Detection of Circovirus in Foxes with Meningoencephalitis, United Kingdom, 2009-2013

Epidemiological and evolutionary analysis of canine circovirus from 1996 to 2023

BACKGROUND

Canine circovirus (CanineCV), a non-enveloped virus with a circular DNA genome, has been identified in various avian and mammalian species, including domestic and wild canids. This study aimed to comprehensively analyze the prevalence of CanineCV across diverse animal species in 11 provinces of China.

RESULTS

A total of 1,666 serum samples were collected, revealing a 5.82% prevalence of CanineCV in dogs, with the highest rates being observed in southern and eastern China. Phylogenetic analysis of 266 global CanineCV genomes sourced from the NCBI identified six distinct genotypes, elucidating the complex dynamics of their evolution. Evidence suggested a potential bat origin for CanineCV, with positive selection and high rates of evolution being observed. Recombination analysis revealed dynamic genetic exchange, highlighting the intricate nature of CanineCV evolution. Mutational analysis identified key amino acid substitutions likely to influence the virus's adaptation. Additionally, glycosylation, palmitoylation, and SUMOylation sites were predicted, shedding light on crucial functional properties of the virus.

CONCLUSIONS

This study provides a global perspective on the origin, genetic diversity, and evolutionary dynamics of CanineCV. Understanding these factors is crucial for elucidating its epidemiology and potential health risks.

Molecular Detection of Viral and Bacterial Pathogens in Red Foxes (Vulpes vulpes) from Italy

Animals, including wildlife, are part of One-Health concept since many infectious diseases can affect both humans and animals. In this study, 126 red foxes (Vulpes vulpes) from Northern Italy in 2022-2023 were tested by molecular assays for Protoparvovirus carnivoran 1 (PPVC-1), Canine adenovirus type 1 and 2 (CAdV-1 and CAdV-2), Circovirus canine (CanineCV), Canine distemper virus (CDV), and Leptospira spp. A total of 39 of 126 (30.9%) red foxes were infected with at least one pathogen and five of these were coinfected: 20/126 (15.9%) red foxes tested positive for PPVC-1, 3/126 (2.4%) for CAdV, 20/126 (15.9%) for CanineCV, and 2/126 (1.6%) for Leptospira spp. DNA. No foxes tested positive for CDV RNA. The pathogens identified were genetically analysed. New findings were reported such as a fox with multiple feline panleukopenia virus (FPV) and canine parvovirus type 2b (CPV-2b) infection associated with quasispecies dynamics, typical genetic characteristics of the identified CanineCV, and the first detection in red foxes of Leptospira ST198 related to L. interrogans serogroup Australis. Further studies are necessary to investigate the transmission between domestic animals and wildlife and to understand the role of red foxes in the maintenance of these pathogens not only in the wild but also in urban and peri-urban environments.

Effect of formalin-fixation and paraffin-embedded tissue storage times on RNAscope in situ hybridization signal amplification

RNAscope in situ hybridization (ISH) detects target RNA in formalin-fixed, paraffin-embedded (FFPE) tissues. Protocols suggest that prolonged FFPE storage and formalin fixation may impact signal detection, potentially limiting the utility of RNAscope ISH in retrospective studies. To develop parameters for RNAscope use with archived specimens, we evaluated the effect of formalin-fixation time by measuring the signal of a reference gene (16srRNA) in selected tissues fixed in 10% neutral-buffered formalin for 1, 2, 3, 5, 7, 10, 14, 21, 28, 60, 90, 180, and 270 d. The signal intensity and percent area of signal decreased after 180 d. Tissues had detectable signal at 180 d but not at 270 d of formalin fixation. To assess target detection in paraffin blocks, we qualitatively compared the signal of canine distemper virus (CDV) antigen via immunohistochemistry and CDV RNA via RNAscope ISH in replicate sections from blocks stored at room temperature for 6 mo, 1, 3, 6, 8, 11, 13, and 15 y; RNA was detected in FFPE tissues stored for up to 15 y. Our results demonstrate that RNAscope ISH can detect targets in tissues with prolonged paraffin storage intervals and formalin-fixation times.

