<term>Humans</term>
<term>Models, Biological</term>
</keywords>
</textClass>
</profileDesc>
</teiHeader>
<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>
</TEI>
<pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><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>
</Journal>
<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>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Lu</LastName>
<ForeName>Hongchao</ForeName>
<Initials>H</Initials>
<AffiliationInfo><Affiliation>Bioinformatics Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P R China. lhc@ict.ac.cn</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Zhao</LastName>
<ForeName>Yi</ForeName>
<Initials>Y</Initials>
</Author>
<Author ValidYN="Y"><LastName>Zhang</LastName>
<ForeName>Jingfen</ForeName>
<Initials>J</Initials>
</Author>
<Author ValidYN="Y"><LastName>Wang</LastName>
<ForeName>Yuelan</ForeName>
<Initials>Y</Initials>
</Author>
<Author ValidYN="Y"><LastName>Li</LastName>
<ForeName>Wei</ForeName>
<Initials>W</Initials>
</Author>
<Author ValidYN="Y"><LastName>Zhu</LastName>
<ForeName>Xiaopeng</ForeName>
<Initials>X</Initials>
</Author>
<Author ValidYN="Y"><LastName>Sun</LastName>
<ForeName>Shiwei</ForeName>
<Initials>S</Initials>
</Author>
<Author ValidYN="Y"><LastName>Xu</LastName>
<ForeName>Jingyi</ForeName>
<Initials>J</Initials>
</Author>
<Author ValidYN="Y"><LastName>Ling</LastName>
<ForeName>Lunjiang</ForeName>
<Initials>L</Initials>
</Author>
<Author ValidYN="Y"><LastName>Cai</LastName>
<ForeName>Lun</ForeName>
<Initials>L</Initials>
</Author>
<Author ValidYN="Y"><LastName>Bu</LastName>
<ForeName>Dongbo</ForeName>
<Initials>D</Initials>
</Author>
<Author ValidYN="Y"><LastName>Chen</LastName>
<ForeName>Runsheng</ForeName>
<Initials>R</Initials>
</Author>
</AuthorList>
<Language>eng</Language>
<PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType>
<PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType>
</PublicationTypeList>
<ArticleDate DateType="Electronic"><Year>2004</Year>
<Month>02</Month>
<Day>06</Day>
</ArticleDate>
</Article>
<MedlineJournalInfo><Country>England</Country>
<MedlineTA>BMC Infect Dis</MedlineTA>
<NlmUniqueID>100968551</NlmUniqueID>
<ISSNLinking>1471-2334</ISSNLinking>
</MedlineJournalInfo>
<CitationSubset>IM</CitationSubset>
<MeshHeadingList><MeshHeading><DescriptorName UI="D002681" MajorTopicYN="N" Type="Geographic">China</DescriptorName>
<QualifierName UI="Q000453" MajorTopicYN="N">epidemiology</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D002910" MajorTopicYN="N">Chronology as Topic</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D004196" MajorTopicYN="N">Disease Outbreaks</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D019143" MajorTopicYN="N">Evolution, Molecular</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D015497" MajorTopicYN="N">HIV-1</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D008954" MajorTopicYN="N">Models, Biological</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D045473" MajorTopicYN="N">SARS Virus</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D045169" MajorTopicYN="N">Severe Acute Respiratory Syndrome</DescriptorName>
<QualifierName UI="Q000453" MajorTopicYN="Y">epidemiology</QualifierName>
<QualifierName UI="Q000821" MajorTopicYN="N">virology</QualifierName>
</MeshHeading>
</MeshHeadingList>
</MedlineCitation>
<PubmedData><History><PubMedPubDate PubStatus="received"><Year>2003</Year>
<Month>09</Month>
<Day>28</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="accepted"><Year>2004</Year>
<Month>02</Month>
<Day>06</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="pubmed"><Year>2004</Year>
<Month>3</Month>
<Day>19</Day>
<Hour>5</Hour>
<Minute>0</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="medline"><Year>2004</Year>
<Month>6</Month>
<Day>17</Day>
<Hour>5</Hour>
<Minute>0</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="entrez"><Year>2004</Year>
<Month>3</Month>
<Day>19</Day>
<Hour>5</Hour>
<Minute>0</Minute>
</PubMedPubDate>
</History>
<PublicationStatus>epublish</PublicationStatus>
<ArticleIdList><ArticleId IdType="pubmed">15028113</ArticleId>
<ArticleId IdType="doi">10.1186/1471-2334-4-3</ArticleId>
<ArticleId IdType="pii">1471-2334-4-3</ArticleId>
<ArticleId IdType="pmc">PMC516801</ArticleId>
</ArticleIdList>
<ReferenceList><Reference><Citation>Science. 2000 Jun 9;288(5472):1789-96</Citation>
<ArticleIdList><ArticleId IdType="pubmed">10846155</ArticleId>
</ArticleIdList>
</Reference>
<Reference><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>
<ArticleIdList><ArticleId IdType="pubmed">12690091</ArticleId>
</ArticleIdList>
</Reference>
</ReferenceList>
</PubmedData>
</pubmed>
</record>
Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/SrasV1/Data/PubMed/Corpus
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 002F13 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/PubMed/Corpus/biblio.hfd -nk 002F13 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Sante |area= SrasV1 |flux= PubMed |étape= Corpus |type= RBID |clé= pubmed:15028113 |texte= Date of origin of the SARS coronavirus strains. }}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/PubMed/Corpus/RBID.i -Sk "pubmed:15028113" \ | HfdSelect -Kh $EXPLOR_AREA/Data/PubMed/Corpus/biblio.hfd \ | NlmPubMed2Wicri -a SrasV1
![]() | This area was generated with Dilib version V0.6.33. | ![]() |