Full-length genome of wild-type hepatitis A virus (DL3) isolated in China

AIM: To characterize the genome of an wild-type HAV isolate (DL3) in China. METHODS: A stool specimen was collected from hepatitis A patient from Dalian, China. HAV (DL3) was isolated and viral RNA was extracted. The genome of DO was amplified by reverse transcription and polymerase chain reaction (RT-PCR), followed by cloning into pGEM-T vector. The positive colonies were selected and sequenced. The full-length genome of DO was analyzed and compared with other wild-type HAV isolates. RESULTS: The genome of DO was 7 476 nucleotides (nt) in size, containing 732-nt 5'untranslated region (UTR), 6 681-nt open reading frame (ORF) which encoded a polyprotein of 2 227 amino acids (aa), and 63-nt 3'UTR. The base composition was 28.96% A (2 165), 16.08% C (1202), 22.11% G(1653) and 32.85% U (2 456). Genomic comparisons with wildtype HAV isolates revealed that DO had the highest identity of 97.5% for nt (185 differences) with AH1, the lowest identity of 85.7% (1 066 differences) with SLF88. The highest identity of 99.2% for amino acid (18 differences) appeared among DL3, AH2 and FH3, and the lowest identity of 96.8% (72 differences) between DL3 and SLF88. Based upon comparisons of the VP1/2A junction and the VP1 amino terminus, DL3 was classified as subgenotype IA. Phylogenetic analysis showed that DL3 was closest to the isolates in Japan. CONCLUSION: The sequence comparison and phylogenetic analysis revealed that DO is most similar to the isolates in Japan, suggesting the epidemiological link of hepatitis A happened in China and Japan.