Columbiform Pediatrics

Pigeons have been bred by humans for thousands of years as a source of food and feathers, as messengers, but also for their beauty, and more recently for sport. Pediatric medicine of pigeons has risen in importance given the interest at stake during international competitions. Young pigeons have a unique development and an increased sensitivity to both infectious and nutritional disorders compared with adults. Preventive medicine is of paramount importance and relies on measures targeting parents before breeding and chicks after hatching. Vaccination has been especially studied in pigeons.

Detection of circovirus in free-ranging brown rats (Rattus norvegicus)

Accidentally found, two poisoned brown rats from Hungary were surveyed for presence of circoviral DNA, using specific nested primers, designed against the rep gene of the virus. Both specimens were positive. The whole genomes were amplified using inverse PCR based on the Rep sequence parts and sequenced by the primer walking method. Genomic analyses revealed that these novel rat viruses, together with tawny owl-associated circovirus reported by Italian researchers in 2022, are sequence variations of the same virus from genus Circovirus. In phylogenetic reconstructions, these circovirus strains detected from brown rats clustered closest to circoviruses derived from faeces samples of various predatory mammals. Molecular data as well as the phylogenetic analyses of the complete derived replication-associated protein and the capsid protein, as well as the prey preference of the host species of the recently described tawny owl-associated virus suggest that brown rat could be the evolutionary adapted host of the viruses described in this paper (brown rat circovirus types 1 and 2) and the previously reported tawny owl-associated virus. Possible pathogenic and zoonotic role of these viruses need further studies.

Detection and genetic characterization of circoviruses in more than 80 bat species from eight countries on four continents

Several bat-associated circoviruses and circular rep-encoding single-stranded DNA (CRESS DNA) viruses have been described, but the exact diversity and host species of these viruses are often unknown. Our goal was to describe the diversity of bat-associated circoviruses and cirliviruses, thus, 424 bat samples from more than 80 species were collected on four continents. The samples were screened for circoviruses using PCR and the resulting amino acid sequences were subjected to phylogenetic analysis. The majority of bat strains were classified in the genus Circovirus and some strains in the genus Cyclovirus and the clades CRESS1 and CRESS3. Some strains, however, could only be classified at the taxonomic level of the order and were not classified in any of the accepted or proposed clades. In the family Circoviridae, 71 new species have been predicted. This screening of bat samples revealed a great diversity of circoviruses and cirliviruses. These studies underline the importance of the discovery and description of new cirliviruses and the need to establish new species and families in the order Cirlivirales.

Investigating the genetic diversity of CRESS DNA viruses in cats identifies a novel feline circovirus and unveils exposure of cats to canine circovirus

Circular replication-associated protein (Rep)-encoding single stranded (CRESS) DNA viruses include Circoviruses which have been found in several animal species and in human specimens. Circoviruses are associated with severe disease in pigs and birds and with respiratory and gastrointestinal disorders and systemic disease in dogs. In cats there are only a few anecdotical studies reporting CRESS DNA viruses. In this study, a total of 530 samples (361 sera, 131 stools, and 38 respiratory swabs) from cats, were screened for the presence of CRESS DNA viruses. Overall, 48 (9.0%) of 530 samples tested positive using a pan-Rep PCR. A total of 30 Rep sequences were obtained. Ten sequences of fecal origin were tightly related to each other (82.4-100% nt identity) and more distantly related to mongoose circoviruses (68.3 to 77.2% nt identity). At genome level these circoviruses displayed the highest nt identity (74.3-78.7%) to mongoose circoviruses thus representing a novel circovirus species. Circoviruses from different animal hosts (n = 12) and from humans (n = 8) were also identified. However, six Rep sequences were obtained from serum samples, including canine circoviruses, a human cyclovirus and human and fish-associated CRESS DNA viruses. The presence of these viruses in the sera would imply, to various extent, virus replication in the animal host, able to sustain viremia. Overall, these findings indicate a wide genetic diversity of CRESS DNA viruses in cats and warrant further investigations.

Unknown Circovirus in Immunosuppressed Patient with Hepatitis, France, 2022

Hepatitis of undetermined origin can be caused by a wide variety of pathogens, sometimes emerging pathogens. We report the discovery, by means of routine shotgun metagenomics, of a new virus belonging to the family Circoviridae, genus Circovirus, in a patient in France who had acute hepatitis of unknown origin.

A remarkably diverse and well-organized virus community in a filter-feeding oyster

BACKGROUND

Viruses play critical roles in the marine environment because of their interactions with an extremely broad range of potential hosts. Many studies of viruses in seawater have been published, but viruses that inhabit marine animals have been largely neglected. Oysters are keystone species in coastal ecosystems, yet as filter-feeding bivalves with very large roosting numbers and species co-habitation, it is not clear what role they play in marine virus transmission and coastal microbiome regulation.

RESULTS

Here, we report a Dataset of Oyster Virome (DOV) that contains 728,784 nonredundant viral operational taxonomic unit contigs (≥ 800 bp) and 3473 high-quality viral genomes, enabling the first comprehensive overview of both DNA and RNA viral communities in the oyster Crassostrea hongkongensis. We discovered tremendous diversity among novel viruses that inhabit this oyster using multiple approaches, including reads recruitment, viral operational taxonomic units, and high-quality virus genomes. Our results show that these viruses are very different from viruses in the oceans or other habitats. In particular, the high diversity of novel circoviruses that we found in the oysters indicates that oysters may be potential hotspots for circoviruses. Notably, the viruses that were enriched in oysters are not random but are well-organized communities that can respond to changes in the health state of the host and the external environment at both compositional and functional levels.

CONCLUSIONS

In this study, we generated a first "knowledge landscape" of the oyster virome, which has increased the number of known oyster-related viruses by tens of thousands. Our results suggest that oysters provide a unique habitat that is different from that of seawater, and highlight the importance of filter-feeding bivalves for marine virus exploration as well as their essential but still invisible roles in regulating marine ecosystems. Video Abstract.