Emergence of novel circoviruses in humans and pigs and their possible importance for xenotransplantation and blood transfusions

BACKGROUND

As sequencing is becoming more broadly available, virus discovery continues. Small DNA viruses contribute to up to 60% of the overall virus load in pigs. Porcine circoviruses (PCVs) are small DNA viruses with a single-stranded circular genome. They are common in pig breeds and have not been properly addressed for their potential risk in xenotransplantation. Whereas PCV1 is non-pathogenic in pigs, PCV2 has been associated with various disease manifestations. Recently two new circoviruses have been described, PCV3 and PCV4. While PCV4 is currently present mainly in Asia, PCV3 is widely distributed, and has been identified in commercial pigs, wild boars, and pigs generated for xenotransplantation. In one case PCV3 was transmitted by pigs to baboons via heart transplantation. PCV3 pathogenicity in pigs was controversial initially, however, the virus was found to be associated with porcine dermatitis and nephropathy syndrome (PDNS), reproductive failure, and multisystemic inflammation. Inoculation studies with PCV3 infectious clones confirmed that PCV3 is pathogenic. Most importantly, recently discovered human circoviruses (CV) are closely related to PCV3.

METHODS

Literature was evaluated and summarized. A dendrogram of existing circoviruses in pigs, humans, and other animal species was created and assessed at the species level.

RESULTS

We found that human circoviruses can be divided into three species, human CV1, CV2, and CV3. Human CV2 and CV3 are closest to PCV3.

CONCLUSIONS

Circoviruses are ubiquitous. This communication should create awareness of PCV3 and the newly discovered human circoviruses, which may be a problem for blood transfusions and xenotransplantation in immune suppressed individuals.

Epidemiology and genotypic diversity of canine circovirus identified in pet dogs in Harbin, China

Canine circovirus (CanineCV) is a single-stranded DNA virus that circulates in dogs and wild carnivores around the world. It has been suggested to be associated with diseases of respiratory and gastrointestinal systems, though its pathogenic potential remains unclear. Currently, CanineCV is divided into six genotypes (genotype 1-6), and genotypes 2, 3, and 4 have been described in China. In this study, 359 blood samples from pet dogs with or without clinical signs were collected in Harbin city. After PCR screening, a total of 34 samples were tested positive for CanineCV, and nine full-length genome sequences were recovered from positive samples. Pairwise sequence comparison showed that they shared 82.4-99.3% genome-wide identity with other CanineCVs available in GenBank. Additionally, recombination events were detected, all of which were determined to be associated with sequences obtained in China. The reconstructed phylogenetic tree based on the recombination-free complete genome sequences revealed that the complete genome sequences generated herein were clustered into genotypes 1 and 3. Furthermore, purifying selection was the dominant evolutionary pressure acting on the genomes of CanineCV. These results expand the knowledge about the genetic diversity of CanineCV circulating in China, and also promote us to better understand the evolution of CanineCV.

Canine circovirus among dogs and cats in China: first identification in cats

Canine circovirus (CanineCV) is a virus associated with respiratory and digestive diseases in dogs and often occurs in coinfections with other pathogens, thereby aggravating the symptoms of infected dogs. CanineCV was first reported in the United States in 2012. Subsequently, it was reported among dogs in Europe, Asia, and South America. To investigate the prevalence of CanineCV in dogs in China, 331 dog samples were collected in this study. The PCR results showed that 9.06% (30/331, 95% CI = 6.2% ~ 12.7%) of the dog samples were CanineCV positive. CanineCV has also been detected in some carnivorous wild animals, indicating the potential risk of cross-species transmission of this virus. And, cats are also one of the most common pets in our daily lives, who is close contact with dogs. Thus, this study first investigated the prevalence of CanineCV in cats. The PCR results showed that 3.42% (14/409, 95% CI = 1.9% ~ 5.7%) of the cat samples were CanineCV positive. Moreover, 14 canine-derived CanineCV whole genomes and the first cat-derived CanineCV whole genome were obtained in this study. Rep and Cap are the major nonstructural proteins and structural proteins of CanineCV, respectively. In nucleic acid homology analyses, these 15 CanineCV strains showed a high degree of variation in Rep (85.9 ~ 99%) and Cap (85.6 ~ 100%). In phylogenetic analyses, the 15 CanineCV strains clustered into 3 different genotypes (genotypes 1, 3, and 4). Among them, the first cat-derived CanineCV belonged to CanineCV-3. In addition, 4 genetic recombination events were predicted in these 15 CanineCV strains, occurring in multiple regions of the genome. In conclusion, this study is the first to provide evidence of CanineCV infection in cats and successfully obtained the first whole genome of cat-derived CanineCV. The complex circulation and high prevalence of CanineCV among dogs and cats emphasize the importance of continuous monitoring of this virus in various animal species.

