Fecal Virome Diversity of Diarrheic Pigs in the Philippines

Pigs frequently act as reservoirs for zoonotic viruses and novel viruses which have zoonotic potential. In the Philippines, the enteric viruses community of pigs is largely unknown. This study aimed to investigate the viral... [ view full abstract ]

Pigs frequently act as reservoirs for zoonotic viruses and novel viruses which have zoonotic potential. In the Philippines, the enteric viruses community of pigs is largely unknown. This study aimed to investigate the viral composition of the fecal flora of diarrheic pigs from commercial farms in the country. Using high-throughput sequencing, the genetic material from fecal samples of 2 diarrheic pigs was sequenced to generate a total of 60.7 million reads. Contigs were assembled using de novo and reference-based assembly tools and were identified with the sequences available in the NCBI Genbank database. The sequences were further validated by performing Sanger sequencing using virus-specific primers. The RNA viruses identified in the samples belonged to the viral genera Rotavirus, Mamastrovirus, Sapelovirus, Enterovirus, and Kobuvirus. Pairwise identity comparisons of the nucleotide and amino acid sequences of the samples and Genbank references also indicated the presence of novel viral genotypes. The results provide the first description of the diversity of viral communities present in the fecal samples of diarrheic pigs in the Philippines. This can help determine the etiology of diarrhea in pigs and, if possible, the emerging enteric viruses in humans. Comparison of the incidence of these viruses in healthy and sick pigs must be further studied to establish their potential to be pathogenic.