Molecular insights into astrovirus, kobuvirus and rotavirus a coinfection in pigs (Sus domesticus) from Haryana, India.

The multiple viral agents, either individually or in combination, are associated with enteritis and diarrhoea in pigs, including porcine astrovirus (PAstV), porcine kobuvirus (PKV), and porcine rotavirus A (PRV-A). In this study, 182 faecal samples were collected from diarrheic (n = 116) and asymptomatic (n = 66) pigs of different age groups from Haryana, India. The presence of these three viruses (PAstV, PKV, and PRV-A) was examined in the samples using reverse transcription-polymerase chain reaction (RT-PCR). The results showed that 54 samples tested positive for PAstV, 90 for PKV, and 60 for PRV-A. Of these, 35, 73, and 50 positive cases were found in pigs with diarrhoea, while 19, 17, and 10 positive cases were identified in pigs without diarrhoea for PAstV, PKV, and PRV-A, respectively. Single virus infection was detected in 63 samples, whereas mixed infections were found in 59 samples, with 37 and 22 samples having two and three viruses, respectively. PAstV was more prevalent in weaning pigs (37/95), whereas PKV and PRV-A were more predominant (36/59 and 30/59) in suckling piglets. Phylogenetic analysis revealed the circulation of lineage 1, 2, and 4 of PAstV, and genotypes I1, I2, and I5 of PRV-A in this region. The study shows that PAstV’s specific role in causing diarrhoea is unclear; however, the presence of PKV or PRV-A has led to an increase in diarrhoea cases among pigs.