Epidemiological investigation of PCV2 and PCV3 in three provinces of Northeast China in 2025

Abstract Background Porcine circovirus type 2 (PCV2) and porcine circovirus type 3 (PCV3) have emerged as significant pathogens jeopardizing the swine industry in China in recent years, and caused substantial economic losses to pig farms. Objective This study aimed to conduct an epidemiological investigation and genetic evolutionary analysis of PCV2 and PCV3 in three provinces of Northeast China in 2025. Methods A total of 322 clinical samples suspected of PCV infection were collected from 25 cities across the three provinces of Northeast China. All samples were tested for PCV2 and PCV3 by a duplex nested PCR. The genomes of selected PCV2 and PCV3 strains were sequenced for the subsequent homology and phylogenetic analysis. Results Among the 322 samples, the number and prevalence of PCV2-positive samples were 68 (21.12%), and the number and prevalence of PCV3-positive samples were 122 (37.89%). The highest positive rate for PCV2 was in Jilin Province, and the highest positive rate for PCV3 was in Liaoning Province. The positive rate of PCV2 and PCV3 were both higher in winter than that in other seasons. Homology and phylogenetic analysis performed on 17 sequenced PCV2 genomes revealed the nucleotide identity ranging from 96.20% to 99.90%, and all strains were classified as the genotype PCV2d. The 17 sequenced PCV3 genomes showed the nucleotide identity between 98.60% and 99.90%. Among these PCV3 strains, 5 strains belonged to the PCV3a, and 12 strains belonged to the PCV3c. The results of the amino acid sequence analysis of Cap showed that the 17 PCV2 strains exhibited multiple amino acid mutations within the antibody recognition domain. Among these, 16 strains harbored variations in the immunodominant decoy epitope. Additionally, amino acid mutations were detected in the nuclear localization signal of 5 strains. The results of PCV3 amino acid analysis showed that the residues at the position 24 and 27 were consistent with the phylogenetic analysis. Beyond these, only four amino acid mutations were observed and all of them were not located within the reported antibody recognition domain of the PCV3 Cap. Conclusion The currently predominant strains circulating in three provinces of Northeast China in 2025 were PCV2d and PCV3c. Seasonal analysis indicated a higher prevalence in winter for both PCV2 and PCV3. PCV2 Cap displayed amino acid variations at multiple key sites, while the amino acid of PCV3 Cap is relatively conserved. This study provided the crucial data for understanding the epidemiology of PCV2 and PCV3 and for the development of PCVAD control strategies in these regions.