Ten Previously Unassigned Human Cosavirus Genotypes Detected in Feces of Children with Non-Polio Acute Flaccid Paralysis in Nigeria in 2020
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 <i>Picornaviridae</...
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| author | Toluwani Goodnews Ajileye Toluwanimi Emmanuel Akinleye Temitope O. C. Faleye Lander De Coninck Uwem Etop George Anyebe Bernard Onoja Sheriff Tunde Agbaje Ijeoma Maryjoy Ifeorah Oluseyi Adebowale Olayinka Elijah Igbekele Oni Arthur Obinna Oragwa Bolutife Olubukola Popoola Olaitan Titilola Olayinka Oluwadamilola Gideon Osasona Oluwadamilola Adefunke George Philip G. Ajayi Adedolapo A. Suleiman Ahmed Iluoreh Muhammad Isaac Komolafe Adekunle Johnson Adeniji Jelle Matthijnssens Moses Olubusuyi Adewumi |
| author_facet | Toluwani Goodnews Ajileye Toluwanimi Emmanuel Akinleye Temitope O. C. Faleye Lander De Coninck Uwem Etop George Anyebe Bernard Onoja Sheriff Tunde Agbaje Ijeoma Maryjoy Ifeorah Oluseyi Adebowale Olayinka Elijah Igbekele Oni Arthur Obinna Oragwa Bolutife Olubukola Popoola Olaitan Titilola Olayinka Oluwadamilola Gideon Osasona Oluwadamilola Adefunke George Philip G. Ajayi Adedolapo A. Suleiman Ahmed Iluoreh Muhammad Isaac Komolafe Adekunle Johnson Adeniji Jelle Matthijnssens Moses Olubusuyi Adewumi |
| author_sort | Toluwani Goodnews Ajileye |
| collection | DOAJ |
| description | 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 <i>Picornaviridae</i> 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 <i>Cosavirus asiani</i>, <i>Cosavirus bepakis</i>, <i>Cosavirus depakis</i>, and <i>Cosavirus eaustrali</i>, 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 <i>Cosavirus bepakis</i> and <i>Cosavirus eaustrali</i> genotypes, respectively (including those described here). We report the first near-complete genomes of <i>Cosavirus bepakis</i> and <i>Cosavirus depakis</i> 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. |
| format | Article |
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| issn | 1999-4915 |
| language | English |
| publishDate | 2025-06-01 |
| publisher | MDPI AG |
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| series | Viruses |
| spelling | doaj-art-5bb1202a01ce430c80363e5e953cb7ba2025-08-20T02:21:58ZengMDPI AGViruses1999-49152025-06-0117684410.3390/v17060844Ten Previously Unassigned Human Cosavirus Genotypes Detected in Feces of Children with Non-Polio Acute Flaccid Paralysis in Nigeria in 2020Toluwani Goodnews Ajileye0Toluwanimi Emmanuel Akinleye1Temitope O. C. Faleye2Lander De Coninck3Uwem Etop George4Anyebe Bernard Onoja5Sheriff Tunde Agbaje6Ijeoma Maryjoy Ifeorah7Oluseyi Adebowale Olayinka8Elijah Igbekele Oni9Arthur Obinna Oragwa10Bolutife Olubukola Popoola11Olaitan Titilola Olayinka12Oluwadamilola Gideon Osasona13Oluwadamilola Adefunke George14Philip G. Ajayi15Adedolapo A. Suleiman16Ahmed Iluoreh Muhammad17Isaac Komolafe18Adekunle Johnson Adeniji19Jelle Matthijnssens20Moses Olubusuyi Adewumi21Department of Virology, College of Medicine, University of Ibadan, Ibadan 200212, NigeriaPhytomedicine Unit, Department of Pharmacognosy, Faculty of Pharmacy, University of Ibadan, Ibadan 200005, NigeriaCenter for Environmental Health Engineering, Biodesign Institute, Arizona State University, Tempe, AZ 85281, USALaboratory of Viral Metagenomics, Department of Microbiology, Immunology and Transplantation, Rega Institute, Universiteit Leuven, 3000 Leuven, BelgiumAfrican Centre of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede 232101, NigeriaDepartment of Virology, College of Medicine, University of Ibadan, Ibadan 200212, NigeriaDepartment of Virology, College of Medicine, University of Ibadan, Ibadan 200212, NigeriaDepartment of Medical Laboratory Science, Faculty of Health Science and Technology, College of Medicine, University of Nigeria Enugu Campus, Enugu 400241, NigeriaDepartment of Virology, College