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

Characterization of a duck circovirus propagated in duck embryos: from genome to pathogenesis in SPF ducks

Duck circovirus (DuCV) is a major pathogen in duck farming that causes immunosuppression and increases the susceptibility to secondary infections. This study focused on a Chinese DuCV strain, designated SDDC, which was isolated and characterized from Cherry Valley ducks in Shandong Province in 2022. The SDDC strain was successfully propagated in specific-pathogen-free (SPF) duck embryos and confirmed by transmission electron microscopy. Genomic analysis identified a complete genome of 1994 bp, with a critical amino acid mutation (I to T) at the 160th position in the Cap protein, potentially influencing viral tropism. Pathogenicity studies in 2-day-old SPF ducks revealed a multi-organ infection, with the spleen as the primary target, exhibiting the highest viral load and significant histopathological alterations. Analysis of multi-organ viral dynamics indicated a detectable viral presence across target organs as early as 3 dpi, followed by a progressive decline in viral load until day 7. A pronounced replication peak was observed on day 14, after which a gradual viral clearance occurred. This study provides critical insights into the genomics, pathogenicity, and tropism of DuCV, establishing a foundation for elucidating its infection mechanisms, and developing targeted control strategies to protect duck farming.

Host-driven evolution of PCV2: insights into genetic diversity and adaptation

Introductions

Porcine circovirus type 2 (PCV2) is a significant pathogen in swine, exhibiting notable genetic and phenotypic diversity. This study explores the evolutionary mechanisms influencing PCV2 variability, emphasizing the role of viral features and host environment.

Methods

An extensive collection of globally available ORF2 sequences of the main PCV2 genotypes (i.e., PCV2a, PCV2b, and PCV2d) sampled from wild boars and domestic pigs was analyzed, using a combination of phylodynamic approaches and biostatistical methods to infer the presence and patterns of selective pressures in different virus population subsets.

Results

Significant differences were observed between strains collected from domestic and wild populations, with the former appearing to be under stronger selective pressures at specific capsid positions. These pressures are likely driven by immune-mediated selection acting on critical residues for immune system recognition and evasion. A comprehensive evaluation of substitution patterns also revealed a trend toward maintaining or enhancing amino acid polarity, with neutral residues often replaced by polar or charged ones. This shift may influence the virus interaction with host proteins, particularly glycosaminoglycans such as heparan sulfate-like molecules. The observed variability among hosts and genotypes highlights both the importance of host environment as a key driver of viral evolution and the plasticity of PCV2 adaptability, with multiple alternative evolutionary pathways seemingly being selected.

Discussion

The findings underscore the complex evolutionary trajectories followed by PCV2 on a global scale and suggest that the intensification of pig farming and associated management practices may have significantly shaped PCV2 evolution, contributing to the current epidemiological landscape.

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

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

Molecular characterization of canine circovirus based on the Capsid gene in Thailand

BACKGROUND

Canine circovirus (CanineCV) is a single-stranded circular DNA virus that infects domestic and wild canids in many countries. CanineCV is associated with gastroenteritis and diarrhea, respiratory disease, and generalized vasculitis leading to a fatal event. The Capsid protein (Cap) is a structural protein of the virus which has high genetic variability and plays a role in the canine immune response. In this study, we cloned the full-length CanineCV Capsid gene (Cap). In-silico analyses were used to explore the genomic and amino acid variability and natural selection acting on the Cap gene. The immune relevance for T-cell and B-cell epitopes was predicted by the immunoinformatic approach.

RESULTS

According to the Cap gene, our results showed that CanineCV was separated into five phylogenetic groups. The obtained CanineCV strain from this study was grouped with the previously discovered Thai strain (MG737385), as supported by a haplotype network. Entropy analyses revealed high nucleotide and amino acid variability of the Capsid region. Selection pressure analysis revealed four codons at positions 24, 50, 103, and 111 in the Cap protein evolved under diversifying selection. Prediction of B-cell epitopes exhibited four consensus sequences based on physiochemical properties, and eleven peptide sequences were predicted as T-cell epitopes. In addition, the positive selection sites were located within T-cell and B-cell epitopes, suggesting the role of the host immune system as a driving force in virus evolution.

