Search Results (5)

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. Full article

In this study, we analyzed the potential of viral infections in the species Homo sapiens as environmental causes of orofacial clefts (OFCs). A scoring system was adapted for qualitatively assessing the potential of viruses to cause cleft lip and/or palate (CL/P). This assessment considered factors such as information from the literature, nucleotide and amino acid similarities, and the presence of Endogenous Viral Elements (EVEs). The analysis involved various algorithm packages within Basic Local Alignment Search Tool 2.13.0 software and databases from the National Center for Biotechnology Information and the International Committee on Taxonomy of Viruses. Twenty significant viral species using different biosynthesis strategies were identified: Human coronavirus NL63, Rio Negro virus, Alphatorquevirus homin9, Brisavirus, Cosavirus B, Torque teno mini virus 4, Bocaparvovirus primate2, Human coronavirus HKU1, Monkeypox virus, Mammarenavirus machupoense, Volepox virus, Souris mammarenavirus, Gammapapillomavirus 7, Betainfluenzavirus influenzae, Lymphocytic choriomeningitis mammarenavirus, Ledantevirus kern, Gammainfluenzavirus influenzae, Betapolyomavirus hominis, Vesiculovirus perinet, and Cytomegalovirus humanbeta5. The evident viral etiological potential in relation to CL/P varies depending on the Baltimore class to which the viral species belongs. Given the multifactorial nature of CL/P, this relationship appears to be dynamic. Full article

Metagenomics based on the next-generation sequencing (NGS) technique is a target-independent assay that enables the simultaneous detection and genomic characterization of all viruses present in a sample. There is a limited amount of data about the virome of individuals with gastroenteritis (GI). In this study, the enteric virome of 250 individuals (92% were children under 5 years old) with GI living in the northeastern and northern regions of Brazil was characterized. Fecal samples were subjected to NGS, and the metagenomic analysis of virus-like particles (VLPs) identified 11 viral DNA families and 12 viral RNA families. As expected, the highest percentage of viral sequences detected were those commonly associated with GI, including rotavirus, adenovirus, norovirus (94.8%, 82% and 71.2%, respectively). The most common co-occurrences, in a single individual, were the combinations of rotavirus-adenovirus, rotavirus-norovirus, and norovirus-adenovirus (78%, 69%, and 62%, respectively). In the same way, common fecal-emerging human viruses were also detected, such as parechovirus, bocaporvirus, cosavirus, picobirnavirus, cardiovirus, salivirus, and Aichivirus. In addition, viruses that infect plants, nematodes, fungi, protists, animals, and arthropods could be identified. A large number of unclassified viral contigs were also identified. We show that the metagenomics approach is a powerful and promising tool for the detection and characterization of different viruses in clinical GI samples. Full article

In the post-polio eradication era, increasing attention is given to non-polio enteroviruses. Most of the data about enteroviruses in sub-Saharan Africa are related to acute flaccid paralysis surveillance and target the pediatric population. This study aimed to investigate the presence of enterovirus in PLHIV (people living with HIV) and HIV-negative individuals in Ghana. Stool samples from HIV-positive individuals (n = 250) and healthy blood donors (n = 102) attending the Komfo Anokye Teaching Hospital in Kumasi, Ghana, were screened by real-time PCR for enterovirus. Molecular typing of the VP1 region was performed. Enterovirus-positive samples were tested for norovirus, adenovirus, rotavirus, sapovirus, and cosaviruses. Twenty-six out of 250 HIV-positive subjects (10.4%) and 14 out of 102 HIV-negative individuals (13.7%) were detected enterovirus-positive, not showing a significant different infection rate between the two groups. HIV-negative individuals were infected with Enterovirus C strains only. HIV-positive participants were detected positive for species Enterovirus A, Enterovirus B, and Enterovirus C. Co-infections with other viral enteric pathogens were almost exclusively detected among HIV-positive participants. Overall, the present study provides the first data about enteroviruses within HIV-positive and HIV-negative adults living in Ghana. Full article

Human enteroviruses and human parechoviruses are associated with a broad range of diseases and even severe and fatal conditions. For human cosaviruses, the etiological role is yet unknown. Little is known about the circulation of non-polio enteroviruses, human parechoviruses, and human cosaviruses in Nigeria. A total of 113 stool samples were collected from healthy individuals in Osun State between February 2016 and May 2017. RT-PCR assays targeting the 5′ non-coding region (5′ -NCR) were used to screen for human enteroviruses, human parechoviruses, and human cosaviruses. For human enteroviruses, species-specific RT-PCR assays targeting the VP1 regions were used for molecular typing. Inoculation was carried out on RD-A, CaCo-2, HEp-2C, and L20B cell lines to compare molecular and virological assays. Ten samples tested positive for enterovirus RNA with 11 strains detected, including CV-A13 (n = 3), E-18 (n = 2), CV-A20 (n = 1), CV-A24 (n = 1), EV-C99 (n = 1), and EV-C116 (n = 2). Three samples tested positive for human parechovirus RNA, and full genome sequencing on two samples allowed assignment to a new Parechovirus A type (HPeV-19). Thirty-three samples tested positive for cosavirus with assignment to species Cosavirus D and Cosavirus A based on the 5′-NCR region. Screening of stool samples collected from healthy individuals in Nigeria in 2016 and 2017 revealed a high diversity of circulating human enteroviruses, human parechoviruses, and human cosaviruses. Molecular assays for genotyping showed substantial benefits compared with those of cell-culture assays. Full article