Genome analysis and epidemiological investigation of goose circovirus detected in eastern China

Goose circovirus (GoCV), a potential immuno-suppressive virus, was detected in a sample collected from Yongkang avian influenza (AI) case in Zhejiang Province of eastern China. Further, epidemiological investigation showed that, four farms located in the two major rearing areas of Yongkang and Xiangshan out of eight in Zhejiang Province were positive for GoCV. However, the geese in these GoCV positive farms exhibited no apparent clinical abnormality. The complete genomes of ten isolates from Yongkang AI case (yk1) and other four different farms were sequenced. They had 90.8-99.9% nucleotide (nt) identity with each other and had 91.3-95.8% nt identity to that of the Taiwan and German strains. Genome analysis showed that the GoCVs isolated in Zhejiang Province possessed common features of circovirus, including the potentially replication-associated stem-loop structure, the Rep protein motifs, etc. Highly variable region was also detected between nt27 and nt72 in the intergenic region. Phylogenetic analysis showed that GoCVs could be divided into three distinct genetic groups, where groups I and II could each be further divided into two subgroups (I1, I2 and II1, II2, respectively). No obvious characteristic was found between subclinical strains and clinical strains. However, both the phylogenetic result and analysis of highly variable region revealed that GoCVs isolated from different locations had some geographically dependent characteristics. This is the first epidemiological investigation of GoCV in the mainland of China.