Complete Genome Sequence of a 2019 Novel Coronavirus (SARS-CoV-2) Strain Isolated in Nepal
Identifieur interne : 000913 ( Pmc/Corpus ); précédent : 000912; suivant : 000914Complete Genome Sequence of a 2019 Novel Coronavirus (SARS-CoV-2) Strain Isolated in Nepal
Auteurs : Ranjit Sah ; Alfonso J. Rodriguez-Morales ; Runa Jha ; Daniel K. W. Chu ; Haogao Gu ; Malik Peiris ; Anup Bastola ; Bibek Kumar Lal ; Hemant Chanda Ojha ; Ali A. Rabaan ; Lysien I. Zambrano ; Anthony Costello ; Kouichi Morita ; Basu Dev Pandey ; Leo L. M. PoonSource :
- Microbiology Resource Announcements [ 2576-098X ] ; 2020.
Abstract
A complete genome sequence was obtained for a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strain isolated from an oropharyngeal swab specimen of a Nepalese patient with coronavirus disease 2019 (COVID-19), who had returned to Nepal after traveling to Wuhan, China.
Url:
DOI: 10.1128/MRA.00169-20
PubMed: 32165386
PubMed Central: 7067954
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Complete Genome Sequence of a 2019 Novel Coronavirus (SARS-CoV-2) Strain Isolated in Nepal</title><author><name sortKey="Sah, Ranjit" sort="Sah, Ranjit" uniqKey="Sah R" first="Ranjit" last="Sah">Ranjit Sah</name><affiliation><nlm:aff id="aff1"><addr-line>National Public Health Laboratory, Kathmandu, Nepal</addr-line></nlm:aff></affiliation></author><author><name sortKey="Rodriguez Morales, Alfonso J" sort="Rodriguez Morales, Alfonso J" uniqKey="Rodriguez Morales A" first="Alfonso J." last="Rodriguez-Morales">Alfonso J. Rodriguez-Morales</name><affiliation><nlm:aff id="aff2"><addr-line>Public Health and Infection Research Group, Faculty of Health Sciences, Universidad Tecnologica de Pereira, Pereira, Risaralda, Colombia</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff3"><addr-line>Grupo de Investigación Biomedicina, Faculty of Medicine, Fundación Universitaria Autónoma de las Américas, Pereira, Risaralda, Colombia</addr-line></nlm:aff></affiliation></author><author><name sortKey="Jha, Runa" sort="Jha, Runa" uniqKey="Jha R" first="Runa" last="Jha">Runa Jha</name><affiliation><nlm:aff id="aff1"><addr-line>National Public Health Laboratory, Kathmandu, Nepal</addr-line></nlm:aff></affiliation></author><author><name sortKey="Chu, Daniel K W" sort="Chu, Daniel K W" uniqKey="Chu D" first="Daniel K. W." last="Chu">Daniel K. W. Chu</name><affiliation><nlm:aff id="aff4"><addr-line>School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China</addr-line></nlm:aff></affiliation></author><author><name sortKey="Gu, Haogao" sort="Gu, Haogao" uniqKey="Gu H" first="Haogao" last="Gu">Haogao Gu</name><affiliation><nlm:aff id="aff4"><addr-line>School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China</addr-line></nlm:aff></affiliation></author><author><name sortKey="Peiris, Malik" sort="Peiris, Malik" uniqKey="Peiris M" first="Malik" last="Peiris">Malik Peiris</name><affiliation><nlm:aff id="aff4"><addr-line>School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China</addr-line></nlm:aff></affiliation></author><author><name sortKey="Bastola, Anup" sort="Bastola, Anup" uniqKey="Bastola A" first="Anup" last="Bastola">Anup Bastola</name><affiliation><nlm:aff id="aff5"><addr-line>Sukraraj Tropical and Infectious Disease Hospital, Kathmandu, Nepal</addr-line></nlm:aff></affiliation></author><author><name sortKey="Lal, Bibek Kumar" sort="Lal, Bibek Kumar" uniqKey="Lal B" first="Bibek Kumar" last="Lal">Bibek Kumar Lal</name><affiliation><nlm:aff id="aff6"><addr-line>Epidemiology and Disease Control Division, Government of Nepal, Kathmandu, Nepal</addr-line></nlm:aff></affiliation></author><author><name sortKey="Ojha, Hemant Chanda" sort="Ojha, Hemant Chanda" uniqKey="Ojha H" first="Hemant Chanda" last="Ojha">Hemant Chanda Ojha</name><affiliation><nlm:aff id="aff6"><addr-line>Epidemiology and Disease Control Division, Government of Nepal, Kathmandu, Nepal</addr-line></nlm:aff></affiliation></author><author><name sortKey="Rabaan, Ali A" sort="Rabaan, Ali A" uniqKey="Rabaan A" first="Ali A." last="Rabaan">Ali A. Rabaan</name><affiliation><nlm:aff id="aff7"><addr-line>Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia</addr-line></nlm:aff></affiliation></author><author><name sortKey="Zambrano, Lysien I" sort="Zambrano, Lysien I" uniqKey="Zambrano L" first="Lysien I." last="Zambrano">Lysien I. Zambrano</name><affiliation><nlm:aff id="aff8"><addr-line>Departments of Physiological and Morphological Sciences, School of Medical Sciences, Universidad Nacional Autónoma de Honduras (UNAH), Tegucigalpa, Honduras</addr-line></nlm:aff></affiliation></author><author><name sortKey="Costello, Anthony" sort="Costello, Anthony" uniqKey="Costello A" first="Anthony" last="Costello">Anthony Costello</name><affiliation><nlm:aff id="aff9"><addr-line>Global Health and Sustainable Development, University College London, London, United Kingdom</addr-line></nlm:aff></affiliation></author><author><name sortKey="Morita, Kouichi" sort="Morita, Kouichi" uniqKey="Morita K" first="Kouichi" last="Morita">Kouichi Morita</name><affiliation><nlm:aff id="aff10"><addr-line>Department of Virology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan</addr-line></nlm:aff></affiliation></author><author><name sortKey="Pandey, Basu Dev" sort="Pandey, Basu Dev" uniqKey="Pandey B" first="Basu Dev" last="Pandey">Basu Dev Pandey</name><affiliation><nlm:aff id="aff5"><addr-line>Sukraraj Tropical and Infectious Disease Hospital, Kathmandu, Nepal</addr-line></nlm:aff></affiliation></author><author><name sortKey="Poon, Leo L M" sort="Poon, Leo L M" uniqKey="Poon L" first="Leo L. M." last="Poon">Leo L. M. Poon</name><affiliation><nlm:aff id="aff4"><addr-line>School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China</addr-line></nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">32165386</idno><idno type="pmc">7067954</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7067954</idno><idno type="RBID">PMC:7067954</idno><idno type="doi">10.1128/MRA.00169-20</idno><date when="2020">2020</date><idno type="wicri:Area/Pmc/Corpus">000913</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000913</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Complete Genome Sequence of a 2019 Novel Coronavirus (SARS-CoV-2) Strain Isolated in Nepal</title><author><name sortKey="Sah, Ranjit" sort="Sah, Ranjit" uniqKey="Sah R" first="Ranjit" last="Sah">Ranjit Sah</name><affiliation><nlm:aff id="aff1"><addr-line>National Public Health Laboratory, Kathmandu, Nepal</addr-line></nlm:aff></affiliation></author><author><name sortKey="Rodriguez Morales, Alfonso J" sort="Rodriguez Morales, Alfonso J" uniqKey="Rodriguez Morales A" first="Alfonso J." last="Rodriguez-Morales">Alfonso J. Rodriguez-Morales</name><affiliation><nlm:aff id="aff2"><addr-line>Public Health and Infection Research Group, Faculty of Health Sciences, Universidad Tecnologica de Pereira, Pereira, Risaralda, Colombia</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff3"><addr-line>Grupo de Investigación Biomedicina, Faculty of Medicine, Fundación Universitaria Autónoma de las Américas, Pereira, Risaralda, Colombia</addr-line></nlm:aff></affiliation></author><author><name sortKey="Jha, Runa" sort="Jha, Runa" uniqKey="Jha R" first="Runa" last="Jha">Runa Jha</name><affiliation><nlm:aff id="aff1"><addr-line>National Public Health Laboratory, Kathmandu, Nepal</addr-line></nlm:aff></affiliation></author><author><name sortKey="Chu, Daniel K W" sort="Chu, Daniel K W" uniqKey="Chu D" first="Daniel K. W." last="Chu">Daniel K. W. Chu</name><affiliation><nlm:aff id="aff4"><addr-line>School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China</addr-line></nlm:aff></affiliation></author><author><name sortKey="Gu, Haogao" sort="Gu, Haogao" uniqKey="Gu H" first="Haogao" last="Gu">Haogao Gu</name><affiliation><nlm:aff id="aff4"><addr-line>School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China</addr-line></nlm:aff></affiliation></author><author><name sortKey="Peiris, Malik" sort="Peiris, Malik" uniqKey="Peiris M" first="Malik" last="Peiris">Malik Peiris</name><affiliation><nlm:aff id="aff4"><addr-line>School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China</addr-line></nlm:aff></affiliation></author><author><name sortKey="Bastola, Anup" sort="Bastola, Anup" uniqKey="Bastola A" first="Anup" last="Bastola">Anup Bastola</name><affiliation><nlm:aff id="aff5"><addr-line>Sukraraj Tropical and Infectious Disease Hospital, Kathmandu, Nepal</addr-line></nlm:aff></affiliation></author><author><name sortKey="Lal, Bibek Kumar" sort="Lal, Bibek Kumar" uniqKey="Lal B" first="Bibek Kumar" last="Lal">Bibek Kumar Lal</name><affiliation><nlm:aff id="aff6"><addr-line>Epidemiology and Disease Control Division, Government of Nepal, Kathmandu, Nepal</addr-line></nlm:aff></affiliation></author><author><name sortKey="Ojha, Hemant Chanda" sort="Ojha, Hemant Chanda" uniqKey="Ojha H" first="Hemant Chanda" last="Ojha">Hemant Chanda Ojha</name><affiliation><nlm:aff id="aff6"><addr-line>Epidemiology and Disease Control Division, Government of Nepal, Kathmandu, Nepal</addr-line></nlm:aff></affiliation></author><author><name