Demonstration of nicking/joining activity at the origin of DNA replication associated with the rep and rep' proteins of porcine circovirus type 1

Genomoviruses in Liver Samples of Molossus molossus Bats

CRESS-DNA encompasses a broad spectrum of viruses documented across diverse organisms such as animals, plants, diatoms, fungi, and marine invertebrates. Despite this prevalence, the full extent of these viruses' impact on the environment and their respective hosts remains incompletely understood. Furthermore, an increasing number of viruses within this category lack detailed characterization. This investigation focuses on unveiling and characterizing viruses affiliated with the Genomoviridae family identified in liver samples from the bat Molossus molossus. Leveraging viral metagenomics, we identified seven sequences (MmGmV-PA) featuring a circular DNA genome housing two ORFs encoding replication-associated protein (Rep) and capsid protein (Cap). Predictions based on conserved domains typical of the Genomoviridae family were established. Phylogenetic analysis revealed the segregation of these sequences into two clades aligning with the genera Gemycirculavirus (MmGmV-06-PA and MmGmV-07-PA) and Gemykibivirus (MmGmV-01-PA, MmGmV-02-PA, MmGmV-03-PA, MmGmV-05-PA, and MmGmV-09-PA). At the species level, pairwise comparisons based on complete nucleotide sequences indicated the potential existence of three novel species. In summary, our study significantly contributes to an enhanced understanding of the diversity of Genomoviridae within bat samples, shedding light on previously undiscovered viral entities and their potential ecological implications.

From obscurity to urgency: a comprehensive analysis of the rising threat of duck circovirus

Duck circovirus (DuCV) is a small, nonenveloped, single-stranded DNA virus with immunosuppressive effects on ducks that leads to slow growth and elevated mortality following mixed infections. Its infection manifests as feather loss, slow growth, swelling of respiratory tissue, and damage to immune organs in ducks. Although single infections with DuCV do not cause noticeable clinical symptoms, its ability to compromise the immune system and facilitate infections caused by other pathogens poses a serious threat to duck farming. Given the prevalence of this disease and the increasing infection rates in recent years, which have resulted in significant economic losses in duck farming and related sectors, research and control of DuCV infection have become especially important. The aim of this review is to provide a summary of the current understanding of DuCV, serving as a reference for subsequent research and effective control of the virus. We focus mainly on the genetics and molecular biology, epidemiology, clinical symptoms, and pathology of DuCV. Additionally, topics such as the isolation and culture of the virus, vaccines and antiviral therapies, diagnostics, and preventative measures are discussed.

Characterization of a novel reporter system for beak and feather disease virus

Beak and feather disease virus (BFDV) belongs to the Circoviridae family, which has a relatively simple replication mechanism. As BFDV lacks a mature cell culture system, a novel mini-replicon system based on the reporter plasmid that contains the origin of replication, which can bind to the Rep protein expressed from another plasmid and thus trigger its replication and induce/increase luminescence was developed. The dual-luciferase assay was used in this system to measure replicative efficiency by comparing relative light units (RLU) of firefly luciferase. Linear relationships between the luciferase activity of the reporter plasmids with the BFDV origin of replication and the amounts of the Rep protein and vice versa were found, suggesting the mini-replicon system can be used to quantify viral replication. Moreover, the activities of reporter plasmids driven by mutated Rep proteins or the activities of reporter plasmids with mutations were significantly downregulated. The Rep and Cap promoter activities can be characterized using this luciferase reporter system. Notably, the RLU of the reporter plasmid was considerably inhibited in the presence of sodium orthovanadate (Na₃VO₄). When BFDV-infected birds were treated with Na₃VO₄, the viral loads of BFDV rapidly decreased. In conclusion, this mini-replicon reporter gene-based system provides a practical means to screen for anti-viral drug candidates.

Watson-Crick Base-Pairing Requirements for ssDNA Recognition and Processing in Replication-Initiating HUH Endonucleases

Replication-initiating HUH endonucleases (Reps) are sequence-specific nucleases that cleave and rejoin single-stranded DNA (ssDNA) during rolling-circle replication. These functions are mediated by covalent linkage of the Rep to its substrate post cleavage. Here, we describe the structures of the endonuclease domain from the Muscovy duck circovirus Rep in complex with its cognate ssDNA 10-mer with and without manganese in the active site. Structural and functional analyses demonstrate that divalent cations play both catalytic and structural roles in Reps by polarizing and positioning their substrate. Further structural comparisons highlight the importance of an intramolecular substrate Watson-Crick (WC) base pairing between the -4 and +1 positions. Subsequent kinetic and functional analyses demonstrate a functional dependency on WC base pairing between these positions regardless of the pair's identity (i.e., A·T, T·A, G·C, or C·G), highlighting a structural specificity for substrate interaction. Finally, considering how well WC swaps were tolerated in vitro, we sought to determine to what extent the canonical -4T·+1A pairing is conserved in circular Rep-encoding single-stranded DNA viruses and found evidence of noncanonical pairings in a minority of these genomes. Altogether, our data suggest that substrate intramolecular WC base pairing is a universal requirement for separation and reunion of ssDNA in Reps. IMPORTANCE Circular Rep-encoding single-stranded DNA (CRESS-DNA) viruses are a ubiquitous group of viruses that infect organisms across all domains of life. These viruses negatively impact both agriculture and human health. All members of this viral family employ a multifunctional nuclease (Rep) to initiate replication. Reps are structurally similar throughout this family, making them targets of interest for viral inhibition strategies. Here, we investigate the functional dependencies of the Rep protein from Muscovy duck circovirus for ssDNA interaction. We demonstrate that this Rep requires an intramolecular Watson-Crick base pairing for origin of replication (Ori) recognition and interaction. We show that noncognate base pair swaps are well tolerated, highlighting a local structural specificity over sequence specificity. Bioinformatic analysis found that the vast majority of CRESS-DNA Oris form base pairs in conserved positions, suggesting this pairing is a universal requirement for replication initiation in the CRESS-DNA virus family.

