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A Pneumonia Outbreak Associated with a New Coronavirus of Probable Bat Origin

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A Pneumonia Outbreak Associated with a New Coronavirus of Probable Bat Origin Article A pneumonia outbreak associated with a new coronavirus of probable bat origin https://doi.org/10.1038/s41586-020-2012-7 Peng Zhou1,5, Xing-Lou Yang1,5, Xian-Guang Wang2,5, Ben Hu1, Lei Zhang1, Wei Zhang1, Hao-Rui Si1,3, Yan Zhu1, Bei Li1, Chao-Lin Huang2, Hui-Dong Chen2, Jing Chen1,3, Yun Luo1,3, Received: 20 January 2020 Hua Guo1,3, Ren-Di Jiang1,3, Mei-Qin Liu1,3, Ying Chen1,3, Xu-Rui Shen1,3, Xi Wang1,3, Accepted: 29 January 2020 Xiao-Shuang Zheng1,3, Kai Zhao1,3, Quan-Jiao Chen1, Fei Deng1, Lin-Lin Liu4, Bing Yan1, Fa-Xian Zhan4, Yan-Yi Wang1, Geng-Fu Xiao1 & Zheng-Li Shi1 ✉ Published online: 3 February 2020 Open access Since the outbreak of severe acute respiratory syndrome (SARS) 18 years ago, a large Check for updates number of SARS-related coronaviruses (SARSr-CoVs) have been discovered in their natural reservoir host, bats1–4. Previous studies have shown that some bat SARSr-CoVs have the potential to infect humans5–7. Here we report the identifcation and characterization of a new coronavirus (2019-nCoV), which caused an epidemic of acute respiratory syndrome in humans in Wuhan, China. The epidemic, which started on 12 December 2019, had caused 2,794 laboratory-confrmed infections including 80 deaths by 26 January 2020. Full-length genome sequences were obtained from fve patients at an early stage of the outbreak. The sequences are almost identical and share 79.6% sequence identity to SARS-CoV. Furthermore, we show that 2019-nCoV is 96% identical at the whole-genome level to a bat coronavirus. Pairwise protein sequence analysis of seven conserved non-structural proteins domains show that this virus belongs to the species of SARSr-CoV. In addition, 2019-nCoV virus isolated from the bronchoalveolar lavage fuid of a critically ill patient could be neutralized by sera from several patients. Notably, we confrmed that 2019-nCoV uses the same cell entry receptor—angiotensin converting enzyme II (ACE2)—as SARS-CoV. Coronaviruses have caused two large-scale pandemics in the past Samples from seven patients with severe pneumonia (six of whom are two decades, SARS and Middle East respiratory syndrome (MERS)8,9. sellers or deliverymen from the seafood market), who were admitted to It has generally been thought that SARSr-CoV—which is mainly found the intensive care unit of Wuhan Jin Yin-Tan Hospital at the beginning in bats—could cause a future disease outbreak10,11. Here we report of the outbreak, were sent to the laboratory at the Wuhan Institute of on a series of cases caused by an unidentified pneumonia disease Virology (WIV) for the diagnosis of the causative pathogen (Extended outbreak in Wuhan, Hubei province, central China. This disease out- Data Table 1). As a laboratory investigating CoV, we first used pan-CoV break—which started from a local seafood market—has grown sub- PCR primers to test these samples13, given that the outbreak occurred in stantially to infect 2,761 people in China, is associated with 80 deaths winter and in a market—the same environment as SARS infections. We and has led to the infection of 33 people in 10 additional countries found five samples to be PCR-positive for CoVs. One sample (WIV04), as of 26 January 202012. Typical clinical symptoms of these patients collected from the bronchoalveolar lavage fluid (BALF), was analysed by are fever, dry cough, breathing difficulties (dyspnoea), headache metagenomics analysis using next-generation sequencing to identify and pneumonia. Disease onset may result in progressive respiratory potential aetiological agents. Of the 10,038,758 total reads—of which failure owing to alveolar damage (as observed by transverse chest 1,582 total reads were retained after filtering of reads from the human computerized-tomography images) and even death. The disease was genome—1,378 (87.1%) sequences matched the sequence of SARSr- determined to be caused by virus-induced pneumonia by clinicians CoV (Fig. 1a). By de novo assembly and targeted PCR, we obtained a according to clinical symptoms and other criteria, including a rise in 29,891-base-pair CoV genome that shared 79.6% sequence identity body temperature, decreases in the number of lymphocytes and white to SARS-CoV BJ01 (GenBank accession number AY278488.2). High blood cells (although levels of the latter were sometimes normal), new genome coverage was obtained by remapping the total reads to this pulmonary infiltrates on chest radiography and no obvious improve- genome (Extended Data Fig. 1). This sequence has been submitted to ment after treatment with antibiotics for three days. It appears that GISAID (https://www.gisaid.org/) (accession number EPI_ISL_402124). most of the early cases had contact history with the original seafood Following the name given by the World Health Organization (WHO), market; however, the disease has now progressed to be transmitted we tentatively call it novel coronavirus 2019 (2019-nCoV). Four more by human-to-human contact. full-length genome sequences of 2019-nCoV (WIV02, WIV05, WIV06 and 1CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China. 