Complete genome sequences and phylogenetic analysis of encephalomyocarditis virus strains isolated from pigs and rats origin

In order to evaluate the genetic variability of encephalomyocarditis virus (EMCV), the whole genomes of six EMCV field isolates originating from pigs and rats origin in different regions of central China, were phylogenetically and comparatively analyzed. Phylogenetic analysis of whole genome sequences, open reading frame (ORF), capsid coding region (CCR) and VP3/VP1 using neighbor-joining analysis revealed that these isolates belonged to lineage 1. Nucleotide sequences of six isolates showed more than 99% pairwise identity rates, and the sequences of isolates from pig and boar in the same region were completely identical with each other, without any genetic deletion or insertion. From comparative analysis of variability of each EMCV protein coding region, 3D and VP3 regions showed that the highest average identity rates, and was confirmed as highly conserved. In contrast, the protein coding regions 3A and 3B was confirmed to be highly variable region with the lowest average identity rate. Our data confirmed that the EMCV strains isolated from pigs and rats origin had high homology with each other, which implied rats may play an important role in EMCV transmission between domestic pigs and wild boars.