Complete genome sequence analysis of one genotype 1 HEV strain from a sporadic acute hepatitis E patient

Abstract

Objective To sequence and analyze the full-length genome of one HEV strain,W2-1 isolated from a sporadic hepatitis E patient hospitalized in 1999 in Xinjiang,China.Methods Nested RT-PCR assays with 4 sets primers were used to amplify the entire genome.The PCR products were purified and sequenced.The full-length genome was acquired by assembling the fragmental sequences using the DNAstar 5.01 software.The genome of W2-1 was analyzed by comparing with the reference HEVs from GenBank.Results The complete genome of W2-1 is 7212 nt in length,including three open reading frames (ORF1-3) with 5079,1980 and 345 nt respectively,27 nt 5'UTR and 83 nt 3'UTR,and a 3' poly A tail.Phylogenetic analysis based on full-length genome showed that W2-1 belonged to genotype 1,subtype 1b.W2-1 had high homology with the HEV strains isolated in the large hepatitis E epidemic in Xinjiang in 1987-1989,sharing 97.2％-98.5％ nucleotide identity in the full length genome.W2-1 also showed high homology with 1b strains isolated in China after 2000,with 97.6％-99.2％ nucleotide identity.The specific amino acid sites in ORF1-3 proteins that distinct between genotype 1 HEV and the potential zoonotic strains did not change in W2-1.Conclusion W2-1 belongs to subtype 1b.The study indicates subtype 1b HEV has been circulating in China in a long period after hepatitis E outbreak in Xinjiang in 1986-1989.The amino acids of ORF1-3 of subtype 1b are conserved. Key words: Hepatitis E virus; Complete genome; Sequence analysis; Genotype