CONCLUSIONS

Our study provides knowledge of CanineCV genetic diversity, virus evolution, and potential epitopes for host cell immune response.

Molecular basis for the different PCV2 susceptibility of T-lymphoblasts in Landrace and Piétrain pigs

Clinically, Landrace pigs are more susceptible to porcine circovirus-associated diseases (PCVADs) than Piétrain pigs. We previously found that porcine circovirus type 2 (PCV2) can infect T-lymphoblasts. The present study examined the replication kinetics of six PCV2 strains in the lymphoblasts of Landrace and Piétrain pigs. The results showed that T-lymphoblasts from Landrace pigs are much more susceptible to PCV2 infection than those from Piétrain pigs. In addition, PCV2 replication was strain-dependent. PCV2 binding to T-lymphoblasts was partially mediated by chondroitin sulfate (CS) and dermatan sulfate (DS). Phosphacan, an effective internalization mediator in monocytes that contains several CS chains, was also demonstrated to be involved in PCV2 internalization. Viral binding and internalization were not different between the two breeds, however, the subsequent step, the disassembly was. Although inhibition of serine proteases blocked PCV2 replication in both Landrace and Piétrain pigs, this only occurred at a neutral pH in Piétrain pigs, whereas this occurred also at a low pH in Landrace. This suggested that more proteases can cleave PCV2 in Landrace lymphoblasts than in Piétrain lymphoblasts, explaining the better replication. Through co-localization studies of viral particles with endo-lysosomal markers, and quantitative analysis of organelle sizes during viral internalization, it was observed that PCV2 may exhibit a higher propensity for viral escape from late endosomes in Landrace pigs (smaller) compared to Piétrain pigs. These results provide new understandings of the different PCV2 susceptibility in Landrace and Piétrain pigs.

Both recombinant Bacillus subtilis Expressing PCV2d Cap protein and PCV2d-VLPs can stimulate strong protective immune responses in mice

Porcine circovirus type 2 (PCV2) is one of the most serious pathogens in pig herds worldwide. The Capsid protein (Cap), a structural protein of PCV2, is involved in the host's immune response; it induces neutralizing-antibody production and has good immunogenicity. The main PCV2 subtype currently prevalent in the Chinese pig herd is PCV2d. In this study, We constructed a recombinant Bacillus subtilis (B. subtilis) capable of secreting Cap protein, named pHT43-Cap/B. subtilis; we concentrated the supernatant of the recombinant bacteria and observed virus-like particles (VLPs) of PCV2d formed by Cap protein under transmission electron microscopy, named PCV2d-VLPs. The immunocompetence of the pHT43-Cap/B. subtilis and PCV2d-VLPs were then assessed by oral administration and by intramuscular injection into mice, respectively. The results showed that the levels of PCV2d-Cap protein-specific IgG in the serum and of PCV2d-Cap protein-specific sIgA in the small intestinal fluid of pHT43-Cap/B. subtilis immunized mice were elevated compared to the control group, both of them highly significant (p < 0.01), and the corresponding serum-specific IgG antibodies were effective in neutralizing PCV2d virulence. The virus load in the liver of the immunized mice was significantly lower than that in the control group (p < 0.01), as was the virus load in the spleen and lungs of the immunized mice (p < 0.05). In addition, the serum levels of PCV2d-Cap-specific IgG in mice immunized with PCV2d-VLPs by intramuscular injection were significantly elevated compared to the control group (p < 0.05), and the viral load in all tissues was significantly lower in immunized mice (p < 0.05). In conclusion, the recombinant bacterium pHT43-Cap/B. subtilis can induce effective mucosal and humoral immunity in mice, PCV2d-VLPs can induce humoral immunity in mice, and both vaccines have good immunogenicity; these results provide a theoretical and material basis for the development of a new vaccine against PCV2d.

