GENOME ANNOUNCEMENT
Complete Genome Sequence of a Novel Duck Hepatitis A Virus Discovered in Southern China Chun-ya Wei, Shuo Su, Zhen Huang, Wan-jun Zhu, Ji-dang Chen, Fu-rong Zhao, Yan-jing Wang, Jie-xiong Xie, Heng Wang, and Guihong Zhang College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province, China
We report here the complete genomic sequence of a novel duck hepatitis A virus (DHAV) isolated from mixed infections with DHAV type 1 (DHAV-1) and DHAV-3 in ducklings in Southern China. The whole nucleotide sequence had the highest homology with the sequence of DHAV-3 (GenBank accession number DQ812093) (96.2%). To our knowledge, this is the first report of gene rearrangement between DHAV-1 and DHAV-3, and it will help to understand the epidemiology and molecular characteristics of duck hepatitis A virus in Southern China.
D
uck hepatitis virus is an acute and fatal disease in ducklings which is characterized by its rapid transmission. Duck hepatitis A virus (DHAV) was originally isolated from mule ducklings and goslings between 3 and 6 weeks of age. Coinfection with DHAV type 1 (DHAV-1) and DHAV-2 is common in Taiwan (3). DHAV-3 isolates were first reported in Korea (1), were also recently reported in the northeast of China, and more interestingly, were isolated from 60- to 90-day-old geese (2). In June 2011, duck hepatitis A virus type 3 was isolated from a commercial duck farm with an outbreak of an infectious disease whose clinical symptoms manifested with hemorrhagic liver lesions in ducklings in Guangdong Province, Southern China. Coinfection with DHAV-1 and DHAV-3 was found. Subsequently, nucleotide sequences were amplified through reverse transcription-PCR (RT-PCR). Amplified products were purified and cloned into the pMD18-T vector (TaKaRa) and sequenced with an ABI 3730 XL genome sequencer. Sequences were assembled and manually edited to produce the final genome sequence. The isolate virus was identified as DHAV-3 and named A/duck/ Guangdong/B-N/2011(DHAV-3) (B-N). Sequence analysis showed that the full genomic length of B-N is 7,782 nucleotides (nt) without the poly(A) tail, and the 5= and 3= terminal noncoding regions are 652 and 374 nucleotides, respectively. Additionally, the coding region of B-N includes a single open reading frame (ORF) which encodes a polypeptide of 2,252 amino acids. Compared with other relative DHAV strains, the nucleotide sequence homology was about 72.9% to 96.2%. The whole nucleotide sequence had the highest homology with the sequence of DHAV-3 (GenBank accession number DQ812093) (96.2%), medium homology with that of DHAV-2 (GenBank accession number EF067924) (78.3%), and the lowest homology with that of DHAV-1 (GenBank accession number DQ249299) (73.2%). The putative translation initiation site of B-N is located in an optimal Kozak context (GCAAUGG) at position 654. There is a conserved cis-acting element, the Yn-Xm-AUG motif, in the 3= border of the picornavirus internal ribosome entry site (IRES) element. Yn is a pyrimidine-rich region, and Xm is a spacer with a length of 15 to 25 nt, followed by AUG (4). The sequence of the B-N Yn-Xm-AUG motif is Y7-X66-AUG-CA-AUG. The 100 nt before the initiator codon of the B-N polyprotein have high similarity to those of DHAV-1.
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Amino acid sequence analysis showed that the most variable region of the capsid protein of B-N is located in P1. Positions 48 to 57, 138 to 147, and 180 to 223 are the hypervariable regions of VP1. There are 24 amino acids which are exactly the same as those in both DHAV-2 (GenBank accession number EF067923) and DHAV-3 (GenBank accession number DQ812093). All of these findings indicate that B-N is in a transitional state between DHAV-1 and DHAV-3. It might also be a recombinant strain with gene rearrangement in ducklings with coinfection of DHAV-1 and DHAV-3. Therefore, continuing duck hepatitis A virus surveillance in poultry is critical to understanding the genesis and emergence of future pandemic strains in Southern China. Nucleotide sequence accession number. The GenBank accession number of A/duck/Guangdong/B-N/2011(DHAV-3) is JX235698. ACKNOWLEDGMENTS This work was supported by the International Science & Technology Cooperation Program (2010DFB33920) and the Modern Agricultural Industry Technology System (CARS-36). The funding organizations had no role in the study design, data collection and analysis, ownership of the materials, or preparation of the manuscript.
REFERENCES 1. Kim MC. 2007. Recent Korean isolates of duck hepatitis virus reveal the presence of a new geno- and serotype when compared to duck hepatitis virus type 1 type strains. Arch. Virol. 152:2059 –2072. 2. Liu M, et al. 2011. Goose haemorrhagic hepatitis caused by a new subtype duck hepatitis type 1 virus. Vet. Microbiol. 152: 280 –283. 3. Tseng CH, Tsai, HJ. 2007. Molecular characterization of a new serotype of duck hepatitis virus. Virus Res. 126:19 –31. 4. Tseng CH, Knowles NJ, Tsai HJ. 2007. Molecular analysis of duck hepatitis virus type 1 indicates that it should be assigned to a new genus. Virus Res. 123:190 –203.
Received 28 June 2012 Accepted 28 June 2012 Address correspondence to Guihong Zhang,
[email protected]. C-Y.W. and S.S. contributed equally to this study. Copyright © 2012, American Society for Microbiology. All Rights Reserved. doi:10.1128/JVI.01643-12
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