Epidemiological investigation and whole-genome genetic characterization of duck circovirus in Shandong Province of eastern China.

INTRODUCTION

Duck circovirus (DuCV) is a contagious immunosuppressive pathogen in duck populations, causing severe economic losses in the global waterfowl breeding industry. Shandong Province is a major duck-producing region in China, with one of the country's largest duck populations.

METHODS

In this study, we systematically investigated the prevalence, genetic characteristics, and major proteins of DuCV strains found in Shandong Province. A total of 630 cloacal swab samples were collected from more than 60 duck farms across 17 cities of Shandong province in 2023. Duck circovirus and other common duck pathogens were detected by the polymerase chain reaction (PCR) method. Whole-genome sequencing was further performed to acquire three representative complete DuCV genome sequences, followed by comprehensive phylogenetic and genotypic analyses.

RESULTS

The positive rate for duck circovirus was 12.54% (79/630), with variation in detection rates among the sampled cities. Riemerella anatipestifer and duck parvovirus were identified as the dominant co-infecting pathogens. Genomic analysis showed that the full-genome lengths of the three complete DuCV genome sequences ranged from 1988 bp to 1993 bp. The three sequenced DuCV genome sequences belonged to the DuCV-1b and DuCV-2c sub-genotypes. Notable differences were observed in the N-glycosylation site and 3D structure of the cap proteins between the two genotypes. The three novel DuCV genome sequences shared 56.40-99.79% nucleotide sequence identity with global reference DuCV sequences. Phylogenetic trees of DuCV based on the whole genome, Cap gene, and Rep gene were constructed using reference strains from around the world.

CONCLUSION

This study provides updated epidemiological survey data and genetic information on DuCV in Shandong Province, China, which provides reference data for further research on the prevention and control of DuCV infection.