Viruses Infecting the European Catfish (Silurus glanis)

In aquaculture, disease management and pathogen control are key for a successful fish farming industry. In past years, European catfish farming has been flourishing. However, devastating fish pathogens including limiting fish viruses are considered a big threat to further expanding of the industry. Even though mainly the ranavirus (Iridoviridea) and circovirus (Circoviridea) infections are considered well- described in European catfish, more other agents including herpes-, rhabdo or papillomaviruses are also observed in the tissues of catfish with or without any symptoms. The etiological role of these viruses has been unclear until now. Hence, there is a requisite for more detailed information about the latter and the development of preventive and therapeutic approaches to complete them. In this review, we summarize recent knowledge about viruses that affect the European catfish and describe their origin, distribution, molecular characterisation, and phylogenetic classification. We also highlight the knowledge gaps, which need more in-depth investigations in the future.

Identification of a novel circovirus in blood sample of giant pandas (Ailuropoda melanoleuca)

The members of the family Circoviridae are considered to be one of the smallest autonomously replicating viruses that are classified into two genera, Circovirus and Cyclovirus. Circoviruses have been found in a variety of vertebrates, but whether they infect endangered protected animals has not been studied in much detail. Here, viral metagenomics and PCR methods were used to detect and verify viral nucleic acid in the blood sample from giant pandas. According to these methods, the complete genome sequence of a novel circovirus, the giant panda associated circovirus (GPCV) from the blood sample of three giant pandas was identified. The GPCV genome is 2090 bp in size and reveals two putative ambisense open-reading frames, encoding the major structural capsid protein and the replication associated protein, respectively, the latter having two predicted introns. Pairwise sequence comparison and phylogenetic analyses indicated GPCV was a putative new species within genus Circovirus based on the species demarcation criteria of the International Committee on the Taxonomy of Viruses. It is the first time that circovirus has been identified from blood sample of giant pandas. These efforts will contribute to future analyses to illuminate the evolutionary relationships between classified and newly identified members of the family Circoviridae.

Correlation between goose circovirus and goose parvovirus with gosling feather loss disease and goose broke feather disease in southern Taiwan

BACKGROUND

Goslings in several Taiwanese farms experienced gosling feather loss disease (GFL) at 21-35 days and goose broke feather disease (GBF) at 42-60 days. The prevalence ranges from a few birds to 500 cases per field. It is estimated that about 12,000 geese have been infected, the morbidity is 70-80% and the mortality is 20-30%.

OBJECTIVES

This study aims to investigate the pathogens that cause GFL and GBF. Focus on the study of the correlation between goose circovirus (GoCV) and goose parvovirus (GPV) with the goose feather loss in southern Taiwan. Furthermore, a phylogenetic tree was established to align the differences between southern and northern Taiwan and compare with virus strains from China and Europe.

METHODS

Samples were collected from animal hospitals. Molecular and microscopy diagnostics were used to examine 92 geese. Specific quantitative polymerase chain reaction (Q-PCR) assays are performed to evaluate GPV and GoCV viral loads and simultaneously evaluated the feather loss conditions in geese with the scoring method.

RESULTS

High prevalence of GoCV and GPV infection in geese showing signs of GFL and GBF. Inclusion body was detected in the feather follicles and Lieberkühn crypt epithelial cells. The Q-PCR showed the high correlation between feather loss and viruses during 3rd-5th week. However, the infection was not detected using the same test in 60 healthy geese.

CONCLUSIONS

Thus, GFL and GBF appear to be significantly closely related to GoCV and GPV. The geese feathers showed increasing recovery after being quarantined and disinfected.

Nucleolar protein NPM1 is essential for circovirus replication by binding to viral capsid

Entry of circovirus into the host cell nucleus is essential for viral replication during the early stage of infection. However, the mechanisms by which nucleolar shuttle proteins are used during viral replication is still not well understood. Here, we report a previously unidentified nucleolar localization signal in circovirus capsid protein (Cap), and that circovirus hijacks the nucleolar phosphoprotein nucleophosmin-1 (NPM1) to facilitate its replication. Colocalization analysis showed that NPM1 translocates from the nucleolus to the nucleoplasm and cytoplasm during viral infection. Coimmunoprecipitation and glutathione S-transferase pull-down assays showed that Cap interacts directly with NPM1. Binding domain mapping showed that the arginine-rich N-terminal motif ¹MTYPRRRYRRRRHRPRSHLG²⁰ of Cap, and residue serine-48 of the N-terminal oligomerization domain of NPM1, are essential for the interaction. Virus rescue experiments showed that all arginine to alanine substitution in the N-terminal arginine-rich motif of Cap resulted in diminished viral replication. Knockdown of NPM1 and substitution of serine-48 in NPM1 to glutamic acid also decreased viral replication. In addition, binding assays showed that the arginine-rich motif of Cap is a nucleolar localization signal. Taken together, our findings demonstrate that circovirus protein Cap is a nucleolus-located, and regulates viral replication by directly binding to NPM1.

REPEAT SPILLOVER OF BEAK AND FEATHER DISEASE VIRUS INTO AN ENDANGERED PARROT HIGHLIGHTS THE RISK ASSOCIATED WITH ENDEMIC PATHOGEN LOSS IN ENDANGERED SPECIES

Conservation efforts for the orange-bellied parrot (Neophema chrysogaster), one of the world's most critically endangered bird species, have been hampered by beak and feather disease virus (BFDV) spillover infection. To understand the vulnerability of orange-bellied parrots to potential reservoirs of infection we investigated geographic versus taxonomic structure in 160 full-genome and 319 partial Rep gene BFDV sequences from captive and wild orange-bellied parrots and other wild parrot species in Australia. We found that Australian BFDV populations are structured by host taxonomy. By identifying genetic stratification of BFDV in reservoir hosts we characterized three separate recent incursions of BFDV into orange-bellied parrots from other wild parrots, which demonstrates the susceptibility of critically endangered species to multiple threats of pathogen re-emergence. Our study highlighted how loss of endemic circulating BFDV in orange-bellied parrots precipitated repeated spillover into an immunologically naïve population, causing significant disease.

