Whole genome sequencing and molecular characterization of porcine astrovirus from Haryana, India

Porcine astrovirus (PAstV) is an enteropathogen that belongs to the family Astroviridae and the genus Mamastrovirus, and is divided into five distinct genotypes (PAstV1-PAstV5). PAstV has been reported in pigs from several countries worldwide. In India, there are limited reports of genetic characterization of PAstV. The present study aimed to characterize the whole genome of PAstV from Haryana, a state in Northern India. Initially, 70 porcine fecal samples were screened for the presence of PAstV using RT-PCR that targeted the partial RdRp region. Three PAstV-positive samples were selected and their complete genomes successfully amplified by RT-PCR in two overlapping segments: segment A (∼3.6 kb) and segment B (∼3.1 kb). The phylogenetic analysis of PAstV, based on complete nucleotide sequences, revealed that PV247173 and PV247174 clustered within the PAstV1 group, whereas PV455027 clustered within the PAstV4 group. In contrast, analysis of the ORF2 amino acid sequence revealed that only PV247173 was classified in PAstV1, while PV455027 and PV247174 were classified in PAstV4. This study reports the first whole-genome molecular characterization of PAstV from Northern India.