Genomic Insights into SARS-CoV-2 Evolution: Nucleocapsid Gene Mutations in West Sumatra, Indonesia

Abstract

The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic has necessitated a comprehensive understanding of viral mutations, particularly in the nucleocapsid protein, which plays a crucial role in the virus's life cycle and interaction with the host immune system. This study aims to analyze the nucleocapsid (N) gene mutations in SARS-CoV-2 variants isolated from West Sumatra during the pandemic. A dataset of 352 SARS-CoV-2 sequences from local COVID-19 cases was examined to identify N gene mutations and assess their prevalence across different variants. The primary mutations identified were R203K and G204R in the ancestral and Omicron variants. However, the D63G and D377Y mutation is present in the Delta variant. These mutations are implicated in enhancing viral infectivity and potential immune evasion. Notably, the Omicron variant showed additional deletions and mutations (P13L, E31-, R32-, S33-, and S413R) that harm protein expansion for structural stability and functionality of the nucleocapsid protein. The conservation of specific mutations across variants suggests their fundamental role in viral replication and immune interaction. Variant-specific mutations may represent adaptive responses to immune pressure or other environmental factors, with significant implications for viral transmissibility and pathogenicity. Understanding the impact of nucleocapsid protein mutations provides critical insights into the evolutionary dynamics of SARS-CoV-2 and aids in developing effective vaccines and therapeutics. Continued surveillance and detailed functional studies are essential to manage the pandemic and prepare for future viral outbreaks. Keywords: SARS-CoV-2, nucleocapsid protein, N gene, mutations, viral evolution.