Detection of two porcine circovirus type 2 genotypic groups in United States swine herds

Isolation and pathogenicity of porcine circovirus type 2 in mice from Guangxi province, China

BACKGROUND

Porcine circovirus type 2 (PCV2), a member of the genus Circovirus and family Circoviridae, is a closed, small, circular, and single-stranded DNA virus, and it is a crucial swine pathogen of porcine circovirus-associated diseases (PCVADs). PCV2 was first detected in PK-15(ATCC-CCL) cells in 1974, which has caused significant economic loss to the swine industry throughout the world. And the first case of PCV2 was reported in China in 2000. At present, PCV2d is the main genotype circulating widely in China.

METHODS

Lymph samples were obtained from piglets with emaciation and respiratory disease in Guangxi province, China. The main pathogens were detected via PCR from lymph samples, and then PCV2-single positive samples were used to inoculate with PK-15 cells. After successive generations, the isolate was subsequently identified by polymerase chain reaction (PCR), immunofluorescence assay (IFA), Western blot (WB), and transmission electron microscopic (TEM). The full-length genome and genetic characterization of isolates were analyzed by Sanger sequencing. The TCID50 of the PCV2-GX-6 was determined by IFA, and the pathogenicity of PCV2 in BALB/c mice was analyzed via the mouse model.

RESULTS

The isolates were successfully isolated from clinical samples. The complete genome of PCV2-GX-4, PCV2-GX-6, PCV2-GX-7, PCV2-GX-11 and PCV2-GX-16 have been amplified, sequenced, and deposited in GenBank (accession no.: OR133747, OQ803314, OR133748, OR133749, OR133750). Homology and phylogenetic analysis with reference strains showed that the isolates belonged to the PCV2d genotype. The PCV2-GX-6 could be stably passaged more than 30 times in PK-15 cells. PCV2-GX-6 was identified by PCR, IFA, WB and TEM. The results of homology showed that PCV2-GX-6 was closely related to the reference strains PCV2-JS17-8 (GenBank accession no.: MH211363). Pathogenicity studies in mice have shown that PCV2-GX-6 can lead to growth inhibition of mice. Meanwhile PCV2-GX-6 caused the typical lesions of spleen, lung and kidney. The results of qPCR showed that PCV2 can effectively proliferate in the liver, spleen, lung, and kidney.

CONCLUSION

PCV2-GX-6 can successfully infect BLAB/c mice, effectively proliferate in major organs, and possessed high pathogenicity. In conclusion, combined with the genotype and pathogenicity of PCV2d currently prevalent, PCV2-GX-6 can be used as a candidate vaccine strain.

Revisiting Porcine Circovirus Infection: Recent Insights and Its Significance in the Piggery Sector

Porcine circovirus (PCV), a member of the Circoviridae family within the genus Circovirus, poses a significant economic risk to the global swine industry. PCV2, which has nine identified genotypes (a-i), has emerged as the predominant genotype worldwide, particularly PCV2d. PCV2 has been commonly found in both domestic pigs and wild boars, and sporadically in non-porcine animals. The virus spreads among swine populations through horizontal and vertical transmission routes. Despite the availability of commercial vaccines for controlling porcine circovirus infections and associated diseases, the continuous genotypic shifts from a to b, and subsequently from b to d, have maintained PCV2 as a significant pathogen with substantial economic implications. This review aims to provide an updated understanding of the biology, genetic variation, distribution, and preventive strategies concerning porcine circoviruses and their associated diseases in swine.

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.

First detection and complete genome analysis of porcine circovirus-like virus P1 and porcine circovirus-2 in yak in China

Porcine circovirus-like virus P1, like porcine circovirus type 2 (PCV2), is a potential pathogen of post-weaning multisystemic wasting syndrome in swine. Yaks are a valuable species and an iconic symbol of the Tibet Plateau which is the highest and largest plateau in the world. In this study, a total of 105 yak diarrheal samples, collected from 13 farms in Linzhi in the Tibet Plateau from January 2019 to December 2021, that were screened for P1 and PCV2 by polymerase chain reaction, 10.48% (n = 11) were positive for P1, 4.76% (n = 5) for PCV2, and 5.71% (n = 6) were positive for coinfection of P1 and PCV2. In addition, the whole genomes of eight P1 strains and eight PCV2 strains were sequenced. Alignment of deduced amino acid sequences of P1 ORF1 and PCV2 ORF2 gene revealed that ON012566 had one unique amino acid mutation at residues 137 (T to P). This mutation has important implication for the study of virus virulence, tissue tropism, and immune response. Phylogenetic analysis shows that the yak-origin P1 strains in this study with cattle-origin P1 reference strains were grouped into one cluster. The yak-origin PCV2 (ON012566) and a buffalo-origin PCV2 (KM116514) reference strain clustered in the same branch in the PCV2b regions. Meanwhile, the remaining PCV2 strains and buffalo-origin PCV2 reference strain (ON012565) clustered in the PCV2d regions. To summarize, to our knowledge, this is the first report on the molecular prevalence and genome characteristics of P1 and PCV2 in yaks in the world and will contribute to further study of the molecular epidemiology, source, and evolution of P1 and PCV2 strains.

Pathological Evaluation of Porcine Circovirus 2d (PCV2d) Strain and Comparative Evaluation of PCV2d and PCV2b Inactivated Vaccines against PCV2d Infection in a Specific Pathogen-Free (SPF) Yucatan Miniature Pig Model

Porcine circovirus type 2 (PCV2) is an economically important swine pathogen that causes porcine circovirus-associated diseases (PCVADs). The objective of this study was to evaluate the use of specific pathogen-free Yucatan miniature pigs (YMPs) as an experimental model for PCV2d challenge and vaccine assessment because PCV2-negative pigs are extremely rare in conventional swine herds in Korea. In the first experiment, every three pigs were subjected to PCV2d field isolate or mock challenge. During three weeks of experiments, the PCV2d infection group exhibited clinical outcomes of PCVAD with high viral loads, lymphoid depletion, and detection of PCV2d antigens in lymphoid organs by immunohistochemistry. In the second experiment, three groups of pigs were challenged with PCV2d after immunization for three weeks: a nonvaccinated group (three pigs), a PCV2b-Vac group vaccinated with a commercial PCV2b-based inactivated vaccine SuiShot^® Circo-ONE (five pigs), and a PCV2d-Vac group vaccinated with an experimental PCV2d-based inactivated vaccine (five pigs). During the three weeks of the challenge period, nonvaccinated pigs showed similar clinical outcomes to those observed in the PCV2d infection group from the first experiment. In contrast, both the PCV2b and PCV2d vaccinations produced good levels of protection against PCV2d challenge, as evidenced by reduced viral loads, improved growth performance, high virus-neutralizing antibody titers, and less development of PCV2-associated pathological lesions. Taken together, these data suggest that YMPs could be an alternative model for PCV2 challenge experiments, and these animals displayed typical clinical and pathological features and characteristics of protective immunity induced by the vaccines that were consistent with those resulting from PCV2 infections in conventional pigs.

