Pangolin homology associated with 2019-nCoV

Tao Zhang; Qunfu Wu; Zhigang Zhang

High S-protein amino acid identity implies function similarity between Pangolin-Cov and 16 2019-nCoV. 17 To determine the evolutionary relationships among Pangolin-Cov, 2019-nCoV and 18 previously identified coronaviruses, we estimated phylogenetic trees based on the 19 nucleotide sequences of the whole genome sequence, RNA-dependent RNA polymerase 20 . CC-BY-NC-ND 4.0 International license author/funder. It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the . https: //doi.org/10.1101 //doi.org/10. /2020 gene (RdRp), non-structural protein genes ORF1a and 1b, and the main structural proteins 1 encoded by the S and M genes. In all phylogenies, Pangolin-CoV, RaTG13 and 2019-nCoV 2 were clustered into a well-supported group, here named as "SARS-CoV-2 group" ( Figure 3 2 and Figures S1 to S2) . This group represents a novel Beta-coronaviruses group. Within 4 this group, RaTG13 and 2019-nCoV was grouped together, and the Pangolin-CoV was 5 their lowest common ancestor. However, whether the basal position of the SARS-CoV-2 6 group is SARSr-CoV ZXC21 and/or SARSr-CoV ZC45 or not is still in debate. Such 7 debate also occurred in both Wu et al.(3) and Zhou et al. (2) studies. Possible explanation 8 is due to a past history of recombination in Beta-CoV group(3). It is noteworthy that our 9 discovered evolutionary relationships of coronaviruses shown by the whole genome, RdRp 10 gene, and S-gene were highly consistent with that discovered by complete genome 11 information in Zhou et al. study(2) . It indicates our Pangolin-CoV draft genome has enough 12 genomic information to trace true evolutionary position of Pangolin-CoV in coronaviruses. 13 The coronavirus spike (S) protein consisting of 2 subunits (S1 and S2) mediates 14 infection of receptor-expressing host cells and is a critical target for antiviral neutralizing 15 antibodies. S1 contains a receptor binding domain (RBD) about 193 amino acid fragment, 16 which is responsible for recognizing and binding with the cell surface receptor (8, 9) . Zhou 17 et al. had experimentally confirmed that 2019-nCoV is able to use human, Chinese 18 horseshoe bats, civet, and pig ACE2 as an entry receptor in the ACE2-expressing cells(2), 19 suggesting the RBD of 2019-nCoV mediates infection to human and other animals. To gain 20 . CC-BY-NC-ND 4.0 International license author/funder. It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.02.19.950253 doi: bioRxiv preprint a sequence-level insight into understanding pathogen potential of Pangolin-Cov, we 1 investigated the amino acid variation pattern of S1 protein from Pangolin-CoV, 2019-2 nCoV, RaTG13, and other representative SARS-CoVs. The amino acid phylogenetic tree 3 showed the S1 protein of Pangolin-CoV is more closely related to that of 2019-CoV than 4 RaTG13. Within the RBD, we further found Pangolin-CoV and 2019-nCOV was highly 5 conserved with only one amino acid change (500H/500Q) (Figure 3) but not belonging to 6 five key residues involved in the interaction with human ACE2 (2, 9) . In contrast, RaTG13 7 has 17 amino acid residue changes and 4 of them belonged to key amino acid residue 8 (Figure 3) . These results indicate Pangolin-Cov has similar pathogen potential to 2019-9 nCoV. 10 The nucleocapsid protein (N-protein) is the most abundant protein in coronavirus.