Characterization of SARS-CoV-2 intrahost genetic evolution in vaccinated and non-vaccinated patients from the Kenyan population

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cg.authorship.typesCGIAR and developing country instituteen
cg.authorship.typesCGIAR and advanced research instituteen
cg.contributor.affiliationInternational Livestock Research Instituteen
cg.contributor.affiliationUniversity of Texas Medical Branchen
cg.contributor.affiliationKEMRI-Wellcome Trust Research Programmeen
cg.contributor.affiliationStellenbosch Universityen
cg.contributor.affiliationWashington State Universityen
cg.contributor.affiliationScripps Researchen
cg.contributor.donorRockefeller Foundationen
cg.contributor.donorAfrica Centres for Disease Control and Preventionen
cg.contributor.donorFederal Ministry for Economic Cooperation and Development, Germanyen
cg.contributor.donorCGIAR Trust Funden
cg.contributor.donorNational Institutes of Health, United Statesen
cg.coverage.countryKenya
cg.coverage.iso3166-alpha2KE
cg.coverage.regionAfrica
cg.coverage.regionEastern Africa
cg.creator.identifierDoreen Lugano: 0009-0000-9542-0558en
cg.creator.identifierKennedy Mwangi: 0000-0003-2561-1521en
cg.creator.identifierBenard Mware: 0000-0003-2214-5457en
cg.creator.identifierGilbert Kibet-Rono: 0000-0001-8043-5423en
cg.creator.identifierShebbar Osiany: 0009-0008-4829-0277en
cg.creator.identifierEdward Kiritu: 0000-0003-0513-8300en
cg.creator.identifierPAUL DOBI: 0000-0002-8722-8301en
cg.creator.identifierCollins Muthini Muli: 0000-0003-1775-0468en
cg.creator.identifierRegina Njeru: 0000-0001-9828-2621en
cg.creator.identifierSamuel O. Oyola: 0000-0002-6425-7345en
cg.howPublishedFormally Publisheden
cg.identifier.dataurlhttps://epicov.org/epi3/epi_set/250403bw?main=trueen
cg.identifier.dataurlhttps://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA1256765en
cg.identifier.dataurlhttps://github.com/andrewrouth/ARTIC_ViReMa/tree/mainen
cg.identifier.doihttps://doi.org/10.1128/jvi.00482-25en
cg.isijournalISI Journalen
cg.issn0022-538Xen
cg.journalJournal of Virologyen
cg.reviewStatusPeer Reviewen
cg.subject.ilriCOVID19en
cg.subject.ilriHUMAN HEALTHen
cg.subject.impactAreaNutrition, health and food security
cg.subject.sdgSDG 3 - Good health and well-beingen
dc.contributor.authorLugano, Doreenen
dc.contributor.authorMwangi, Kennedyen
dc.contributor.authorMware, Bernarden
dc.contributor.authorKibet, Gilberten
dc.contributor.authorOsiany, Shebbaren
dc.contributor.authorKiritu, Edwarden
dc.contributor.authorDobi, Paulen
dc.contributor.authorMuli, Collinsen
dc.contributor.authorNjeru, Reginaen
dc.contributor.authorOliveira, T. deen
dc.contributor.authorNjenga, M.K.en
dc.contributor.authorRouth, A.en
dc.contributor.authorOyola, Samuel O.en
dc.contributor.editorSchultz-Cherry, Staceyen
dc.date.accessioned2025-05-08T06:31:11Zen
dc.date.available2025-05-08T06:31:11Zen
dc.identifier.urihttps://hdl.handle.net/10568/174472
dc.titleCharacterization of SARS-CoV-2 intrahost genetic evolution in vaccinated and non-vaccinated patients from the Kenyan populationen
dcterms.abstractVaccination is a key control measure of coronavirus disease 2019 by preventing severe effects of disease outcomes, reducing hospitalization rates and death, and increasing immunity. However, vaccination can affect the evolution and adaptation of SARS-CoV-2 largely through vaccine-induced immune pressure. Here, we investigated intrahost recombination and single nucleotide variations (iSNVs) on the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome in non-vaccinated and vaccinated sequences from the Kenyan population to profile intrahost viral genetic evolution and adaptations driven by vaccine-induced immune pressure. We identified recombination hotspots in the S, N, and ORF1a/b genes and showed the genetic evolution landscape of SARS-CoV-2 by comparing within- and inter-wave recombination events from the beginning of the pandemic (June 2020 to December 2022) in Kenya. We further reveal differential expression of recombinant RNA species between vaccinated and non-vaccinated individuals and perform an in-depth analysis of iSNVs to identify and characterize the functional properties of non-synonymous mutations found in ORF-1 a/b, S, and N genes. Lastly, we detected a minority variant in non-vaccinated patients in Kenya, with an immune escape mutation S255F of the spike gene, and showed differential recombinant RNA species. Overall, this work identified unique in vivo mutations and intrahost recombination patterns in SARS-CoV-2, which could have significant implications for virus evolution, virulence, and immune escape.en
dcterms.accessRightsOpen Access
dcterms.audienceAcademicsen
dcterms.audienceScientistsen
dcterms.available2025-05-06en
dcterms.bibliographicCitationLugano, D., Mwangi, K., Mware, B., Kibet, G., Osiany, S., Kiritu, E., Dobi, P., Muli, C., Njeru, R., Oliveira T. de, Njenga, M.K., Routh, A. and Oyola, S.O. 2025. Characterization of SARS-CoV-2 intrahost genetic evolution in vaccinated and non-vaccinated patients from the Kenyan population. Journal of Virology e00482-25.en
dcterms.extente0048225en
dcterms.issued2025en
dcterms.languageen
dcterms.licenseCC-BY-4.0
dcterms.publisherAmerican Society for Microbiologyen
dcterms.subjectcovid-19en
dcterms.subjecthealthen
dcterms.typeJournal Article

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