Diversity of CRESS DNA Viruses in Squamates Recapitulates Hosts Dietary and Environmental Sources of Exposure

Replication-associated protein (Rep)-encoding single-stranded (CRESS) DNA viruses comprise viruses with covalently closed, circular, single-stranded DNA (ssDNA) genomes, and are considered the smallest known autonomously replicating, capsid-encoding animal pathogens. CRESS DNA viruses (phylum Cressdnaviricota) encompass several viral families including Circoviridae. Circoviruses are classified into two genera, Circovirus and Cyclovirus, and they are known to cause fatal diseases in birds and pigs. Circoviruses have also been identified in human stools, blood, and cerebrospinal fluid (CSF), as well as in various wild and domestic vertebrates, including reptiles. The synanthropic presence of Squamata reptiles has increased in the last century due to the anthropic pressure, which has shifted forested animal behavior to an urban and peri-urban adaptation. In this paper, we explored the diversity of CRESS DNA viruses in Squamata reptiles from different Italian areas representative of the Mediterranean basin. CRESS DNA viruses were detected in 31.7% (33/104) of sampled lizards and geckoes. Different CRESS DNA viruses likely reflected dietary composition or environmental contamination and included avian-like (n = 3), dog (n = 4), bat-like (n = 1), goat-like (n = 1), rodent-like (n = 4), and insect-like (n = 2) viruses. Rep sequences of at least two types of human-associated cycloviruses (CyV) were identified consistently, regardless of geographic location, namely, TN9-like (n = 11) and TN12-like (n = 6). A third human-associated CyV, TN25-like, was detected in a single sample. The complete genome of human-like CyVs, of a rodent-like, insect-like, and of a bat-like virus were generated. Collectively, the results recapitulate hosts dietary and environmental sources of exposure and may suggest unexpected ecological niches for some CRESS DNA viruses.

IMPORTANCE CRESS DNA viruses are significant pathogens of birds and pigs and have been detected repeatedly in human samples (stools, serum, and cerebrospinal fluid), both from healthy individuals and from patients with neurological disease, eliciting in 2013 a risk assessment by the European Centre for Disease Prevention and Control (ECDC). Sequences of CRESS DNA viruses previously reported in humans (TN9, TN12, and TN25), and detected in different animal species (e.g., birds, dogs, and bats) were herein detected in fecal samples of synanthropic squamates (geckos and lizards). The complete genome sequence of six viruses was generated. This study extends the information on the genetic diversity and ecology of CRESS DNA viruses. Because geckos and lizards are synanthropic animals, a role in sustaining CRESS DNA virus circulation and increasing viral pressure in the environment is postulated.

Detection and Molecular Characterization of a Novel Species of Circovirus in a Tawny Owl (Strix aluco) in Southern Italy

Simple Summary

The genus Circovirus groups some of the smallest viruses capable of autonomous replication, including some notable swine and avian pathogens. Among domestic and wild birds, circoviruses are often associated with immunosuppression and integumental disorders, but, despite their relevance, nothing is known about their circulation in birds of prey. By conducting molecular analyses on samples from birds of prey recovered by a wildlife rescue centre in Italy, we identified a new viral species in the spleen of a tawny owl (Strix aluco). However, there is contrasting evidence regarding its definitive host. On one hand, the virus was discovered to be phylogenetically closer to mammalian rather than avian circoviruses, which allows speculations on its host being a micromammal preyed by the tawny owl, rather than the bird itself. On the other hand, its detection in the spleen, a lymphoid organ in which other avian circoviruses are often detected, supports the tawny owl being its actual host, perhaps following a spillover event associated with predation. Adding to the growing number of circoviruses found in recent years in a diverse range of hosts, this discovery represents another step forward in the characterization of this genus of remarkable veterinary importance.

Abstract

Thanks to recent developments in molecular methods, many new species have been discovered within the genus Circovirus, which comprises viruses of veterinary relevance found in a broad range of hosts. In particular, several circoviruses are known to infect birds, often causing immunosuppression and feathering disorders. Nonetheless, nothing is known about their circulation in birds of prey. In this study, samples from 61 birds of prey representing ten different species, recovered by a wildlife rescue centre in Southern Italy, were taken at necropsy and analysed by PCR with pan-Circovirus primers. Only one sample, collected from a tawny owl (Strix aluco), tested positive. Its genome, sequenced by primer walking, displays the typical features of circoviruses. Based on demarcation criteria, the detected strain qualifies as a novel species, which was named “tawny owl-associated circovirus” (ToCV). Phylogenetically, ToCV clustered with mammalian rather than avian circoviruses, and its closeness to a rodent circovirus suggests that its host may have been a micromammal eaten by the tawny owl. On the other hand, its detection in the spleen fits with the tropism of other avian circoviruses. Little can be therefore said on its biology and pathogenicity, and further efforts are needed to better characterize its epidemiology.

Mitochondrial Localization Signal of Porcine Circovirus Type 2 Capsid Protein Plays a Critical Role in Cap-Induced Apoptosis

Porcine circovirus 2 (PCV2), considered one of the most globally important porcine pathogens, causes postweaning multisystemic wasting syndrome (PMWS). This virus is localized in the mitochondria in pigs with PMWS. Here, we identified, for the first time, a mitochondrial localization signal (MLS) in the PCV2 capsid protein (Cap) at the N-terminus. PK-15 cells showed colocalization of the MLS-EGFP fusion protein with mitochondria. Since the PCV2 Cap also contained a nuclear localization signal (NLS) that mediated entry into the nucleus, we inferred that the subcellular localization of the PCV2 Cap is inherently complex and dependent on the viral life cycle. Furthermore, we also determined that deletion of the MLS attenuated Cap-induced apoptosis. More importantly, the MLS was essential for PCV2 replication, as absence of the MLS resulted in failure of virus rescue from cells infected with infectious clone DNA. In conclusion, the MLS of the PCV2 Cap plays critical roles in Cap-induced apoptosis, and MLS deletion of Cap is lethal for virus rescue.

Novel Cyclovirus Species in Dogs with Hemorrhagic Gastroenteritis

Nested PCRs with circovirus/cyclovirus pan-rep (replicase gene) primers detected eukaryotic circular Rep-encoding single-stranded DNA (CRESS DNA) viruses in three (samples CN9E, CN16E and CN34) of 18 canine parvovirus-2-positive fecal samples from household dogs with hemorrhagic gastroenteritis on the Caribbean island of Nevis. The complete genomes of CRESS DNA virus CN9E, CN16E and CN34 were determined by inverse nested PCRs. Based on (i) genome organization, (ii) location of the putative origin of replication, (iii) pairwise genome-wide sequence identities, (iv) the presence of conserved motifs in the putative replication-associated protein (Rep) and the arginine-rich region in the amino terminus of the putative capsid protein (Cp) and (v) a phylogenetic analysis, CN9E, CN16E and CN34 were classified as cycloviruses. Canine-associated cycloviruses CN16E and CN34 were closely related to each other and shared low genome-wide nucleotide (59.642–59.704%), deduced Rep (35.018–35.379%) and Cp (26.601%) amino acid sequence identities with CN9E. All the three canine-associated cycloviruses shared < 80% genome-wide pairwise nucleotide sequence identities with cycloviruses from other animals/environmental samples, constituting two novel species (CN9E and CN16E/34) within the genus Cyclovirus. Considering the feeding habits of dogs, we could not determine whether the cycloviruses were of dietary origin or infected the host. Interestingly, the CN9E putative Rep-encoding open reading frame was found to use the invertebrate mitochondrial genetic code with an alternative initiation codon (ATA) for translation, corroborating the hypothesis that cycloviruses are actually arthropod-infecting viruses. To our knowledge, this is the first report on the detection and complete genome analysis of cycloviruses from domestic dogs.

