Detection of natural inter- and intra-genotype recombination events revealed by cap gene analysis and decreasing prevalence of PCV2 in wild boars

Intra- and inter-host origin, evolution dynamics and spatial-temporal transmission characteristics of circoviruses

Introduction

Since their identification in 1974, circoviruses have caused clinicopathological diseases in various animal species, including humans. However, their origin, transmission, and genetic evolution remain poorly understood.

Methods

In this study, the genome sequences of circovirus were obtained from GenBank, and the Bayesian stochastic search variable selection algorithm was employed to analyzed the evolution and origin of circovirus.

Results

Here, the evolutionary origin, mode of transmission, and genetic recombination of the circovirus were determined based on the available circovirus genome sequences. The origin of circoviruses can be traced back to fish circovirus, which might derive from fish genome, and human contributes to transmission of fish circovirus to other species. Furthermore, mosquitos, ticks, bats, and/or rodents might play a role as intermediate hosts in circovirus intra- and inter-species transmission. Two major lineages (A and B) of circoviruses are identified, and frequent recombination events accelerate their variation and spread. The time to the most recent common ancestor of circoviruses can be traced back to around A.D. 600 and has been evolving at a rate of 10-4 substitutions site-1 year-1 for a long time.

Discussion

These comprehensive findings shed light on the evolutionary origin, population dynamics, transmission model, and genetic recombination of the circovirus providing valuable insights for the development of prevention and control strategies against circovirus infections.

Virome of wild rats (Rattus norvegicus) captured far from pig farms in Jiangsu province of China reveals novel porcine circovirus type 2d (PCV2d) sequences

BACKGROUND

Porcine circovirus type 2 (PCV2) has caused great economic losses in the global pig industry. There have been published records of wild rats acting as the reservoirs of PCV2 (only PCV2a and PCV2b), but almost all of which were related to the PCV2-infected swine herds.

RESULTS

In this study, we carried out the detection, amplification, and characterization of novel PCV2 strains in wild rats that were captured far from pig farms. Nested PCR assay demonstrated that the kidney, heart, lung, liver, pancreas, and large and small intestines of rats were screened positive for PCV2. We subsequently sequenced two full genomes of PCV2 in positive sample pools, designated as js2021-Rt001 and js2021-Rt002. Genome sequence analysis indicated that they had the highest similarity to nucleotide sequences of porcine-origin PCV2 isolates in Vietnam. Phylogenetically, js2021-Rt001 and js2021-Rt002 were a part of the PCV2d genotype cluster, which is a predominant genotype circulating worldwide in recent years. The antibody recognition regions, immunodominant decoy epitope, and heparin sulfate binding motif of the two complete genome sequences coincided with those previously reported.

CONCLUSIONS

Our research reported the genomic characterization of two novel PCV2 strains (js2021-Rt001 and js2021-Rt002) and provided the first supported evidence that PCV2d could naturally infect wild rats in China. However, whether the newly identified strains have potential for circulating in nature in vertical and horizontal transmission or inter-species jumping between rats and pigs needs further research.

First complete genomic sequence analysis of porcine circovirus type 4 (PCV4) in wild boars

Porcine circovirus type 4 (PCV4), a unique circovirus with a different classification from other existing circovirus, was discovered in domestic pigs in several provinces of China. In this study, in order to investigate the epidemiology and genetic diversity of PCV4 in wild boars (Sus scrofa), a total number of 138 wild boar samples were collected from five different areas in Jiangxi Province of China, between January 2020 and December 2020. Taqman based real-time PCR were used to test PCV4 as well as PCV1, PCV2, and PCV3. Among 138 samples, 30 samples (21.7%) were positive for PCV1, 31 samples (22.5%) were positive for PCV2, 8 samples (5.8%) were positive for PCV3 and 27 samples (19.6%) were positive for PCV4, respectively. Some of the samples were co-infected with multiple PCVs. In this study, we successfully sequenced the complete genome of two PCV4 strains, which shared 98.5-99.8% of their genomic nucleotide similarity with the other five PCV4 strains discovered in domestic pigs. Phylogenetic analysis showed that the two PCV4 strains derived from wild boars were located in a closed relative branch with other PCV4 strains derived from domestic pigs, but were distinguished from other circovirus. These results of this study not only expand our understanding of the prevalence of PCVs, especially PCV4, in wild boars in Jiangxi province of China, but also showed the molecular epidemiology of PCV4. Nevertheless, the impact of wild boars infected with PCV4 on intensive farmed pigs industry remains to be further explored.

