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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Comments to the predecessor of human SARS coronavirus in 2003–2004 epidemic</title><author><name sortKey="Lam, Tommy Tsan Yuk" sort="Lam, Tommy Tsan Yuk" uniqKey="Lam T" first="Tommy Tsan-Yuk" last="Lam">Tommy Tsan-Yuk Lam</name></author><author><name sortKey="Hon, Chung Chau" sort="Hon, Chung Chau" uniqKey="Hon C" first="Chung-Chau" last="Hon">Chung-Chau Hon</name></author><author><name sortKey="Lam, Pui Yi" sort="Lam, Pui Yi" uniqKey="Lam P" first="Pui-Yi" last="Lam">Pui-Yi Lam</name></author><author><name sortKey="Yip, Chi Wai" sort="Yip, Chi Wai" uniqKey="Yip C" first="Chi-Wai" last="Yip">Chi-Wai Yip</name></author><author><name sortKey="Zeng, Fanya" sort="Zeng, Fanya" uniqKey="Zeng F" first="Fanya" last="Zeng">Fanya Zeng</name></author><author><name sortKey="Leung, Frederick Chi Ching" sort="Leung, Frederick Chi Ching" uniqKey="Leung F" first="Frederick Chi-Ching" last="Leung">Frederick Chi-Ching Leung</name></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">17884305</idno><idno type="pmc">7117273</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7117273</idno><idno type="RBID">PMC:7117273</idno><idno type="doi">10.1016/j.vetmic.2007.08.014</idno><date when="2007">2007</date><idno type="wicri:Area/Pmc/Corpus">000B32</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000B32</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Comments to the predecessor of human SARS coronavirus in 2003–2004 epidemic</title><author><name sortKey="Lam, Tommy Tsan Yuk" sort="Lam, Tommy Tsan Yuk" uniqKey="Lam T" first="Tommy Tsan-Yuk" last="Lam">Tommy Tsan-Yuk Lam</name></author><author><name sortKey="Hon, Chung Chau" sort="Hon, Chung Chau" uniqKey="Hon C" first="Chung-Chau" last="Hon">Chung-Chau Hon</name></author><author><name sortKey="Lam, Pui Yi" sort="Lam, Pui Yi" uniqKey="Lam P" first="Pui-Yi" last="Lam">Pui-Yi Lam</name></author><author><name sortKey="Yip, Chi Wai" sort="Yip, Chi Wai" uniqKey="Yip C" first="Chi-Wai" last="Yip">Chi-Wai Yip</name></author><author><name sortKey="Zeng, Fanya" sort="Zeng, Fanya" uniqKey="Zeng F" first="Fanya" last="Zeng">Fanya Zeng</name></author><author><name sortKey="Leung, Frederick Chi Ching" sort="Leung, Frederick Chi Ching" uniqKey="Leung F" first="Frederick Chi-Ching" last="Leung">Frederick Chi-Ching Leung</name></author></analytic><series><title level="j">Veterinary Microbiology</title><idno type="ISSN">0378-1135</idno><idno type="eISSN">1873-2542</idno><imprint><date when="2007">2007</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Guindon, S" uniqKey="Guindon S">S. Guindon</name></author><author><name sortKey="Gascuel, O" uniqKey="Gascuel O">O. Gascuel</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kan, B" uniqKey="Kan B">B. Kan</name></author><author><name sortKey="Wang, M" uniqKey="Wang M">M. Wang</name></author><author><name sortKey="Jing, H" uniqKey="Jing H">H. Jing</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kumar, S" uniqKey="Kumar S">S. Kumar</name></author><author><name sortKey="Tamura, K" uniqKey="Tamura K">K. Tamura</name></author><author><name sortKey="Nei, M" uniqKey="Nei M">M. Nei</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Posada, D" uniqKey="Posada D">D. Posada</name></author><author><name sortKey="Crandall, K A" uniqKey="Crandall K">K.A. Crandall</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ronquist, F" uniqKey="Ronquist F">F. Ronquist</name></author><author><name sortKey="Huelsenbeck, J P" uniqKey="Huelsenbeck J">J.P. Huelsenbeck</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Song, H D" uniqKey="Song H">H.D. Song</name></author><author><name sortKey="Tu, C C" uniqKey="Tu C">C.C. Tu</name></author><author><name sortKey="Zhang, G W" uniqKey="Zhang