Redondovirus Diversity and Evolution on Global, Individual, and Molecular Scales

Redondoviridae is a newly established family of circular Rep-encoding single-stranded (CRESS) DNA viruses found in the human ororespiratory tract. Redondoviruses were previously found in ∼15% of respiratory specimens from U.S. urban subjects; levels were elevated in individuals with periodontitis or critical illness. Here, we report higher redondovirus prevalence in saliva samples: four rural African populations showed 61 to 82% prevalence, and an urban U.S. population showed 32% prevalence. Longitudinal, limiting-dilution single-genome sequencing revealed diverse strains of both redondovirus species (Brisavirus and Vientovirus) in single individuals, persistence over time, and evidence of intergenomic recombination. Computational analysis of viral genomes identified a recombination hot spot associated with a conserved potential DNA stem-loop structure. To assess the possible role of this site in recombination, we carried out in vitro studies which showed that this potential stem-loop was cleaved by the virus-encoded Rep protein. In addition, in reconstructed reactions, a Rep-DNA covalent intermediate was shown to mediate DNA strand transfer at this site. Thus, redondoviruses are highly prevalent in humans, found in individuals on multiple continents, heterogeneous even within individuals and encode a Rep protein implicated in facilitating recombination. IMPORTANCE Redondoviridae is a recently established family of DNA viruses predominantly found in the human respiratory tract and associated with multiple clinical conditions. In this study, we found high redondovirus prevalence in saliva from urban North American individuals and nonindustrialized African populations in Botswana, Cameroon, Ethiopia, and Tanzania. Individuals on both continents harbored both known redondovirus species. Global prevalence of both species suggests that redondoviruses have long been associated with humans but have remained undetected until recently due to their divergent genomes. By sequencing single redondovirus genomes in longitudinally sampled humans, we found that redondoviruses persisted over time within subjects and likely evolve by recombination. The Rep protein encoded by redondoviruses catalyzes multiple reactions in vitro, consistent with a role in mediating DNA replication and recombination. In summary, we identify high redondovirus prevalence in humans across multiple continents, longitudinal heterogeneity and persistence, and potential mechanisms of redondovirus evolution by recombination.

Detection and Complete Genome Analysis of Circoviruses and Cycloviruses in the Small Indian Mongoose (Urva auropunctata): Identification of Novel Species

Fecal samples from 76 of 83 apparently healthy small Indian mongooses (Urva auropunctata) were PCR positive with circovirus/cyclovirus pan-rep (replicase gene) primers. In this case, 30 samples yielded high quality partial rep sequences (~400 bp), of which 26 sequences shared maximum homology with cycloviruses from an arthropod, bats, humans or a sheep. Three sequences exhibited maximum identities with a bat circovirus, whilst a single sequence could not be assigned to either genus. Using inverse nested PCRs, the complete genomes of mongoose associated circoviruses (Mon-1, -29 and -66) and cycloviruses (Mon-20, -24, -32, -58, -60 and -62) were determined. Mon-1, -20, -24, -29, -32 and -66 shared <80% maximum genome-wide pairwise nucleotide sequence identities with circoviruses/cycloviruses from other animals/sources, and were assigned to novel circovirus, or cyclovirus species. Mon-58, -60 and -62 shared maximum pairwise identities of 79.90–80.20% with human and bat cycloviruses, which were borderline to the cut-off identity value for assigning novel cycloviral species. Despite high genetic diversity, the mongoose associated circoviruses/cycloviruses retained the various features that are conserved among members of the family Circoviridae, such as presence of the putative origin of replication (ori) in the 5′-intergenic region, conserved motifs in the putative replication-associated protein and an arginine rich region in the amino terminus of the putative capsid protein. Since only fecal samples were tested, and mongooses are polyphagous predators, we could not determine whether the mongoose associated circoviruses/cycloviruses were of dietary origin, or actually infected the host. To our knowledge, this is the first report on detection and complete genome analysis of circoviruses/cycloviruses in the small Indian mongoose, warranting further studies in other species of mongooses.

StemLoop-Finder: a Tool for the Detection of DNA Hairpins with Conserved Motifs

Nucleic acid secondary structures play important roles in regulating biological processes. StemLoop-Finder is a computational tool to recognize and annotate conserved structural motifs in large data sets. The program is optimized for the detection of stem-loop structures that may serve as origins of replication in circular replication-associated protein (Rep)-encoding single-stranded (CRESS) DNA viruses.

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.

C1QBP inhibits proliferation of porcine circovirus type 2 by restricting nuclear import of the capsid protein

Complement component 1 Q subcomponent-binding protein (C1QBP) has been shown to interact with the porcine circovirus type 2 (PCV2) Cap protein. Here, using yeast two-hybrid (Y2H) and co-immunoprecipitation assays, as well as laser confocal microscopy, the interaction between C1QBP and Cap was confirmed. Furthermore, overexpression of C1QBP in cells altered the intracellular location of Cap, which was observed using confocal microscopy and verified by detection of Cap in nuclear protein extracts in a Western blot assay. By inhibiting nuclear transport of Cap, overexpression of C1QBP downregulated PCV2 proliferation in PK-15 cells, as determined by quantitative polymerase chain reaction (qPCR). As C1QBP plays a similar role in a fusion of green fluorescent protein (GFP) with the Cap nuclear localisation signal (NLS) sequence, (CapNLS-GFP), we propose that the target site for C1QBP in Cap is possibly located in the NLS region. Considering all the results together, this study demonstrated that C1QBP interacts with the Cap NLS region, resulting in changes in the intracellular localisation of the Cap protein. We confirmed that overexpression of C1QBP inhibits the proliferation of PCV2, and this is possibly related to the function of C1QBP in controlling nuclear transport of Cap.

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.

