The natural history of porcine circovirus type 2: From an inoffensive virus to a devastating swine disease?

Comparative infectivity and horizontal transmission ability of the isolates PCV2a, PCV2b, and PCV2d

Porcine circovirus type 2 (PCV2) causes postweaning multisystemic wasting syndrome in piglets. Differences in the infectivity and horizontal transmissibility of different isolates of PCV2a, PCV2b, and PCV2d in pigs were evaluated by HE and IHC staining, PCR, virus titration, and IPMA to determine their clinical symptoms, pathological changes, levels of virus and antibody, and cohabitation infectivity. In the cohabitation infection experiment, weak viremia and low levels of antibodies were detected in the pigs challenged with PCV2a-CL, whereas no viremia or antibodies were detected in the corresponding cohabiting pigs. Furthermore, no PCV2 was isolated from any organ of pigs that were challenged with PCV2a-CL, as well as from those of their cohabiting pigs. In contrast, persistent viremia and pathological changes, including swollen inguinal lymph nodes, were detected in both the challenged and cohabiting pigs after PCV2b-BY or PCV2d-LNHC infection. Alive PCV2 was detected in the tonsils, inguinal lymph nodes, spleen, and kidneys of the experimental pigs by virus titration, and the highest viral titer was detected in the tonsils, followed by the inguinal lymph nodes. In a comparative analysis of the challenged and cohabiting pigs, a 1-week delay in viremia and specific antibodies was observed in the cohabiting pigs. Moreover, the number of viruses isolated from the tonsils and inguinal lymph nodes of the pigs cohabiting with PCV2d-LNHC-challenged pigs was significantly greater than those in the pigs that were directly challenged with PCV2d-LNHC in cohabitation infection experiment (P<0.05). Together, these results indicated that the infectivity and horizontal transmissibility of the strains PCV2b-BY and PCV2d-LNHC were much greater than those of the strain PCV2a-CL and provided some insights into PCV2 pathogenicity.

Development of a novel PCV2 and PCV3 vaccine using virus-like vesicles incorporating Venezuelan equine encephalomyelitis virus-containing vesicular stomatitis virus glycoprotein

Porcine circovirus disease (PCV) causes substantial economic losses in the pig industry, primarily from porcine circovirus type 2 (PCV2) and porcine circovirus type 3 (PCV3). Novel vaccines are necessary to prevent and control PCV infections. PCV coat proteins are crucial for eliciting immunogenic proteins that induce the production of antibodies and immune responses. A vaccine platform utilizing Semliki Forest virus RNA replicons expressing vesicular stomatitis virus glycoprotein (VSV-G), was recently developed. This platform generates virus-like vesicles (VLVs) containing VSV-G exclusively, excluding other viral structural proteins. In our study, we developed a novel virus-like vesicle vaccine by constructing recombinant virus-like vesicles (rVLVs) that also express EGFP. These rVLVs were created using the RNA replicon of Venezuelan equine encephalomyelitis (VEEV) and New Jersey serotype VSV-G. The rVLVs underwent characterization and safety evaluation in vitro. Subsequently, rVLVs expressing PCV2d-Cap and PCV3-Cap proteins were constructed. Immunization of C57 mice with these rVLVs led to a significant increase in anti-porcine circovirus type 2 and type 3 capsid protein antibodies in mouse serum. Additionally, a cellular immune response was induced, as evidenced by high production of IFN-γ and IL-4 cytokines. Overall, this study demonstrates the feasibility of developing a novel porcine circovirus disease vaccine based on rVLVs.

Comparison of immune effects of porcine circovirus type 2d (PCV2d) capsid protein expressed by Escherichia coli and baculovirus-insect cells

Porcine circovirus type 2 (PCV2) is an important pathogen harmful to global pig production, which causes immunosuppression and serious economic losses. PCV2 capsid (Cap) protein expressed by E. coli or baculovirus-insect cells are often used in preparation of PCV2 subunit vaccines, but the latter is expensive to produce. It is therefore crucial to comparison of the immune effects of Cap protein expressed by the above two expression systems for reducing the production cost and guaranteeing PCV2 vaccine quality. In this study, the PCV2d-Cap protein lacking nuclear localization signal (NLS), designated as E. coli-Cap and Bac-Cap, was expressed by E. coli and baculovirus-Spodoptera frugiperda Sf9 (Bac-Sf9) cells, respectively. The expressed Cap proteins could self-assemble into virus-like particles (VLPs), but the Bac-Cap-assembled VLPs were more regular. The two system-expressed Cap proteins induced similar specific IgG responses in mice, but the neutralizing antibody levels of Bac-Cap-immunized mice was higher than those of E. coli-Cap. After PCV2 challenge, IL-10 in Bac-Cap immunized mice decreased significantly than that in E. coli-Cap. The lesions and PCV2 antigen positive cells in tissues of mice immunized with E. coli-Cap and Bac-Cap were significantly reduced, and Bac-Cap appeared mild lesions and fewer PCV2 antigen-positive cells compared with E. coli-Cap immunized mice. The study indicated that Cap proteins expressed by E. coli and Bac-Sf9 cells could induce specific protective immunity, but the latter induced more effective immunity, which provides valuable information for the research and development of PCV2 vaccine.

Conflicting Evidence between Clinical Perception and Molecular Epidemiology: The Case of Fowl Adenovirus D

Fowl adenoviruses (FAdVs, species FAdV-A/-E) are responsible for several clinical syndromes reported with increasing frequency in poultry farms in the last decades. In the present study, a phylodynamic analysis was performed on a group of FAdV-D Hexon sequences with adequate available metadata. The obtained results demonstrated the long-term circulation of this species, at least several decades before the first identification of the disease. After a period of progressive increase, the viral population showed a high-level circulation from approximately the 1960s to the beginning of the new millennium, mirroring the expansion of intensive poultry production and animal trade. At the same time, strain migration occurred mainly from Europe to other continents, although other among-continent connections were estimated. Thereafter, the viral population declined progressively, likely due to the improved control measures, potentially including the development and application of FAdV vaccines. An increase in the viral evolutionary rate featured this phase. A role of vaccine-induced immunity in shaping viral evolution could thus be hypothesized. Accordingly, several sites of the Hexon, especially those targeted by the host response were proven under a significant pervasive or episodic diversifying selection. The present study results demonstrate the role of intensive poultry production and market globalization in the rise of FAdV. The applied control strategies, on the other hand, were effective in limiting viral circulation and shaping its evolution.

Evidence of Porcine Circovirus Type 2 (PCV2) Genetic Shift from PCV2b to PCV2d Genotype in Sardinia, Italy

Porcine Circovirus type 2 (PCV2) is the etiological agent of a disease syndrome named Porcine Circovirus disease (PCVD), representing an important threat for the pig industry. The increasing international trade of live animals and the development of intensive pig farming seem to have sustained the spreading of PCVD on a global scale. Recent classification criteria allowed the identification of nine different PCV2 genotypes (PCV2a-i). PCV2a was the first genotype detected with the highest frequency from the late 1990s to 2000, which was then superseded by PCV2b (first genotype shift). An ongoing genotype shift is now determining increasing prevalence rates of PCV2d, in replacement of PCV2b. In Italy, a complete genotype replacement was not evidenced yet. The present study was carried out on 369 samples originating from domestic pigs, free-ranging pigs, and wild boars collected in Sardinia between 2020 and 2022, with the aim to update the last survey performed on samples collected during 2009-2013. Fifty-seven complete ORF2 sequences were obtained, and the phylogenetic and network analyses evidenced that 56 out of 57 strains belong to the PCV2d genotype and only one strain to PCV2b, thus showing the occurrence of a genotype shift from PCV2b to PCV2d in Sardinia.

Wilder than intense: higher frequency, variability, and viral flows of porcine circovirus 3 in wild boars and rural farms compared to intensive ones in northern Italy

Introduction

Porcine circovirus 3 (PCV-3) was firstly reported in 2017. Although evidence of its pathogenic role has been provided, its clinical relevance seems lower than Porcine circovirus 2 (PCV-2), as well as its evolutionary rate. Different studies have reported a high PCV-3 prevalence in wild boars, sometimes higher than the one observed in commercial pigs. Nevertheless, to date, few studies have objectively investigated the relationships between these populations when inhabiting the same area. Moreover, the role of small-scale, backyard pig production in PCV-3 epidemiology is still obscure.

