Genetic variability of porcine circovirus 2 in vaccinating and non-vaccinating commercial farms

Molecular evolution and genotype shift of Porcine circoviruses type 2 in Vietnam

Porcine Circovirus Type 2 (PCV2), a significant pathogen in the global swine industry, causes Porcine Circovirus Associated Diseases (PCVAD), contributing to substantial economic losses. This study investigates the genetic diversity and evolutionary dynamics of PCV2 in Vietnam from 2007 to 2023. We sequenced and analyzed 47 PCV2 genomes isolated from swine farms across Vietnam between 2022 and 2023, revealing predominant circulation of PCV2d (80.85%) followed by PCV2b (19.15%). Phylogenetic analysis identified PCV2 genotypes PCV2a, PCV2b, PCV2d, PCV2g, and PCV2h circulating in Vietnam, with PCV2d emerging as the most prevalent genotype. Comparison with historical data highlighted genotype shifts from PCV2b to PCV2d in 2014. Interestingly, PCV2h genotype was mainly observed between 2008 and 2012 but have not been detected since 2014. Regional analysis indicated varied PCV2 epidemiological patterns between northern and southern Vietnam. Amino acid substitutions within the capsid protein were identified, predominantly in antigenic regions critical for immune recognition. Positive selection analysis identified multiple sites under evolutionary pressure, indicating ongoing adaptation of Vietnamese PCV2 strains. These findings enhance understanding of PCV2 dynamics in Vietnam and underscore the importance of continuous surveillance and adaptive management strategies in controlling PCV2-associated diseases in swine populations.

Evaluation of cross-immunity among major porcine circovirus type 2 genotypes by infection with PCV2b and PCV2d circulating strains

There are three main genotypes of porcine circovirus type 2 (PCV2), namely PCV2a, PCV2b and PCV2d, of which PCV2b and PCV2d are currently the most common. There are antigenic differences between these different genotypes. To explore the effect of PCV2 antigen differences on the immune protection provided by vaccines, a cross-immune protection test was carried out in pigs. Three genotype strains, PCV2a-CL, PCV2b-MDJ and PCV2d-LNHC, were inactivated and emulsified to prepare inactivated vaccines to immunize pigs, who were then challenged with the circulating strains PCV2b-BY and PCV2d-LNHC. Immunoperoxidase monolayer assays (IPMAs) and micro-neutralization assays were used to detect antibodies against the three different genotypes of PCV2. The results showed that the three genotype vaccines induced pigs to produce antibodies against the same and different genotypes of PCV2, but the levels of IPMA and neutralizing antibodies against the same genotype were higher than those against different genotypes. Quantitative Polymerase Chain Reaction (qPCR), virus titration and immunohistochemistry were used to detect PCV2 genomic DNA, live virus and antigen, respectively, in inguinal lymph nodes of experimental pigs. Following challenge with the PCV2b-BY strain, the viral DNA load in the inguinal lymph nodes of pigs immunized with the three genotype vaccines was reduced by more than 99 % compared to the unimmunized group. Following challenge with the PCV2d-LNHC strain, the viral DNA loads in the inguinal lymph nodes of pigs immunized with PCV2a, PCV2b and PCV2d genotype vaccines were reduced by 93.8 %, 99.8 % and 98.3 %, respectively, compared to unimmunized controls. In addition, neither live PCV2 virus nor antigen were detected in the inguinal lymph nodes of pigs immunized with any of the genotype vaccines (0/18), but both were detected in the lymph nodes of experimental pigs in the unimmunized control group (6/6). These findings suggest that, although the antigenic differences of the three genotype strains induce significant differences in antibody levels, they seem to have little effect on cross-protection between different genotypes.

