A Novel Coronavirus Genome Identified in a Cluster of Pneumonia Cases

<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> <html> <head> <meta http-equiv="X-UA-Compatible" content="IE=edge" /> <title>A Novel Coronavirus Genome Identified in a Cluster of Pneumonia Cases — Wuhan, China 2019−2020</title> <title>A Novel Coronavirus Genome Identified in a Cluster of Pneumonia Cases — Wuhan, China 2019−2020</title> <meta name="keywords" content="" /> <meta name="hw.ad-path" content="https://weekly.chinacdc.cn/en/article/doi/10.46234/ccdcw2020.017" /> <meta name="hw.identifier" content="https://weekly.chinacdc.cn/en/article/doi/10.46234/ccdcw2020.017" /> <meta name="dc.format" content="text/html" /> <meta name="dc.title" content="A Novel Coronavirus Genome Identified in a Cluster of Pneumonia Cases — Wuhan, China 2019−2020" /> <meta name="dc.identifier" content="10.46234/ccdcw2020.017" /> <meta name="dc.contributor" content="Wenjie Tan" /> <meta name="dc.contributor" content="Xiang Zhao" /> <meta name="dc.contributor" content="Xuejun Ma" /> <meta name="dc.contributor" content="Wenling Wang" /> <meta name="dc.contributor" content="Peihua Niu" /> <meta name="dc.contributor" content="Wenbo Xu" /> <meta name="dc.contributor" content="George F. Gao" /> <meta name="dc.contributor" content="Guizhen Wu" /> <meta name="dc.creator" content="Wenjie Tan" /> <meta name="dc.creator" content="Xiang Zhao" /> <meta name="dc.creator" content="Xuejun Ma" /> <meta name="dc.creator" content="Wenling Wang" /> <meta name="dc.creator" content="Peihua Niu" /> <meta name="dc.creator" content="Wenbo Xu" /> <meta name="dc.creator" content="George F. Gao" /> <meta name="dc.creator" content="Guizhen Wu" /> <meta name="dc.date" content="2020-01-01" /> <meta name="dc.keywords" content=""/> <meta name="citation_journal_title" content="China CDC Weekly" /> <meta name="citation_publisher" content="China CDC Weekly" /> <meta name="citation_journal_abbrev" content="CCDCW" /> <meta name="citation_issn" content="2096-7071" /> <meta name="citation_date" content="2020-01-01" /> <meta name="citation_authors" content="Wenjie Tan, Xiang Zhao, Xuejun Ma, Wenling Wang, Peihua Niu, Wenbo Xu, George F. Gao, Guizhen Wu" /> <meta name="citation_online_date" content="2020-01-01"/> <meta name="citation_abstract_html_url" content="https://weekly.chinacdc.cn/en/article/doi/10.46234/ccdcw2020.017?viewType=HTML" /> <meta name="citation_pdf_url" content="https://weekly.chinacdc.cn/en/article/pdf/preview/10.46234/ccdcw2020.017" /> <meta name="citation_public_url" content="https://weekly.chinacdc.cn/en/article/doi/10.46234/ccdcw2020.017" /> <meta name="robots" content="noarchive" /> <meta name="dc.type" content="Notes from the Field"/> <meta name="dc.source" content="China CDC Weekly, 2020, Vol. 2, Issue 4, Pages: 61-62"/> <meta name="dc.publisher" content="China CDC Weekly"/> <meta name="dc.rights" content="http://creativecommons.org/licenses/by/3.0/"/> <meta name="dc.format" content="application/pdf" /> <meta name="dc.language" content="en" /> <meta name="dc.description" content="" />  <meta name="citation_title" content="A Novel Coronavirus Genome Identified in a Cluster of Pneumonia Cases — Wuhan, China 2019−2020" /> <meta name="citation_author" content="Wenjie Tan"/> <meta name="citation_author" content="Xiang Zhao"/> <meta name="citation_author" content="Xuejun Ma"/> <meta name="citation_author" content="Wenling Wang"/> <meta name="citation_author" content="Peihua Niu"/> <meta name="citation_author" content="Wenbo Xu"/> <meta name="citation_author" content="George F. 