Prevalence and genetic diversity of porcine circovirus type 2 in Henan Province of China during 2020-2023

Abstract

Abstract The genetic diversity and widespread of porcine circovirus type 2 (PCV2), mainly lead to porcine circovirus-associated diseases (PCVADs), seriously threatens the swine industry worldwide. In the present study, to investigate the recent prevalence and genetic diversity of PCV2 in Henan Province of China, a total of 385 tissue samples collected from pig farms of different sizes during 2020 and 2023 were analyzed by PCR. Overall, 71.17% (274/385) tissue samples of pigs were positive for PCV2, with the detection rates of PCV2 were 81.16% (112/138), 72.41% (84/116), 62.50% (55/88), 53.49% (23/43) in 2020, 2021, 2022, 2023, respectively, indicating the detection rates of PCV2 decreased progressively in Henan Province of China in recent years. Additionally, the complete genomes of 34 PCV2 strains were sequenced and analyzed, which indicated that their nucleotide identities were 93.9–100.0%, 96.70–100.0%, and 88.90–100.0% in the complete genome, ORF1, ORF2, respectively, and amino acid identities were 98.10–100.0% and 88.60–100.0% in the replicase and capsid proteins, respectively. Phylogenetic analysis based on the complete genome sequences and deduced amino acids of ORF2 showed that the PCV2 strains obtained in the present study could be classified into three sub-clades, with the most strains clustered into clade PCV2d, indicated PCV2d is the predominated subtype in Henan Province, China. Moreover, four substitution sites (V57I, I89R/L, P134T, D210E) were observed in PCV2b ORF2 that were absent in PCV2a and PCV2d, and 4 substitution sites (S68N, I89L, T/P134N, S169G/R) were observed in PCV2d ORF2 that were absent in PCV2a and PCV2b. In general, the present study revealed a high prevalence and high genetic divergence of PCV2 among Chinese swine herds, provided an insight into the ongoing emerged PCV2, and enriched our understanding of the genetic diversity and evolution of PCV2.