Genetic Diversity of Porcine Circovirus 2 in Wild Boar and Domestic Pigs in Ukraine

Porcine circovirus type 2 (PCV2) is responsible for a number of porcine circovirus-associated diseases (PCVAD) that can severely impact domestic pig herds. For a non-enveloped virus with a small genome (1.7 kb ssDNA), PCV2 is remarkably diverse, with eight genotypes (a–h). New genotypes of PCV2 can spread through the migration of wild boar, which are thought to infect domestic pigs and spread further through the domestic pig trade. Despite a large swine population, the diversity of PCV2 genotypes in Ukraine has been under-sampled, with few PCV2 genome sequences reported in the past decade. To gain a deeper understanding of PCV2 genotype diversity in Ukraine, samples of blood serum were collected from wild boars (n = 107) that were hunted in Ukraine during the November–December 2012 hunting season. We found 34/107 (31.8%) prevalence of PCV2 by diagnostic PCR. For domestic pigs, liver samples (n = 16) were collected from a commercial market near Kharkiv in 2019, of which 6 out of 16 (37%) samples were positive for PCV2. We sequenced the genotyping locus ORF2, a gene encoding the PCV2 viral capsid (Cap), for 11 wild boar and six domestic pig samples in Ukraine using an Oxford Nanopore MinION device. Of 17 samples with resolved genotypes, the PCV2 genotype b was the most common in wild boar samples (10 out of 11, 91%), while the domestic pigs were infected with genotypes b and d. We also detected genotype b/d and b/a co-infections in wild boars and domestic pigs, respectively, and for the first time in Ukraine we detected genotype f in a wild boar from Poltava. Building a maximum-likelihood phylogeny, we identified a sublineage of PCV2 genotype b infections in both wild and domestic swine, suggesting a possible epizootic cluster and an ecological interaction between wild boar and domestic pig populations in northeastern Ukraine.

Epidemiology and Genetic Diversity of PCV2 Reveals That PCV2e Is an Emerging Genotype in Southern China: A Preliminary Study

Porcine circovirus-associated disease (PCVAD), caused by porcine circovirus type 2 (PCV2), has ravaged the pig industry, causing huge economic loss. At present, PCV2b and PCV2d are highly prevalent genotypes worldwide, while in China, in addition to PCV2b and PCV2d, a newly emerged PCV2e genotype detected in the Fujian province has attracted attention, indicating that PCV2 genotypes in China are more abundant. A preliminary study was conducted to better understand the genetic diversity and prevalence of PCV2 genotypes in southern China. We collected 79 random lung samples from pigs with respiratory signs, from 2018 to 2021. We found a PCV2-positivity rate of 29.1%, and frequent co-infections of PCV2 with PCV3, Streptococcus suis (S. suis), and other porcine pathogens. All PCV2-positive samples were sequenced and subjected to whole-genome analysis. Phylogenetic analysis, based on the PCV2 ORF2 gene and complete genomes, found that PCV2 strains identified in this study belonged to genotypes PCV2a (1), PCV2b (6), PCV2d (10), and PCV2e (6). Importantly, PCV2e was identified for the first time in some provinces, including Guangdong and Jiangxi. Additionally, we found two positively selected sites in the ORF2 region, located on the previously reported antigenic epitopes. Moreover, codon 63, one of the positively selected sites, has different types of amino acids in different genotypes. In conclusion, this study shows that PCV2e is an emerging genotype circulating in southern China, which warrants urgent, specific surveillance to aid the development of prevention and control strategies in China.

Occurrence and Associated Risk Factors of Porcine Reproductive and Respiratory Syndrome Virus and Porcine Circovirus Type 2 Infections in Greece

The objective of the present study was to identify factors associated with the probability of being polymerase chain reaction (PCR) positive and the level of porcine reproductive and respiratory syndrome virus (PRRSV), porcine circovirus type 2 (PCV2) occurrence in Greek farms. The study included 56 pig farms, with a total population of 22.500 sows, which represent about 40% of the entire capacity of the Greek swine production. A total of 896 blood samples (224 pools*4 samples/pool = 896 samples) from breeding stock, weaners, growers, and finishers were collected from each farm and organized in pools of 4 samples size. Further, data regarding herd health management protocols were collected. The sera were tested for PRRSV and PCV2, using real-time PCR (RT-PCR). The results indicated that both viruses remain a major challenge for the Greek swine industry. Main risk factors involved in the infection process by these viruses were identified. In particular, vaccination programs such as the mass PRRSV vaccination with modified-live virus (MLV) in breeding stock during the last stages of gestation or with killed-virus (KV) during the middle of gestation are more likely to be associated with PRRSV PCR-positivity. Farms with low biosecurity level are associated with higher PRRSV circulation. It has also been revealed that breeding stock is more likely to be associated with PCV2 circulation compared to weaners and growers. In conclusion, our results could be the basis of the development of surveillance protocols for a national monitoring system for PRRSV and PCV2, which could prevent future infection of Greek farms.

