The Prevalence and Genetic Diversity of Porcine Circoviruses (PCVs) during 2017-2023 in Guangdong Province, China

Simple Summary Porcine circovirus (PCV2 and PCV3) currently stands as the primary viral agent afflicting intensive pig farming, inflicting substantial economic losses on farms. This study endeavored to explore the prevalence and genetic diversity of PCVs that have circulated in Guangdong province in recent years, a prominent hub for pig production within China. In the current investigation, the prevalence of PCV2, PCV3, and PCV2/3 co-infection was found to be 56.48%, 8.81%, and 8.81%, respectively. Nonetheless, no evidence of PCV4 presence materialized in the course of this study. Moreover, the co-occurrence of PCV2 with classical swine fever virus (CSFV), porcine reproductive and respiratory syndrome virus (PRRSV), pseudo-rabies virus (PRV), and porcine epidemic diarrhea virus (PEDV) emerged as a common phenomenon, with the co-infection rate with PEDV (23.85%) surpassing that of PRV (9.17%), PRRSV (18.35%), or CSFV (0.92%). Subsequently, a detailed analysis of the Cap protein sequence of the PCV2 and PCV3 isolates unveiled several high-frequency mutation sites within the epitope regions. Collectively, this study imparts valuable insights into the prevalence and evolution of PCV2 and PCV3 in China between 2017 and 2023, thereby contributing to the formulation of efficacious prevention and control strategies.Abstract Porcine circovirus disease poses a significant threat to the pig farming industry. Globally, four genotypes of porcine circovirus are circulating, with porcine circovirus type 2 and 3 (PCV2 and PCV3) being most strongly associated with clinical manifestations. The recently discovered porcine circovirus type 4 (PCV4) exhibits clinical symptoms resembling porcine dermatitis nephropathy syndrome. This study aimed to assess the prevalence and genetic characteristics of PCVs in Guangdong province, China. A comprehensive analysis was conducted on 193 samples collected from 83 distinct pig farms during the period of 2017-2023. A conventional PCR was employed to investigate the presence of PCV2, PCV3, and PCV4. Among the samples, 56.48%, 8.81%, and 8.81% tested positive for PCV2, PCV3, and PCV2/3 co-infection, respectively. Interestingly, PCV4 was not detected. Whole-genome sequencing was performed on 80 PCV2 isolates and 7 PCV3 isolates. A phylo-genetic analysis revealed that 12 strains belonged to PCV2a, 8 strains belonged to PCV2b, and 60 strains belonged to PCV2d, indicating the prevailing presence of PCV2d in Guangdong province, China. Furthermore, two PCV3 isolates were classified as PCV3a and five strains as PCV3b. Notably, an in-depth analysis of the Cap protein sequence of the PCV2 and PCV3 isolates identified high-frequency mutation sites located in predicted epitope regions. Overall, this study provides valuable insights into the prevalence and evolution of PCV2 and PCV3 during the period of 2017-2023 in Guangdong province, China, thereby contributing to the development of effective prevention and control measures.