Reference Based Genome Assembly And Partial Genetic Characterization Of Rotavirus Segments VP4 And VP7 in Fecal Samples from Diarrheic Pigs from Commercial and Backyard Farms in Nueva Ecija and Batangas, Philippines

Abstract

Rotavirus is the major cause of diarrhea in young animals and children worldwide. There is a lack of research done on porcine rotavirus in the Philippines hence, this study was conceptualized. This study aims to molecularly characterize the Rotavirus VP4 and VP7 genome segments from fecal samples of diarrheic pigs from commercial and backyard farms in Nueva Ecija and Batangas. Six (6) diarrheic pools samples were derived from the fecal samples collected by the Institute of Molecular Biology and Biotechnology - National Institutes of Health. Assembly and annotation of VP4 and VP7 genome segments involved the use of reference based assembly generating a consensus sequence for all six diarrheic pools for both VP4 and VP7 genome segments. The use of new pairs of oligonucleotide primers modified from that of Tonietti et al. revealed putative RT-PCR bands for VP7. Sanger sequencing and basic local alignment sequencing technique (NCBI-BLAST) confirmed VP7 identity as porcine rotavirus (ProV). Phylogenetic analysis revealed the clustering of VP4 consensus sequences with genotype P [13] for the first [D1], second [D2], third [D3], and sixth [D6] diarrheic pools and genotype P [23] for the fourth [D4] and fifth [D5] diarrheic pools of the fecal samples. Phylogenetic analysis revealed clustering of VP7 consensus and sanger sequences with genotype G9 for the first [D1] diarrheic pool, genotype G6 for the second [D2], third [D3], and sixth [D6] diarrheic pools, and genotype G3 for the fourth [D4] and fifth [D5] diarrheic pools.