Unveiling Crucivirus Diversity by Mining Metagenomic Data

Viruses are the most abundant biological entities on Earth. In addition to their impact on animal and plant health, viruses have important roles in ecosystem dynamics as well as in the evolution of the biosphere. Circular Rep-encoding single-stranded (CRESS) DNA viruses are ubiquitous in nature, many are agriculturally important, and they appear to have multiple origins from prokaryotic plasmids. A subset of CRESS-DNA viruses, the cruciviruses, have homologues of capsid proteins encoded by RNA viruses. The genetic structure of cruciviruses attests to the transfer of capsid genes between disparate groups of viruses. However, the evolutionary history of cruciviruses is still unclear. By collecting and analyzing cruciviral sequence data, we provide a deeper insight into the evolutionary intricacies of cruciviruses. Our results reveal an unexpected diversity of this virus group, with frequent recombination as an important determinant of variability.

The discovery of cruciviruses revealed the most explicit example of a common protein homologue between DNA and RNA viruses to date. Cruciviruses are a novel group of circular Rep-encoding single-stranded DNA (ssDNA) (CRESS-DNA) viruses that encode capsid proteins that are most closely related to those encoded by RNA viruses in the family Tombusviridae. The apparent chimeric nature of the two core proteins encoded by crucivirus genomes suggests horizontal gene transfer of capsid genes between DNA and RNA viruses. Here, we identified and characterized 451 new crucivirus genomes and 10 capsid-encoding circular genetic elements through de novo assembly and mining of metagenomic data. These genomes are highly diverse, as demonstrated by sequence comparisons and phylogenetic analysis of subsets of the protein sequences they encode. Most of the variation is reflected in the replication-associated protein (Rep) sequences, and much of the sequence diversity appears to be due to recombination. Our results suggest that recombination tends to occur more frequently among groups of cruciviruses with relatively similar capsid proteins and that the exchange of Rep protein domains between cruciviruses is rarer than intergenic recombination. Additionally, we suggest members of the stramenopiles/alveolates/Rhizaria supergroup as possible crucivirus hosts. Altogether, we provide a comprehensive and descriptive characterization of cruciviruses.

Nuclear transporter karyopherin subunit alpha 3 levels modulate Porcine circovirus type 2 replication in PK-15 cells

Entering the nucleus is important for Porcine circovirus type 2 (PCV2) replication. Karyopherins (KPNs) mediate the nuclear import of many cytoplasmic proteins. Our previous study showed that KPNA3 is involved in interferon production during PCV2 infection induced by Poly I:C and ISD (Interferon stimulatory DNA). However, it remains unclear whether PCV2 replication is associated with KPNA3. In the present study, knockdown of KPNA3 promoted the replication of PCV2, whereas overexpression of KPNA3 inhibited PCV2 replication in PK-15 cells. Furthermore, KPNA3 knockdown inhibited IRF3 and reduced the expression of antiviral genes including IFN-β, ISG54, Mx1 and ISG56, while the opposite results were obtained after KPNA3 overexpression. KPNA3 knockdown also promoted p65 nuclear translocation and increased the mRNA expression of IL-10 and IL-1β. These results suggested that KPNA3 facilitates IRF3 entry into the nucleus and the production of an antiviral response, resulting in PCV2 replication inhibition and blockage of NF-κB signal activation.

Click-Type Protein-DNA Conjugation for Mn2+ Imaging in Living Cells

A click-type protein-DNA conjugation, named as MnDDC (Mn²⁺-activated DCV-DNA conjunction), is presented, where DCV (rep protein of duck circovirus) and its target DNA work as the modular blocks to rapidly and effectively generate Mn²⁺-dependent and site-specific protein-DNA linkage. On the basis of MnDCC, a fluorescent Mn²⁺ biosensor composed of DCV and a molecular beacon, was developed for rapid sensing of Mn²⁺ within 2 min with nanomolar sensitivity. Using the proposed biosensor, not only analysis of Mn²⁺ in real samples (e.g., serum and food), but also wash-free fluorescent imaging of Mn²⁺ in extracellular environment and cytoplasm have been achieved. Moreover, the MnDDC-based sensor was proved to be a powerful tool for visualization of Mn²⁺ during exploration of the associated cytotoxicity in living neural cells, which is helpful to reveal the cellular responses toward the disordered homeostasis of Mn²⁺ in both extracellular and intracellular microenvironments.

Eukaryotic Circular Rep-Encoding Single-Stranded DNA (CRESS DNA) Viruses: Ubiquitous Viruses With Small Genomes and a Diverse Host Range

While single-stranded DNA (ssDNA) was once thought to be a relatively rare genomic architecture for viruses, modern metagenomics sequencing has revealed circular ssDNA viruses in most environments and in association with diverse hosts. In particular, circular ssDNA viruses encoding a homologous replication-associated protein (Rep) have been identified in the majority of eukaryotic supergroups, generating interest in the ecological effects and evolutionary history of circular Rep-encoding ssDNA viruses (CRESS DNA) viruses. This review surveys the explosion of sequence diversity and expansion of eukaryotic CRESS DNA taxonomic groups over the last decade, highlights similarities between the well-studied geminiviruses and circoviruses with newly identified groups known only through their genome sequences, discusses the ecology and evolution of eukaryotic CRESS DNA viruses, and speculates on future research horizons.

Crystal Structure of the Dimerized N Terminus of Porcine Circovirus Type 2 Replicase Protein Reveals a Novel Antiviral Interface

Two replicase (Rep) proteins, Rep and Rep', are encoded by porcine circovirus (PCV) ORF1; Rep is a full ORF1 transcript, and Rep' is a truncated transcript generated by splicing. These two proteins are crucial for the rolling-circle replication (RCR) of PCV. The N-terminal sequences of Rep and Rep' are identical and interact to form homo- or heterodimers. The three types of dimers perform different functions during replication. A structural examination of the interfacing termini has not been performed. In this study, a crystal structure of dimerized Rep protein N termini was resolved at 2.7 Å. The dimerized protein was maintained by nine intermolecular hydrogen bonds and 15 pairs of hydrophobic interactions. The amino acid residue Ile37 participates in 11 of the hydrophobic interactions, mostly with its side chain. To find the predominant sites for protein dimerization and virus replication, a series of mutant proteins and virus replicons were generated by alanine substitution. Of all the single amino acid substitutions, the mutation at Ile37 showed the greatest effect on protein dimerization and virus replication. A double mutation at Leu35 and Ile37 almost eliminated protein dimerization and had the greatest negative effect on virus replication. These studies demonstrate that Leu35 and Ile37 are the most important residues for protein dimerization and are crucial for virus replication. Our results also show that PCV replication can be decreased by disrupting the dimerization of Rep or Rep' at the N terminus, suggesting that the structural interface responsible for dimerization offers a promising antiviral target.IMPORTANCE Porcine circovirus type 2 (PCV2) is one of the most economically damaging pathogens affecting the swine industry. Although vaccines have been available for more than 10 years, the virus still remains prevalent. More effective strategies for disease prevention are clearly required. The Rep and Rep' proteins of the virus have identical N-terminal regions that interact with each other, allowing the formation of homo- or heterodimers. The heterodimer has crucial functions during different stages of viral replication. Here, we resolved the crystal structure of the Rep (Rep') dimerization domain. The individual residues involved in the intermolecular interaction were visualized in the protein structure, and several interactions were verified by mutant analysis. Our studies show that disrupting the interaction decreases viral replication, thus revealing a new target for the design of antiviral agents.

