Prevalence, Genetics, and Evolution of Porcine Astrovirus 3 in China

Porcine astrovirus 3 (PAstV3) is an emerging virus associated with porcine polioencephalomyelitis outbreaks and is frequently detected in the feces of both healthy and diarrheal pigs. Despite its significance, the prevalence, genetic characteristics, and evolutionary features of PAstV3 in China remain poorly understood. Here, a retrospective study of PAstV3 infection was conducted using 634 tissue or fecal specimens collected from diseased pigs across 29 regions in China between 1990 and 2024. As a result, eight tissue samples and 32 fecal samples from seven regions tested positive for PAstV3, yielding an overall positive rate of 6.3% (40/634). Through a combination of metatranscriptomics (MTT) and RT-PCR, nearly complete genome sequences of 14 PAstV3 strains and full-length open reading frame (ORF) 2 sequences of another 13 PAstV3 strains were successfully obtained. Sequence analysis revealed that these strains exhibited a sequence identity of 59.8%-100% in the capsid protein. Phylogenetic analysis demonstrated that global PAstV3 strains could be classified into four genotypes: PAstV3a-d. The intergenotype strains showed nucleotide (nt) and amino acid sequence identities of 59.7%-69.8% and 59.5%-72.0%, respectively, in the ORF2 region. Notably, PAstV3b was identified as the predominant genotype in China. Sequence comparisons further confirmed the close genetic relationship between PAstV3 and neurotropic mammalian astroviruses, suggesting the potential interspecies transmission or a shared evolutionary origin. Phylodynamic analysis estimated that the most recent common ancestor (tMRCA) of PAstV3 emerged around the year 1660 and the effective population size of PAstV3 has been continuously expanding over time.