Abstract: Thousands of individuals are affected every day by the current covid-19 pandemic, which is caused by a novel coronavirus called SARSCoV2. As a result, medicines and vaccines that are effective against all SARSCoV2 subtypes are critical today. Viral genome mutations are prevalent, and they can affect the encoded proteins, resulting in varying levels of detection and illness treatment effectiveness. Despite its clinical relevance, the SARS-CoV-2 gene set remains uncertain, making COVID-19 biology difficult to understand. A single type of mutation in the S gene that was changed the anticodon 614 from aspartic acid to glycine (D614G) consequence in increased virus infection. Herein, we report the gene mutation of structural proteins particularly spike and nucleocapsid proteins in viral genome. The overall prevalence of S and N gene mutations in SARS-CoV-2 were investigated. Among the structural proteins, our findings suggest that nucleocapsid had the highest mutation density, whereas Spike D614G was the most prevalent 93.9 %, found largely in genomes worldwide. These findings indicate that while designing diagnostics tools and therapeutic alternatives, the virus genotype in a certain community should be taken into account.