ICTV Virus Taxonomy Profile: Circoviridae

The family Circoviridae comprises viruses with small, circular, single-stranded DNA (ssDNA) genomes, including the smallest known animal viruses. Members of this family are classified into two genera, Circovirus and Cyclovirus, which are distinguished by the position of the origin of replication relative to the coding regions and the length of the intergenic regions. Within each genus, the species demarcation threshold is 80 % genome-wide nucleotide sequence identity. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Circoviridae, which is available at www.ictv.global/report/circoviridae.

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

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

Revisiting the taxonomy of the family Circoviridae: establishment of the genus Cyclovirus and removal of the genus Gyrovirus

The family Circoviridae contains viruses with covalently closed, circular, single-stranded DNA (ssDNA) genomes, including the smallest known autonomously replicating, capsid-encoding animal pathogens. Members of this family are known to cause fatal diseases in birds and pigs and have been historically classified in one of two genera: Circovirus, which contains avian and porcine pathogens, and Gyrovirus, which includes a single species (Chicken anemia virus). However, over the course of the past six years, viral metagenomic approaches as well as degenerate PCR detection in unconventional hosts and environmental samples have elucidated a broader host range, including fish, a diversity of mammals, and invertebrates, for members of the family Circoviridae. Notably, these methods have uncovered a distinct group of viruses that are closely related to members of the genus Circovirus and comprise a new genus, Cyclovirus. The discovery of new viruses and a re-evaluation of genomic features that characterize members of the Circoviridae prompted a revision of the classification criteria used for this family of animal viruses. Here we provide details on an updated Circoviridae taxonomy ratified by the International Committee on the Taxonomy of Viruses in 2016, which establishes the genus Cyclovirus and reassigns the genus Gyrovirus to the family Anelloviridae, a separate lineage of animal viruses that also contains circular ssDNA genomes. In addition, we provide a new species demarcation threshold of 80% genome-wide pairwise identity for members of the family Circoviridae, based on pairwise identity distribution analysis, and list guidelines to distinguish between members of this family and other eukaryotic viruses with circular, ssDNA genomes.

Sequence-based taxonomic framework for the classification of uncultured single-stranded DNA viruses of the family Genomoviridae

With the advent of metagenomics approaches, a large diversity of known and unknown viruses has been identified in various types of environmental, plant, and animal samples. One such widespread virus group is the recently established family Genomoviridae which includes viruses with small (∼2-2.4 kb), circular ssDNA genomes encoding rolling-circle replication initiation proteins (Rep) and unique capsid proteins. Here, we propose a sequence-based taxonomic framework for classification of 121 new virus genomes within this family. Genomoviruses display ∼47% sequence diversity, which is very similar to that within the well-established and extensively studied family Geminiviridae (46% diversity). Based on our analysis, we establish a 78% genome-wide pairwise identity as a species demarcation threshold. Furthermore, using a Rep sequence phylogeny-based analysis coupled with the current knowledge on the classification of geminiviruses, we establish nine genera within the Genomoviridae family. These are Gemycircularvirus (n = 73), Gemyduguivirus (n = 1), Gemygorvirus (n = 9), Gemykibivirus (n = 29), Gemykolovirus (n = 3), Gemykrogvirus (n = 3), Gemykroznavirus (n = 1), Gemytondvirus (n = 1), Gemyvongvirus (n = 1). The presented taxonomic framework offers rational classification of genomoviruses based on the sequence information alone and sets an example for future classification of other groups of uncultured viruses discovered using metagenomics approaches.

Diverse circular replication-associated protein encoding viruses circulating in invertebrates within a lake ecosystem

Over the last five years next-generation sequencing has become a cost effective and efficient method for identifying known and unknown microorganisms. Access to this technique has dramatically changed the field of virology, enabling a wide range of environmental viral metagenome studies to be undertaken of organisms and environmental samples from polar to tropical regions. These studies have led to the discovery of hundreds of highly divergent single stranded DNA (ssDNA) virus-like sequences encoding replication-associated proteins. Yet, few studies have explored how viruses might be shared in an ecosystem through feeding relationships. Here we identify 169 circular molecules (160 CRESS DNA molecules, nine circular molecules) recovered from a New Zealand freshwater lake, that we have tentatively classified into 51 putatively novel species and five previously described species (DflaCV-3, -5, -6, -8, -10). The CRESS DNA viruses identified in this study were recovered from molluscs (Echyridella menzeisii, Musculium novaezelandiae, Potamopyrgus antipodarum and Physella acuta) and insect larvae (Procordulia grayi, Xanthocnemis zealandica, and Chironomus zealandicus) collected from Lake Sarah, as well as from the lake water and benthic sediments. Extensive diversity was observed across most CRESS DNA molecules recovered. The putative capsid protein of one viral species was found to be most similar to those of members of the Tombusviridae family, thus expanding the number of known RNA-DNA hybrid viruses in nature. We noted a strong association between the CRESS DNA viruses and circular molecules identified in the water and browser organisms (C. zealandicus, P. antipodarum and P. acuta), and between water sediments and undefended prey species (C. zealandicus). However, we were unable to find any significant correlation of viral assemblages to the potential feeding relationships of the host aquatic invertebrates.

T-cell reprogramming through targeted CD4-coreceptor and T-cell receptor expression on maturing thymocytes by latent Circoviridae family member porcine circovirus type 2 cell infections in the thymus

Although porcine circovirus type 2 (PCV2)-associated diseases have been evaluated for known immune evasion strategies, the pathogenicity of these viruses remained concealed for decades. Surprisingly, the same viruses that cause panzootics in livestock are widespread in young, unaffected animals. Recently, evidence has emerged that circovirus-like viruses are also linked to complex diseases in humans, including children. We detected PCV2 genome-carrying cells in fetal pig thymi. To elucidate virus pathogenicity, we developed a new pig infection model by in vivo transfection of recombinant PCV2 and the immunosuppressant cofactor cyclosporine A. Using flow cytometry, immunofluorescence and fluorescence in situ hybridization, we found evidence that PCV2 dictates positive and negative selection of maturing T cells in the thymus. We show for the first time that PCV2-infected cells reside at the corticomedullary junction of the thymus. In diseased animals, we found polyclonal deletion of single positive cells (SPs) that may result from a loss of major histocompatibility complex class-II expression at the corticomedullary junction. The percentage of PCV2 antigen-presenting cells correlated with the degree of viremia and, in turn, the severity of the defect in thymocyte maturation. Moreover, the reversed T-cell receptor/CD4-coreceptor expression dichotomy on thymocytes at the CD4⁺CD8^interm and CD4SP cell stage is viremia-dependent, resulting in a specific hypo-responsiveness of T-helper cells. We compare our results with the only other better-studied member of Circoviridae, chicken anemia virus. Our data show that PCV2 infection leads to thymocyte selection dysregulation, adding a valuable dimension to our understanding of virus pathogenicity.

