Simultaneous detection and genetic characterization of porcine circovirus 2 and 4 in Henan province of China

• Published in: Gene 2022-01, Vol.808, p.145991-145991, Article 145991
• Main Authors: Xu, Tong, Hou, Cheng-Yao, Zhang, Yuan-Hang, Li, Hong-Xuan, Chen, Xi-Meng, Pan, Jia-Jia, Chen, Hong-Ying
• Format: Article
• Language: English
• Subjects: Animals; China; Circoviridae Infections - virology; Circovirus - classification; Circovirus - genetics; Circovirus - isolation & purification; Genetic Variation - genetics; Genome, Viral - genetics; Genomics - methods; Genotype; Molecular characteristics; Molecular Epidemiology - methods; Phylogeny; Porcine circovirus 2; Porcine circovirus 4; Prevalence; Real-Time Polymerase Chain Reaction - methods; Real-Time Polymerase Chain Reaction - veterinary; Sus scrofa - genetics; Sus scrofa - virology; Swine - genetics; Swine - virology; Swine Diseases - genetics; SYBR Green I-based duplex qPCR
• ISSN: 0378-1119; 1879-0038
• DOI: 10.1016/j.gene.2021.145991

•A SYBR Green I-based duplex qPCR assay was developed to detect PCV2 and PCV4 simultaneously.•Three PCV2 genotypes (PCV2a, PCV2b and PCV2d) existed in Henan province of China, and 6 PCV4 strains in this study belonged to PCV4a.•Eleven putative recombination events were found in newly emerging isolates of PCV2 in Henan province of China.•The functional regions of PCV4 strains were predicted by comparison with other circoviruses. Porcine circovirus 4 (PCV4) was identified as a novel porcine circovirus in China in 2019. To investigate the prevalence and genetic characteristics of PCV2 and PCV4, 133 clinical samples (103 tissue samples and 30 serum samples) were collected from 30 different pig farms in Henan province of China, and a SYBR Green I-based duplex quantitative real-time polymerase chain reaction assay was established to detect PCV2 and PCV4 genomes simultaneously. The complete genome sequences of 20 PCV2 and 6 PCV4 strains from 19 and 6 clinical samples respectively were sequenced and analyzed. The results showed the detection limits of this assay were 80.2 copies/μL for PCV2 and 58.6 copies/μL for PCV4. The detection results of clinical samples revealed the PCV2 positive rate was 63.16% (84/133), the PCV4 positive rate was 33.33% (45/133), and the PCV2 and PCV4 co-infection positive rate was 21.05% (28/133). Among 20 PCV2 strains, 6 belonged to PCV2a, 6 belonged to PCV2b and 8 belonged to PCV2d. Co-infection with JZ1 (PCV2b) and JZ2 (PCV2d) strains was identified in one sample (JZ-1). Eleven putative recombination events were found through the recombination analysis, suggesting that the new PCV2 variant strains had circulated in Henan province, which contributes to our understanding of evolutionary characteristics of PCV2 in China. The possible genotypes of PCV4 strains were determined based on genomic sequences of 6 PCV4 strains in this study and 29 PCV4 reference strains available at GenBank. According to three different phylogenetic trees (ORF1, ORF2 and complete genome), all 35 PCV4 strains were clustered into two major genotypes (PCV4a and PCV4b), and 6 PCV4 strains in this study belonged to PCV4a. Additionally, the functional regions of PCV4 strains were predicted by comparison with other circoviruses, which are conducive to the further study of the biological functions of PCV4 genome.