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class="fl text input"> <input name="pageType" type="hidden" value="en"> <input type="submit" class="sub fl" value=""> </form> </div> </div> </div> <div class="article-main"> <div class="inner clear content" style="position:relative;"> <div class="article-main-mid fl"> <div class="articleNav"> <strong>Article Navigation</strong> >  <span class="jounralName"><a class="mainColor" href="//weekly.chinacdc.cn/">China CDC Weekly</a></span>  > <span class="aIssue"><a class="mainColor" href="//weekly.chinacdc.cn/en/zcustom/volume/1/2020">2020, 2(4): 61-62</a></span> </div> <div class="article-left"> <div class="articleEn"> <div class="article-title" style="text-align:center;"> <h1>Notes from the Field: A Novel Coronavirus Genome Identified in a Cluster of Pneumonia Cases — Wuhan, China 2019−2020</h1> </div> <ul class="article-author clear">  <li> <a href="javascript:void(0);" class="mainColor" data-relate="tanwj@ivdc.chinacdc.cn" onclick="">Wenjie Tan</a><sup class="authorTag"><span class="com-num" data-tagVal="1,2" style="color:#0178d6;">1,2</span>, <a href="javascript:void(0);" class="com-user" title="Corresponding author: Wenjie Tan, tanwj@ivdc.chinacdc.cn"></a>, <a href="mailto:tanwj@ivdc.chinacdc.cn" class="com-mail" title="tanwj@ivdc.chinacdc.cn"></a></sup>; </li>  <li> <a href="javascript:void(0);" class="mainColor" data-relate="" onclick="">Xiang Zhao</a><sup class="authorTag"><span class="com-num" data-tagVal="1" style="color:#0178d6;">1</span></sup>; </li>  <li> <a href="javascript:void(0);" class="mainColor" data-relate="" onclick="">Xuejun Ma</a><sup class="authorTag"><span class="com-num" data-tagVal="1" style="color:#0178d6;">1</span></sup>; </li>  <li> <a href="javascript:void(0);" class="mainColor" data-relate="" onclick="">Wenling Wang</a><sup class="authorTag"><span class="com-num" data-tagVal="1" style="color:#0178d6;">1</span></sup>; </li>  <li> <a href="javascript:void(0);" class="mainColor" data-relate="" onclick="">Peihua Niu</a><sup class="authorTag"><span class="com-num" data-tagVal="1" style="color:#0178d6;">1</span></sup>; </li>  <li> <a href="javascript:void(0);" class="mainColor" data-relate="" onclick="">Wenbo Xu</a><sup class="authorTag"><span class="com-num" data-tagVal="1" style="color:#0178d6;">1</span></sup>; </li>  <li> <a href="javascript:void(0);" class="mainColor" data-relate="" onclick="">George F. Gao</a><sup class="authorTag"><span class="com-num" data-tagVal="1" style="color:#0178d6;">1</span></sup>; </li>  <li> <a href="javascript:void(0);" class="mainColor" data-relate="wugz@ivdc.chinacdc.cn" onclick="">Guizhen Wu</a><sup class="authorTag"><span class="com-num" data-tagVal="1,2" style="color:#0178d6;">1,2</span>, <a href="javascript:void(0);" class="com-user" title="Corresponding author: Guizhen Wu, wugz@ivdc.chinacdc.cn"></a>, <a href="mailto:wugz@ivdc.chinacdc.cn" class="com-mail" title="wugz@ivdc.chinacdc.cn"></a></sup></li> </ul> <p style="margin: 10px 0 "></p> <a class="affibtn" href="javascript:void(0)">View author affiliations</a> </div> </div> <ul class="article-tab-box tab-content" id="myTabContent">  <li id="Abstract" class="articleListBox">  </li> <li id="FullText" class="articleListBox FullText-all"> <img style="display:block;margin:10px auto;" src="//weekly.chinacdc.cn/style/web/images/public/1.gif" alt="loading..." /> </li>   <h3 class="navTitle" id="about-articletit">Author Affiliations</h3> <ul class="about-author" id="affiliations"> <li class="article-author-address" > <span class=""> 1. </span> <p class="lostOf"> MHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China</p> </li> <li class="article-author-address" > <span class=""> 2. </span> <p class="lostOf"> Center for Biosafety Mega-Science, Chinese