2Wuhan Jin Yin-Tan Hospital, Wuhan, China. 3University of Chinese Academy of Sciences, Beijing, China. 4Hubei Provincial Center for Disease Control and Prevention, Wuhan, China. 5These authors contributed equally: Peng Zhou, Xing-Lou Yang, Xian-Guang Wang. ✉e-mail: [email protected] 270 | Nature | Vol 579 | 12 March 2020 Bat SARSr-CoV WIV16 a d 100 Saccharomyces cerevisiae Bat SARSr-CoV Rs4231 89 killer virus M1, complete genome (52) SARS-CoV SZ3 93 SARS-CoV BJ01 Glypta fumiferanae ichnovirus 100 Bat SARSr-CoV SHC014 segment C9, complete sequence (36) Bat SARSr-CoV WIV1 96 Glypta fumiferanae ichnovirus Bat SARSr-CoV LYRa11 segment C10, complete sequence (36) 99 Bat SARSr-CoV Rs672 99 Bat SARSr-CoV GX2013 Bat SARSr-CoV Rp3 Dulcamara mottle virus, 99 SARSr-CoV (1,378) complete genome (28) Bat SARSr-CoV YNLF31C 100 Bat SARSr-CoV SC2018 Proteus phage VB_PmiS-Isfahan, 100 Bat SARSr-CoV Rf1 complete genome (28) Bat SARSr-CoV SX2013 100 Bat SARSr-CoV HuB2013 Hyposoter fugitivus ichnovirus Bat SARSr-CoV HKU3-1 segment B5, complete sequence (24) 100 Bat SARSr-CoV Longquan-140 V 2019-nCoV BetaCoV/Wuhan/WIV02 100 M 7a 7b 2019-nCoV BetaCoV/Wuhan/WIV07 63 b 2019-nCoV BetaCoV/Wuhan/WIV04 100 ORF1a S3a N 2019-nCoV BetaCoV/Wuhan/WIV06 BetaCo ORF1b 100 E 6 8 100 2019-nCoV BetaCoV/Wuhan/WIV05 100 Bat CoV RaTG13 Bat SARSr-CoV ZXC21 5,000 10,000 15,000 20,000 25,000 30,000 100 Genome nucleotide position 100 Bat SARSr-CoV ZC45 100 Bat SARSr-CoV BM48-31 c Bat Hp BetaCoV Zhejiang2013 100 100 Rousettus bat CoV HKU9 76 Bat CoV GCCDC1 90 92 MHV 100 100 Human CoV OC43 80 Human CoV HKU1 96 Tylonycteris bat CoV HKU4 100 70 Pipistrellus bat CoV HKU5 MERS-CoV PEDV 60 100 100 Scotophilus bat CoV 512 SARS-CoV BJ01 Miniopterus bat CoV 1 100 V 85 50 Bat CoV RaTG13 Miniopterus bat CoV HKU8 Nucleotide identity (%) Bat CoV ZC45 86 86 Human CoV NL63 40 Bat SARSr-CoV WIV1 Human CoV 229E 100 Rhinolophus bat CoV HKU2 Bat SARSr-CoV HKU3-1 AlphaCo 100 Mink CoV TGEV 0 5,000 10,000 15,000 20,000 25,000 30,000 Genome nucleotide position 0.4 Fig. 1 | Genome characterization of 2019-nCoV. a, Metagenomics analysis of nucleotide sequences of complete genomes of coronaviruses. MHV, murine next-generation sequencing of BALF from patient ICU06. b, Genomic hepatitis virus; PEDV, porcine epidemic diarrhoea virus; TGEV, porcine organization of 2019-nCoV WIV04. M, membrane. c, Similarity plot based on transmissible gastroenteritis virus.The scale bars represent 0.1 substitutions the full-length genome sequence of 2019-nCoV WIV04. Full-length genome per nucleotide position. Descriptions of the settings and software that was sequences of SARS-CoV BJ01, bat SARSr-CoV WIV1, bat coronavirus RaTG13 and used are included in the Methods. ZC45 were used as reference sequences. d, Phylogenetic tree based on WIV07) (GISAID accession numbers EPI_ISL_402127–402130) that were identity to all previously described SARSr-CoVs, except for a 93.1% more than 99.9% identical to each other were subsequently obtained nucleotide identity to RaTG13 (Extended Data Table 3). The S genes of from four additional patients using next-generation sequencing and 2019-nCoV and RaTG13 are longer than other SARSr-CoVs. The major PCR (Extended Data Table 2). differences in the sequence of the S gene of 2019-nCoV are the three The virus genome consists of six major open-reading frames (ORFs) short insertions in the N-terminal domain as well as changes in four out that are common to coronaviruses and a number of other accessory of five of the key residues in the receptor-binding motif compared with genes (Fig. 1b). Further analysis indicates that some of the 2019-nCoV the sequence of SARS-CoV (Extended Data Fig. 3). Whether the inser- genes shared less than 80% nucleotide sequence identity to SARS-CoV. tions in the N-terminal domain of the S protein of 2019-nCoV confer However, the amino acid sequences of the seven conserved replicase sialic-acid-binding activity as it does in MERS-CoV needs to be further domains in ORF1ab that were used for CoV species classification were studied. The close phylogenetic relationship to RaTG13 provides evi- 94.4% identical between 2019-nCoV and SARS-CoV, suggesting that dence that 2019-nCoV may have originated in bats. the two viruses belong to the same species, SARSr-CoV. We rapidly developed a qPCR-based detection method on the basis We then found that a short region of RNA-dependent RNA polymerase of the sequence of the receptor-binding domain of the S gene, which (RdRp) from a bat coronavirus (BatCoV RaTG13)—which was previously was the most variable region of the genome (Fig.
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