Background: Natural selection such as
mutations is known as a constant process for viral fitness and selective adaptation. Understanding the effects of each mutation, especially on structural proteins in the viral life cycle, is important in tracking the viruses behavior. Here, we evaluated the effects of
mutations in
SARS-CoV-۲ nucleoprotein (N) and
spike (S) genes on the protein stability, immunogenicity, and pathogenicity in Iranian
COVID-۱۹ patients from Golestan province. Methods: In this study, ۸
SARS-CoV-۲ RNA samples were enrolled from referral hospitals in Golestan province. These samples were confirmed using a real-time RT-PCR assay targeting the
SARS-CoV-۲ nucleoprotein (N) and ORF۱ab genes (Pishtazteb, Iran). Next-generation sequencing (NGS) was done on samples and subsequent sequences were retrieved from Global Initiative on Sharing All Influenza Data (GISAID) EpiCoV database. Structural analysis was performed between wild type (Wuhan accession number: NC_۰۴۵۵۱۲.۲) and mutant N and S proteins to evaluate their stability, immunogenicity, and pathogenicity via bioinformatics servers such as Dynamut, Prodigy, IEDB, and software’s (Mega XI and Pymol II.V.II visualizer). Results: Amino acid codon changes in N and S proteins show that
mutations could alter the translation efficiency. Normal Mode Analysis (NMA) by Dynamut server shows that stability and flexibility are changed by the
mutations of these proteins. Immunogenicity analysis indicates the potential effects of some
mutations such as P۶۸۱H, Q۶۷۵R, L۶۹۹I, and D۳L on immune escape. Interaction complex binding energy and affinity are higher in the mutant type compared to the Wuhan wild type, indicating higher pathogenicity. Conclusion: The results indicate that there are some important
mutations in N and S genes that affect the virus behavior in the infectivity. Regarding the sample size limitation and various
mutations in
SARS-CoV-۲ variants, other studies using whole-genome sequencing with larger sample sizes will be required. Therefore, continuous monitoring of the
SARS-CoV-۲ genome seems important.