Identification and whole-genome characterization of a novel Porcine Circovirus 3 subtype b strain from swine populations in Vietnam

Porcine circovirus 3 (PCV3) is a novel circovirus detected in pigs suffering from porcine dermatitis and nephropathy syndrome (PDNS), reproductive failure, and multisystemic infection. In this study, we identified PCV3 infection in aborted fetuses and reported the full-length genome sequence of a PCV3 strain identified from southern Vietnam. The complete genome of this PCV3 strain is 2000 nucleotides in length. We found that it shares 98.5-99.25% sequence identity with other reference sequences and that it clusters with the PCV3b subtype. Several specific mutated sites were found to be unique to this Vietnamese PCV3b strain, including I14M in the Rep protein and K139R, I150F, and P169T in the Cap protein. The sequence data that have been made publically available as part of this study will help investigators to better understand the molecular characteristics, genetic diversity, and evolutionary history of PCV3. Careful and in-depth investigations into the epidemiology, pathogenicity, and the evolution of this novel virus is a matter of urgent economic and agricultural interest in Vietnam.

Characterization and purification of pentameric chimeric protein particles using asymmetric flow field-flow fractionation coupled with multiple detectors

Porcine circovirus causes the post-weaning multi-systemic wasting syndrome. Despite the existence of commercial vaccines, the development of more effective and cheaper vaccines is expected. The usage of chimeric antigens allows serological differentiation between naturally infected and vaccinated animals. In this work, recombinant pentameric vaccination protein particles spontaneously assembled from identical subunits-chimeric fusion proteins derived from circovirus capsid antigen Cap and a multimerizing subunit of mouse polyomavirus capsid protein VP1 were purified and characterized using asymmetric flow field-flow fractionation (AF4) coupled with UV and MALS/DLS (multi-angle light scattering/dynamic light scattering) detectors. Various elution profiles were tested, including constant cross-flow and decreasing cross-flow (linearly and exponentially). The optimal sample retention, separation efficiency, and resolution were assessed by the comparison of the hydrodynamic radius (R_h) measured by online DLS with the R_h values calculated from the simplified retention equation according to the AF4 theory. The results show that the use of the combined elution profiles (exponential and constant cross-flow rates) reduces the time of the separation, prevents undesirable sample-membrane interaction, and yields better resolution. Besides, the results show no self-associations of the individual pentameric particles into larger clusters and no sample degradation during the AF4 separation. The R_g/R_h ratios for different fractions are in good correlation with morphological analyses performed by transmission electron microscopy (TEM). Additionally to the online analysis, the individual fractions were subjected to offline analysis, including batch DLS, TEM, and SDS-PAGE, followed by Western blot.

Analysis of the beak and feather disease viral genome indicates evidence of multiple introduction events into Saudi Arabia

Psittacine beak and feather disease (PBFD), caused by beak and feather disease virus (BFDV) is a highly contagious disease in wild and captive psittacine populations and has an almost global presence. However, the BFDV infection in Saudi Arabia remains largely unknown. In the present study, we report the full genome sequence of BFDV strains from Saudi Arabia and its genetic diversity. The complete genome sequences were analyzed for 14 BFDV-infected birds representing 6 psittacine species. The complete genome sequence of BFDV strains was compared with 201 previously reported sequences to evaluate their diversity and possible recombination events, if any. Our analysis revealed that newly sequenced BFDV genomes from Saudi Arabia belonged to six different strains. Phylogenetic analysis suggested that the isolated BFDV genomes were highly recombinant with a high degree of diversity. It is evident from the study that psittacine species in Saudi Arabia are at risk from the spread of BFDV. As per the CITES trade database, about 190,000 parrots have been imported to Saudi Arabia since 1975 over a thousand instances. Presumably, during any of these trade events or unregulated trade of birds has predisposed the introduction of BFDV to Saudi Arabia. Understanding the epidemiology of BFDV is necessitated to address the threat posed by the virus to the psittacine population of Saudi Arabia.

Viruses belonging to Anelloviridae or Circoviridae as a possible cause of chronic fatigue

Chronic fatigue often starts with an acute viral infection-as witnessed in the case of SARS-CoV-2-but indirect consequences of these infections are presumably the actual cause of the condition. As recently reviewed in this journal, the culprit could be a virus already present in the patient. The review covers several types of viruses, but concludes that the question is still open. The focus is on well known, pathogenic viruses for which there are ample diagnostic tools. I argue that there is one lesser-known group of viruses, the related anello- and circoviruses, which ought to be investigated. More or less everyone harbours at least one strain of these viruses in the blood, while not in the spinal fluid. They normally replicate at a low level, but their activity increases in an immune suppressed host; and there are cases where they do reach the brain. The initial infection could facilitate their access to the brain.

Investigation on porcine circovirus type 3 in serum of farrowing sows with stillbirths

Since its first identification in 2016, porcine circovirus 3 (PCV3) has been detected in healthy and/or diseased swine in many countries worldwide. In a previous study by our group, PCV3 was detected in sera of sows which had at least one stillborn piglet in the last parturition. As such, it became important to investigate if the presence of PCV3 in sows' sera could be associated to the occurrence of stillbirths. With that aim, the frequency of PCV3 infections and viral DNA loads in sows' sera was investigated through a real-time quantitative PCR in 89 serum samples of just farrowed sows with or without stillbirths. PCV3 genomes were identified in most samples, with genome loads ranging between less than 10 to 200,000 copies per mL of serum. No significant differences were observed either in the frequency of infection or PCV3 viral loads in sows with or without stillbirths. Thus, no association could be established between PCV3 infection of sows at farrowing and stillbirths' occurrence.