Detection and characterisation of porcine circoviruses in wild boars in northeastern Serbia

The objective was to expand and update the knowledge on the presence and genotype diversity of porcine circoviruses 2 and 3 (PCV2 and PCV3) in the wild boar populations from the hunting grounds in northeastern Serbia. The presence of PCV3 was not determined, and PCV2 was confirmed in 40.32% of the organ samples from 124 wild boars hunted from 2018 to 2019, indicating their significance in virus circulation since traditional pig farms with irregular PCV2 vaccination strategies are widespread in this region. The most prevalent genotype was PCV2d, followed by PCV2b and PCV2a in 55.6%, 38.9%, and 5.5% of the examined samples, respectively. Nucleotide sequences of the detected strains were homogenous within the genotype and clustered within the subgroups PCV2d-2, PCV2b-1A/B, and PCV2a-2D with high identity to European, Chinese, and Serbian domestic pig sequences suggesting their origin. Wild boars presented with no clinical or pathological signs of infection, implying that these animals might be less susceptible to disease, particularly since the cofactors present in pig farming systems that support the disease development are absent in the wild. The high PCV2 detection frequency demonstrates the importance of wildlife monitoring to track virus population dynamics, especially in regions with free-range pig farming in order to plan adequate disease control strategies.

Molecular Epidemic Characteristics and Genetic Evolution of Porcine Circovirus Type 2 (PCV2) in Swine Herds of Shanghai, China

Porcine Circovirus 2 (PCV2) is a crucial swine pathogen and considered a primary causative agent of porcine circovirus-associated diseases (PCVADs), posing a serious economic threat to the swine industry across globe. The world’s biggest agricultural conglomerates have teamed up to create giant commercial pig farms across Shanghai due to the proximity of this region to more affluent lean-pork markets. Since its discovery, PCV2 has displayed extraordinary genetic diversity, and its genome is swiftly evolving through a series of mutations and recombinations. However, limited information on epidemiology, molecular characteristics, vaccine cross-protection, and the co-infection rate of PCV2 with other lethal swine diseases can adversely impact the pig production in the region. To investigate the molecular epidemic characteristics and genetic evolution of PCV2, pigs with doubtful symptoms of PCVADs were sampled from various commercial pig farms with a history of PWMS and/or PDNS across Shanghai from 2014 to 2018. Our results revealed the coexistence of multiple PCV2 genotypes (PCV2b, PCV2e, and PCV2d) among Shanghai pig herds and dominance of PCV2d among them. We also found critical amino acid substitutions in epitope regions of important capsid proteins in PCV2 isolates involved in viral replication and host immune escape. Spotted mutations may favor the prevalence and survival of various PCV2 genotypes despite availability of commercial vaccines. This study also provides insight into the co-infection status of PCV2 with major lethal swine viral diseases such as PPV and PPRSV. Collectively, these investigations will contribute to understanding the molecular epidemiology and evolution of PCV2 across the region.

Discriminating the eight genotypes of the porcine circovirus type 2 with TaqMan-based real-time PCR

Background

The porcine circovirus type 2 (PCV2) is divided into eight genotypes including the previously described genotypes PCV2a to PCV2f and the two new genotypes PCV2g and PCV2h. PCV2 genotyping has become an important task in molecular epidemiology and to advance research on the prophylaxis and pathogenesis of PCV2 associated diseases. Standard genotyping of PCV2 is based on the sequencing of the viral genome or at least of the open reading frame 2. Although, the circovirus genome is small, classical sequencing is time consuming, expensive, less sensitive and less compatible with mass testing compared with modern real-time PCR assays. Here we report about a new PCV2 genotyping method using qPCR.

Methods

Based on the analysis of several hundred PCV2 full genome sequences, we identified PCV2 genotype specific sequences or single-nucleotide polymorphisms. We designed six TaqMan PCR assays that are specific for single genotypes PCV2a to PCV2f and two qPCRs targeting two genotypes simultaneously (PCV2g/PCV2d and PCV2h/PCV2c). To improve specific binding of oligonucleotide primers and TaqMan probes, we used locked nucleic acid technology. We evaluated amplification efficiency, diagnostic sensitivity and tested assay specificity for the respective genotypes.