sortKey="Rabaan, Ali A" sort="Rabaan, Ali A" uniqKey="Rabaan A" first="Ali A." last="Rabaan">Ali A. Rabaan</name><affiliation><nlm:aff id="aff7"><addr-line>Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia</addr-line></nlm:aff></affiliation></author><author><name sortKey="Zambrano, Lysien I" sort="Zambrano, Lysien I" uniqKey="Zambrano L" first="Lysien I." last="Zambrano">Lysien I. Zambrano</name><affiliation><nlm:aff id="aff8"><addr-line>Departments of Physiological and Morphological Sciences, School of Medical Sciences, Universidad Nacional Autónoma de Honduras (UNAH), Tegucigalpa, Honduras</addr-line></nlm:aff></affiliation></author><author><name sortKey="Costello, Anthony" sort="Costello, Anthony" uniqKey="Costello A" first="Anthony" last="Costello">Anthony Costello</name><affiliation><nlm:aff id="aff9"><addr-line>Global Health and Sustainable Development, University College London, London, United Kingdom</addr-line></nlm:aff></affiliation></author><author><name sortKey="Morita, Kouichi" sort="Morita, Kouichi" uniqKey="Morita K" first="Kouichi" last="Morita">Kouichi Morita</name><affiliation><nlm:aff id="aff10"><addr-line>Department of Virology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan</addr-line></nlm:aff></affiliation></author><author><name sortKey="Pandey, Basu Dev" sort="Pandey, Basu Dev" uniqKey="Pandey B" first="Basu Dev" last="Pandey">Basu Dev Pandey</name><affiliation><nlm:aff id="aff5"><addr-line>Sukraraj Tropical and Infectious Disease Hospital, Kathmandu, Nepal</addr-line></nlm:aff></affiliation></author><author><name sortKey="Poon, Leo L M" sort="Poon, Leo L M" uniqKey="Poon L" first="Leo L. M." last="Poon">Leo L. M. Poon</name><affiliation><nlm:aff id="aff4"><addr-line>School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China</addr-line></nlm:aff></affiliation></author></analytic><series><title level="j">Microbiology Resource Announcements</title><idno type="eISSN">2576-098X</idno><imprint><date when="2020">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>A complete genome sequence was obtained for a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strain isolated from an oropharyngeal swab specimen of a Nepalese patient with coronavirus disease 2019 (COVID-19), who had returned to Nepal after traveling to Wuhan, China.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Huang, C" uniqKey="Huang C">C Huang</name></author><author><name sortKey="Wang, Y" uniqKey="Wang Y">Y Wang</name></author><author><name sortKey="Li, X" uniqKey="Li X">X Li</name></author><author><name sortKey="Ren, L" uniqKey="Ren L">L Ren</name></author><author><name sortKey="Zhao, J" uniqKey="Zhao J">J Zhao</name></author><author><name sortKey="Hu, Y" uniqKey="Hu Y">Y Hu</name></author><author><name sortKey="Zhang, L" uniqKey="Zhang L">L Zhang</name></author><author><name sortKey="Fan, G" uniqKey="Fan G">G Fan</name></author><author><name sortKey="Xu, J" uniqKey="Xu J">J Xu</name></author><author><name sortKey="Gu, X" uniqKey="Gu X">X Gu</name></author><author><name sortKey="Cheng, Z" uniqKey="Cheng Z">Z Cheng</name></author><author><name sortKey="Yu, T" uniqKey="Yu T">T Yu</name></author><author><name sortKey="Xia, J" uniqKey="Xia J">J Xia</name></author><author><name sortKey="Wei, Y" uniqKey="Wei Y">Y Wei</name></author><author><name sortKey="Wu, W" uniqKey="Wu W">W Wu</name></author><author><name sortKey="Xie, X" uniqKey="Xie X">X Xie</name></author><author><name sortKey="Yin, W" uniqKey="Yin W">W Yin</name></author><author><name sortKey="Li, H" uniqKey="Li H">H Li</name></author><author><name sortKey="Liu, M" uniqKey="Liu M">M Liu</name></author><author><name sortKey="Xiao, Y" uniqKey="Xiao Y">Y Xiao</name></author><author><name sortKey="Gao, H" uniqKey="Gao H">H Gao</name></author><author><name sortKey="Guo, L" uniqKey="Guo L">L Guo</name></author><author><name sortKey="Xie, J" uniqKey="Xie J">J Xie</name></author><author><name sortKey="Wang, G" uniqKey="Wang G">G Wang</name></author><author><name sortKey="Jiang, R" uniqKey="Jiang R">R Jiang</name></author><author><name sortKey="Gao, Z" uniqKey="Gao Z">Z Gao</name></author><author><name sortKey="Jin, Q" uniqKey="Jin Q">Q Jin</name></author><author><name sortKey="Wang, J" uniqKey="Wang J">J Wang</name></author><author><name sortKey="Cao, B" uniqKey="Cao B">B Cao</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Rodriguez Morales, Aj" uniqKey="Rodriguez Morales A">AJ Rodriguez-Morales</name></author><author><name sortKey="Macgregor, K" uniqKey="Macgregor K">K MacGregor</name></author><author><name