[Genomic analysis of a 2019-nCoV strain in the first COVID-19 patient found in Hangzhou, Zhejiang, China].
Identifieur interne : 000069 ( Main/Exploration ); précédent : 000068; suivant : 000070[Genomic analysis of a 2019-nCoV strain in the first COVID-19 patient found in Hangzhou, Zhejiang, China].
Auteurs : H. Yu [République populaire de Chine] ; X C Wang [République populaire de Chine] ; J. Li [République populaire de Chine] ; X. Qian [République populaire de Chine] ; X F Yu [République populaire de Chine] ; Z. Sun [République populaire de Chine] ; J F Chen [République populaire de Chine] ; Q J Kao [République populaire de Chine] ; H Q Wang [République populaire de Chine] ; J C Pan [République populaire de Chine]Source :
- 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
Affiliations:
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Yu</name><affiliation wicri:level="1"><nlm:affiliation>Hangzhou Center for Disease Prevention and Control, Health Inspection Center, Hangzhou 310021, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Hangzhou Center for Disease Prevention and Control, Health Inspection Center, Hangzhou 310021</wicri:regionArea><placeName><settlement type="city">Hangzhou</settlement><region type="province">Zhejiang</region></placeName></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 wicri:level="1"><nlm:affiliation>Hangzhou Center for Disease Prevention and Control, Health Inspection Center, Hangzhou 310021, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Hangzhou Center for Disease Prevention and Control, Health Inspection Center, Hangzhou 310021</wicri:regionArea><placeName><settlement type="city">Hangzhou</settlement><region type="province">Zhejiang</region></placeName></affiliation></author><author><name sortKey="Li, J" sort="Li, J" uniqKey="Li J" first="J" last="Li">J. Li</name><affiliation wicri:level="1"><nlm:affiliation>Hangzhou Center for Disease Prevention and Control, Health Inspection Center, Hangzhou 310021, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Hangzhou Center for Disease Prevention and Control, Health Inspection Center, Hangzhou 310021</wicri:regionArea><placeName><settlement type="city">Hangzhou</settlement><region type="province">Zhejiang</region></placeName></affiliation></author><author><name sortKey="Qian, X" sort="Qian, X" uniqKey="Qian X" first="X" last="Qian">X. Qian</name><affiliation wicri:level="1"><nlm:affiliation>Hangzhou Center for Disease Prevention and Control, Health Inspection Center, Hangzhou 310021, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Hangzhou Center for Disease Prevention and Control, Health Inspection Center, Hangzhou 310021</wicri:regionArea><placeName><settlement type="city">Hangzhou</settlement><region type="province">Zhejiang</region></placeName></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 wicri:level="1"><nlm:affiliation>Hangzhou Center for Disease Prevention and Control, Health Inspection Center, Hangzhou 310021, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Hangzhou Center for Disease Prevention and Control, Health Inspection Center, Hangzhou 310021</wicri:regionArea><placeName><settlement type="city">Hangzhou</settlement><region type="province">Zhejiang</region></placeName></affiliation></author><author><name sortKey="Sun, Z" sort="Sun, Z" uniqKey="Sun Z" first="Z" last="Sun">Z. Sun</name><affiliation wicri:level="1"><nlm:affiliation>Hangzhou Center for Disease Prevention and Control, Health Inspection Center, Hangzhou 310021, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Hangzhou Center for Disease Prevention and Control, Health Inspection Center, Hangzhou 310021</wicri:regionArea><placeName><settlement type="city">Hangzhou</settlement><region type="province">Zhejiang</region></placeName></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 wicri:level="1"><nlm:affiliation>Hangzhou Center for Disease Prevention and Control, Health Inspection Center, Hangzhou 310021, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Hangzhou Center for Disease Prevention and Control, Health Inspection Center, Hangzhou 310021</wicri:regionArea><placeName><settlement type="city">Hangzhou</settlement><region type="province">Zhejiang</region></placeName></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 wicri:level="1"><nlm:affiliation>Hangzhou Center for Disease Prevention and Control, Health Inspection Center, Hangzhou 310021, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Hangzhou Center for Disease Prevention and Control, Health Inspection Center, Hangzhou 310021</wicri:regionArea><placeName><settlement type="city">Hangzhou</settlement><region type="province">Zhejiang</region></placeName></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 wicri:level="1"><nlm:affiliation>Hangzhou Center for Disease Prevention and Control, Health Inspection Center, Hangzhou 310021, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Hangzhou Center for Disease Prevention and Control, Health Inspection Center, Hangzhou 310021</wicri:regionArea><placeName><settlement type="city">Hangzhou</settlement><region type="province">Zhejiang</region></placeName></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 wicri:level="1"><nlm:affiliation>Hangzhou Center for Disease Prevention and Control, Health Inspection Center, Hangzhou 310021, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Hangzhou Center for Disease Prevention and Control, Health Inspection Center, Hangzhou 310021</wicri:regionArea><placeName><settlement type="city">Hangzhou</settlement><region type="province">Zhejiang</region></placeName></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><affiliations><list><country><li>République populaire de Chine</li></country><region><li>Zhejiang</li></region><settlement><li>Hangzhou</li></settlement></list><tree><country name="République populaire de Chine"><region name="Zhejiang"><name sortKey="Yu, H" sort="Yu, H" uniqKey="Yu H" first="H" last="Yu">H. Yu</name></region><name sortKey="Chen, J F" sort="Chen, J F" uniqKey="Chen J" first="J F" last="Chen">J F Chen</name><name sortKey="Kao, Q J" sort="Kao, Q J" uniqKey="Kao Q" first="Q J" last="Kao">Q J Kao</name><name sortKey="Li, J" sort="Li, J" uniqKey="Li J" first="J" last="Li">J. Li</name><name sortKey="Pan, J C" sort="Pan, J C" uniqKey="Pan J" first="J C" last="Pan">J C Pan</name><name sortKey="Qian, X" sort="Qian, X" uniqKey="Qian X" first="X" last="Qian">X. Qian</name><name sortKey="Sun, Z" sort="Sun, Z" uniqKey="Sun Z" first="Z" last="Sun">Z. Sun</name><name sortKey="Wang, H Q" sort="Wang, H Q" uniqKey="Wang H" first="H Q" last="Wang">H Q Wang</name><name sortKey="Wang, X C" sort="Wang, X C" uniqKey="Wang X" first="X C" last="Wang">X C Wang</name><name sortKey="Yu, X F" sort="Yu, X F" uniqKey="Yu X" first="X F" last="Yu">X F Yu</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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