Genotype Shift of Malaysian Porcine Circovirus 2 (PCV2) from PCV2b to PCV2d within a Decade

Simple Summary

This study aims to provide an updated Malaysian porcine circovirus 2 (PCV2) situation after a knowledge gap of one decade. Molecular detection rates of 83.78% and 83.54% at farm and sample population level were reported, close to previous publication. However, an obvious genotype shift from genotype PCV2b to PCV2d was revealed. Substitution rate for PCV2 cap gene sequences in this study was estimated at 1.102 × 10⁻³ substitutions/site/year, in agreement with the high substitution rate expected from PCV2 strains. Phylogenetic clustering pattern according to the year of sample origin was observed, suggesting possible nucleotide mutation occurring over time. Concurrent circulation of different PCV2 strains within one farm and within a single individual were also observed. This study also reports detection of PCV2 antigen across all production age groups from fetuses to sows; in abattoir lung samples from clinically healthy finishers; and in the wild boar population roaming Peninsular Malaysia. These observations of high molecular detection rates in farms, clinically healthy abattoir samples and in the wild boar population; and most importantly, a new wave of genotype shift from PCV2b to PCV2d—warrant further attention on the Malaysian PCV2 situation pertinent to the control and management strategy applicable to local swine farming.

Abstract

This paper aims to update the molecular status of porcine circovirus 2 (PCV2) in Malaysia. Firstly, the molecular detection rate of PCV2 in farm and sampled pig population were reported to be 83.78% (31/37 farms) and 83.54% (66/79 pigs) positive for PCV2, respectively. PCV2 was detected across all age groups, from fetuses, porkers to sows. Co-detection of PCV2 and PCV3 antigens was also reported at a rate of 28.77% (21/73). Secondly, PCV2 antigen was also detected in Malaysian abattoir lung samples: 18 out of 19 (94.74%) samples originating from clinically healthy finishers were tested positive. Further, this is the first study to confirm the circulation of PCV2 in the wild boar population roaming Peninsular Malaysia, where 28 out of 28 (100%) wild boar lung samples were found positive. One decade earlier, only genotype PCV2b was reported in Malaysia. This most recent update revealed that genotypes PCV2a, PCV2b and PCV2d were present, with PCV2d being the predominant circulating genotype. PCV2 cap gene nucleotide sequences in this study were found to be under negative selection pressure, with an estimated substitution rate of 1.102 × 10⁻³ substitutions/site/year (ssy).

Molecular genotypic analysis of porcine circovirus type 2 reveals the predominance of PCV2d in Vietnam (2018-2020) and the association between PCV2h, the recombinant forms, and Vietnamese vaccines

We conducted nucleotide and amino acid sequence alignment and phylogenetic analysis of porcine circovirus ORF2 (Cap protein) from 17 PCV2-positive clinical samples from nine different northern Vietnamese provinces (Mar 2018-Nov 2020), four local vaccines, and 77 reference strains. We identified one PCV2a (1/17 = 5.9%), five PCV2b (5/17 = 29.9%), and 11 PCV2d (11/17 = 64.7%) isolates, while only PCV2d was detected in 2020. Timeline analysis indicated an increasing predominance of PCV2d nationwide (2018-2020). With strong nodal support (98% for nucleotides and 74% for amino acids), the phylogenetic tree topology revealed a distinct PCV2h clade including recombinant/intermediate strains and local vaccines. The Cap protein sequences from 11 PCV2d field strains had the 2d-genotype-typical motif ⁸⁶SNPLSV⁹¹ in loop CD, the motif TGID in loop GH-HI, and the motif ²³⁰PLNPK²³⁴ in loop CT. The PCV2h isolates (and vaccines) had the ⁸⁶SNPLSV⁹¹, SAID, and ²³⁰L(N/H)PK²³⁴ motifs. Selection pressure analysis indicated positive selection at seven sites: A⁶⁸N in immunoreactive region (IRR)-A; ¹¹⁹G and ¹³⁰V in IRR-B; and ¹⁶⁷L, T¹⁹⁰(A/S), ¹⁹⁴D and ²⁰²F in IRR-C. We identified PCV2h as the genotype of the recombinant strains, which resulted from intergenotype recombination of PCV2a, PCV2b, and PCV2d. The current data provide new information about the diversity, distribution, and dominance of the PCV2 genotype in Vietnam.

Evaluation of Methylotrophic Yeast Ogataea thermomethanolica TBRC 656 as a Heterologous Host for Production of an Animal Vaccine Candidate

Multiple yeast strains have been developed into versatile heterologous protein expression platforms. Earlier works showed that Ogataea thermomethanolica TBRC 656 (OT), a thermotolerant methylotrophic yeast, can efficiently produce several industrial enzymes. In this work, we demonstrated the potential of this platform for biopharmaceutical manufacturing. Using a swine vaccine candidate as a model, we showed that OT can be optimized to express and secrete the antigen based on porcine circovirus type 2d capsid protein at a respectable yield. Crucial steps for yield improvement include codon optimization and reduction of OT protease activities. The antigen produced in this system could be purified efficiently and induce robust antibody response in test animals. Improvements in this platform, especially more efficient secretion and reduced extracellular proteases, would extend its potential as a competitive platform for biopharmaceutical industries.

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.

Efficacy of bivalent vaccines of porcine circovirus type 2 and Mycoplasma hyopneumoniae in specific pathogen-free pigs challenged with porcine circovirus type 2d

Background

Porcine circovirus type 2 (PCV2) and Mycoplasma hyopneumoniae (MHP) are economically significant pathogens in the pig industry. The use of combined vaccines against PCV2 and MHP is one of the most effective ways of protecting pigs from both diseases, and it has become a part of general management.

Objectives

This study evaluated the efficacy of two new bivalent vaccines of PCV2 and MHP (Myco-X and Myco-XD) in SPF pigs. Myco-X and Myco-XD are a combined vaccine of MHP with PCV2b and PCV2d, respectively.

Methods

Sixteen pigs were divided into four groups: Myco-X-vaccinated challenged, Myco-XD-vaccinated challenged, unvaccinated challenged, and unvaccinated unchallenged. Two milliliters of Myco-X were administered intramuscularly, and 0.5 mL of Myco-XD was injected intradermally at 3 wk of age. The pigs were challenged with virulent PCV2d via the intramuscular and intranasal route 4 wk post-vaccination.

Results

All vaccinated pigs showed effective reduction of the clinical signs, the PCV2d load in the blood and nasal swab samples, as well as lung and lymphoid tissue lesions in the challenge test. Compared to unvaccinated challenged animals, the vaccinated challenged animals showed significantly higher (p < 0.05) levels of anti-PCV2 IgG, PCV2d-specific interferon-γ (IFN-γ), and anti-MHP IgG.

Conclusions

Based on clinical, microbiological, serological, and pathological assessments, this study confirmed that both combined vaccines could protect pigs against PCV2 infection caused by PCV2d. On the other hand, further research on the efficacy evaluation of these new vaccines against the MHP challenge and PCV2d/MHP co-challenge is needed.

Minimal Dosage of Porcine Circovirus Type 2d Based Virus-like Particles to Induce Stable Protective Immunity against Infection

In recent years, porcine circovirus type 2d (PCV2d) has achieved a dominant position worldwide. Various PCV2d capsid-based vaccines have been used to alleviate concerns regarding the emergence of the variant. This study aimed to determine the dosage of recombinant PCV2d capsid protein to induce protective efficacy against experimental challenge with a virulent PCV2d strain. Conventional 3-week-old pigs were intramuscularly inoculated with different doses of the protein (60, 20, 10 and 2 µg). Four weeks after vaccination, all pigs were challenged with pathogenic PCV2d (SNU140003), which was isolated from a farm severely experiencing PCV2-associated disease in Korea. Vaccination with greater than 10 µg of the capsid protein caused a significant (p < 0.05) reduction in PCV2d viremia, lymphoid lesions and lymphoid PCV2 antigen levels in vaccinated challenged pigs compared to unvaccinated challenged pigs. The vaccination also resulted in significantly higher (p < 0.05) titers of neutralizing antibodies against PCV2d. However, the pigs vaccinated with 2 µg had significantly lower neutralizing antibody titers than the other vaccinated groups. They showed a similar level of challenged PCV2d in serum and lymphoid lesion score compared to unvaccinated challenged pigs. The difference in efficacy among the vaccinated groups indicates that there may be a baseline dosage to induce sufficient neutralizing antibodies to prevent viral replication in pigs. In conclusion, at least 10 µg dosage of capsid protein is essential for stable protective efficacy against PCV2d in a pig model.

