title: Analysis of the full-length genome of a subgenotype IIIB hepatitis A virus isolate: primers for broadly reactive PCR and genotypic analysis.
abstract: Among six known subgenotypes (IA, IB, IIA, IIB, IIIA, and IIIB) of human hepatitis A virus (HAV), the complete genomic sequence has not been determined for IIIB. In this study, the full-length genomic sequence of a IIIB HAV isolate (HA-JNG06-90F) recovered from a Japanese patient who contracted sporadic hepatitis A in 1990, was determined. The HA-JNG06-90F genome, which comprised 7462 nt excluding the poly(A) tail, was related most closely to NOR-21 of subgenotype IIIA with an identity of 89.1%, and was only 82.6-83.4% similar to human HAV isolates of genotypes I and II over the entire genome. Comparison of full-length genomic sequences of 20 reported isolates and HA-JNG06-90F generated optimal results for separation of different levels: the nucleotide identities were 80.7-86.6% at the genotype level, 89.1-91.9% at the subgenotype level, and 94.6-99.7% at the isolate level. Similar ranges of nucleotide identity were observed when comparing partial nucleotide sequences of the VP1-2B (481 nt; primer sequences at both ends excluded) and 3C/3D (590 nt) regions, which were amplifiable by PCR with primers designed from well-conserved areas of the HAV genome. All 66 samples with IgM-class HAV antibodies tested positive for HAV RNA by both VP1-2B (481 nt)-PCR and 3C/3D (590 nt)-PCR: subgenotype assignment was concordant in all samples tested (IA [n = 61], IB [n = 1], IIIA [n = 2] and IIIB [n = 2]). These results suggest that two broadly reactive PCRs using primers derived from the VP1-2B and 3C/3D regions, respectively, may be applicable to universal detection and phylogenetic analysis of various HAV strains.
authors.affiliation: Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, Tochigi-Ken, Japan.
authors.forename: Kazunori
authors.initials: K
authors.lastname: Endo
authors.forename: Jun
authors.initials: J
authors.lastname: Inoue
authors.forename: Masaharu
authors.initials: M
authors.lastname: Takahashi
authors.forename: Takehiro
authors.initials: T
authors.lastname: Mitsui
authors.forename: Kazuo
authors.initials: K
authors.lastname: Masuko
authors.forename: Yoshihiro
authors.initials: Y
authors.lastname: Akahane
authors.forename: Hiroaki
authors.initials: H
authors.lastname: Okamoto
mesh_terms: D017931:DNA Primers; D004279:DNA, Viral / Q000097:blood; D016679:Genome, Viral; D005838:Genotype; D006506:Hepatitis A / Q000453:epidemiology / Q000235:genetics* / Q000821:virology; D030041:Hepatitis A virus / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D006801:Humans; D008969:Molecular Sequence Data; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D017421:Sequence Analysis
chemical_list: D017931:DNA Primers; D004279:DNA, Viral