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Date of origin of the SARS coronavirus strains

Identifieur interne : 001693 ( Pmc/Checkpoint ); précédent : 001692; suivant : 001694

Date of origin of the SARS coronavirus strains

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

Source :

RBID : PMC:516801

Abstract

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.

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.

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.

Conclusion

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.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2334-4-3) contains supplementary material, which is available to authorized users.


Url:
DOI: 10.1186/1471-2334-4-3
PubMed: 15028113
PubMed Central: 516801


Affiliations:


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PMC:516801

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<title>Background</title>
<p>A new respiratory infectious epidemic,
<italic>severe acute respiratory syndrome</italic>
(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.</p>
</sec>
<sec>
<title>Methods</title>
<p>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 (T
<sub>0</sub>
) can be deduced. We then implemented the least square method to estimate K and T
<sub>0</sub>
from the dataset of sequences and corresponding times. Monte Carlo stimulation was employed to discuss the results.</p>
</sec>
<sec>
<title>Results</title>
<p>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.</p>
</sec>
<sec>
<title>Conclusion</title>
<p>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.</p>
</sec>
<sec>
<title>Electronic supplementary material</title>
<p>The online version of this article (doi:10.1186/1471-2334-4-3) contains supplementary material, which is available to authorized users.</p>
</sec>
</div>
</front>
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<name sortKey="Wei, Cl" uniqKey="Wei C">CL Wei</name>
</author>
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<name sortKey="Ee, Al" uniqKey="Ee A">AL Ee</name>
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<name sortKey="Vega, Vb" uniqKey="Vega V">VB Vega</name>
</author>
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<name sortKey="Thoreau, H" uniqKey="Thoreau H">H Thoreau</name>
</author>
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<name sortKey="Su, St" uniqKey="Su S">ST Su</name>
</author>
<author>
<name sortKey="Chia, Jm" uniqKey="Chia J">JM Chia</name>
</author>
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<name sortKey="Ng, P" uniqKey="Ng P">P Ng</name>
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<author>
<name sortKey="Chiu, Kp" uniqKey="Chiu K">KP Chiu</name>
</author>
<author>
<name sortKey="Lim, L" uniqKey="Lim L">L Lim</name>
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<author>
<name sortKey="Zhang, T" uniqKey="Zhang T">T Zhang</name>
</author>
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<name sortKey="Peng, Ck" uniqKey="Peng C">CK Peng</name>
</author>
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<name sortKey="Lin, Eo" uniqKey="Lin E">EO Lin</name>
</author>
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<author>
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<author>
<name sortKey="Korber, B" uniqKey="Korber B">B Korber</name>
</author>
<author>
<name sortKey="Muldoon, M" uniqKey="Muldoon M">M Muldoon</name>
</author>
<author>
<name sortKey="Theiler, J" uniqKey="Theiler J">J Theiler</name>
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<author>
<name sortKey="Gao, F" uniqKey="Gao F">F Gao</name>
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<name sortKey="Gupta, R" uniqKey="Gupta R">R Gupta</name>
</author>
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<name sortKey="Lapedes, A" uniqKey="Lapedes A">A Lapedes</name>
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</author>
<author>
<name sortKey="Wolinsky, S" uniqKey="Wolinsky S">S Wolinsky</name>
</author>
<author>
<name sortKey="Bhattacharya, T" uniqKey="Bhattacharya T">T Bhattacharya</name>
</author>
</analytic>
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</back>