Methods

The present study investigated PCV-3 occurrence in 216 samples collected from the same area of Northern Italy from commercial and rural pigs, and wild boars. PCV-3 presence was tested by qPCR and complete genome or ORF2 sequences were obtained when possible and analysed using a combination of statistical, phylogenetic and phylodynamic approaches.

Results

A higher infection risk in wild boars and rural pigs compared to the commercial ones was demonstrated. The phylodynamic analysis confirmed a larger viral population size in wild and rural populations and estimated a preferential viral flow from these populations to commercial pigs. A significant flow from wild to rural animals was also proven. The analysis of the Italian sequences and the comparison with a broader international reference dataset highlighted the circulation of a highly divergent clade in Italian rural pigs and wild boars only.

Discussion

Overall, the present study results demonstrate the role of non-commercial pig populations in PCV-3 maintenance, epidemiology and evolution, which could represent a threat to intensive farming.

Production of virus-like particles of porcine circovirus 2 in baculovirus expression system and its application for antibody detection

BACKGROUND

Porcine circovirus 2 (PCV-2) is one of the pathogens that leads to a growing and persistent threat in pigs. Thus, the development of serological detection methods for PCV-2 is of great necessity for clinical diagnosis as well as epidemiological investigations. This study aimed to establish an indirect enzyme-linked immunosorbent assay (ELISA) to examine antibodies against PCV-2 based on virus-like particles (VLPs).

RESULTS

Recombinant PCV-2 Cap protein was expressed in the baculovirus-insect cells system and PCV-2 VLPs were observed over transmission electron microscopy (TEM). The PCV-2 VLPs were shown to have good immunogenicity in mice and stimulated a high level of PCV-2 antibody titers. Using PCV-2 VLPs as coating antigen, the indirect ELISA can detect PCV-2 antibodies in animals with diagnostic sensitivity and specificity of 98.33% and 93.33% compared to immunofluorescence assay (IFA), respectively. The intra- and inter-assay coefficient variations (CVs) were < 10% in a batch, and < 15% in different batches, indicating good repeatability. There was no cross-reaction of this ELISA with antibodies against other porcine viruses. A total of 170 serum samples collected from different pig farms in China were tested for PCV-2 antibodies, and 151 (88.8%) samples were PCV-2 antibody positive.

CONCLUSION

Our findings suggest that this ELISA was rapid, specific, and reproducible and can be used for large-scale serological investigations of PCV-2 antibodies in pigs.

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.

Into the backyard: Multiple detections of PCV-2e in rural pig farms of Northern Italy. An unexpected ecological niche?

Porcine circovirus type 2 (PCV-2) is among the most burdensome viruses of the swine industry globally. Several genotypes have been periodically emerging, but just three of them (PCV-2a, PCV-2b, and PCV-2d) seem to circulate worldwide and be associated with the disease. Conversely, the spatial-temporal distribution of minor genotypes appears limited and their clinical relevance is still unclear. Recently PCV-2e was incidentally detected for the first time in Europe in a breeding farm in Northeastern Italy, while no connection could be established with countries where this genotype had been previously detected. To investigate circulating genotypes in the neglected rural context and provide a comparison with the most explored industrial context, a molecular survey was performed on samples collected in rural (n = 72) and industrial farms (n = 110) located in the same geographic area. Phylogenetic analysis surprisingly evidenced PCV-2e circulation only in pigs reared in backyard farms (n = 5), while major genotypes (PCV-2a, -2b, -2d) circulate in both rearing contexts. However, the close genetic similarity between the herein detected PCV-2e strains and the previously reported one testify that, although unusual, such rural-to-industrial strains exchange affected also PCV-2e. The greater genetic and phenotypic diversity of PCV-2e genotype compared to other ones might threaten the protection granted by current vaccines. The present study suggests the rural context as an ecological niche for the circulation of PCV-2e, and even of other minor genotypes. PCV-2e detection in pigs with outdoor access further stresses the epidemiological role of backyard farms as interfaces for pathogen introduction, potentially ascribable to the different rearing approaches, lower managerial and biosecurity capabilities, and easier contacts with wildlife.

Is Penguin Circovirus Circulating Only in the Antarctic Circle? Lack of Viral Detection in Namibia

The known host range of circoviruses is continuously expanding because of more intensive diagnostic activities and advanced sequencing tools. Recently, a new circovirus (penguin circovirus (PenCV)) was identified in the guano and cloacal samples collected from Adélie penguins (Pygoscelis adeliae) and chinstrap penguins (Pygoscelis antarcticus) in Antarctica. Although the virus was detected in several asymptomatic subjects, a potential association with feather disease was speculated. To investigate the occurrence and implications of PenCV in other penguin species located outside of Antarctica, a broad survey was undertaken in African penguins (Spheniscus demersus) on two islands off the southern Namibian coast. For this purpose, specific molecular biology assays were developed and validated. None of the 151 blood samples tested positive for PenCV. Several reasons could explain the lack of PenCV positive samples. African penguins and Pygoscelis species are separated by approximately 6000 km, so there is almost no opportunity for transmission. Similarly, host susceptibility to PenCV might be penguin genus-specific. Overall, the present study found no evidence of PenCV in African penguin colonies in Namibia. Further dedicated studies are required to assess the relevance of PenCV among different penguin species.

Co-infections of respiratory pathogens and gastrointestinal parasites in smallholder pig production systems in Uganda

A cross-sectional study was conducted to identify factors for infections of pigs with key respiratory pathogens: porcine circovirus type 2 (PCV2), porcine reproductive and respiratory syndrome virus (PPRSv), Mycoplasma hyopneumoniae (M. hyo), Actinobacillus pleuropneumoniae (App), and gastrointestinal (GI) parasites in Uganda. A structured questionnaire was used to collect data on management practices associated with infections. Ninety (90) farms and 259 pigs were sampled. Sera were screened against 4 pathogens using commercial ELISA tests. The Baerman's method was used to identify parasite species in faecal samples. Logistic regression was done to identify risk factors for infections. Results showed individual animal seroprevalence of PCV2 was 6.9% (95% CI 3.7-11.1), PRRSv 13.8% (95% CI 8.8-19.6), M. hyo 6.4% (95% CI 3.5-10.5), and App 30.4% (95% CI 24.8-36.5). The prevalence of Ascaris spp. was 12.7% (95% CI 8.6-16.8), Strongyles spp was 16.2% (95% CI 11.7-20.7), and Eimeria spp. was 56.4% (95% CI 50.3-62.4). Pigs infested with Ascaris spp. were more likely to test positive to PCV2, odds ratio (OR) 1.86 (CI 1.31-2.60; p = 0.0002). For M. hyo, infection with Strongyles spp. was a risk factor (OR 12.9, p < 0.001). Pigs that had Strongyles and Ascaris spp. Infections (ORs 3.5 and 3.4, p < 0.001 respectively) were likely to have co-infections. The model showed that use of cement, elevated floor, and limiting contacts with outside pigs were protective while using mud and helminth infestations increased risks of co-infections. This study provided evidence that improved housing and biosecurity are critical in reducing pathogen incidence in herds.

Porcine circovirus 3 (PCV-3) variability: Is it in the virus or in the classification criteria?

The continuous discovery of new viruses during the last decades has increased the need for new classification approaches and rules. Currently, the International Committee on Taxonomy of Viruses classifies viruses up to the species level. However, because of the higher variability of most of these infectious agents, a below-species categorization is often required for proper epidemiological investigations. Unfortunately, variable criteria are typically proposed by different research groups, leading to misleading and poorly reproducible results. This scenario occurred for the recently identified Porcine circovirus 3. Although genotype definition standards had been defined by a group of experts in the field, recent articles have been published introducing new genotypes, whose classification rules are not reported. We therefore would like to stress the usefulness of defining and maintaining a common language to allow proper results comparison among groups. We consider the consensus opinion of a heterogeneous expert team as the most valuable approach. Nevertheless, if other approaches are proposed, the disclosure of the criteria and the comparison with previous literature should be deemed mandatory to allow effective results reproducibility, interpretation and sharing.

