COMPLETE GENOME SEQUENCE OF PORCINE EPIDEMIC DIARRHEA VIRUS IN VIETNAM

Abstract

Porcine epidemic diarrhea (PED) is caused by PED virus (PEDV), an enveloped, positive-sense, single-stranded RNA virus belonging to the genus Alphacoronavirus, family Coronaviridae, order Nidovirales. PEDV first emerged in Vietnam in 2009. In this study, the complete genomes of three Vietnamese PEDV isolates were characterized. These three isolates were isolated from 3-day-old pigs experiencing diarrhea. Two isolates were from swine farms in the south, and the other was from North Vietnam. The whole genome sequences of these isolates are 28,035 nucleotides in length and have a genome characterization similar to that of other PEDV isolates with gene order 5’-ORF1a/1b-S-ORF3-E-M-N-3’. All three Vietnamese PEDV isolates share 99.8% and 99.6% sequence identity at the nucleotide and amino acid levels, respectively and have characteristics including deletion and insertion in the spike gene, namely, the insertion of 4 amino acids (GENQ) and 1 amino acid (N) at positions 56-59 and 140, respectively, and one deletion of 2 amino acids (DG) at positions 160 and 161. Phylogenetic analysis based on the whole genome revealed that the three Vietnamese PEDV isolates are grouped together with new variants from China that were responsible for an outbreak of PEDV from 2011 to 2012, and genetically distinct from US isolates and the classical PEDV variant. The results suggest that Vietnamese PEDV isolates are new variants as evidenced by their unique genetic composition of insertions and a deletion in the spike gene and share high genetic similarity with the new variants of Chinese PEDV isolates. This study provides a better understanding of the molecular characteristics of PEDV in Vietnam.