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

To characterize the genome of an wild-type HAV isolate (DL3) in China.

A stool specimen was collected from hepatitis A patient from Dalian, China. HAV (DL3) was isolated and viral RNA was extracted. The genome of DL3 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 DL3 was analyzed and compared with other wild-type HAV isolates.

The genome of DL3 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 (1 202), 22.11 % G(1 653) and 32.85% U (2 456). Genomic comparisons with wild-type HAV isolates revealed that DL3 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.

The sequence comparison and phylogenetic analysis revealed that DL3 is most similar to the isolates in Japan, suggesting the epidemiological link of hepatitis A happened in China and Japan.