Genomic characterization of a novel bat-associated Circovirus detected in European Miniopterus schreibersii bats

Circoviruses are small circular DNA viruses causing severe pig and poultry disease, recently identified in various bat species worldwide. We report the detection and full-genome molecular characterization of a novel bat-associated Circovirus identified in faecal samples of Miniopterus schreibersii bats (Schreiber’s bent-winged bats) from Sardinia, Italy. Full-genomic sequencing revealed a new putative member of Circoviridae family, with a genome size of 2063 nt. Sequencing allowed the characterization of the two major ORFs, inversely arranged, encoding replicase and capsid proteins, as well as the finding of a polythymidine tract within the genome, and highlighted phylogenetic relationships of the novel virus. This is the first report of circovirus in European bats. Giving the high level of genetic diversity of bat circoviruses, it is paramount to further investigate the relationships between these viruses and bats.

Molecular survey of avian circoviruses in some non-psittacine birds and detection of a novel canary circovirus in a pigeon

BACKGROUND

Circoviruses are small, non-enveloped, single stranded DNA viruses. There is scarce information about these agents in non-psittacine birds.

AIMS

It is attempted to detect and characterize circoviruses in non-psittacine birds.

METHODS

Forty-five samples were collected from different non-psittacine species belonging to seven avian orders. A nested polymerase chain reaction (nested-PCR) for the detection of rep gene of circoviruses was applied.

RESULTS

Two different types of circoviruses were detected in two pigeon samples (2/11, 18.2%). One of the detected circoviruses was placed in clade A next to a polish strain based on phylogenetic analysis. Interestingly, the other detected circovirus was closely related to canary circoviruses (CaCVs).

CONCLUSION

In addition to the molecular diagnosis of a pigeon circovirus (PiCV), this is the first report of the detection of CaCv in a pigeon. The possible hypotheses of such circumstance are discussed.

Genomic characterization of a novel circovirus from a stranded Longman's beaked whale (Indopacetus pacificus)

Tissues from a juvenile Longman's beaked whale that stranded in Hawaii in 2010 were screened for viruses using a Next-Generation Sequencing (NGS) approach. From the NGS data, the full genome (1,849 bp) of a novel beaked whale circovirus (BWCV) was determined. Two open reading frames (ORF) were annotated, including ORF1 that encodes the capsid gene, ORF2 that encodes the replication-associated gene, and a 9-bp conserved nonamer on the apex of the open loop found in all circoviruses. Independent phylogenetic analyses based on amino acid sequence alignments of the two CV proteins supported the BWCV as a member of the genus Circovirus, branching as the sister species to the recently discovered canine circovirus. A sequence identity matrix generated from complete genome alignments revealed the BWCV displays between from 51.1 to 56.7% nucleotide identity to other circoviruses, which is lower than the 80% threshold proposed for species demarcation. Considering the genetic and phylogenetic analyses, we propose the formal species designation of beaked whale circovirus. An endpoint PCR assay targeting the BWCV genome confirmed the presence of the BWCV DNA in every tissue from which DNA was extracted, including spleen, muscle, left ventricle, left adrenal gland, liver, lung, cerebrum, cerebellum, and lymph node. An automated in situ hybridization assay utilizing RNAscope® technology and targeting the replication-associated gene resulted in labeling of individual cells morphologically resembling mononuclear leukocytes and cells of blood vessels in diaphragm, liver, lymph nodes, lung, pericardium, oral mucosa and tongue, adrenal gland, testis, aorta, intestine, stomach and heart. The clinical or pathologic significance of BWCV is undetermined, as are its host range, prevalence, and pathogenicity in cetaceans of Hawaiian waters and elsewhere.

Structural characterization of the PCV2d virus-like particle at 3.3 Å resolution reveals differences to PCV2a and PCV2b capsids, a tetranucleotide, and an N-terminus near the icosahedral 3-fold axes

Porcine circovirus 2 (PCV2) has a major impact on the swine industry. Eight PCV2 genotypes (a-h) have been identified using capsid sequence analysis. PCV2d has been designated as the emerging genotype. The cryo-electron microscopy molecular envelope of PCV2d virus-like particles identifies differences between PCV2a, b and d genotypes that accompany the emergence of PCV2b from PCV2a, and PCV2d from PCV2b. These differences indicate that sequence analysis of genotypes is insufficient, and that it is important to determine the PCV2 capsid structure as the virus evolves. Structure-based sequence comparison demonstrate that each genotype possesses a unique combination of amino acids located on the surface of the capsid that undergo substitution. We also demonstrate that the capsid N-terminus moves in response to increasing amount of nucleic acid packaged into the capsid. Furthermore, we model a tetranucleotide between the 5- and 2-fold axes of symmetry that appears to be responsible for capsid stability.

Assessing circovirus gene flow in multiple spill-over events

The establishment of viral pathogens in new host environments following spillover events probably requires adaptive changes within both the new host and pathogen. After many generations, signals for ancient cross-species transmission may become lost and a strictly host-adapted phylogeny may mimic true co-divergence while the virus may retain an inherent ability to jump host species. The mechanistic basis for such processes remains poorly understood. To study the dynamics of virus-host co-divergence and the arbitrary chances of spillover in various reservoir hosts with equal ecological opportunity, we examined structural constraints of capsid protein in extant populations of Beak and feather disease virus (BFDV) during known spillover events. By assessing reservoir-based genotype stratification, we identified co-divergence defying signatures in the evolution BFDV which highlighted primordial processes of cryptic host adaptation and competing forces of host co-divergence and cross-species transmission. We demonstrate that, despite extensive surface plasticity gathered over a longer span of evolution, structural constraints of the capsid protein allow opportunistic host switching in host-adapted populations. This study provides new insights into how small populations of endangered psittacine species may face multidirectional forces of infection from reservoirs with apparently co-diverging genotypes.

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.

Detection and Characterization of Circovirus in Canary Flocks

Circovirus infections have been documented in adult and nestling canaries (Fringillidae) but the distribution of the virus in the world is not yet known. In captive canary flocks, Circovirus infections have been reported based on the clinical observations. In this study, the presence of both canary circovirus (CaCV) and chicken anemia virus (CAV) in canary flocks was investigated. Virus strains were detected by PCR and direct sequencing of amplified products. Nucleotide sequences were aligned and compared with existing data in GenBank. PCR identified CaCV-positive birds, giving an overall positivity rate of 25%, but all samples were negative for CAV. According to the sequencing data, three distinct strains were identified. Our results indicated a relationship between genetic variation in the replicase gene ( rep) and the geographic regions as well as the feasibility of using the rep gene for virus detection and molecular epidemiology investigations. We are reporting detection and characterization of canary circovirus based on the rep gene. Sequencing results and sequence identity analysis revealed that the rep gene could be used for detecting and discriminating the members of family Circoviridae. This manuscript is the first report of canary circovirus in Iran and of three new strains in the world.

