Full genomic analysis of hepatitis delta virus prevalent on Miyako Island, Japan

The aims of this study were to determine the full-length genome sequences of hepatitis delta virus (HDV) in HDV RNA-positive subjects, and to elucidate the molecular specificity of the HDVs that are clustered on a distant island in Japan. This study included 3 subjects with chronic hepatitis who were positive for hepatitis B surface (HBs) antigen and HDV RNA, and who were admitted to the Okinawa Prefectural Miyako Hospital in 1998. The full-length genome sequence of HDV was determined by nested polymerase chain reaction (PCR) using four kinds of primer sets. The genomic length of HDV was 1,675, 1,679 and 1,681 base pairs, respectively. There was 90-92% nucleotide homology between each pair of isolates. In comparison with HDV isolates in geographically neighboring regions, the nucleotide homology of the 3 HDV isolates were 73-75% with the China isolate of genotype I; 77-78% with the Taiwan isolate of genotype I; 83-84% with a Japan isolate of genotype IIa; 85-87% with the Taiwan isolate of genotype IIa, and 87-88% with the Taiwan isolates of genotype IIb. Therefore, the Miyako Island isolates had high homology with the Taiwan isolate of genotype IIa and IIb. Phylogenetic analysis of the full-length genome sequences of HDV revealed that the two Miyako Island isolates were classified into a genotype IIb'. The other one was classified as genotype IIb. In conclusion, the HDV of Miyako Island isolates can be classified as a novel subgroup of genotype IIb, designated type IIb', and genotype IIb.