Comprehensive Analysis of Codon Usage Patterns in Chinese Porcine Circoviruses Based on Their Major Protein-Coding Sequences

Porcine circoviruses (PCVs) are distributed in swine herds worldwide and represent a threat to the health of domestic pigs and the profits of the swine industry. Currently, four PCV species, including PCV-1, PCV-2, PCV-3 and PCV-4, have been identified in China. Considering the ubiquitous characteristic of PCVs, the new emerged PCV-4 and the large scale of swine breeding in China, an overall analysis on codon usage bias for Chinese PCV sequences was performed by using the major proteins coding sequences (ORF1 and ORF2) to better understand the relationship of these viruses with their host. The data from genome nucleotide frequency composition and relative synonymous codon usage (RSCU) analysis revealed an overrepresentation of AT pair and the existence of a certain codon usage bias in all PCVs. However, the values of an effective number of codons (ENC) revealed that the bias was of low magnitude. Principal component analysis, ENC-plot, parity rule two analysis and correlation analysis suggested that natural selection and mutation pressure were both involved in the shaping of the codon usage patterns of PCVs. However, a neutrality plot revealed a stronger effect of natural selection than mutation pressure on codon usage patterns. Good host adaptation was also shown by the codon adaptation index analysis for all these viruses. Interestingly, obtained data suggest that PCV-4 might be more adapted to its host compared to other PCVs. The present study obtained insights into the codon usage pattern of PCVs based on ORF1 and ORF2, which further helps the understanding the molecular evolution of these swine viruses.

One Dose of a Novel Vaccine Containing Two Genotypes of Porcine Circovirus (PCV2a and PCV2b) and Mycoplasma hyopneumoniae Conferred a Duration of Immunity of 23 Weeks

Porcine circovirus type 2 (PCV2) and Mycoplasma hyopneumoniae (Mhyo) are important swine pathogens for which vaccination is a key control strategy. Three separate studies were performed to evaluate the duration of immunity (DOI) conferred by a novel vaccine combining PCV2a/PCV2b and Mhyo into a ready-to-use formulation. In each study, three-week-old naïve piglets were vaccinated (Day 0) and challenged 23-weeks later (Day 159) with either PCV2a, PCV2b or Mhyo. Pigs were euthanized three-to-four-weeks post-challenge. Vaccinated pigs had significantly lower PCV2 viremia from Day 168 until Day 175 (PCV2a study) or until euthanasia (PCV2b study), respectively. Fecal shedding was significantly lower for PCV2a-challenged from Day 171 until Day 178, and for PCV2b-challenged from Day 172 until euthanasia. In the PCV2a challenge study, there were no differences among vaccinates and controls in terms of percent of pigs positive for PCV2 immunohistochemistry, histiocytic replacement, or lymphoid depletion. However, significant differences for immunohistochemistry and histiocytic replacement, not lymphoid depletion, were observed among vaccinates and controls following PCV2b challenge. Vaccination supposed a significant reduction in the mean percentage of Mhyo-like lesions in the lung. Percentages of lung tissues positive for Mhyo via immunohistochemistry were 49.3% and 67.1% for vaccinated and control groups, respectively. One dose of the novel PCV2a/PCV2b/Mhyo vaccine conferred robust protection against challenge 23-weeks later for all three fractions.

Porcine Circovirus 2 Genotypes, Immunity and Vaccines: Multiple Genotypes but One Single Serotype