Functional and evolutionary analysis of host Synaptogyrin-2 in porcine circovirus type 2 susceptibility

Mammalian evolution has been influenced by viruses for millions of years, leaving signatures of adaptive evolution within genes encoding for viral interacting proteins. Synaptogyrin-2 (SYNGR2) is a transmembrane protein implicated in promoting bacterial and viral infections. A genome-wide association study of pigs experimentally infected with porcine circovirus type 2b (PCV2b) uncovered a missense mutation (SYNGR2 p.Arg63Cys) associated with viral load. In this study, CRISPR/Cas9-mediated gene editing of the porcine kidney 15 (PK15, wtSYNGR2+p.63Arg) cell line generated clones homozygous for the favorable SYNGR2 p.63Cys allele (emSYNGR2+p.63Cys). Infection of edited clones resulted in decreased PCV2 replication compared to wildtype PK15 (P<0.05), with consistent effects across genetically distinct PCV2b and PCV2d isolates. Sequence analyses of wild and domestic pigs (n>700) revealed the favorable SYNGR2 p.63Cys allele is unique to domestic pigs and more predominant in European than Asian breeds. A haplotype defined by the SYNGR2 p.63Cys allele was likely derived from an ancestral haplotype nearly fixed within European (0.977) but absent from Asian wild boar. We hypothesize that the SYNGR2 p.63Cys allele arose post-domestication in ancestral European swine. Decreased genetic diversity in homozygotes for the SYNGR2 p.63Cys allele compared to SYNGR2 p.63Arg, corroborates a rapid increase in frequency of SYGNR2 p.63Cys via positive selection. Signatures of adaptive evolution across mammalian species were also identified within SYNGR2 intraluminal loop domains, coinciding with the location of SYNGR2 p.Arg63Cys. Therefore, SYNGR2 may reflect a novel component of the host-virus evolutionary arms race across mammals with SYNGR2 p.Arg63Cys representing a species-specific example of putative adaptive evolution.

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.

PCV2 Uptake by Porcine Monocytes Is Strain-Dependent and Is Associated with Amino Acid Characteristics on the Capsid Surface

Porcine circovirus type 2 (PCV2) is associated with several economically important diseases that are described as PCV2-associated diseases (PCVADs). PCV2 is replicating in lymphoblasts, and PCV2 particles are taken up by monocytes without effective replication or complete degradation. Glycosaminoglycans (GAGs) have been demonstrated to be important receptors for PCV2 binding and entry in T-lymphocytes and continuous cell lines. The objective of this study was to determine whether differences exist in viral uptake and outcome among six PCV2 strains from different disease outbreaks in primary porcine monocytes: Stoon-1010 (PCV2a; PMWS), 1121 (PCV2a; abortion), 1147 (PCV2b; PDNS), 09V448 (PCV2d-1; PCVAD with high viral load in lymphoid tissues [PCVADhigh]), DE222-13 (PCV2d-2; PCVADhigh), and 19V245 (PCV2d-2; PCVADhigh). The uptake of PCV2 in peripheral blood monocytes was different among the PCV2 strains. A large number of PCV2 particles were found in the monocytes for Stoon-1010, DE222-13, and 19V245, while a low number was found for 1121, 1147, and 09V448. Competition with, and removal of GAGs on the cell surface, demonstrated an important role of chondroitin sulfate (CS) and dermatan sulfate (DS) in PCV2 entry into monocytes. The mapping of positively/negatively charged amino acids exposed on the surface of PCV2 capsids revealed that their number and distribution could have an impact on the binding of the capsids to GAGs, and the internalization into monocytes. Based on the distribution of positively charged amino acids on PCV2 capsids, phosphacan was hypothesized, and further demonstrated, as an effective candidate to mediate virus attachment to, and internalization in, monocytes. IMPORTANCE PCV2 is present on almost every pig farm in the world and is associated with a high number of diseases (PCV2-associated diseases [PCVADs]). It causes severe economic losses. Although vaccination is successfully applied in the field, there are still a lot of unanswered questions on the pathogenesis of PCV2 infections. This article reports on the uptake difference of various PCV2 strains by peripheral blood monocytes, and reveals the mechanism of the strong viral uptake ability of monocytes of Piétrain pigs. We further demonstrated that: (i) GAGs mediate the uptake of PCV2 particles by monocytes, (ii) positively charged three-wings-windmill-like amino acid patterns on the capsid outer surface are activating PCV2 uptake, and (iii) phosphacan is one of the potential candidates for PCV2 internalization. These results provide new insights into the mechanisms involved in PCVAD and contribute to a better understanding of PCV2 evolution. This may lead to the development of resistant pigs.

