An immunoinformatics approach to study the epitopes contributed by Nsp13 of SARS-CoV-2

Kumar, Sushant; Azad, Gajendra Kumar

doi:10.1101/2021.04.02.438155

Cited by 1 publication

(1 citation statement)

References 40 publications

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“…Thus, this mutation may lead to a slight change in protein folding. The [114] study also suggests the ability of this mutation to alter the secondary structure of the protein.…”

Section: Non-spike Mutationsmentioning

confidence: 99%

Follow-up investigation and detailed mutational characterization of the SARS-CoV-2 Omicron variant lineages (BA.1, BA.2, BA.3 and BA.1.1)

Abbas

Kusakin

Sharrouf

et al. 2022

Preprint

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Aided by extensive protein mutations, the SARS-CoV-2 Omicron (B.1.1.529) variant overtook the previously dominant Delta variant and rapidly spread around the world. It was shown to exhibit significant resistance to current vaccines and evasion from neutralizing antibodies. It is therefore critical to investigate the Omicron mutations trajectories. In this study, a literature search of published articles and SARS-CoV-2 databases was conducted, We explored the full list of mutations in Omicron BA.1, BA.1.1, BA.2, and BA.3 lineages. We described in detail the prevalence and occurrence of the mutations across variants, and how Omicron differs from them. We used GISAID as our primary data source, which provides open access to genomics data of the SARS-CoV-2 virus, in addition to epidemiological and geographical data. We examined how these mutations interact with each other, their co-occurrence and clustering. Our study offers for the first time a comprehensive description of all mutations with a focus on non-spike mutations and demonstrated that mutations in regions other than the Spike (S) genes are worth investigating further. Our research established that the Omicron variant has retained some mutations reported in other SARS-CoV-2 variants, yet many of its mutations are extremely rare in other variants and unique to Omicron. Some of these mutations have been linked to the transmissibility and immune escape of the virus, and indicate a significant shift in SARS-CoV-2 evolution. The most likely theories for the evolution of the Omicron variant were also discussed.

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“…Thus, this mutation may lead to a slight change in protein folding. The [114] study also suggests the ability of this mutation to alter the secondary structure of the protein.…”

Section: Non-spike Mutationsmentioning

confidence: 99%