Investigating the Genetic Evolution of PCV2 and PCV3 across Six Swine Herds in China from 2020 to 2021

Abstract

To elucidate the prevalence, molecular evolution, and coinfection of PCV2 and PCV3 in China, we collected samples from six large-scale swine herds located in Heilongjiang, Henan, Hebei, and Hubei provinces and Xinjiang Uygur autonomous region from 2020 to 2021. Overall, 1,201 samples were analyzed and sequenced by PCR to identify the dominant genotypes of PCV2 and PCV3, and genetic variations in the capsid protein genes of PCV2 and PCV3 were evaluated. The major epidemic genotypes of PCV2 and PCV3 were different across different regions. The infection rate of PCV2 and PCV3 was 72.1% and 26.3%, respectively, and the coinfection rate was 18.6%. PCV2d was the dominant genotype across all herds. The PCV2d-positive rate in PCV2-positive samples was 93.5%–100% in five out of six herds, indicative of its predominance. PCV3 prevalence in China widely varied, and no dominant genotype was identified. Four, 21, 11, and 11 strains with PCV2a, PCV2d, PCV3a, and PCV3c genotypes were detected, respectively, with the capsid protein containing four, five, eight, and three aa sites with mutations, respectively. Overall, our findings revealed the dominant epidemic genotypes of PCV2 and PCV3 in six herds across five provinces in China, in addition to the main aa sites with mutations in the capsid protein. We believe that these results will facilitate the diagnosis, prevention, and control of PCV2 and PCV3 in China.