Isolation and genetic analysis of Porcine circovirus 2 in southern India evidences high circulation of Porcine circovirus 2d genotype

BACKGROUND

Porcine circovirus 2 is globally noted swine pathogen with multiple genotypes associated with vast clinical and subclinical outcomes. This study aimed to isolate and characterize PCV2 genotypes circulating in southern states of India.

METHODS AND RESULTS

A total of 434 field samples comprising of serum (n = 273), tissues (n = 109) and swabs (n = 52) collected from swine during 2019 to 2021 from southern states of India were screened for PCV2 by specific polymerase chain reaction (PCR) assay. Molecular prevalence of PCV2 in southern India was found to be 12.21% (n = 53). All the 53 PCV2 positive samples were further subjected to the PCR assay with designed primers targeting full length amplification of ORF2 gene of PCV2 for molecular characterization. Randomly 32 positive samples by full length PCV2-ORF2 gene PCR were sequenced for genotyping. Signature motif and phylogenetic analysis of 32 PCV2 sequences revealed 62.5% (n = 20) prevalence of PCV2d genotype followed by 21.8% (n = 7) of PCV2h or PCV2-IM1 and 15.6% (n = 5) of PCV2b genotypes. Twenty five PCR positive field samples were subjected for virus isolation in PK15 cells and characterized. Out of 25 samples processed 5 (20%) PCV2 isolates obtained in this study were confirmed by PCR and immune fluorescence assay. Molecular characterization of PK15 adapted five PCV2 isolates confirmed circulation of PCV2d, PCV2h and PCV2b genotypes in pigs under field conditions in southern India.

CONCLUSIONS

Isolation and molecular epidemiological study of PCV2 in southern states of India evidences high circulation of PCV2d genotypes in field conditions in comparison to other genotypes.

Survey of porcine circovirus type 2 and parvovirus in swine breeding herds of Colombia

Background

One of the consequences of the presentation of reproductive failures in sows is the economic losses in production because it alters the estimated values of the volume of production, decreasing the productivity of the farm. Porcine circovirosis by porcine circovirus 2 (PCV2) has been associated with reproductive disorders, and porcine parvovirus (PVP) is one of the pathological agents most related to the presentation of reproductive failure in pigs. In Colombia, there are reports of the presence of PCV2 through molecular techniques, and PVP through serum tests; however, in the department of Tolima, the prevalence of these two viruses is unknown.

Objective

In this study, the aim was to establish a report of the prevalence of viruses in five municipalities of the department of Tolima‐Colombia.

Methods

Blood samples from 150 breeding sows of five municipalities in Tolima, Colombia, were obtained. Quantitative polymerase chain reaction (qPCR) was used to detect the PCV2 and PVP virus in the blood samples followed by PCR and sequencing of 16 PCR products of the amplification of the cap gene of PCV2. A phylogenetic tree was constructed to identify the genotype of the PCV2 virus.

Results

The presence of PCV2d in sows was detected in 135 samples (90%), as well as the identification of PVP in 2.6% of the samples. In addition, the phylogenetic analysis showed that 16 isolates were the PCV2d2 genotype.

Conclusion

PCV2d and PVP were found to coinfect the females, and the identification of variability in regions in the predicted amino acid sequence of the PCV2 capsid may be associated with virus pathogenicity.

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

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 102.5 TCID50/0.1 ml, 100.7 TCID50/0.1 ml, and 101.5 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.

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.

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.

