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

Autor:	Choga WT; Botswana Harvard Health Partnership, Gaborone, Botswana.; School of Allied Health Sciences, Faculty of Health Sciences, Gaborone, Botswana., Gobe I; School of Allied Health Sciences, Faculty of Health Sciences, Gaborone, Botswana., Seru K; Botswana Harvard Health Partnership, Gaborone, Botswana., Maruapula D; Botswana Harvard Health Partnership, Gaborone, Botswana., Ndlovu NS; Botswana Harvard Health Partnership, Gaborone, Botswana., Zuze BJL; Botswana Harvard Health Partnership, Gaborone, Botswana., Motshosi P; Botswana Harvard Health Partnership, Gaborone, Botswana., Matsuru T; Botswana Harvard Health Partnership, Gaborone, Botswana., Sabone P; Botswana Harvard Health Partnership, Gaborone, Botswana., Yu X; Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, Scotland, UK., Blackard JT; University of Cincinnati College of Medicine, Cincinnati, USA., San JE; Duke Human Vaccine Institute (DHVI), Durham, USA.; University of KwaZulu-Natal (UKZN), Durban, South Africa., Makhema J; Botswana Harvard Health Partnership, Gaborone, Botswana., Gaseitsiwe S; Botswana Harvard Health Partnership, Gaborone, Botswana.; Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, Scotland, UK., Moyo S; Botswana Harvard Health Partnership, Gaborone, Botswana.; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, USA.; School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa.; Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa.
Jazyk:	angličtina
Zdroj:	IJID regions [IJID Reg] 2024 Nov 02; Vol. 13, pp. 100484. Date of Electronic Publication: 2024 Nov 02 (Print Publication: 2024).
DOI:	10.1016/j.ijregi.2024.100484
Abstrakt:	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. Competing Interests: The authors declare no conflicts of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript; or in the decision to publish the results. (© 2024 The Author(s).)
Databáze:	MEDLINE
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