RNA based mNGS approach identifies a novel human coronavirus from two individual pneumonia cases in 2019 Wuhan outbreak.
Identifieur interne : 000208 ( new/Analysis ); précédent : 000207; suivant : 000209RNA based mNGS approach identifies a novel human coronavirus from two individual pneumonia cases in 2019 Wuhan outbreak.
Auteurs : Liangjun Chen [République populaire de Chine] ; Weiyong Liu [République populaire de Chine] ; Qi Zhang [République populaire de Chine] ; Ke Xu [République populaire de Chine] ; Guangming Ye [République populaire de Chine] ; Weichen Wu [République populaire de Chine] ; Ziyong Sun [République populaire de Chine] ; Fang Liu [République populaire de Chine] ; Kailang Wu [République populaire de Chine] ; Bo Zhong [République populaire de Chine] ; Yi Mei [République populaire de Chine] ; Wenxia Zhang [République populaire de Chine] ; Yu Chen [République populaire de Chine] ; Yirong Li [République populaire de Chine] ; Mang Shi [République populaire de Chine] ; Ke Lan [République populaire de Chine] ; Yingle Liu [République populaire de Chine]Source :
- Emerging microbes & infections [ 2222-1751 ] ; 2020.
Descripteurs français
- KwdFr :
- MESH :
- génétique : ARN viral.
- épidémiologie : Infections à coronavirus, Pneumopathie virale.
- Adulte, Chine, Femelle, Flambées de maladies, Génome viral, Humains, Jeune adulte, Mâle, Phylogénie.
- Wicri :
- geographic : République populaire de Chine.
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : RNA, Viral.
- geographic : China.
- epidemiology : Coronavirus Infections, Pneumonia, Viral.
- genetics : Betacoronavirus.
- Adult, Disease Outbreaks, Female, Genome, Viral, Humans, Male, Phylogeny, Young Adult.
Abstract
From December 2019, an outbreak of unusual pneumonia was reported in Wuhan with many cases linked to Huanan Seafood Market that sells seafood as well as live exotic animals. We investigated two patients who developed acute respiratory syndromes after independent contact history with this market. The two patients shared common clinical features including fever, cough, and multiple ground-glass opacities in the bilateral lung field with patchy infiltration. Here, we highlight the use of a low-input metagenomic next-generation sequencing (mNGS) approach on RNA extracted from bronchoalveolar lavage fluid (BALF). It rapidly identified a novel coronavirus (named 2019-nCoV according to World Health Organization announcement) which was the sole pathogens in the sample with very high abundance level (1.5% and 0.62% of total RNA sequenced). The entire viral genome is 29,881 nt in length (GenBank MN988668 and MN988669, Sequence Read Archive database Bioproject accession PRJNA601736) and is classified into β-coronavirus genus. Phylogenetic analysis indicates that 2019-nCoV is close to coronaviruses (CoVs) circulating in Rhinolophus (Horseshoe bats), such as 98.7% nucleotide identity to partial RdRp gene of bat coronavirus strain BtCoV/4991 (GenBank KP876546, 370 nt sequence of RdRp and lack of other genome sequence) and 87.9% nucleotide identity to bat coronavirus strain bat-SL-CoVZC45 and bat-SL-CoVZXC21. Evolutionary analysis based on ORF1a/1b, S, and N genes also suggests 2019-nCoV is more likely a novel CoV independently introduced from animals to humans.