Results

All eight PCV2 genotype specific qPCRs demonstrated appropriate amplification efficiencies between 91 and 97%. Testing samples from an epidemiological field study demonstrated a diagnostic sensitivity of the respective genotype specific qPCR that was comparable to a highly sensitive pan-PCV2 qPCR system. Genotype specificity of most qPCRs was excellent. Limited unspecific signals were obtained when a high viral load of PCV2b was tested with qPCRs targeting PCV2d or PCV2g. The same was true for the PCV2a specific qPCR when high copy numbers of PCV2d were tested. The qPCR targeting PCV2h/PCV2c showed some minor cross-reaction with PCV2d, PCV2f and PCV2g.

Conclusion

Genotyping of PCV2 is important for routine diagnosis as well as for epidemiological studies. The introduced genotyping qPCR system is ideal for mass testing and should be a valuable complement to PCV2 sequencing, especially in the case of simultaneous infections with multiple PCV2 genotypes, subclinically infected animals or research studies that require large sample numbers.

Genetic Diversity of Porcine Circovirus Isolated from Korean Wild Boars

In Korea, three genotypes of porcine circovirus type 2 (PCV2a, PCV2b, and PCV2d) have been identified on domestic pig farms, while two genotypes (PCV2a and PCV2b) have been identified in wild boar populations. Here, we investigated genotype diversity and genotypic shift in 91 PCV2 isolates from 1340 wild boars captured in South Korea between 2013 and 2017. Phylogenetic analyses based on the complete ORF2 showed that the 91 PCV2 strains were detected as four genotypes by qPCR screening assay: PCV2a (2.2%, 2/91), PCV2b (16.5%, 15/91), PCV2d (80.2%, 73/91), and PCV2h (1.1%, 1/91). Only one intergenotype recombinant event was detected between PCV2 ORF2 in wild boars (PCV2b) and domestic pigs (PCV2a). Amino acid positions 86–89 within ORF2, which distinguishes the different genotypes, were conserved in all PCV2 genotypes isolated from South Korean wild boars, including TNKI in PCV2a/PCV2h, SNPR in PCV2b, and SNPL in PCV2d. The estimated nucleotide substitution rates in the ORF2 region of viruses from South Korean wild boars and domestic pigs were 5.8145 × 10⁻⁴ and 4.5838 × 10⁻⁴ substitutions per site per year (s/s/y), respectively. The times to the most recent common ancestor (tMRCA) for South Korean domestic pig PCV2 were 1937 (PCV2a), 1972 (PCV2b), 1999 (PCV2d-1), and 2000 (PCV2d-2). By contrast, the tMRCA for South Korean wild boar PCV2b and PCV2d were 1989 and 2001, respectively. Thus, the PCV2d genotype is prevalent among South Korean wild boars and domestic pigs.

Porcine circovirus 2 (PCV-2) genotype update and proposal of a new genotyping methodology

Porcine circovirus 2 (PCV-2) is one of the most widespread viral infections of swine, causing a remarkable economic impact because of direct losses and indirect costs for its control. As other ssDNA viruses, PCV-2 is characterized by a high evolutionary rate, leading to the emergence of a plethora of variants with different biological and epidemiological features. Over time, several attempts have been made to organize PCV-2 genetic heterogeneity in recognized genotypes. This categorization has clearly simplified the epidemiological investigations, allowing to identify different spatial and temporal patterns among genotypes. Additionally, variable virulence and vaccine effectiveness have also been hypothesized. However, the rapid increase in sequencing activity, coupled with the per se high viral variability, has challenged the previously established nomenclature, leading to the definition of several study-specific genotypes and hindering the capability of performing comparable epidemiological studies.

Based on these premises, an updated classification scheme is herein reported. Recognizing the impossibility of defining a clear inter-cluster p-distance cut-off, the present study proposes a phylogeny-grounded genotype definition based on three criteria: maximum intra-genotype p-distance of 13% (calculated on the ORF2 gene), bootstrap support at the corresponding internal node higher than 70% and at least 15 available sequences. This scheme allowed defining 8 genotypes (PCV-2a to PCV-2h), which six of those had been previously proposed. To minimize the inconvenience of implementing a new classification, the most common names already adopted have been maintained when possible. The analysis of sequence-associated metadata highlighted a highly unbalanced sequencing activity in terms of geographical, host and temporal distribution. The PCV-2 molecular epidemiology scenario appears therefore characterized by a severe bias that could lead to spurious associations between genetic and epidemiological/biological viral features. While the suggested classification can establish a “common language” for future studies, further efforts should be paid to achieve a more homogeneous and informative representation of the PCV-2 global scenario.

