Mutation Profile Analysis of 3,252 SARS-CoV-2 Genomes from January to Early May 2025: Evidence of High Diversity and Limited Convergent Evolution in NSP7, NSP8, NSP12, and NSP14

This study presents a mutation profile analysis of 3,252 SARS-CoV-2 genomes collected between January and early May 2025 , focusing on non-structural proteins (NSP7, NSP8, NSP12, and NSP14).It is suggested that there is high diversity, low convergence which suggests ongoing evolutionary process with no fixed substitutions in key replicase components (nsp7, nsp8, nsp12, nsp14) as of early May 2025.After rigorous alignment, filtering, and quality control steps, sequences were reduced due to gaps, misalignment, or incomplete coverage. No recurrent mutations were identified at standard thresholds (≥1% frequency), suggesting high genomic diversity and limited convergent evolution during this period.QC check was set to 90%This analysis began with 3,252 SARS-CoV-2 genome accessions downloaded from NCBI, covering samples collected between January and early May 2025. Following alignment using MAFFT and extensive quality control to remove duplicates, incomplete sequences, and misaligned entries, the dataset was reduced to 2,731 high-quality sequences . Mutation matrices were generated for four key non-structural protein regions: nsp7, nsp8, nsp12, and nsp14 . Despite lowering mutation frequency thresholds down to 0.1%, no recurrent mutations were identified across these genes that indicate a high degree of genetic diversity and limited evidence of convergent evolution during this time window.The results highlight the importance of careful sequence curation when analyzing public NCBI surveillance data. Most observed changes were rare or private, indicating an evolving population without dominant variants emerging by early May 2025.All mutation matrices are provided for reproducibility.