Genetic distance of SARS coronavirus from the recent natural case
Identifieur interne : 000928 ( Pmc/Corpus ); précédent : 000927; suivant : 000929Genetic distance of SARS coronavirus from the recent natural case
Auteurs : Zhi-Gang Wang ; Shu-Ping Xu ; Yan-Jun Zhang ; Qi-Yu BaoSource :
- Veterinary Microbiology [ 0378-1135 ] ; 2006.
Abstract
Phylogenetic analysis of SARS coronavirus isolates based on the spike gene and protein sequence using Neighbor-Joining, maximum likelihood and Bayesian inference methods indicated that a recent human SARS-CoV isolate was closer to some human SARS-CoV isolates from earlier epidemic phase than to the SARS-CoV-like viruses isolated from wild animals during previous epidemic phase. A reasonable judgment based on phylogenetic relationship and sequence variations it is likely that the recent human SARS-CoV isolate is closer to an unknown SARS-CoV predecessor.
Url:
DOI: 10.1016/j.vetmic.2006.10.022
PubMed: 17141432
PubMed Central: 7117388
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PMC:7117388Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Genetic distance of SARS coronavirus from the recent natural case</title><author><name sortKey="Wang, Zhi Gang" sort="Wang, Zhi Gang" uniqKey="Wang Z" first="Zhi-Gang" last="Wang">Zhi-Gang Wang</name><affiliation><nlm:aff id="aff1">Zhejiang Provincial Center for Disease Prevention and Control, 17 Laozhedazhi Road, Hangzhou 310009, China</nlm:aff></affiliation></author><author><name sortKey="Xu, Shu Ping" sort="Xu, Shu Ping" uniqKey="Xu S" first="Shu-Ping" last="Xu">Shu-Ping Xu</name><affiliation><nlm:aff id="aff2">College of Biosystems Engineering and Food Science, University of Zhejiang, Hangzhou 310029, China</nlm:aff></affiliation></author><author><name sortKey="Zhang, Yan Jun" sort="Zhang, Yan Jun" uniqKey="Zhang Y" first="Yan-Jun" last="Zhang">Yan-Jun Zhang</name><affiliation><nlm:aff id="aff1">Zhejiang Provincial Center for Disease Prevention and Control, 17 Laozhedazhi Road, Hangzhou 310009, China</nlm:aff></affiliation></author><author><name sortKey="Bao, Qi Yu" sort="Bao, Qi Yu" uniqKey="Bao Q" first="Qi-Yu" last="Bao">Qi-Yu Bao</name><affiliation><nlm:aff id="aff3">Institute of Biomedical Informatics, Wenzhou Medical College, Wenzhou 325000, China</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">17141432</idno><idno type="pmc">7117388</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7117388</idno><idno type="RBID">PMC:7117388</idno><idno type="doi">10.1016/j.vetmic.2006.10.022</idno><date when="2006">2006</date><idno type="wicri:Area/Pmc/Corpus">000928</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000928</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Genetic distance of SARS coronavirus from the recent natural case</title><author><name sortKey="Wang, Zhi Gang" sort="Wang, Zhi Gang" uniqKey="Wang Z" first="Zhi-Gang" last="Wang">Zhi-Gang Wang</name><affiliation><nlm:aff id="aff1">Zhejiang Provincial Center for Disease Prevention and Control, 17 Laozhedazhi Road, Hangzhou 310009, China</nlm:aff></affiliation></author><author><name sortKey="Xu, Shu Ping" sort="Xu, Shu Ping" uniqKey="Xu S" first="Shu-Ping" last="Xu">Shu-Ping Xu</name><affiliation><nlm:aff id="aff2">College of Biosystems Engineering and Food Science, University of Zhejiang, Hangzhou 310029, China</nlm:aff></affiliation></author><author><name sortKey="Zhang, Yan Jun" sort="Zhang, Yan Jun" uniqKey="Zhang Y" first="Yan-Jun" last="Zhang">Yan-Jun Zhang</name><affiliation><nlm:aff id="aff1">Zhejiang Provincial Center for Disease Prevention and Control, 17 Laozhedazhi Road, Hangzhou 310009, China</nlm:aff></affiliation></author><author><name sortKey="Bao, Qi Yu" sort="Bao, Qi Yu" uniqKey="Bao Q" first="Qi-Yu" last="Bao">Qi-Yu Bao</name><affiliation><nlm:aff id="aff3">Institute of Biomedical Informatics, Wenzhou Medical College, Wenzhou 325000, China</nlm:aff></affiliation></author></analytic><series><title level="j">Veterinary Microbiology</title><idno type="ISSN">0378-1135</idno><idno type="eISSN">1873-2542</idno><imprint><date when="2006">2006</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Phylogenetic analysis of SARS coronavirus isolates based on the spike gene and protein sequence using Neighbor-Joining, maximum likelihood and Bayesian inference methods indicated that a recent human SARS-CoV isolate was closer to some human SARS-CoV isolates from earlier epidemic phase than to the SARS-CoV-like viruses isolated from wild animals during previous epidemic phase. A reasonable judgment based on phylogenetic relationship and sequence variations it is likely that the recent human SARS-CoV isolate is closer to an unknown SARS-CoV predecessor.