Porcine Circovirus type 2 (PCV2) is a small non-enveloped virus, member of the genus Circovirus, family Circoviridae [1]. PCV2 is primary causative agent of postweaning multisystemic wasting syndrome (PMWS) and other diseases in swine referred to as porcine circovirus associated diseases (PCVAD) [2]. PMWS was first described in Canada in 1991, and nowadays it has been described in pig population worldwide, having a serious economic impact on the global swine industry. Pigs affected with PMWS show decreased weight gain, progressive weight loss, enlarged lymph nodes, and others non-specific clinical signs such as dyspnea and diarrhea [3] .

The genome of PCV2 is a 1.76–1.77 kb single-stranded circular DNA, containing three main open reading frames (ORFs) which encode viral proteins [4]. ORF1 encodes for the replicase protein (Rep) and splice variants involved in viral replication, ORF2 encodes for the capsid (Cap), an exclusive structural protein [5], and ORF3 encodes a non-structural protein which causes apoptosis in PCV2 infected cells and has been associated with pathogenicity [6]. PCV2 isolates could be classified into four different genotypes, PCV2a, PCV2b, PCV2c and PCV2d, based on pairwise sequence comparisons (PASC) [7], and most recently based on reference sequences and/or marker positions [8]. PCV2a and PCV2b are the major groups, worldwide distributed, while PCV2c has been described only in Denmark from swine historic archived tissues [9] and recently from wild boar in Brazil [10]. PCV2d correspond to a PCV2b mutant (mPCV2b) described in some countries of Europe, Asia, North America and South America [8, 11]. Moreover, a new cluster of PCV2 has been recently described and proposed as the PCV2e genotype [12].

In South America, PMWS and PCVAD have been reported; phylogenetic studies have only been conducted in Brazil, Argentina, Uruguay and Colombia [10, 13, 14]. The objective of this study is to evaluate the genetic diversity of PCV2 using sequences in pig affected by PMWS obtained from intensive swine farms in Chile.

The study conducts the first phylogenetic analysis of PCV2 in Chile. PCV2 isolated from Chilean intensive swine farms, covering over the 90% of the pork production, resulting a complete national perspective of PCV2. The results confirm the high presence of PCV2b (52%) and less represented PCV2a (14%). Surprisingly, 34% of sequences were PCV2a/PCV2d recombinant viruses. The no amplification of these 10 sequences by the selective PCR was further explained due to these primers were not able to amplified PCV2d, the major parenteral of these viruses. Furthermore, we were not able to detect PCV2d variant in the Chilean PCV2 diversity even if was the major parent of the recombinant viruses, probably this event occurred years before and the recombinant remained. PCV2a and PCV2b, and the recombinant viruses were found since 2005. Nevertheless, were not observed geographical, temporal and other patterns, most likely due to there is not enough sequences per farm.

Recently, a large-scale study determinates that the PCV2 vaccination is important factor in the PCV2 ecology, driving the evolution and epidemiology of the virus. PCV2 vaccination by selective pressure generates vaccine scape-mutants, which become new genotypes waves [19]. Interestingly, the vaccination against PCV2 in Chile started in 2007 and massive in swine farms around 2008–2009. This study includes samples since 2005 to 2013, but differences before and after massive vaccination were not reported mostly due low number of isolates per farm and year.

Six farms presented PCV2 recombinant viruses; this event was observed in samples from 2005. However, even if geographical or others patterns were not identified, probably the presence of these recombinant viruses is linked between farms. There are not similar sequences reported with this particular recombination in the world; therefore, probably this recombination event occurred in Chile and then was spread to the rest of the farms.

Recombination events are common among PCV2 strains, which have been reported in several countries [20, 21]. Also, different patterns of recombination have been described, with break points in both ORF1 and ORF2, which suggest that the recombination can occur easily in PCV2 co-infections [22].

On the other hand, PCV2b was the most common genotype in Chilean farms during the PMWS outbreak, as has been found of the rest of the world, where more than 50% of the viral sequences belonged into PCV2b [11]. PCV2b sequences did not show divergence over time among samples obtained in 2005 to 2008 from several different farms and present 99.9% identity with viruses found in the rest of the world.

This is the first study that revealed the genetic diversity of PCV2 in Chile during a PWMS outbreak. Our findings suggested that a novel cluster of Chilean sequences emerged resulting from recombination between genotypes PCV2a and PCV2d within ORF2. However, analysis of the complete PCV2 genome and further surveillance of PCV2 is needed to confirm the real impact of these recombinant viruses.