RNA based mNGS approach identifies a novel human coronavirus from two individual pneumonia cases in 2019 Wuhan outbreak
ABSTRACTFrom 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 mar...
| Main Authors: | , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Taylor & Francis Group
2020-01-01
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| Series: | Emerging Microbes and Infections |
| Subjects: | |
| Online Access: | https://www.tandfonline.com/doi/10.1080/22221751.2020.1725399 |
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| author | Liangjun Chen Weiyong Liu Qi Zhang Ke Xu Guangming Ye Weichen Wu Ziyong Sun Fang Liu Kailang Wu Bo Zhong Yi Mei Wenxia Zhang Yu Chen Yirong Li Mang Shi Ke Lan Yingle Liu |
| author_facet | Liangjun Chen Weiyong Liu Qi Zhang Ke Xu Guangming Ye Weichen Wu Ziyong Sun Fang Liu Kailang Wu Bo Zhong Yi Mei Wenxia Zhang Yu Chen Yirong Li Mang Shi Ke Lan Yingle Liu |
| author_sort | Liangjun Chen |
| collection | DOAJ |
| description | ABSTRACTFrom 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. |
| first_indexed | 2024-03-07T17:24:06Z |
| format | Article |
| id | doaj.art-836f5e3b275a4dde8eecf76b13d30f00 |
| institution | Directory Open Access Journal |
| issn | 2222-1751 |
| language | English |
| last_indexed | 2024-04-25T00:51:47Z |
| publishDate | 2020-01-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | Emerging Microbes and Infections |
| spelling | doaj.art-836f5e3b275a4dde8eecf76b13d30f002024-03-11T16:04:23ZengTaylor & Francis GroupEmerging Microbes and Infections2222-17512020-01-019131331910.1080/22221751.2020.1725399RNA based mNGS approach identifies a novel human coronavirus from two individual pneumonia cases in 2019 Wuhan outbreakLiangjun Chen0Weiyong Liu1Qi Zhang2Ke Xu3Guangming Ye4Weichen Wu5Ziyong Sun6Fang Liu7Kailang Wu8Bo Zhong9Yi Mei10Wenxia Zhang11Yu Chen12Yirong Li13Mang Shi14Ke Lan15Yingle Liu16State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of ChinaDepartment of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People’s Republic of ChinaState Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of ChinaState Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of ChinaDepartment of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, People’s Republic of ChinaSchool of Medicine, Sun yat-Sen University, Guangzhou, People’s Republic of ChinaDepartment of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People’s Republic of ChinaState Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of ChinaState Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of ChinaState Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of ChinaState Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of ChinaState Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of ChinaState Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of ChinaDepartment of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, People’s Republic of ChinaSchool of Medicine, Sun yat-Sen University, Guangzhou, People’s Republic of ChinaState Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of ChinaState Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of ChinaABSTRACTFrom 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.https://www.tandfonline.com/doi/10.1080/22221751.2020.17253992019-nCoVWuhan pneumoniametagenomic next-generation sequencingphylogenetic analysesvirus evolution |
| spellingShingle | Liangjun Chen Weiyong Liu Qi Zhang Ke Xu Guangming Ye Weichen Wu Ziyong Sun Fang Liu Kailang Wu Bo Zhong Yi Mei Wenxia Zhang Yu Chen Yirong Li Mang Shi Ke Lan Yingle Liu RNA based mNGS approach identifies a novel human coronavirus from two individual pneumonia cases in 2019 Wuhan outbreak Emerging Microbes and Infections 2019-nCoV Wuhan pneumonia metagenomic next-generation sequencing phylogenetic analyses virus evolution |
| title | RNA based mNGS approach identifies a novel human coronavirus from two individual pneumonia cases in 2019 Wuhan outbreak |
| title_full | RNA based mNGS approach identifies a novel human coronavirus from two individual pneumonia cases in 2019 Wuhan outbreak |
| title_fullStr | RNA based mNGS approach identifies a novel human coronavirus from two individual pneumonia cases in 2019 Wuhan outbreak |
| title_full_unstemmed | RNA based mNGS approach identifies a novel human coronavirus from two individual pneumonia cases in 2019 Wuhan outbreak |
| title_short | RNA based mNGS approach identifies a novel human coronavirus from two individual pneumonia cases in 2019 Wuhan outbreak |
| title_sort | rna based mngs approach identifies a novel human coronavirus from two individual pneumonia cases in 2019 wuhan outbreak |
| topic | 2019-nCoV Wuhan pneumonia metagenomic next-generation sequencing phylogenetic analyses virus evolution |
| url | https://www.tandfonline.com/doi/10.1080/22221751.2020.1725399 |
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