DOI: 10.1080/22221751.2020.1725399
PubMed: 32020836
Affiliations:
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pubmed:32020836Le document en format XML
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Medicine, Sun yat-Sen University, Guangzhou, People's Republic of China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>School of Medicine, Sun yat-Sen University, Guangzhou</wicri:regionArea><placeName><settlement type="city">Jiangmen</settlement><region type="province">Guangdong</region></placeName></affiliation></author><author><name sortKey="Lan, Ke" sort="Lan, Ke" uniqKey="Lan K" first="Ke" last="Lan">Ke Lan</name><affiliation wicri:level="4"><nlm:affiliation>State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan</wicri:regionArea><placeName><settlement type="city">Wuhan</settlement><region type="région">Hubei</region></placeName><orgName type="university">Université de Wuhan</orgName></affiliation></author><author><name sortKey="Liu, Yingle" sort="Liu, Yingle" uniqKey="Liu Y" first="Yingle" last="Liu">Yingle Liu</name><affiliation wicri:level="4"><nlm:affiliation>State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan</wicri:regionArea><placeName><settlement type="city">Wuhan</settlement><region type="région">Hubei</region></placeName><orgName type="university">Université de Wuhan</orgName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2020">2020</date><idno type="RBID">pubmed:32020836</idno><idno 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coronavirus from two individual pneumonia cases in 2019 Wuhan outbreak.</title><author><name sortKey="Chen, Liangjun" sort="Chen, Liangjun" uniqKey="Chen L" first="Liangjun" last="Chen">Liangjun Chen</name><affiliation wicri:level="4"><nlm:affiliation>State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan</wicri:regionArea><placeName><settlement type="city">Wuhan</settlement><region type="région">Hubei</region></placeName><orgName type="university">Université de Wuhan</orgName></affiliation></author><author><name sortKey="Liu, Weiyong" sort="Liu, Weiyong" uniqKey="Liu W" first="Weiyong" last="Liu">Weiyong Liu</name><affiliation wicri:level="3"><nlm:affiliation>Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan</wicri:regionArea><placeName><settlement type="city">Wuhan</settlement><region type="région">Hubei</region></placeName></affiliation></author><author><name sortKey="Zhang, Qi" sort="Zhang, Qi" uniqKey="Zhang Q" first="Qi" last="Zhang">Qi Zhang</name><affiliation wicri:level="4"><nlm:affiliation>State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan</wicri:regionArea><placeName><settlement type="city">Wuhan</settlement><region type="région">Hubei</region></placeName><orgName type="university">Université de Wuhan</orgName></affiliation></author><author><name sortKey="Xu, Ke" sort="Xu, Ke" uniqKey="Xu K" first="Ke" last="Xu">Ke Xu</name><affiliation wicri:level="4"><nlm:affiliation>State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan</wicri:regionArea><placeName><settlement type="city">Wuhan</settlement><region type="région">Hubei</region></placeName><orgName type="university">Université de Wuhan</orgName></affiliation></author><author><name sortKey="Ye, Guangming" sort="Ye, Guangming" uniqKey="Ye G" first="Guangming" last="Ye">Guangming Ye</name><affiliation wicri:level="3"><nlm:affiliation>Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, People's Republic of China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan</wicri:regionArea><placeName><settlement type="city">Wuhan</settlement><region type="région">Hubei</region></placeName></affiliation></author><author><name sortKey="Wu, Weichen" sort="Wu, Weichen" uniqKey="Wu W" first="Weichen" last="Wu">Weichen Wu</name><affiliation wicri:level="3"><nlm:affiliation>School of Medicine, Sun yat-Sen University, Guangzhou, People's Republic of China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>School of Medicine, Sun yat-Sen University, Guangzhou</wicri:regionArea><placeName><settlement type="city">Jiangmen</settlement><region type="province">Guangdong</region></placeName></affiliation></author><author><name sortKey="Sun, Ziyong" sort="Sun, Ziyong" uniqKey="Sun Z" first="Ziyong" last="Sun">Ziyong Sun</name><affiliation wicri:level="3"><nlm:affiliation>Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan</wicri:regionArea><placeName><settlement type="city">Wuhan</settlement><region type="région">Hubei</region></placeName></affiliation></author><author><name sortKey="Liu, Fang" sort="Liu, Fang" uniqKey="Liu F" first="Fang" last="Liu">Fang Liu</name><affiliation wicri:level="4"><nlm:affiliation>State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan</wicri:regionArea><placeName><settlement type="city">Wuhan</settlement><region type="région">Hubei</region></placeName><orgName