A Phylogeographic Analysis of Porcine Parvovirus 1 in Africa

Porcine parvovirus 1 (PPV1) is recognized as a major cause of reproductive failure in pigs, leading to several clinical outcomes globally known as SMEDI. Despite being known since the late 1960s its circulation is still of relevance to swine producers. Additionally, the emergence of variants such as the virulent 27a strain, for which lower protection induced by vaccines has been demonstrated, is of increasing concern. Even though constant monitoring of PPV1 using molecular epidemiological approaches is of pivotal importance, viral sequence data are scarce especially in low-income countries. To fill this gap, a collection of 71 partial VP2 sequences originating from eight African countries (Burkina Faso, Côte d'Ivoire, Kenya, Mozambique, Namibia, Nigeria, Senegal, and Tanzania) during the period 2011-2021 were analyzed within the context of global PPV1 variability. The observed pattern largely reflected what has been observed in high-income regions, i.e., 27a-like strains were more frequently detected than less virulent NADL-8-like strains. A phylogeographic analysis supported this observation, highlighting that the African scenario has been largely shaped by multiple PPV1 importation events from other continents, especially Europe and Asia. The existence of such an international movement coupled with the circulation of potential vaccine-escape variants requires the careful evaluation of the control strategies to prevent new strain introduction and persistence.

Clinical Efficacy of Two Novel, Differentially Administered (IM, ID) Vaccines against Mycoplasma hyopneumoniae and PCV2 in Swine under Field Conditions

Enzootic pneumonia (EP) of pigs is caused by Mycoplasma hyopneumoniae (M.hp.), which is, together with the porcine circovirus type 2 (PCV2), among the most prominent inducers of the porcine respiratory disease complex (PRDC). Therefore, vaccination of piglets against M.hp. and PCV2 is crucial in the fight against pulmonary infections. In this field study, we tested the clinical efficacy of two novel vaccines, one delivered IM (Hyogen^® + Circovac^®) and the other ID (MHyo-Sphere^®PCV ID), on a fattening farm in Lower Austria with a history of still ongoing EP. Average daily weight gain, coughing/sneezing index, losses due to morbidity/mortality, and lung scoring data at slaughter by means of CLP (Ceva Lung Program) were recorded for three consecutive fattening cohorts to achieve a powerful number of animals, one half each vaccinated with the IM vaccine and the other half with the ID vaccine (n = 659 in total). No statistically significant differences could be observed between the two vaccination groups for the parameters investigated, but the total median EP score, which categorizes pulmonary lesions due to infection by M.hp. with a theoretical range of 0-28, was lowered from initially 1.9 to 1.0, indicating that both vaccines proved very suitable measures in the fight against EP.

Porcine respiratory disease complex: Dynamics of polymicrobial infections and management strategies after the introduction of the African swine fever

A few decades ago, porcine respiratory disease complex (PRDC) exerted a major economic impact on the global swine industry, particularly due to the adoption of intensive farming by the latter during the 1980's. Since then, the emerging of porcine reproductive and respiratory syndrome virus (PRRSV) and of porcine circovirus type 2 (PCV2) as major immunosuppressive viruses led to an interaction with other endemic pathogens (e.g., Mycoplasma hyopneumoniae, Actinobacillus pleuropneumoniae, Streptococcus suis, etc.) in swine farms, thereby exacerbating the endemic clinical diseases. We herein, review and discuss various dynamic polymicrobial infections among selected swine pathogens. Traditional biosecurity management strategies through multisite production, parity segregation, batch production, the adoption of all-in all-out production systems, specific vaccination and medication protocols for the prevention and control (or even eradication) of swine diseases are also recommended. After the introduction of the African swine fever (ASF), particularly in Asian countries, new normal management strategies minimizing pig contact by employing automatic feeding systems, artificial intelligence, and robotic farming and reducing the numbers of vaccines are suggested. Re-emergence of existing swine pathogens such as PRRSV or PCV2, or elimination of some pathogens may occur after the ASF-induced depopulation. ASF-associated repopulating strategies are, therefore, essential for the establishment of food security. The "repopulate swine farm" policy and the strict biosecurity management (without the use of ASF vaccines) are, herein, discussed for the sustainable management of small-to-medium pig farms, as these happen to be the most potential sources of an ASF re-occurrence. Finally, the ASF disruption has caused the swine industry to rapidly transform itself. Artificial intelligence and smart farming have gained tremendous attention as promising tools capable of resolving challenges in intensive swine farming and enhancing the farms' productivity and efficiency without compromising the strict biosecurity required during the ongoing ASF era.

Molecular Epidemiology and Genetic Characterization of PCV2 Circulating in Wild Boars in Southwestern Ethiopia

Porcine circovirus type 2 (PCV2) is one of the most relevant infectious agents affecting domestic pigs. Recently, a surprising PCV2 genetic heterogenicity has been reported in Africa. Nevertheless, the knowledge of the epidemiology of PCV2 in African countries, in both domestic and wild species, is limited and sparse. Having this in mind, in the present study, the PCV2 circulation and its molecular epidemiology in Southwestern Ethiopia have been investigated by collecting 64 samples from domestic pigs, wild boars, and warthogs. PCV2 genome presence was detected and quantified using qPCR and ORF2 sequencing was attempted on positive samples. Ten samples, 8 wild boars, 1 domestic pig, and 1 warthog, tested PCV2 positive. Complete ORF2 sequences were obtained from 5 wild boars; 4 of those were classified as PCV2d and 1 as PCV2b. Both PCV2b and PCV2d were related to strains of Asian origin, most commonly from China. The role of this country in the exportation of PCV2 strains in Ethiopia, and Africa in general, might be supported by the crescent economic relationship between the two continents. The obtained evidence also testifies to the inadequacy and/or poor application of biosecurity measures separating wild and domestic animals. Further, extensive and systematic studies should be performed to more deeply characterize the molecular epidemiology of PCV2 in this region, in order to improve our understanding of these ecological niches in the evolution and dispersal of PCV2.

LAMP Coupled CRISPR-Cas12a Module for Rapid, Sensitive and Visual Detection of Porcine Circovirus 2

Porcine circovirus 2 (PCV2) is the main pathogen of porcine circovirus-associated disease (PCVAD), which can cause considerable economic loss to the pig industry. The diagnosis of PCVAD is complicated and requires a series of clinical, pathological, and virological methods. Therefore, a rapid, highly sensitive, on-site, and visual diagnostic approach would facilitate dealing with the spread of PCV2. In this study, we intended to establish a new and effective PCV2 detection method through combining the no specific equipment requirement advantage of loop-mediated isothermal amplification (LAMP) with the property of clustered regular interspaced short palindromic repeats (CRISPR)/Cas12a system possessing the huLbCas12a collateral cleavage activity able to cleave single-stranded DNA fluorophore quencher probe sensor (designed as LAPM-CRISPR). Following a series of optimizations of its reaction conditions, this LAMP-CRISPR-based PCV2 detection could be conducted in constant temperature equipment, with the result reflected in a direct visual readout way. This established PCV2 detection approach presented fine sensitivity, rapidity, specificity, and reliability, as demonstrated by a low detectable limit of 1 copy/μL, completed within an hour, no cross-reaction with main porcine DNA or RNA viruses like PCV1, PCV3, and PEDV, and a 100% coincidence rate with that of the quantitative PCR (qPCR) method in the evaluation of 30 clinical blood samples, respectively. Therefore, this novel method makes rapid, on-site, visual, highly sensitive, and specific detection of PCV2 possible, facilitating the prevention of this pathogen in the field.

Phylodynamic and phylogeographic reconstruction of porcine reproductive and respiratory syndrome virus (PRRSV) in Europe: Patterns and determinants

Porcine reproductive and respiratory syndrome (PRRS) is among the most devastating diseases affecting the pig industry. Despite vaccines having been available for decades, the remarkable genetic variability of this virus, leading to poor cross-protection, has limited their efficacy, and other measures must be adopted to effectively control the viral circulation. Some recent studies have investigated the factors involved in viral spreading and persistence, at least at the local level. However, despite the topic's relevance, no statistically grounded evidence is currently available evaluating the variables more involved in porcine reproductive and respiratory syndrome virus (PRRSV) epidemiological success at a broader scale, such as the European scale. In the present study, an extensive phylodynamic and phylogeographic analysis was performed on more than 1000 ORF5 sequences to investigate the history, dynamics and spreading patterns of PRRSV within European borders. Moreover, several potential predictors, representative of swine population features and trade, human population, economy and geographic characteristics, were evaluated through a specifically designed generalized linear model (GLM) to assess their weight on viral migration rate between countries over time. Although pig stock density, mean PRRSV strain genetic diversity, investments in agriculture (including a likely role of vaccination) and farmer education were involved to a certain extent, the major determinant was proven to be by far the live pig trade. Providing a robust depiction of PRRSV European molecular epidemiology patterns and determinants, the present study could contribute to a more rational allocation of limited resources based on an effective prioritization of control measures.

