Prevalence and genetic features of hepatitis E virus in swine, in Gansu, China

The prevalence of hepatitis E virus (HEV) in domestic swine threats the public health, due to the risk of zoonotic transmission. In this study, we investigated the prevalence and genetic features of HEV in swine, in Gansu, which is geographically an important province in China. 377 fecal samples were collected from pig farms in Gansu province of China and tested for HEV RNA by RT-PCR. The prevalence rate is about 23% in pig farms of Gansu province. By RT-nPCR, 5' and 3' RACE methods, a whole genome with 7,284 nt in length, termed as swCH189, was obtained and investigated by nucleotide, codon and amino acid usage analyses. Phylogenetic tree analysis classified swCH189 strain into genotype 4e. Although this subtype has never been reported in the local population, genotype 4 is known as zoonotic and more pathogenic than other genotypes. According to the synonymous codon usage patterns of the three open reading frames (ORFs) of swCH189, compositional constraint mainly influences usage patterns of synonymous codons with A-end, while natural selections dominate in usage patterns of synonymous codons with G, C and U-ends. Genetic diversities of each ORFs, in respect to codon and amino acid usage patterns, are closely related to other members of genotype 4 in general, but with distinct features. Thus, the prevalence rate and the genetic features of HEV determined by this study are important for the prevention of zoonotic transmission of HEV from swine to human in this region as well as in China.