title: Full genomic sequence analysis of swine genotype 3 hepatitis E virus isolated from Shanghai.
abstract: The full genomic nucleotide sequence of a previously identified genotype 3 hepatitis E virus (HEV), strain SAAS-JDY5, was obtained using RT-PCR and rapid amplification of cDNA ends (RACE). The genome consisted of 7225 nucleotides, excluding a poly-A tail at the 3' terminus, and contained three open reading frames (ORFs), ORF-1, ORF-2 and ORF-3, encoding 1702, 660 and 113 amino acids, respectively. Phylogenetic analysis confirmed that SAAS-JDY5 belonged to genotype 3 HEV and was most closely related to the Japanese isolate wbJYG1 (AB222184). SAAS-JDY5 shared approximately 87% nucleotide similarity to human and swine strains from the United States, compared with 74-75% similarity to Asian (genotype 4) and Mexican strains (genotype 2). Alignment of the SAAS-JDY5 genomic sequence with reference sequences of the same genotype revealed one nucleotide substitution and one deletion at positions 5145 and 7189 (3' UTR), respectively. Moreover, SAAS-JDY5 contained two additional nucleotides (AC) at the very end of the 3'-terminus preceding the poly-A tail of the genome. Comparison of the putative amino acid sequence encoded by the SAAS-JDY5 genome with sequences of other genotype 3 isolates revealed 15 unique amino acid substitutions and one deletion in ORF-1, and three substitutions in ORF-2.
authors.affiliation: Institute of Animal Science and Veterinary Medicine, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China.
authors.forename: Fu-sheng
authors.initials: FS
authors.lastname: Si
authors.forename: Yu-min
authors.initials: YM
authors.lastname: Zhu
authors.forename: Shi-juan
authors.initials: SJ
authors.lastname: Dong
authors.forename: Shui-sheng
authors.initials: SS
authors.lastname: Yu
authors.forename: Rui-song
authors.initials: RS
authors.lastname: Yu
authors.forename: Shi-yuan
authors.initials: SY
authors.lastname: Shen
authors.forename: Qian
authors.initials: Q
authors.lastname: Yang
authors.forename: Zhen
authors.initials: Z
authors.lastname: Li
mesh_terms: D000818:Animals; D002681:China; D016000:Cluster Analysis; D018076:DNA, Complementary / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D005243:Feces / Q000821:virology; D016679:Genome, Viral; D005838:Genotype; D016752:Hepatitis E virus / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification*; D006801:Humans; D016254:Mutagenesis, Insertional; D016366:Open Reading Frames; D010802:Phylogeny; D017354:Point Mutation; D012367:RNA, Viral / Q000235:genetics*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D017384:Sequence Deletion; D013552:Swine / Q000821:virology*
chemical_list: D018076:DNA, Complementary; D012367:RNA, Viral