[Genomic analysis of a 2019-nCoV strain in the first COVID-19 patient found in Hangzhou, Zhejiang, China].
Identifieur interne : 000508 ( PubMed/Corpus ); précédent : 000507; suivant : 000509[Genomic analysis of a 2019-nCoV strain in the first COVID-19 patient found in Hangzhou, Zhejiang, China].
Auteurs : H. Yu ; X C Wang ; J. Li ; X. Qian ; X F Yu ; Z. Sun ; J F Chen ; Q J Kao ; H Q Wang ; J C PanSource :
- Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine] [ 0253-9624 ] ; 2020.
Abstract
Objective: To understand the viral genomic characteristics of a 2019-nCoV strain in the first COVID-19 patient found in Hangzhou, China. Methods: Viral RNA was extracted in throat swab and sputum sample of the patient and was performed real-time reverse transcription PCR detection and obtained viral genome by high-throughput sequencing method. Phylogenetic analysis was conducted using 29 2019-nCoV genomes and 30 β-coronavirus genomes deposited in NCBI GenBank. Fifteen genomes from Wuhan were grouped by mutation sites and others were identified by Wuhan's or specific mutation sites. Results: A 29 833 bp length genome of the first 2019-nCoV strain in Hangzhou was obtained, covering full length of the coding regions of coronavirus. Phylogenetic analysis showed that the genome was closest to the genome of a bat SARS-like coronavirus strain RaTG13 with an identity of 96.11% (28 666/29 826). Among the genes between two genomes, E genes were highly conserved (99.56%), while S genes had lowest identity (92.87%), suggesting that S gene was of a faster evolutionary rate. The genome sequence similarities among 29 strains from China (Hangzhou, Wuhan, and Shenzhen), Japan, USA, and Finland, were all more than 99.9%; however, some single nucleotide polymorphisms were identified in some strains. Conclusion: The genome of Hangzhou 2019-nCoV strain was very close to the genomes of strains from other cities in China and overseas collected at early epidemic phase. The 2019-nCoV genome sequencing method used in this paper provides an useful tool for monitoring variation of viral genes.
DOI: 10.3760/cma.j.cn112150-20200217-00128
PubMed: 32171191
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">[Genomic analysis of a 2019-nCoV strain in the first COVID-19 patient found in Hangzhou, Zhejiang, China].</title><author><name sortKey="Yu, H" sort="Yu, H" uniqKey="Yu H" first="H" last="Yu">H. Yu</name><affiliation><nlm:affiliation>Hangzhou Center for Disease Prevention and Control, Health Inspection Center, Hangzhou 310021, China.</nlm:affiliation></affiliation></author><author><name sortKey="Wang, X C" sort="Wang, X C" uniqKey="Wang X" first="X C" last="Wang">X C Wang</name><affiliation><nlm:affiliation>Hangzhou Center for Disease Prevention and Control, Health Inspection Center, Hangzhou 310021, China.</nlm:affiliation></affiliation></author><author><name sortKey="Li, J" sort="Li, J" uniqKey="Li J" first="J" last="Li">J. Li</name><affiliation><nlm:affiliation>Hangzhou Center for Disease Prevention and Control, Health Inspection Center, Hangzhou 310021, China.</nlm:affiliation></affiliation></author><author><name sortKey="Qian, X" sort="Qian, X" uniqKey="Qian X" first="X" last="Qian">X. Qian</name><affiliation><nlm:affiliation>Hangzhou Center for Disease Prevention and Control, Health Inspection Center, Hangzhou 310021, China.</nlm:affiliation></affiliation></author><author><name sortKey="Yu, X F" sort="Yu, X F" uniqKey="Yu X" first="X F" last="Yu">X F Yu</name><affiliation><nlm:affiliation>Hangzhou Center for Disease Prevention and Control, Health Inspection Center, Hangzhou 310021, China.</nlm:affiliation></affiliation></author><author><name sortKey="Sun, Z" sort="Sun, Z" uniqKey="Sun Z" first="Z" last="Sun">Z. Sun</name><affiliation><nlm:affiliation>Hangzhou Center for Disease Prevention and Control, Health Inspection Center, Hangzhou 310021, China.</nlm:affiliation></affiliation></author><author><name sortKey="Chen, J F" sort="Chen, J F" uniqKey="Chen J" first="J F" last="Chen">J F Chen</name><affiliation><nlm:affiliation>Hangzhou Center for Disease Prevention and Control, Health Inspection Center, Hangzhou 310021, China.