An update on the origin of SARS-CoV-2: Despite closest identity, bat (RaTG13) and pangolin derived coronaviruses varied in the critical binding site and O-linked glycan residues

Abstract

The initial cases of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) occurred in Wuhan, China, in December 2019 and swept the world by 23 June 2020 with 8 993 659 active cases, 469 587 deaths across 216 countries, areas or territories. This strongly implies global transmission occurred before the lockdown of China. However, the initial source's transmission routes of SARS-CoV-2 remain obscure and controversial. Research data suggest bat (RaTG13) and pangolin carried CoV were the proximal source of SARS-CoV-2. In this study, we used systematic phylogenetic analysis of Coronavirinae subfamily along with wild type human SARS-CoV, MERS-CoV, and SARS-CoV-2 strains. The key residues of the receptor-binding domain (RBD) and O-linked glycan were compared. SARS-CoV-2 strains were clustered with RaTG13 (97.41% identity), Pangolin-CoV (92.22% identity) and Bat-SL-CoV (80.36% identity), forms a new clade-2 in lineage B of beta-CoV. The alignments of RBD contact residues to ACE2 justified? Those SARS-CoV-2 strains sequences were 100% identical by each other, significantly varied in RaTG13 and pangolin-CoV. SARS-CoV-2 has a polybasic cleavage site with an inserted sequence of PRRA compared to RaTG13 and only PRR to pangolin. Only serine (Ser) in pangolin and both threonine (Thr) and serine (Ser) O-linked glycans were seen in RaTG13, suggesting that a detailed study needed in pangolin (Manis javanica) and bat (Rhinolophus affinis) related CoV.

Keywords: COVID-19; RaTg13; SARS-CoV-2; intermediate host; pangolins.

Figure 1

Phylogenetic analysis of S protein of SARS‐CoV‐2 strains and representative viruses of the Coronavirinae subfamily. Countrywide first reported SARS‐CoV‐2 isolates were closely clustered to RaTG13 (97.41% identity), pangolins‐CoV (92.22% identity), and bat‐SL‐CoV (80.36% identity) forms a new clade 2 in lineage B of β CoV. SARS‐CoV‐2, severe acute respiratory syndrome coronavirus‐2

Figure 2

Features of the spike protein in human SARS‐CoV‐2, RaTG13 and pangolin‐CoV. A, Mutations in contact residues of the SARS‐CoV‐2 S protein. Key residues in the spike protein that make contact to the ACE2 receptor are marked with yellow in both SARS‐CoV‐2 and related viruses. B, Acquisition of polybasic cleavage site (Red) and O‐linked glycans (yellow). SARS‐CoV‐2, severe acute respiratory syndrome coronavirus‐2