Analysis of the full-length genome of a subgenotype IIIB hepatitis A virus isolate: Primers for broadly reactive PCR and genotypic analysis

Kazunori Endo, Jun Inoue, Masaharu Takahashi, Takehiro Mitsui, Kazuo Masuko, Yoshihiro Akahane, Hiroaki Okamoto

Research output: Contribution to journalArticlepeer-review

19 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)8-17
Number of pages10
JournalJournal of Medical Virology
Volume79
Issue number1
DOIs
Publication statusPublished - 2007 Jan

Keywords

  • Complete genome
  • Genotype
  • Hepatitis A virus
  • Phylogenetic analysis
  • RT-PCR

ASJC Scopus subject areas

  • Virology
  • Infectious Diseases

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