Molecular epidemiology of Canine circovirus in domestic dogs and wildlife in Namibia, Africa

Canine circovirus (CanineCV) is a DNA virus affecting domestic dogs and other wild carnivore species. Despite the potential implications for dogs' health and wildlife conservation, data on CanineCV presence, epidemiology and genetic features from Africa is still poor. In the present study, biological specimens collected between 2020 and 2022 from a total of 32 jackals and 575 domestic dogs were tested for the presence of CanineCV DNA to evaluate its frequency. Furthermore, sequencing was conducted on positive samples to characterize the strains and compare them with publicly available sequences through phylogenetic analysis. A high CanineCV prevalence was observed both in jackals (43.75%; 95 CI: 28.17% - 60.67%) and domestic dogs (27.13%; 95 CI: 23.66% - 30.91%). All aside from one Namibian strain formed an independent clade, suggestive of extremely rare introduction events, followed by local persistence, circulation, and evolution. Remarkably, different recombination events were observed involving strains from both jackals and domestic dogs, which testify to the likely strain exchange between these populations. Distinctive amino acid residues were also observed in jackals. The limitations of the considered host populations however prevent a definitive conclusion on host adaptation, biological, and clinical features. Further studies should be performed to expand our current knowledge of the CanineCV disease scenario in Namibia, other African regions, and associated host species in Africa.

Canine circovirus: An emerging or an endemic undiagnosed enteritis virus?

Canine Circovirus (CanineCV) belongs to the family Circoviridae. It is an emerging virus described for the first time in 2011; since then, it has been detected in different countries and can be defined as worldwide distribution virus. CanineCV infects domestic and wild canids and is mainly related to hemorrhagic enteritis in canines. However, it has been identified in fecal samples from apparently healthy animals, where in most cases it is found in coinfection with other viral agents such as the canine parvovirus type-2 (CPV). The estimated prevalence/frequency of CanineCV has been variable in the populations and countries where it has been evaluated, reaching from 1 to 30%, and there are still many concepts to define the epidemiological characteristics of the virus. The molecular characterization and phylo-evolutive analyses that allow to postulate the wild origin and intercontinental distribution of the virus. This review focuses on the importance on continuing research and establish surveillance systems for this emerging virus.

Viromic analysis of feces from laboratory rabbits reveals a new Circovirus

BACKGROUND

Members of the genus Circovirus with the family Circoviridae are responsible for fatal diseases that can affect mammals and birds. Beak and feather disease virus (BFDV) is responsible for fatal diseases that could affect birds, causing the psittacine beak and feather disease. The current study discovered a new Circovirus from feces of laboratory rabbits and name it RabCV, which shows close relationship to BFDVs.

RESULTS

We investigated the feces virome of 10 laboratory rabbits using the viral metagenomic method. In these samples, we detected a new rabbit-associated Circovirus (RabCV) and performed phylogenetic analysis based on replication-associated (Rep) protein. The result showed that the RabCV was closely clustered with BFDVs, sharing the identity of 56.7%-57.2% with them based on the whole genome sequence. PCR screening in a cohort of 38 laboratory rabbits showed that 3 out of the 38 rabbits were positive for this new rabbit-associated Circovirus.

CONCLUSION

A new Circovirus was discovered from feces of rabbits, which showed low prevalence in the healthy laboratory rabbits. BFDV is responsible for fatal diseases that could affect birds, which suggested that the potential threat of the new rabbit-associated Circovirus to the health of laboratory rabbits needs further study.

