Ajileye Toluwani Goodnews, Akinleye Toluwanimi Emmanuel, Faleye Temitope O C, De Coninck Lander, George Uwem Etop, Onoja Anyebe Bernard, Agbaje Sheriff Tunde, Ifeorah Ijeoma Maryjoy, Olayinka Oluseyi Adebowale, Oni Elijah Igbekele, Oragwa Arthur Obinna, Popoola Bolutife Olubukola, Olayinka Olaitan Titilola, Osasona Oluwadamilola Gideon, George Oluwadamilola Adefunke, Ajayi Philip G, Suleiman Adedolapo A, Muhammad Ahmed Iluoreh, Komolafe Isaac, Adeniji Adekunle Johnson, Matthijnssens Jelle, Adewumi Moses Olubusuyi
Department of Virology, College of Medicine, University of Ibadan, Ibadan 200212, Nigeria.
Phytomedicine Unit, Department of Pharmacognosy, Faculty of Pharmacy, University of Ibadan, Ibadan 200005, Nigeria.
Viruses. 2025 Jun 12;17(6):844. doi: 10.3390/v17060844.
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 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 , , , and , 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 and genotypes, respectively (including those described here). We report the first near-complete genomes of and 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.
自2008年通过宏基因组学发现人类柯萨病毒（HCoSV）以来，已在患有脑膜炎、急性弛缓性麻痹（AFP）和急性胃肠炎的人类脑脊液（CSF）和粪便中检测到该病毒。迄今为止，该研究小组已记录了34种HCoSV基因型。然而，尼日利亚记录的HCoSV遗传多样性有限。在此，我们使用宏基因组学方法描述尼日利亚HCoSV的遗传多样性。对来自尼日利亚五个州诊断为非脊髓灰质炎AFP的15岁以下儿童的存档匿名粪便标本进行了分析。使用NetoVIR方案从55个样本池（由254个样本制成）中纯化病毒样颗粒。对样本池进行核酸提取和宏基因组测序。对读数进行修剪和组装，将归类为HCoSV的重叠群进行系统发育、成对同一性、重组分析，并在必要时进行免疫信息学和衣壳结构预测。15个样本池产生了23个HCoSV基因组。系统发育和成对同一性分析表明，所有基因组均属于四个物种（分别为、、和的11个、3个、3个和6个成员）和17个基因型。10个基因组属于7个先前指定的基因型（HCoSV-A3/A10、A15、A17、A19、A24、D3和E1），而其余13个基因组基于柯萨病毒基因组的近乎完整的VP1区域（VP1*）属于四个HCoSV物种中的10个新提出的基因型。我们的分析表明分别至少存在7个和8个和基因型（包括此处描述的那些）。我们报告了来自尼日利亚的首个近乎完整的和基因组，这有助于增加对HCoSV多样性的了解，将暂定基因型的数量从34个增加到40多个。我们的研究结果表明，HCoSV的遗传多样性可能比目前记录的更广泛，突出了加强监测的必要性。