Novel canine circovirus strains from Thailand: Evidence for genetic recombination

Canine circoviruses (CanineCV's), belonging to the genus Circovirus of the Circoviridae family, were detected by next generation sequencing in samples from Thai dogs with respiratory symptoms. Genetic characterization and phylogenetic analysis of nearly complete CanineCV genomes suggested that natural recombination had occurred among different lineages of CanineCV's. Similarity plot and bootscaning analyses indicated that American and Chinese viruses had served as major and minor parental viruses, respectively. Positions of recombination breakpoints were estimated using maximum-likelihood frameworks with statistical significant testing. The putative recombination event was located in the Replicase gene, intersecting with open reading frame-3. Analysis of nucleotide changes confirmed the origin of the recombination event. This is the first description of naturally occurring recombinant CanineCV's that have resulted in the circulation of newly emerging CanineCV lineages.

Phylogenetic and genetic variation analyses of porcine circovirus type 2 isolated from China

Porcine circovirus type 2 (PCV2) is a causative agent of PCV2-associated disease, which is a growing problem in the swine industry worldwide. High nucleotide substitution occurs in the capsid (Cap) gene of PCV2, which allows the continuous evolution and the emergence of novel PCV2 strains. In this study, we sequenced 24 Chinese PCV2 strains collected from healthy and diseased pigs between 2013 and 2015. Analyses of the genome, Cap and phylogeny classified the 24 Chinese PCV2 strains as PCV-2a (four of 24), PCV-2b (five of 24) and PCV-2d (15 of 24). All strains shared 89.5%-100% and 87.2%-100% identities with the nucleotide and amino acid (aa) sequences of Cap, respectively. Selection pressure analysis showed that five sites at the epitope regions in Cap were under positive selection. Further analysis by Jameson-Wolf antigenic index indicated that aa substitutions occurring at the epitope regions contributed to the antigenic alterations of the different PCV2 strains. High genetic variation and genotype shift to PCV2d occurred in recent years, and different genotypes coexisted in Chinese pig herds. The data provide evidence for the increased genetic diversity and insights into the molecular epidemiology of PCV2.

Porcine Circovirus Type 2 (PCV2) Vaccines in the Context of Current Molecular Epidemiology

Porcine circovirus type 2 (PCV2) is an economically important swine pathogen and, although small, it has the highest evolution rate among DNA viruses. Since the discovery of PCV2 in the late 1990s, this minimalistic virus with a 1.7 kb single-stranded DNA genome and two indispensable genes has become one of the most important porcine pathogens, and presently is subjected to the highest volume of prophylactic intervention in the form of vaccines in global swine production. PCV2 can currently be divided into five different genotypes, PCV2a through PCV2e. It is well documented that PCV2 continues to evolve, which is reflected by changes in the prevalence of genotypes. During 2006, commercial vaccines for PCV2 were introduced on a large scale in a pig population mainly infected with PCV2b. Since 2012, the PCV2d genotype has essentially replaced the previously predominant PCV2b genotype in North America and similar trends are also documented in other geographic regions such as China and South Korea. This is the second major PCV2 genotype shift since the discovery of the virus. The potential increase in virulence of the emergent PCV2 genotype and the efficacy of the current vaccines derived from PCV2a genotype against the PCV2d genotype viruses has received considerable attention. This review attempts to synthesize the understanding of PCV2 biology, experimental studies on the antigenic variability, and molecular epidemiological analysis of the evolution of PCV2 genotypes.

