{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T01:23:45Z","timestamp":1760059425490,"version":"build-2065373602"},"reference-count":47,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2025,6,12]],"date-time":"2025-06-12T00:00:00Z","timestamp":1749686400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Since its discovery via metagenomics in 2008, human cosavirus (HCoSV) has been detected in the cerebrospinal fluid (CSF) and feces of humans with meningitis, acute flaccid paralysis (AFP), and acute gastroenteritis. To date, 34 HCoSV genotypes have been documented by the Picornaviridae study group. However, the documented genetic diversity of HCoSV in Nigeria is limited. Here we describe the genetic diversity of HCoSV in Nigeria using a metagenomics approach. Archived and anonymized fecal specimens from children (under 15 years old) diagnosed with non-polio AFP from five states in Nigeria were analyzed. Virus-like particles were purified from 55 pools (made from 254 samples) using the NetoVIR protocol. Pools were subjected to nucleic acid extraction and metagenomic sequencing. Reads were trimmed and assembled, and contigs classified as HCoSV were subjected to phylogenetic, pairwise identity, recombination analysis, and, when necessary, immuno-informatics and capsid structure prediction. Fifteen pools yielded 23 genomes of HCoSV. Phylogenetic and pairwise identity analysis showed that all belonged to four species (eleven, three, three, and six members of Cosavirus asiani, Cosavirus bepakis, Cosavirus depakis, and Cosavirus eaustrali, respectively) and seventeen genotypes. Ten genomes belong to seven (HCoSV-A3\/A10, A15, A17, A19, A24, D3, and E1) previously assigned genotypes, while the remaining thirteen genomes belonged to ten newly proposed genotypes across the four HCoSV species, based on the near-complete VP1 region (VP1*) of the cosavirus genome. Our analysis suggests the existence of at least seven and eight Cosavirus bepakis and Cosavirus eaustrali genotypes, respectively (including those described here). We report the first near-complete genomes of Cosavirus bepakis and Cosavirus depakis from Nigeria, which contributes to the increasing knowledge of the diversity of HCoSV, raising the number of tentative genotypes from 34 to over 40. Our findings suggest that the genetic diversity of HCoSV might be broader than is currently documented, highlighting the need for enhanced surveillance.<\/jats:p>","DOI":"10.3390\/v17060844","type":"journal-article","created":{"date-parts":[[2025,6,13]],"date-time":"2025-06-13T03:53:12Z","timestamp":1749786792000},"page":"844","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Ten Previously Unassigned Human Cosavirus Genotypes Detected in Feces of Children with Non-Polio Acute Flaccid Paralysis in Nigeria in 2020"],"prefix":"10.3390","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0009-0002-1294-3519","authenticated-orcid":false,"given":"Toluwani Goodnews","family":"Ajileye","sequence":"first","affiliation":[{"name":"Department of Virology, College of Medicine, University of Ibadan, Ibadan 200212, Nigeria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7202-8112","authenticated-orcid":false,"given":"Toluwanimi Emmanuel","family":"Akinleye","sequence":"additional","affiliation":[{"name":"Phytomedicine Unit, Department of Pharmacognosy, Faculty of Pharmacy, University of Ibadan, Ibadan 200005, Nigeria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7706-9493","authenticated-orcid":false,"given":"Temitope O. C.","family":"Faleye","sequence":"additional","affiliation":[{"name":"Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6847-2379","authenticated-orcid":false,"given":"Lander","family":"De Coninck","sequence":"additional","affiliation":[{"name":"Laboratory of Viral Metagenomics, Department of Microbiology, Immunology and Transplantation, Rega Institute, Universiteit Leuven, 3000 Leuven, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5474-1048","authenticated-orcid":false,"given":"Uwem Etop","family":"George","sequence":"additional","affiliation":[{"name":"African Centre of Excellence for Genomics of Infectious Diseases, Redeemer\u2019s University, Ede 232101, Nigeria"},{"name":"Department of Biological Sciences, Faculty of Natural Sciences, Redeemer\u2019s University, Ede 232101, Nigeria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5502-3224","authenticated-orcid":false,"given":"Anyebe Bernard","family":"Onoja","sequence":"additional","affiliation":[{"name":"Department of Virology, College of Medicine, University of Ibadan, Ibadan 