A pneumonia outbreak associated with a new coronavirus of probable bat origin
Authors: Xing-Lou Yang
Bei Li
Kai Zhao
Ying Chen
Yun Luo
Lin-Lin Liu
Ren-Di Jiang
Yan-Yi Wang
Xiao-Shuang Zheng
Fei Deng
Bing Yan
Fa-Xian Zhan
Hua Guo
Quan-Jiao Chen
Ben Hu
Hao-Rui Si
Yan Zhu
Xu-Rui Shen
Wei Zhang
Jing Chen
Chao-Lin Huang
Hui-Dong Chen
Geng-Fu Xiao
Xian-Guang Wang
Xi Wang
Peng Zhou
Lei Zhang
Zheng-Li Shi
Mei-Qin Liu
Journal: Nature (2020)
Discipline: Multidisciplinary
Keywords: SARS; coronavirus; 2019-nCoV; epidemic; Wuhan
Affiliations: CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China., Wuhan Jin Yin-Tan Hospital, Wuhan, China., University of Chinese Academy of Sciences, Beijing, China., Hubei Provincial Center for Disease Control and Prevention, Wuhan, China., CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China. .

Abstract:  Since the outbreak of severe acute respiratory syndrome (SARS) 18 years ago, a large 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 identification 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-confirmed infections including 80 deaths by 26 January 2020. Full-length genome sequences were obtained from five 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 fluid of a critically ill patient could be neutralized by sera from several patients. Notably, we confirmed that 2019-nCoV uses the same cell entry receptor-angiotensin converting enzyme II (ACE2)-as SARS-CoV. 

Retracted: No

PubPeer comments:
 The authors state that a short region of RdRp from a bat coronavirus (BatCoV RaTG13)u2014which was previously detected in Rhinolophus affinis from Yunnan provinceu2014showed high sequence identity to 2019-nCoV ( SARS-CoV-2). Another paper published at the same time reported 98.7% nucleotide identity of 2019-nCoV with BtCoV 4991 (GenBank KP876546, only 370 nt sequence of RdRp gene) [[Chen L 2020 Emerging Microbes Infections] ]. I wonder if BtCov 4991 could be the origin of SARS-CoV-2 instead? As BtCov 4991 was reported by the authors of this paper previously [[Ge XY 2016 Virol Sin] ], are these viruses the same or it is just a sample mislabeling? , 
 https: www.preprints.org manuscript 202006.0044 v1 *Abstract* A recent manuscript (Zhou, P. et al. u201cA pneumonia outbreak associated with a new coronavirus of probable bat originu201d, Nature 579, 270u2013273 (2020). https: doi.org 10.1038 s41586-020- 2012-7) from Wuhan Institute of Virology claimed the identification of a bat coronavirus, RaTG13, which showed 96.2% genome homology with SARS-CoV-2. In this paper, we raise the puzzling observations surrounding the identification, characterization, unique genome features of this RaTG13 strain, as well as its 100% nucleotide identity in partial RdRp gene with another bat coronavirus strain BtCoV 4991. And the paper presented premature hypothesis of potential bat origin of SARS-CoV-2 while RaTG13 strain was not successfully isolated. We also present the concerns on the methodology, data quality and experiment procedures described in this paper. We call for the authors to provide additional data, to share related samples to be verified and further characterized by other scientists. , 
 https: www.minervanett.no alina-chan-coronavirus-covid19 contradicting-statements-cast-doubts-on-chinese-raw-data 364540 , 
 I am happy to see the answer to my question through an [addendum] . The authors claim that BtCov 4991 (KP876546) and RaTG13 (MN996532) are the same. The next step might be to update the NCBI record to show that both are equivalent. ,