Emerging XBB variants in Vietnam show high affinity for hACE2

Since the beginning of 2022, the Omicron variant of the SARS-CoV-2 virus responsible for the COVID-19 pandemic has been the dominant variant. Numerous subvariants of Omicron have been identified, including BA.2.75, BA.4, and BA.5, which are classified as Variants of Concern (VOCs) due to their potential to cause severe illness. Additionally, an emerging variant called XBB has recently caused outbreaks and is believed to be highly lethal. To better understand the XBB variant, we compared the variation in the S protein to that of the other variants. Our initial findings indicate that the XBB variant has spread in Vietnam and carries unique nucleotide changes in the S gene. Specifically, we observed two mutations, G22317T (G252V) and C23123T (P521S), that have resulted in a new subvariant called XBB.1 on the phylogenetic tree. Our analysis also suggests that the XBB variant has a high affinity for hACE2, as indicated by an increase in the interface's number of residues and van der Waals energy. We found that XBB has conserved mutations in RBD that enhance its binding affinity for hACE2. In this report, we noted the mutation V83A, H146Q, and G252V in the NTD increased the binding free energy of the XBB spike protein in the complex with hACE2.