Academy of Sciences, Beijing, China</p> </li> </ul> <ul class="about-article"> <li> <b>Corresponding authors:</b> Wenjie Tan, <a href="mailto:tanwj@ivdc.chinacdc.cn">tanwj@ivdc.chinacdc.cn</a>; Guizhen Wu, <a href="mailto:wugz@ivdc.chinacdc.cn">wugz@ivdc.chinacdc.cn</a></li> <li class="com-author-info"> <b>Online Date: </b>January 21 2020</li> <li class="com-author-info"> <b>Issue Date: </b>January 24 2020</li> <li class="com-author-info"> <b>doi: </b><a href="//weekly.chinacdc.cn/en/article/doi/10.46234/ccdcw2020.017" target="_blank">10.46234/ccdcw2020.017</a> </li> <li class="com-author-info"> </li> </ul> <li id="References" class="articleListBox"> <h3 class="navTitle" id="References-list">References</h3> <div class="References-wrap" style="word-break:break-all;"> <table class="reference-tab"> <tr class="document-box" id="b1"> <td valign="top" class="td1" style="width:28px;"> [1] </td> <td class="td2"> George F. Gao. From “A”IV to “Z”IKV: attacks from emerging and Re-emerging pathogens. Cell 2018;172(6):1157 − 9. http://dx.doi.org/10.1016/j.cell.2018.02.025.</td> </tr> <tr class="document-box" id="b2"> <td valign="top" class="td1" style="width:28px;"> [2] </td> <td class="td2"> Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 2013;30(4):772 − 80. http://dx.doi.org/10.1093/molbev/mst010.</td> </tr> <tr class="document-box" id="b3"> <td valign="top" class="td1" style="width:28px;"> [3] </td> <td class="td2"> Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 2003;52(5):696 − 704. http://dx.doi.org/10.1080/10635150390235520.</td> </tr> </table> </div></li>  <li class="article-box article-chart" id="figTab"> <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> <html> <head> <meta name="renderer" content="webkit" /> <meta http-equiv="X-UA-Compatible" content="IE=edge" /> </head> <body> <div class="_figclass figure"> <div class="figureTextBox"> <div> <a class="" title="FIGURE 1. Phylogenetic relationships between the genomes of the new types of Betacoronavirus and other Orthocoronavirinae genomes. The viruses in the subfamily Orthocoronavirinae were classified into four genera (prototype or Refseq strains shown): Alphacoronavirus (purple), Betacoronavirus (orange), Gammacoronavirus (green), and Deltacoronavirus (blue). Classic subgroup clusters for the Betacoronavirus were labelled 2a–2d. The tree was based on complete genomes shown above using the maximum likelihood method under the GTR + I + Γ model of nucleotide substitution as implemented in PhyML. The new types of Betacoronavirus, labelled with red stars, were placed into the lineage of Betacoronavirus 2b, which contain the following: avian infectious bronchitis virus (AIBV), Middle East respiratory syndrome coronavirus (MERS-CoV), mouse hepatitis virus (MHV), porcine enteric diarrhea virus (PEDV), severe acute respiratory syndrome coronavirus (SARS-CoV), SARS-related coronavirus (SARSr-CoV), and Human coronavirus (HCoV)." href="/fileCCDCW/journal/article/ccdcw/2020/4/PIC/Wuhan-1.jpg" > <img src="/fileCCDCW/journal/article/ccdcw/2020/4/PIC/Wuhan-1.jpg" onerror="this.onerror=null;this.src='/fileCCDCW/journal/article/ccdcw/2020/4/PIC/Wuhan-1.jpg'" class="figure_img figure_type2 " id="Fig-Figure1" ref="#Fig-Figure1"/> </a> </div> <div class="figureTitle">  <p class="figTabSpan"> <span class="FigText" id="Figure1"> <b>FIGURE 1.