Genetic Diversity of Porcine Circovirus Types 2 and 3 in Wild Boar in Italy

Porcine circovirus (PCV) infection is associated with relevant economic impact to the pig industry. To date, four species of PCV (PCV1 to 4) have been identified but only PCV2 has been associated firmly with disease in pigs. The objective of this study was to assess the prevalence of PCV2 and PCV3 in the wild boar population in Basilicata region, Southern Italy, since this region is characterized by large forested and rural areas and the anthropic pressure is lower than in other Italian regions. Liver samples from 82 hunted wild boar were collected in 2021 from 3 different hunting districts. Sixty (73%, 95%CI: 63-82) samples tested positive for PCVs by quantitative PCR. In detail, 22 (27%, 95%CI: 18-37) were positive for PCV2, 58 (71%, 95%CI: 60-79) for PCV3, and 20 (24.4%, 95%CI 16-35) for both PCV2 and PCV3. On genome sequencing, different types and sub-types of PCV2 and PCV3 were identified, remarking a genetic diversity and hinting to a global circulation for the identified PCV strains. Overall, the high prevalence suggests that PCV2 and PCV3 infections are endemic in the wild boar population, posing risks for semi-intensive and free-range pig farming, typical of this region, due to contact with PCV-infected wild boar.

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.

The Oryx Antelope (Oryx gazella): An Unexpected Host for Porcine Circovirus-2 (PCV-2)

For several years after its discovery, Porcine circovirus 2 (PCV-2) represented a major threat to the swine industry through economic losses due to the associated clinical syndromes, decreased production performances in both symptomatic and asymptomatic animals and disease management costs. Widespread vaccination administration has largely reduced the impact of this infection and represents the most effective control measure. The efficacy of vaccination is threatened by the emergence of novel (or uncommon) PCV-2 genotypes. In addition to domestic pigs, PCV-2 has been detected in several other species, a fact which could have an impact on new variant emergence and maintenance. Considering this, the present study assessed the distribution of the minor PCV-2c genotype in non-Suidae ungulates in Namibia. Red hartebeests (Alcelaphus buselaphus caama) (n = 44), kudus (Tragelaphus strepsiceros) (n = 10) and oryxes (Oryx gazella) (n = 54), whose mediastinal lymph nodes were sampled after slaughtering during the period 2019–2021, were included in the study. Two oryxes (3.7%; 95% CI = 0.45–12.75%) were PCV-2-positive by PCR. Complete genome sequence was obtained for the two samples identifying them as PCV-2c genotype. The sequences were identical and shared a high percentage of identity (~99.9%) with those recently obtained from warthogs living in the same area. The present study confirms the presence of the PCV-2c genotype (previously considered extinct) in Namibian wild animal populations and demonstrates greater than expected PCV-2 host plasticity. Because of the role these niches can have in the maintenance and evolution of minor PCV-2 genotypes, more extensive and dedicated studies should be performed to prepare authorities to promptly react to potential emerging threats from these viruses.

Genotyping of Porcine Circovirus 2 (PCV-2) in Vaccinated Pigs Suffering from PCV-2-Systemic Disease between 2009 and 2020 in Spain

Vaccination against porcine circovirus 2 (PCV-2) is a common practice all over the world. Vaccines can prevent PCV-2-systemic disease (PCV-2-SD) outbreaks but not PCV-2 infection, which can be detectable in a percentage of vaccinated animals. Occasionally, PCV-2-SD is diagnosed in vaccinated farms. The objective of this study was to genotype the PCV-2 strains detected in vaccinated animals diagnosed with PCV-2-SD. Additionally, the evolution of the frequency of PCV-2 genotype detection at Spanish, European, and world levels was assessed. Fifty cases diagnosed as PCV-2-SD between 2009 and 2020 were included in this study. PCV-2 genotype was determined by sequencing the Cap gene region. Among them, only PCV-2b (23/50, 46%) and PCV-2d (27/50, 54%) genotypes were detected. Although the frequency of detection of these two genotypes was similar, their temporal distribution was different. Whereas most PCV-2b sequences (17/23, 74%) were detected between 2009 and 2012, PCV-2d sequences were obtained from 2013 to 2020. Indeed, a predominance of the PCV-2d genotype was observed from 2013 onwards, a trend also noticed at European and world levels. The results suggest that detection of particular genotypes in vaccinated animals probably reflects the general prevalence of the genotypes over time rather than genotype-specific vaccine-immunity escaping.