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.

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.

Emergence of porcine circovirus 2g (PCV2g) and evidence for recombination between genotypes 2g, 2b and 2d among field isolates from non-vaccinated pigs in Mizoram, India

The molecular genetics of fourteen Porcine Circovirus 2 (PCV2) isolates from non-vaccinated pigs that died of porcine circovirus associated disease (PCVAD) between 2012 and 2019 in the Mizoram state of North East India, was studied. The PCVAD in these pigs, that had shown characteristic clinical signs and lesions associated with post-weaning multi-systemic wasting syndrome and reproductive failure was confirmed with detection of PCV2 DNA in the tissue samples. Complete viral genomes of these fourteen field isolates were sequenced following in house developed overlapping PCR. The multiple sequence alignment of viral capsid proteins or the open reading frame 2 (ORF2) sequences showed highly conserved residues known for antibody recognition and genotype specificity, however, variations were noticed in the amino acid residues previously known as important for in vitro replication of PCV2. The phylogenetic analyses based on the complete genome sequences enabled identification of genotype PCV2g (9/14, 64.29%) for the first time in India along with genotypes PCV2d (3/14, 21.43%) and PCV2b (2/14, 14.29%). Further, recombination analyses showed evidence for recombination between the genotypes 2b, 2g and 2d. This is the first report on the prevalence of genotype PCV2g and natural inter-genotypic (2g-2b, 2g-2d and 2d-2g) recombinants in India. The findings indicate a non-vaccine driven, natural genotypic shift and signify the need for routine PCV2 surveillance and genotyping. Our analyses also provide a solid ground for future studies to understand the consequences of multiple PCV2 genotypes within a pig population with respect to vaccination, diagnostics and emergence of new genotypes.

Porcine circovirus genotypes and their copathogens in pigs with respiratory disease in southern provinces of Vietnam

This study was conducted to investigate the genetic diversity of porcine circovirus type 2 (PCV2) and its coinfecting pathogens in pigs with respiratory disease in Vietnam. Samples from 127 clinical cases were obtained from different southern provinces of Vietnam from January 2018 to January 2020 for PCR and sequence analysis. The infection rate of PCV2 was 78.8%, and the major pathogens found in coinfections with PCV2 were porcine reproductive and respiratory syndrome virus, Mycoplasma hyopneumoniae, and Haemophilus parasuis. Forty-three PCV2-positive clinical samples were selected for amplification and sequencing of the ORF2 region. Phylogenetic analysis of PCV2 ORF2 showed that five of the sequences belonged to PCV2b (11.6%) and 38 belonged to PCV2d (88.4%), indicating that PCV2d strains were predominant in southern provinces of Vietnam. Alignment of the predicted amino acid sequences of the PCV2 capsid protein revealed polymorphic sites in the antibody recognition regions. This study demonstrates the prevalence of the PCV2d genotype in southern Vietnam and presents a comprehensive overview of the coinfecting pathogens associated with PCV2 in young pigs with respiratory disease.

Co-infection status of novel parvovirus's (PPV2 to 4) with porcine circovirus 2 in porcine respiratory disease complex and porcine circovirus-associated disease from 1997 to 2012

As global pig health diseases, porcine respiratory disease complex (PRDC) and porcine circovirus-associated disease (PCVAD) generate substantial economic losses despite pigs been vaccinated against the primary causative virus, highlighting the importance of understanding virome interactions and specifically co-factor infections. Established primary endemic pathogens for PRDC include porcine circovirus 2 (PCV2), porcine reproductive and respiratory syndrome virus (PRRSv) and swine influenza virus (SIV), and PCV2 aetiology in interaction with other co-infecting viruses can result in PCVAD. Porcine parvovirus (PPV) 1 is a well-characterized virus with an available vaccine preventing reproductive failure in sows. However, whilst novel PPV 2 to 7 viruses have been identified since 2001, their viral pathogenic potential in clinical and subclinical disease remains to be determined. Therefore, this study has sought to develop a better understanding of their potential role as associated co-infections in PRDC and PCVAD by examining archival samples for the presence of PCV2 and the novel parvoviruses PPV2-4 from clinically diseased pigs across production age stages. Epidemiologically, the novel PPV2 was found to be the most prevalent within the fattener age group with PPV2-4 statistically associated with pig respiratory disease and enteric ulcers. Additionally, statistical modelling by latent class analysis (LCA) on veterinary pathology scored pigs found a clustering co-factor association between PPV2 and PCV2, suggesting the novel PPV may be involved in PRDC and PCVAD. Phylogenetic analysis of novel PPVs revealed the PPV2 capsid evolution to be diverged from the original strains with a low nucleotide homology of 88%-96% between two distinct clades. These findings determine that novel PPV 2-4 viruses are statistically associated as co-infectors in a diseased pig population, and significantly detected PPV2 clustering co-infection frequency with PCV2 in PRDC and PCVAD diseased pigs through LCA analysis.

Porcine Circovirus Type 2 Pathogenicity Alters Host's Central Tolerance for Propagation

Porcine circovirus type 2 (PCV2) infections and resulting diseases are a worldwide threat to pig production. PCV2 bears a uniqueness that allows for us to understand more about chronic infections and the immune system in general. The virus can be phylogenetically subdivided into PCV2a to PCV2h genotypes. Although vaccination against PCV2 has been seen to prevent the manifestation of PCV disease, PCV2 still lingers as subclinical infections in all developmental stages of pigs. The “slow and low” tactic gives PCV2 a particular advantage in a host’s immune surveillance. Since the inception of the PCV2 associated panzootic, research scientists have been trying to understand the pathogenicity of PCV2. Different research groups found that one genotype group member was more pathogenic than others. We found, in our weaner infection model with in vivo transfection of different recombinant PCV2 genotype group members that these viruses alter T cell maturation in the thymus, including host’s central tolerance. Here, we extend these original observations by showing that PCV2 infected cells were also found in proximity within the female and male reproductive organs of stillborn pig fetuses. These PCV2 pools were sufficient in infecting three and half-day-old embryos in sows. Furthermore, the dominant PCV2 group member was more pathogenic in our weaner infection model. PCV2 pre-immunocompetence infection makes PCV2 recognized by central immune tolerance as belonging to the host. This also explains why pathogenicity is not a genetically intrinsic characteristic of PCV2; however, the dominance of any one PCV2 genotype group member leads to a more efficient deletion of the T cells against that specific genotype group member in the thymus.

Development of a differential multiplex real-time PCR assay for porcine circovirus type 2 (PCV2) genotypes PCV2a, PCV2b and PCV2d

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A multiplex real-time PCR (mqPCR) is developed for PCV2a, 2b, and 2d differentiations.

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Sequencing of 74 strains confirmed genotyping results generated by the mqPCR.

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The mqPCR did not detect any non-target swine pathogens included in this study.

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This genotyping assay is recommended following a general PCV2 diagnostic testing.

