Analysing complete genome sequence of swine hepatitis E virus (HEV), strain CHN-XJ-SW13 isolated from Xinjiang, China: putative host range, and disease severity determinants in HEV

Abstract

Hepatitis E is a worldwide public health problem, particular in areas where hygiene conditions are poor. Hepatitis E virus (HEV) has at least four genotypes: genotypes 1 and 2 exclusively infect human; while genotypes 3 and 4, are considered to be a zoonotic agent, infecting both humans and animals. This study was aimed at determining why genotype 3 and 4 HEV strains isolated from swine are able to cross species borders, whereas genotype1 and 2 strains isolated from humans are not. The full length genome of the swine HEV isolate CHN-XJ-SW13 was amplified as overlapping fragments using reverse-transcription-nested polymerase chain reaction (RT-nPCR) and rapid amplification of cDNA ends (RACE). The sequence of CHN-XJ-SW13 was compared with those of 90 HEV strains covering genotype 1-4 retrieved from GenBank. Possible regions of the viral genome, specifying the host range of HEV or associated with the severity of hepatitis E disease, were then screened for with the aid of the ALIGNX sequences alignment software package. The CHN-XJ-SW13 swine HEV isolate was determined to be a novel subtype of genotype 4, whose sequence provided several valuable clues for tracing the sources of human HEV infection. 25 specific nucleotide positions were identified to possibly being involved specifying the host range of HEV or determining the severity of hepatitis E disease.