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.

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.

Evaluation of novel recombinant porcine circovirus type 2d (PCV2d) vaccine in pigs naturally infected with PCV2d

INTRODUCTION

The pathogenic porcine circovirus type 2 (PCV2) causes significant economic losses in pig production. Emergence of the PCV2d genotype has been linked with PCV2-associated disease (PCVAD) outbreaks. However, no study has been conducted efficacy of an experimental PCV2d-based subunit vaccine in pigs. Therefore, PCV2b- and PCV2d-based capsid (CP) proteins were generated using a baculovirus (Bac) expression system, and we evaluated the protective immune responses in a commercial pig farm where predominant PCV2d is circulating.

METHODS

Eighteen 3-week-old pigs with maternal antibodies were randomly divided into four groups, and were immunized with purified Bac-2dCP, mixed 1:1 ratio with purified Bac-2bCP and Bac-2dCP (Bac-mCP), a commercial PCV2a-based subunit vaccine (VAC) or phosphate-buffered saline (PBS) as controls.

RESULTS

The Bac-2dCP and Bac-mCP groups had significantly higher PCV2b- or PCV2d- specific IgG and neutralizing antibody without interference by maternal antibody compared to control group in pigs naturally infected with PCV2d. Interestingly, not only serum IL-4 level was significantly increased in the Bac-2dCP group, but also PCV2d viremia level was significantly reduced than the control group.

CONCLUSIONS

The recombinant Bac-2dCP subunit vaccine is a good candidate for the effective reduction against PCV2d infection.

Structural Perspectives of Beak and Feather Disease Virus and Porcine Circovirus Proteins

Circoviruses represent a rapidly expanding group of viruses that infect both vertebrate and invertebrate hosts. Members are responsible for diseases of veterinary and economic importance, including postweaning multisystemic wasting syndrome in pigs, and beak and feather disease (BFD) in birds. These viruses are associated with lymphoid depletion and immunosuppressive conditions in infected animals leading to systemic illness. Circoviruses are small nonenveloped DNA viruses containing a single-stranded circular genome, encoding two major proteins: the capsid-associated protein (Cap), comprising the entirety of the viral capsid, and the replication-associated protein (Rep). Cap is the only protein component of the virion and plays crucial roles throughout the virus replication cycle, including viral attachment, cell entry, genome uncoating, and packaging of newly formed viral particles. Rep mediates recognition of replication origin motifs in the viral genome sequence and is responsible for endonuclease activity enabling nicking of the circular DNA and initiation of rolling-circle replication (RCR). Porcine circovirus 2 (PCV2) was the first circovirus capsid structure to be solved at atomic resolution using X-ray crystallography. The structure revealed an assembly comprising 60 monomeric subunits to form virus-like particles. Each Cap monomer harbors a canonical viral jelly roll domain composed of two, four-stranded antiparallel β-sheets. Crystal structures of two distinct macromolecular assemblies from BFD virus Cap were also resolved at high resolution. In these structures, the exposure of the N-terminal arginine-rich motif, responsible for DNA binding and nuclear localization is reversed. Additional structural investigations have also elucidated a PCV2 type-specific neutralizing epitope, and interaction between the PCV2 capsid and polymers such as heparin. In this review, we provide a snapshot of the structural and functional aspects of circovirus proteins.

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.

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.

