Partial Molecular Characterization of Sapovirus and Astrovirus Isolated from Healthy and Diarrheic Swine from Batangas and Nueva Ecija

Abstract

Porcine sapovirus (PSaV) and porcine astrovirus (PAstV) are economically significant viruses that are associated with diarrhea. Both viruses have been detected in pigs from Korea, Japan, China, and the USA with prevalences from 0.9%-64% (Cai et al., 2016; Lee et al., 2013; Nakanishi et al., 2011; Shen et al., 2009; Wang, Souza et al., 2006; Xiao et al., 2013; Yu et al., 2008). In the Philippines there is no documentation on their presence in pigs. Thus, in this study the complete genome of sapovirus and astrovirus were assembled through reference-based assembly using Bowtie2 (version 2.2.9) and Burrows Wheeler Alignment tool (BWA, version 0.7.12). Reads were generated from pooled fecal samples of healthy and diarrheic pigs from Batangas and Nueva Ecija. Two (2) pools (one diarrheic and one healthy) were collected from Nueva Ecija while nine pools (five diarrheic and four healthy) were collected from Batangas. PSaV sequences were assembled from one diarrheic from Nueva Ecija, five diarrheic pools from Batangas, and two healthy pools from Batangas (D1 NE, D2 B, D3 B, D4 B, D5 B, D6 B, H2 B & H3 B), while PAstV sequences were assembled from one diarrheic pool from Nueva Ecija, five diarrheic pools from Batangas, and three healthy pools from Batangas (D1 NE, D2 B, D3 B, D4 B, D5 B, D6 B, H2 B, H3 B & H5 B). Coinfection of PSaV and PAstV is suspected as in some cases, sequences of both viruses were assembled from the same pools. Amplification of the capsid and ORF2 regions for PSaV and PAstV, respectively, in a portion of the samples confirmed the presence of the viruses in pools D1 B and H5 NE. Phylogenetic analysis using the consensus sequences classified all eight PSaV assemblies into GIII, 1 PAstV assembly into lineage 2, and eight PAstV sequences into lineage 5. Moreover, the percent nucleotide identity of the PAstV (85.40%-94.70%) assemblies to strains from China and the USA indicate that the assembled sequences may be novel.