type="university">Université de Wuhan</orgName></affiliation></author><author><name sortKey="Wu, Kailang" sort="Wu, Kailang" uniqKey="Wu K" first="Kailang" last="Wu">Kailang Wu</name><affiliation wicri:level="4"><nlm:affiliation>State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan</wicri:regionArea><placeName><settlement type="city">Wuhan</settlement><region type="région">Hubei</region></placeName><orgName type="university">Université de Wuhan</orgName></affiliation></author><author><name sortKey="Zhong, Bo" sort="Zhong, Bo" uniqKey="Zhong B" first="Bo" last="Zhong">Bo Zhong</name><affiliation wicri:level="4"><nlm:affiliation>State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan</wicri:regionArea><placeName><settlement type="city">Wuhan</settlement><region type="région">Hubei</region></placeName><orgName type="university">Université de Wuhan</orgName></affiliation></author><author><name sortKey="Mei, Yi" sort="Mei, Yi" uniqKey="Mei Y" first="Yi" last="Mei">Yi Mei</name><affiliation wicri:level="4"><nlm:affiliation>State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan</wicri:regionArea><placeName><settlement type="city">Wuhan</settlement><region type="région">Hubei</region></placeName><orgName type="university">Université de Wuhan</orgName></affiliation></author><author><name sortKey="Zhang, Wenxia" sort="Zhang, Wenxia" uniqKey="Zhang W" first="Wenxia" last="Zhang">Wenxia Zhang</name><affiliation wicri:level="4"><nlm:affiliation>State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan</wicri:regionArea><placeName><settlement type="city">Wuhan</settlement><region type="région">Hubei</region></placeName><orgName type="university">Université de Wuhan</orgName></affiliation></author><author><name sortKey="Chen, Yu" sort="Chen, Yu" uniqKey="Chen Y" first="Yu" last="Chen">Yu Chen</name><affiliation wicri:level="4"><nlm:affiliation>State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan</wicri:regionArea><placeName><settlement type="city">Wuhan</settlement><region type="région">Hubei</region></placeName><orgName type="university">Université de Wuhan</orgName></affiliation></author><author><name sortKey="Li, Yirong" sort="Li, Yirong" uniqKey="Li Y" first="Yirong" last="Li">Yirong Li</name><affiliation wicri:level="3"><nlm:affiliation>Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, People's Republic of China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan</wicri:regionArea><placeName><settlement type="city">Wuhan</settlement><region type="région">Hubei</region></placeName></affiliation></author><author><name sortKey="Shi, Mang" sort="Shi, Mang" uniqKey="Shi M" first="Mang" last="Shi">Mang Shi</name><affiliation wicri:level="3"><nlm:affiliation>School of Medicine, Sun yat-Sen University, Guangzhou, People's Republic of China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>School of Medicine, Sun yat-Sen University, Guangzhou</wicri:regionArea><placeName><settlement type="city">Jiangmen</settlement><region type="province">Guangdong</region></placeName></affiliation></author><author><name sortKey="Lan, Ke" sort="Lan, Ke" uniqKey="Lan K" first="Ke" last="Lan">Ke Lan</name><affiliation wicri:level="4"><nlm:affiliation>State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan</wicri:regionArea><placeName><settlement type="city">Wuhan</settlement><region type="région">Hubei</region></placeName><orgName type="university">Université de Wuhan</orgName></affiliation></author><author><name sortKey="Liu, Yingle" sort="Liu, Yingle" uniqKey="Liu Y" first="Yingle" last="Liu">Yingle Liu</name><affiliation wicri:level="4"><nlm:affiliation>State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan</wicri:regionArea><placeName><settlement type="city">Wuhan</settlement><region type="région">Hubei</region></placeName><orgName type="university">Université de Wuhan</orgName></affiliation></author></analytic><series><title level="j">Emerging microbes & infections</title><idno type="eISSN">2222-1751</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Adult</term><term>Betacoronavirus (genetics)</term><term>China</term><term>Coronavirus Infections (epidemiology)</term><term>Disease Outbreaks</term><term>Female</term><term>Genome, Viral</term><term>Humans</term><term>Male</term><term>Phylogeny</term><term>Pneumonia, Viral (epidemiology)</term><term>RNA, Viral (genetics)</term><term>Young Adult</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ARN viral (génétique)</term><term>Adulte</term><term>Chine</term><term>Femelle</term><term>Flambées de maladies</term><term>Génome viral</term><term>Humains</term><term>Infections à coronavirus (épidémiologie)</term><term>Jeune adulte</term><term>Mâle</term><term>Phylogénie</term><term>Pneumopathie virale (épidémiologie)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>RNA, Viral</term></keywords><keywords