GENOME ANNOUNCEMENT
Complete Genome Sequence of a Duck Hepatitis A Virus Type 3 Identified in Eastern China Qian Xu,a,b Ruihua Zhang,a,b Linlin Chen,a,b Lei Yang,a,b Jingxin Li,a,b Pengfei Dou,a,b Hui Wang,a,b Zhijing Xie,a,b Yu Wang,c and Shijin Jianga,b Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Taian, Shandong, Chinaa; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian, Shandong, Chinab; and Department of Basic Medical Sciences, Taishan Medical College, Taian, Shandong, Chinac
We report here the complete genome sequence of a novel duck hepatitis A virus type 3 (DHAV-3) isolated from a dead Cherry Valley duckling in eastern China. The whole genomic nucleotide sequence and polyprotein amino acid sequence of the virus had higher homology with those of Chinese DHAV-3 isolates, medium homology with those of Korean DHAV-3 isolates, and the lowest homology with those of Vietnamese isolate DN2. The result indicated that the genetic evolution of DHAV-3 isolates had obvious geographical features.
D
uck virus hepatitis (DVH) is an acute, rapidly spreading, and fatal disease of ducklings, characterized by liver necrosis, hemorrhage, and high mortality. The disease is caused by duck hepatitis A virus (DHAV), duck astrovirus type 1 (DAstV-1), and DAstV-2, and no antigenic relationships have been found between the three different viruses (2, 5, 7). DHAV is divided into three serotypes: DHAV type 1 (DHAV-1), DHAV-2, and DHAV-3. There is no cross-neutralization between DHAV-1 and DHAV-2 (6) and limited cross-neutralization between DHAV-1 and DHAV-3 (3). DHAV-3 was first reported in Korea (3) and was recently reported in China (1, 4, 8). Here we report a new DHAV-3 strain isolated from a 4-day-old dead duckling. In September 2011, DHAV-3 strain SD1101 was isolated from a commercial Cherry Valley duck farm in Shandong Province, eastern China. The mortality of the duck flock was more than 60%, and the sick ducklings died quickly with typical hemorrhagic hepatitis. To determine the complete genome sequence of the isolate, 10 pairs of primers were designed based on DHAV-3 strains AP-04203, AP-03337, AP-04009, and AP-04114 to generate overlapping amplicons by reverse transcription-PCR (RT-PCR). The terminal sequences were obtained by using a TaKaRa kit for rapid amplification of cDNA ends (RACE). The PCR products were purified and cloned into the pMD18-T vector (TaKaRa) and sequenced by Sangon Biotech Co., Ltd. (China). DNAStar version 7.0 and the ClustalW method were applied to the genomic analysis. The full genomic length of SD1101 is 7,774 nucleotides (nt), with a 5=-terminal untranslated region (UTR) of 652 nt and a 3=-terminal UTR of 386 nt, including a 20-nt poly(A) tail. The coding region of SD1101 includes a single long open reading frame (ORF), which encodes a polyprotein of 2,251 amino acids (aa), and the polyprotein is processed by viral proteases into mature viral polypeptides. Comparative genomic analysis revealed that SD1101 showed high nucleotide similarity (96.2% to 98.7%) to Chinese DHAV-3 isolates (including 1v, SD01, SD02, GD, C-GY, C-YDF, C-BLZ, C-YCZ, C-YCW, FS, G, and JT), medium nucleotide homology (95.3% to 95.6%) to Korean DHAV-3 isolates (AP-04203, AP-03337, AP-04009, and AP-04114), and the lowest nucleotide homology (90.8%) to the DN2 strain isolated from Vietnam. Amino acid sequence analysis showed that the most variable region of the polyprotein of DHAV-3 is located at positions 178 to 219 in the most external and dominant regions of capsid protein VP1. The hypervariable region of SD1101 was similar to
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that of other Chinese DHAV-3 isolates but different from those of Korean and Vietnamese DHAV-3 isolates. There does seem to be close relationship between the geographic distribution and antigenic evolution of DHAV-3. The genome data of a new DHAV-3 strain isolated from a dead duckling in eastern China reported in our study will be helpful for understanding the epidemiology and evolution of DHAV-3. Nucleotide sequence accession number. The complete genome sequence of the DHAV-3 SD1101 strain has been submitted to GenBank under accession no. JQ409566. ACKNOWLEDGMENTS This work was supported by Shandong Province Higher Educational Science and Technology Program (J08LF07) and the Science and Technology Commission of Shandong Province (2010GNC10914), China.
REFERENCES 1. Fu Y, et al. 2008. Molecular detection and typing of duck hepatitis A virus directly from clinical specimens. Vet. Microbiol. 131:247–257. 2. Haider SA, Calnek BW. 1979. In vitro isolation, propagation, and characterization of duck hepatitis virus type III. Avian Dis. 23:715–729. 3. Kim MC, et al. 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. 4. Liu M, Fanyi-Meng, Li XJ, Zhang Z, Liu S, Zhang Y. 2011. Goose haemorrhagic hepatitis caused by a new subtype duck hepatitis type 1 virus. Vet. Microbiol. 152:280 –283. 5. Toth TE. 1969. Studies of an agent causing mortality among ducklings immune to duck virus hepatitis. Avian Dis. 13:834 – 846. 6. Tseng CH, Tsai HJ. 2007. Molecular characterization of a new serotype of duck hepatitis virus. Virus Res. 126:19 –31. 7. Wang X, Wang Y, Xie X, Zhang B, Zhang D. 2011. Expression of the C-terminal ORF2 protein of duck astrovirus for application in a serological test. J. Virol. Methods 171:8 –12. 8. Wei CY, et al. 2012. Complete genome sequence of a novel duck hepatitis A virus discovered in Southern China. J. Virol. 86:10247.
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Received 26 September 2012 Accepted 27 September 2012 Address correspondence to Shijin Jiang,
[email protected]. Q.X. and R.Z. contributed equally to this work. Copyright © 2012, American Society for Microbiology. All Rights Reserved. doi:10.1128/JVI.02651-12
December 2012 Volume 86 Number 24
