Marked genomic heterogeneity of rat hepatitis E virus strains in Indonesia demonstrated on a full-length genome analysis.
Rat hepatitis E virus (HEV) strains have recently been isolated in several areas of Germany, Vietnam, the United States, Indonesia and China. However, genetic information regarding these rat HEV strains is limited. A total of 369 wild rats (Rattus rattus) captured in Central Java (Solo) and on Lombok Island, Indonesia were tested for the presence of rat HEV-specific antibodies and RNA. Overall, 137 rats (37.1%) tested positive for rat anti-HEV antibodies, while 97 (26.3%) had rat HEV RNA detectable on reverse transcription-PCR with primers targeting the ORF1-ORF2 junctional region. The 97 HEV strains recovered from these viremic rats were 76.3-100% identical to each other in an 840-nucleotide sequence and 75.4-88.4% identical to the rat HEV strains reported in Germany and Vietnam. Five representative Indonesian strains, one from each of five phylogenetic clusters, whose entire genomic sequence was determined, were segregated into three genetic groups (a German type, Vietnamese type and novel type), which differed from each other by 19.5-23.5 (22.0 ± 1.7)% over the entire genome. These results suggest the presence of at least three genetic groups of rat HEV and indicate the circulation of polyphyletic strains of rat HEV belonging to three distinct genetic groups in Indonesia.
West Nusa Tenggara Hepatitis Laboratory, Mataram, Indonesia; Immunobiology Laboratory, Faculty of Medicine, University of Mataram, Mataram, Indonesia.
Mulyanto
Department of Clinical Pathology, Moewardi Hospital, University of Sebelas Maret, Solo, Indonesia.
Joseph Benedictus
JB
Suparyatmo
Immunobiology Laboratory, Faculty of Medicine, University of Mataram, Mataram, Indonesia.
I Gusti Ayu Sri
IG
Andayani
Immunobiology Laboratory, Faculty of Medicine, University of Mataram, Mataram, Indonesia.
Khalid
Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, 3311-1 Yakushiji, Shimotsuke-Shi, Tochigi-Ken 329-0498, Japan.
Masaharu
M
Takahashi
Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, 3311-1 Yakushiji, Shimotsuke-Shi, Tochigi-Ken 329-0498, Japan.
Hiroshi
H
Ohnishi
Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, 3311-1 Yakushiji, Shimotsuke-Shi, Tochigi-Ken 329-0498, Japan.
Suljid
S
Jirintai
Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, 3311-1 Yakushiji, Shimotsuke-Shi, Tochigi-Ken 329-0498, Japan.
Shigeo
S
Nagashima
Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, 3311-1 Yakushiji, Shimotsuke-Shi, Tochigi-Ken 329-0498, Japan.
Tsutomu
T
Nishizawa
Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, 3311-1 Yakushiji, Shimotsuke-Shi, Tochigi-Ken 329-0498, Japan. Electronic address: hokamoto@jichi.ac.jp.
Hiroaki
H
Okamoto
D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D016679:Genome, Viral; D023281:Genomics; D016751:Hepatitis E / Q000453:epidemiology / Q000662:veterinary* / Q000821:virology; D016752:Hepatitis E virus / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification*; D007214:Indonesia / Q000453:epidemiology; D008969:Molecular Sequence Data; D010802:Phylogeny; D051381:Rats; D012376:Rodent Diseases / Q000453:epidemiology / Q000821:virology*; D016415:Sequence Alignment
Genotype; Hepatitis E virus; Indonesia; Phylogeny; Rat