scheme="MESH" type="geographic" xml:lang="en"><term>China</term></keywords><keywords scheme="MESH" qualifier="epidemiology" xml:lang="en"><term>Coronavirus Infections</term><term>Pneumonia, Viral</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Betacoronavirus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ARN viral</term></keywords><keywords scheme="MESH" qualifier="épidémiologie" xml:lang="fr"><term>Infections à coronavirus</term><term>Pneumopathie virale</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Adult</term><term>Disease Outbreaks</term><term>Female</term><term>Genome, Viral</term><term>Humans</term><term>Male</term><term>Phylogeny</term><term>Young Adult</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Adulte</term><term>Chine</term><term>Femelle</term><term>Flambées de maladies</term><term>Génome viral</term><term>Humains</term><term>Jeune adulte</term><term>Mâle</term><term>Phylogénie</term></keywords><keywords scheme="Wicri" type="geographic" xml:lang="fr"><term>République populaire de Chine</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">From December 2019, an outbreak of unusual pneumonia was reported in Wuhan with many cases linked to Huanan Seafood Market that sells seafood as well as live exotic animals. We investigated two patients who developed acute respiratory syndromes after independent contact history with this market. The two patients shared common clinical features including fever, cough, and multiple ground-glass opacities in the bilateral lung field with patchy infiltration. Here, we highlight the use of a low-input metagenomic next-generation sequencing (mNGS) approach on RNA extracted from bronchoalveolar lavage fluid (BALF). It rapidly identified a novel coronavirus (named 2019-nCoV according to World Health Organization announcement) which was the sole pathogens in the sample with very high abundance level (1.5% and 0.62% of total RNA sequenced). The entire viral genome is 29,881 nt in length (GenBank MN988668 and MN988669, Sequence Read Archive database Bioproject accession PRJNA601736) and is classified into β-coronavirus genus. Phylogenetic analysis indicates that 2019-nCoV is close to coronaviruses (CoVs) circulating in Rhinolophus (Horseshoe bats), such as 98.7% nucleotide identity to partial RdRp gene of bat coronavirus strain BtCoV/4991 (GenBank KP876546, 370 nt sequence of RdRp and lack of other genome sequence) and 87.9% nucleotide identity to bat coronavirus strain bat-SL-CoVZC45 and bat-SL-CoVZXC21. Evolutionary analysis based on ORF1a/1b, S, and N genes also suggests 2019-nCoV is more likely a novel CoV independently introduced from animals to humans.</div></front></TEI><affiliations><list><country><li>République populaire de Chine</li></country><region><li>Guangdong</li><li>Hubei</li></region><settlement><li>Jiangmen</li><li>Wuhan</li></settlement><orgName><li>Université de Wuhan</li></orgName></list><tree><country name="République populaire de Chine"><region name="Hubei"><name sortKey="Chen, Liangjun" sort="Chen, Liangjun" uniqKey="Chen L" first="Liangjun" last="Chen">Liangjun Chen</name></region><name sortKey="Chen, Yu" sort="Chen, Yu" uniqKey="Chen Y" first="Yu" last="Chen">Yu Chen</name><name sortKey="Lan, Ke" sort="Lan, Ke" uniqKey="Lan K" first="Ke" last="Lan">Ke Lan</name><name sortKey="Li, Yirong" sort="Li, Yirong" uniqKey="Li Y" first="Yirong" last="Li">Yirong Li</name><name sortKey="Liu, Fang" sort="Liu, Fang" uniqKey="Liu F" first="Fang" last="Liu">Fang Liu</name><name sortKey="Liu, Weiyong" sort="Liu, Weiyong" uniqKey="Liu W" first="Weiyong" last="Liu">Weiyong Liu</name><name sortKey="Liu, Yingle" sort="Liu, Yingle" uniqKey="Liu Y" first="Yingle" last="Liu">Yingle Liu</name><name sortKey="Mei, Yi" sort="Mei, Yi" uniqKey="Mei Y" first="Yi" last="Mei">Yi Mei</name><name sortKey="Shi, Mang" sort="Shi, Mang" uniqKey="Shi M" first="Mang" last="Shi">Mang Shi</name><name sortKey="Sun, Ziyong" sort="Sun, Ziyong" uniqKey="Sun Z" first="Ziyong" last="Sun">Ziyong Sun</name><name sortKey="Wu, Kailang" sort="Wu, Kailang" uniqKey="Wu K" first="Kailang" last="Wu">Kailang Wu</name><name sortKey="Wu, Weichen" sort="Wu, Weichen" uniqKey="Wu W" first="Weichen" last="Wu">Weichen Wu</name><name sortKey="Xu, Ke" sort="Xu, Ke" uniqKey="Xu K" first="Ke" last="Xu">Ke Xu</name><name sortKey="Ye, Guangming" sort="Ye, Guangming" uniqKey="Ye G" first="Guangming" last="Ye">Guangming Ye</name><name sortKey="Zhang, Qi" sort="Zhang, Qi" uniqKey="Zhang Q" first="Qi" last="Zhang">Qi Zhang</name><name sortKey="Zhang, Wenxia" sort="Zhang, Wenxia" uniqKey="Zhang W" first="Wenxia" last="Zhang">Wenxia Zhang</name><name sortKey="Zhong, Bo" sort="Zhong, Bo" uniqKey="Zhong B" first="Bo" last="Zhong">Bo Zhong</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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