Molecular characterization of a novel bat-associated circovirus with a poly-T tract in the 3' intergenic region

The family Circoviridae comprises a large group of small circular single-stranded DNA viruses with several members causing severe pig and poultry diseases. In recent years the number of new viruses within the family has had an explosive increase showing a high level of genetic diversity and a broad host range. In this report we describe two more circoviruses identified from bats in Yunnan and Heilongjiang provinces in China. Full genome sequencing has revealed that these bat associated circoviruses (bat ACV) should be classified as new species within the genus Circovirus based on the demarcation criteria of the International Committee on the Taxonomy of Viruses (ICTV). The most striking result is the novel finding of a 21-28 nt polythymidine (poly-T) tract in the 3' terminal intergenic region of bat ACV isolates from Heilongjiang province. To understand its role in viral replication, a wild type bat ACV and a mutated version with the entire poly-T deleted were rescued through construction of infectious clones. Replication comparison in vitro showed that the poly-T is not essential for viral replication. Identification of additional bat ACV isolates and study of their biological characteristics will be the main task in future to understand the potential roles of bats in transmission of circoviruses to terrestrial mammals and humans.

The evolution, distribution and diversity of endogenous circoviral elements in vertebrate genomes

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Sequences derived from circoviruses occur sporadically in vertebrate genomes.

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The vast majority of fixed circovirus sequences in vertebrate genomes are derived from rep genes.

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Some ancient circoviruses were closely related to modern circoviruses.

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Integrated circovirus sequences are highly duplicated in some carnivore lineages.

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Sequences in the Mus spretus genome are closely related to modern canine circoviruses.

Circoviruses (family Circoviridae) are small, non-enveloped viruses that have short, single-stranded DNA genomes. Circovirus sequences are frequently recovered in metagenomic investigations, indicating that these viruses are widespread, yet they remain relatively poorly understood. Endogenous circoviral elements (CVe) are DNA sequences derived from circoviruses that occur in vertebrate genomes. CVe are a useful source of information about the biology and evolution of circoviruses. In this study, we screened 362 vertebrate genome assemblies in silico to generate a catalog of CVe loci. We identified a total of 179 CVe sequences, most of which have not been reported previously. We show that these CVe loci reflect at least 19 distinct germline integration events. We determine the structure of CVe loci, identifying some that show evidence of potential functionalization. We also identify orthologous copies of CVe in snakes, fish, birds, and mammals, allowing us to add new calibrations to the timeline of circovirus evolution. Finally, we observed that some ancient CVe group robustly with contemporary circoviruses in phylogenies, with all sequences within these groups being derived from the same host class or order, implying a hitherto underappreciated stability in circovirus-host relationships. The openly available dataset constructed in this investigation provides new insights into circovirus evolution, and can be used to facilitate further studies of circoviruses and CVe.

High prevalence of Mycobacterium genavense within flocks of pet birds

Mycobacterium genavense is regarded as the primary cause of mycobacteriosis in psittaciform and passeriform birds, which are commonly kept as pets. In humans, Mycobacterium genavense is especially pathogenic for young, old, pregnant and immunocompromised people (YOPIs). In birds, only few studies, mainly case reports, exist and there is still little e information about occurrence and relevance of this zoonotic pathogen. In this first pilot study concerning the prevalence of Mycobacterium genavense within flocks of naturally infected pet birds, real-time PCR examinations of 170 individual passeriform and psittaciform birds, including commonly kept budgerigars, lovebirds and zebra finches as well as gold finches and weaver finches, were conducted to determine the infection rate in six different aviaries. Antemortem examinations of faeces and cloacal swabs were compared with postmortem examinations of tissue samples to evaluate the reliability of antemortem diagnostics. Additional ophthalmologic examinations were performed to evaluate their diagnostic potential. Molecular examinations for viral co-infections, including circovirus, polyomavirus and adenovirus, were conducted to identify potential risk factors. PCR results revealed a detection prevalence of Mycobacterium genavense in the flocks varying from 3% to 91% based on postmortem testing, while antemortem diagnostics of faecal samples and swabs showed 64% discrepant (false negative) results. Ophthalmologic examinations were not useful in identifying infected birds within the flocks. Viral co-infections, especially with polyomavirus, were common. It has to be assumed that Mycobacterium genavense infections are widespread and underdiagnosed in companion birds. Viral infections might be an important risk factor. There is urgent need to improve antemortem diagnostics.

Molecular detection of novel circoviruses in ticks in northeastern China

Novel circular single-stranded DNA (ssDNA) genomes have been found in various animals using high-throughput sequencing techniques. In this study, two circular ssDNA genomes were detected in adult ticks from northeastern China by Solexa sequencing and PCR. The two sequences shared a similar genomic organization to circoviruses, with genomes of 1936 bp (TiCV-1) and 1812 bp (TiCV-2), each including two major open read frames (ORFs), ORF1 and ORF2, encoding putative replicase and capsid proteins, respectively. The potential stem-loop structure of a circovirus was predicted in the intergenic region between the two ORFs. Sequence comparison showed that the genome of TiCV-2 was almost the same as that of TiCV-1, except for two deletions and several mutations, and they had a high identity of 71.3-72.9% with Raven circovirus. The infection rates of circoviruses were calculated by the maximum likelihood estimation as 3.2% (95% CI, 1.9-5.2%) for TiCV-1 in the investigated Haemaphysalis longicornis, and 1.2% (95% CI, 0.2-4.0%) for TiCV-2 in Ixodes crenulatus from Yichun of Heilongjiang Province. These results indicate that the two sequences are distantly related to known circovirus genomes and may represent novel species in the family Circoviridae.