</nlm:affiliation></affiliation></author><author><name sortKey="Kao, Q J" sort="Kao, Q J" uniqKey="Kao Q" first="Q J" last="Kao">Q J Kao</name><affiliation><nlm:affiliation>Hangzhou Center for Disease Prevention and Control, Health Inspection Center, Hangzhou 310021, China.</nlm:affiliation></affiliation></author><author><name sortKey="Wang, H Q" sort="Wang, H Q" uniqKey="Wang H" first="H Q" last="Wang">H Q Wang</name><affiliation><nlm:affiliation>Hangzhou Center for Disease Prevention and Control, Health Inspection Center, Hangzhou 310021, China.</nlm:affiliation></affiliation></author><author><name sortKey="Pan, J C" sort="Pan, J C" uniqKey="Pan J" first="J C" last="Pan">J C Pan</name><affiliation><nlm:affiliation>Hangzhou Center for Disease Prevention and Control, Health Inspection Center, Hangzhou 310021, China.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2020">2020</date><idno type="RBID">pubmed:32171191</idno><idno type="pmid">32171191</idno><idno type="doi">10.3760/cma.j.cn112150-20200217-00128</idno><idno type="wicri:Area/PubMed/Corpus">000508</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000508</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">[Genomic analysis of a 2019-nCoV strain in the first COVID-19 patient found in Hangzhou, Zhejiang, China].</title><author><name sortKey="Yu, H" sort="Yu, H" uniqKey="Yu H" first="H" last="Yu">H. Yu</name><affiliation><nlm:affiliation>Hangzhou Center for Disease Prevention and Control, Health Inspection Center, Hangzhou 310021, China.</nlm:affiliation></affiliation></author><author><name sortKey="Wang, X C" sort="Wang, X C" uniqKey="Wang X" first="X C" last="Wang">X C Wang</name><affiliation><nlm:affiliation>Hangzhou Center for Disease Prevention and Control, Health Inspection Center, Hangzhou 310021, China.</nlm:affiliation></affiliation></author><author><name sortKey="Li, J" sort="Li, J" uniqKey="Li J" first="J" last="Li">J. Li</name><affiliation><nlm:affiliation>Hangzhou Center for Disease Prevention and Control, Health Inspection Center, Hangzhou 310021, China.</nlm:affiliation></affiliation></author><author><name sortKey="Qian, X" sort="Qian, X" uniqKey="Qian X" first="X" last="Qian">X. Qian</name><affiliation><nlm:affiliation>Hangzhou Center for Disease Prevention and Control, Health Inspection Center, Hangzhou 310021, China.</nlm:affiliation></affiliation></author><author><name sortKey="Yu, X F" sort="Yu, X F" uniqKey="Yu X" first="X F" last="Yu">X F Yu</name><affiliation><nlm:affiliation>Hangzhou Center for Disease Prevention and Control, Health Inspection Center, Hangzhou 310021, China.</nlm:affiliation></affiliation></author><author><name sortKey="Sun, Z" sort="Sun, Z" uniqKey="Sun Z" first="Z" last="Sun">Z. Sun</name><affiliation><nlm:affiliation>Hangzhou Center for Disease Prevention and Control, Health Inspection Center, Hangzhou 310021, China.</nlm:affiliation></affiliation></author><author><name sortKey="Chen, J F" sort="Chen, J F" uniqKey="Chen J" first="J F" last="Chen">J F Chen</name><affiliation><nlm:affiliation>Hangzhou Center for Disease Prevention and Control, Health Inspection Center, Hangzhou 310021, China.</nlm:affiliation></affiliation></author><author><name sortKey="Kao, Q J" sort="Kao, Q J" uniqKey="Kao Q" first="Q J" last="Kao">Q J Kao</name><affiliation><nlm:affiliation>Hangzhou Center for Disease Prevention and Control, Health Inspection Center, Hangzhou 310021, China.</nlm:affiliation></affiliation></author><author><name sortKey="Wang, H Q" sort="Wang, H Q" uniqKey="Wang H" first="H Q" last="Wang">H Q Wang</name><affiliation><nlm:affiliation>Hangzhou Center for Disease Prevention and Control, Health Inspection Center, Hangzhou 310021, China.</nlm:affiliation></affiliation></author><author><name sortKey="Pan, J C" sort="Pan, J C" uniqKey="Pan J" first="J C" last="Pan">J C Pan</name><affiliation><nlm:affiliation>Hangzhou Center for Disease Prevention and Control, Health Inspection Center, Hangzhou 310021, China.