Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades.

ABSTRACT

SARS-CoV-2 is currently causing major havoc worldwide with its efficient transmission and propagation. To track the emergence as well as the persistence of mutations during the early stage of the pandemic, a comparative analysis of SARS-CoV-2 whole proteome sequences has been performed by considering manually curated 31,389 whole genome sequences from 84 countries. Among the 7 highly recurring (percentage frequency≥10%) mutations (Nsp2T85I, Nsp6L37F, Nsp12P323L, SpikeD614G, ORF3aQ57H, N proteinR203K and N proteinG204R), N proteinR203K and N protein G204R are co-occurring (dependent) mutations. Nsp12P323L and SpikeD614G often appear simultaneously. The highly recurring SpikeD614G, Nsp12P323L and Nsp6L37F as well as moderately recurring (percentage frequency between ≥1 and <10%) ORF3aG251V and ORF8L84S mutations have led to4 major clades in addition to a clade that lacks high recurring mutations. Further, the occurrence of ORF3aQ57H&Nsp2T85I, ORF3aQ57H and N proteinR203K&G204R along with Nsp12P323L&SpikeD614G has led to 3 additional sub-clades. Similarly, occurrence of Nsp6L37F and ORF3aG251V together has led to the emergence of a sub-clade. Nonetheless, ORF8L84S does not occur along with ORF3aG251V or Nsp6L37F. Intriguingly, ORF3aG251V and ORF8L84S are found to occur independent of Nsp12P323L and SpikeD614G mutations. These clades have evolved during the early stage of the pandemic and have disseminated across several countries. Further, Nsp10 is found to be highly resistant to mutations, thus, it can be exploited for drug/vaccine development and the corresponding gene sequence can be used for the diagnosis. Concisely, the study reports the SARS-CoV-2 antigens diversity across the globe during the early stage of the pandemic and facilitates the understanding of viral evolution.