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Chen, W" uniqKey="Chen W">W. Chen</name></author><author><name sortKey="Yan, M" uniqKey="Yan M">M. Yan</name></author><author><name sortKey="Yang, L" uniqKey="Yang L">L. Yang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wu, C Y" uniqKey="Wu C">C.Y. Wu</name></author><author><name sortKey="Jan, J T" uniqKey="Jan J">J.T. Jan</name></author><author><name sortKey="Ma, S H" uniqKey="Ma S">S.H. Ma</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Guan, Y" uniqKey="Guan Y">Y. Guan</name></author><author><name sortKey="Zheng, B J" uniqKey="Zheng B">B.J. Zheng</name></author><author><name sortKey="He, Y Q" uniqKey="He Y">Y.Q. 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Luo</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Zhao, G P" uniqKey="Zhao G">G.P. Zhao</name></author><author><name sortKey="He, J F" uniqKey="He J">J.F. He</name></author><author><name sortKey="Peng, G W" uniqKey="Peng G">G.W. Peng</name></author></analytic></biblStruct></listBibl></div1></back></TEI><pmc article-type="brief-report"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Vet Microbiol</journal-id><journal-id journal-id-type="iso-abbrev">Vet. Microbiol</journal-id><journal-title-group><journal-title>Veterinary Microbiology</journal-title></journal-title-group><issn pub-type="ppub">0378-1135</issn><issn pub-type="epub">1873-2542</issn><publisher><publisher-name>Elsevier B.V.</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">17141432</article-id><article-id pub-id-type="pmc">7117388</article-id><article-id pub-id-type="publisher-id">S0378-1135(06)00394-4</article-id><article-id pub-id-type="doi">10.1016/j.vetmic.2006.10.022</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>Genetic distance of SARS coronavirus from the recent natural case</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Wang</surname><given-names>Zhi-Gang</given-names></name><email>wzg188@126.com</email><xref rid="aff1" ref-type="aff">a</xref><xref rid="cor1" ref-type="corresp">⁎</xref></contrib><contrib contrib-type="author"><name><surname>Xu</surname><given-names>Shu-Ping</given-names></name><xref rid="aff2" ref-type="aff">b</xref></contrib><contrib contrib-type="author"><name><surname>Zhang</surname><given-names>Yan-Jun</given-names></name><xref rid="aff1" ref-type="aff">a</xref></contrib><contrib contrib-type="author"><name><surname>Bao</surname><given-names>Qi-Yu</given-names></name><xref rid="aff3" ref-type="aff">c</xref></contrib></contrib-group><aff id="aff1"><label>a</label>Zhejiang Provincial Center for Disease Prevention and Control, 17 Laozhedazhi Road, Hangzhou 310009, China</aff><aff id="aff2"><label>b</label>College of Biosystems Engineering and Food Science, University of Zhejiang, Hangzhou 310029, China</aff><aff id="aff3"><label>c</label>Institute of Biomedical Informatics, Wenzhou Medical College, Wenzhou 325000, China</aff><author-notes><corresp id="cor1"><label>⁎</label>Corresponding author. Tel.: +86 571 87235078; fax: +86 571 87235111. <email>wzg188@126.com</email></corresp></author-notes><pub-date pub-type="pmc-release"><day>25</day><month>10</month><year>2006</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on .</pmc-comment>
<pub-date pub-type="ppub"><day>25</day><month>2</month><year>2007</year></pub-date><pub-date pub-type="epub"><day>25</day><month>10</month><year>2006</year></pub-date><volume>120</volume><issue>1</issue><fpage>167</fpage><lpage>172</lpage><history><date date-type="received"><day>14</day><month>6</month><year>2005</year></date><date date-type="rev-recd"><day>26</day><month>7</month><year>2006</year></date><date date-type="accepted"><day>10</day><month>10</month><year>2006</year></date></history><permissions><copyright-statement>Copyright © 2006 Elsevier B.V. All rights reserved.</copyright-statement><copyright-year>2006</copyright-year><copyright-holder>Elsevier B.V.</copyright-holder><license><license-p>Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.</license-p></license></permissions><abstract><p>Phylogenetic analysis of SARS coronavirus isolates based on the spike gene and protein sequence using Neighbor-Joining, maximum likelihood and Bayesian inference methods indicated that a recent human SARS-CoV isolate was closer to some human SARS-CoV isolates from earlier epidemic phase than to the SARS-CoV-like viruses isolated from wild animals during previous epidemic phase. A reasonable judgment based on phylogenetic relationship and sequence variations it is likely that the recent human SARS-CoV isolate is closer to an unknown SARS-CoV predecessor.