Geminivirus protein structure and function

Geminiviruses are a family of plant viruses that cause economically important plant diseases worldwide. These viruses have circular single-stranded DNA genomes and four to eight genes that are expressed from both strands of the double-stranded DNA replicative intermediate. The transcription of these genes occurs under the control of two bidirectional promoters and one monodirectional promoter. The viral proteins function to facilitate virus replication, virus movement, the assembly of virus-specific nucleoprotein particles, vector transmission and to counteract plant host defence responses. Recent research findings have provided new insights into the structure and function of these proteins and have identified numerous host interacting partners. Most of the viral proteins have been shown to be multifunctional, participating in multiple events during the infection cycle and have, indeed, evolved coordinated interactions with host proteins to ensure a successful infection. Here, an up-to-date review of viral protein structure and function is presented, and some areas requiring further research are identified.

Attenuation of porcine circovirus type-2b by replacement with the Rep gene of porcine circovirus type-1

Porcine circovirus type-2 (PCV2) is the primary causative agent of porcine circovirus-associated diseases and has 4 main ORFs, ORF1 (Rep gene), ORF2 (Cap gene), ORF3 within ORF1, and ORF4, which is overlapped with ORF3, and 1 origin (Ori) of replication located between ORF1 and ORF2. The chimeric PCV1-2, containing the PCV2 capsid, PCV1 rep, and Ori genes, is attenuated in pigs. In order to verify the role of the Rep gene or Ori in the virulence of PCV2, 3 chimeric viruses [PCV2b-Ori1 (PCV1 Ori gene cloned into the backbone of PCV2b), PCV2b-rep1 (PCV1 Rep gene cloned into the backbone of PCV2b), and PCV2b-rep1-Ori1 (PCV1 Rep and Ori genes cloned into the backbone of PCV2b)] and 2 wild-type recombinant PCV2b and PCV1 were constructed and identified. The experimental results in piglets showed that clinical symptoms, viremia, viral load, lesions in lymphoid and lung tissues, and IL-10 and TNF-α expression levels in PBMCs in the PCV2b-rep1-Ori1 and PCV2b-rep1 groups were significantly decreased, compared to PCV2-infected piglets. Meanwhile, histological lesions of lymphoid and lung tissues, viral loads in lymphoid tissues, viremia, and TNF-α expression in PBMCs were not significantly different between groups PCV2b-Ori1 and PCV2b, suggesting that the Rep gene (ORF1) likely contributes to viral pathogenicity in vivo.

Replicative intermediates of porcine circovirus in animal tissue cultured cells or in bacteria undergoing copy-release replication

Porcine circovirus (PCV) has been assumed to replicate its genome via the rolling-circle replication (RCR) mechanism because it encodes a Rep protein that contains several amino acid motifs commonly found in other RCR biological systems. Two proteins, Rep and Rep', are essential for PCV DNA replication in mammalian cells. In this work, replicative intermediates of PCV-infected porcine kidney (PK15) cells or copy-release of PCV genomes from a head-to-tail tandem construct (without Rep') in Escherichia coli were examined. In PK15 cells, replicative intermediates consistent with complementary-strand replication which converts single-stranded circular genome to double-stranded supercoiled DNA and RCR which generates single-stranded plus strand progeny genome were observed. To a lesser extent, intermediates suggestive of recombination-dependent replication were also detected. In Escherichia coli, copy release of the single-stranded circular PCV genome with conversion to a supercoiled molecule by complementary-strand synthesis was observed. However, replicative intermediates indicative of RCR were not detected.

Tracking viral evolution during a disease outbreak: the rapid and complete selective sweep of a circovirus in the endangered Echo parakeet

Circoviruses are among the smallest and simplest of all viruses, but they are relatively poorly characterized. Here, we intensively sampled two sympatric parrot populations from Mauritius over a period of 11 years and screened for the circovirus Beak and feather disease virus (BFDV). During the sampling period, a severe outbreak of psittacine beak and feather disease, which is caused by BFDV, occurred in Echo parakeets. Consequently, this data set presents an ideal system for studying the evolution of a pathogen in a natural population and to understand the adaptive changes that cause outbreaks. Unexpectedly, we discovered that the outbreak was most likely caused by changes in functionally important regions of the normally conserved replication-associated protein gene and not the immunogenic capsid. Moreover, these mutations were completely fixed in the Echo parakeet host population very shortly after the outbreak. Several capsid alleles were linked to the replication-associated protein outbreak allele, suggesting that whereas the key changes occurred in the latter, the scope of the outbreak and the selective sweep may have been influenced by positive selection in the capsid. We found evidence for viral transmission between the two host populations though evidence for the invasive species as the source of the outbreak was equivocal. Finally, the high evolutionary rate that we estimated shows how rapidly new variation can arise in BFDV and is consistent with recent results from other small single-stranded DNA viruses.

Porcine circovirus: transcription and DNA replication

This review summarizes the molecular studies pertaining to porcine circovirus (PCV) transcription and DNA replication. The genome of PCV is circular, single-stranded DNA and contains 1759-1768 nucleotides. Both the genome-strand (packaged in the virus particle) and the complementary-strand (synthesized in the new host) encode viral proteins. Among a multitude of RNAs synthesized by alternate splicing, only rep and rep' are essential for virus DNA replication via the rolling-circle replication (RCR) mechanism. In contrast to other RCR biological systems which utilize only one multi-functional protein, Rep, to replicate their respective genomes, PCV requires two proteins, Rep and Rep'. During DNA synthesis, the PCV origin of DNA replication (Ori), which contains a pair of inverted repeats (palindrome), exists in a destabilized four-stranded configuration (the melting-pot model) and permits both the palindromic-strand and the complementary-strand to serve as templates simultaneously for initiation and termination. Inherent in the "melting-pot" model is the template-strand-switching mechanism. This mechanism is the basis for the "correction or conversion" of any mutated nucleotide sequences engineered into either arm of the palindrome and the incorporation of "illegitimate recombination" (addition or deletion of nucleotides) events that are commonly observed at the Ori of other RCR biological systems during DNA replication.