</TEI>
<pmc article-type="research-article">
<pmc-dir>properties open_access</pmc-dir>
<front>
<journal-meta>
<journal-id journal-id-type="nlm-ta">BMC Infect Dis</journal-id>
<journal-id journal-id-type="iso-abbrev">BMC Infect. Dis</journal-id>
<journal-title-group>
<journal-title>BMC Infectious Diseases</journal-title>
</journal-title-group>
<issn pub-type="epub">1471-2334</issn>
<publisher>
<publisher-name>BioMed Central</publisher-name>
<publisher-loc>London</publisher-loc>
</publisher>
</journal-meta>
<article-meta>
<article-id pub-id-type="pmid">15028113</article-id>
<article-id pub-id-type="pmc">516801</article-id>
<article-id pub-id-type="publisher-id">88</article-id>
<article-id pub-id-type="doi">10.1186/1471-2334-4-3</article-id>
<article-categories>
<subj-group subj-group-type="heading">
<subject>Research Article</subject>
</subj-group>
</article-categories>
<title-group>
<article-title>Date of origin of the SARS coronavirus strains</article-title>
</title-group>
<contrib-group>
<contrib contrib-type="author">
<name>
<surname>Lu</surname>
<given-names>Hongchao</given-names>
</name>
<address>
<email>lhc@ict.ac.cn</email>
</address>
<xref ref-type="aff" rid="Aff2">2</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Zhao</surname>
<given-names>Yi</given-names>
</name>
<address>
<email>biozy@ict.ac.cn</email>
</address>
<xref ref-type="aff" rid="Aff2">2</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Zhang</surname>
<given-names>Jingfen</given-names>
</name>
<address>
<email>jfzhang@ict.ac.cn</email>
</address>
<xref ref-type="aff" rid="Aff2">2</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Wang</surname>
<given-names>Yuelan</given-names>
</name>
<address>
<email>wyl_lisa@sina.com</email>
</address>
<xref ref-type="aff" rid="Aff1">1</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Li</surname>
<given-names>Wei</given-names>
</name>
<address>
<email>liw@genomics.org.cn</email>
</address>
<xref ref-type="aff" rid="Aff1">1</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Zhu</surname>
<given-names>Xiaopeng</given-names>
</name>
<address>
<email>nimezhu@163.com</email>
</address>
<xref ref-type="aff" rid="Aff1">1</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Sun</surname>
<given-names>Shiwei</given-names>
</name>
<address>
<email>dwsun@ict.ac.cn</email>
</address>
<xref ref-type="aff" rid="Aff2">2</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Xu</surname>
<given-names>Jingyi</given-names>
</name>
<address>
<email>cailun@ict.ac.cn</email>
</address>
<xref ref-type="aff" rid="Aff2">2</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Ling</surname>
<given-names>Lunjiang</given-names>
</name>
<address>
<email>xjy@ict.ac.cn</email>
</address>
<xref ref-type="aff" rid="Aff1">1</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Cai</surname>
<given-names>Lun</given-names>
</name>
<address>
<email>ling@sun5.ibp.ac.cn</email>
</address>
<xref ref-type="aff" rid="Aff2">2</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Bu</surname>
<given-names>Dongbo</given-names>
</name>
<address>
<email>bdb@ict.ac.cn</email>
</address>
<xref ref-type="aff" rid="Aff2">2</xref>
</contrib>
<contrib contrib-type="author" corresp="yes">
<name>
<surname>Chen</surname>
<given-names>Runsheng</given-names>
</name>
<address>
<email>crs@sun5.ibp.ac.cn</email>
</address>
<xref ref-type="aff" rid="Aff1">1</xref>
<xref ref-type="aff" rid="Aff2">2</xref>
</contrib>
<aff id="Aff1">
<label>1</label>
<institution-wrap>
<institution-id institution-id-type="GRID">grid.418856.6</institution-id>
<institution-id institution-id-type="ISNI">0000000417925640</institution-id>
<institution>Bioinformatics Laboratory,</institution>
<institution>Institute of Biophysics, Chinese Academy of Sciences,</institution>
</institution-wrap>
Beijing, P.R. China</aff>
<aff id="Aff2">
<label>2</label>
<institution-wrap>
<institution-id institution-id-type="GRID">grid.424936.e</institution-id>
<institution-id institution-id-type="ISNI">0000000122213902</institution-id>
<institution>Bioinformatics Research Group, Key Laboratory of Intelligent Information Processing,</institution>
