Genetic profile of Omicron subvariants in Vietnam by May 2024: The emergence of JN.1

SARS-CoV-2 Omicron and its subvariants continue to significantly impact global infection and mortality rates. Omicron is characterized by its rapid transmissibility and its ability to evade immune defenses and neutralizing antibodies. The widespread prevalence of Omicron and its subvariants is attributed to mutations within the spike (S) gene. This study update the status of the nucleotide changes and genetic diversity of Omicron in Vietnam. Our analysis recorded new Omicron variants, including BA.2.86 and its descendant: BA.2.86.1; JN.1 and its descendants: JN.1.20, JN.1.4, JN.1.4.5, JN.1.11, and JN.1.16 since December of 2023. These newly found variants formed a separated group in the haplotype network. Our analysis identified five Omicron subvariants isolated in Vietnam: BA.1*, BA.2*, BA.4*, BA.5*, and XBB*. Among these, BA.2* exhibited the highest frequency and haplotype diversity index. We observed that mutations in the S gene predominantly occur in the S1 region, while the S2 region remains relatively conserved across Omicron subvariants.

This study provides a comprehensive analysis of the nucleotide alterations and genetic diversity of Omicron in Vietnam, confirming the critical role of the S gene in the evolution and control of SARS-CoV-2.