Phylogenetic analysis of Omicron subvariants in Vietnam

Abstract

The COVID-19 pandemic is still exposed worldwide and dominated by Omicron and its subvariants. The evolution of Omicron is mainly influenced by protein S mutations encoded by the Spike gene. Therefore, this study aimed to investigate the diversity of the S gene from Omicron isolated in Vietnam, focusing on haplotype and nucleotide levels. A total of 6348 sequences of Omicron originated from Vietnam were collected, aligned to identify the nucleotide variations before being used to build phylogenetic tree. The analysis showed that Omicron in Vietnam had a high level of haplotype diversity, leading to the identification of five subvariants, in which BA.2* and BA.5* were the most prevalent, followed by XBB* variant. Phylogenetic analysis showed close relationships between BA.2* and XBB* based on S gene sequences. The S1 region exhibited the highest genetic variation, characterized by indels and numerous missense mutations in NTD and RBD. Notably, the analysis also showed that transition mutations, including C → T and A → G, as well as reversible changes, were commonly observed. Our study provided valuable insights into the genetic diversity of Omicron variants in Vietnam, emphasizing the significant role of the S gene mutations in the evolution of SARS-CoV-2. Understanding these genetic variations is crucial for efforts to combat the ongoing COVID-19 pandemic.