Detection of canine circovirus in dogs infected with canine parvovirus

Since the first detection of canine circovirus (CanineCV), several reports have been published over the last decade about the worldwide distribution of this emerging virus of dogs. In order to investigate the prevalence and genomic features of CanineCV in Iranian dogs, a total of 203 dog faecal samples was collected between February and November 2018 from five different geographical regions and screened by real-time PCR (qPCR). Thirteen dogs (6.4%) tested positive for CanineCV DNA, all being detected in co-infections with the highly virulent canine parvovirus (CPV). Three partial replicase nucleotide sequences of the detected CanineCV strains were obtained and compared with the reference sequences deposited in the GenBank database. The Iranian CanineCV sequences had a nucleotide identity of 96.4-98.2% each to other and of 88.3-98.2% with other sequences available on the GenBank. Phylogenetic analysis showed that the Iranian sequences are more closely related to Turkish strains than to strains reported from other countries. The present study provides new insights into the CanineCV molecular epidemiology and its possible role as a co-infectious pathogen.

Pathogen Screening for Possible Causes of Meningitis/Encephalitis in Wild Carnivores From Saxony-Anhalt

Inflammation in meninges and/or brain is regularly noticed in red foxes and other wild carnivores during rabies control programs. Despite negative rabies virus (RABV) results, the etiologies of these cases remain unknown. Thus, the aim of this study was to provide an overview of the occurrence of pathogens that may cause diseases in the brains of wild carnivores and pose a risk to humans and other animals. In addition to RABV and canine distemper virus (CDV), a variety of pathogens, including members of Flaviviridae, Bornaviridae, Herpesviridae, Circoviridae, as well as bacteria and parasites can also cause brain lesions. In 2016 and 2017, brain samples of 1,124 wild carnivores were examined by direct fluorescent antibody test for RABV as well as (reverse-transcriptase) quantitative polymerase chain reaction (PCR) for the presence of CDV as part of a monitoring program in Saxony-Anhalt, Germany. Here, we applied similar methods to specifically detect suid herpesvirus 1 (SuHV-1), West Nile virus (WNV), Borna disease virus 1 (BoDV-1), canid alphaherpesvirus 1 (CaHV-1), canine parvovirus type 2 (CPV-2), fox circovirus (FoxCV), and Neospora caninum (N. caninum). Further, bacteriogical examination for the existence of Listeria monocytogenes (L. monocytogenes) and immunohistochemistry of selected cases to detect Toxoplasma gondii (T. gondii) antigen were performed. Of all pathogens studied, CDV was found most frequently (31.05%), followed by FoxCV (6.80%), CPV-2 (6.41%), T. gondii (4/15; 26.67%), nematode larvae (1.51%), L. monocytogenes (0.3%), and various other bacterial pathogens (1.42%). In 68 of these cases (6.05%), multiple pathogen combinations were present simultaneously. However, RABV, WNV, BoDV-1, SuHV-1, CaHV-1, and N. caninum were not detected. The majority of the histopathological changes in 440 animals were inflammation (320/440; 72.73%), predominantly non-suppurative in character (280/320; 87.50%), and in many cases in combination with gliosis, satellitosis, neuronophagia, neuronal necrosis, and/or vacuolization/demyelination, or in single cases with malacia. Thus, it could be shown that wild carnivores in Saxony-Anhalt are carriers mainly for CDV and sometimes also for other, partly zoonotic pathogens. Therefore, the existing monitoring program should be expanded to assess the spill-over risk from wild carnivores to humans and other animals and to demonstrate the role of wild carnivores in the epidemiology of these zoonotic pathogens.

Detection and Genetic Characterization of Canine Adenoviruses, Circoviruses, and Novel Cycloviruses From Wild Carnivores in Italy