</b>  </span> Phylogenetic relationships between the genomes of the new types of <i>Betacoronavirus</i> and other <i>Orthocoronavirinae</i> genomes. The viruses in the subfamily <i>Orthocoronavirinae</i> were classified into four genera (prototype or Refseq strains shown): <i>Alphacoronavirus</i> (purple), <i>Betacoronavirus</i> (orange), <i>Gammacoronavirus</i> (green), and <i>Deltacoronavirus</i> (blue). Classic subgroup clusters for the <i>Betacoronavirus</i> were labelled 2a–2d. The tree was based on complete genomes shown above using the maximum likelihood method under the GTR + I + Γ model of nucleotide substitution as implemented in PhyML. The new types of <i>Betacoronavirus</i>, labelled with red stars, were placed into the lineage of <i>Betacoronavirus</i> 2b, which contain the following: avian infectious bronchitis virus (AIBV), Middle East respiratory syndrome coronavirus (MERS-CoV), mouse hepatitis virus (MHV), porcine enteric diarrhea virus (PEDV), severe acute respiratory syndrome coronavirus (SARS-CoV), SARS-related coronavirus (SARSr-CoV), and Human coronavirus (HCoV).</p> </div> </div>  <div class="figure_button"> <img src="//weekly.chinacdc.cn/style/web/images/public/download.png"/>Download: <a href="javascript:void(0);" onclick="downloadImg('73680759-5f97-493c-bf0c-cb7174d4c623','figure')">Full-Size Img</a> <a href="javascript:void(0);" onclick="downloadPPT('73680759-5f97-493c-bf0c-cb7174d4c623','figure')" style="border-left: 1px solid #ccc;padding-left: 5px;">PowerPoint</a> </div>  </div> </body> </html> </li> <li id="Supplements" class="articleListBox"> </li>   <li> <script defer 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tanwj@ivdc.chinacdc.cn"></a>, <a href="mailto:tanwj@ivdc.chinacdc.cn" class="com-mail" title="mailto: tanwj@ivdc.chinacdc.cn"></a></sup>; </li> <li> <a onclick='searchLike("authorNameEn","Xiang Zhao");' href="javascript:void(0);">Xiang Zhao</a><sup class="authorTag"><a href="javascript:void(0);" title="">1</a></sup>; </li> <li> <a onclick='searchLike("authorNameEn","Xuejun Ma");' href="javascript:void(0);">Xuejun Ma</a><sup class="authorTag"><a href="javascript:void(0);" title="">1</a></sup>; </li> <li> <a onclick='searchLike("authorNameEn","Wenling Wang");' href="javascript:void(0);">Wenling Wang</a><sup class="authorTag"><a href="javascript:void(0);" title="">1</a></sup>; </li> <li> <a onclick='searchLike("authorNameEn","Peihua Niu");' href="javascript:void(0);">Peihua Niu</a><sup class="authorTag"><a href="javascript:void(0);" title="">1</a></sup>; </li> <li> <a onclick='searchLike("authorNameEn","Wenbo Xu");' href="javascript:void(0);">Wenbo Xu</a><sup class="authorTag"><a href="javascript:void(0);" title="">1</a></sup>; </li> <li> <a onclick='searchLike("authorNameEn","George F. Gao");' href="javascript:void(0);">George F. Gao</a><sup class="authorTag"><a href="javascript:void(0);" title="">1</a></sup>; </li> <li> <a onclick='searchLike("authorNameEn","Guizhen Wu");' href="javascript:void(0);">Guizhen Wu</a><sup class="authorTag"><a href="javascript:void(0);" title="">1,2</a>, <a href="javascript:void(0);" class="com-user" title="Corresponding author: Guizhen Wu, wugz@ivdc.chinacdc.cn"></a>, <a href="mailto:wugz@ivdc.chinacdc.cn" class="com-mail" title="mailto: wugz@ivdc.chinacdc.cn"></a></sup></li> </ul> <p style="margin: 10px 0 " ></p> <a class="affibtnPhone" href="javascript:void(0)">View author affiliations</a>  <div class="summary">  </div>  <h6 class="navTitle" id="about-articletit-app" style="padding-top:15px;"><b>Author Affiliations</b></h6> <ul class="about-author" id ="articleAffiliations"> <li style="margin-bottom:8px;line-height: 18px;">1. MHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China</li> <li style="margin-bottom:8px;line-height: 18px;">2. Center for Biosafety Mega-Science, Chinese Academy of Sciences, Beijing, China</li> <h6><b>Corresponding authors: </b> <p style="margin-bottom:2px;display:inline-block;">Wenjie Tan, <a