A multiplex quantitative real-time polymerase chain reaction (mqPCR) assay was developed and validated for detection and differentiation of porcine circovirus type 2 (PCV2) genotypes, PCV2a, PCV2b and PCV2d. Single nucleotide polymorphism in primers or probes was deployed for different genotype detections, while conserved sequence in the 3' end of a primer and in the middle of a probe was used for the targeted genotype. In silico analysis of 2601 PCV2 ORF2 sequences showed that the predicted strain coverage of the assay was 93.4 % (409/438) for PCV2a, 95.1 % (1161/1221) for PCV2b and 93.6 % (882/942) for PCV2d strains. The PCR amplification efficiencies were 94.5 %, 100.2 %, and 99.2 % for PCV2a, PCV2b and PCV2d, respectively, with correlation coefficients >0.995 for all genotypes. The limits of detection (LOD) were 1.58 × 10⁻⁴ TCID50/mL for PCV2a, 5.62 × 10⁻⁴ TCID50/mL for PCV2b, and 3.16 × 10⁻³ TCID50/mL for PCV2d. Sanger sequencing of 74 randomly selected PCV2 positive clinical samples confirmed the genotypes of strains identified by the mqPCR. Validation with clinical samples co-positive for target and non-target pathogens demonstrated that the mqPCR assay specifically detected targeted viruses without cross reacting to each other or to other common porcine viruses.

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.

Comparison of Multiplex Real-Time PCR and PCR-Reverse Blot Hybridization Assays for the Direct and Rapid Detection of Porcine Circovirus Type 2 Genotypes

Porcine circovirus type 2 (PCV2), the causative agent of porcine circovirus-associated diseases (PCVAD), poses a serious economic threat for the swine industry. Currently, PCV2 is classified into five major genotypes: PCV2a, PCV2b, PCV2c, PCV2d, and PCV2e. The aim of this study is to evaluate the performance of two commercially available methods, multiplex real-time PCR assay and PCR-reverse blot hybridization assay (REBA), for the rapid detection of PCV2 and direct identification of PCV2 genotypes from clinical samples as well as to compare the results with that of sequence analysis. Molecular diagnostic methods were used to evaluate a total of 180 samples, including tissues and blood samples from pigs that were suspected of PCVAD infection. The results of this study showed that the detection rate for positive PCV2 was 48.3% (n = 87) in both multiplex real-time PCR and PCR-REBA methods. Using sequence analysis, which is the gold standard, and multiplex real time PCR assay, the sensitivity, specificity, positive predictive value, and negative predictive value of PCV2 genotyping were found to be 97.1% (n = 67, 95% CI 0.894–0.998, p < 0.001), 100% (n = 93, 95% CI 0.966–1.000, p < 0.001), 100% (95% CI 0.953–1.000, p < 0.001), 97.9% (95% CI 0.921–0.998, p < 0.001), respectively. The results of PCR-REBA were found to be consistent with those of sequence analysis for all the samples and showed good agreement (κ = 1). The most prevalent genotypes detected in this study were PCV2d (n = 53, 60.9%), followed by PCV2a (n = 17, 19.5%), PCV2b (n = 14, 16.1%), and PCV2a/b co-infection (n = 3, 3.5%). Both the methods required ~3 h for completion. Therefore, we conclude that two molecular methods are rapid and reliable for the characterization of the causative pathogen with PCV2 genotypes.

High rates of detection and complete genomic analysis of porcine circovirus 2 (PCV2) in the Lesser Antilles island of St. Kitts: Identification of PCV2b-PCV2d recombinants

Although porcine circovirus 2 (PCV2) is an economically important pathogen of swine, there is a lack of information on PCV2 from the Lesser Antilles. In this retrospective study, we report high rates of detection of PCV2 DNA in porcine faecal (41.3%, 26/63) and kidney (32.8%, 20/61) samples from the Lesser Antilles island of St. Kitts. Most of the PCV2-positive faecal samples were from diarrhoeic piglets (23/26), with 15 animals exhibiting stunted growth and/or weight loss. Although the PCV2-positive kidneys were from slaughter age, clinically healthy pigs, microscopically, various degrees of inflammation (mild, moderate or severe) were observed in 18 kidneys. Rotavirus-A, porcine parvovirus and torque teno sus virus were detected in 2, 4 and 14 PCV2-positive samples, respectively. The complete genomes of 18 St. Kitts PCV2 strains were amplified using three overlapping nested PCR assays designed in the present study. By phylogenetic analysis of PCV2 open reading frame 2 (ORF2) and complete genomes, 15 St. Kitts strains were assigned to genotype PCV2b. The remaining three PCV2 strains were identified as PCV2b-PCV2d recombinants, with the involvement of ORF2 in two of the strains. To our knowledge, this is the first report on detection and genotyping of PCV2 strains from the Lesser Antilles. Considering the significant contributions of pig farming to the regional livestock economy and increasing demand for local pork in the Lesser Antilles, our findings emphasize the importance of future studies on surveillance and genotyping of PCV2 in other Caribbean islands of the region.

Neutralization Mechanism of a Monoclonal Antibody Targeting a Porcine Circovirus Type 2 Cap Protein Conformational Epitope

Porcine circovirus type 2 (PCV2) is an important pathogen in swine herds, and its infection of pigs has caused severe economic losses to the pig industry worldwide. The capsid protein of PCV2 is the only structural protein that is associated with PCV2 infection and immunity. Here, we report a neutralizing monoclonal antibody (MAb), MAb 3A5, that binds to intact PCV2 virions of the PCV2a, PCV2b, and PCV2d genotypes. MAb 3A5 neutralized PCV2 by blocking viral attachment to PK15 cells. To further explore the neutralization mechanism, we resolved the structure of the PCV2 virion in complex with MAb 3A5 Fab fragments by using cryo-electron microscopy single-particle analysis. The binding sites were located at the topmost edges around 5-fold icosahedral symmetry axes, with each footprint covering amino acids from two adjacent capsid proteins. Most of the epitope residues (15/18 residues) were conserved among 2,273 PCV2 strains. Mutations of some amino acids within the epitope had significant effects on the neutralizing activity of MAb 3A5. This study reveals the molecular and structural bases of this PCV2-neutralizing antibody and provides new and important information for vaccine design and therapeutic antibody development against PCV2 infections.IMPORTANCE PCV2 is associated with several clinical manifestations collectively known as PCV2-associated diseases (PCVADs). Neutralizing antibodies play a crucial role in the prevention of PCVADs. We demonstrated previously that a MAb, MAb 3A5, neutralizes the PCV2a, PCV2b, and PCV2d genotypes with different degrees of efficiency, but the underlying mechanism remains elusive. Here, we report the neutralization mechanism of this MAb and the structure of the PCV2 virion in complex with MAb 3A5 Fabs, showing a binding mode in which one Fab interacted with more than two loops from two adjacent capsid proteins. This binding mode has not been observed previously for PCV2-neutralizing antibodies. Our work provides new and important information for vaccine design and therapeutic antibody development against PCV2 infections.

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

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.

The Role of Non-animal Origin Feed Ingredients in Transmission of Viral Pathogens of Swine: A Review of Scientific Literature

The emergence of porcine epidemic diarrhea (PED) in commercial swine in North America and growing concerns about the potential for the introduction of African swine fever (ASF) from China, the European Union, or other affected regions has put a spotlight on the possible role of contaminated feed and feed ingredients in the introduction and transmission of viral swine pathogens. This paper systematically reviews the scientific literature regarding whether non-animal origin ingredients of commercial swine feed could introduce or transmit viral pathogens of swine into or within the United States. The purpose of this review is to identify, evaluate, and summarize the relevant scientific knowledge, published through March 2018, and to identify information gaps and research needs, thereby making the available evidence more accessible to policy makers, the swine industry, and the scientific community. A total of 26 documents were selected for the final review process, which included experimental studies, case reports, epidemiological investigations, and scientific opinion, among others. The review found that the scientific literature has addressed some critical experimental questions pertaining to transmission of swine viruses via feed and feed ingredients, but the current body of scientific knowledge lacks conclusive evidence of virus contamination of non-animal origin feed ingredients of commercial swine feed, particularly for imported commodities, and further investigation into the epidemiology of virus transmission via feed to swine under field conditions through natural feeding behavior is warranted. Additional studies of how imported ingredients of commercial swine feed are sourced, processed, transported and, thus, contaminated prior to importation into the United States are needed. Moving forward, studies designed to examine the likely source(s) of contamination and subsequent virus mitigation steps in processing and post-processing may be the most fruitful focus of research.

