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J Virol. Dec 2012; 86(23): 13136.
PMCID: PMC3497624

Complete Genome Sequence Analysis of a Duck Circovirus from Guangxi Pockmark Ducks

Abstract

We report here the complete genomic sequence of a novel duck circovirus (DuCV) strain, GX1104, isolated from Guangxi pockmark ducks in Guangxi, China. The whole nucleotide sequence had the highest homology (97.2%) with the sequence of strain TC/2002 (GenBank accession number AY394721.1) and had a low homology (76.8% to 78.6%) with the sequences of other strains isolated from China, Germany, and the United States. This report will help to understand the epidemiology and molecular characteristics of Guangxi pockmark duck circovirus in southern China.

GENOME ANNOUNCEMENT

Duck circovirus (DuCV), isolated from Muscovy duck (3) and mulard duck (5), is involved in duck diseases, with the main clinical symptoms including immunosuppression and feather disorders in young ducks. The genome of DuCV is circular and 1,996 nucleotides (nt) in size. Two major open reading frames (ORFs) were identified, encoding the replicase (V1) and the capsid protein (C1) (4). DuCV was first reported in Germany (3) and was also recently reported in China (1, 2, 6). The whole nucleotide sequences of these strains had a homology of 83.2% to 99.8%.

In April 2011, DuCV was isolated from a commercial Guangxi pockmark duck farm with an outbreak of an infectious disease whose clinical symptoms manifested with severe immunosuppression and feather disorders in ducklings in Guangxi Province, southern China. Subsequently, nucleotide sequences of DuCV were amplified through PCR. The amplified products were purified and cloned into the pMD18-T vector (TaKaRa) and then sequenced (TaKaRa, Dalian, China). Sequences were assembled and manually edited to produce the final genome sequence. The isolate's virus was named duck/Guangxi/04/2011 (GX1104).

Sequence analysis showed that the full genomic length of GX1104 is 1,988 nt. Additionally, the coding region of GX1104 includes two major ORFs, V1 and C1, encoding polypeptides of 292 and 257 amino acids, respectively. Compared with other relative DuCV strains, the V1 and C1 nucleotide sequence homologies were about 85.6% to 97.8% and 74.4 to 96.4%, respectively. The complete genome sequence homology was about 76.8% to 97.2%.

The whole nucleotide sequence had the highest homology (97.2%) with the sequence of strain TC/2002 (GenBank accession number AY394721.1; origin, Taiwan, China), a medium homology (76.8% to 78.6%) with that of five Chinese strains (GenBank accession numbers EF451157.1, GQ334371.1, GU131342.1, HM162345.1, and HQ180265.1; origin, China), strain 33753-52 (GenBank accession number DQ100076.1; origin, the United States), and a German strain (GenBank accession number NC_005053.1; origin, Germany), and the lowest homology (54.2%) with that of strain JX1(Goose circovirus) (GenBank accession number GU320569.1; origin, Jiangxi, China).

The homologies of the whole nucleotide sequence of GX1104, with the sequences of two mallard duck circovirus strains (GenBank accession numbers NC_005053 and HQ180266), two Mule duck circovirus strains (GenBank accession numbers EU344803 and EU499309), two Muscovy duck circovirus (GenBank accession numbers EF451157 and AY394721), two Perkin duck circovirus (GenBank accession numbers NC_007220 and DQ100076), and two Cherry valley duck circovirus (GenBank accession numbers GU131342 and HM162352), were 76.8%, 77.1%, 80.4%, 95.5%, 77.9%, 97.1%, 78.6%, 78.6%, 78.6%, and 78.4%, respectively. The homology of the whole nucleotide sequence of GX1104 with the sequence of all 14 Cherry valley duck circovirus in GenBank was less than 80%. The results indicated that Guangxi pockmark duck circovirus was different from Cherry valley duck circovirus.

Phylogenetic analysis of the whole nucleotide sequence of GX1104 indicates that Guangxi pockmark duck circovirus has been mutated, resulting in Guangxi pockmark clinical symptoms manifested with severe immunosuppression and feather disorders. Further study is required.

Nucleotide sequence accession number.

The GenBank accession number of duck/Guangxi/04/2011(GX1104) is JX241046.

ACKNOWLEDGMENTS

This work was supported by the Science and Technology Projects of Guangxi Province (grants 10100014-5 and 11-3) and Guangxi government senior scientist foundation project from the Guangxi Science and Technology Department of China.

REFERENCES

1. Fu G, Cheng LF, Shi SH, Peng CX, Chen HM, Huang Y. 2008. Genome cloning and sequence analysis of duck circovirus. Bing Du Xue Bao 24:138–143 (In Chinese.) 18533346 [PubMed]
2. Fu G, et al. 2011. Genetic diversity and genotype analysis of duck circovirus. Avian Dis. 55:311–318 [PubMed]
3. Hattermann K, Schmitt C, Soike D, Mankertz A. 2003. Cloning and sequencing of duck circovirus (DuCV). Arch. Virol. 148:2471–2480 [PubMed]
4. Johne R, Fernández-de-Luco D, Höfle U, Müller H. 2006. Genome of a novel circovirus of starlings, amplified by multiply primed rolling-circle amplification. J. Gen. Virol. 87:1189–1195 [PubMed]
5. Soike D, Albrecht K, Hattermann K, Schmitt C, Mankertz A. 2004. Novel circovirus in mulard ducks with developmental and feathering disorders. Vet. Rec. 154:792–793 [PubMed]
6. Wan CH, et al. 2011. Epidemiological investigation and genome analysis of duck circovirus in Southern China. Virol. Sin. 26:289–296 [PubMed]

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