The rat HEV used in this study was isolated from a 10% lung homogenate of a wild rat from Vietnam, which was positive for rat HEV RNA by reverse transcription PCR (RT-PCR) (14). Because of the limited availability of rat specimens that are positive for HEV RNA, we first transmitted the rat HEV to a laboratory rat (Wistar) to produce a large amount of virus for RNA extraction and genome amplification. After intravenous inoculation of the rat, fecal specimens positive for HEV RNA were collected, and a 10% suspension was prepared as described (15). RT-PCR was performed by using Superscript II RNase H^– (Invitrogen, Carlsbad, CA, USA) and primer TX30SXN (14). The full-length genome of the V-105 strain was amplified by RT-PCR with primers based on the nucleotide sequences of GU345042 and JN040433 (Table 1). All PCR products were purified by using the QIAquick PCR Purification Kit (QIAGEN, Valencia, CA, USA) and cloned into TA cloning vector pCR2.1 (Invitrogen). The nucleotide sequencing was carried out by using an ABI 3130 Genetic Analyzer automated sequencer (Applied Biosystems, Foster City, CA, USA).

Because 901 nt of V-105, corresponding to nt 4108–5008 of the R63 genome, were already known (14), primers F13 and open reading frame (ORF) 1–R12 were designed. An ≈2,100-nt fragment of the C-terminus of the rat HEV V-105, nt 4923-poly (A) tail, was amplified with a pair of primers, F13 and TX30SXN, by the first RT-PCR. The ORF1 region was amplified with primers ORF1-F1 and ORF1-R12. Two fragments, 440 nt (nt 11–450) and 1,182 nt (nt 2990–4171), were amplified by nested PCR with 2 sets of primers, ORF1-F2/ORF1-R1 and ORF1-F7/ORF1-R12, respectively. On the basis of the nucleotide sequences of those amplified fragments, ORF1-F9, ORF1-F16, ORF1-R16, ORF1-F18, and ORF2-R21 were designed, and 3 fragments, 1,830 nt (nt 388–2217), 996 nt (nt 2080–3075), and 1,110 nt (nt 3991–5100), were amplified with 3 sets of primers, ORF1-F9/ORF1-R10, ORF1-F16/ORF1-R16, and ORF1-F18/ORF2-R21, respectively.

To amplify the N-terminus nonstructural region of V-105, we synthesized cDNA with primer ORF1-R14, and a DNA anchor (P-CACGAATTCACTATCGATTCTGGAACCTTCAGAGG-NH₃) was linked to the N-terminus of the cDNA by T4 RNA Ligase I (BioLabs, Tokyo, Japan). By using this anchor-cDNA as the template, the first and the nested PCRs were carried out with 2 sets of primers, anchor-1/ORF1-R14 and anchor-2/ORF1-R13, respectively.

The V-105 genome consisted of 6,927 nt plus a poly (A) tail of a still-undetermined length (GenBank accession no. JX120573). The genomic structure of V-105 was, from the N-terminus toward the C-terminus, the N 5′–untranslated region (UTR) at nt 1–10, ORF1at nt 11–4900, ORF3 at nt 4917–5225, ORF2 at nt 4928–6862, the 3′-UTR at nt 6863–6927, and the poly (A) tail starting at nt 6928. ORF2 and ORF3 encode 644 aa and 102 aa, respectively, as do R63 and R68. However, ORF1 of V-105 encodes 1,629 aa, which is 7 aa shorter than either R63 or R68. The V-105 genome possessed 2 aa insertions (Ser-Pro) between the aa residues 591 and 592 and 9 aa deletions (Ser-Pro-Pro-Gly-Pro-Pro-Pro-Ala-Gly) between aa residues 852 and 853, corresponding to those of R63. The 3′-UTR was 65 nt as were R63 and R68. Unlike R63 and R68, only 1 additional putative ORF, corresponding to ORF4 (nt residues 27–578), was found in V-105, suggesting that other putative ORFs, ORF5 and ORF6 found in R63 and R68, are not common in rat HEV.

When the V-105 genome was compared with reported HEV genomes, the V-105 genome shared identities of only 50.5% with avian HEV, 53.6% with rabbit HEV, 53.7%–54.0% with wild boar HEV, and 53.1%–53.5% with HEV genotypes 1–4. In contrast, V-105 shared relatively high nucleotide sequence identities (76.8%–76.9%) with rat HEV strains (R63 and R68) (Table 2). The nucleotide and amino acid sequences of ORF1, ORF2, and ORF3 of V-105 were compared with those of other HEV genotypes, and the identities among them are shown in Table 2. Together, these results suggest that V-105 is more similar to rat HEV than to other HEV genotypes.

Figure

Figure. . Phylogenetic relationships among genotypes 1–4, wild boar, rabbit, avian (chicken), and rat hepatitis E virus (HEV) isolates. The nucleic acid sequence alignment was performed by using ClustalX 1.81 (www.clustal.org)....

Phylogenetic trees were generated on the basis of the nucleotide sequences derived from the entire genome and ORF3 of the genotypes 1–4, wild boar, rabbit, chicken, and rat HEV isolates. These trees demonstrated that V-105 does not belong to any known genotype and should probably be classified into a new genotype (Figure).

In this study we successfully amplified the entire genome of an HEV strain isolated from a wild rat in Vietnam. Phylogenetic analyses and nucleotide and amino acid sequence comparisons demonstrated that the complete rat HEV genome sequences were consistently well separated from those of mammalian genotypes 1–4, wild boar, rabbit, and chicken HEV and close to those of the rat HEV strains. Although the entire genome of V-105 shared nucleotide sequence identities of only 76.8%–76.9% with the isolates from Germany (R63 and R68), the ORF1 and ORF3 amino acid identities between V-105 and these isolates were 86.4%–87.0% and 66.7%, respectively, which suggests that V-105 can be classified into a new genotype of rat HEV. However, ORF2 has relatively high amino acid identities with R63 and R68 (91.6%–92.1%), indicating that the V-105 and rat HEV isolates from Germany share similar antigenicity. In fact, rat HEV–like particles derived from R63 are cross-reactive to serum from V-105–infected wild rats (14).

In conclusion, we isolated and identified rat HEV strain V-105 from a wild rat in Vietnam, and this strain was highly divergent from known rat HEV isolates. We propose that the strain from Vietnam, V-105, is a new member of the rat HEV genotype.