Detection and Complete Genome Analysis of Porcine Circovirus 2 (PCV2) and an Unclassified CRESS DNA Virus from Diarrheic Pigs in the Dominican Republic: First Evidence for Predominance of PCV2d from the Caribbean Region

We report here high rates (47.5%, 48/101) of detection of porcine circovirus 2 (PCV2) in diarrheic pigs from three pig farms in the Dominican Republic. Seventeen of the PCV2 positive samples, representing the three pig farms, different age groups and sampling periods (2020–2021), were amplified for the complete PCV2 genome. Based on analysis of open reading frame 2 and complete genome sequences, the 17 PCV2 strains were assigned to the PCV2d genotype. Significant differences were observed in PCV2 detection rates between the vaccinated (20% (10/50)) and unvaccinated (62.5% (10/16) and 80% (28/35)) farms, corroborating previous observations that PCV2a-based vaccines confer protection against heterologous PCV2 genotypes. The present study is the first to report detection and molecular characterization of PCV2 from the Dominican Republic, warranting large-scale molecular epidemiological studies on PCV2 in pig farms and backyard systems across the country. For the first time, PCV2d was identified as the predominant PCV2 genotype in a study from the Caribbean region, suggesting that a genotype shift from PCV2b to PCV2d might be happening in the Caribbean region, which mirrored the current PCV2 genotype scenario in many other parts of the world. Besides PCV2, we also identified a pigeon circovirus-like virus, and a circular Replication-associated protein (Rep)-encoding single-stranded (CRESS) DNA virus, which was characterized for the complete genome. The CRESS DNA virus shared a similar genomic organization and was related to unclassified CRESSV2 DNA viruses (belonging to the Order Cirlivirales) from porcine feces in Hungary, indicating that related unclassified CRESS DNA viruses are circulating among pigs in different geographical regions, warranting further studies on the epidemiology and biology of these novel viruses.

Rapid detection of porcine circovirus type 2 by a red latex microsphere immunochromatographic strip

Abstract

To establish a rapid and specific antigen detection method for porcine circovirus type 2 (PCV2), monoclonal antibodies (mAbs) were produced against the PCV2 epidemic strains and a red latex microsphere immunochromatographic strip was established. A total of eight anti-PCV2b and four anti-PCV2d mAbs were produced, and seven mAbs were confirmed to react with PCV2a, PCV2b, and PCV2d strains using an immunoperoxidase monolayer assay. The results of micro-neutralization tests showed that the mAbs 2C8, 9H4, 10G7, 7B9, and 7C7 had good neutralizing activity, whereas the neutralizing activity of the mAbs 4B3, 4C9, 6H9, and 7E2 was lower than 50%. Three mAbs, 4B3, 7C7, and 9H4, and PCV2 pAb were selected for the establishment of a red latex microsphere immunochromatographic strip, and the combination of mAb 7C7 labeled with red latex microspheres and mAb 9H4 exhibited the greatest detection ability. The immunochromatographic strip had minimum detection limits of 10^2.5 TCID₅₀/0.1 ml, 10^0.7 TCID₅₀/0.1 ml, and 10^1.5 TCID₅₀/0.1 ml for PCV2a/CL, PCV2b/MDJ, and PCV2d/LNHC, respectively. Furthermore, no cross-reactivity was found for African swine fever virus, classical swine fever virus, porcine respiratory and reproductive syndrome virus, porcine parvovirus, porcine pseudorabies virus, porcine circovirus type 1, transmissible gastroenteritis virus, porcine epidemic diarrhea virus, porcine rotavirus, or porcine deltacoronavirus using the immunochromatographic strip. Using PCR as a reference standard, the detection sensitivity, specificity, and overall coincidence rate of the immunochromatographic strip were 81.13%, 100%, and 90.00%. Additionally, the detection ability of the immunochromatographic strip was correlated with that of virus titration. The immunochromatographic strip was used to detect 183 clinical disease samples, and the average positive detection rate was 22.95%. In summary, this method has good sensitivity and specificity and is simple, convenient, and quick to operate. It has high application value for on-site diagnosis of PCV2 and virus quantification.

Key points

• A red latex microsphere immunochromatographic strip for PCV2 detection was developed.

• The method was not only simple to operate, but also takes less time.

• The method had good sensitivity and specificity.

Genetic Variation Analysis of Porcine Circovirus Type 4 in South China in 2019 to 2021

Porcine circovirus type 4 (PCV4) is a novel virus associated with porcine dermatitis and nephropathy syndrome (PDNS)-like signs identified firstly in China in 2019. However, the details of the molecular epidemiology of PCV4 are unclear at this time. A total of forty-two related sequences were selected from the GenBank database to explore the spread of PCV4 and its rule in genetic evolution. Of the selected strains, 41 were from south China in 2019 to 2021 and the other was a foreign representative strain. Phylogenetic tree construction, nucleotide and amino acid (aa) sequence alignment, gene recombination and antigen structure prediction were performed on the collected sequences using bioinformatics softwares. The 42 PCV4 strains were divided into two subgenotypes: PCV4a (35/42) and PCV4b (7/42), according to the constructed genetic evolution tree. PCV4a is the main epidemic strain, and it can be further divided into two different gene clusters: PCV4a-1 (22/35) and PCV4a-2 (13/35). The pairwise comparison analysis showed that the complete genome sequence similarity of the 42 PCV4 strains ranged between 97.9% and 100%, and the aa sequences of the Cap proteins of 42 PCV4 strains had three major heterogenic or hypervariable regions—27–28, 96 and 212—all located near the antigenic epitope of the Cap protein. The results of this study can provide some basis for further studying the spread and epidemic growth of PCV4, and the prevention and control of PCV4 infection in China.

Comparison of effects of a single dose of MHYOSPHERE® PCV ID with three commercial porcine vaccine associations against Mycoplasma hyopneumoniae (Mhyo) and porcine circovirus type 2 (PCV2) on piglet growth during the nursery period under field conditions

Pigs routinely undergo stressful vaccination procedures, which are often unavoidable given the unavailability of safer alternatives, challenging animal welfare. The available vaccines for Mycoplasma hyopneumoniae (Mhyo) or Porcine circovirus type 2 (PCV2) are mostly administered intramuscularly in association to prevent Porcine respiratory disease complex (PRDC). MHYOSPHERE® PCV ID is the first vaccine protecting from both agents by intradermal route. This randomized, blind-field trial aimed to compare the effects of MHYOSPHERE® PCV ID with those of three different intramuscular associations of commercially available vaccines. A total of 7072 21-day-old piglets from 12 consecutive batches in one farm were randomly vaccinated with MHYOSPHERE® PCV ID (G1) or Ingelvac CircoFLEX® + Hyogen® (G2), Porcilis® PCV + M + PAC® (G3), and Porcilis® PCV + Hyogen® (G4). Growth performance during the nursery period and adverse reactions (ARs) after vaccine administration were monitored. Average Daily Weight Gain (ADWG) during the first 7 days post-weaning in G1 was 10.92, 3.03, and 20.08 g/day higher than in G2, G3, and G4, respectively, and 0.65, 4.06, and 9.58 g/day higher than in G2, G3, and G4 during the entire nursery period, respectively. G1 ADWG was significantly higher than G4 during both periods and significantly higher than G2 during the first 7 days post-weaning. Incidence of systemic ARs in G2 and G4 was 0.03% and 0.32%, respectively; none were recorded in G1 and G3. Replacing the usual intramuscular vaccination with MHYOSPHERE® PCV ID results in higher growth performance during the first weeks after weaning with no systemic ARs.

