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Article 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 .
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 × 10⁵). 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.
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| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC11636131 | PMC |
| http://dx.doi.org/10.1016/j.ijregi.2024.100484 | DOI Listing |
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