G">G.W. Zhang</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Thompson, J D" uniqKey="Thompson J">J.D. Thompson</name></author><author><name sortKey="Higgins, D G" uniqKey="Higgins D">D.G. Higgins</name></author><author><name sortKey="Gibson, T J" uniqKey="Gibson T">T.J. Gibson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wang, M" uniqKey="Wang M">M. Wang</name></author><author><name sortKey="Yan, M" uniqKey="Yan M">M. Yan</name></author><author><name sortKey="Xu, H" uniqKey="Xu H">H. Xu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wang, Z G" uniqKey="Wang Z">Z.G. Wang</name></author><author><name sortKey="Xu, S P" uniqKey="Xu S">S.P. Xu</name></author><author><name sortKey="Zhang, Y J" uniqKey="Zhang Y">Y.J. Zhang</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="letter"><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">17884305</article-id><article-id pub-id-type="pmc">7117273</article-id><article-id pub-id-type="publisher-id">S0378-1135(07)00403-8</article-id><article-id pub-id-type="doi">10.1016/j.vetmic.2007.08.014</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>Comments to the predecessor of human SARS coronavirus in 2003–2004 epidemic</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Lam</surname><given-names>Tommy Tsan-Yuk</given-names></name></contrib><contrib contrib-type="author"><name><surname>Hon</surname><given-names>Chung-Chau</given-names></name></contrib><contrib contrib-type="author"><name><surname>Lam</surname><given-names>Pui-Yi</given-names></name></contrib><contrib contrib-type="author"><name><surname>Yip</surname><given-names>Chi-Wai</given-names></name></contrib><contrib contrib-type="author"><name><surname>Zeng</surname><given-names>Fanya</given-names></name></contrib><contrib contrib-type="author"><name><surname>Leung</surname><given-names>Frederick Chi-Ching</given-names></name><email>fcleung@hkucc.hku.hk</email><xref rid="cor1" ref-type="corresp">⁎</xref></contrib></contrib-group><aff>Department of Zoology, The University of Hong Kong, HKSAR, China</aff><author-notes><corresp id="cor1"><label>⁎</label>Corresponding author at: 5N-01, 5/F, North Wing, Kadoorie Biological Science Building, The University of Hong Kong, HKSAR, China. Tel.: +852 2299 0817; fax: +852 2857 4672. <email>fcleung@hkucc.hku.hk</email></corresp></author-notes><pub-date pub-type="pmc-release"><day>17</day><month>8</month><year>2007</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>1</month><year>2008</year></pub-date><pub-date pub-type="epub"><day>17</day><month>8</month><year>2007</year></pub-date><volume>126</volume><issue>4</issue><fpage>390</fpage><lpage>393</lpage><history><date date-type="received"><day>15</day><month>1</month><year>2007</year></date></history><permissions><copyright-statement>Copyright © 2007 Elsevier B.V. All rights reserved.</copyright-statement><copyright-year>2007</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><kwd-group><title>Keywords</title><kwd>SARS</kwd><kwd>Coronavirus</kwd><kwd>Civet cats</kwd></kwd-group></article-meta></front><body><p content-type="salutation">Dear Editor-in-Chief,</p><p><xref rid="bib10" ref-type="bibr">Wang et al. (2006)</xref> analyzed the spike gene sequences of SARS coronavirus (SARS-CoV) from the recent sporadic (December 2003–January 2004) and 2002–2003 epidemic human cases and SARS-like-CoV from civet cats. The authors claimed that SARS-CoV strain GD03T0013 from the recent sporadic cases (<xref rid="bib11" ref-type="bibr">WHO, 2004</xref>) was genetically closer to the human SARS-CoV from the early phase of the 2002–2003 epidemic than to the wild animal SARS-like-CoV from the 2002–2003 epidemic. <xref rid="bib10" ref-type="bibr">Wang et al. (2006)</xref> therefore concluded that the recent sporadic human SARS-CoV was closer to an unknown SARS-CoV predecessor, which is remarkably different from the conclusions of previous studies (<xref rid="bib2" ref-type="bibr">Kan et al., 2005</xref>, <xref rid="bib6" ref-type="bibr">Song et al., 2005</xref>, <xref rid="bib9" ref-type="bibr">Wang et al., 2005</xref>). A drawback of the study by <xref rid="bib10" ref-type="bibr">Wang et al. (2006)</xref> is the exclusion of a number of civet cats SARS-like-CoV sequences, leading to the inability of their analyses to fully delineate the phylogenetic origin of strain GD03T0013.