The prevalence of PCV2 viremia in newborn piglets on four endemically infected Dutch sow farms is very low

Porcine circovirus type 2 (PCV2) systemic disease is currently considered one of the most relevant infectious diseases in swine industry worldwide from an economical point of view. Although piglets generally become diseased between 8 and 16 weeks of age, they can be infected much earlier, even already in utero. However, data on the prevalence of PCV2 infection in newborn piglets are very variable (lower than 40 up to 82%) and most of the studies have been performed in US. In European pig farms, using group-housing systems for gestating sows, a different herd PCV2 infection and immunological status may be expected and was recently reported in Germany. If that is the current scenario in most European farms, strategies to prevent horizontal transmission become essential for the control of the infection. The aim of our study was to determine the PCV2 prevalence in newborn piglets on 4 endemically infected farms in the Netherlands under European conditions. Eleven sows and 8 piglets per litter from 4 farms selected by their assumed PCV2 endemic infection status were sampled. Plasma from piglets was analysed with a PCV2 qPCR and serum from the sows was analysed with a commercial circovirus IgG ELSIA, circovirus IgM ELISA and PCV2 qPCR. In none of the samples from the piglets PCV2 was detected by the qPCR. None of the samples from the sows tested positive in the qPCR and circovirus IgM ELISA. The true- and apparent prevalence of IgG at herd and sow level were 0.75 and 0.81 and, 0.30 and 0.32, respectively, and no statistically significant association with sow parity was observed. These results reveal a very low prevalence of PCV2 in newborn piglets on endemically infected farms in The Netherlands, opening the opportunity of re-evaluation of the control measures applied in these farms.

Recombinant expression of beak and feather disease virus capsid protein and assembly of virus-like particles in Nicotiana benthamiana

BACKGROUND

Beak and feather disease virus (BFDV) is an important disease causing agent affecting psittacines. BFDV is highly infectious and can present as acute, chronic or subclinical disease. The virus causes immunodeficiency and is often associated with secondary infections. No commercial vaccine is available and yields of recombinant BFDV capsid protein (CP) expressed in insect cells and bacteria are yet to be seen as commercially viable, although both systems produced BFDV CP that could successfully assemble into virus-like particles (VLPs). Plants as expression systems are increasingly becoming favourable for the production of region-specific and niche market products. The aim of this study was to investigate the formation and potential for purification of BFDV VLPs in Nicotiana benthamiana.

METHODS

The BFDV CP was transiently expressed in N. benthamiana using an Agrobacterium-mediated system and plant expression vectors that included a bean yellow dwarf virus (BeYDV)-based replicating DNA vector. Plant-produced BFDV CP was detected using immunoblotting. VLPs were purified using sucrose cushion and CsCl density gradient centrifugation and visualised using transmission electron microscopy.

RESULTS

In this study we demonstrate that the BFDV CP can be successfully expressed in N. benthamiana, albeit at relatively low yield. Using a purification strategy based on centrifugation we demonstrated that the expressed CP can self-assemble into VLPs that can be detected using electron microscopy. These plant-produced BFDV VLPs resemble those produced in established recombinant expression systems and infectious virions. It is possible that the VLPs are spontaneously incorporating amplicon DNA produced from the replicating BeYDV plant vector.

CONCLUSIONS

This is the first report of plant-made full-length BFDV CP assembling into VLPs. The putative pseudovirions could be used to further the efficacy of vaccines against BFDV.

A molecular survey for selected viral enteropathogens revealed a limited role of Canine circovirus in the development of canine acute gastroenteritis

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A molecular survey for selected viral enteropathogens was conducted in dogs with and without acute gastroenteritis.

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Canine parvovirus and coronavirus were strongly associated with occurrence of enteric disease.

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Canine circovirus infections correlated with acute gastroenteritis only when associated with other enteric viruses.

Canine circovirus (CanineCV) is a canine virus, whose pathogenetic role is still uncertain. Based on recent data suggesting its role as entheropathogen, a case-control study was conducted between 2013 and 2016 to investigate the association of CanineCV with gastroenteritis in dogs, alone or in combination with other viral pathogens, including canine parvovirus (CPV), canine coronavirus (CCoV) and canine distemper virus (CDV). A total of 219 dogs suffering from acute gastroenteritis disorders and 67 controls randomly recruited among healthy dogs or patients presenting without enteric signs were screened by a panel of real-time (RT-)PCR assays for CanineCV, CPV, CCoV and CDV. A high prevalence of viral infections was detected in dogs with gastroenteritis (77.16%), with CPV representing the most frequently detected enteropathogen, followed by CanineCV and CCoV. While CPV and CCoV infections displayed a strong association with occurrence of acute gastroenteritis (p < 0.00001), detection of CanineCV in control dogs (28.35%) occurred with prevalence comparable to that of clinical cases (32.42%), so that its correlation with gastrointestinal disease was not statistically supported (p = 0.530988). Different from the clinical cases, where co-infections were frequently observed, all positive samples from the control group contained single infections. Noteworthy, a significant association was calculated between co-infections with CanineCV and occurrence of acute gastroenteritis (p < 0.00001). This study supports the role of CanineCV as a co-pathogen in the development of gastrointestinal disease, mainly acting in synergism with other enteric viruses.