sortKey="Kanagarajah, S" uniqKey="Kanagarajah S">S Kanagarajah</name></author><author><name sortKey="Patel, D" uniqKey="Patel D">D Patel</name></author><author><name sortKey="Schlagenhauf, P" uniqKey="Schlagenhauf P">P Schlagenhauf</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Rodriguez Morales, Aj" uniqKey="Rodriguez Morales A">AJ Rodriguez-Morales</name></author><author><name sortKey="Bonilla Aldana, Dk" uniqKey="Bonilla Aldana D">DK Bonilla-Aldana</name></author><author><name sortKey="Balbin Ramon, Gj" uniqKey="Balbin Ramon G">GJ Balbin-Ramon</name></author><author><name sortKey="Paniz Mondolfi, A" uniqKey="Paniz Mondolfi A">A Paniz-Mondolfi</name></author><author><name sortKey="Rabaan, A" uniqKey="Rabaan A">A Rabaan</name></author><author><name sortKey="Sah, R" uniqKey="Sah R">R Sah</name></author><author><name sortKey="Pagliano, P" uniqKey="Pagliano P">P Pagliano</name></author><author><name sortKey="Esposito, S" uniqKey="Esposito S">S Esposito</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bastola, A" uniqKey="Bastola A">A Bastola</name></author><author><name sortKey="Sah, R" uniqKey="Sah R">R Sah</name></author><author><name sortKey="Rodriguez Morales, Aj" uniqKey="Rodriguez Morales A">AJ Rodriguez-Morales</name></author><author><name sortKey="Lal, Bk" uniqKey="Lal B">BK Lal</name></author><author><name sortKey="Jha, R" uniqKey="Jha R">R Jha</name></author><author><name sortKey="Ojha, Hc" uniqKey="Ojha H">HC Ojha</name></author><author><name sortKey="Shrestha, B" uniqKey="Shrestha B">B Shrestha</name></author><author><name sortKey="Chu, Dkw" uniqKey="Chu D">DKW Chu</name></author><author><name sortKey="Poon, Llm" uniqKey="Poon L">LLM Poon</name></author><author><name sortKey="Costello, A" uniqKey="Costello A">A Costello</name></author><author><name sortKey="Morita, K" uniqKey="Morita K">K Morita</name></author><author><name sortKey="Pandey, Bd" uniqKey="Pandey B">BD Pandey</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chu, Dkw" uniqKey="Chu D">DKW Chu</name></author><author><name sortKey="Pan, Y" uniqKey="Pan Y">Y Pan</name></author><author><name sortKey="Cheng, Sms" uniqKey="Cheng S">SMS Cheng</name></author><author><name sortKey="Hui, Kpy" uniqKey="Hui K">KPY Hui</name></author><author><name sortKey="Krishnan, P" uniqKey="Krishnan P">P Krishnan</name></author><author><name sortKey="Liu, Y" uniqKey="Liu Y">Y Liu</name></author><author><name sortKey="Ng, Dym" uniqKey="Ng D">DYM Ng</name></author><author><name sortKey="Wan, Ckc" uniqKey="Wan C">CKC Wan</name></author><author><name sortKey="Yang, P" uniqKey="Yang P">P Yang</name></author><author><name sortKey="Wang, Q" uniqKey="Wang Q">Q Wang</name></author><author><name 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Microbiol Resour Announc</journal-id><journal-id journal-id-type="iso-abbrev">Microbiol Resour Announc</journal-id><journal-id journal-id-type="hwp">ga</journal-id><journal-id journal-id-type="pmc">mra</journal-id><journal-id journal-id-type="publisher-id">MRA</journal-id><journal-title-group><journal-title>Microbiology Resource Announcements</journal-title></journal-title-group><issn pub-type="epub">2576-098X</issn><publisher><publisher-name>American Society for Microbiology</publisher-name><publisher-loc>1752 N St., N.W., Washington, DC</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">32165386</article-id><article-id pub-id-type="pmc">7067954</article-id><article-id pub-id-type="publisher-id">MRA00169-20</article-id><article-id pub-id-type="doi">10.1128/MRA.00169-20</article-id><article-categories><subj-group subj-group-type="heading"><subject>Genome Sequences</subject></subj-group></article-categories><title-group><article-title>Complete Genome Sequence of a 2019 Novel Coronavirus (SARS-CoV-2) Strain Isolated in Nepal</article-title><alt-title alt-title-type="running-head">Microbiology Resource Announcement</alt-title><alt-title alt-title-type="short-authors">Sah et al.</alt-title></title-group><contrib-group><contrib contrib-type="author" corresp="yes" equal-contrib="yes"><contrib-id contrib-id-type="orcid" authenticated="false">https://orcid.org/0000-0002-2695-8714</contrib-id><name><surname>Sah</surname><given-names>Ranjit</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref></contrib><contrib contrib-type="author" equal-contrib="yes"><contrib-id contrib-id-type="orcid" authenticated="false">http://orcid.org/0000-0001-9773-2192</contrib-id><name><surname>Rodriguez-Morales</surname><given-names>Alfonso J.