Identified for the first time in the 1990s, Porcine circovirus 2 (PCV-2) should not be considered an emerging virus anymore. Nevertheless, many aspects of its biology and epidemiology are still controversial. Particularly, its high evolutionary rate has caused the emergence of several variants and genotypes, alternating on the worldwide proscenium. The biological and practical implications of such heterogenicity are unfortunately largely unknown. The effectiveness of currently available vaccines against new genotypes that have emerged over time has been the topic of an intense debate and often inconclusive or contradictory results between experimental, field, and epidemiological studies have been gathered. The challenge in establishing an effective PCV-2 disease model, the peculiarities in experimental design and settings and the strains involved could justify the observed differences. The present work aims to summarize and critically review the available knowledge on PCV-2 genetic heterogeneity, immunity, and vaccine efficacy, organizing and harmonizing the available data from different sources, shedding light on this complex field and highlighting current knowledge gaps and future perspectives. So far, all vaccines in the market have shown great efficacy in reducing clinical signs associated to diseases caused by PCV-2, independently of the genotype present in the farm. Moreover, experimental data demonstrated the cross-protection of PCV-2a vaccines against the most widespread genotypes (PCV-2a, PCV-2b, and PCV-2d). Therefore, despite the significant number of genotypes described/proposed (PCV-2a to PCV-2i), it seems one single PCV-2 serotype would exist so far.

Porcine circovirus 2 (PCV2) population study in experimentally infected pigs developing PCV2-systemic disease or a subclinical infection

Porcine circovirus 2 (PCV2) is a single stranded DNA virus with one of the highest mutation rates among DNA viruses. This ability allows it to generate a cloud of mutants constantly providing new opportunities to adapt and evade the immune system. This pig pathogen is associated to many diseases, globally called porcine circovirus diseases (PCVD) and has been a threat to pig industry since its discovery in the early 90's. Although 11 ORFs have been predicted from its genome, only two main proteins have been deeply characterized, i.e. Rep and Cap. The structural Cap protein possesses the majority of the epitopic determinants of this non-enveloped virus. The evolution of PCV2 is affected by both natural and vaccine-induced immune responses, which enhances the genetic variability, especially in the most immunogenic Cap region. Intra-host variability has been also demonstrated in infected animals where long-lasting infections can take place. However, the association between this intra-host variability and pathogenesis has never been studied for this virus. Here, the within-host PCV2 variability was monitored over time by next generation sequencing during an experimental infection, demonstrating the presence of large heterogeneity. Remarkably, the level of quasispecies diversity, affecting particularly the Cap coding region, was statistically different depending on viremia levels and clinical signs detected after infection. Moreover, we proved the existence of hyper mutant subjects harboring a remarkably higher number of genetic variants. Altogether, these results suggest an interaction between genetic diversity, host immune system and disease severity.

Genetic diversity and different cross-neutralization capability of porcine circovirus type 2 isolates recently circulating in South Korea

Background

Porcine circovirus type 2 (PCV2) is a small single-stranded DNA virus and a primary cause of PCV-associated diseases (PCVAD) that result insubstantial economic loss for swine farms. Between 2016 and 2018, PCV2 field viruses were isolated from PCVAD-affected swine farms in South Korea and investigated for genetic and antigenic heterogeneity.

Results

The genetic analysis of ORF2 showed that the genotype of the Korean PCV2 field isolates has been rapidly shifted from PCV2a or 2b to mutant PCV2b known as PCV2d with 82.6 to 100% amino acid sequence similarity. PCV2-specific monoclonal antibodies (mAbs) demonstrated variable antigen-binding activity to four representative Korean PCV2 field isolates [QIA215 (PCV2a), QIA418 (PCV2b), QIA169 (PCV2d), and QIA244 (PCV2d)] without genotype specificity, and one mAb showed neutralization activity to QIA215. In a cross-virus neutralization assay using anti-PCV2 sera of pigs and guinea pigs injected with a commercial vaccine and the Korean PCV2 field isolates, the anti-porcine sera of a commercial vaccine had high neutralization activity against QIA215 and QIA418 with statistically lower activity against PCV2d viruses. Anti-guinea pig sera of QIA215, QIA418, QIA169, and a commercial vaccine had high neutralization activity against all of the viruses with significantly lower activity against QIA244. Importantly, anti-guinea pig sera of QIA244 had high neutralization activity against all of the viruses.

Conclusions

This study confirmed genetic and antigenic diversity among recent PCV2 field isolates in Korean swine farms, and the strain-based difference in virus neutralization capability should be considered for more effective control by vaccination.

