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Grant","doi-asserted-by":"publisher","award":["23\/58"],"award-info":[{"award-number":["23\/58"]}],"id":[{"id":"10.13039\/501100001323","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>While a global downward trend in rotavirus diarrhea cases has been observed following vaccine introduction, reassortment, genetic drift, and vaccine-escaping strains remain a concern, particularly in Sub-Saharan Africa. Here, we provide genomic insights into three equine-like G3P[8] rotavirus strains detected in Benin during the post-vaccine era. Whole-genome sequencing was performed using the Illumina MiSeq platform, and genomic analysis was conducted using bioinformatics tools. The G3 of the study strains clustered within the recently described lineage IX, alongside the human-derived equine-like strain D388. The P[8] is grouped within the lineage III, along with cognate strains from the GenBank database. Both the structural and non-structural gene segments of these study strains exhibited genetic diversity, highlighting the ongoing evolution of circulating strains. Notably, we identified a novel NSP2 lineage, designated NSP2-lineage VI. Amino acid comparisons of the G3 gene showed two conservative substitutions at positions 156 (A156V) and 260 (I260V) and one radical substitution at position 250 (K250E) relative to the prototype equine-like strain D388, the equine strain Erv105, and other non-equine-like strains. In the P[8] gene, three conservative (N195G, N195D, N113D) and one radical (D133N) substitutions were observed when compared with vaccine strains Rotarix and RotaTeq. These findings suggest continuous viral evolution, potentially driven by vaccine pressure. Ongoing genomic surveillance is essential to monitor genotype shifts as part of the efforts to evaluate the impact of emerging strains and to assess vaccine effectiveness in Sub-Saharan Africa.<\/jats:p>","DOI":"10.3390\/v17081091","type":"journal-article","created":{"date-parts":[[2025,8,8]],"date-time":"2025-08-08T08:09:35Z","timestamp":1754640575000},"page":"1091","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Unveiling a Shift in the Rotavirus Strains in Benin: Emergence of Reassortment Intergenogroup and Equine-like G3P[8] Strains in the Post-Vaccination Era"],"prefix":"10.3390","volume":"17","author":[{"given":"Jijoho M.","family":"Agbla","sequence":"first","affiliation":[{"name":"National Public Health Laboratory, Ministry of Public Health, Cotonou 01 P.O. Box 418, Benin"},{"name":"Next Generation Sequencing Unit, School of Biomedical Sciences, Faculty of Health Sciences, Bloemfontein 9300, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Milton T.","family":"Mogotsi","sequence":"additional","affiliation":[{"name":"Next Generation Sequencing Unit, School of Biomedical Sciences, Faculty of Health Sciences, Bloemfontein 9300, South Africa"},{"name":"Division of Virology, School of Pathology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alban G.","family":"Zohoun","sequence":"additional","affiliation":[{"name":"National Public Health Laboratory, Ministry of Public Health, Cotonou 01 P.O. Box 418, Benin"},{"name":"Faculty of Health Sciences, University of Abomey-Calavi, Cotonou 01 P.O. Box 526, Benin"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8967-3820","authenticated-orcid":false,"given":"Nkosazana D.","family":"Shange","sequence":"additional","affiliation":[{"name":"Next Generation Sequencing Unit, School of Biomedical Sciences, Faculty of Health Sciences, Bloemfontein 9300, South Africa"},{"name":"Division of Virology, School of Pathology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Annick","family":"Capochichi","sequence":"additional","affiliation":[{"name":"Centre Hospitalier Universitaire de Zone (CHUZ)\u2014Suru L\u00e9r\u00e9 Hospital, Ministry of Public Health, Cotonou 01 P.O. Box 418, Benin"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ayodeji E.","family":"Ogunbayo","sequence":"additional","affiliation":[{"name":"Next Generation Sequencing Unit, School of Biomedical Sciences, Faculty of Health Sciences, Bloemfontein 9300, South Africa"},{"name":"Division of Virology, School of Pathology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rolande","family":"Assogba","sequence":"additional","affiliation":[{"name":"National Public Health Laboratory, Ministry of Public Health, Cotonou 01 P.O. Box 418, Benin"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9831-9081","authenticated-orcid":false,"given":"Shainey","family":"Khakha","sequence":"additional","affiliation":[{"name":"Wellcome Trust Research Laboratory, Christian Medical College and Hospital Vellore, Tamil Nadu 632004, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aristide","family":"Sossou","sequence":"additional","affiliation":[{"name":"World Health Organization-Benin (WCO-Benin), Cotonou 01 P.O. Box 918, Benin"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hlengiwe","family":"Sondlane","sequence":"additional","affiliation":[{"name":"Next Generation Sequencing Unit, School of Biomedical Sciences, Faculty of Health Sciences, Bloemfontein 9300, South Africa"},{"name":"Division of Virology, School of Pathology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jason M.","family":"Mwenda","sequence":"additional","affiliation":[{"name":"Diarrhea Pathogens Research Unit, Department of Virology, Sefako Makgatho Health Sciences University, Pretoria 0208, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4069-947X","authenticated-orcid":false,"given":"Mathew D.","family":"Esona","sequence":"additional","affiliation":[{"name":"Diarrhea Pathogens Research Unit, Department of Virology, Sefako Makgatho Health Sciences University, Pretoria 0208, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5017-5584","authenticated-orcid":false,"given":"Martin M.","family":"Nyaga","sequence":"additional","affiliation":[{"name":"Next Generation Sequencing Unit, School of Biomedical Sciences, Faculty of Health Sciences, Bloemfontein 9300, South Africa"},{"name":"Division of Virology, School of Pathology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,8,7]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"958","DOI":"10.1001\/jamapediatrics.2018.1960","article-title":"Rotavirus Vaccination and the Global Burden of Rotavirus Diarrhea Among Children Younger Than 5 Years","volume":"172","author":"Troeger","year":"2018","journal-title":"JAMA Pediatr."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1016\/j.cll.2015.02.012","article-title":"Rotavirus","volume":"35","author":"Esona","year":"2015","journal-title":"Clin. 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