Genetic analysis of porcine circovirus type 2 from pigs affected with PMWS in Chile reveals intergenotypic recombination

Abstract

Background: Porcine circovirus type 2 (PCV2) is a very small, non-enveloped and icosahedral virus, with circular single stranded DNA genome. This virus is the most ubiquitous and persistent pathogen currently affecting the swine industry worldwide. PCV2 has been implicated as the major causative agent of postweaning multisystemic wasting syndrome (PMWS), a disease which is characterized by severe immunosuppressive effects in the porcine host. Worldwide PCV2 isolates have been classified into four different genotypes, PCV2a, PCV2b, PCV2c and PCVd. The goal of this work was to conduct the first phylogenetic analysis of PCV2 in Chile.

Methods: PCV2 partial ORF2 sequences (462 nt) obtained from 29 clinical cases of PMWS in 22 Chilean intensive swine farms, covering over the 90% of the local pork-production, were analyzed.

Results: 14% and 52% of sequences belonged to the genotypes PCV2a and PCV2b, respectively. Surprisingly, 34% of sequences were PCV2a/PCV2d recombinant viruses.

Conclusions: Our findings suggested that a novel cluster of Chilean sequences emerged resulting from intergenotypic recombination between PCV2a and PCV2d.

Keywords: Genetic diversity; PCV2; PMWS; Recombination.

Fig. 1

Phylogenetic tree generated by neighbor-joining method using 462-nt sequence of ORF2 PCV2. Chilean strains were compared with twenty-five PCV2 reference strains. PCV1 was included as out-group. GenBank accession numbers and country of origin are specified. Genotypes are indicated with straight brackets

Fig. 2

Recombination analysis. a Similarity plot generated by SIMPLOT software based on 462 nt of ORF2 sequence using B2/2005 as query sequence and representative parent sequence of genotypes PCV2d (red) and PCV2a (blue) (JX535296 and AY180397, respectively). A PCV1 isolate was used as outgroup (green). The analysis was performed with a window size of 100 nt and a step size of 20 nt. b BootScan analysis and potential breakpoints for B2/2005 predicted by RDP3 software

Fig. 3

Phylogenetic trees generated by neighbor-joining method based on a the minor parent region estimated with SIMPLOT and RDP software (nt 100–389) and b the major parent region (concatenated alignment of nt 1–99 and nt 390–462). Chilean strains were compared with twenty-five PCV2 reference strains. GenBank accession numbers and country of origin are specified. Genotypes are indicated with straight brackets. Discordant clustering patterns of potential Chilean recombinant strains with different genotypes are observed (◆)