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine]</title><idno type="ISSN">0253-9624</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><b>Objective:</b> To understand the viral genomic characteristics of a 2019-nCoV strain in the first COVID-19 patient found in Hangzhou, China. <b>Methods:</b> Viral RNA was extracted in throat swab and sputum sample of the patient and was performed real-time reverse transcription PCR detection and obtained viral genome by high-throughput sequencing method. Phylogenetic analysis was conducted using 29 2019-nCoV genomes and 30 β-coronavirus genomes deposited in NCBI GenBank. Fifteen genomes from Wuhan were grouped by mutation sites and others were identified by Wuhan's or specific mutation sites. <b>Results:</b> A 29 833 bp length genome of the first 2019-nCoV strain in Hangzhou was obtained, covering full length of the coding regions of coronavirus. Phylogenetic analysis showed that the genome was closest to the genome of a bat SARS-like coronavirus strain RaTG13 with an identity of 96.11% (28 666/29 826). Among the genes between two genomes, E genes were highly conserved (99.56%), while S genes had lowest identity (92.87%), suggesting that S gene was of a faster evolutionary rate. The genome sequence similarities among 29 strains from China (Hangzhou, Wuhan, and Shenzhen), Japan, USA, and Finland, were all more than 99.9%; however, some single nucleotide polymorphisms were identified in some strains. <b>Conclusion:</b> The genome of Hangzhou 2019-nCoV strain was very close to the genomes of strains from other cities in China and overseas collected at early epidemic phase. The 2019-nCoV genome sequencing method used in this paper provides an useful tool for monitoring variation of viral genes.</div></front></TEI><pubmed><MedlineCitation Status="Publisher" Owner="NLM"><PMID Version="1">32171191</PMID><DateRevised><Year>2020</Year><Month>03</Month><Day>15</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">0253-9624</ISSN><JournalIssue CitedMedium="Print"><Volume>54</Volume><Issue>0</Issue><PubDate><Year>2020</Year><Month>Mar</Month><Day>15</Day></PubDate></JournalIssue><Title>Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine]</Title><ISOAbbreviation>Zhonghua Yu Fang Yi Xue Za Zhi</ISOAbbreviation></Journal><ArticleTitle>[Genomic analysis of a 2019-nCoV strain in the first COVID-19 patient found in Hangzhou, Zhejiang, China].</ArticleTitle><Pagination><MedlinePgn>E026</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.3760/cma.j.cn112150-20200217-00128</ELocationID><Abstract><AbstractText><b>Objective:</b> To understand the viral genomic characteristics of a 2019-nCoV strain in the first COVID-19 patient found in Hangzhou, China. <b>Methods:</b> Viral RNA was extracted in throat swab and sputum sample of the patient and was performed real-time reverse transcription PCR detection and obtained viral genome by high-throughput sequencing method. Phylogenetic analysis was conducted using 29 2019-nCoV genomes and 30 β-coronavirus genomes deposited in NCBI GenBank. Fifteen genomes from Wuhan were grouped by mutation sites and others were identified by Wuhan's or specific mutation sites. <b>Results:</b> A 29 833 bp length genome of the first 2019-nCoV strain in Hangzhou was obtained, covering full length of the coding regions of coronavirus. Phylogenetic analysis showed that the genome was closest to the genome of a bat SARS-like coronavirus strain RaTG13 with an identity of 96.11% (28 666/29 826). Among the genes between two genomes, E genes were highly conserved (99.56%), while S genes had lowest identity (92.87%), suggesting that S gene was of a faster evolutionary rate. The genome sequence similarities among 29 strains from China (Hangzhou, Wuhan, and Shenzhen), Japan, USA, and Finland, were all more than 99.9%; however, some single nucleotide polymorphisms were identified in some strains. <b>Conclusion:</b> The genome of Hangzhou 2019-nCoV strain was very close to the genomes of strains from other cities in China and overseas collected at early epidemic phase. The 2019-nCoV genome sequencing method used in this paper provides an useful tool for monitoring variation of viral genes.