href="mailto:tanwj@ivdc.chinacdc.cn">tanwj@ivdc.chinacdc.cn</a>; </p> <p style="margin-bottom:2px;display:inline-block;">Guizhen Wu, <a href="mailto:wugz@ivdc.chinacdc.cn">wugz@ivdc.chinacdc.cn</a></p> </h6> <h6> <b>Online Date: </b>January 21 2020</h6> <h6> <b>Issue Date: </b>January 24 2020</h6> <h6> <b>doi: </b><a href="//weekly.chinacdc.cn/en/article/doi/10.46234/ccdcw2020.017" target="_blank">10.46234/ccdcw2020.017</a> </h6> <h6 style="margin:8px 0 3px;"> </h6> </ul>    </section>  <section class="article-content FullText-all"> <ul id="htmlContent2" class="current">  <div class="box box-top box-tan"> <table class="box-content reference-tab"></table> <div class="triangle"> <div class="triangle-bg"></div> <div class="triangle-content"></div> </div> <i class="close-box articleFont icon-cuo"></i> </div> <h3 class="full-text navTitle">HTML</h3>        <li vid="s00" >  <p id="18b0fb4e-53a7-43b6-adc7-85773f88d2ff"> Emerging and re-emerging pathogens are great challenges to the public health (<span class="xref"><a href="#b1" ref-type="bibr">1</a></span>). A cluster of pneumonia cases with an unknown cause occurred in Wuhan starting on December 21, 2019. As of January 20, 2020, a total of 201 cases of pneumonia in China have been confirmed. A team of professionals from the National Health Commission and China CDC conducted epidemiological and etiological investigations. On January 3, 2020, the first complete genome of the novel β genus coronaviruses (2019-nCoVs) was identified in samples of bronchoalveolar lavage fluid (BALF) from a patient from Wuhan by scientists of the National Institute of Viral Disease Control and Prevention (IVDC) through a combination of Sanger sequencing, Illumina sequencing, and nanopore sequencing. Three distinct strains have been identified, the virus has been designated as 2019-nCoV, and the disease has been subsequently named novel coronavirus-infected pneumonia (NCIP).</p>      <p id="6d14ab40-6429-4144-bf10-8121400d5f44"> Phylogenetic analysis was conducted to determine the relationship between 2019-nCoVs and other sequences under the <i>Orthocoronavirinae</i> subfamily using MAFFT v7.455 (<span class="xref"><a href="#Figure1" ref-type="fig">Figure 1</a></span>) (<span class="xref"><a href="#b2" ref-type="bibr">2</a></span>), and maximum likelihood inference was calculated using PhyML v3.3 (<span class="xref"><a href="#b3" ref-type="bibr">3</a></span>), employing the GTR + I + Γ model of nucleotide substitution, and 1,000 bootstrap replicates. The 2019-nCoVs have features typical of the coronavirus family and were placed in the <i>Betacoronavirus</i> 2b lineage. Alignment of these strains’ full genomes and other available genomes of <i>Betacoronavirus</i> showed the closest relationship with Bat SARS-like coronavirus isolate bat-SL-CoVZC45 (Accession Number: MG772933.1) (Identity 87.99%). The typical crown-like particles of the 2019-nCoVs can be observed under transmission electron microscope (TEM) with negative staining (<ext-link ext-link-type="uri" xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="http://www.gisaid.org">www.gisaid.org</ext-link>). The origin of the 2019-nCoVs is still being investigated. However, all current evidence points to wild animals sold illegally in the Huanan Seafood Wholesale Market.</p>        <div class="_figclass figure"> <a href="/fileCCDCW/journal/article/ccdcw/2020/4/PIC/Wuhan-1.jpg"> <img src="/fileCCDCW/journal/article/ccdcw/2020/4/PIC/Wuhan-1.jpg" onerror="this.onerror=null;this.src='/fileCCDCW/journal/article/ccdcw/2020/4/PIC/Wuhan-1.jpg'" style=" border: 1px solid #d9d4d4;float:none; cursor: pointer;height: auto; margin: auto !important; width: 100% !important;" class="figure_img" id="Fig-Figure1" ref="#Fig-Figure1"/> </a> <div class="figTitle">  <div class="figTitleEn" id="Figure1"> <b>Figure 1.