Phylogenetic analysis of porcine circovirus type 2 (PCV2) between 2015 and 2018 in Henan Province, China

Abstract

Background: Porcine circovirus type 2 (PCV2) is the pathogen of porcine circovirus associated diseases (PCVAD) and one of the main pathogens in the global pig industry, which has brought huge economic losses to the pig industry. In recent years, there has been limited research on the prevalence of PCV2 in Henan Province. This study investigated the genotype and evolution of PCV2 in this area.

Results: We collected 117 clinical samples from different regions of Henan Province from 2015 to 2018. Here, we found that the PCV2 infection rate of PCV2 was 62.4%. Thirty-seven positive clinical samples were selected to amplify the complete genome of PCV2 and were sequenced. Based on the phylogenetic analysis of PCV2 ORF2 and complete genome, it was found that the 37 newly detected strains belonged to PCV2a (3 of 37), PCV2b (21 of 37) and PCV2d (13 of 37), indicating the predominant prevalence of PCV2b and PCV2d strains. In addition, we compared the amino acid sequences and found several amino acid mutation sites among different genotypes. Furthermore, the results of selective pressure analysis showed that there were 5 positive selection sites.

Conclusions: This study indicated the genetic diversity, molecular epidemiology and evolution of PCV2 genotypes in Henan Province during 2015-2018.

Keywords: Evolution; Genetic diversity; Molecular epidemiology; PCV2; Phylogenetic analysis.

Fig. 1

Geographical distribution and PCV2 test results of clinical tissue samples in Henan province from 2015 to 2018. The first number in parentheses represents the total number of samples detected in this area, and the latter number represents the number of PCV2 positive samples detected in this area. The map in this figure is my own

Fig. 2

Phylogenetic tree based on ORF2 (a) and genome (b). Phylogenetic trees were constructed with the MEGA 7.0.14 software using the neighbor-joining (NJ) method, with the Jukes-cantor model as a nucleotide substitution model. The reliability of the generated trees was determined with 1000 replicates of the data set. 37 isolates and 19 reference sequences were used for this analysis. The isolations detected in this study were labeled by the red star, and reference strains downloaded from NCBI weren’t labeled

Fig. 3

Sequence alignment of multiple sequence amino acids in PCV2 Cap protein. This alignment included deduced amino acid sequences of ORF2 from 37 PCV2 isolates and 15 PCV2 reference strains. The diagram was plotted by EPSprint 3.0. The antibody recognition domains (A (51–81), B (113–134), C (161–208) and D (228–233)) and immunodominant decoy epitope E (168–180), were demarcated by the colored boxes, in bright green, blue, white, black and dark red, respectively