Genetic characterization of porcine circovirus type 2 in captive wild boars in southern Brazil

Porcine circovirus type 2 (PCV2) has been identified in pig population in Brazil since 2000, but scarce studies involving wild boars with PCV2 infection are reported in the country. This study aimed to perform the genetic characterization of PCV2 detected in clinically healthy captive wild boars from farms located in Southern Brazil. Bronchial and mesenteric lymph nodes from 129 clinically healthy captive wild boars were tested by nested PCR for PCV2 detection. Six out of 38 positive samples (29.5%) were submitted to a quantitative real time PCR (qPCR) and genetic sequencing. Viral load up to 1.19 × 10⁹ viral DNA copies/uL was detected in lymph nodes samples by qPCR. According to the ORF2 gene sequence analysis, all PCV2 samples were classified into PCV2b genotype. Comparisons based on a 702 nt region of the ORF2 of all six isolates revealed a high degree of similarity between these isolates. The ORF2 sequences characterized here share 97.1-100% of nucleotide identity and 95.7-100% of amino acid identity with other PCV2b isolated in Brazil from wild boars and feral pigs. This study reports the first detection and genetic characterization of PCV2b in captive wild boars in Brazil and provides important information on PCV2 infection in this domesticated species.

Wild boars harboring porcine epidemic diarrhea virus (PEDV) may play an important role as a PEDV reservoir

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First detection of PEDV in wild boar population.

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PEDV positive samples were spread throughout the mainland of South Korea.

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Our results provide novel insight into the epidemiology of PEDV infection.

Porcine epidemic diarrhea virus (PEDV) is a burdensome pathogen in the swine industry. Wild boar population poses a high risk for reservoir of viral pathogen. Two hundred eighty seven samples from wild boar (Sus scrofa) collected in South Korea during 2010/11 were analyzed using RT-PCR, revealing a PEDV infection rate of 9.75% (28/287). PEDV positive samples were distributed throughout the mainland of South Korea, clustering at the northern border adjacent to the Demilitarized Zone (DMZ) and in mountainous regions. PEDV in wild boar was genetically similar to Chinese PEDV strains in phylogenetic investigations. Our results indicated that PEDV is circulating in the wild boar and provided a novel knowledge into epidemiology of PEDV infection.

Porcine circovirus 2 immunology and viral evolution

Porcine circovirus 2 (PCV2) has and is still causing important economic losses to pig industry. This is due to PCV2-systemic disease (PCV2-SD), formerly known as postweaning multi-systemic wasting syndrome (PMWS), which increases mortality rates and slows down the growth of the animals, as well as other conditions collectively included within the so-called porcine circovirus diseases (PCVD). PCV2-SD affected pigs are considered to be immunosuppressed, with severe lymphocyte depletion and evidence of secondary infections. However, PCV2-infected pigs not developing the disease are able to mount humoral and cellular immune responses and clear the virus or limit the infection. On the contrary, insufficient amounts of neutralizing antibodies have been linked to increased PCV2 replication, severe lymphoid lesions and development of PCV2-SD. Central role in controlling PCV2 infection are played by the antigen specific memory T cells. These cells persist long term post-infection or vaccination and are able to expand rapidly after recall antigen recognition. Most farms in the main pig producing countries are applying vaccination against PCV2 to prevent the disease and improve the farm performance. Vaccines do not induce sterilizing immunity and PCV2 keeps on circulating even in farms applying vaccination. This, together with the high mutation rate of PCV2, world-wide fluctuations in the genotype dominance and emergence of novel genetic variants, warrant close molecular survey of the virus in the field.

Novel circovirus from mink, China

A long-established epidemic of enteritis, caused by an unidentified pathogen distinct from parvovirus, has now been recognized in mink. In 2013, we identified a novel circovirus by degenerate PCR and fully sequenced its genome. This virus differs substantially from currently known members of the genus Circovirus and represents a new species.

CHARACTERIZATION OF PORCINE PARVOVIRUS TYPE 3 AND PORCINE CIRCOVIRUS TYPE 2 IN WILD BOARS (SUS SCROFA) IN SLOVAKIA

As the number of free-living wild boars (Sus scrofa L.) continues to rise in Slovakia, the probability of pathogen transmission between susceptible species increases. We investigated the distribution and genetic characterization of porcine parvovirus type 3 (PPV3), porcine circovirus type 2 (PCV2), and their coinfection in wild boars. Among 194 animals tested, 19.1% were positive for PPV3 and 43.8% for PCV2. Similar rates of coinfection with both viruses reaching 11.0% and 11.8% were observed in juvenile and mature wild boars, respectively. Phylogenetic analysis of PPV3 sequences from VP1 and NS1 genomic regions revealed a close genetic relationship among isolates from Slovakia and those sampled worldwide. Prevalence of PCV2 in wild boars was lower than that reported in domestic pigs in Slovakia. The PCV2 variants originating from sylvatic and domestic hosts in Slovakia were grouped in the same clusters, namely PCV2b-1A/1B and PCV2a-2D.