Changes on the viral capsid surface during the evolution of porcine circovirus type 2 (PCV2) from 2009 till 2018 may lead to a better receptor binding

Porcine circovirus type 2 (PCV2) is the primary causative agent of porcine circovirus-associated diseases (PCVAD). Three major PCV2 genotypes (PCV2a, PCV2b, and PCV2d) have been identified globally. Despite their worldwide distribution, the prevalence and genetic evolution of PCV2 in Belgium has not previously been determined. In this study, 319 samples from animals suffering from diseases likely to be associated with PCV2 were collected from 2009 to 2018 and analysed by virus titration. The overall prevalence of PCV2 in PCVAD-suspected cases was 15.7 per cent (50/319). The phylogenetic analysis demonstrated that at least three genotypes (PCV2a, PCV2b, and PCV2d) circulated in Belgium from 2009 till 2018, and that PCV2 evolved from PCV2a to PCV2b and from PCV2d-1 to PCV2d-2. Sequence comparison among the forty-three PCV2 isolates showed that they had 89.7–100 per cent nucleotide-sequence and 88.5–100 per cent amino-acid-sequence identities. Three amino acid sites were under positive selection. Three-dimensional analysis of genotype-specific amino acids revealed that most of the mutations were on the outside of the cap protein with a few conserved mutations present on the inner side. Mutations toward more basic amino acids were found on the upper and tail parts of two connecting capsid proteins which form one big contact region, most probably involved in receptor binding. The lower part was relatively conserved. This polarity change together with the formation of an extruding part drive the virus to a more efficient GAG receptor binding. Taken together, these results showed a genotype shift from PCV2a to PCV2b and later on from PCV2d-1 to PCV2d-2, and a PCV2 evolution toward a better receptor binding capacity.

Phylogeographic and genetic characterization of porcine circovirus type 2 in Taiwan from 2001-2017

Porcine circovirus type 2 (PCV2) is an important pathogen that causes significant economic losses in the swine industry worldwide. Five major PCV2 genotypes have been identified, including PCV2a, PCV2b, PCV2c, PCV2d, and PCV2e. To investigate the prevalence and phylodynamics of the different PCV2 genotypes in Taiwan, 214 PCV2 ORF2 sequences from Taiwan and other countries were analyzed. Genotypic differences were observed among PCV2a, 2b, and 2d at amino acid position 89 in ORF2, with isoleucine (I), arginine (R), and leucine (L), respectively. Similar to other countries, a genotypic shift was also observed in Taiwan, where the predominant genotype shifted from PCV2b to 2d after 2010. The estimated nucleotide substitution rate of Taiwanese strains in the ORF2 region was 8.467 × 10⁻⁴ substitutions per site per year. This rapid evolution rate of PCV2 may lead to the genotypic shift observed in Taiwan. The times to the most recent common ancestor (TMRCA) for PCV2a, -2b, and -2d-2 was dated to 1970, 1992 and 2004, respectively. Thus, the PCV2a, -2b, and -2d genotypes were already present in Taiwan before the introduction of the PCV2 vaccine.

Genetic analysis of porcine circovirus type 2 (PCV2) strains between 2002 and 2016 reveals PCV2 mutant predominating in porcine population in Guangxi, China

Background

Porcine circovirus 2-associated disease (PCVAD) is acknowledged as one of the most economically important diseases for the swine industry worldwide. The aim of this study was to characterize and determine the genetic diversity of PCV2 in the porcine population of Guangxi, China.

Methods

The full length genome and open reading frame 2 (ORF2) of 95 PCV2 strains collected from the tissues and sera of pigs that had either died as a result of PCVAD or did not exhibit disease symptoms were analyzed.

Results

The results of multiple sequence alignments showed that there is considerable diversity among the PCV2 ORF2 sequences. Phylogenetic analyses based on the complete genome showed that current PCV2 strains in this study could be divided into PCV2a (1/95), PCV2b (39/95), PCV2d (43/95), PCV2e (10/95) and PCV2h (2/95). Among the 5 sub-genotypes, PCV2b was dominant in the porcine population from 2002 to 2008. The newly identified sub-genotype, PCV2d, was seen from 2003 and has increased every year. PCV2b and PCV2d formed two predominant genetic groups circulating in southern China between 2009 and 2013 and the sub-genotype PCV2d has become the dominant virus in China since 2014.

Conclusions

This study reveals the complex genetic diversity of PCV2 and improves our understanding regarding the epidemiological trends of PCV2 sub-genotypes in China.

Electronic supplementary material

The online version of this article (10.1186/s12917-019-1859-z) contains supplementary material, which is available to authorized users.

Evaluation of a porcine circovirus type 2a (PCV2a) vaccine efficacy against experimental PCV2a, PCV2b, and PCV2d challenge

The objective of this study was to compare the efficacy of a commercial porcine circovirus type 2a (PCV2a) subunit vaccine against experimental PCV2a, PCV2b, and PCV2d challenge. A total of 105 pigs were randomly divided into 7 groups (15 pigs per group). At 21 days old the pigs were intramuscularly administered the PCV2a vaccine as a 1.0 mL dose. Four weeks following vaccination, pigs were challenged with either Korean PCV2a, PCV2b, or PCV2d. All vaccinated pigs showed a significant (P <  0.05) reduction of clinical signs, PCV2 viremia, lymphoid lesions, and lymphoid PCV2 antigen levels compared to unvaccinated control pigs. Vaccination resulted also in significantly higher (P <  0.05) titers of neutralizing antibody against PCV2, and an increase in the frequency of PCV2-specific interferon-γ secreting cells (IFN-γ-SC). The vaccine showed similar protection among the vaccinated groups regardless of the genotype of the challenge. Interestingly, vaccinated pigs had higher levels of neutralizing antibody titers against PCV2a compared to PCV2b or PCV2d while the number of PCV2a-, PCV2b-, and PCV2d-specific IFN-γ-SC were similar. Taken together, the results presented here demonstrate that a PCV2a vaccine can be effective against experimental PCV2a, PCV2b, and PCV2d challenge.