</given-names></name><xref ref-type="aff" rid="aff2"><sup>b</sup></xref><xref ref-type="aff" rid="aff3"><sup>c</sup></xref></contrib><contrib contrib-type="author" equal-contrib="no"><name><surname>Jha</surname><given-names>Runa</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref></contrib><contrib contrib-type="author" equal-contrib="no"><name><surname>Chu</surname><given-names>Daniel K. W.</given-names></name><xref ref-type="aff" rid="aff4"><sup>d</sup></xref></contrib><contrib contrib-type="author" equal-contrib="no"><name><surname>Gu</surname><given-names>Haogao</given-names></name><xref ref-type="aff" rid="aff4"><sup>d</sup></xref></contrib><contrib contrib-type="author" equal-contrib="no"><name><surname>Peiris</surname><given-names>Malik</given-names></name><xref ref-type="aff" rid="aff4"><sup>d</sup></xref></contrib><contrib contrib-type="author" equal-contrib="no"><name><surname>Bastola</surname><given-names>Anup</given-names></name><xref ref-type="aff" rid="aff5"><sup>e</sup></xref></contrib><contrib contrib-type="author" equal-contrib="no"><name><surname>Lal</surname><given-names>Bibek Kumar</given-names></name><xref ref-type="aff" rid="aff6"><sup>f</sup></xref></contrib><contrib contrib-type="author" equal-contrib="no"><name><surname>Ojha</surname><given-names>Hemant Chanda</given-names></name><xref ref-type="aff" rid="aff6"><sup>f</sup></xref></contrib><contrib contrib-type="author" equal-contrib="no"><contrib-id contrib-id-type="orcid" authenticated="false">https://orcid.org/0000-0002-6774-9847</contrib-id><name><surname>Rabaan</surname><given-names>Ali A.</given-names></name><xref ref-type="aff" rid="aff7"><sup>g</sup></xref></contrib><contrib contrib-type="author" equal-contrib="no"><contrib-id contrib-id-type="orcid" authenticated="false">http://orcid.org/0000-0001-9002-5807</contrib-id><name><surname>Zambrano</surname><given-names>Lysien I.</given-names></name><xref ref-type="aff" rid="aff8"><sup>h</sup></xref></contrib><contrib contrib-type="author" equal-contrib="no"><name><surname>Costello</surname><given-names>Anthony</given-names></name><xref ref-type="aff" rid="aff9"><sup>i</sup></xref></contrib><contrib contrib-type="author" equal-contrib="no"><name><surname>Morita</surname><given-names>Kouichi</given-names></name><xref ref-type="aff" rid="aff10"><sup>j</sup></xref></contrib><contrib contrib-type="author" equal-contrib="no"><name><surname>Pandey</surname><given-names>Basu Dev</given-names></name><xref ref-type="aff" rid="aff5"><sup>e</sup></xref></contrib><contrib contrib-type="author" equal-contrib="no"><name><surname>Poon</surname><given-names>Leo L. M.</given-names></name><xref ref-type="aff" rid="aff4"><sup>d</sup></xref></contrib><aff id="aff1"><label>a</label><addr-line>National Public Health Laboratory, Kathmandu, Nepal</addr-line></aff><aff id="aff2"><label>b</label><addr-line>Public Health and Infection Research Group, Faculty of Health Sciences, Universidad Tecnologica de Pereira, Pereira, Risaralda, Colombia</addr-line></aff><aff id="aff3"><label>c</label><addr-line>Grupo de Investigación Biomedicina, Faculty of Medicine, Fundación Universitaria Autónoma de las Américas, Pereira, Risaralda, Colombia</addr-line></aff><aff id="aff4"><label>d</label><addr-line>School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China</addr-line></aff><aff id="aff5"><label>e</label><addr-line>Sukraraj Tropical and Infectious Disease Hospital, Kathmandu, Nepal</addr-line></aff><aff id="aff6"><label>f</label><addr-line>Epidemiology and Disease Control Division, Government of Nepal, Kathmandu, Nepal</addr-line></aff><aff id="aff7"><label>g</label><addr-line>Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia</addr-line></aff><aff id="aff8"><label>h</label><addr-line>Departments of Physiological and Morphological Sciences, School of Medical Sciences, Universidad Nacional Autónoma de Honduras (UNAH), Tegucigalpa, Honduras</addr-line></aff><aff id="aff9"><label>i</label><addr-line>Global Health and Sustainable Development, University College London, London, United Kingdom</addr-line></aff><aff id="aff10"><label>j</label><addr-line>Department of Virology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan</addr-line></aff></contrib-group><contrib-group><contrib contrib-type="editor"><name><surname>Roux</surname><given-names>Simon</given-names></name><role>Editor</role><aff>DOE Joint Genome Institute</aff></contrib></contrib-group><author-notes><corresp id="cor1">Address correspondence to Ranjit Sah, <email>ranjitsah@iom.edu.np</email>.</corresp><fn fn-type="equal"><p>Ranjit Sah and Alfonso J. Rodriguez-Morales contributed equally. Author order was determined by order of increasing seniority.