Molecular epidemiology and genetic diversity of duck hepatitis A virus type 3 in Shandong province of China, 2012-2014.

The infections with duck hepatitis A virus type 3 (DHAV-3) become common in eastern Asia. To better understand the molecular evolution and genetic variation of DHAV-3, a total of 482 dead Cherry Valley duckling liver samples collected from Shandong province of China during 2012-2014 were tested, and the complete P1 coding sequences of 18 DHAV-3 strains were analyzed. The detection rate of DHAV-3 was 64.5% (311/482) in clinical liver samples and 73.0% (92/126) in duckling flocks. The P1 genes of the 18 DHAV-3 isolates shared 91.9%-99.0% nucleotide similarity and 95.2%-100% amino acid similarity with those of the other 26 reference strains. Based on the P1 and VP1 gene sequences, phylogenetic analysis results indicated that the genotyping of DHAV-3 strains presented a distinct geographical distribution. Except B63 strain, all Chinese strains isolated from different host species (duck or goose) at different time were classed into the CH genotype. All Korean and Vietnamese strains belonged to the KV genotype, and all the Korean strains were clustered into KV1 subgenotype, while B63 strain and the Vietnamese strains from different host species (duck or goose) were clustered into KV2 subgenotype. Ten variable amino acid residues were highly conserved within genotypes or subgenotypes in the VP0, VP3 and VP1, respectively, which were possibly the geographic molecular markers of DHAV-3. To the best of our knowledge, this is the first study about the genetic variation of the P1 gene of different DHAV-3 strains, which will be helpful for understanding of the molecular epidemiology of DHAV-3.