Structural roles of PCV2 capsid protein N-terminus in PCV2 particle assembly and identification of PCV2 type-specific neutralizing epitope

Postweaning multisystemic wasting disease (PMWS) in piglets caused by porcine circovirus type 2 (PCV2) is one of the major threats to most pig farms worldwide. Among all the PCV types, PCV2 is the dominant genotype causing PMWS and associated diseases. Considerable efforts were made to study the virus-like-particle (VLP) assembly and the specific PCV2-associated epitope(s) in order to establish the solid foundation for engineered PCV2 vaccine development. Although the N-terminal fragment including Nuclear Localization Signal (NLS) sequence seems important for recombinant PCV2 capsid protein expression and VLP assembly, the detailed structural and functional information regarding this important fragment are largely unknown. In this study, we report crystal structure of PCV2 VLP assembled from N-terminal NLS truncated PCV2 capsid protein at 2.8 Å resolution and cryo-EM structure of PCV2 VLP assembled from full-length PCV2 capsid protein at 4.1Å resolution. Our in vitro PCV2 VLP assembly results show that NLS-truncated PCV2 capsid protein only forms instable VLPs which were easily disassembled in solution, whereas full-length PCV2 capsid protein forms stable VLPs due to interaction between ¹⁵PRSHLGQILRRRP²⁷(α-helix) and ³³RHRYRWRRKN⁴²(NLS-B) in a repeated manner. In addition, our results also showed that N-terminal truncation of PCV2 capsid protein up to 27 residues still forms PCV2 particles in solution with similar size and immunogenicity, while N-terminal truncation of PCV2 capsid protein with more than 30 residues is not able to form stable PCV2 particles in solution, demonstrating the importance of interaction between the α-helix at N-terminal and NLS-B in PCV2 VLP formation. Moreover, we also report the cryo-EM structure of PCV2 VLP in complex with 3H11-Fab, a PCV2 type-specific neutralizing antibody, at 15 Å resolution. MAb-3H11 specifically recognizes one exposed epitope located on the VLP surface EF-loop (residues 128–143), which is further confirmed by PCV1-PCV2 epitope swapping assay. Hence, our results have revealed the structural roles of N-terminal fragment of PCV2 capsid protein in PCV2 particle assembly and pinpointed one PCV2 type-specific neutralizing epitope for the first time, which could provide clear clue for next generation PCV2 vaccine and diagnostic kits development.

Porcine circovirus type 2 (PCV2) is considered as one of the most wide-spread pathogens threatening swine production by causing postweaning multisystemic wasting disease (PMWS) in piglets worldwide. Several VLP-based PCV2 vaccines are commercially available which significantly reduce the viral burden and virally induced lesions. However, prophylactic efficacy of VLP-based PCV2 vaccine largely relies on the correct VLP assembly from the individual PCV2 capsid protein. Notably, limited structural information of PCV2 N-terminal fragment containing arginine-rich patches significantly delays our understanding of PCV2 assembly at the molecular level, and the lack of solid evidence in identification of PCV2 type-specific epitope delays the development of PCV2 type-specific diagnosis kits. In this study, through the combination of structural and immunological approaches, we are able, for the first time, to disclose the structural details of the N-terminal Nuclear Localization Signal (NLS) region of PCV2 capsid protein. We show that the interaction between the α-helix from one capsid protein and the NLS-B from an adjacent capsid protein within the pentamer stabilizes the assembled PCV2 VLP in solution. Moreover, by the combination of structural determination and biochemical mapping, we have identified that a short linear sequence (¹³⁴KATALT¹³⁹) located within PCV2 EF-loop is a unique PCV2 type-specific neutralizing epitope. Therefore, our work has revealed the detailed structural information of PCV2 particle assembly and a PCV2 type-specific neutralizing epitope, which should provide insightful information for virus-host interaction studies and next-generation PCV2 vaccine and type-specific diagnostic kits development.

Genetic characterization and diversity of porcine circovirus type 2 in non-vaccinated South African swine herds

The porcine circovirus type 2 (PCV2) is a swine infectious viral pathogen of great significance in global swine herds. It was recently detected at another Province of South Africa sequel to the first detection of North American-like strain (PCV2a) at Gauteng about two decades ago, but there is a dearth of information about the genomic features and diversity of the viral strains in circulation within the country and the entire sub-Saharan Africa region. To date, only one complete genome of the virus from South Africa is available on global data base. This current effort is therefore geared towards the full-genome characterization of the circulating PCV2 strains in the pigs of Eastern Cape Province. With the use of conventional polymerase chain reaction method, fifteen complete PCV2 genomes were successfully amplified, sequenced and assembled from field samples obtained from non-vaccinated pigs in the region. Neighbor Joining and Maximum Likelihood phylogenetic analyses of the ORF2 gene and full genomes unanimously showed that most of the assembled genomes (11) belong to genotype PCV2b. Furthermore, three of the characterized sequences formed clade with other reference mutant PCV2b and PCV2b subtype 1C (i.e. PCV2d) strains from the USA, China and South Korea. The last sequence, however, clustered with other reference strains belonging to PCV2 intermediate clade 2 (PCV2-IM2), recently identified in a global PCV2 strains phylogenetic analysis. This study reports the first complete genome sequences of PCV2b, PCV2d and PCV2-IM2 in pigs from South Africa, and it gives a possible insight into the genetic characteristics and variability of the viral strains presently in circulation within the country. It further emphasizes the need for more stringent measures in curtailing the introduction and spread of transboundary swine pathogens in the country and entire Southern African region.

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.

Genetic diversity of porcine circovirus type 2 (PCV2) in Thailand during 2009-2015

Porcine circovirus type 2 (PCV2), the essential cause of porcine circovirus associated disease (PCVAD), has evolved rapidly and it has been reported worldwide. However, genetic information of PCV2 in Thailand has not been available since 2011. Herein, we studied occurrence and genetic diversity of PCV2 in Thailand and their relationships to the global PCV2 based on ORF2 sequences. The results showed that 306 samples (44.09%) from 56 farms (80%) were PCV2 positive by PCR. Phylogenetic trees constructed by both neighbor-joining and Bayesian Inference yielded similar topology of the ORF2 sequences. Thai PCV2 comprise four clusters: PCV2a (5.5%), PCV2b (29.41%), intermediate clade 1 (IM1) PCV2b (11.03%) and PCV2d (54.41%). Genetic shift of PCV2 in Thailand has occurred similarly to the global situation. The shift from PCV2b to PCV2d was clearly observed during 2013-2014. The viruses with genetically similar to the first reported PCV2 in 2004 have still circulated in Thailand. The first Thai PCV2b and PCV2d were closely related to the neighboring countries. The haplotype network analysis revealed the relationship of PCV2 in Thailand and other countries. These results indicate that genetic diversity of PCV2 in Thailand is caused by genetic drift of the local strains and intermittent introduction of new strains or genotypes from other countries. Genetic evolution of PCV2 in Thailand is similar to that occurs globally.

[Occurrence of genotypes of porcine circovirus (PCV2) in pig farms using different vaccination strategies against PCV2]

OBJECTIVE

Since 2004/2005 a worldwide shift of the detection rate of porcine circovirus (PCV) has been observed from PCV2a towards PCV2b. Currently commercially available vaccines are based on genotype PCV2a. The study was conducted as a pilot study to evaluate the occurrence of PCV2a and PCV2b in farms with different vaccination strategies against PCV2.

MATERIAL AND METHODS

For this purpose a total of 405 piglets originating from nine farms (three farms with sow vaccination [SI], piglet vaccination [FI] and no vaccination [NI] against PCV2, respectively) were enrolled and followed from day 3 of life until slaughter. Serum of the piglets was examined for PCV2-DNA by quantitative PCR, genotype differentiating duplex PCR, and after sequencing of the total genome, PCV2 isolates were phylogenetically assigned. The evaluation included the data from 383 animals.

RESULTS

In eight farms PCV2 could be detected (1x PCV2a; 6x PCV2b; 1x PCV2a and PCV2b). PCV2b was found in SI-, NI- and FI-farms, whereas PCV2a was only detected in SI- and NI-farms. A proportion of 55.4% was PCV2-positive at least once during the entire study period (FI: 7.8%, SI: 65.4%, NI: 93.7%). Of these samples 4.7% were PCV2a-, 92.2% PCV2b- and 2.4% PCV2a- and PCV2b-positive. The mean content of PCV2-DNA in the serum of PCV2b positive animals was significantly higher than from PCV2a positive animals. PCV2 isolates were identified as PCV2b-1A (5/9 farms), PCV2b-1B (1/9 farms) und PCV2a-2D (2/9 farms).