Epidemiology and evolutionary analysis of Torque teno sus virus

Single stranded (ss) DNA viruses are increasingly being discovered due to the ongoing development of modern technologies in exploring the virosphere. Characterized by high rates of recombination and nucleotide substitutions, it could be comparable to RNA virus ones. Torque teno sus virus (TTSuV) is a standard ssDNA virus with a high population diversity, whose evolution is still obscure, further, it is frequently found in co-infections with other viruses threatening the porcine industry and therefore share the same host and epidemiological context. Here, we implement and describe approach to integrate viral nucleotide sequence analysis, surveillance data, and a structural approach to examine the evolution of TTSuVs, we collected samples from pigs displaying respiratory signs in China and revealed a high prevalence of TTSuV1 and TTSuVk2, frequently as part of co-infections with porcine circoviruses (PCVs), especially in spleen and lung. In addition, thirty six strains sequenced were obtained to investigate their genetic diversity in China. The evolutionary history of TTSuVs were unveiled as following: At the nucleotide sequence level, TTSuVs ORF1 was confirmed to be a robust phylogenetic maker to study evolution comparably to full genomes. Additionally, extensive recombination discovered within TTSuVk2a (also 5 out of the 36 sequenced strains in this study revealed to be recombination). Then, pairwise distance, phylogenetic trees, and amino acid analysis confirmed TTSuVs species, and allowed to define circulating genotypes (TTSuV1a-1, 1a-2, 1b-1, 1b-2, 1b-3, and k2a-1, k2a-2, k2b). Selection analysis uncovered seven and six positive selected sites in TTSuV1 and TTSuVk2, respectively. At the protein structure level, mapping of sites onto the three-dimensional structure revealed that several positive selected sites locate into potential epitopes, which might related to the potential escaping from host immune response. Our result could assist future studies on swine ssDNA virus classification, surveillance and control.

A Methodology for Porcine Circovirus 2 (PCV-2) Quantification Based on Gold Nanoparticles

The aim of the current study is to introduce a methodology aimed at producing a biosensor that uses gold nanoparticles (AuNPs) to detect porcine circovirus 2 (PCV-2). This biosensor was based on AuNPs, which were modified with self-assembled monolayers (SAMs) and antibodies. The AuNPs’ surface and virus modification process applied to enable antibody binding was accompanied by localized surface plasmon resonance (LSPR), surface plasmon resonance (SPR), transmission electron microscopy (TEM), and energy-dispersive X-ray spectroscopy (EDX). Virus quantification was possible by the light absorption difference in the spectrum at concentrations of 10⁵, 10⁶, 10⁷, 10⁸, and 10⁹ DNA copies/mL PCV-2 in relation to quantitative PCR (qPCR), with an R² value >0.98. The visualization of colorimetric changes in the different PCV-2 concentrations was possible without the use of equipment. The biosensor production methodology presented reproducibility and specificity, as well as easy synthesis and low cost. An enhanced version of it may be used in the future to replace traditional tests such as PCR.

Strain-Dependent Porcine Circovirus Type 2 (PCV2) Entry and Replication in T-Lymphoblasts

Porcine circovirus type 2 (PCV2) is the etiological agent of PCV2-associated diseases (PCVAD). PCV2 targets lymphoblasts, and pigs suffering from PCVAD display lymphocyte depletion in lymphoid tissues. PCV2 infection of lymphoblasts has not been studied. Here, the replication cycle of PCV2 (abortion strain 1121 and PMWS strain Stoon1010) in T-lymphoblasts was examined. The expression of Rep and Cap were found for both viral strains, while progeny virus was detected for Stoon1010 but not for 1121. PCV2 attached to 11–26% (1121-Stoon1010) of the T-lymphoblasts while 2.6–12.7% of cells showed virus internalization. Chondroitin sulfate (CS) was present on 25% of T-lymphoblasts, and colocalized with PCV2 on 31–32% of the PCV2+ cells. Enzymatic removal of CS reduced PCV2 infection. PCV2 infection was decreased by chlorpromazine, cytochalasin D and Clostridium difficile toxin B for both viral strains and by amiloride for 1121 but not for Stoon1010. Inhibiting either endosome acidification or serine proteases strongly reduced PCV2 infection. Three-dimensional analysis of Cap structure demonstrated a better Cap-nucleic acid affinity for Stoon1010 than for 1121. Taken together, PCV2 binds to T-lymphoblasts partially via CS, enters via clathrin-mediated endocytosis, and disassembles under functions of a pH-drop and serine proteases. Strain Stoon1010 displayed an enhanced viral binding, a specific receptor-mediated endocytosis, an increased Cap-nucleic acid affinity, and a more productive infection in T-lymphoblasts than 1121 did, indicating an evolution from 1121 to Stoon1010.