Metatranscriptomic Assessment of Diarrhoeic Faeces in Rotavirus group A Infected Piglets and Calves from India

Neonatal diarrhoea caused by enteric viruses is common cause of morbidity and mortality in human and animal. We investigated, metagenomics-derived RNA virome in rotavirus group A (RVA) positive diarrheic faecal samples from piglets and calves. The viruses identified belonged to Astrovirdae in both species while Picornavirade in pigs. Among the porcine RNA viruses detected, astroviruses (PAstV2, PAstV4, BAstV) were predominant followed by enterovirus (EV-G1, EV-G15), sapelovirus, kobuvirus, teschovirus (PTV-17) in decreasing order of sequence reads. However, in bovines astrovirus accounted for more than 96% of reads. The most variable portion of detected viruses were selected and phylogenetically analysed.In summary, an unbiased survey of viruses in the feces of intensely farmed animals revealed frequent coinfections with a highly diverse set of viruses providing favorable conditions for viral recombination.