Date of origin of the SARS coronavirus strains
Identifieur interne : 005395 ( Main/Exploration ); précédent : 005394; suivant : 005396Date 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 :
- BMC Infectious Diseases [ 1471-2334 ] ; 2004.
Descripteurs français
- KwdFr :
- Chine (épidémiologie), Chronologie comme sujet, Flambées de maladies, Humains, Modèles biologiques, Syndrome respiratoire aigu sévère (virologie), Syndrome respiratoire aigu sévère (épidémiologie), VIH-1 (Virus de l'Immunodéficience Humaine de type 1) (génétique), Virus du SRAS (génétique), Évolution moléculaire.
- MESH :
- génétique : VIH-1 (Virus de l'Immunodéficience Humaine de type 1), Virus du SRAS.
- virologie : Syndrome respiratoire aigu sévère.
- épidémiologie : Chine, Syndrome respiratoire aigu sévère.
- Chronologie comme sujet, Flambées de maladies, Humains, Modèles biologiques, Évolution moléculaire.
- Wicri :
- geographic : République populaire de Chine.
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,
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.
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.
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.
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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Le document en format XML
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China</nlm:aff><country xml:lang="fr" wicri:curation="lc">République populaire de Chine</country><wicri:regionArea>Beijing</wicri:regionArea></affiliation></author><author><name sortKey="Chen, Runsheng" sort="Chen, Runsheng" uniqKey="Chen R" first="Runsheng" last="Chen">Runsheng Chen</name><affiliation wicri:level="1"><nlm:aff id="Aff1"><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</nlm:aff><country xml:lang="fr" wicri:curation="lc">République populaire de Chine</country><wicri:regionArea>Beijing</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff2"><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</nlm:aff><country xml:lang="fr" wicri:curation="lc">République populaire de Chine</country><wicri:regionArea>Beijing</wicri:regionArea></affiliation></author></analytic><series><title level="j">BMC Infectious Diseases</title><idno type="eISSN">1471-2334</idno><imprint><date when="2004">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="KwdFr" xml:lang="fr"><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></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="génétique" xml:lang="fr"><term>VIH-1 (Virus de l'Immunodéficience Humaine de type 1)</term><term>Virus du SRAS</term></keywords><keywords scheme="MESH" qualifier="virologie" xml:lang="fr"><term>Syndrome respiratoire aigu sévère</term></keywords><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></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><keywords scheme="MESH" xml:lang="fr"><term>Chronologie comme sujet</term><term>Flambées de maladies</term><term>Humains</term><term>Modèles biologiques</term><term>Évolution moléculaire</term></keywords><keywords scheme="Wicri" type="geographic" xml:lang="fr"><term>République populaire de Chine</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><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></div></front><back><div1 type="bibliography"><listBibl><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Tsang, Kw" uniqKey="Tsang K">KW Tsang</name></author><author><name sortKey="Ho, Pl" uniqKey="Ho P">PL Ho</name></author><author><name sortKey="Ooi, Gc" uniqKey="Ooi G">GC Ooi</name></author><author><name sortKey="Yee, Wk" uniqKey="Yee W">WK Yee</name></author><author><name sortKey="Wang, T" uniqKey="Wang T">T Wang</name></author><author><name sortKey="Chan Yeung, M" uniqKey="Chan Yeung M">M Chan-Yeung</name></author><author><name 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Hong, SHI Jianping, TONG Zongzhong, ZHANG Feng, LI Songgang, LIU Bin, LIU Siqi, DONG Wei, WANG Jun, Gane K-S Wong, YU Jun & YANG Huanming WANG Cui’e</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ruan, Yj" uniqKey="Ruan Y">YJ Ruan</name></author><author><name sortKey="Wei, Cl" uniqKey="Wei C">CL Wei</name></author><author><name sortKey="Ee, Al" uniqKey="Ee A">AL Ee</name></author><author><name sortKey="Vega, Vb" uniqKey="Vega V">VB Vega</name></author><author><name sortKey="Thoreau, H" uniqKey="Thoreau H">H Thoreau</name></author><author><name sortKey="Su, St" uniqKey="Su S">ST Su</name></author><author><name sortKey="Chia, Jm" uniqKey="Chia J">JM Chia</name></author><author><name sortKey="Ng, P" uniqKey="Ng P">P Ng</name></author><author><name sortKey="Chiu, Kp" uniqKey="Chiu K">KP Chiu</name></author><author><name sortKey="Lim, L" uniqKey="Lim L">L Lim</name></author><author><name sortKey="Zhang, T" uniqKey="Zhang T">T Zhang</name></author><author><name sortKey="Peng, Ck" uniqKey="Peng C">CK Peng</name></author><author><name sortKey="Lin, Eo" uniqKey="Lin E">EO Lin</name></author><author><name sortKey="Lee, Nm" uniqKey="Lee N">NM Lee</name></author><author><name sortKey="Yee, Sl" uniqKey="Yee S">SL Yee</name></author><author><name sortKey="Ng, Lf" uniqKey="Ng L">LF Ng</name></author><author><name sortKey="Chee, Re" uniqKey="Chee R">RE Chee</name></author><author><name sortKey="Stanton, Lw" uniqKey="Stanton L">LW Stanton</name></author><author><name sortKey="Long, Pm" uniqKey="Long P">PM Long</name></author><author><name sortKey="Liu, Et" uniqKey="Liu E">ET Liu</name></author></analytic></biblStruct><biblStruct><analytic><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></author><author><name sortKey="Gao, F" uniqKey="Gao F">F Gao</name></author><author><name sortKey="Gupta, R" uniqKey="Gupta R">R Gupta</name></author><author><name sortKey="Lapedes, A" uniqKey="Lapedes A">A Lapedes</name></author><author><name sortKey="Hahn, Bh" uniqKey="Hahn B">BH Hahn</name></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></biblStruct></listBibl></div1></back></TEI><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>Pour manipuler ce document sous Unix (Dilib)
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