Wild carnivores are known to play a role in the epidemiology of several canine viruses, including canine adenoviruses types 1 (CAdV-1) and 2 (CAdV-2), canine circovirus (CanineCV) and canine distemper virus (CDV). In the present study, we report an epidemiological survey for these viruses in free ranging carnivores from Italy. A total of 262 wild carnivores, including red foxes (Vulpes vulpes), wolves (Canis lupus) and Eurasian badgers (Meles meles) were sampled. Viral nucleic acid was extracted and screened by real-time PCR assays (qPCR) for the presence of CAdVs and CanineCV DNA, as well as for CDV RNA. CAdV-1 DNA was detected only in red foxes (4/232, 1.7%) whilst the wolves (0/8, 0%) and Eurasian badgers (0/22, 0%) tested negative. CanineCV DNA was detected in 4 (18%) Eurasian badgers, 4 (50%) wolves and 0 (0%) red foxes. None of the animals tested positive for CDV or CAdV-2. By sequence and phylogenetic analyses, CAdV-1 and CanineCV sequences from wild carnivores were closely related to reference sequences from domestic dogs and wild carnivores. Surprisingly, two sequences from wolf intestines were identified as cycloviruses with one sequence (145.20-5432) displaying 68.6% nucleotide identity to a cyclovirus detected in a domestic cat, while the other (145.201329) was more closely related (79.4% nucleotide identity) to a cyclovirus sequence from bats. A continuous surveillance in wild carnivores should be carried out in order to monitor the circulation in wildlife of viruses pathogenic for domestic carnivores and endangered wild species.

Detection and Genomic Characterization of Canine Circovirus in Iran

Simple Summary

During the last decade, canine circovirus (CaCV) has been repeatedly reported in domestic dogs with and without acute enteritis. Here we report the detection and full genome characterization of CaCV strains from non-diarrheic dogs in Iran. The results showed the circulation of the virus in this country, with Iranian strains segregating from the CaCVs detected in other countries.

Abstract

Canine circovirus (CaCV) is a single-stranded DNA virus that globally circulates in dogs and wild carnivores. Although the pathogenic potential of the virus has not been fully understood yet, CaCV has been suggested to exacerbate the clinical course of other canine viral infections but also to circulate in dogs without clinical signs. In this study, we carried out real-time PCR assays to detect enteric pathogens from 156 canine rectal swabs collected from dogs without enteritis in 3 different regions in Iran. A total of 14 samples tested positive for CaCV and full-length genome sequences were obtained from 6 of the detected strains. Sequence and phylogenetic analyses showed that, despite the distance between the different sample collection sites, all Iranian CaCV strains were closely related and formed a separate clade from extant CaCVs. The present study shows that CaCV is circulating in non-diarrheic dogs in Iran, thus highlighting the need for further epidemiological investigations in Iranian domestic and wild carnivores.

Genomic Rearrangement and Recombination of Porcine Circovirus Type 2 and Porcine Circovirus-Like Virus P1 in China

Porcine circovirus type 2 (PCV2) belongs to the genus Circovirus of the family Circoviridae, and it has been associated with porcine circovirus (associated) disease (PCVD or PCVAD) in pigs. PCVAD is the generic term for a series of disease syndromes that have caused economic losses to the pig industry worldwide. Since the discovery of PCV2 in the late 1990s, the virus has continued to evolve, and novel genotypes have continued to appear. Moreover, there has been recombination between different genotypes of PCV2. This review attempts to illustrate some progress concerning PCV2 in genome rearrangement and genomic recombination with non-PCV2-related nucleic acids, particularly focusing on the porcine circovirus-like virus P1 formed by the recombination of PCV2. The presence of rearranged PCV2 genomes can be demonstrated both in vivo and in vitro, and these subviral molecules ranged from 358 to 1,136 bp. Depending on whether it has the ability to encode a protein, the agents formed by PCV2 recombination can be divided into two categories: porcine circovirus-like viruses and porcine circovirus-like mini agents. We mainly discuss the porcine circovirus-like virus P1 regarding genomic characterization, etiology, epidemiology, and pathogenesis. Further research needs to be conducted on the pathogenicity of other porcine circovirus-like viruses and porcine circovirus-like mini agents and the effects of their interactions with PCV2, especially for the porcine circovirus-like mini agents that do not have protein-coding functions in the genome.

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.

