Analysis of genetic variation of porcine circovirus type 2 within pig populations in central China.

In order to investigate the genetic diversity of porcine circovirus type 2 (PCV2), 284 clinical tissue samples were collected from different pig farms in central China from 2015 to 2017. A total of 162 tissue samples (162/284, 57.04%) were positive for PCV2 by PCR, and subsequently, the complete genome of 36 of these PCV2 samples was cloned and sequenced. The sequencing results showed that 37 complete PCV2 sequences were obtained from 36 PCV2-positive clinical samples. These PCV2 strains were relatively conserved and extremely homologous to the representative classical PCV2 strains. Of these, 20 PCV2 strains belonged to genotype PCV2d, 14 belonged to PCV2b, and three others belonged to PCV2a. Coinfection with PCV2b and PCV2d was identified in one sample (DF-2). These results show that PCV2d may be gradually replacing PCV2b as the predominant PCV2 genotype in central China, and that other genotypes also exist in individual regions. The results of this study will aid in our understanding of the molecular epidemiology of PCV2.

Development of a SYBR green I-based duplex real-time fluorescence quantitative PCR assay for the simultaneous detection of porcine epidemic diarrhea virus and porcine circovirus 3.

The development of a rapid, specific, and sensitive SYBR Green I-based duplex real-time quantitative PCR assay is described for the simultaneous detection of porcine epidemic diarrhea virus (PEDV) and porcine circovirus type 3 (PCV3). The assay specifically detected PEDV and PCV3, with no fluorescence detected for other non-targeted pig pathogens. The assay showed a good linear relationship, and the limits of detection for this assay were 34.6 copies/µL and 61.2 copies/µL for PEDV and PCV3, respectively. The assay exhibited high repeatability and reproducibility, with intra-assay and inter-assay variation coefficients less than 2.0%. A clinical evaluation using intestinal tissue and fecal samples from piglets suffering from diarrhea at different pig farms in China revealed that the singular infection rates of PEDV and PCV3 were 43.94% (29/66) and 16.67% (11/66), respectively, while the co-infection rate of PCV3 with PEDV was 27.27% (18/66). The results indicate this assay is a rapid and reliable diagnostic tool for PEDV and PCV3 monitoring and surveillance in the field, and provides technical support for the quantitative detection of clinical samples infected or co-infected with PEDV and PCV3.

Detection and phylogenetic analysis of porcine circovirus type 3 in central China.

Porcine circovirus type 3 (PCV3) is the pathogen responsible for a new infectious disease that was first reported in 2016 in the United States. To further investigate the epidemic profile and genetic diversity of the virus, one hundred and seventy clinical samples (110 tissue samples and 60 serum samples) were collected from 41 different pig farms in 14 cities in central China, and a SYBR Green I-based quantitative real-time PCR method was developed to detect PCV3. The partial cap genes of four field strains from four different farms were sequenced and analysed. The results showed the detection limit was 2.19 × 101 genome copies/µl. Fifty-three of 170 samples were detected as positive for PCV3, giving a PCV3-positive rate of 31.18%, with 48.78% (20/41) of pig farms harbouring PCV3, which varied from 20% to 42.86% between 2013 and 2017. PCV3 could be detected in samples from pigs with different clinical presentations, and the PCV3-positive rates varied for these different clinical presentations. The partial capsid genes of four PCV3 strains (designated YZ, LY-03, NY and SP) shared 96.3%-99.4% nucleotide identity with those available in GenBank. Phylogenetic analysis based on the capsid gene of 32 PCV3 strains showed that the four PCV3 strains in this study were clustered with the China/GD2016 and South Korea Ku-1606 strains. The results of this study will aid our understanding of the molecular epidemiology of PCV3.