SARS-CoV-2 variants in Vietnam: A comprehensive analysis of nucleotide changes in the spike gene

Abstract

SARS-CoV-2, causing the COVID-19 pandemic, has claimed millions of lives worldwide. SARS-CoV-2 has a high mutation rate in its genome, resulting in thousands of variants. The success of SARS-CoV-2 is attributed to a mutation in the S gene, which encodes the spike protein that interacts directly with hACE2. Mutations in this gene are known to increase the transmission rate and the ability to escape the immune system of the virus. This study focused on analyzing the nucleotide changes in the S gene of the SARS-CoV-2 variants that appeared in Vietnam. The results showed that Vietnam recorded many VOC variants, including Alpha, Beta, Delta, and Omicron, with Delta and Omicron being the most prevalent. The S1 region of the S gene had the highest mutation rate, with missense and C to T mutations being the most common. The NTD region contained all deletion and insertion mutations, with the nucleotide at 22198 to 22206 being the hotspot for insertion. The RBD region showed a positive selection during evolution, indicating that it had undergone harsh missense mutation. Overall, this study demonstrates that the S gene in Vietnam has high haplotype and nucleotide diversity. The Omicron variant in Vietnam had the highest nucleotide, haplotype diversity indexes, and average number of mutations in the S gene. These findings provide insights into the genetic diversity of SARS-CoV-2 variants in Vietnam and the impact of the S gene mutations on the evolution of the virus.