Complexity of Diarrhea-Associated Viruses in Stunted Pigs Identified by Viral Metagenomics

Viral diarrhea poses a severe threat to the health and growth of piglets, especially when caused by co-infection with multiple diarrhea-associated viruses. In this study anal swabs were collected from pigs older than 3 months from a farm in Gansu province, China, and subjected to viral metagenomic analysis. They had been suffering from diarrhea and their growth was significantly retarded. A total of 18 viruses were identified by high-throughput sequencing (HTS) in pooled samples from 22 stunted pigs and (separately) three healthy pigs. They included 15 diarrhea-associated RNA viruses with five porcine rotaviruses (PoRVs), porcine epidemic diarrhea virus (PEDV), a torovirus, and a sapelovirus present only in the stunted pigs. Among the identified PoRVs, PoRVBs showed a much greater genetic diversity than other PoRVs with multiple variant gene sequences identified in segments VP1 (2), VP2 (3), VP3 (4), VP4 (5), VP7 (5), NSP1 (2), NSP3 (3), NSP4 (2), and NSP5 (4), with 1–3 new genotypes being defined within each segment except NSP5. Unexpectedly, PoRVF was identified for the first time in pigs, with all gene segments exhibiting low nucleotide (56.5%−79.4%) and amino acid sequence identities (46.2%−92.0%) with previously identified avian RVF reference strains. Phylogenetic analysis showed that multiple variant strains of PAstV2 (6) and PAstV4 (13) were found in stunted pigs, and other enteric viruses were highly homologous with reference strains. Overall, the findings indicate that the stunted pigs may serve as a hotbed for the propagation of diarrhea-associated viruses and that they should be isolated and treated as early as possible.