New Pathways of Mutational Change in SARS-CoV-2 Proteomes Involve Regions of Intrinsic Disorder Important for Virus Replication and Release

Abstract

The massive worldwide spread of the SARS-CoV-2 virus is fueling the COVID-19 pandemic. Since the first whole-genome sequence was published in January 2020, a growing database of tens of thousands of viral genomes has been constructed. This offers opportunities to study pathways of molecular change in the expanding viral population that can help identify molecular culprits of virulence and virus spread. Here we investigate the genomic accumulation of mutations at various time points of the early pandemic to identify changes in mutationally highly active genomic regions that are occurring worldwide. We used the Wuhan NC_045512.2 sequence as a reference and sampled 15,342 indexed sequences from GISAID, translating them into proteins and grouping them by month of deposition. The per-position amino acid frequencies and Shannon entropies of the coding sequences were calculated for each month, and a map of intrinsic disorder regions and binding sites was generated. The analysis revealed dominant variants, most of which were located in loop regions and on the surface of the proteins. Mutation entropy decreased between March and April of 2020 after steady increases at several sites, including the D614G mutation site of the spike (S) protein that was previously found associated with higher case fatality rates and at sites of the NSP 12 polymerase and the NSP13 helicase proteins. Notable expanding mutations include R203K and G204R of the nucleocapsid (N) protein inter-domain linker region and G251V of the viroporin encoded by ORF3a between March and April. The regions spanning these mutations exhibited significant intrinsic disorder, which was enhanced and decreased by the N-protein and viroporin 3a protein mutations, respectively. These results predict an ongoing mutational shift from the spike and replication complex to other regions, especially to encoded molecules known to represent major beta-interferon antagonists. The study provides valuable information for therapeutics and vaccine design, as well as insight into mutation tendencies that could facilitate preventive control.

The seasonal behaviour of COVID-19 and its galectin-like culprit of the viral spike

“…During a pandemic, the evolving viral quasispecies will develop protein ‘variants’ with sets of co-occurring amino acid changes that will strive to survive the environmental challenges imposed by weather or geographic location. One proposed mechanism is protection of integrity of the viral envelope ( Minhaz Ud-Dean, 2010 ), which could be accomplished by favouring mutations in protein regions of intrinsic disorder ( Tomaszewski et al, 2020 ). Following a selective sweep, mutations take over the quasispecies population in search for new cycles of better variant proteins.…”

Evolutionary trajectory of SARS-CoV-2 and emerging variants

“…Positively selected for residues within SARS-CoV-2 Nsp6 [74,[123][124][125][126] are intriguing since Nsp6 is relatively conserved in other coronaviruses [126] (Fig. 2, Table 2).…”

“…Another mutation of interest (L84S) lies within ORF8 [123,124,135], a protein implicated in evasion of host immune responses [136,137] (Table 4). ORF8 was under strong directional selection at the beginning of both SARS-CoV-2 [124] and SARS-CoV outbreaks [138], supporting the theory that it facilitates zoonotic transmission and adaptation in alternate hosts [139,140].…”

“…Sites are indicated as nucleotide (nt) position or amino acid (aa) position. Empty cells in the table represent lack of evidence for positive selection or lack of publications on positive selection within these regions clade GR [123]. RG203KR alters N protein morphology, resulting in increased intraviral protein binding affinity [132].…”

Emerging SARS-CoV-2 Variants: A Review of Its Mutations, Its Implications and Vaccine Efficacy

“…It is also involved in inflammation as it interacts with the inflammasome complex. Mutation F206F affects the fitness of the virus and is a part of G glade (four mutations—NSP12, 5′ UTR, D614G of Spike, and NSP3) that originated in China [ 40 ]. The S1197R and T1198K mutations in the NSP3 protein have been related to increased severity of infection [ 41 ].…”