Molecular Epidemiological Investigation and Genetic Evolution Analysis of Porcine Circovirus 3 in Hunan Province, China, from 2021 to 2024.

Abstract

Porcine circovirus 3 (PCV3), first reported in 2016, is associated with diverse clinical conditions, including porcine dermatitis and nephropathy syndrome, reproductive disorders, and systemic inflammation, and affects pigs of all ages. To investigate the prevalence and genetic evolution of PCV3 in Hunan Province, China, 700 lymph node tissue specimens were collected from slaughterhouses and hazard-free disposal centers across 14 prefecture-level cities between 2021 and 2024 and screened using real-time quantitative PCR (qPCR). Epidemiological investigation revealed an overall PCV3 positivity rate of 29.4% (206/700) in the province. The highest prevalence was observed in Yiyang City (56%, 28/50), whereas no positive samples were detected in Zhuzhou City (0/30). Among the positive samples, 34 specimens from different cities with Ct values < 25 were selected for Cap gene amplification and sequencing. Phylogenetic analysis showed that PCV3c was the predominant genotype (67.6%, 23/34), followed by PCV3a (32.4%, 11/34), while PCV3b was not detected. We identified twelve amino acid substitution sites within Cap proteins. Furthermore, B-cell linear epitope prediction and homology modeling of the Cap protein identified seven linear epitopes, with ten amino acid variation sites located within these epitopic regions. This study enriches the molecular epidemiological data of PCV3 in southern China and provides a reference for future PCV3 control strategies.