Characterization of swine hepatitis E virus genotype 3 open reading frames

Abstract

The goal of this study was a determination of structural organization features of swine hepatitis E virus genotype 3 open reading frames. Gene selective pressure for genes was estimated using the Tajima’s neutrality test as implemented in MEGA 6. Shannon entropy was used for diversity detection at each position of open reading frames. Shannon entropy plots representing quantitative diversity at each amino acid (nucleotide) position of 11 swine HEV-3 isolates aligned sequences were calculated by software BioEdit. For phylogenetic analysis, nucleotide distances were analyzed using the neighbour-joining algorithm. Analysis of nucleotide, non-synonymous and synonymous distances was performed using MEGA6. Parameters of mutational analysis for swine hepatitis E virus genotype 3 open reading frames ORF1 – ORF3 were determined using Tajima’s neutrality test. Shannon entropy technique revealed that ORF3 is characterized by the most number of diverse amino acid residues (21,7 %) comparing with ORF1, ORF2 coding regions. Analysis of non-synonymous distances in ORF3 allowed to determine an order of evolutionary events in the history of swine HEV-3 isolates. Avian astroviruses strains were used as control because phylogenetic relationships among them correspond to the evolution history of their host species. Tree topology for swine HEV-3 ORF3 based on non-synonymous distances differs from tree structures based on nucleotide and synonymous distances. Positive values of D Tajima’s factor for ORF1, ORF2 of swine HEV-3 show on operating positive selection onto these coding regions. Negative value of D Tajima’s factor for ORF3 coding region indicates onto purifying selection