First molecular detection and complete sequence analysis of porcine circovirus type 3 (PCV3) in Peninsular Malaysia

Porcine circovirus type 3 (PCV3) is a newly emerging virus in the swine industry, first reported recently in 2016. PCV3 assembles into a 2000 bp circular genome; slightly larger than PCV1 (1758-1760 bp), PCV2 (1766-1769 bp) and PCV4 (1770 bp). Apart from being associated with porcine dermatitis and nephropathy syndrome (PDNS), PCV3 has been isolated from pigs with clinical signs of reproductive failures, myocarditis, porcine respiratory disease complex (PRDC) and neurologic disease. Given that PCV3 is increasingly reported in countries including Thailand and U.S. with whom Malaysia shares trade and geographical relationship; and that PCV3 is associated with several clinical presentations that affect productivity, there is a need to study the presence and molecular characteristics of PCV3 in Malaysian swine farms. Twenty-four commercial swine farms, three abattoirs and retail shops in Peninsular Malaysia were sampled using convenience sampling method. A total of 281 samples from 141 pigs, including 49 lung archive samples were tested for PCV3 by conventional PCR. Twenty-eight lung samples from wild boar population in Peninsular Malaysia were also included. Nucleotide sequences were analyzed for maximum likelihood phylogeny relationship and pairwise distances. Results revealed that PCV3 is present in Peninsular Malaysia at a molecular prevalence of 17.02%, with inguinal lymph nodes and lungs showing the highest molecular detection rates of 81.82% and 71.43% respectively. Despite wide reports of PCV3 in healthy animals and wild boars, no positive samples were detected in clinically healthy finishers and wild boar population of this study. PCV3 strain A1 and A2 were present in Malaysia, and Malaysian PCV3 strains were found to be phylogenetically related to Spanish, U.S. and Mexico strains.

Quasispecies dynamics in disease prevention and control

Medical interventions to prevent and treat viral disease constitute evolutionary forces that may modify the genetic composition of viral populations that replicate in an infected host and influence the genomic composition of those viruses that are transmitted and progress at the epidemiological level. Given the adaptive potential of viruses in general and the RNA viruses in particular, the selection of viral mutants that display some degree of resistance to inhibitors or vaccines is a tangible challenge. Mutant selection may jeopardize control of the viral disease. Strategies intended to minimize vaccination and treatment failures are proposed and justified based on fundamental features of viral dynamics explained in the preceding chapters. The recommended use of complex, multiepitopic vaccines, and combination therapies as early as possible after initiation of infection falls under the general concept that complexity cannot be combated with simplicity. It also follows that sociopolitical action to interrupt virus replication and spread as soon as possible is as important as scientifically sound treatment designs to control viral disease on a global scale.

Generation and Immunogenicity of a Recombinant Pseudorabies Virus Co-Expressing Classical Swine Fever Virus E2 Protein and Porcine Circovirus Type 2 Capsid Protein Based on Fosmid Library Platform

Pseudorabies (PR), classical swine fever (CSF), and porcine circovirus type 2 (PCV2)-associated disease (PCVAD) are economically important infectious diseases of pigs. Co-infections of these diseases often occur in the field, posing significant threat to the swine industry worldwide. gE/gI/TK-gene-deleted vaccines are safe and capable of providing full protection against PR. Classical swine fever virus (CSFV) E2 glycoprotein is mainly used in the development of CSF vaccines. PCV2 capsid (Cap) protein is the major antigen targeted for developing PCV2 subunit vaccines. Multivalent vaccines, and especially virus-vectored vaccines expressing foreign proteins, are attractive strategies to fight co-infections for various swine diseases. The gene-deleted pseudorabies virus (PRV) can be used to develop promising and economical multivalent live virus-vectored vaccines. Herein, we constructed a gE/gI/TK-gene-deleted PRV co-expressing E2 of CSFV and Cap of PCV2 by fosmid library platform established for PRV, and the expression of E2 and Cap proteins was confirmed using immunofluorescence assay and western blotting. The recombinant virus propagated in porcine kidney 15 (PK-15) cells for 20 passages was genetically stable. The evaluation results in rabbits and pigs demonstrate that rPRVTJ-delgE/gI/TK-E2-Cap elicited detectable anti-PRV antibodies, but not anti-PCV2 or anti-CSFV antibodies. These findings provide insights that rPRVTJ-delgE/gI/TK-E2-Cap needs to be optimally engineered as a promising trivalent vaccine candidate against PRV, PCV2 and CSFV co-infections in future.

