Dominant Clade-featured SARS-CoV-2 Co-occurring Mutations Reveals Plausible Epistasis: An in silico based Hypothetical Model

Abstract

Background: SARS-CoV-2 is continuously spreading worldwide at an unprecedented scale and evolved into seven clades according to GISAID where four (G, GH, GR and GV) are globally prevalent in 2020. These major predominant clades of SARS-CoV-2 are continuously increasing COVID-19 cases worldwide; however, after an early rise in 2020, the death-case ratio has been decreasing to a plateau. G clade viruses contain four co-occurring mutations in their genome (C241T+C3037T+C14408T: RdRp.P323L+A23403G:spike.D614G). GR, GH, and GV strains are defined by the presence of these four mutations in addition to the clade-featured mutation in GGG28881-28883AAC:N. RG203-204KR, G25563T:ORF3a.Q57H, and C22227T:spike.A222V+C28932T-N.A220V+G29645T, respectively. The research works are broadly focused on the spike protein mutations that have direct roles in receptor binding, antigenicity, thus viral transmission and replication fitness. However, mutations in other proteins might also have effects on viral pathogenicity and transmissibility. How the clade-featured mutations are linked with viral evolution in this pandemic through gearing their fitness and virulence is the main question of this study. Methodology: We thus proposed a hypothetical model, combining a statistical and structural bioinformatics approach, endeavors to explain this infection paradox by describing the epistatic effects of the clade-featured co-occurring mutations on viral fitness and virulence. Results and Discussion: The G and GR/GV clade strains represent a significant positive and negative association, respectively, with the death-case ratio (incidence rate ratio or IRR = 1.03, p <0.001 and IRR= 0.99/0.97, p < 0.001), whereas GH clade strains showed no association with the Docking analysis showed the higher infectiousness of a spike mutant through more favorable binding of G614 with the elastase-2. RdRp mutation p.P323L significantly increased genome-wide mutations (p<0.0001) since more expandable RdRp (mutant)-NSP8 interaction may accelerate replication. Superior RNA stability and structural variation at NSP3:C241T might impact upon protein or RNA interactions. Another silent 5'UTR:C241T mutation might affect translational efficiency and viral packaging. These G-featured co-occurring mutations might increase the viral load, alter immune responses in host and hence can modulate intra-host genomic plasticity. An additional viroporin ORF3a:p.Q57H mutation, forming GH-clade, prevents ion permeability by cysteine (C81)-histidine (H57) inter-transmembrane-domain interaction mediated tighter constriction of the channel pore and possibly reduces viral release and immune response. GR strains, four G clade mutations and N:p.RG203-204KR, would have stabilized RNA interaction by more flexible and hypo-phosphorylated SR-rich region. GV strains seemingly gained the evolutionary advantage of superspreading event through confounder factors; nevertheless, N:p.A220V might affect RNA binding. Conclusion: These hypotheses need further retrospective and prospective studies to understand detailed molecular and evolutionary events featuring the fitness and virulence of SARS-CoV-2.

Demographic Analysis of Mutations in Indian SARS-CoV-2 Isolates

“…Being a non-genic mutation, the C241T mutation does not cause an amino acid change. However, since it is part of the stem-loop region upstream of the ORF1ab gene, it may involve in differential RNA binding affinity to the ribosome and affect translational efficiency of the virus, though no change in the RNA structure was observed for the mutant form [8]. The study by Chaudhari et al [9] analysed the role of C241T mutation in the interaction of the stem-loop region with the host replication factors, MADP1 Zinc finger CCHC-type and RNA-binding motif 1 (hnRNP1).…”

“…Being a non-genic mutation, it does not cause an amino acid change. However, being part of the stem-loop region upstream of the ORF1ab gene, it may involve in differential RNA binding affinity to the ribosome and affect translational efficiency of the virus, though no change in the RNA structure was observed for the mutant form (Alam et al . 2021).…”

“…This mutation is unique to the Indian region (~5% frequency) with no presence globally (Figure 3(a) and 3(b)). It co-occurs with the synonymous mutation, C313T, and is observed in 33 Indian samples: Maharashtra (21), Telangana (8) and Gujarat (4). The first observed sample with this mutation was on 4 th April 2020 in Maharashtra and its presence has also been reported in an earlier study on 90 sequences from western India [18].…”

Evolutionary trajectory of SARS-CoV-2 and emerging variants

“…Clade L dominated the beginning of the pandemic [38], prior to the appearances of clade S and the less defined clade O in early January, 2020 [73,93,96]. Clades V and G appeared in mid-January, followed by clades GH and GR at the end of February, clade GV at the end of June, and clade GRY in September, 2020 [94,97,98] 5), we may see the rise of other variants, selected by mounting population-level immunity and other yet unidentified factors [89,[99][100][101], highlighting the need for international genome surveillance efforts and global data sharing via the established GISAID resource [102].…”