CONCLUSION AND CLINICAL RELEVANCE

The increased detection rate of PCV2b in comparison to PCV2a could be confirmed. The present study gives hint that the vaccination of piglets using PCV2a-based vaccines may lead to a further shift of the detection rate from PCV2a to PCV2b. To assess the clinical relevance of this observation, extensive comparative studies should be taken into account, which also evaluate the efficacy of PCV2a-based vaccines in PCV2a- and PCV2b-positive farms.

Global Status of Porcine circovirus Type 2 and Its Associated Diseases in Sub-Saharan Africa

Globally, Porcine circovirus type 2 (PCV2) is a recognized viral pathogen of great economic value in pig farming. It is the major cause of ravaging postweaning multisystemic wasting syndrome (PMWS) and many other disease syndromes generally regarded as Porcine circovirus associated diseases (PCVAD) in Europe. PCV2 infections, specifically PMWS, had impacted huge economic loss on swine production at different regions of the world. It has been studied and reported at different parts of the globe including: North and South America, Europe, Asia, Oceania, Middle East, and the Caribbean. However, till date, this virus and its associated diseases have been grossly understudied in sub-Sahara African region and the entire continent at large. Two out of forty-nine, representing just about 4% of countries that make up sub-Sahara Africa presently, have limited records on reported cases and occurrence of the viral pathogen despite the ubiquitous nature of the virus. This review presents an overview of the discovery of Porcine circovirus and its associated diseases in global pig herds and emphasizes the latest trends in PCV2 vaccines and antiviral drugs development and the information gaps that exist on the occurrence of this important viral pathogen in swine herds of sub-Saharan Africa countries. This will serve as wake-up call for immediate and relevant actions by stakeholders in the region.

Evidence of natural co-infection with PCV2b subtypes in vivo

Porcine circovirus type 2 (PCV2) is the causative pathogen of porcine circovirus-associated diseases (PCVAD). This virus evolves mostly through point mutations and genome recombination between different PCV2 genotypes (e.g. PCV2a and PCV2b), as has been confirmed in swine herds. In the current work, the complete PCV2 genome sequences of 69 clones derived from various tissues (lymph node, spleen and lung,) of an infected individual, were subjected to phylogenetic and alignment analyses. The results not only demonstrate co-infection with distinct PCV2b subtypes (e.g. 1B and 1C) in the same animal, but also highlight another mechanism of evolution - diverse point mutations acquired during immune evasion by this virus.

A Novel Porcine Circovirus Distantly Related to Known Circoviruses Is Associated with Porcine Dermatitis and Nephropathy Syndrome and Reproductive Failure

Porcine circovirus-associated disease (PCVAD) is clinically manifested by postweaning multisystemic wasting syndrome (PMWS), respiratory and enteric disease, reproductive failure, and porcine dermatitis and nephropathy syndrome (PDNS). Porcine circovirus 2 (PCV2) is an essential component of PCVAD, although an etiologic role in PDNS is not well established. Here, a novel circovirus, designated porcine circovirus 3 (PCV3), was identified in sows that died acutely with PDNS-like clinical signs. The capsid and replicase proteins of PCV3 are only 37% and 55% identical to PCV2 and bat circoviruses, respectively. Aborted fetuses from sows with PDNS contained high levels of PCV3 (7.57 × 10⁷ genome copies/ml), and no other viruses were detected by PCR and metagenomic sequencing. Immunohistochemistry (IHC) analysis of sow tissue samples identified PCV3 antigen in skin, kidney, lung, and lymph node samples localized in typical PDNS lesions, including necrotizing vasculitis, glomerulonephritis, granulomatous lymphadenitis, and bronchointerstitial pneumonia. Further study of archived PDNS tissue samples that were negative for PCV2 by IHC analysis identified 45 of 48 that were PCV3 positive by quantitative PCR (qPCR), with 60% of a subset also testing positive for PCV3 by IHC analysis. Analysis by qPCR of 271 porcine respiratory disease diagnostic submission samples identified 34 PCV3-positive cases (12.5%), and enzyme-linked immunosorbent assay detection of anti-PCV3 capsid antibodies in serum samples found that 46 (55%) of 83 samples tested were positive. These results suggest that PCV3 commonly circulates within U.S. swine and may play an etiologic role in reproductive failure and PDNS. Because of the high economic impact of PCV2, this novel circovirus warrants further studies to elucidate its significance and role in PCVAD.

IMPORTANCE

While porcine circovirus 2 (PCV2) was first identified in sporadic cases of postweaning multisystemic wasting syndrome in Canada in the early 1990s, an epidemic of severe systemic disease due to PCV2 spread worldwide in the ensuing decade. Despite being effectively controlled by commercial vaccines, PCV2 remains one of the most economically significant viruses of swine. Here, a novel porcine circovirus (PCV3) that is distantly related to known circoviruses was identified in sows with porcine dermatitis and nephropathy syndrome (PDNS) and reproductive failure. PCV2, which has previously been associated with these clinical presentations, was not identified. High levels of PCV3 nucleic acid were observed in aborted fetuses by quantitative PCR, and PCV3 antigen was localized in histologic lesions typical of PDNS in sows by immunohistochemistry (IHC) analysis. PCV3 was also identified in archival PDNS diagnostic samples that previously tested negative for PCV2 by IHC analysis. The emergence of PCV3 warrants further investigation.

In silico analysis of surface structure variation of PCV2 capsid resulting from loop mutations of its capsid protein (Cap)

Outbreaks of porcine circovirus (PCV) type 2 (PCV2)-associated diseases have caused substantial economic losses worldwide in the last 20 years. The PCV capsid protein (Cap) is the sole structural protein and main antigenic determinant of this virus. In this study, not only were phylogenetic trees reconstructed, but variations of surface structure of the PCV capsid were analysed in the course of evolution. Unique surface patterns of the icosahedral fivefold axes of the PCV2 capsid were identified and characterized, all of which were absent in PCV type 1 (PCV1). Icosahedral fivefold axes, decorated with Loops BC, HI and DE, were distinctly different between PCV2 and PCV1. Loops BC, determining the outermost surface around the fivefold axes of PCV capsids, had limited homology between Caps of PCV1 and PCV2. A conserved tyrosine phosphorylation motif in Loop HI that might be recognized by non-receptor tyrosine kinase(s) in vivo was present only in PCV2. Particularly, the concurrent presence of 60 pairs of the conserved tyrosine and a canonical PXXP motif on the PCV2 capsid surface could be a mechanism for PXXP motif binding to and activation of an SH3-domain-containing tyrosine kinase in host cells. Additionally, a conserved cysteine in Loop DE of the PCV2 Cap was substituted by an arginine in PCV1, indicating potentially distinct assembly mechanisms of the capsid in vitro between PCV1 and PCV2. Therefore, these unique patterns on the PCV2 capsid surface, absent in PCV1 isolates, might be related to cell entry, virus function and pathogenesis.