</b>  <p>Phylogenetic relationships between the genomes of the new types of <i>Betacoronavirus</i> and other <i>Orthocoronavirinae</i> genomes. The viruses in the subfamily <i>Orthocoronavirinae</i> were classified into four genera (prototype or Refseq strains shown): <i>Alphacoronavirus</i> (purple), <i>Betacoronavirus</i> (orange), <i>Gammacoronavirus</i> (green), and <i>Deltacoronavirus</i> (blue). Classic subgroup clusters for the <i>Betacoronavirus</i> were labelled 2a–2d. The tree was based on complete genomes shown above using the maximum likelihood method under the GTR + I + Γ model of nucleotide substitution as implemented in PhyML. The new types of <i>Betacoronavirus</i>, labelled with red stars, were placed into the lineage of <i>Betacoronavirus</i> 2b, which contain the following: avian infectious bronchitis virus (AIBV), Middle East respiratory syndrome coronavirus (MERS-CoV), mouse hepatitis virus (MHV), porcine enteric diarrhea virus (PEDV), severe acute respiratory syndrome coronavirus (SARS-CoV), SARS-related coronavirus (SARSr-CoV), and Human coronavirus (HCoV).</p>  </div> </div> </div>    <p id="b7dcf897-f414-4f6e-9362-54475f521d29"> Several complete genome sequences of 2019-nCoVs were successfully obtained and released recently via www.gisaid.org to provide a first look at the molecular characteristics of this emerging pathogen, and all related information has also been reported to the World Health Organization (WHO). Several rapid and sensitive detection tests have been developed by China CDC and will be applied to the prevention and control of this 2019-nCoV outbreak.</p>      <p id="f61a7929-c7f7-4be8-91e5-6a1b6cda7d3c"> <b>Data availability.</b> The new <i>Betacoronavirus</i> genome sequence has been deposited in GISAID (<ext-link ext-link-type="uri" xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="http://www.gisaid.org">www.gisaid.org</ext-link>) under the accession number EPI_ISL_402119, EPI_ISL_ 402020 and EPI_ISL_402121.</p>     </li> </ul></figure> </ul>   <a class="tabJump" href="//weekly.chinacdc.cn/en/article/app/id/a3907201-f64f-4154-a19e-4253b453d10c/reference">Reference <num>(3)</num></a> <div class="" > <p class="quot"> <div class="copyCitationInfo" style="width: 0px;height: 0px;opacity:0;overflow: hidden;"></div> <table class="article-tab"> <tr> <td valign="top" width="70"><span class=""><b>Citation:</b></span></td> <td> <span class="info" id="infoEn"></span> <div class="modal-footer"> <span class="copy-citation" onclick="copyArticle2(this)" title="copy to clipboard"> <img class="shu" src="//weekly.chinacdc.cn/style/web/images/public/shu.png" alt="shu" /> </span> </div> </td> </tr> </table> </p> </div> <div class="References-wrap" style="display:none;"> <table class="reference-tab reference-tab-app"> <tr id="b1"> <td class="mainColor td1" valign="top">[1]</td> <td class="article-ref td2">George F. Gao. From “A”IV to “Z”IKV: attacks from emerging and Re-emerging pathogens. Cell 2018;172(6):1157 − 9. http://dx.doi.org/10.1016/j.cell.2018.02.025.</td> </tr> <tr id="b2"> <td class="mainColor td1" valign="top">[2]</td> <td class="article-ref td2">Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 2013;30(4):772 − 80. http://dx.doi.org/10.1093/molbev/mst010.</td> </tr> <tr id="b3"> <td class="mainColor td1" valign="top">[3]</td> <td class="article-ref td2">Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 2003;52(5):696 − 704. http://dx.doi.org/10.1080/10635150390235520.