200212, Nigeria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sheriff Tunde","family":"Agbaje","sequence":"additional","affiliation":[{"name":"Department of Virology, College of Medicine, University of Ibadan, Ibadan 200212, Nigeria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0911-7179","authenticated-orcid":false,"given":"Ijeoma Maryjoy","family":"Ifeorah","sequence":"additional","affiliation":[{"name":"Department of Medical Laboratory Science, Faculty of Health Science and Technology, College of Medicine, University of Nigeria Enugu Campus, Enugu 400241, Nigeria"},{"name":"Centre for Translation and Implementation Research, University of Nigeria, Nsukka 410001, Nigeria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Oluseyi Adebowale","family":"Olayinka","sequence":"additional","affiliation":[{"name":"Department of Virology, College of Medicine, University of Ibadan, Ibadan 200212, Nigeria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Elijah Igbekele","family":"Oni","sequence":"additional","affiliation":[{"name":"Department of Virology, College of Medicine, University of Ibadan, Ibadan 200212, Nigeria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Arthur Obinna","family":"Oragwa","sequence":"additional","affiliation":[{"name":"Department of Veterinary Microbiology, Faculty of Veterinary Medicine, University of Jos, Jos 930003, Nigeria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-5868-7412","authenticated-orcid":false,"given":"Bolutife Olubukola","family":"Popoola","sequence":"additional","affiliation":[{"name":"Department of Virology, College of Medicine, University of Ibadan, Ibadan 200212, Nigeria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Olaitan Titilola","family":"Olayinka","sequence":"additional","affiliation":[{"name":"National Polio Laboratory, College of Medicine, University of Ibadan, Ibadan 200212, Nigeria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4887-9336","authenticated-orcid":false,"given":"Oluwadamilola Gideon","family":"Osasona","sequence":"additional","affiliation":[{"name":"Department of Medical Laboratory Sciences, Faculty of Basic Medical Sciences, Redeemer\u2019s University, Ede 232101, Nigeria"},{"name":"Hospitals Management Board, Ado-Ekiti 360102, Nigeria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Oluwadamilola Adefunke","family":"George","sequence":"additional","affiliation":[{"name":"National Veterinary Research Institute, Vom 930101, Nigeria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-1692-7612","authenticated-orcid":false,"given":"Philip G.","family":"Ajayi","sequence":"additional","affiliation":[{"name":"Department of Virology, College of Medicine, University of Ibadan, Ibadan 200212, Nigeria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Adedolapo A.","family":"Suleiman","sequence":"additional","affiliation":[{"name":"Department of Virology, College of Medicine, University of Ibadan, Ibadan 200212, Nigeria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7679-5052","authenticated-orcid":false,"given":"Ahmed Iluoreh","family":"Muhammad","sequence":"additional","affiliation":[{"name":"African Centre of Excellence for Genomics of Infectious Diseases, Redeemer\u2019s University, Ede 232101, Nigeria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Isaac","family":"Komolafe","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Faculty of Natural Sciences, Redeemer\u2019s University, Ede 232101, Nigeria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Adekunle Johnson","family":"Adeniji","sequence":"additional","affiliation":[{"name":"Department of Virology, College of Medicine, University of Ibadan, Ibadan 200212, Nigeria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1188-9733","authenticated-orcid":false,"given":"Jelle","family":"Matthijnssens","sequence":"additional","affiliation":[{"name":"Laboratory of Viral Metagenomics, Department of Microbiology, Immunology and Transplantation, Rega Institute, Universiteit Leuven, 3000 Leuven, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5172-5808","authenticated-orcid":false,"given":"Moses Olubusuyi","family":"Adewumi","sequence":"additional","affiliation":[{"name":"Department of Virology, College of Medicine, University of Ibadan, Ibadan 200212, Nigeria"},{"name":"Infectious Disease Institute, College of Medicine, University of Ibadan, Ibadan 200212, Nigeria"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,6,12]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"2864","DOI":"10.1098\/rstb.2011.0354","article-title":"Chase-Topping. 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