Molecular evolution and adaptation of SARS-CoV-2 omicron XBB sub-lineage Spike protein under African Selection pressure.

The Omicron variant of SARS-CoV-2, which is a cause of concern, has various mutations in its spike protein. This protein is responsible for both viral infection and immunity. We have analyzed a particular sub-lineage of Omicron, designated XBB, which has undergone structural and functional changes in its spike protein as a response to the African selection pressures. Using molecular modeling, we compared the S protein structures of Omicron and XBB and discovered that XBB has a reduced receptor-binding domain (RBD) because of the loss of some β-sheets. This change may result in an increased affinity of XBB towards the human angiotensin-converting enzyme 2 (hACE2) receptor. We also conducted selection and recombination analysis of the S protein sequences of Omicron and XBB using Fast Unconstrained Bayesian Approximation (FUBAR) and Recombination Detection Program 4 (RDP 4). Our analysis detected signals of positive selection and recombination in the N-terminal domain (NTD) of the S1 subunit, which contains antibody-binding epitopes, and the RBD, which is involved in viral entry. Our findings reveal the structural and functional adaptation of the Omicron XBB variant in Africa and its potential implications for viral pathogenesis and immunity.