Evolution of Delta variant by non-Spike signature co-appearing mutations: trailblazer of COVID-19 disease outcome

Abstract

The high transmissibility and infectivity of a SARS-CoV-2 variant is usually ascribed to the Spike mutations, while emerging non-spike mutations might be a serious threat to the current Spike-recombinant vaccines. In addition to mutations in structural Spike glycoprotein, rapid accumulation of mutations across non-structural genes is leading to continuous virus evolution, altering its pathogenicity. We performed whole genome sequencing of SARS-CoV-2 positive samples collected from different clinical groups from eastern India, during the second pandemic wave (April-May, 2021). In addition to the several common spike mutations in Delta variant, two mutually explicit signature constellations of non-spike co-appearing mutations were identified, driving symptomatic and asymptomatic infections. We attempted to correlate these unique signatures of non-Spike co-appearing mutations to COVID-19 disease outcome. Results revealed that the Delta strains harboring a unique constellation of 9 non-spike co-appearing mutations could be the wheeler and dealer of symptomatic infection, even post vaccination. The strains predominantly driving asymptomatic infection possessed 7 non-spike co-appearing mutations, which were mutually exclusive in contrast to the set of mutations causing symptomatic disease. Phylodynamic analysis depicted high probability of emergence of these unique sub-clusters within India, with subsequent spread worldwide. Interestingly, some mutations of this signature were selected in Omicron and IHU variants, which suggest that gradual accumulation of such co-existing mutations may lead to emergence of more “vaccine-evading variants” in future. Hence, unfaltering genome sequencing and tracking of non-Spike mutations might be significant in formulation of any future vaccines against emerging SARS-CoV-2 variants that might evade the current vaccine-induced immunity.

In-depth genetic characterization of the SARS-CoV-2 pandemic in a two-year frame in North Macedonia using second and third generation sequencing technologies

“…Predicting the success of these novel mutations in the population might be possible by tracing their interactions with the genetic background in which they appear. The only characterized breakthrough infection belonged to haplotype 2C_2 and it harbored a signature set of 7 co-appearing mutations and the same set of mutations was found in a small number of samples from India and Europe (Denmark) (53). Even though we had only one breakthrough infection in our study, we suspect that the real number has probably been higher.…”

“…All cases belonging to the haplotype 2C_1 were hospitalized for at least three weeks, due to the severity of their condition and all had oxygen requirement, but none was put on mechanical ventilation. Significant variations across the ORF1ab, N region and the S protein caused the divergence of this haplotype from the prototype 21A Delta, which might be a consequence of selection pressure due to growing vaccination rates (53). One of the signature mutations of the haplotype 2C_1, S:A222V, emerged first in 2020 in the B.1.177 lineage.…”

“…A SARS-CoV-2 variant's high transmissibility and infectivity are typically attributed to spike protein alterations, while the rapid accumulation of mutations across non-structural genes is causing the virus to continuously evolve and change in pathogenicity (53). By grouping the mutations into haplotypes, we attempted to find an association with a signature set of both spike and non-spike constellation substitutions with the clinical manifestation of the disease.…”

SARS-CoV-2 VOCs, Mutational diversity and clinical outcome: Are they modulating drug efficacy by altered binding strength?

“…Contrarily, we observed a greater percentage of significant mutations in the Spike (5) followed by mutations in the Nucleocapsid (2), 3’UTR (2), 5’UTR (1), and the ORF1ab (1) genes in the Omicron patients. Furthermore, we found the co-presence of five mutations (P309L in NSP2, P1640L in NSP3, A3209V in NSP4, V3718A in NSP6, and R385K in the N gene) in the Delta mortality patients, which has been recently reported to be more prevalent in the symptomatic patients than the asymptomatic ones [ 4 ]. On the other hand, three co-occurring mutations, G142D in the Spike, P2287S in the Nsp3 and T3255I in the Nsp4 region of the ORF1ab were observed in the Delta recovered patients, which has been previously reported for their correlation with milder infectious cases of SARS-CoV-2 [ 38 ].…”

Unraveling the genetic evolution of SARS-CoV-2 Recombinants using mutational dynamics across the different lineages

“…Notably, these progressively increasing mutations were long accumulating mutations since majority of them were present in low frequency in Pre-VOC and substantially resurfaced in the Omicron and Recombinants. Mutations, such as ORF1ab: T3255I, are reported to be responsible for symptomatic disease outcome and changed interactome toward avoidance of antiviral response, improving viral spread and infectivity as seen in the Omicron ( 68 ), while ORF3a: T223I, ORF1a: P3395H and ORF1ab: I5967V were retained till BA.2 and BA.3, but the functional significance of such mutations are still unknown ( 69 , 70 ).…”