The Prevalence and Genetic Diversity of PCV3 and PCV2 in Colombia and PCV4 Survey during 2015–2016 and 2018–2019

Four genotypes of circovirus have been recognized in swine, with PCV2 and PCV3 being the most associated with clinical manifestations, while PCV4 does not have a defined disease. In addition, PCV2 is associated with different syndromes grouped as diseases associated with porcine circovirus (PCVAD), while PCV3 causes systemic and reproductive diseases. In the present study, we retrospectively detected PCV2, PCV3, and PCV4 in Colombia during two periods: A (2015–2016) and B (2018–2019). During period A, we evaluated stool pools from the 32 Colombian provinces, finding a higher prevalence of PCV3 compared to PCV2 as well as PCV2/PCV3 co-infection. Furthermore, we determined that PCV3 had been circulating since 2015 in Colombia. Regarding period B, we evaluated sera pools and tissues from abortions and stillborn piglets from the five provinces with the highest pig production. The highest prevalence found was for PCV3 in tissues followed by sera pools, while PCV2 was lower and only in sera pools. In addition, PCV2/PCV3 co-infection in sera pools was also found for this period. The complete genome sequences of PCV3 and PCV3-ORF2 placed the Colombian isolates within clade 1 as the majority in the world. For PCV2, the predominant genotype currently in Colombia is PCV2d. Likewise, in some PCV3-ORF2 sequences, a mutation (A24V) was found at the level of the Cap protein, which could be involved in PCV3 immunogenic recognition. Regarding PCV4, retrospective surveillance showed that there is no evidence of the presence of this virus in Colombia.

Revisiting Porcine Circovirus Disease Diagnostic Criteria in the Current Porcine Circovirus 2 Epidemiological Context

Current knowledge on porcine circovirus diseases (PCVD) caused by Porcine circovirus 2 (PCV-2) includes the subclinical infection (PCV-2-SI), systemic (PCV-2-SD) and reproductive (PCV-2-RD) diseases, and porcine dermatitis and nephropathy syndrome (PDNS). Criteria to establish the diagnosis of these conditions have not changed over the years; thus, the triad composed by clinical signs, lesions and viral detection in lesions are still the hallmark for PCV-2-SD and PCV-2-RD. In contrast, PCV-2-SI diagnosis is not usually performed since this condition is perceived to be controlled by default through vaccination. PDNS is diagnosed by gross and histopathological findings, and PCV-2 detection is not recognized as a diagnostic criterion. Molecular biology methods as a proxy for PCVD diagnoses have been extensively used in the last decade, although these techniques should be mainly considered as monitoring tools rather than diagnostic ones. What has changed over the years is the epidemiological picture of PCV-2 through the massive use of vaccination, which allowed the decrease in infectious pressure paralleled with a decrease in overall herd immunity. Consequently, the need for establishing the diagnosis of PCVD has increased lately, especially in cases with a PCV-2-SD-like condition despite vaccination. Therefore, the objective of the present review is to update the current knowledge on diagnostic criteria for PCVDs and to contextualize the interest of using molecular biology methods in the overall picture of these diseases within variable epidemiological scenarios of PCV-2 infection.

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.

The Swine IFN System in Viral Infections: Major Advances and Translational Prospects

Interferons (IFNs) are a family of cytokines that play a pivotal role in orchestrating the innate immune response during viral infections, thus representing the first line of defense in the host. After binding to their respective receptors, they are able to elicit a plethora of biological activities, by initiating signaling cascades which lead to the transcription of genes involved in antiviral, anti-inflammatory, immunomodulatory and antitumoral effector mechanisms. In hindsight, it is not surprising that viruses have evolved multiple IFN escape strategies toward efficient replication in the host. Hence, in order to achieve insight into preventive and treatment strategies, it is essential to explore the mechanisms underlying the IFN response to viral infections and the constraints thereof. Accordingly, this review is focused on three RNA and three DNA viruses of major importance in the swine farming sector, aiming to provide essential data as to how the IFN system modulates the antiviral immune response, and is affected by diverse, virus-driven, immune escape mechanisms.

Novel Porcine Circoviruses in View of Lessons Learned from Porcine Circovirus Type 2-Epidemiology and Threat to Pigs and Other Species

Porcine circovirus type 2 (PCV2) plays a key role in PCV2-associated disease (PCVAD) etiology and has yielded significant losses in the pig husbandry in the last 20 years. However, the impact of two recently described species of porcine circoviruses, PCV3 and PCV4, on the pork industry remains unknown. The presence of PCV3 has been associated with several clinical presentations in pigs. Reproductive failure and multisystemic inflammation have been reported most consistently. The clinical symptoms, anatomopathological changes and interaction with other pathogens during PCV3 infection in pigs indicate that PCV3 might be pathogenic for these animals and can cause economic losses in the swine industry similar to PCV2, which makes PCV3 worth including in the differential list as a cause of clinical disorders in reproductive swine herds. Moreover, subsequent studies indicate interspecies transmission and worldwide spreading of PCV3. To date, research related to PCV3 and PCV4 vaccine design is at early stage, and numerous aspects regarding immune response and virus characteristics remain unknown.

Purification of Porcine Circovirus Type 2 Using an Affinity Chromatography Based on a Neutralizing Monoclonal Antibody against Viral Capsid Protein

Porcine circovirus type 2 (PCV2) is a DNA virus without an envelope. The viral particle is icosahedral and has a diameter of approximately 17 nm. In order to obtain the purified virus, a broad-spectrum monoclonal antibody 3A5 against PCV2 was coupled to CNBr-activated Sepharose^TM 4B, and an affinity chromatography was established for PCV2 purification. A total of 6.5 mg of purified PCV2a/LG with 97% purity was obtained from 120 mL of the viral culture medium, and only PCV2 was detected by electron microscopy. No significant changes in the antigenic characteristics of the purified virus were detected by a capture enzyme-linked immunosorbent assay (ELISA). Furthermore, the titer of the purified PCV2 was 100 times higher than that of the unpurified virus. This affinity chromatography method was also used to purify PCV2b/LN590516 and PCV2d/SD446F16, and the purified viruses were detected by electron microscopy, capture ELISA, and virus titration, respectively. The results showed that these two strains can be successfully purified, but the yield is lower than that of the PCV2a strain. In addition, the purified virus could be used to study the viral adsorption and invasion of PK15 cells using indirect immunofluorescence assays. A large number of PCV2 signals were detected to transfer from the cellular surface to the periphery of the nucleus of the PK15 cells after 30 min of adsorption of the PCV2 to the PK15 cells. The affinity chromatography is a simple and convenient tool to obtain PCV2 with high purity. It could be applied for virus structure analysis, antibody preparation, and viral adsorption and invasion research.

Prevalence of Infection with Porcine Circovirus Types 2 and 3 in the Wild Boar Population in the Campania Region (Southern Italy)

In recent years, porcine circovirus (PCV) infection has been documented as an important and emerging health concern for livestock and wildlife worldwide. The purpose of the present study was to assess the molecular prevalence of PCV-2 and PCV-3 and to clarify the epidemiological role of wild boars in the circulation of this virus in Campania, Southern Italy. For this purpose, samples from several organs were collected during the hunting season 2017-2018 from 148 wild boars in the Campania region. Quantitative real-time PCR was used for the detection and quantification of PCV-2 and PCV-3 genomes. The combined prevalence of PCV-2 and PCV-3 was 74.32% in the wild boars tested. The proportions of wild boars positive for PCV-2 or PCV-3, or coinfected, were 47.30%, 49.32%, and 22.30%, respectively. No link was detected between PCV positivity and location, but gender was a risk factor for the disease (female; p < 0.0001; OR 0.29). Furthermore, our study provides a snapshot of PCV-2 and PCV-3 circulation in wild boars in the Campania region: our findings can help us to better understand the role of wildlife in PCV circulation.

Balantidium coli in pig farms suspected of porcine circovirus type 2 (PCV2) associated enteritis

Introduction

Diarrhoea in growing-finishing pigs is a common problem of commercial pig farms. Among many causative factors, porcine circovirus type 2 (PCV2) is one considered an important pathogen in modern pig production. The aim of the study was to verify if PCV2 was responsible for antibiotic non-responsive diarrhoea and wasting in pigs.

Material and Methods

A total of 13 dead pigs aged between 12 and 15 weeks from three Polish farms with persistent herd symptoms suggestive of PCV2 infection were provided for evaluation. Sections of lymph nodes and intestines were analysed by in situ hybridization (ISH) for PCV2 and histopathological examination. Faeces and intestinal scrapings were tested for Lawsonia intracellularis and Brachyspira hyodysenteriae by real-time PCR and for parasitic infection by flotation and decantation.

Results

ISH and histopathological examination showed that all pigs were PCV2 systemic disease negative. Swine dysentery was confirmed by real-time PCR on two farms, and proliferative enteropathy on one farm. In histological examinations, erosions of the caecal and colonic mucosa were found, together with cysts and trophozoites of Balantidium coli. The protozoa were present in the intestinal lumen and mucosa. B. coli cysts were identified in faeces from all examined pigs.

