Detection and molecular characterization of human cosavirus in a pediatric patient with acute gastroenteritis, Japan

•This is the first report of HCoSV detection in a child with diarrhea in Japan.•Other common diarrhea-causal pathogens were not detected in the clinical sample.•The strain in this study was found to belong to a new genotype in the HCoSV-A.

Human cosavirus (HCoSV) is a genus recently identified in the family Picornaviridae, which includes important pathogens in human health. The pathogenicity of HCoSV remains unclear. This study reports that an HCoSV strain, 10928/2012/JPN, was identified and collected from the stool sample of a child with acute gastroenteritis in Japan, with the detection rate of 0.16%. The patient was not co-infected with other common diarrhea-causal viruses, suggesting HCoSV as a causal pathogen in this pediatric patient. Phylogenetic and sequence analyses exhibited that the virus strain was classified as a new genotype in HCoSV A species, and this study is first to detect HCoSV in a clinical specimen collected in Japan. These results showed that surveillance of HCoSV is important for detecting viral agents in children with diarrhea, despite being the low detection rate.