Inactivated chimeric porcine circovirus (PCV) 1-2 vaccines based on genotypes 2b and 2d exhibit similar immunological effectiveness in protecting pigs against challenge with PCV2b strain 0233

Porcine circovirus type 2 (PCV2) is subdivided into four genotypes: PCV2a, PCV2b, PCV2c and PCV2d. Here, for the first time, we compared the efficacy of two experimental inactivated chimeric PCV1-2 vaccines based on genotypes 2b and 2d. Seventeen 3-week-old pigs were divided randomly into four groups. Group 1 and 2 pigs were inoculated with genotype 2b- and 2d-based inactivated vaccines, respectively. At 28 days post-vaccination (DPV), pigs in groups 1-3 were challenged with the PCV2b 0233 strain. All experimental pigs were necropsied at 21 days post-challenge (DPC). Pigs vaccinated with the genotype 2b- or 2d-based vaccine had high antibody titres and lower PCV2b copy numbers in samples of sera, faeces and nasal secretions compared with pigs in the unvaccinated challenge group. Interestingly, we detected no DNA from the challenge strain in the superficial inguinal lymph nodes of the pigs immunized with the PCV2b vaccine, while one pig in the PCV2d- immunized group had detectable DNA from the challenge strain at 21 DPC. We found no significant differences in the humoral immune response, PCV2b load, or PCV-related microscopic lesions between the two vaccinated groups post-challenge. Therefore, both vaccines were equally effective at inducing immunity against challenge with PCV2b strain 0233.

Molecular detection and genome characterization of porcine circovirus type 2 in rats captured on commercial swine farms

Porcine circovirus type 2 (PCV2) is considered the major etiological pathogen of porcine circovirus-associated diseases (PCVADs) in pigs. Recently, PCV2 was also found in non-porcine animals such as cattle, rats, and mice. However, there was no record of PCV2 in rats in China. The goal of this study was to investigate whether PCV2 was present in rats (Rattus norvegicus, RN) on three swine farms, using molecular tools. PCR results showed that 30 of 95 (31.6 %) rat samples were positive for PCV2. Moreover, further genotype analysis suggested that 10 of 30 (33.3 %) were positive for PCV2a, 19 of 30 (63.3 %) were positive for PCV2b, and only one sample (1/30, 3.33 %) was co-infected by PCV2a and PCV2b. To determine the possible origin of PCV2, 60 serum samples were also collected from weaned pigs on those swine farms, and 23 out of 60 samples were positive for PCV2. In addition, two distinct RN-origin and two distinct porcine-origin PCV2 full-length nucleotide sequences were obtained from the farms. Sequence and phylogenetic analysis indicated that they had the highest nucleotide similarity and closest genetic relationships to each other. In this study, we report the infection and genome characterization of PCV2 in rats and compare RN-origin and porcine-origin PCV2 sequences obtained from the same pig farm, revealing possible cross-species transmission of PCV2.

The expression level of gC1qR is down regulated at the early time of infection with porcine circovirus of type 2 (PCV-2) and gC1qR interacts differently with the Cap proteins of porcine circoviruses

Porcine circoviruses (PCV) are small, non-enveloped single-stranded DNA-viruses. Porcine circovirus type 2 (PCV-2) is the causal agent of post-weaning multisystemic wasting syndrome (PMWS) whereas porcine circovirus of type 1 (PCV-1) is non- pathogenic. gC1qR is a membrane-located receptor of the complement protein subunit C1q and interacts with PCV capsid proteins. The mechanisms associated with the triggering of PMWS are not well known and gC1qR may have a role in the life cycle and eventually in the pathogenicity of PCV. The objectives of this study were to determine the level of expression of gC1qR during early PCV-2 infection, to determine the region of PCV-2 capsid protein (Cap) required for the interaction with gC1qR and to evaluate the interaction of gC1qR with Cap proteins of different PCV strains. The results indicate that gC1qR transcripts are downregulated in the tonsils and the tracheo-bronchial lymph nodes of piglets infected by PCV-2 at the early time of the infection. The N-terminal amino acids (a.a. 1-59) of PCV-2b Cap, an arginine rich region, are involved in the interaction with gC1qR. Porcine gC1qR interacts with Cap proteins of two pathogenic viral strains, PCV-2a and PCV-2b, while interaction has been observed with only one Cap protein of two investigated strains of PCV-1. The amino acids 30 and 49 of PCV-1Cap, solely, were not responsible of the difference of interaction observed. We have also shown that gC1qR interacts strongly with PCV-2Caps and PCV-1 GER Cap. This result suggests that the different interaction of gC1qR with PCV Cap proteins may have an impact on the pathogenicity of the PCV.

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.

Vaccination with a Porcine Reproductive and Respiratory Syndrome (PRRS) Modified Live Virus Vaccine Followed by Challenge with PRRS Virus and Porcine Circovirus Type 2 (PCV2) Protects against PRRS but Enhances PCV2 Replication and Pathogenesis Compared to Results for Nonvaccinated Cochallenged Controls

Coinfections involving porcine reproductive and respiratory syndrome virus (PRRSV) and porcine circovirus type 2 (PCV2) contribute to a group of disease syndromes known as porcine circovirus-associated disease (PCVAD). Presumably, PRRSV infection enhances PCV2 replication as a result of modulation of host immunity. The purpose of this study was to evaluate PCV2 replication and pathogenesis in pigs vaccinated with a PRRS modified live virus (MLV) vaccine and subsequently challenged with a combination of PRRSV and PCV2. During the early postchallenge period, the number of pigs with PRRSV-associated clinical signs was decreased, and average daily gain (ADG) was increased, in the vaccinated group, demonstrating the protective effect of PRRS vaccination. However, during the later postchallenge period, more pigs in the vaccinated group showed increased PCV2 viremia, decreased ADG, increased PCVAD clinical signs, and increased mortality. In this disease model, the early benefits of PRRSV vaccination were outweighed by the later amplification of PCVAD.

Genetic and phylogenetic analysis of a new porcine circovirus type 2 (PCV2) strain in China

Porcine circovirus type 2 (PCV2) is the etiological agent associated with several pig diseases that are collectively referred to as porcine circovirus-associated disease (PCVAD). Unfortunately, PCV2 has had a serious economic impact on the swine industry. In this study, we report the genome sequence of a novel PCV2 isolate (JS2015) identified in pigs in Jiang Su, China. The complete DNA sequence was 1766 nucleotides long with an A+T content of 52.7%. It lacked a guanine (G) at nucleotide position 1045 compared to other reference PCV2 strains with a sequence length of 1766 nucleotides. Genetic characterization and phylogenetic analysis showed that the isolate JS2015 was most closely related to members of the PCV2d (AY181946) lineage. Our data provide insight into the epidemiology of porcine circovirus and may facilitate further study of the origin and evolution of PCV2.

Revisiting the taxonomical classification of Porcine Circovirus type 2 (PCV2): still a real challenge

BACKGROUND

PCV2 has emerged as one of the most devastating viral infections of swine farming, causing a relevant economic impact due to direct losses and control strategies expenses. Epidemiological and experimental studies have evidenced that genetic diversity is potentially affecting the virulence of PVC2. The growing number of PCV2 complete genomes and partial sequences available at GenBank questioned the accepted PCV2 classification.

METHODS

Nine hundred seventy five PCV2 complete genomes and 1,270 ORF2 sequences available from GenBank were subjected to recombination, PASC and phylogenetic analyses and results were used for comparison with previous classification scheme.

RESULTS

The outcome of these analyses favors the recognition of four genotypes on the basis of ORF2 sequences, namely PCV2a, PCV2b, PCV2c and PCV2d-mPCV2b. To deal with the difficulty of founding an unambiguous classification and accounting the impossibility to define a p-distance cut-off, a set of reference sequences that could be used in further phylogenetic studies for PCV2 genotyping was established. Being aware that extensive phylogenetic analyses are time-consuming and often impracticable during routine diagnostic activity, ORF2 nucleotide positions adequately conserved in the reference sequences were identified and reported to allow a quick genotype differentiation.

CONCLUSIONS

Globally, the present work provides an updated scenario of PCV2 genotypes distribution and, based on the limits of the previous classification criteria, proposes new rapid and effective schemes for differentiating the four defined PCV2 genotypes.