Truncated Rep protein of porcine circovirus 2 (PCV2) caused by a naturally occurring mutation reduced virus replication in PK15 cells

BACKGROUND

Porcine circovirus 2 (PCV2) is the causative agent of porcine circovirus-associated diseases (PCVADs). The infection of PCV2 is widespread and has serious consequence, thereby causing significant economic losses in the swine industry worldwide. Previously, we found that a strain named YiY-3-2-3 has a naturally occurring point mutation (G⁷¹⁰ to A⁷¹⁰) in ORF1 region, which leads to a shorten product of the rep gene (945 to 660 base pair). Importantly, the Rep protein is responsible for genome replication of PCV2. To explore the effects of this mutation on the PCV2 replication, in the current study we constructed infectious clone of this IF-YiY-3-2-3, as well as those of its two parental strains of IF-YiY-3-2-1 and IF-YiY-3-2-10. Subsequently, these infectious clones which have 1.1 copy of PCV2 genome of their corresponding strains were transfected into PK15 cells to obtain rescued viruses, respectively.

RESULTS

Though all of the three infectious clones could be rescued, the copy number and infectivity of these rescued viruses were significantly different, as analyzed by fluorescence quantitative PCR, Tissue culture infectious dose 50 (TCID₅₀), and indirect immunofluorescence assay (IFA). Notably, whether the PCV2 copy number, viral titer or the infectivity of rescued viruses from infectious clone IF-YiY-3-2-3 was significantly less than those of its parental clones. Meanwhile, the spatial structure of the Rep protein from the IF-YiY-3-2-3 displayed an apparent truncation at the C-terminal.

CONCLUSIONS

These findings therefore suggest that the Rep protein with truncated C-terminal would reduce virus replication and infectivity, and there might also exist both favorable and unfavorable mutations in the ORF1 of PCV2 in the process of its evolution.

Porcine circovirus 2 (PCV-2) genetic variability under natural infection scenario reveals a complex network of viral quasispecies

Porcine circovirus 2 (PCV-2) is a virus characterized by a high evolutionary rate, promoting the potential emergence of different genotypes and strains. Despite the likely relevance in the emergence of new PCV-2 variants, the subtle evolutionary patterns of PCV-2 at the individual-host level or over short transmission chains are still largely unknown. This study aimed to analyze the within-host genetic variability of PCV-2 subpopulations to unravel the forces driving PCV-2 evolution. A longitudinal weekly sampling was conducted on individual animals located in three farms after the first PCV-2 detection. The analysis of polymorphisms evaluated throughout the full PCV-2 genome demonstrated the presence of several single nucleotide polymorphisms (SNPs) especially in the genome region encoding for the capsid gene. The global haplotype reconstruction allowed inferring the virus transmission network over time, suggesting a relevant within-farm circulation. Evidences of co-infection and recombination involving multiple PCV-2 genotypes were found after mixing with pigs originating from other sources. The present study demonstrates the remarkable within-host genetic variability of PCV-2 quasispecies, suggesting the role of the natural selection induced by the host immune response in driving PCV-2 evolution. Moreover, the effect of pig management in multiple genotype coinfections occurrence and recombination likelihood was demonstrated.

Structure analysis of capsid protein of Porcine circovirus type 2 from pigs with systemic disease

Economic losses with high mortality rate associated with Porcine circovirus type 2 (PCV2) is reported worldwide. PCV2 commercial vaccine was introduced in 2006 in U.S. and in 2008 in Brazil. Although PCV2 vaccines have been widely used, cases of PCV2 systemic disease have been reported in the last years. Eleven nursery or fattening pigs suffering from PCV2 systemic disease were selected from eight PCV2-vaccinated farms with historical records of PCV2 systemic disease in Southern Brazil. PCV2 genomes were amplified and sequenced from lymph node samples of selected pigs. The comparison among the ORF2 amino acid sequences of PCV2 isolates revealed three amino acid substitutions in the positions F57I, N178S and A190T, respectively. Using molecular modeling, a structural model for the capsid protein of PCV2 was built. Afterwards, the mutated residues positions were identified in the model. The structural analysis of the mutated residues showed that the external residue 190 is close to an important predicted region for antibodies recognition. Therefore, changes in the viral protein conformation might lead to an inefficient antibody binding and this could be a relevant mechanism underlying the recent vaccine failures observed in swine farms in Brazil.

