Identification and characterization of a novel circovirus species in domestic laying ducks designated as duck circovirus 3 (DuCV3) from Hunan province, China

Duck circovirus (DuCV) is an immunosuppressive virus and can induce immunosuppression increasing rates of infection caused by other pathogens, which has resulted in gross economic losses in poultry industries. The genome sizes of DuCVs varied from 1987 to 1996 nucleotides (nt). Up to date two DuCV genotypes/lineages, DuCV1 and DuCV2, have been defined, with genome identities of around 83% between each other. In this study, a novel duck circovirus having a genome size of 1755 nt was identified from laying ducks with a disease of egg production declining or abrogation from Hunan province, China. Two major open reading frames (ORFs) were identified, with ORF1 (882 nt) and ORF2 (738 nt) encoding replicase (Rep) and capsid protein (Cap), respectively. Its genome showed the highest identities of 62.3–63.7% and 66.3%− 67.8% to the known genomes of DuCVs and goose circoviruses (GoCVs) available in GenBank, respectively, while it showed less than 50% identities to the genomes of other circoviruses. The amino acid sequence of capsid of this virus showed the highest identities of 45.4%− 47.3% and 42.9%− 44.5% to capsids of the known DuCVs and GoCVs, respectively, while it showed less than 27% identity to the capsid proteins of other circoviruses available in GenBank. Further phylogenetic analyses based on genomes, amino acid sequences of Rep and Cap proteins demonstrated that the present duck circovirus was clustered in a separate clade, distinct from other DuCVs and GoCVs, corroborating it is a distinct novel circovirus species in ducks, tentatively designated as duck cirovirus 3 (DuCV3). The clinical significance and pathogenesis of this virus needs further investigation.