Efficacy and future prospects of commercially available and experimental vaccines against porcine circovirus type 2 (PCV2)

Porcine circovirus type 2 (PCV2) is the causative agent of an economically significant collection of disease syndromes in pigs, now known as porcine circovirus associated diseases (PCVADs) in the United States or porcine circovirus diseases (PCVDs) in Europe. Inactivated and subunit vaccines based on PCV2a genotype are commercially available and have been shown to be effective at decreasing mortality and increasing growth parameters in commercial swine herds. Since 2003, there has been a drastic global shift in the predominant prevalence of PCV2b genotype in swine populations, concurrently in most but not all cases with increased severity of clinical disease. Although the current commercial vaccines based on PCV2a do confer cross-protection against PCV2b, novel experimental vaccines based on PCV2b genotype such as modified live-attenuated vaccines are being developed and may provide a superior protection and reduce vaccine costs. In this review, we discuss the current understanding of the impact of PCV2 infection on the host immune response, review the efficacy of the currently available commercial PCV2 vaccines in experimental and field conditions, and provide insight into novel experimental approaches that are useful in the development of next generation vaccines against PCV2.

Coreplication of the major genotype group members of porcine circovirus type 2 as a prerequisite to coevolution may explain the variable disease manifestations

A member of the family Circoviridae, porcine circovirus type 2 (PCV2), is associated with postweaning multisystemic wasting syndrome (PMWS), a recent emerging disease worldwide. PCV2 is also found in clinically asymptomatic animals. This paradoxical finding makes the syndrome etiology challenging. We developed new assays to study PCV2 with links to syndrome etiology. For analysis, we used PCV2-infected tissues from subclinically infected and diseased piglets. We compared antigen- and PCV2 DNA-derived signals for tissue localization and intensity. Oligonucleotides were designed to the signature motif of the PCV2 capsid open reading frame to discriminate experimentally between PCV2 genotype groups by PCR, in situ hybridization (ISH), and fluorescence in situ hybridization (FISH). Unexpectedly, all PCV2-infected animals carried both PCV2a and PCV2b genotype group members. Using confocal microscopy, genotype single-cell infections and cell superinfections were visible. Additionally, we discriminated replicative DNA from total PCV2 DNA isoforms with FISH. This aided in our inquiry into cellular genotype-specific replication. Importantly, single-genotype-group replication was not observed. In infected cells with replicating virus, both genotype groups were equally present. These findings suggest PCV2 genotype group members relaxed replication regulation requirements and may even point to PCV2 replication cooperativity in vivo. These observations explain the readily seen PCV2 DNA recombinations and the high overall PCV2 genome plasticity. Hence, we suggest a novel mechanism of syndrome etiology that consists of a continuously changing PCV2 genome pool in hosts and pig herds, posing a constant challenge to the individual maturing immune system.

A dimeric Rep protein initiates replication of a linear archaeal virus genome: implications for the Rep mechanism and viral replication

The Rudiviridae are a family of rod-shaped archaeal viruses with covalently closed, linear double-stranded DNA (dsDNA) genomes. Their replication mechanisms remain obscure, although parallels have been drawn to the Poxviridae and other large cytoplasmic eukaryotic viruses. Here we report that a protein encoded in the 34-kbp genome of the rudivirus SIRV1 is a member of the replication initiator (Rep) superfamily of proteins, which initiate rolling-circle replication (RCR) of diverse viruses and plasmids. We show that SIRV Rep nicks the viral hairpin terminus, forming a covalent adduct between an active-site tyrosine and the 5' end of the DNA, releasing a 3' DNA end as a primer for DNA synthesis. The enzyme can also catalyze the joining reaction that is necessary to reseal the DNA hairpin and terminate replication. The dimeric structure points to a simple mechanism through which two closely positioned active sites, each with a single tyrosine residue, work in tandem to catalyze DNA nicking and joining. We propose a novel mechanism for rudivirus DNA replication, incorporating the first known example of a Rep protein that is not linked to RCR. The implications for Rep protein function and viral replication are discussed.

Phylogenetic analysis of six isolates of beak and feather disease virus from African grey parrots in Portugal

Beak and feather disease virus (BFDV), a member of the genus Circovirus, was detected in six dead African grey parrots (Psittacus erithacus) in Portugal. The complete nucleotide sequences of these six BFDVs (PT05, PT08, PT08-2, PT08-3, PT09, and PT09-2) were determined and analyzed. The seven open reading frames (ORFs) described for other BFDVs were detected in all strains, except for PT05 and PT08, in which ORFs 4 and 7 are absent. Bayesian inference of phylogeny based on complete genomes of BFDVs isolated in Portugal and 32 other BFDVs found in other parts of the world revealed that PT05 is included in lineage IV, whereas the others form a new proposed genotype lineage IX. The nucleotide diversity ranged from 2% to 12% between the BFDV strains isolated in Portugal and other BFDVs found worldwide.

Replacement of the replication factors of porcine circovirus (PCV) type 2 with those of PCV type 1 greatly enhances viral replication in vitro

Porcine circovirus type 1 (PCV1), originally isolated as a contaminant of PK-15 cells, is nonpathogenic, whereas porcine circovirus type 2 (PCV2) causes an economically important disease in pigs. To determine the factors affecting virus replication, we constructed chimeric viruses by swapping open reading frame 1 (ORF1) (rep) or the origin of replication (Ori) between PCV1 and PCV2 and compared the replication efficiencies of the chimeric viruses in PK-15 cells. The results showed that the replication factors of PCV1 and PCV2 are fully exchangeable and, most importantly, that both the Ori and rep of PCV1 enhance the virus replication efficiencies of the chimeric viruses with the PCV2 backbone.

