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RNA based mNGS approach identifies a novel human coronavirus from two individual pneumonia cases in 2019 Wuhan outbreak.
Emerg Microbes Infect. 2020; 9(1):313-319.EM

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.

Authors+Show Affiliations

State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China. Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, People's Republic of China.Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China.State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China.State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China.Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, People's Republic of China.School of Medicine, Sun yat-Sen University, Guangzhou, People's Republic of China.Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China.State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China.State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China.State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China.State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China.State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China.State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China.Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, People's Republic of China.School of Medicine, Sun yat-Sen University, Guangzhou, People's Republic of China.State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China.State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China.

Pub Type(s)

Case Reports
Journal Article

Language

eng

PubMed ID

32020836

Citation

Chen, Liangjun, et al. "RNA Based mNGS Approach Identifies a Novel Human Coronavirus From Two Individual Pneumonia Cases in 2019 Wuhan Outbreak." Emerging Microbes & Infections, vol. 9, no. 1, 2020, pp. 313-319.
Chen L, Liu W, Zhang Q, et al. RNA based mNGS approach identifies a novel human coronavirus from two individual pneumonia cases in 2019 Wuhan outbreak. Emerg Microbes Infect. 2020;9(1):313-319.
Chen, L., Liu, W., Zhang, Q., Xu, K., Ye, G., Wu, W., Sun, Z., Liu, F., Wu, K., Zhong, B., Mei, Y., Zhang, W., Chen, Y., Li, Y., Shi, M., Lan, K., & Liu, Y. (2020). RNA based mNGS approach identifies a novel human coronavirus from two individual pneumonia cases in 2019 Wuhan outbreak. Emerging Microbes & Infections, 9(1), 313-319. https://doi.org/10.1080/22221751.2020.1725399
Chen L, et al. RNA Based mNGS Approach Identifies a Novel Human Coronavirus From Two Individual Pneumonia Cases in 2019 Wuhan Outbreak. Emerg Microbes Infect. 2020;9(1):313-319. PubMed PMID: 32020836.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - RNA based mNGS approach identifies a novel human coronavirus from two individual pneumonia cases in 2019 Wuhan outbreak. AU - Chen,Liangjun, AU - Liu,Weiyong, AU - Zhang,Qi, AU - Xu,Ke, AU - Ye,Guangming, AU - Wu,Weichen, AU - Sun,Ziyong, AU - Liu,Fang, AU - Wu,Kailang, AU - Zhong,Bo, AU - Mei,Yi, AU - Zhang,Wenxia, AU - Chen,Yu, AU - Li,Yirong, AU - Shi,Mang, AU - Lan,Ke, AU - Liu,Yingle, Y1 - 2020/02/05/ PY - 2020/2/6/entrez PY - 2020/2/6/pubmed PY - 2020/3/17/medline KW - 2019-nCoV KW - Wuhan pneumonia KW - metagenomic next-generation sequencing KW - phylogenetic analyses KW - virus evolution SP - 313 EP - 319 JF - Emerging microbes & infections JO - Emerg Microbes Infect VL - 9 IS - 1 N2 - 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. SN - 2222-1751 UR - https://www.unboundmedicine.com/medline/citation/32020836/RNA_based_mNGS_approach_identifies_a_novel_human_coronavirus_from_two_individual_pneumonia_cases_in_2019_Wuhan_outbreak_ DB - PRIME DP - Unbound Medicine ER -