</p></abstract><kwd-group><title>Keywords</title><kwd>SARS coronavirus</kwd><kwd>Phylogeny</kwd><kwd>Human and palm civet</kwd><kwd>Spike gene sequence</kwd></kwd-group></article-meta></front><body><sec><label>1</label><title>Introduction</title><p>SARS coronavirus (SARS-CoV) phylogeny and genotyping studies have processed since SARS emergence (<xref rid="bib9" ref-type="bibr">Ruan et al., 2003</xref>, <xref rid="bib14" ref-type="bibr">Tsui et al., 2003</xref>, <xref rid="bib17" ref-type="bibr">Zhao et al., 2004</xref>). Genotype C and T were first suggested at the end of May 2003 (<xref rid="bib7" ref-type="bibr">Li et al., 2003</xref>), and were further improved and named as the Yexin genotype and Xiaohong genotype (<xref rid="bib15" ref-type="bibr">Wang et al., 2004</xref>). SARS virus was supposed to be transmitted from the wild animal to human being. This hypothesis was then supported by identification of a SARS-CoV-like virus in wild animals, such as palm civet, sold in markets in south China, for it had more than 99% of sequence identity to the SARS-CoV (<xref rid="bib3" ref-type="bibr">Guan et al., 2003</xref>), and indicating that the virus could have recently transferred its hosts, from animals to human beings. However, recent reports indicated that SARS-CoV was distinct from the virus in palm civet and no direct evidence so far to demonstrate if the palm civet virus was the origin of the SARS-CoV or if palm civets were also infected from other species (<xref rid="bib10" ref-type="bibr">Stadler et al., 2003</xref>). Although unlikely, the possibility that humans infected these SARS-CoV positive animals cannot be formally excluded, and there was a report of SARS-CoV transmitted from human to pig (<xref rid="bib1" ref-type="bibr">Chen et al., 2005</xref>). Where is the SARS-CoV-like virus of palm civet in the chain? Are they getting it from another animal? Are palm civets infecting rodents as well as humans? These still are not known exactly.</p><p>Here, the evolutional relationship among the previous epidemic and newly occurred (<xref rid="bib16" ref-type="bibr">WHO, 2004</xref>) (at the end of 2003) SARS-CoVs, and the previous epidemic SARS-CoV-like viruses of animal source are analyzed.</p></sec><sec><label>2</label><title>Materials and methods</title><p>The complete spike glycoprotein gene sequences of SARS-CoVs or SARS-CoV-like viruses download from NCBI GenBank database. GenBank accession numbers see <xref rid="tbl1" ref-type="table">Table 1</xref>. Multiple sequences of nucleic acid or amino acid were aligned by ClustalW 1.83 (<xref rid="bib13" ref-type="bibr">Thompson et al., 1994</xref>). Phylogenetic trees were constructed by MEGA3.1 (<xref rid="bib6" ref-type="bibr">Kumar et al., 2004</xref>) (Neighbor-Joining (NJ) for gene and protein sequences), PAUP* 4.0b2 (<xref rid="bib12" ref-type="bibr">Swofford, 2002</xref>) (Maximum likelihood for gene sequences) and MrBayes 3.1.2 (<xref rid="bib5" ref-type="bibr">Huelsenbeck and Ronquist, 2001</xref>) (Bayesian inference for gene and protein sequences). The FIPV-X06170 (Feline infectious peritonitis virus) was used as an outgroup within the spike gene data set. SARS-CoV and FIPV are known to be highly identical throughout the spike gene sequence (<xref rid="bib11" ref-type="bibr">Stavrinides and Guttman, 2004</xref>).<table-wrap position="float" id="tbl1"><label>Table 1</label><caption><p>The variant locations and substitution types in the spike protein sequences</p></caption><graphic xlink:href="fx1"></graphic></table-wrap></p></sec><sec><label>3</label><title>Results</title><p>Neighbor-Joining (NJ) trees of the spike gene sequences (<xref rid="fig1" ref-type="fig">Fig. 1</xref>) indicated that the SARS-CoV (GD03T0013) of newly occurred case is closer to the human SARS-CoVs detected in the previous epidemic early phase (such as GZ02, GZ-B and BJ02, etc) than to the palm civet or raccoon dog SARS-CoV-like viruses (SZ1, SZ3, SZ13 and SZ16) detected in the previous epidemic. The <italic>p</italic>-distances of new isolate (GD03T0013) with GZ02 and GZ-B isolates are smaller than with SZ3 isolate (<xref rid="fig1" ref-type="fig">Fig. 1</xref>). The similar results of gene sequence analysis were obtained from other models of phylogenetic trees such as Bayesian inference and Maximum likelihood methods (<xref rid="fig2" ref-type="fig">Fig. 2</xref>). The phylogenetic trees of the spike protein sequences were also showed similar characteristics as above (<xref rid="fig3" ref-type="fig">Fig. 3</xref>). The variant locations in the spike protein and the substitution types occurring in these isolates were markedly different between the human SARS-CoVs and the animal-origin SARS-CoV-like viruses comparing with the new isolate, the former has 5–7 mutual variant locations, the latter 8–9 mutual variant locations (<xref rid="tbl1" ref-type="table">Table 1</xref>).