GENETIC CHARACTERIZATION OF H13 AND H16 INFLUENZA A VIRUSES IN GULLS (LARUS SPP.) WITH CLINICALLY SEVERE DISEASE AND CONCURRENT CIRCOVIRUS INFECTION

Influenza A viruses (IAVs) of the subtypes H13 and H16 are primarily found in gulls ( Larus spp., order Charadriiformes). Although the gull-adapted subtypes replicate efficiently during infection, gulls usually remain apparently healthy during infection. Avian influenza virus isolates are generally separated into two distinct populations, North American and Eurasian, because of the limited gene flow between the continents. Reassortment between these lineages does occur occasionally; however, direct intercontinental transmission of all eight gene segments is rare. Extensive research has been done to understand the ecology of IAV subtypes that naturally circulate in ducks (order Anseriformes), but the ecology of H13 and H16 IAVs in gulls remains far less studied. In Finland, gulls were screened for IAVs for passive (dead and diseased gulls) and active (clinically healthy gulls) surveillance purposes during the years 2005-10. During that period, 11 H13, two H16 viruses, and one H3N8 IAV were detected. We sequenced partial and full-length hemagglutinin genes of these gull-origin IAVs for phylogenetic assessments. All but one of the H13 genes clustered together with northern European and northeastern Asian viruses, whereas one virus clustered with North American viruses. Interestingly, a high rate (10/14) of these low-pathogenic IAVs was detected in dead or diseased gulls. The atypical clinical status of the IAV-positive gulls and previous observations of circovirus-like inclusion bodies in diseased gulls during autopsies, led us to screen for concurrent circovirus infections in our samples. The DNA of circovirus, an immunosuppressive pathogen of both birds and mammals, was detected in 54% (7/13) of the tested IAV-positive gulls, whereas only 25% (14/56) of our panel of IAV-negative gulls tested positive by circovirus PCR.

Detection of virus particles resembling circovirus and porcine circovirus 2a (PCV2a) sequences in feces of dogs

During routine electron microscopy of fecal samples from diarrheic dogs dated from 2000 virus particles resembling circovirus in shape and size were detected in two samples (V2177/00; V3374/00). Polymerase chain reaction (PCR) using primers specific for porcine circovirus type 2 (PCV2) amplified DNA recovered from both samples. Sequencing of PCR amplificates (V2177/00) obtained with PCV2-specific primer pairs revealed a genome size of 1768 bp. The nucleotide sequence was highly similar (98% nucleotide identity) to the PCV2a reference sequence.

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Electron microscopy has revealed circoviruses in two fecal samples of diarrheic dogs.

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PCV2-specific PCR amplified DNA extracted from the samples.

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By sequencing one sample a genome size of 1768 bp and a nucleotide sequence identity of 98% to PCV2a were achieved.

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This is the first time that PCV2 has been reported in dogs.

Detection of a novel circovirus PCV3 in pigs with cardiac and multi-systemic inflammation

BACKGROUND

Porcine circovirus 2 causes different clinical syndromes resulting in a significant economic loss in the pork industry. Three pigs with unexplained cardiac and multi-organ inflammation that tested negative for PCV2 and other known porcine pathogens were further analyzed.

METHODS

Histology was used to identify microscopic lesions in multiple tissues. Metagenomics was used to detect viral sequences in tissue homogenates. In situ hybridization was used to detect viral RNA expression in cardiac tissue.

RESULTS

In all three cases we characterized the genome of a new circovirus we called PCV3 with a replicase and capsid proteins showing 55 and 35 % identities to the genetically-closest proteins from a bat-feces associated circovirus and were even more distant to those of porcine circovirus 1 and 2. Common microscopic lesions included non-suppurative myocarditis and/or cardiac arteriolitis. Viral mRNA was detected intralesionally in cardiac cells. Deep sequencing in tissues also revealed the presence of porcine astrovirus 4 in all three animals as well as rotavirus A, porcine cytomegalovirus and porcine hemagglutinating encephalomyelitis virus in individual cases.

CONCLUSION

The pathogenicity and molecular epidemiology of this new circovirus, alone or in the context of co-infections, warrants further investigations.

Faecal virome of red foxes from peri-urban areas

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High-throughput sequencing and viral metagenomic analysis were performed on faecal samples of juvenile and adult foxes.

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Fox picobirnavirus was more closely related to the porcine and human picobirnaviruses than to fox picobirnavirus.

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New fox circovirus highly similar to dog circovirus of is de novo asembled from the high-throughput sequencing data.

Red foxes (Vulpes vulpes) are the most abundant carnivore species in the Northern Hemisphere. Since their populations are well established in peri-urban and urban areas, they represent a potential reservoir of viruses that transmit from wildlife to humans or domestic animals. In this study, we evaluated the faecal virome of juvenile and adult foxes from peri-urban areas in central Croatia. The dominating mammalian viruses were fox picobirnavirus and parvovirus. The highest number of viral reads (N = 1412) was attributed to a new fox circovirus and complete viral genome was de novo assembled from the high-throughput sequencing data. Fox circovirus is highly similar to dog circoviruses identified in diseased dogs in USA and Italy, and to a recently discovered circovirus of foxes with neurologic disease from the United Kingdom. Our fox picobirnavirus was more closely related to the porcine and human picobirnaviruses than to known fox picobirnaviruses.

Incidence and detection of beak and feather disease virus in psittacine birds in the UAE

Beak and feather disease is caused by Circovirus, which affects actively growing beak and feather cells of avian species. The disease affects mainly young birds while older birds may overcome the disease with few lasting effects. Due to lack of treatment, the only way to control the disease is through hygiene and early diagnosis. As a diagnostic tool, we have established a Taqman probe based real-time PCR assay to detect the presence of the viral genome in psittacine birds in UAE and reported the incidence of circovirus in different species of psittacine birds. The sensitivity of our assay was found to be very high with detection limit of up to 3.5 fg of DNA in the sample. The mean prevalence of circovirus was found to be 58.33% in African Grey Parrots, 34.42% in Cockatoos, 31.8% in amazon parrots and 25.53% in Macaws.

The Taqman assay is a quick, reliable and sensitive detection method that has been instrumental in identifying this disease that was not previously reported in the region.

False-positive PCR detection of cyclovirus Malawi strain VS5700009 in human cerebrospinal fluid

BACKGROUND

Cyclovirus (CyCV) Malawi strain VS5700009 has recently been discovered and reported in clinical cerebrospinal fluid (CSF) samples. Further epidemiological and case-control studies are warranted. The availability of a highly sensitive and specific detection assay for this new virus is thus crucial.

OBJECTIVES

To evaluate the performance of the first and the only available PCR assay for CyCV-VS5700009.

STUDY DESIGN

A total of 100 CSF samples collected during January-December 2010 were selected for PCR detection of CyCV-VS5700009. Positive PCR amplicons were subjected to sequencing confirmation and BLAST analysis.

