Genomic epidemiology and immune escape of SARS-CoV-2 recombinant strains circulating in Botswana

Abstract

OBJECTIVES : We characterized the molecular and mutational landscape of SARS-CoV-2 recombinant strains in Botswana. METHODS : We performed genomic, phylogenetic, and immunoinformatic analyses of 5254 near-complete genomes from 2020 to 2023. We assessed the presence of mutations of interested (MutOI) that may be associated with immune escape in silico . RESULTS : We observed a few recombinant strains in Botswana, with the majority being descendants of Omicron (XBB∗ ), except for XV and XM. Most recombinant sequences corresponded to transmission clusters. Most recombination events occurred within the receptor-binding domain (RDB) of the spike (S) protein. We identified 16 MutOI among different proteins, with the majority occurring at a very low global prevalence ( < 4.8 ×10− 5). We also observed S:Q474K, a MutOI in the RBD, that was predicted to escape human leukocyte antigen class I–mediated immune responses. Molecular surveillance is vital to inform early detection and response to potential variants with heightened immune and vaccine breakthrough properties. CONCLUSIONS : These results underscore the need for continued molecular surveillance to map the evolutionary landscape of SARS-CoV-2.