Conclusion

These results suggest that monitoring of B. coli infections should be an additional measure of control and prevention of gastrointestinal tract disorders in modern swine husbandry.

A retrospective study reveals the Porcine circovirus-2f genotype predominant in the indigenous pig population of North-eastern India

Porcine circovirus-2 (PCV2) is a widespread virus and presents sub-clinically in most of the swineherd. Globally, eight genotypes of PCV2 have been identified that is PCV2a to 2h. To determine the region-wide genotype distribution of PCV2 infection, with additional reference to indigenous breeds, a total of 1314 pig's clinical samples from the eight states of North-eastern India between 2011 and 2014; were analyzed. The overall prevalence rate of PCV2 in this region was 28.2% (370/1314) by PCR. The state-wise PCR based PCV2 prevalence rate was: Tripura (20.8%), Nagaland (25.0%), Meghalaya (25.8%), Assam (32.1%), Sikkim (32.6%), Manipur (33.3%), Mizoram (36.7%) and Arunachal Pradesh (42.3%). Subsequently, a total of 29 complete genomes of PCV2 were amplified and sequenced from these PCV2 positive samples. The phylogenetic tree represents that the 29 PCV2 isolates of this study were divided into four distinct genetic groups; PCV2a, PCV2b, PCV2d, and PCV2f. Among these, 14 PCV2 strains were classified as PCV2f, 13 classified as PCV2d, and one isolate of each classified as PCV2a and PCV2b. All the 14 PCV2f strains appeared from indigenous pigs of this region. Based on the date of collection, the present study further describes that the PCV2f genotypes circulate in the indigenous pigs' population back in 2011. The amino acid residues and the atomic coordinate structure (3D model) of PCV2f capsid protein represents similarity to PCV2d capsid protein support the efficacy of the existing PCV2 vaccine against the PCV2f. The observation of this study helps to understand the genotype distribution of PCV2 and stands as a reference for future molecular epidemiological studies in North-eastern India.

Correlations between lung pneumonic lesions and serologic status for key respiratory pathogens in slaughtered pigs in northern Uganda

Background

A cross-sectional study of slaughtered pigs was conducted in Lira district, Uganda, to (1) determine the prevalence and severity of pneumonia and (2) establish relationships between pneumonia types and the serological status for key respiratory pathogens. Using enzyme-linked immunosorbent assays (ELISAs), sera were screened for antibodies against Mycoplasma hyopneumoniae (M. hyo), Actinobacillus pleuropneumoniae (App), porcine reproductive and respiratory syndrome virus (PRRSv) and porcine circovirus type 2 (PCV2). Postmortem, lungs were grossly scored for pneumonia types and pneumonic lesions. Pneumonia types were characterized as catarrhal purulent bronchopneumonia (CPBP), pleuropneumonia (PLP) and pleuritis. The percent of lung surface affected by pneumonia was determined by estimating the affected surface area of each lung lobe. Each lobe was assigned scores based on the approximate volume represented and the total percentage of lung surface affected obtained as a sum of individual lobe scores. Metastrongylus spp. helminth infection was determined by examining lungs for gross presence or absence. RStudio was used for data analysis and presentation. Wilcoxon rank sum tests were used to compare median pneumonia lesion scores and serostatus for each studied pathogen. An ordinal logistic regression model was fitted to evaluate the odds of multiple pneumonia, with pathogen serostatus and Metastrongylus spp. infection as predictors.

Results

One hundred sixty-seven (n = 167) lungs were examined for pneumonic lesions. The prevalences of CPBP, PLP and pleuritis were 29.9% (95% CI 22.9–36.9), 74.2% (95% CI 67.5–80.9) and 17.3% (95% CI 22.4–36.3), respectively. The true prevalence of PCV2 was 9.7% (95% CI 4.5–16.8), that of PRRSv was 7.5% (95% CI 2.7–14.2), that of M. hyo was 11.5% (95% CI 7.2–18.0), that of App was 25.1% (95% CI 18.5–38.0), and that of Metastrongylus spp. was 29.3% (95% CI 22.9–36.6). The odds of multiple pneumonia forms increased in pigs with multiple pathogens (ORs 2.6, p = 0.01) and Metastrongylus spp. infestation (OR 2.5, p = 0.003), suggesting synergistic effects of coinfections in the induction of lesions.

Conclusions

This study revealed a high prevalence and severity of pneumonic lesions in slaughtered pigs. It provides baseline information and evidence for the magnitude of pneumonia associated with the studied pathogens and justifies future studies on their potential economic impacts on Ugandan pigs.

Circoviruses and cycloviruses identified in Weddell seal fecal samples from McMurdo Sound, Antarctica

Circoviridae is a family of circular single-stranded DNA viruses whose members infect a wide variety of hosts. While well characterized in avian and mammalian hosts, little is known about circoviruses associated with Antarctic animals. From 48 Weddell seal (Leptonychotes weddellii) fecal samples collected on the sea ice in McMurdo between Nov 2014 and Dec 2014, we identified and determined the genomes of novel viruses that fall within two genera of the family Circoviridae, i.e. Circovirus (n = 7) and Cyclovirus (n = 45). We named these viruses as werosea circovirus (WerCV) and werosea cyclovirus (WerCyV). The genomes of WerCV and WerCyV share ~63-64% genome-wide pairwise identity with classified circoviruses and cycloviruses, respectively. Based on the species demarcation threshold of 80% for members of the Circoviridae, the genomes of WerCV and WerCyV represent new species in their respective genera. Evidence indicated recombination in five of the 45 WerCyV genomes identified in this study. These are the first circoviruses found associated with Antarctic pinnipeds, adding to those recently identified associated with Adélie (Pygoscelis adeliae) and chinstrap penguins (P. antarcticus).

Open reading frame 5 protein of porcine circovirus type 2 induces RNF128 (GRAIL) which inhibits mRNA transcription of interferon-β in porcine epithelial cells

A previous study has indicated that mRNA transcript of Rnf128 (Grail) is significantly increased in porcine epithelial cells expressing porcine circovirus type 2 (PCV2) open reading frame 5 (ORF5). RNF128 is an E3 ubiquitin ligase that can modulate the activity of target protein via ubiquitination of specific lysine residues. However, the function of RNF128 in PCV2-infected epithelial cells has not been well studied yet. Thus, the objective of the present study was to examine the functional role of RNF128 in porcine epithelial cells (PK15 cells) after PCV2 infection. Results clearly indicated that PCV2 ORF5 increased the expression of RNF128 which inhibited type I IFN production and enhanced viral replication of PCV2 in PK15 cells. Therefore, up-regulating RNF128 by PCV2 ORF5 can help PCV2 circumvent initial immune surveillance of porcine epithelial cells.

Efficacy of Simultaneous Intradermal Vaccination of Swine against Porcine Circovirus 2, Porcine Reproductive and Respiratory Syndrome Virus, Mycoplasma hyopneumoniae and Lawsonia intracellularis

The combined application of vaccines in swine offers many benefits, including reduced time and labour costs, and improved animal welfare, due to fewer injections and manipulations. This study investigated if simultaneous intradermal vaccinations against porcine circovirus 2, porcine reproductive and respiratory syndrome virus, Mycoplasma hyopneumoniae, and Lawsonia intracellularis, using a specialised needle-free applicator would confer comparable protection against experimental infection compared to the single vaccines. In all cases, the administration of the vaccines together was as efficacious as the administration of the vaccines alone, significantly reducing clinical signs associated with each of the four pathogens.

Porcine circovirus 3 (PCV-3) as a causal agent of disease in swine and a proposal of PCV-3 associated disease case definition

Porcine circovirus 3 (PCV‐3) was discovered in 2015 using next‐generation sequencing (NGS) methods. Since then, the virus has been detected worldwide in pigs displaying several clinical–pathological outcomes as well as in healthy animals. The objective of this review is to critically discuss the evidence existing so far regarding PCV‐3 as a swine pathogen. In fact, a significant number of publications claim PCV‐3 as a disease causal infectious agent, but very few of them have shown strong evidence of such potential causality. The most convincing proofs of disease association are those that demonstrate a clinical picture linked to multisystemic lymphoplasmacytic to lymphohistiocytic perivascular inflammation and presence of viral nucleic acid within these lesions. Based on these evidence, individual case definitions for PCV‐3‐reproductive disease and PCV‐3‐systemic disease are proposed to standardize diagnostic criteria for PCV‐3‐associated diseases. However, the real frequency of these clinical–pathological conditions linked to the novel virus is unknown, and the most frequent outcome of PCV‐3 infection is likely subclinical based on its worlwide distribution.