</td> </tr> </table> </div> </section>  <footer> <a href="/fileCCDCW/journal/article/ccdcw/2020/4/PDF/Wuhan.pdf"> <div class="pdfView"> <div class="in-bl"> <i class="fa fa-file-pdf-o"></i> <span>PDF  view</span> </div> </div> </a> <div class="WeChatView" style="display:block;"> <img style="display:block;" src="/fileCCDCW/journal/article/ccdcw/2020/4/PIC/wechat_en_a3907201-f64f-4154-a19e-4253b453d10c.jpg" alt="WeChat"> <span>follow<i></i>share</span> </div> <div class="metrics own-metrics" style="display:block;"> <div class="shareBox shareMargin clearfix" style="display:block;"> <ul class="shareTool text-center"> <li onclick="shareTools('twitter');" title="share this content in twitter"><img src="//weekly.chinacdc.cn/style/web/images/public/share_twitter.png"/></li>  <li onclick="shareTools('sina');" title="share this content in sina"><img src="//weekly.chinacdc.cn/style/web/images/public/share_sina.png"/></li>  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data-ppt="downloadPPT('73680759-5f97-493c-bf0c-cb7174d4c623','figure')"> <a href="/fileCCDCW/journal/article/ccdcw/2020/4/PIC/Wuhan-1.jpg"> <img src="/fileCCDCW/journal/article/ccdcw/2020/4/PIC/Wuhan-1.jpg" onerror="this.onerror=null;this.src='/fileCCDCW/journal/article/ccdcw/2020/4/PIC/Wuhan-1.jpg'"/> </a> </li> </ul> </div> <div id="imgNext"> <a href="javascript:void(0);"><span class="imgShowIcon imgShowIcon-next"></span> </a> </div> </div>  <div id="imgBack"> <a href="javascript:void(0);"> Return<span class="triangle"></span> </a> </div> </div>  <div class="show-table"> <div class="new-back"> <a href="javascript:;"> Return<span class="triangle"></span></a> </div> <div class="picbox"> <ul class="piclist"> </ul> <div id="big_play_prev" class="home-picprev thePrev"></div> <div id="big_play_next" class="home-picnext theNext"></div> </div> <div class="picsmallbox"> <a href="javascript:;" id="play_prev" class="play_prev"> <span class="imgShowIcon imgShowIcon-prev"></span> </a> <div class="picboxpic"> <ul id="picsmall" class="picsmall clear"> </ul> </div> <a href="javascript:;" id="play_next" class="play_next"> <span class="imgShowIcon imgShowIcon-next"></span> </a> </div> </div> <ul id="miniImgs_title" hidden> <li> Figure 1. Phylogenetic relationships between the genomes of the new types of <i>Betacoronavirus</i> and other <i>Orthocoronavirinae</i> genomes. The viruses in the subfamily <i>Orthocoronavirinae</i> were classified into four genera (prototype or Refseq strains shown): <i>Alphacoronavirus</i> (purple), <i>Betacoronavirus</i> (orange), <i>Gammacoronavirus</i> (green), and <i>Deltacoronavirus</i> (blue). Classic subgroup clusters for the <i>Betacoronavirus</i> were labelled 2a–2d. The tree was based on complete genomes shown above using the maximum likelihood method under the GTR + I + Γ model of nucleotide substitution as implemented in PhyML. The new types of <i>Betacoronavirus</i>, labelled with red stars, were placed into the lineage of <i>Betacoronavirus</i> 2b, which contain the following: avian infectious bronchitis virus (AIBV), Middle East respiratory syndrome coronavirus (MERS-CoV), mouse hepatitis virus (MHV), porcine enteric diarrhea virus (PEDV), severe acute respiratory syndrome coronavirus (SARS-CoV), SARS-related coronavirus (SARSr-CoV), and Human coronavirus (HCoV).</li> </ul> <script type="text/javascript"> $(document).ready(function () { //访问文章记录 var articleId = $("#articleId").val(); if(!isNull(articleId)){ var nowUrl = window.location.href; var number = nowUrl.indexOf("viewType=HTML"); getVisitInfo(articleId,3); } }); </script> </body> </html>

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A Novel Coronavirus Genome Identified in a Cluster of Pneumonia Cases — Wuhan, China 2019−2020