<fig id="fig1"><label>Fig. 1</label><caption><p>NJ trees of the newly occurred, animal-origin and previous epidemic SARS-CoVs. Red hollow circle indicates genotype T isolate, red solid circle indicates genotype C isolate, both from human in previous epidemic. Yellow solid triangle indicates animal-origin virus in previous epidemic. Blue solid circle indicates newly occurred virus. Purple hollow triangle indicates an out-group. Left tree: the tree was constructed using the <italic>p</italic>-distance of nucleotide difference. Bootstrap = 5000. The length indicated number of nucleotide difference per site of the spike gene. Right tree: the topologic tree was constructed using the <italic>p</italic>-distance of nucleotide difference. Bootstrap = 5000. Below table: <sup>*</sup>the genetic distance between SARS-CoV GD03T0013 and three groups. Here, genotype C composed of 43 isolates, genotype T composed of 76 isolates, animal-origin virus composed of SARS-CoV SZ1, SZ3, SZ13 and SZ16.</p></caption><graphic xlink:href="gr1"></graphic></fig><fig id="fig2"><label>Fig. 2</label><caption><p>Other model phylogenetic trees of the spike protein gene sequences, Bayesian inference (Bayes) tree was conducted with MrBayes 3.1.2 using the GTR model with 60,000 generations, sampling trees every 10th generation, and calculating a consensus tree with 25% alltrees, branch lengths indicating gamma-distributed rate variation across sites and a proportion of invariable sites, the probability of the partition indicated by the branch. Maximum likelihood (ML) tree was tested by the program MODELTEST 3.7 (<xref rid="bib8" ref-type="bibr">Posada and Crandall, 1998</xref>) to find out the best model and parameters for PAUP<sup>*</sup> 4.0b2 to build maximum likelihood tree, branch lengths indicating substitutions/site. Confidence in ML tree was determined by analyzing 300 bootstrap replicates.</p></caption><graphic xlink:href="gr2"></graphic></fig><fig id="fig3"><label>Fig. 3</label><caption><p>Phylogenetic trees of the spike protein sequences, Neighbor-Joining (NJ) tree was conducted with MEGA 3.1 using the JTT mode, the confidence in NJ tree was determined by analyzing 1000 bootstrap replicates, the branch length indicating substitutions/site. Bayesian inference (Bayes) tree was conducted with MrBayes 3.1.2 using the JTT model with 50,000 generations, sampling trees every 10th generation, and calculating a consensus tree with 25% alltrees, branch lengths indicated substitutions/site, the probability of the partition indicated by the branch.</p></caption><graphic xlink:href="gr3"></graphic></fig></p></sec><sec><label>4</label><title>Discussion</title><p>Our analysis is markedly different from a conclusion of previous report in SCIENCE journal (<xref rid="bib17" ref-type="bibr">Zhao et al., 2004</xref>) (They claim that phylogenetic analysis of this S gene sequence with those from the human SARS-CoV and palm civet SARS-like coronavirus indicated that this most recent case of SARS-CoV (GD03T0013) is much closer to the palm civet SARS-like coronavirus than to any human SARS-CoV detected in the previous epidemic). Their conclusion was cited by lately reports (<xref rid="bib4" ref-type="bibr">Song et al., 2005</xref>, <xref rid="bib2" ref-type="bibr">Wu et al., 2004</xref>). Here, our opinion, the phylogenetic relationship should be cautiously interpreted.</p><p>In this context, as a reasonable judgment based on phylogenetic relationship and sequence variations it is likely that the recent human SARS-CoV isolate is closer to an unknown SARS-CoV predecessor than the SARS-CoVs from human or SARS-CoV-like viruses from palm civet both detected in the previous epidemic.</p></sec></body><back><ref-list><title>References</title><ref id="bib1"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Chen</surname><given-names>W.</given-names></name><name><surname>Yan</surname><given-names>M.</given-names></name><name><surname>Yang</surname><given-names>L.</given-names></name></person-group><article-title>SARS-associated coronavirus transmitted from human to pig</article-title><source>Emerg. Infect. 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