Probable Pangolin Origin of 2019-nCoV Associated with Outbreak of COVID-19

Abstract

In the late December of 2019, an epidemic pneumonia (announced recently as Corona Virus Disease (COVID-19)) outbreak in city of Wuhan in China and widely spreads all over the world. According to authoritative statistics, the COVID-19 has caused more than 40,000 laboratory-confirmed infections with more than 1000 deaths by 12 February 2020 and is still increasing. It was caused by a novel identified coronavirus 2019-nCoV (renamed this virus as severe acute respiratory syndrome coronavirus 2, SARS-CoV-2). Released complete genomes of 2019-nCoVs have helped rapid identification and diagnosis of the COVID-19. Currently, it is another key task to explore potential intermediate host of SARS-CoV-2, which is vital to control COVID-19 spread. To this end, we re-investigated published data from pangolin lung samples from which SARS-like coronaviruses were detected by Liu et. By both deep assembly and multiple phylogenetic analyses, we found genomic and evolutionary evidences of the occurrence of 2019-nCoV-like coronavirus (named as Pangolin-CoV) from dead Malayan Pangolins. Pangolin-CoV is 91.02% and 90.55% identical at the whole genome level to 2019-nCoV and BatCoV RaTG13, respectively. Pangolin-CoV is the lowest common ancestor of 2019-nCoV and RaTG13. The S1 protein of Pangolin-CoV is much more closely related to 2019-nCoV than RaTG13. Five key amino-acid residues involved in the interaction with human ACE2 are completely consistent between Pangolin-CoV and 2019-nCoV but four amino-acid mutations occur in RaTG13. It indicates Pangolin-CoV has similar pathogenic potential to 2019-nCoV, which would be helpful to trace the origin and probable intermediate host of 2019-nCoV.

Keywords: Pangolin, 2019-nCoV, COVID-19, Origin