Computational based design and tracking of synthetic variants of Porcine circovirus reveal relations between silent genomic information and viral fitness

Viral genomes not only code the protein content, but also include silent, overlapping codes which are important to the regulation of the viral life cycle and affect its evolution. Due to the high density of these codes, their non-modular nature and the complex intracellular processes they encode, the ability of current approaches to decipher them is very limited. We describe the first computational-experimental pipeline for studying the effects of viral silent and non-silent information on its fitness. The pipeline was implemented to study the Porcine Circovirus type 2 (PCV2), the shortest known eukaryotic virus, and includes the following steps: (1) Based on the analyses of 2100 variants of PCV, suspected silent codes were inferred. (2) Five hundred variants of the PCV2 were designed to include various ‘smart’ silent mutations. (3) Using state of the art synthetic biology approaches, the genomes of these five hundred variants were generated. (4) Competition experiments between the variants were performed in Porcine kidney-15 (PK15) cell-lines. (5) The variant titers were analyzed based on novel next-generation sequencing (NGS) experiments. (6) The features related to the titer of the variants were inferred and their analyses enabled detection of various novel silent functional sequence and structural motifs. Furthermore, we demonstrate that 50 of the silent variants exhibit higher fitness than the wildtype in the analyzed conditions.

Retrospective surveillance of porcine circovirus 4 in pigs in Inner Mongolia, China, from 2016 to 2018

A novel circovirus designated "porcine circovirus type 4" (PCV4) was recently reported in pigs with severe clinical disease in Hunan Province, China. Relatively little is known about the molecular epidemiology of this recently discovered virus. In order to assess the prevalence of PCV4 infection in pigs and to analyze its genomic characteristics, 1683 clinical samples were collected in Inner Mongolia, China, from 2016 to 2018. The overall infection rate of PCV4 was 1.6% (27/1683) at the sample level and 21.6% (11/51) at the farm level, with rates ranging from 3.2% (1/31) to 20.0% (6/30) on different PCV4-positive pig farms. In addition, the PCV4 infection rates at both the sample and farm level increased from 2016 to 2018. This also showed that PCV4 was present in pigs in 2016 in China and therefore did not arrive later than this date. Additionally, our findings showed that PCV4 infections had no association with PCV2 or PCV3 infections. We sequenced the complete genomes of three PCV4 strains and found that the PCV4 strains had a high degree of genetic stability but shared less than 80% sequence identity with other circoviruses. We identified six amino acid mutations in the Rep protein and seven in the Cap protein. Phylogenetic analysis based on Cap and Rep sequences confirmed that the PCV4 strains grouped in an independent branch. Our findings provide important information about the prevalence and genetic characteristics of PCV4 strains.

Exploratory field study on the effects of porcine circovirus 2 (PCV-2) sow vaccination at different physiological stages mimicking blanket vaccination

Background

The objective of the present study was to explore the benefits of Porcine circovirus 2 (PCV-2) blanket vaccination in a sow herd on productive parameters, PCV-2 infection and immune status in sows and their progeny. For this purpose, 288 sows were distributed among four balanced experimental groups. One group remained as negative control group and the other three received 1 mL of PCV-2 Ingelvac Circoflex® intramuscularly at different productive cycle moments: before mating, mid gestation (42–49 days post-insemination) or late gestation (86–93 days post-insemination); phosphate buffered saline (PBS) was used as negative control item. Reproductive parameters from sows during gestation and body weight of their progeny from birth to weaning were recorded. Additionally, blood was collected from sows at each vaccination time and piglets at 3 weeks of age. Moreover, up to 4 placental umbilical cords (PUC) per sow were taken at peri-partum. Sera from sows and piglets were analysed for PCV-2 antibody detection using an enzyme-linked immunosorbent assay (ELISA). Sera from sows and PUC were tested to quantify viraemia using a real time quantitative polymerase chain reaction (qPCR) assay.

Results

Globally, results indicated that vaccinated sows showed heavier piglets at birth and at weaning, less cross-fostered piglets, lower viral load at farrowing as well as in PUC, and higher antibody levels at farrowing, compared to non-vaccinated ones. When all groups were compared among them, sows vaccinated at mid or late gestation had heavier piglets at birth than non-vaccinated sows, and lower proportion of PCV-2 positive PUC. Also, cross-fostering was less frequently practiced in sows vaccinated at pre-mating or mid gestation compared to non-vaccinated ones.

Conclusions

In conclusion, the present study points out that PCV-2 sow vaccination at different time points of their physiological status (mimicking blanket vaccination) offers benefits at production and serological and virological levels.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40813-021-00213-2.

Development of cost-effective quantitative PCR method for parallel detection of porcine circovirus2 and porcine parvovirus in perspective of North-eastern India

Pig farming performs as an intricate part in the socio-economic situation in the north-eastern region of India. This region contributes 38% (3.95 million) of total pigs in India. In spite of this, the region unables to flourish as an enterprise as per the expectation due to a low productivity rate. Porcine infectious pathogens like porcine cirovirus2 (PCV2) and porcine parvovirus (PPV) have a direct economic impact on pig farming through slow growth rate, abortion, and mortality and ultimately maximize the production cost by increasing the usage of antibiotic or antiviral drugs. The veterinary diagnostic infrastructure is a fundamental aspect of the development of livestock status by rapid and effective detection of pathogens. Quantitative PCR (qPCR) is a precise and fast-track technique used for the routine diagnostic method. Hence, we developed a highly precise and comparatively cost-effective SYBR Green reporter dye-based qPCR assay for parallel identification of PCV2 and PPV. In the present assay, the correlation coefficient (R²) value was 0.99, and 10 copies of the gene/μl were the least limit of detection (LOD) concerning both viruses. Melt curve analysis of this study represented PCV2-specific melt curve (Tm) at 81.2 °C and PPV-specific melt curve (Tm) at 73.5 °C. Therefore, the assay easily differentiates the true positive amplicons of PCV2 and PPV through specific Tm values. Among the 50 field samples, 26 (52%) samples were PCV2 positive, 18 (36%) samples PPV positive, and 11 (22%) samples were co-infected of both the viruses. This method is cost-effective, precise, and sensitive to diagnose the concurrent or individual infection of the PCV2 and PPV in the pig. Hence, considering the impact of pig farming in the north-eastern part of the country, the present assay gives an unprecedented achievement in disease diagnosis.

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.

Active regional surveillance for early detection of exotic/emerging pathogens of swine: A comparison of statistical methods for farm selection

In this study, five spatially balanced sampling methods, i.e., generalized random-tessellation stratified (GRTS), local pivotal method (LPM), spatially correlated Poisson sampling (SCPS), local cube method (LCUBE), and balanced acceptance sampling (BAS) were compared to simple random sampling (SRS) based on a livestock disease transmission model on a hypothetical region (195 km × 300 km) populated with 6000 farms in terms of the probability of detection by sample size. Given a fixed sample size, four of the five spatially balanced sampling methods provided better performance than SRS, i.e., higher probabilities of detecting at least one infected farms over a range of regional prevalence evaluated (1%-5%). That is, for any given probability of detection, spatially balanced methods required testing fewer farms than SRS. In an era of pandemics, active regional surveillance for early detection of emerging pathogens becomes urgent, yet shrinking budgets impose intractable constraints. The better performance and higher efficiency of spatially balanced sampling methods suggests a potential improvement in regional livestock disease surveillances and a partial solution to the challenge of affordable surveillance.

Characterization of Emerging Swine Viral Diseases through Oxford Nanopore Sequencing Using Senecavirus A as a Model

Emerging viral infectious diseases present a major threat to the global swine industry. Since 2015, Senecavirus A (SVA) has been identified as a cause of vesicular disease in different countries and is considered an emerging disease. Despite the growing concern about SVA, there is a lack of preventive and diagnostic strategies, which is also a problem for all emerging infectious diseases. Using SVA as a model, we demonstrated that Oxford Nanopore MinION sequencing could be used as a robust tool for the investigation and surveillance of emerging viral diseases. Our results identified that MinION sequencing allowed for rapid, unbiased pathogen detection at the species and strain level for clinical cases. SVA whole genome sequences were generated using both direct RNA sequencing and PCR-cDNA sequencing methods, with an optimized consensus accuracy of 94% and 99%, respectively. The advantages of direct RNA sequencing lie in its shorter turnaround time, higher analytical sensitivity and its quantitative relationship between input RNA and output sequencing reads, while PCR-cDNA sequencing excelled at creating highly accurate sequences. This study developed whole genome sequencing methods to facilitate the control of SVA and provide a reference for the timely detection and prevention of other emerging infectious diseases.