RESULTS

Initial PCR screening for CyCV-VS5700009 identified one sample, showing a PCR band of expected size (380 bp). Sequencing and BLAST analysis, however, indicated that the band was 364 bp in length and showed >99% nucleotide homology to a human gene known as nuclear receptor coactivator 6 (NCOA6). Pairwise sequence alignment confirmed that both the forward and reverse PCR primers used had significant homology (>70%) to NCOA6. None of the CSF samples tested were positive for CyCV-VS5700009.

CONCLUSIONS

The original PCR assay for CyCV-VS5700009 detection may have potential cross-reactivity with contaminating human genomic DNA. The assay may be of little diagnostic use on clinical specimens that are rich in host DNA such as biopsy tissues.

Phylogeny of beak and feather disease virus in cockatoos demonstrates host generalism and multiple-variant infections within Psittaciformes

Phylogenetic analyses of the highly genetically diverse but antigenically conserved, single-stranded circular, DNA genome of the avian circovirus, beak and feather disease virus (BFDV) from cockatoo species throughout Australia demonstrated a high mutation rate for BFDV (orders of magnitude fall in the range of 10(-4) substitutions/site/year) along with strong support for recombination indicating active cross-species transmission in various subpopulations. Multiple variants of BFDV were demonstrated with at least 30 genotypic variants identified within nine individual birds, with one containing up to 7 variants. Single genetic variants were detected in feathers from 2 birds but splenic tissue provided further variants. The rich BFDV genetic diversity points to Australasia as the most likely geographical origin of this virus and supports flexible host switching. We propose this as evidence of Order-wide host generalism in the Psittaciformes characterised by high mutability that is buffered by frequent recombination and slow replication strategy.

First detection of circovirus-like sequences in amphibians and novel putative circoviruses in fishes

The negative samples of a collection, established originally for seeking new adeno- and herpesviruses in lower vertebrates, were screened for the pres-ence of circoviruses by a consensus nested PCR targeting the gene coding for the replication-associated protein. Six fish samples representing five species, namely asp (Aspius aspius), roach (Rutilus rutilus), common bream (Abramis brama), round goby (Neogobius melanostomus) and monkey goby (Neogobius fluviatilis), as well as three frog samples were found positive for circoviral DNA. Sequence analysis of the amplicons indicated the presence of three novel putative circo-like viruses and a circovirus in Hungarian fishes and one novel circovirus in a common toad (Bufo bufo), and another one in a dead and an alive specimen of green tree frog (Litoria caerulea), respectively. In phylogeny reconstruction, the putative bream circovirus clustered together with circoviruses discovered in other cyprinid fishes recently. Three other piscine circoviral sequences appeared closest to sequences derived from different environmental samples. Surprisingly, the nucleotide sequence derived from two fish samples (a bream and a monkey goby) proved to be from porcine circovirus 2 (PCV2), almost identical to a sequence detected in Sweden previously. This is the first report on the detection of PCV2 in fish and circoviral DNA in amphibian hosts.

Dynamics of antibody response and viraemia following natural infection of porcine circovirus 2 (PCV-2) in a conventional pig herd

Porcine circovirus 2 (PCV-2) is a primary agent of post-weaning multi-systemic wasting syndrome (PMWS), ubiquitous in pig herds. The course of viraemia and seroconversion in naturally infected pigs were investigated in piglets from the 2nd week of their life. Piglets were divided into seropositive (Ab(+)) and seronegative (Ab(-)) groups. Subsequently, after vaccination against PCV-2 (Ingelvac(®) CIRCOFLEX™, Böehringer Ingelheim), they were further divided into non-vaccinated seronegative (NVAC/Ab(-)) and seropositive (NVAC/Ab(+)), and vaccinated seronegative (VAC/Ab(-)) and seropositive (VAC/Ab(+)). PCV-2 colostral antibodies failed to prevent development of natural PCV-2 infection in conventional piglets; however, this occurred at a higher age in comparison with seronegative pigs. Neither colostral nor post-infection antibodies prevented development of viraemia, which persisted up to the end of the study (the 19th week), but without clinical signs of PMWS. Vaccination failed to prevent development of natural PCV-2 infection, but viraemia was limited to between the 8th and 10th week. The presence of colostral anti-PCV-2 antibodies did not show any untoward effect to vaccination; on the contrary, VAC/Ab(+) animals showed the lowest titre of viraemia.

Ear necrosis syndrome in weaning pigs associated with PCV2 infection: A case report

Porcine necrotic ear syndrome (PNES) in pigs has been reported as an increasing health problem in many countries with intensive pig farming. The etiology of this disease is complex and the presumed triggering factors can be divided into infectious and non-infectious agents. The present report describes a case of Porcine Circovirus type 2 (PCV2), infection associated with lesions of PNES at the weaning stage of a farrow-to-finish pig farm. Approximately 35% of weaners (1-3 weeks after weaning) presented clinical symptoms similar to Post-weaning Multisystemic Wasting Syndrome (PMWS). About 2-3 weeks after weaning the first lesions of PNES occurred in approximately 20% of pigs, resulting in a significant health problem characterized by poor growth or severe wasting and finally mortality up to 15% in some batches. Moreover, approximately 5% of survived weaners, during growing / finishing stage, presented poor growth and secondary co-infections that lead to death. The present study based on the clinical signs, serological and pathological examinations, indicates that weaners suffered by sub-acute PCV2 infection resulting in PMWS associated with PNES. The lesions of PNES were initially observed at the same period (4-8 weeks of age) with the higher seroprevalence of PCV2 infection. Metaphylaxis of this case included intramuscular injection of florfenicol for the treatment and control of skin lesions and respiratory signs. Moreover, piglets were vaccinated against PCV2. In conclusion, sub-acute PCV2 infection could be included in triggering factors PNES in weaners. The mass vaccination against PCV2 of infected piglets might be effective in reduction of clinical signs and losses of PNES in cases of PCV2 infection associated with PNES.