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Genomic Characterisation and Epidemiology of 2019 Novel Coronavirus: Implications for Virus Origins and Receptor Binding

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Genomic Characterisation and Epidemiology of 2019 Novel Coronavirus: Implications for Virus Origins and Receptor Binding Articles Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding Roujian Lu*, Xiang Zhao*, Juan Li*, Peihua Niu*, Bo Yang*, Honglong Wu*, Wenling Wang, Hao Song, Baoying Huang, Na Zhu, Yuhai Bi, Xuejun Ma, Faxian Zhan, Liang Wang, Tao Hu, Hong Zhou, Zhenhong Hu, Weimin Zhou, Li Zhao, Jing Chen, Yao Meng, Ji Wang, Yang Lin, Jianying Yuan, Zhihao Xie, Jinmin Ma, William J Liu, Dayan Wang, Wenbo Xu, Edward C Holmes, George F Gao, Guizhen Wu¶, Weijun Chen¶, Weifeng Shi¶, Wenjie Tan¶ Summary Background In late December, 2019, patients presenting with viral pneumonia due to an unidentified microbial agent Published Online were reported in Wuhan, China. A novel coronavirus was subsequently identified as the causative pathogen, January 29, 2020 provisionally named 2019 novel coronavirus (2019-nCoV). As of Jan 26, 2020, more than 2000 cases of 2019-nCoV https://doi.org/10.1016/ S0140-6736(20)30251-8 infection have been confirmed, most of which involved people living in or visiting Wuhan, and human-to-human *Contributed equally transmission has been confirmed. ¶Contributed equally NHC Key Laboratory of Methods We did next-generation sequencing of samples from bronchoalveolar lavage fluid and cultured isolates from Biosafety, National Institute nine inpatients, eight of whom had visited the Huanan seafood market in Wuhan. Complete and partial 2019-nCoV for Viral Disease Control and genome sequences were obtained from these individuals. Viral contigs were connected using Sanger sequencing to Prevention, Chinese Center for obtain the full-length genomes, with the terminal regions determined by rapid amplification of cDNA ends. Disease Control and Prevention, Beijing, China Phylogenetic analysis of these 2019-nCoV genomes and those of other coronaviruses was used to determine the (Prof R Lu MSc, X Zhao MD, evolutionary history of the virus and help infer its likely origin. Homology modelling was done to explore the likely P Niu PhD, Prof W Wang PhD, receptor-binding properties of the virus. B Huang PhD, N Zhu PhD, Prof X Ma PhD, Prof W Zhou MD, L Zhao PhD, Y Meng PhD, Findings The ten genome sequences of 2019-nCoV obtained from the nine patients were extremely similar, exhibiting J Wang PhD, Prof W J Liu PhD, more than 99·98% sequence identity. Notably, 2019-nCoV was closely related (with 88% identity) to two bat-derived Prof D Wang PhD, Prof W Xu MD, severe acute respiratory syndrome (SARS)-like coronaviruses, bat-SL-CoVZC45 and bat-SL-CoVZXC21, collected Prof G F Gao DPhil, in 2018 in Zhoushan, eastern China, but were more distant from SARS-CoV (about 79%) and MERS-CoV (about 50%). Prof G Wu MD, Prof W Tan MD); Key Laboratory of Etiology and Phylogenetic analysis revealed that 2019-nCoV fell within the subgenus Sarbecovirus of the genus Betacoronavirus, Epidemiology of Emerging with a relatively long branch length to its closest relatives bat-SL-CoVZC45 and bat-SL-CoVZXC21, and was genetically Infectious Diseases in distinct from SARS-CoV. Notably, homology modelling revealed that 2019-nCoV had a similar receptor-binding Universities of Shandong, domain structure to that of SARS-CoV, despite amino acid variation at some key residues. Shandong First Medical University and Shandong Academy of Medical Sciences, Interpretation 2019-nCoV is sufficiently divergent from SARS-CoV to be considered a new human-infecting Tai’an, China (J Li PhD, T Hu MSc, betacoronavirus. Although our phylogenetic analysis suggests that bats might be the original host of this virus, an H Zhou PhD, Prof W Shi PhD); animal sold at the seafood market in Wuhan might represent an intermediate host facilitating the emergence of the Division for Viral Disease Detection, Hubei Provincial virus in humans. Importantly, structural analysis suggests that 2019-nCoV might be able to bind to the angiotensin- Center for Disease Control and converting enzyme 2 receptor in humans. The future evolution, adaptation, and spread of this virus warrant urgent Prevention, Wuhan, China investigation. (B Yang MSc, Prof F Zhan PhD); BGI PathoGenesis Pharmaceutical Technology, Funding National Key Research and Development Program of China, National Major Project for Control and Shenzhen, China (H Wu MSc, Prevention of Infectious Disease in China, Chinese Academy of Sciences, Shandong First Medical University. Y Lin BS, J Yuan MSc, Z Xie BS, J Ma PhD, Prof W Chen PhD); Copyright © 2020 Elsevier Ltd. All rights reserved. Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Introduction Among the several coronaviruses that are pathogenic Chinese Academy of Sciences, Viruses of the family Coronaviridae possess a single- to humans, most are associated with mild clinical Beijing, China (H Song PhD); 1 Chinese Academy of Sciences strand, positive-sense RNA genome ranging from symptoms, with two notable exceptions: severe acute Key Laboratory of Pathogenic 1 26 to 32 kilobases in length. Coronaviruses have been respiratory syndrome (SARS) coronavirus (SARS-CoV), a Microbiology and identified in several avian hosts,2,3 as well as in various novel betacoronavirus that emerged in Guangdong, Immunology, Institute of mammals, including camels, bats, masked palm civets, southern China, in November, 2002,5 and resulted in Microbiology, Chinese Academy of Sciences, Beijing, mice, dogs, and cats. Novel mammalian coronaviruses more than 8000 human infections and 774 deaths in China (Prof Y Bi PhD, 1 6 are now regularly identified. For example, an HKU2- 37 countries during 2002–03; and Middle East respiratory L Wang PhD, Prof G F Gao); related coronavirus of bat origin was responsible for a syndrome (MERS) coronavirus (MERS-CoV), which was Center for Influenza Research fatal acute diarrhoea syndrome in pigs in 2018.4 first detected in Saudi Arabia in 20127 and was responsible and Early-warning (CASCIRE), www.thelancet.com Published online January 29, 2020 https://doi.org/10.1016/S0140-6736(20)30251-8 1 Articles CAS-TWAS Center of Excellence for Emerging Infectious Research in context Diseases (CEEID), Chinese Academy of Sciences, Beijing, Evidence before this study humans and that the outbreak was detected relatively rapidly. China (Prof Y Bi, L Wang, The causal agent of an outbreak of severe pneumonia in 2019-nCoV is most closely related to other betacoronaviruses Prof G F Gao); Central Theater, Wuhan, China, is a novel coronavirus, provisionally named of bat origin, indicating that these animals are the likely People’s Liberation Army 2019 novel coronavirus (2019-nCoV). The first cases were reservoir hosts for this emerging viral pathogen. General Hospital, Wuhan, China reported in December, 2019. (Prof Z Hu MD); Key Laboratory Implications of all the available evidence of Laboratory Medicine, Ministry of Education, Added value of this study By documenting the presence of 2019-nCoV in a sample of and Zhejiang Provincial Key We have described the genomic characteristics of 2019-nCoV patients, our study extends previous evidence that this virus Laboratory of Medical Genetics, and similarities and differences to other coronaviruses, has led to the novel pneumonia that has caused severe disease Institute of Medical Virology, including the virus that caused the severe acute respiratory in Wuhan and other geographical localities. Currently available School of Laboratory Medicine and Life Sciences, Wenzhou syndrome epidemic of 2002–03. Genome sequences of data suggest that 2019-nCoV infected the human population Medical University, Wenzhou, 2019-nCoV sampled from nine patients who were among the from a bat reservoir, although it remains unclear if a currently China (J Chen MSc, Prof W Tan); early cases of this severe infection are almost genetically unknown animal species acted as an intermediate host Marie Bashir Institute for identical, which suggests very recent emergence of this virus in between bats and humans. Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and for 2494 laboratory-confirmed cases of infection and the market between Dec 23 and Dec 27, 2019 (table). School of Medical Sciences, University of Sydney, Sydney, 858 fatalities since September, 2012, including 38 deaths Five of the patients (WH19001, WH19002, WH19004, 8,9 NSW, Australia following a single introduction into South Korea. WH19008, and YS8011) had samples collected by the (Prof E C Holmes PhD); The First In late December, 2019, several patients with viral Chinese Center for Disease Control and Prevention Affiliated Hospital of pneumonia were found to be epidemiologically associ- (CDC) which were tested for 18 viruses and four bac- Shandong First Medical University (Shandong ated with the Huanan seafood market in Wuhan, in the teria using the RespiFinderSmart22 Kit (PathoFinder, Provincial Qianfoshan Hubei province of China, where a number of non-aquatic Maastricht, Netherlands) on the LightCycler 480 Real- Hospital), Jinan, China animals such as birds and rabbits were also on sale Time PCR system (Roche, Rotkreuz, Switzerland). (Prof W Shi); and Center for before the outbreak. A novel, human-infecting corona- Presence of SARS-CoV and MERS-CoV was tested using Biosafety Mega-Science, 10,11 14 Chinese Academy of Sciences, virus, provisionally named 2019 novel coronavirus a previously reported method. All five CDC samples Beijing, China (Prof W Tan) (2019-nCoV), was identified with use of next-generation were negative for all common respiratory pathogens Correspondence to: sequencing. As of Jan 28, 2020, China has reported more screened for. Four of the patients (WH01, WH02, WH03, Prof Wenjie Tan, than 5900 confirmed and more than 9000 suspected and WH04) had samples collected by BGI (Beijing, NHC Key Laboratory of Biosafety, cases of 2019-nCoV infection across 33 Chinese prov- China), and were tested for five viruses and one bacterium National Institute for Viral Disease Control and Prevention, inces or municipalities, with 106 fatalities. In addition, using the RespiPathogen 6 Kit (Jiangsu Macro & Micro Chinese Center for Disease 2019-nCoV has now been reported in Thailand, Japan, Test, Nantong, China) on the Applied Biosystems ABI Control and Prevention, South Korea, Malaysia, Singapore, and the USA.
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