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Yu</LastName><ForeName>H</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Hangzhou Center for Disease Prevention and Control, Health Inspection Center, Hangzhou 310021, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>X C</ForeName><Initials>XC</Initials><AffiliationInfo><Affiliation>Hangzhou Center for Disease Prevention and Control, Health Inspection Center, Hangzhou 310021, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>J</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Hangzhou Center for Disease Prevention and Control, Health Inspection Center, Hangzhou 310021, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Qian</LastName><ForeName>X</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>Hangzhou Center for Disease Prevention and Control, Health Inspection Center, Hangzhou 310021, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yu</LastName><ForeName>X F</ForeName><Initials>XF</Initials><AffiliationInfo><Affiliation>Hangzhou Center for Disease Prevention and Control, Health Inspection Center, Hangzhou 310021, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sun</LastName><ForeName>Z</ForeName><Initials>Z</Initials><AffiliationInfo><Affiliation>Hangzhou Center for Disease Prevention and Control, Health Inspection Center, Hangzhou 310021, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>J F</ForeName><Initials>JF</Initials><AffiliationInfo><Affiliation>Hangzhou Center for Disease Prevention and Control, Health Inspection Center, Hangzhou 310021, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kao</LastName><ForeName>Q J</ForeName><Initials>QJ</Initials><AffiliationInfo><Affiliation>Hangzhou Center for Disease Prevention and Control, Health Inspection Center, Hangzhou 310021, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>H Q</ForeName><Initials>HQ</Initials><AffiliationInfo><Affiliation>Hangzhou Center for Disease Prevention and Control, Health Inspection Center, Hangzhou 310021, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Pan</LastName><ForeName>J C</ForeName><Initials>JC</Initials><AffiliationInfo><Affiliation>Hangzhou Center for Disease Prevention and Control, Health Inspection Center, Hangzhou 310021, China.</Affiliation></AffiliationInfo></Author></AuthorList><Language>chi</Language><PublicationTypeList><PublicationType UI="D004740">English Abstract</PublicationType><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>03</Month><Day>15</Day></ArticleDate></Article><MedlineJournalInfo><Country>China</Country><MedlineTA>Zhonghua Yu Fang Yi Xue Za Zhi</MedlineTA><NlmUniqueID>7904962</NlmUniqueID><ISSNLinking>0253-9624</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><OtherAbstract Type="Publisher" Language="chi"><AbstractText><b>目的：</b> 分析杭州市首例新型冠状病毒（2019-nCoV）肺炎病例病毒全基因组序列特征。 <b>方法：</b> 采集杭州市首例新型冠转病毒肺炎病例咽拭子和深咳痰液呼吸道标本，对标本进行病毒核酸提取和实时逆转录PCR检测，对病毒进行高通量基因组测序；从美国国立生物技术信息中心GeneBank数据库中获取29条（分别来自武汉、深圳、日本、美国、澳大利亚和芬兰）2019-nCoV基因组序列和其他物种来源的30条β冠状病毒基因组进行系统发育分析。对15株武汉地区毒株基因组以突变位点进行分组，鉴定其他地区相同和特异性突变位点。 <b>结果：</b> 获得29 833 bp长度的杭州首例新型冠状病毒肺炎病例病毒的基因组序列，覆盖病毒编码区全长。系统发育分析表明，该病毒与云南蝙蝠中分离到的严重急性呼吸综合征样冠状病毒RaTG13株最为接近，相似性为96.11%；相较其他基因，E基因间相似性最高（99.56%），而编码病毒表面刺突蛋白的S基因间相似性最低（92.87%）。与来自武汉、深圳、日本、美国、澳大利亚和芬兰的29株新型冠状病毒基因组序列进行比对，相似性均大于99.9%，但在一些毒株中也发现了一些单位点核苷酸多态性。 <b>结论：</b> 杭州首例新型冠状病毒肺炎病例病毒基因组序列和来自国内外疫情早期冠状病毒基因组高度近源。.</AbstractText></OtherAbstract><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">2019-nCoV</Keyword><Keyword MajorTopicYN="N">COVID-19</Keyword><Keyword MajorTopicYN="N">Genome</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>3</Month><Day>16</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>3</Month><Day>17</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>3</Month><Day>17</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>aheadofprint</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">32171191</ArticleId><ArticleId IdType="doi">10.3760/cma.j.cn112150-20200217-00128</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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