Genetic characterization and sequence heterogeneity of a canadian isolate of Swine hepatitis E virus

Abstract

Swine hepatitis E virus (HEV) is a newly identified potentially zoonotic agent that is possibly transmitted to humans from pigs. Swine HEV is prevalent in pig populations and does not cause abnormal clinical symptoms in infected pigs, further implicating a likelihood of a risk of transmission to humans by normal contact. To date in North America, only one strain of swine HEV (strain US swine) has been fully sequenced. In the present study, we identified a swine HEV isolate from pigs in Canada, designated the Arkell strain, and determined the full length of the genomic sequence. The genome of Canadian strain Arkell consisted of 7,242 nucleotides, excluding the poly(A) tail of at least 15 A residues. The genome contained three open reading frames (ORFs), ORF1, ORF2, and ORF3, which had coding capacities for proteins of 1,708, 660, and 122 amino acids, respectively. Comparative analysis of the full-length genomic sequence indicated that the sequence of strain Arkell was distinct from those of all other known HEV isolates by 13 to 27% and shared the highest degrees of identity with human HEV isolates US-1 and US-2, HEV isolate US swine, and the human and swine HEV isolates recently isolated in Japan. On the basis of sequence similarities and phylogenetic analyses, HEV strain Arkell was grouped into genotype 3. The sequence of the Arkell swine HEV isolate differed from those of HEV isolate US swine and HEV isolate Japan swine by 13 and 14%, respectively. To date, two isolates of swine HEV (isolates Arkell and SK3 [D. Yoo et al., Clin. Diagn. Lab. Immunol. 8:1213-1219, 2001]) have been identified in Canadian pigs, and their sequences also differ from each other by 11.8%. Our studies indicate that, as with human HEV strains, swine HEV isolates exhibit extensive genetic heterogeneity.

FIG. 1.

Amino acid sequence alignments of the hypervariable region in ORF1 of various human and swine HEV strains. Numbers in parentheses indicate the amino acid positions of the ORF1 protein. Only different amino acid residues are presented. Identical amino acids are indicated by dots, and deletions are indicated by dashes.

FIG. 2.

Nucleotide sequence alignments of the 3′ UTR of different 3 HEV strains. Stop represents the translation termination codon of ORF2. Asterisks indicate conserved nucleotides. Identical nucleotides are indicated by dots, and deletions are indicated by dashes.

FIG. 3.

Unrooted phylogenetic trees depicting the relationships of the genomic sequences of swine and human HEV strains. (A) Full-length genomic sequence; (B) 242 nucleotides encoding the nonstructural methyltransferase gene in ORF1; (C) 304 nucleotides encoding the ORF2 structural gene. HEV strains isolated from pigs are underlined. The scales represent the number of nucleotide changes (nts). The internal node numbers represent the bootstrap values as a percentage of trees obtained from 100 replicates. The GenBank accession numbers for each sequence are presented in Materials and Methods.

FIG. 3.

Unrooted phylogenetic trees depicting the relationships of the genomic sequences of swine and human HEV strains. (A) Full-length genomic sequence; (B) 242 nucleotides encoding the nonstructural methyltransferase gene in ORF1; (C) 304 nucleotides encoding the ORF2 structural gene. HEV strains isolated from pigs are underlined. The scales represent the number of nucleotide changes (nts). The internal node numbers represent the bootstrap values as a percentage of trees obtained from 100 replicates. The GenBank accession numbers for each sequence are presented in Materials and Methods.