Characterization and epitope mapping of monoclonal antibodies recognizing N-terminus of Rep of porcine circovirus type 2

Two genotypes of porcine circovirus (PCV) have been described, the non-pathogenic PCV1 and the pathogenic PCV2 in pigs. PCV-ORF1 encodes Rep and Rep' proteins which have identical N-terminal sequence (RepN) within each PCV strain, but RepN has only 88% similarity between PCV1 and PCV2. Purified RepN of PCV2 was used as an immunogen to produce monoclonal antibodies (mAbs). 11 mAbs were screened out and established, and they were divided into two groups according to Western blot and IFA results. One group, including 1C1, bound only PCV2-RepN, while the other, including 3D10, had cross reactivity with RepN of both PCV1 and PCV2. Epitope mapping indicated that 1C1 and 3D10 recognized the linear epitopes L(39)FDYFIVG(46) and K(99)EGNLLIE(106) in PCV2-RepN, respectively. Protein sequence alignment of RepN indicated L(39)FDYFIVG(46) is conserved in all PCV2 in NCBI database, whereas the PCV1 has amino acid substitutions V(41)C(42) in this region. mAb 3D10 could recognize all PCV because all natural mutations in its epitope did not affect its binding. The information about characteristics and epitope of monoclonal antibodies may be useful for the development of diagnostic methods for PCV2 and for analyzing the function of Rep and Rep' of PCV.

Replication of porcine circoviruses

Porcine circoviruses are circular single-stranded DNA viruses that infect swine and wild boars. Two species of porcine circoviruses exist. Porcine circovirus type 1 is non pathogenic contrary to porcine circovirus type 2 which is associated with the disease known as Post-weaning Multisystemic Wasting Syndrome. Porcine circovirus DNA has been shown to replicate by a rolling circle mechanism. Other studies have revealed similar mechanisms of rolling-circle replication in plasmids and single-stranded viruses such as Geminivirus. Three elements are important in rolling-circle replication: i) a gene encoding initiator protein, ii) a double strand origin, and iii) a single strand origin. However, differences exist between viruses and plasmids and between viruses. Porcine circovirus replication probably involves a "melting pot" rather than "cruciform" rolling-circle mechanism.

This review provides a summary of current knowledge of replication in porcine circoviruses as models of the Circovirus genus. Based on various studies, the factors affecting replication are defined and the mechanisms involved in the different phases of replication are described or proposed.

Porcine circoviruses--small but powerful

When porcine circovirus type 1 (PCV1) was isolated more than 40 years ago as a non-pathogenic contaminant of a porcine kidney cell line, enthusiasm and curiosity kept within reasonable limits. Virologists became more interested, when a second variant was isolated and termed PCV2, because PCV2 is linked to postweaning multisystemic wasting disease (PMWS), a new emerging multifactorial disease in swine. Both PCV1 and PCV2 are small and rather simply organized and express only few proteins. Therefore, it was expected that the factor(s) triggering PMWS should be easily identified, but more than one decade of PCV research has not yet singled out a molecule inducing the disease onset. Unravelling the molecular features of PCV and the channels through which the virus interacts with its host are key to manage, prevent and treat PMWS and other PCV-associated diseases. Since we have learned many aspects of the molecular biology of PCV in the last years, it is time for a résumé!

Porcine circovirus type 2 replication is impaired by inhibition of the extracellular signal-regulated kinase (ERK) signaling pathway

Postweaning multisystemic wasting syndrome, which is primarily caused by porcine circovirus type 2 (PCV2), is an emerging and important swine disease. We have recently shown that PCV2 induces nuclear factor kappa B activation and its activation is required for active replication, but the other cellular factors involved in PCV2 replication are not well defined. The extracellular signal-regulated kinase (ERK) which served as an important component of cellular signal transduction pathways has been shown to regulate many viral infections. In this report, we show that PCV2 activates ERK1/2 in PCV2-infected PK15 cells dependent on viral replication. The PCV2-induced ERK1/2 leads to phosphorylation of the ternary complex factor Elk-1, which kinetically paralleled ERK1/2 activation. Inhibition of ERK activation with U0126, a specific MEK1/2 inhibitor, significantly reduced viral progeny release. Investigations into the mechanism of ERK1/2 regulation revealed that inhibition of ERK activation leads to decreased viral transcription and lower virus protein expression. These data indicate that the ERK signaling pathway is involved in PCV2 infection and beneficial to PCV2 replication in the cultured cells.

Porcine circoviruses: a minuscule yet mammoth paradox

Porcine circovirus type 2 (PCV2) is the primary causative agent for porcine circovirus-associated disease (PCVAD). PCVAD has been the cause of considerable economic losses to the pork industry worldwide. The disease is primarily characterized by wasting, enlarged lymph nodes, jaundice and weight loss in affected weanling pigs. Several other complex syndromes involving reproductive failure, enteritis, pneumonia and necrotizing dermatitis have also been associated with PCV2 infection. Lymphoid depletion, which is the hallmark lesion of PCVAD, predisposes the host to immunosuppression. Disease progression is further complicated by co-infections with other bacterial and viral pathogens. Despite the availability of effective vaccines for the last 2 years, newly emerging strains of the virus have been reported to cause more severe outbreaks in parts of the USA and Canada. While knowledge of the biology and pathogenesis of PCV2 has progressed considerably over the last 12 years since the disease was recognized, many questions still remain to be answered.

Homologous recombination plays minor role in excision of unit-length viral genomes from head-to-tail direct tandem repeats of porcine circovirus during DNA replication in Escherichia coli

In this report, we confirmed previous work that a theta-replicating bacterial plasmid containing 1.75 copies of genomic porcine circovirus (PCV) DNA in head-to-tail tandem (HTT) [a partial copy of PCV type 1 (PCV1), a complete copy of PCV type 2 (PCV2) and two origins of DNA replication (Ori)] yielded three different double-stranded DNA species when transformed into Escherichia coli: the input construct (U), the unit-length PCV1/PCV2 genome with a composite Ori lacking the plasmid vector (Q(RC)) and the remaining left-over 0.75 copy PCV1/PCV2 genome with a different composite Ori inserted in the plasmid vector (L(RC)). Replication of U was presumably via the theta-like replication mechanism utilizing the colicin E1 Ori, while derivation of L(RC) and Q(RC) was via the rolling-circle replication (RCR) copy-release mechanism and required the presence of two PCV Oris and the virus-encoded Rep protein. Essentially, excision of a unit-length PCV1/PCV2 genome (Q(RC)) via RCR from U yielded L(RC). Furthermore, we examined whether homologous recombination may also result in excision of a different type of unit-length PCV genome (Q(H)) from identical HTT constructs to generate L(H). Whereas the generation of L(RC) is Rep-protein-dependent, the generation of L(H) is Rep-protein-independent. Accordingly, the L(RC) and Q(RC) molecules derived from RCR possess different characteristics from the L(H) and Q(H) molecules generated via homologous recombination. In one of the studies in which both L(RC) and L(H) were generated simultaneously from the same HTT construct, out of 69 samples analyzed, 66 were derived via RCR and 3 were derived via homologous recombination. Thus, in comparison with RCR, homologous recombination plays a minor role in the excision of unit-length PCV genomes from HTT constructs in Escherichia coli.