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Updated: Jun 5, 2025

Live Imaging and Quantification of Viral Infection in K18 hACE2 Transgenic Mice Using Reporter-Expressing Recombinant SARS-CoV-2
Published on: November 5, 2021
Genomic epidemiology and immune escape of SARS-CoV-2 recombinant strains circulating in Botswana
Wonderful T Choga1,2, Irene Gobe2, Kedumetse Seru1
1Botswana Harvard Health Partnership, Gaborone, Botswana.
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.
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