</p><p>To clarify the phylogenetic origin of strain GD03T0013 we analyzed the full length spike gene nucleotide sequences (<italic>n</italic> = 60) of human SARS-CoV from both the recent sporadic and 2002–2003 epidemic cases, as well as SARS-like-CoV isolated from wild animals (civet cats, raccoon dogs and bats). In particular, our dataset included the SARS-like-CoV isolated from civet cats in the 2003–2004 epidemic, which were not in the dataset of <xref rid="bib10" ref-type="bibr">Wang et al. (2006)</xref>. The sequences were aligned with ClustalX 1.83 (<xref rid="bib8" ref-type="bibr">Thompson et al., 1994</xref>) and gap columns were removed, generating an alignment of 3672 bp. Phylogenies were reconstructed from the alignment using three methods, including neighbor-joining (NJ) implemented in PAUP* 4.0b (<xref rid="bib7" ref-type="bibr">Swofford, 2002</xref>), maximum likelihood (ML) implemented in PhyML 2.4.4 (<xref rid="bib1" ref-type="bibr">Guindon and Gascuel, 2003</xref>) and Bayesian Markov Chain Monte Carlo (BMCMC) implemented in MrBayes (<xref rid="bib5" ref-type="bibr">Ronquist and Huelsenbeck, 2003</xref>). The substitution model used was the best-fit model suggested by ModelTest 3.7 (<xref rid="bib4" ref-type="bibr">Posada and Crandall, 1998</xref>). Five thousand bootstrap replications were performed in both the NJ and ML methods, whereas two sets of four tempered MCMC chains of 550,000 generations sampled every 100th generation with initial 10% burn-ins were used in the BMCMC method.</p><p>The topologies of NJ, ML and BMCMC phylogenies are essentially similar. Therefore, only the ML phylogeny is presented here and the confidences of its topology were summarized from ML and NJ bootstrapping, as well as the sampled trees in BMCMC chains. The summarized ML phylogeny (<xref rid="fig1" ref-type="fig">Fig. 1</xref>) shows that strain GD03T0013 shares a monophyletic relationship with the wild animal SARS-like-CoV cluster B (isolated in 2003–2004 epidemic) and this conclusion is supported by high confidence values. <xref rid="tbl1" ref-type="table">Table 1</xref>shows the comparison of the pairwise genetic distances (nucleotide p-distances) between the spike gene of strain GD03T0013 and other strains of our dataset. The genetic distance between civet cat SARS-like-CoV strain PC4-115 (and HC/SZ/266/03) from wild animal cluster B and strain GD03T0013 is smaller than that between any strains in the human epidemic cluster and the wild animal cluster A isolated during the 2002–2003 epidemic. Remarkably, only one nucleotide difference was identified between the spike genes of strains GD03T0013 and PC4-115 (and HC/SZ/266/03). In the spike gene phylogeny (<xref rid="fig1" ref-type="fig">Fig. 1</xref>), PC4-115 (and HC/SZ/266/03) could be also interpreted as the direct phylogenetic predecessor of GD03T0013. Although the first patient (GD03T0013) reported no contact with civet cats and other animals in the 2 months preceding the disease onset (<xref rid="bib9" ref-type="bibr">Wang et al., 2005</xref>), these phylogenetic and genetic evidences, as well as those presented by previous studies (<xref rid="bib2" ref-type="bibr">Kan et al., 2005</xref>, <xref rid="bib6" ref-type="bibr">Song et al., 2005</xref>, <xref rid="bib9" ref-type="bibr">Wang et al., 2005</xref>) suggested that the recent human case was a sporadic infection originating from the SARS-like-CoV of a wild animal.