of Medicine, University of Ibadan, Ibadan 200212, NigeriaDepartment of Virology, College of Medicine, University of Ibadan, Ibadan 200212, NigeriaDepartment of Veterinary Microbiology, Faculty of Veterinary Medicine, University of Jos, Jos 930003, NigeriaDepartment of Virology, College of Medicine, University of Ibadan, Ibadan 200212, NigeriaNational Polio Laboratory, College of Medicine, University of Ibadan, Ibadan 200212, NigeriaDepartment of Medical Laboratory Sciences, Faculty of Basic Medical Sciences, Redeemer’s University, Ede 232101, NigeriaNational Veterinary Research Institute, Vom 930101, NigeriaDepartment of Virology, College of Medicine, University of Ibadan, Ibadan 200212, NigeriaDepartment of Virology, College of Medicine, University of Ibadan, Ibadan 200212, NigeriaAfrican Centre of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede 232101, NigeriaDepartment of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede 232101, NigeriaDepartment of Virology, College of Medicine, University of Ibadan, Ibadan 200212, NigeriaLaboratory of Viral Metagenomics, Department of Microbiology, Immunology and Transplantation, Rega Institute, Universiteit Leuven, 3000 Leuven, BelgiumDepartment of Virology, College of Medicine, University of Ibadan, Ibadan 200212, NigeriaSince 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 <i>Picornaviridae</i> 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 <i>Cosavirus asiani</i>, <i>Cosavirus bepakis</i>, <i>Cosavirus depakis</i>, and <i>Cosavirus eaustrali</i>, 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 <i>Cosavirus bepakis</i> and <i>Cosavirus eaustrali</i> genotypes, respectively (including those described here). We report the first near-complete genomes of <i>Cosavirus bepakis</i> and <i>Cosavirus depakis</i> 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.https://www.mdpi.com/1999-4915/17/6/844human cosavirushigh-throughput sequencingmetagenomicsacute flaccid paralysisNigeria |
| spellingShingle | Toluwani Goodnews Ajileye Toluwanimi Emmanuel Akinleye Temitope O. C. Faleye Lander De Coninck Uwem Etop George Anyebe Bernard Onoja Sheriff Tunde Agbaje Ijeoma Maryjoy Ifeorah Oluseyi Adebowale Olayinka Elijah Igbekele Oni Arthur Obinna Oragwa Bolutife Olubukola Popoola Olaitan Titilola Olayinka Oluwadamilola Gideon Osasona Oluwadamilola Adefunke George Philip G. Ajayi Adedolapo A. Suleiman Ahmed Iluoreh Muhammad Isaac Komolafe Adekunle Johnson Adeniji Jelle Matthijnssens Moses Olubusuyi Adewumi Ten Previously Unassigned Human Cosavirus Genotypes Detected in Feces of Children with Non-Polio Acute Flaccid Paralysis in Nigeria in 2020 Viruses human cosavirus high-throughput sequencing metagenomics acute flaccid paralysis Nigeria |
| title | Ten Previously Unassigned Human Cosavirus Genotypes Detected in Feces of Children with Non-Polio Acute Flaccid Paralysis in Nigeria in 2020 |
| title_full | Ten Previously Unassigned Human Cosavirus Genotypes Detected in Feces of Children with Non-Polio Acute Flaccid Paralysis in Nigeria in 2020 |
| title_fullStr | Ten Previously Unassigned Human Cosavirus Genotypes Detected in Feces of Children with Non-Polio Acute Flaccid Paralysis in Nigeria in 2020 |
| title_full_unstemmed | Ten Previously Unassigned Human Cosavirus Genotypes Detected in Feces of Children with Non-Polio Acute Flaccid Paralysis in Nigeria in 2020 |
| title_short | Ten Previously Unassigned Human Cosavirus Genotypes Detected in Feces of Children with Non-Polio Acute Flaccid Paralysis in Nigeria in 2020 |
| title_sort | ten previously unassigned human cosavirus genotypes detected in feces of children with non polio acute flaccid paralysis in nigeria in 2020 |
| topic | human cosavirus high-throughput sequencing metagenomics acute flaccid paralysis Nigeria |
| url | https://www.mdpi.com/1999-4915/17/6/844 |
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