Recombination in truncated genome sequences of porcine circovirus type 2

Porcine circovirus type 2 (PCV2) is the causal agent of a serious disease found in pigs. Here, we report the first detection of truncated genome sequences of PCV2 strain ZJ-R, with the genomic region encoding part of Rep and Cap with a nonviral insertion. To our knowledge, the genome of ZJ-R represents the first PCV2 DNA with a coding insertion. The PCV2 ZJ-R genome is 694 nucleotides long and has two main open reading frames. The whole genome sequence of ZJ-R may facilitate further study of the origin and evolution of PCV2.

Porcine circovirus type 2 in China: an update on and insights to its prevalence and control

Currently, porcine circovirus type 2 (PCV2) is considered the major pathogen of porcine circovirus associated-diseases (PCVAD) that causes large economic losses for the swine industry in the world annually, including China. Since the first report of PCV2 in 1998, it has been drawing tremendous attention for the government, farming enterprises, farmers, and veterinary practitioners. Chinese researchers have conducted a number of molecular epidemiological work on PCV2 by molecular approaches in the past several years, which has resulted in the identification of novel PCV2 genotypes and PCV2-like agents as well as the description of new prevalence patterns. Since late 2009, commercial PCV2 vaccines, including the subunit vaccines and inactivated vaccines, have already been used in Chinese swine farms. The aim of this review is to update the insights into the prevalence and control of PCV2 in China, which would contribute to understanding the epidemiology, control measures and design of novel vaccines for PCV2.

Genetic characterization of porcine circovirus type 2 in the Korean wild boar population

The porcine circovirus type 2 (PCV2) has reached very high levels in the pig population in South Korea and throughout the world since it was first described in the late 1990s. In this study, we found that the prevalence of PCV2 in the Korean wild boar population was 4.98% (91/1825). Interestingly, 19 PCV2 ORF2 sequences that could be completely sequenced showed that they belonged only to genotype PCV2b, subgroup 1A/B (n=16) and 1C (n=3). We suggest that sites potentially under positive selection are responsible for the antigenicity changes and phenotypic switch patterns in the capsid gene of 55 PCV2s from Korean domestic pigs, but the sites potentially under positive selection in the 19 PCV2 ORF2 genes from Korean wild boar are not responsible for antigenicity.

Phylogenetic and phylogeographic analyses of porcine circovirus type 2 among pig farms in Vietnam

This study demonstrated the prevalence of Porcine circovirus type 2 (PCV2) among pig farms in Vietnam. Analyses of the genome, capsid protein and phylogeny classified all 30 Vietnamese PCV2 strains as the PCV2b genotype, belonging to the clusters of 1A, 1B, 1C and recombinant forms. Each viral genome was 1767 nucleotides long and shared 96.0-100% nucleotide sequence identity. The amino acid substitutions in the capsid protein of the Vietnamese PCV2 strains were in immunodominant regions, and the majority of strains (24/30) contained a lysine extension at the C-terminus. Bayesian phylogeographic analysis revealed epidemic links of the PCV2 recombinant cluster within and among countries, which supports a circulating recombinant form of PCV2. Further analysis by the Jameson-Wolf antigenic index indicated antigenic alterations at important sites in the capsid protein (sites 131-133) among the recombinant cluster and the other clusters of PCV2b.

Interclade recombination in porcine parvovirus strains

A detailed analysis of the Ns1/Vp1Vp2 genome region of the porcine parvovirus (PPV) strains isolated from vaccinated animals was performed. We found many inconsistencies in the phylogenetic trees of these viral isolates, such as low statistical support and strains with long branches in the phylogenetic trees. Thus, we used distance-based and phylogenetic methods to distinguish de facto recombinants from spurious recombination signals. We found a mosaic virus in which the Ns1 gene was acquired from one PPV clade and the Vp1Vp2 gene was acquired from a distinct phylogenetic clade. We also described the interclade mosaic structure of the Vp1Vp2 gene of a reference strain. If recombination is an adaptive mechanism over the course of PPV evolution, we would likely observe increasing numbers of chimeric strains over time. However, when the PPV sequences isolated from 1964 to 2011 were analysed, only two chimeric strains were detected. Thus, PPV recombination is an independent event, resulting from close contact between animals housed in high-density conditions.