First molecular detection of porcine circovirus type 3 in dogs in China

Porcine circovirus type 3 (PCV3) has recently been isolated from diseased pigs within the USA. The objective was to detect the presence of PCV3 in dogs. Nested polymerase chain reactions (PCR) with PCV3-specific primers for the capsid gene were used to detect PCV3 genomic DNA in serum samples from dogs (n = 44) in China. There was PCV3 DNA detected in 4 of 44 dogs [all were negative for PCV2 and canine circovirus (CanineCV)]. Based on sequence analysis, positive sequences were grouped into PCV3 genotypes. However, these isolates had close evolutionary relationships with FoxCV (KP941114) and CanineCV (JQ821392). Further investigations of the epidemiology, evolutionary biology, and pathobiology of PCV3 to dogs are warranted.

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.

Genome Sequence of a Novel Porcine Circovirus Type 2 Strain That Reemerged in Southern China

Here, we describe a novel porcine circovirus type 2 (PCV2) variant (GD2014) found in the Guangdong province, southern China. Its complete genome is 1,766 nucleotides and contained a 708-nucleotide open reading frame 2 (ORF2). Sequence analysis suggested that GD2014 is closest to JS2015 originating from the Jiangsu province of China and belongs to the PCV2d genotype.

Porcine circovirus type 2 (PCV2) evolution before and after the vaccination introduction: A large scale epidemiological study

Since their commercialization, vaccines against Porcine circovirus type 2 (PCV2) have been the cornerstone control strategy. Nevertheless, the periodic emergence of new genotype waves and the recent reports of vaccine failure outbreaks have raised the question if widespread vaccination strategies could have driven viral evolution and affected different genotype fitness. To investigate this issue an in-deep analysis, based on a bioinformatics and biostatistics approach, has been implemented. ORF2 sequences from vaccinated and non-vaccinated populations (i.e. domestic pigs before and after vaccine introduction and wild boars) were considered. The action of selective forces on PCV2 strains has been analyzed and compared among groups. Remarkable differences were found in the selective forces acting on viral populations circulating in different “immune environments”. Particularly for PCV2a, a directional selection promoting a change in the viral capsid away from the vaccine specific antigenic determinants has been detected after vaccine introduction. Involved amino acids were previously reported to be part of viral epitopes whose variability is responsible of immune escape. Our findings support a change in PCV2 evolutionary pattern after widespread vaccination introduction and stress once more the compulsoriness of a continuous monitoring of PCV2 epidemiology to promptly act in response to the emergence of possible vaccine-escaping mutants.

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.

Genetic variability of porcine circovirus 2 (PCV2) field isolates from vaccinated and non-vaccinated pig herds in Germany

Porcine circovirus 2 (PCV2) is responsible for a wide range of associated diseases (PCVD) affecting swine production worldwide. Highly efficient commercial vaccines induce protective immunity, but PCV2 is still circulating in vaccinated farms. Thus, and because of the viruś high mutation rate, recent findings provide concerns about PCV2 strains capable to escape vaccination. Based on 2156 samples from individual pigs of 315 herds from Germany we describe a high effectivity of vaccination between 2008 and the third quarter of 2011. In this period, virus load dropped continuously and at the end of this period it hardly reached the limit of quantification. Thereafter, virus loads re-increased, although most of the herds were still vaccinated. Sixty-two randomly selected samples from vaccinated (n=28) and non-vaccinated (n=26) herds between 2008 and 2012 were completely sequenced. As compared to the PCV2b reference sequence 259 polymorphisms were detected. Polymorhisms were analysed for associations to vaccination status, genotype (PCV2a/PCV2b), and virus load. PCV2a sequences were significantly repelled by PCV2b. One SNP at position 1182 (g.1182G>T), involved in capsid epitope formation, was significantly associated with the PCV2 genotype (2a/2b). Moreover, this SNP was affected by vaccination, with effects on allele frequencies and viral load, independent from the PCV2 genotype (2a/2b). We conclude that there is indeed evidence for a selectional impact of vaccination on the PCV2 sequence, especially on nucleotides involved in epitope formation. Such variation might be responsible for the observed re-increase of PCV2-loads in samples from the end of 2011 in Germany.