Analysis of the full‐length genome of a subgenotype IIIB hepatitis A Virus isolate: Primers for broadly reactive PCR and genotypic analysisThe nucleotide sequence data reported in this study have been assigned GenBank/EMBL/DDBJ accession numbers AB258387 (entire HAV sequence) and AB258539‐AB258670 (132 partial HAV sequences).

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. J. Med. Virol. 79:8–17, 2007. © 2006 Wiley‐Liss, Inc. [ABSTRACT FROM AUTHOR]