</p></fn><fn fn-type="other"><p><bold>Citation</bold> Sah R, Rodriguez-Morales AJ, Jha R, Chu DKW, Gu H, Peiris M, Bastola A, Lal BK, Ojha HC, Rabaan AA, Zambrano LI, Costello A, Morita K, Pandey BD, Poon LLM. 2020. Complete genome sequence of a 2019 novel coronavirus (SARS-CoV-2) strain isolated in Nepal. Microbiol Resour Announc 9:e00169-20. <ext-link ext-link-type="uri" xlink:href="https://doi.org/10.1128/MRA.00169-20">https://doi.org/10.1128/MRA.00169-20</ext-link>.</p></fn></author-notes><pub-date pub-type="epub"><day>12</day><month>3</month><year>2020</year></pub-date><pub-date pub-type="collection"><month>3</month><year>2020</year></pub-date><volume>9</volume><issue>11</issue><elocation-id>e00169-20</elocation-id><history><date date-type="received"><day>19</day><month>2</month><year>2020</year></date><date date-type="accepted"><day>26</day><month>2</month><year>2020</year></date></history><permissions><copyright-statement>Copyright © 2020 Sah et al.</copyright-statement><copyright-year>2020</copyright-year><copyright-holder>Sah et al.</copyright-holder><license license-type="open-access" xlink:href="https://creativecommons.org/licenses/by/4.0/"><license-p>This is an open-access article distributed under the terms of the <ext-link ext-link-type="uri" xlink:href="https://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International license</ext-link>.</license-p></license></permissions><self-uri content-type="pdf" xlink:href="MRA.00169-20.pdf"></self-uri><abstract abstract-type="precis"><p>A complete genome sequence was obtained for a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strain isolated from an oropharyngeal swab specimen of a Nepalese patient with coronavirus disease 2019 (COVID-19), who had returned to Nepal after traveling to Wuhan, China.</p></abstract><abstract><title>ABSTRACT</title><p>A complete genome sequence was obtained for a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strain isolated from an oropharyngeal swab specimen of a Nepalese patient with coronavirus disease 2019 (COVID-19), who had returned to Nepal after traveling to Wuhan, China.</p></abstract><funding-group><award-group id="award1"><funding-source><institution-wrap><institution>Ministry of Science and Technology, Government of Nepal</institution><institution-id>https://doi.org/10.13039/100012813</institution-id></institution-wrap></funding-source><principal-award-recipient><name><surname>Sah</surname><given-names>Ranjit</given-names></name></principal-award-recipient></award-group></funding-group><counts><fig-count count="0"></fig-count><table-count count="1"></table-count><equation-count count="0"></equation-count><ref-count count="7"></ref-count><page-count count="3"></page-count><word-count count="1781"></word-count></counts><custom-meta-group><custom-meta><meta-name>cover-date</meta-name><meta-value>March 2020</meta-value></custom-meta></custom-meta-group></article-meta></front><body><sec id="s1"><title>ANNOUNCEMENT</title><p>Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), family <italic>Coronaviridae</italic>, genus <italic>Betacoronavirus</italic>, is spreading widely in China, causing coronavirus disease 2019 (COVID-19) (<xref rid="B1" ref-type="bibr">1</xref>), and is also affecting other Asian and non-Asian countries (<xref rid="B2" ref-type="bibr">2</xref>, <xref rid="B3" ref-type="bibr">3</xref>). Imported cases have been reported in countries such as Japan, Singapore, Hong Kong, Thailand, and Nepal, among others (<xref rid="B4" ref-type="bibr">4</xref>). We report here the complete genome sequence of SARS-CoV-2 from a Nepalese patient; the infection was acquired in Wuhan, China, and imported to Nepal.</p><p>The isolate (BetaCoV/Nepal/61/2020) is from the oropharyngeal swab specimen of a 32-year-old man, a Nepalese student at Wuhan University of Technology in Wuhan, China, with no history of comorbidities, who returned to Nepal presenting with cough, mild fever, and throat congestion, suggesting COVID-19 (<xref rid="B4" ref-type="bibr">4</xref>). An oropharyngeal swab specimen was collected at the National Influenza Centre, National Public Health Laboratory in Kathmandu, Nepal, and submitted to the WHO laboratory at the University of Hong Kong, Hong Kong Special Administrative Region, China, where it was confirmed and sequenced.