Full genome sequence and analysis of Indian swine hepatitis E virus isolate of genotype 4

Abstract

The full-length genomic sequence of an Indian swine hepatitis E virus (HEV) isolate (IND-SW-00-01) recovered from feces of a pig experimentally infected with swine HEV pool from western India was determined. The genome consisted of 7240 nucleotides, excluding the poly (A) tail of at least 22 residues and contained three open reading frames (ORFs), ORF-1 encoding 1707 amino acids, ORF-2 encoding 674 amino acids and ORF-3 encoding 114 amino acids. Comparative full-length genome sequence and phylogenetic analyses suggested that the Indian swine HEV represents a distinct variant among the genotype 4 isolates with a divergence of 15-16.6%. Analyses based on ORF-1, 2 and 3 as well as partial ORF-2 (227 nucleotides) yielded similar results. As compared to type 4 HEV isolates, 26 unique amino acid substitutions were recorded, 16 in ORF-1, 8 in ORF-2 and 2 in ORF-3. IND-SW-00-01 showed insertion of 'C' at 5159 position while all other type 4 isolates have insertion of 'U' at the same position. Whether these changes contribute towards observed absence of type 4 HEV infections in Indian patients needs to be determined.