Deletion of a decoy epitope in porcine circovirus 2 (PCV2) capsid protein affects the protective immune response in mice

The swine pathogen porcine circovirus type 2 (PCV2) causes significant economic damage worldwide. The PCV2 capsid (CP) residues 169-STIDYFQPNNKR-180 have been identified as a decoy epitope that diverts the host immune response away from protective epitopes. However, the decoy epitope may include important linear or conformational protective epitopes against PCV2. In this study, we used the baculovirus system to express recombinant complete CP (1-233) and mutant CP (Δ169-180), in which the decoy epitope was deleted, and evaluated the immune response to these in mice. Immunization with mutant CP (Δ169-180) protein, which formed very low level of virus-like particles (VLPs), elicited significantly lower levels of PCV2 CP-specific IgG antibodies and a slightly lower neutralizing activity than immunization with the complete CP (1-233) protein. This finding suggests that the complete CP is important for efficient VLP assembly and induction of PCV2-specific IgG antibodies and neutralizing antibodies in mice. This study may provide useful information for next-generation vaccine design for PCV2 control.

A novel circular ssDNA virus of the phylum Cressdnaviricota discovered in metagenomic data from otter clams (Lutraria rhynchaena)

In this study, we present an analysis of metagenome sequences obtained from a filtrate of a siphon tissue homogenate of otter clams (Lutraria rhynchaena) with swollen-siphon disease. The viral signal was mined from the metagenomic data, and a novel circular ssDNA virus was identified. Genomic features and phylogenetic analysis showed that the virus belongs to the phylum Cressdnaviricota, which consists of viruses with circular, single-stranded DNA (ssDNA) genomes. Members of this phylum have been identified in various species and in environmental samples. The newly found virus is distantly related to the currently known members of the phylum Cressdnaviricota.

Genetic diversity of Indian porcine circovirus type 2 (PCV2) isolates (2006-2018)

Porcine circovirus type 2 (PCV2) is an emerging viral infection in swine population and results in severe economic loss to piggeries worldwide. The present study was conducted to explore the genetic diversity of PCV2 circulating in swine population of India from 2006–2018. A total of 74 heart, lungs, spleen and lymph nodes collected from different regions in Uttar Pradesh, India were subjected to molecular analysis. For studying genetic diversity, the complete nucleotide and ORF2 sequences of 95 PCV2 including 43 nucleotide sequences from India were used. DNA was extracted from samples and positive samples were subjected to full genome sequencing and phylogenetic analysis was done by maximum likelihood method. Phylogenetic analysis of 40 Indian PCV2 genomes downloaded from GenBank along with three new isolates from the current study based on the complete genome and cap gene together with nucleotide sequences of PCV2 isolates from different countries results in a tree in which Indian isolates clustered in 4 different branches includes PCV2b-1C, PCV2a-2D, PCV 2b-1A/B, PCV 2d-2 recombinant group and two new cluster in which one clustered along with unclassified PCV2 viruses from Indonesia and Croatia. The comparison of ORF2 gene among Indian isolates revealed nucleotide identity ranging from 88.6% to 99.6%, indicating the genetic diversity of PCV2 strains circulating in Indian pig. The present work reports for the first time in India the PCV2-1A/B cluster of 2b genotype and all the Indian isolates available in India from 2006–2018 were used in this analysis.

Prevalence, pathogenesis, and evolution of porcine circovirus type 3 in China from 2016 to 2019

Porcine circovirus type 3 (PCV3) infection causes substantial economic losses in pig populations since its discovery in 2016. However, PCV3 molecular epidemiology remains need further study. In order to assess the prevalence of PCV3 infection in China, 4094 clinical samples from 271 pig farms in 10 provinces of China were evaluated by PCR. It was shown that the overall prevalence of PCV3 infection was 29.3 % (1200/4094) and 74.2 % (201/271) at sample and farm levels respectively, suggesting that PCV3 infection is prevalent in China. Furthermore, a statistical analysis showed PCV3 might exacerbate PCV2 and PRRSV infection rate and have a potential association with pig clinical disease. In addition, we sequenced the entire genome of 57 PCV3 strains; homology analysis showed that PCV3 strains have more than 96 % similarities at the nucleotide level, and PCV3 shares less than 60 % similarities with other circoviruses. By comparing the total 673 PCV3 strains from the NCBI GenBank, we found the major of amino acid mutations are located in predicted epitope regions and the mutations ratio changed during PCV3 evolution. Phylogenetic analysis revealed that all isolates belonged to PCV3a and PCV3b, and increasing PCV3a and decreasing PCV3b trends were observed during PCV3 evolution. Overall, this study provides important insights for understanding PCV3 prevalence, pathogenesis, and evolution and will guide future efforts to develop effective preventive and control measures.

Lack of Porcine circovirus 4 Genome Detection in Pig Samples from Italy and Spain

The genus Circovirus includes several species and mostly causes asymptomatic infections. Porcine circovirus 2 (PCV-2) and, with increasing evidence, Porcine circovirus 3 (PCV-3), have been associated with different clinical conditions all over the world. In 2019, a new porcine circovirus (PCV-4) was identified from diseased animals in China. Because of the lessons learned from PCV-2 and PCV-3, it appears mandatory to investigate the actual distribution of this new virus and its potential association with clinical outcomes. To this purpose, an exploratory study to detect PCV-4 by molecular methods was performed in Italy and Spain by testing more than 300 samples of different types (serum and tissues), collected from both healthy and diseased pigs and wild boar as well. All samples, independently from the country, type, health status and host, tested PCV-4 negative. Therefore, no evidence of PCV-4 presence was found in Italy and Spain through this exploratory study. Considering the dense pig trade among European countries, its presence in the continent can similarly be considered unlikely. The reasons behind the restricted PCV-4 distribution compared to other porcine circoviruses will require further investigations. Careful surveillance might nevertheless be important since prompt recognition of PCV-4 would allow the implementation of effective countermeasures to prevent its spreading and potential economic losses.

Detection and genotyping of Porcine circovirus 2 (PCV-2) and detection of Porcine circovirus 3 (PCV-3) in sera from fattening pigs of different European countries

PCV‐2 is considered one of the most economically important viral agents in swine worldwide. Recently, PCV‐3 has been found in pigs affected by different disorders and in healthy animals. The objective of this epidemiological work was to describe the frequency of detection of PCV‐2 and PCV‐3 in pig farms of 9 European countries. Moreover, a second aim was to assess the most frequent PCV‐2 genotypes found in the studied farms. Sera from 5 to 10 pigs per farm were collected from 2 to 11 farms per studied country. A total of 624 sera of fattening pigs (10–25 week old) from 64 farms from Spain (n = 11), Belgium (n = 10), France (n = 8), Germany (n = 8), Italy (n = 7), Denmark (n = 8), the Netherlands (n = 5), Ireland (n = 5) and Sweden (n = 2) were analysed by conventional PCR. In addition, one or two PCV‐2‐positive samples per farm were genotyped by sequencing the ORF2 gene. PCV‐3 PCR‐positive samples with relatively low Ct values were also sequenced and phylogenetically analysed. PCV‐2 DNA was detected in pig sera from all European tested countries, but Sweden. A total of 132 out of 624 (21%) sera were positive for PCV‐2 PCR, corresponding to 30 out of the 64 (47%) tested farms. PCV‐3 DNA was detected in 52 out of 624 (8%) sera, corresponding also to 30 out of the 64 (47%) studied farms from all tested countries. A total of 48 PCV‐2 PCR‐positive samples were successfully sequenced and genotyped, being PCV‐2d the most frequently genotype found (n = 28), followed by PCV‐2b (n = 11) and PCV‐2a (n = 9). These results pointed out PCV‐2d as the most prevalent genotype currently in Europe. The PCV‐3 phylogenetic analysis showed high identity (>98%) among sequences from all the analysed countries. The relatively low co‐infection (3%), likely suggest an independent circulation patterns of PCV‐2 and PCV‐3.