</p><p>The specimen tested positive for SARS-CoV-2 by real-time reverse transcriptase PCR (rRT-PCR) developed in the University of Hong Kong (<xref rid="B5" ref-type="bibr">5</xref>). Sequencing was done using the Illumina MiSeq system with the Burrows-Wheeler Aligner MEM algorithm (BWA-MEM) 0.7.5a-r405 assembly method. The full genome was amplified directly from the RNA extract from the original specimen using gene-specific primers for open reading frame 1b (ORF1b) and N (<xref rid="tab1" ref-type="table">Table 1</xref>) to produce overlapping PCR products covering the full genome (<xref rid="B5" ref-type="bibr">5</xref>). The expected amplicon sizes of the ORF1b and N gene assays are 132 bp and 110 bp, respectively (<xref rid="B5" ref-type="bibr">5</xref>). The raw reads were first cleaned by trimming low-quality bases with Trimmomatic 0.36 (-phred33, LEADING:20, TRAILING:20, SLIDINGWINDOW:4:20, MINLEN:40). The new genome sequence was obtained by first mapping reads to a reference SARS-CoV-2 genome using BWA-MEM 0.7.5a-r405 with default parameters to generate the consensus sequence. In addition, the assembly produced by MEGAHIT 1.2.9 (<italic>de novo</italic> assembly), using default parameters, was used to cross-validate with the reference-based method as an internal control. The two results were consistent, and our final sequence is based on the reference-based method. The reference sequence we used was from the Global Initiative on Sharing All Influenza Database (GISAID; strain identifier EPI_ISL_405839). The reads mapped to the reference sequence were then curated in a pileup alignment file to obtain the consensus sequence (minimum coverage threshold, 10). FastQC 0.11.8 was used to assess the sequence quality before trimming and after alignment to prevent potential errors. There were 5,246,584 paired-end sequences in the raw data. A total of 9,891,431 records were included in the reference-based alignment after trimming, and 9,887,093 (99.96%) of them were mapped to the SARS-CoV-2 reference genome.</p><table-wrap id="tab1" orientation="portrait" position="float"><label>TABLE 1</label><caption><p>Gene-specific primer and probe sequences used</p></caption><alternatives><table frame="hsides" rules="groups"><colgroup span="1"><col span="1"></col><col span="1"></col></colgroup><thead><tr><th rowspan="1" colspan="1">Gene</th><th rowspan="1" colspan="1">Primer<xref ref-type="table-fn" rid="ngtab1.1"><sup><italic>a</italic></sup></xref></th></tr></thead><tbody><tr><td rowspan="1" colspan="1">ORF1b</td><td rowspan="1" colspan="1"></td></tr><tr><td rowspan="1" colspan="1"> Forward</td><td rowspan="1" colspan="1">5′-TGGGGYTTTACRGGTAACCT-3′</td></tr><tr><td rowspan="1" colspan="1"> Reverse</td><td rowspan="1" colspan="1">5′-AACRCGCTTAACAAAGCACTC-3′</td></tr><tr><td rowspan="1" colspan="1"> Probe</td><td rowspan="1" colspan="1">5′-TAGTTGTGATGCWATCATGACTAG-3′<xref ref-type="table-fn" rid="ngtab1.2"><sup><italic>b</italic></sup></xref></td></tr><tr><td rowspan="1" colspan="1">N</td><td rowspan="1" colspan="1"></td></tr><tr><td rowspan="1" colspan="1"> Forward</td><td rowspan="1" colspan="1">5′-TAATCAGACAAGGAACTGATTA-3′</td></tr><tr><td rowspan="1" colspan="1"> Reverse</td><td rowspan="1" colspan="1">5′-CGAAGGTGTGACTTCCATG-3′</td></tr><tr><td rowspan="1" colspan="1"> Probe</td><td rowspan="1" colspan="1">5′-GCAAATTGTGCAATTTGCGG-3′<xref ref-type="table-fn" rid="ngtab1.2"><sup><italic>b</italic></sup></xref></td></tr></tbody></table><graphic xlink:href="MRA.00169-20-t0001"></graphic></alternatives><table-wrap-foot><fn fn-type="other" id="ngtab1.1"><label>a</label><p>Y is C or T; R is A or G; W is A or T.</p></fn><fn fn-type="other" id="ngtab1.2"><label>b</label><p>In 5′-6-carboxyfluorescein/ZEN internal quencher/3′-Iowa Black fluorescent quencher format.</p></fn></table-wrap-foot></table-wrap><p>We generated a consensus sequence of 29,811 bp with no gap and high average coverage (>77,000×). Primer binding sites at the 5′ and 3′ ends were removed, resulting in this genome being 59 nucleotides (nt) shorter than a reference genome in GenBank (accession number <ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/nuccore/NC_045512" assigning-authority="genbank">NC_045512</ext-link>), excluding the poly(A) tail of the genome.</p><p>For phylogenetic analyses, SARS-CoV-2 full-genome sequences were aligned with CLUSTAL W (<xref rid="B6" ref-type="bibr">6</xref>) using MEGA 10.0.5. (<xref rid="B7" ref-type="bibr">7</xref>). The new SARS-CoV-2 sequence was compared to existing genomes using online NCBI BLAST (<ext-link ext-link-type="uri" xlink:href="https://blast.ncbi.nlm.nih.gov/Blast.cgi">https://blast.ncbi.nlm.nih.gov/Blast.cgi</ext-link>).