<fig id="fig1"><label>Fig. 1</label><caption><p>Phylogenetic tree of spike gene nucleotide sequences from SARS-CoV and SARS-like-CoV isolated from humans, civet cats, raccoon dogs and bats. Sequences from humans, civet cats, raccoon dogs and bats were indicated with symbols (■), (○), (▴), and (♦), respectively. The tree was reconstructed using ML method, with confidences of topology summarized from 5000 sampled trees from ML and NJ bootstrapping and BMCMC chains. Only confidence values of major clusters were shown (ML/NJ/BMCMC, in the parenthesis). The recent human SARS-CoV isolate GD03T0013 (of the index patient) is indicated with an asterisk. GZ0402 was isolated from the second patient (a waitress) in the 2003–2004 epidemic. Accession numbers of the sequences are shown within round brackets after their strain names (in bold). The distance unit was substitutions/site. Rp3 isolated from bats was used as an out-group to root the tree, and the genetic distance of its branch is not shown.</p></caption><graphic xlink:href="gr1"></graphic></fig><table-wrap position="float" id="tbl1"><label>Table 1</label><caption><p>Comparison of pairwise nucleotide p-distances between the spike gene of strain GD03T0013 and other SARS-CoV and SARS-like-CoV isolated from human and wild animals</p></caption><table frame="hsides" rules="groups"><thead><tr><th colspan="2" align="left">Human epidemic cluster (2002–2003)</th><th colspan="2" align="left">Wild animal cluster A (2002–2003)</th><th colspan="2" align="left">Wild animal cluster B (2003–2004)</th></tr></thead><tbody><tr><td align="left">GZ02, HSZ-Bc</td><td align="left">GZ60, GZ60, ZS-B, HSZ-Cc, JMD, HSZ2-A</td><td align="left">SZ3</td><td align="left">SZ13, SZ16</td><td align="left">PC4-115, HC/SZ/266/03, GZ0401*</td><td align="left">PC4-145</td></tr><tr><td align="left">0.004630</td><td align="left">0.004902</td><td align="left">0.005719</td><td align="left">0.005991</td><td align="left">0.000272</td><td align="left">0.000545</td></tr></tbody></table><table-wrap-foot><fn><p>Isolates shared the shortest distances to GD03T0013 are shown for each cluster (human epidemic cluster, wild animal cluster A, wild animal cluster B). The p-distances were calculated based on the sequence alignment (length = 3672 bp) using MEGA 3.1 <xref rid="bib3" ref-type="bibr">Kumar et al. (2004)</xref>.</p><p>* GZ0401 (AY568539) was the complete genome sequence of the SARS-CoV isolated from the same patient (the index patient in 2003–2004 epidemic) from which the GD03T0013 (AY525636) spike gene sequence was obtained.</p></fn></table-wrap-foot></table-wrap></p><p>Our results, based on the genetic analyses of the spike gene, showed that the closest strains to the recent sporadic human SARS-CoV are the civet cat SARS-like-CoV in 2003–2004 epidemic rather than the civet cat SARS-like-CoV in 2002–2003 epidemic suggested by <xref rid="bib12" ref-type="bibr">Zhao et al. (2004)</xref>, or the human SARS-CoV from the earlier phase of 2002–2003 epidemic, or an unknown predecessor suggested by <xref rid="bib10" ref-type="bibr">Wang et al. (2006)</xref>. The major difference between <xref rid="bib10" ref-type="bibr">Wang et al. (2006)</xref> and our analysis is the sample size and diversity of sequences used. They used fewer isolates and, more importantly, did not include the civet cat SARS-like-CoV sequences isolated in 2003–2004 epidemic (shown in <xref rid="fig1" ref-type="fig">Fig. 1</xref> under the wild animal cluster B grouping) in their analysis. Consequently, they could not fully delineate the phylogenetic origin of the SARS-CoV in the recent sporadic human cases. 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