SARS-CoV-2 NSP14 governs mutational instability and assists in making new SARS-CoV-2 variants

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the rapidly evolving RNA virus behind the COVID-19 pandemic, has spawned numerous variants since its 2019 emergence. The multifunctional Nonstructural protein 14 (NSP14) enzyme, possessing exonuclease and messenger RNA (mRNA) capping capabilities, serves as a key player. Notably, single and co-occurring mutations within NSP14 significantly influence replication fidelity and drive variant diversification. This study comprehensively examines 120 co-mutations, 68 unique mutations, and 160 conserved residues across NSP14 homologs, shedding light on their implications for phylogenetic patterns, pathogenicity, and residue interactions. Quantitative physicochemical analysis categorizes 3953 NSP14 variants into three clusters, revealing genetic diversity. This research underscoresthe dynamic nature of SARS-CoV-2 evolution, primarily governed by NSP14 mutations. Understanding these genetic dynamics provides valuable insights for therapeutic and vaccine development. •NSP14 Mutations Drive SARS-CoV-2 Variant Evolution: The study reveals that the Nonstructural protein 14 (NSP14) enzyme, with its exonuclease and mRNA capping capabilities, is a key player in driving the mutational instability of SARS-CoV-2. Single and co-occurring mutations within NSP14 significantly influence replication fidelity, contributing to the emergence of diverse SARS-CoV-2 variants.•Genetic Diversity in NSP14 Variants: A comprehensive analysis of 3953 NSP14 variants categorizes them into three clusters, highlighting substantial genetic diversity.•Mutation and co-mutations in NSP14 variants:The research identifies 120 co-mutations, 68 unique mutations, and 160 conserved residues across NSP14 homologs, shedding light on their implications for phylogenetic patterns, pathogenicity, and residue interactions.•Functional Significance of NSP14 Domains: The study emphasizes the critical roles of the two distinct domains of NSP14—the proofreading ExoN domain and the N7-MTase domain responsible for RNA capping. Mutations in key residues, particularly in the ExoN domain, can significantly impact viral replication, highlighting these regions as potential drug targets for therapeutic interventions.•Balance of Deleterious and Neutral Mutations: Analysis of NSP14 sequences reveals a balance between 548 neutral mutations and 414 deleterious mutations. The interplay between these mutations is crucial for viral fitness and adaptation, with deleterious