</p><p>Full-genome comparison of the isolate revealed >99.99% identity with two previously sequenced genomes available at GenBank (<ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/nuccore/MN988668" assigning-authority="genbank">MN988668</ext-link> and <ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/nuccore/NC_045512" assigning-authority="genbank">NC_045512</ext-link>) for SARS-CoV-2 from Wuhan, China, and >99.9% with seven additional sequences (<ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/nuccore/MN938384.1" assigning-authority="genbank">MN938384.1</ext-link>, <ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/nuccore/MN975262.1" assigning-authority="genbank">MN975262.1</ext-link>, <ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/nuccore/MN985325.1" assigning-authority="genbank">MN985325.1</ext-link>, <ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/nuccore/MN988713.1" assigning-authority="genbank">MN988713.1</ext-link>, <ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/nuccore/MN994467.1" assigning-authority="genbank">MN994467.1</ext-link>, <ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/nuccore/MN994468.1" assigning-authority="genbank">MN994468.1</ext-link>, and <ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/nuccore/MN997409.1" assigning-authority="genbank">MN997409.1</ext-link>). The final genome of sequenced SARS-CoV-2 consists of a single, positive-stranded RNA that is 29,811 nucleotides long, broken down as follows: 8,903 (29.86%) adenosines, 5,482 (18.39%) cytosines, 5,852 (19.63%) guanines, and 9,574 (32.12%) thymines.</p><p>The sequence of BetaCoV/Nepal/61/2020 from coordinates 1 to 29811 is identical to the sequence of isolate 2019-nCoV WHU01 (GenBank accession number <ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/nuccore/MN988668" assigning-authority="genbank">MN988668</ext-link>) from 15 to 29825 (29810/29811), except at site 24019, with a substitution of a C, from 2019-nCoV WHU01, for T. The sequence of BetaCoV/Nepal/61/2020 from coordinates 1 to 29811 is identical to the sequence of isolate Wuhan-Hu-1 (GenBank accession number <ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/nuccore/NC_045512" assigning-authority="genbank">NC_045512</ext-link>) from 16 to 29826 (29810/29811), except at site 24019, with the same substitution of a C from isolate Wuhan-Hu-1 for T.</p><p>The C24019T mutation corresponds to C24034T if we use the sequence located under GISAID strain identifier EPI_ISL_405839 as a reference. This was a silent mutation at the spike gene (codon AAC to AAT). Based on the reference sequence, the following five mutations were also identified: T8782C (in ORF1a, codons AGT to AGC, silent mutation), T9561C (in ORF1a, codons TTA to TCA, nonsilent mutation), C15607T (in ORF1b, codons CTA to TTA, silent mutation), C28144T (in ORF8b, codons TCA to TTA, nonsilent mutation), and T29095C (in nucleocapsid, codons TTT to TTC, silent mutation).</p><p>Additional epidemiological and clinical features of this case of COVID-19 were reported in reference <xref rid="B4" ref-type="bibr">4</xref>.</p><sec id="s1.1"><title>Data availability.</title><p>This sequence has been deposited in GenBank under the accession number <ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/nuccore/MT072688" assigning-authority="genbank">MT072688</ext-link> and at the GISAID EpiCoV newly emerging coronavirus SARS-CoV-2 platform under identifier EPI_ISL_410301. The accession numbers for the Illumina MiSeq sequence raw reads in the NCBI Sequence Read Archive (SRA) are <ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA608651" assigning-authority="bioproject">PRJNA608651</ext-link> (BioProject), <ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/sra/SRP250653" assigning-authority="ncbi:sra">SRP250653</ext-link> (SRA), <ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/biosample/SAMN14180202" assigning-authority="biosample">SAMN14180202</ext-link> (BioSample, BetaCoV/Nepal/61/2020), <ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/sra/SRX7798477" assigning-authority="ncbi:sra">SRX7798477</ext-link> (SRA; GISAID EPI_ISL_410301), and <ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/sra/SRR11177792" assigning-authority="ncbi:sra">SRR11177792</ext-link> (run, WHV-Nepal-61-TW_1.fastq.gz).</p></sec></sec></body><back><ack><title>ACKNOWLEDGMENTS</title><p>The Facultad de Ciencias Médicas (FCM) (2-03-01-01), National Autonomous University of Honduras, Tegucigalpa, MDC, Honduras, supported the publication fees of this article. 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