<institution>Institute of Computing Technology, Chinese Academy of Sciences,</institution>
</institution-wrap>
Beijing, P.R. China</aff>
</contrib-group>
<pub-date pub-type="epub">
<day>6</day>
<month>2</month>
<year>2004</year>
</pub-date>
<pub-date pub-type="pmc-release">
<day>6</day>
<month>2</month>
<year>2004</year>
</pub-date>
<pub-date pub-type="collection">
<year>2004</year>
</pub-date>
<volume>4</volume>
<elocation-id>3</elocation-id>
<history>
<date date-type="received">
<day>28</day>
<month>9</month>
<year>2003</year>
</date>
<date date-type="accepted">
<day>6</day>
<month>2</month>
<year>2004</year>
</date>
</history>
<permissions>
<copyright-statement>© Lu et al; licensee BioMed Central Ltd. 2004, This article is published under license to BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL.</copyright-statement>
<license>
<license-p>This article is made available via the PMC Open Access Subset for unrestricted research re-use and secondary analysis in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic.</license-p>
</license>
</permissions>
<abstract id="Abs1">
<sec>
<title>Background</title>
<p>A new respiratory infectious epidemic,
<italic>severe acute respiratory syndrome</italic>
(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.</p>
</sec>
<sec>
<title>Methods</title>
<p>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 (T
<sub>0</sub>
) can be deduced. We then implemented the least square method to estimate K and T
<sub>0</sub>
from the dataset of sequences and corresponding times. Monte Carlo stimulation was employed to discuss the results.</p>
</sec>
<sec>
<title>Results</title>
<p>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.</p>
</sec>
<sec>
<title>Conclusion</title>
<p>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.</p>
</sec>
<sec>
<title>Electronic supplementary material</title>
<p>The online version of this article (doi:10.1186/1471-2334-4-3) contains supplementary material, which is available to authorized users.</p>
</sec>
</abstract>
<kwd-group xml:lang="en">
<title>Keywords</title>
<kwd>Common Ancestor</kwd>
<kwd>Evolution Rate</kwd>
<kwd>Severe Acute Respiratory Syndrome</kwd>
<kwd>Severe Acute Respiratory Syndrome</kwd>
<kwd>Severe Acute Respiratory Syndrome Patient</kwd>
</kwd-group>
<custom-meta-group>
<custom-meta>
<meta-name>issue-copyright-statement</meta-name>
<meta-value>© The Author(s) 2004</meta-value>
</custom-meta>
</custom-meta-group>
</article-meta>
</front>
</pmc>
<affiliations>
<list>
<country>
<li>République populaire de Chine</li>
</country>
</list>
<tree>
<country name="République populaire de Chine">
<noRegion>
<name sortKey="Lu, Hongchao" sort="Lu, Hongchao" uniqKey="Lu H" first="Hongchao" last="Lu">Hongchao Lu</name>
</noRegion>
<name sortKey="Bu, Dongbo" sort="Bu, Dongbo" uniqKey="Bu D" first="Dongbo" last="Bu">Dongbo Bu</name>
<name sortKey="Cai, Lun" sort="Cai, Lun" uniqKey="Cai L" first="Lun" last="Cai">Lun Cai</name>
<name sortKey="Chen, Runsheng" sort="Chen, Runsheng" uniqKey="Chen R" first="Runsheng" last="Chen">Runsheng Chen</name>
<name sortKey="Chen, Runsheng" sort="Chen, Runsheng" uniqKey="Chen R" first="Runsheng" last="Chen">Runsheng Chen</name>
<name sortKey="Li, Wei" sort="Li, Wei" uniqKey="Li W" first="Wei" last="Li">Wei Li</name>
<name sortKey="Ling, Lunjiang" sort="Ling, Lunjiang" uniqKey="Ling L" first="Lunjiang" last="Ling">Lunjiang Ling</name>
<name sortKey="Sun, Shiwei" sort="Sun, Shiwei" uniqKey="Sun S" first="Shiwei" last="Sun">Shiwei Sun</name>
<name sortKey="Wang, Yuelan" sort="Wang, Yuelan" uniqKey="Wang Y" first="Yuelan" last="Wang">Yuelan Wang</name>
<name sortKey="Xu, Jingyi" sort="Xu, Jingyi" uniqKey="Xu J" first="Jingyi" last="Xu">Jingyi Xu</name>
<name sortKey="Zhang, Jingfen" sort="Zhang, Jingfen" uniqKey="Zhang J" first="Jingfen" last="Zhang">Jingfen Zhang</name>
<name sortKey="Zhao, Yi" sort="Zhao, Yi" uniqKey="Zhao Y" first="Yi" last="Zhao">Yi Zhao</name>
<name sortKey="Zhu, Xiaopeng" sort="Zhu, Xiaopeng" uniqKey="Zhu X" first="Xiaopeng" last="Zhu">Xiaopeng Zhu</name>
</country>
</tree>
</affiliations>
</record>

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