Canine circovirus and Canine adenovirus type 1 and 2 in dogs with parvoviral enteritis

Canine parvovirus type 2 (CPV-2) is one of the most relevant pathogens associated with enteritis in dogs and is frequently reported in association with the detection of other pathogens in faeces. In this study the concomitant presence of Canine circovirus (CanineCV) and Canine adenovirus (CAdV) DNA in faecal or intestine samples of 95 dogs with parvovirus enteritis sampled in Italy (1995–2017) was investigated and the viruses identified were genetically characterised. Potential correlations with the antigenic variant of CPV-2 and with signalment data and outcome were evaluated. Twenty-eight of 95 (29.5%) CPV-2 infected dogs tested positive to other viruses: 7/28 were also positive to CanineCV, 1/28 to CAdV-1, 18/28 to CAdV-2, 1/28 to CanineCV and CAdV-2, and 1/28 to CAdV-1 and CAdV-2. The frequency of CAdV DNA detection and coinfections was significantly higher in purebred dogs compared to mixed breed ones (P = 0.002 and 0.009, respectively). The presence of coinfection was not associated with any other relevant data available, including CPV-2 variant and final outcome. The detection of CanineCV in a dog sampled in 2009 allowed to backdating its circulation in dogs. The eight CanineCV completely sequenced were phylogenetically related to the CanineCV identified in dogs, wolves and a badger from Europe, USA, Argentina and China. Nine CAdV were partially sequenced and phylogenetic analysis showed a separate branch for the oldest CAdV-2 identified (1995). From the results obtained in this study population, CanineCV and CAdV coinfections in dogs with parvoviral enteritis did not result in more severe disease.

Detection and molecular characterization of two canine circovirus genotypes co-circulating in Vietnam

Background

Canine circovirus is reported in dogs in many countries, including the USA, China and Thailand. It has been detected in healthy dogs and dogs with diarrhea, hemorrhagic gastroenteritis, and vasculitis. It comprises five genotypes and is frequently found as a coinfection with canine parvovirus-2 (CPV-2).

Aim

To characterize canine circovirus genotypes co-circulating with CPV-2 in Vietnam.

Method

PCR assessment of 81 CPV-2-positive fecal samples from Vietnamese diarrheic dogs up to seven months of age for other viral enteric pathogens, including canine bocavirus, canine adenovirus, paramyxovirus, canine coronavirus, porcine circovirus-3 and canine circovirus. In addition, eight selected full genome sequences of Vietnamese canine circovirus were analyzed and used for phylogeny.

Results

In total 19.8% of samples were found to be positive for canine circovirus. Phylogeny revealed that the Vietnamese canine circovirus strains were clustered in two different genotypes (genotype-1 and -3). The genetic diversity among Vietnamese canine circovirus was 86.0–87.2%. The nucleotide discrepancy among both genotypes altered the deduced amino acid sequence in 14 and ten residues of the replicase and capsid proteins, respectively. Genetic recombination analysis revealed that the Vietnamese canine circovirus-6 strain has the American and Chinese canine circovirus as its major and minor parents, respectively. Only a single dog revealed triple detections of CPV-2c, Canine circovirus and canine adenovirus (1.2%).

Conclusion

The co-circulation of two different genotypes of canine circovirus and CPV-2c in dogs in Vietnam has been illustrated.

Clinical relevance

The mortality rate with CPV-2 only (22%) doubled in dogs with canine circovirus and CPV-2 co-infection.

Canine Circovirus in Foxes from Northern Italy: Where Did It All Begin?

Canine circovirus (CanineCV) is a recently identified virus affecting both domestic and wild carnivores, including foxes, sometimes in presence of severe clinical signs. Its circulation in wild animals can thus represent a potential threat for endangered species conservation and an infection source for dogs. Nevertheless, no data were available on its circulation in the Alps region of Northern Italy. In the present study, samples collected from 186 foxes in the period 2009–2020 from Valle d’Aosta and Veneto regions were tested using a real-time PCR assay, demonstrating a viral circulation of approximatively 2–5%, depending on the considered regions. Two complete or almost complete genome sequences were obtained, highlighting that the detected strains were part of a so defined “fox only” clade, which suggests that, despite common contact opportunities, Alps foxes are not involved in frequent transmission events to domestic dogs. Such genetic isolation could be at least partially attributed to some sort of independent evolution occurred in the foxes, leading to species barrier. Additionally, CanineCV strains in foxes from Italy were unexpectedly related to those previously identified in foxes from the United Kingdom and Scandinavian area. Combining the history of fox distribution in Europe since the last glacial maximum (LGM) with the viral history allowed us to speculate a long-standing coexistence between European canine circovirus and this host, justifying the peculiar geographic distribution and evolutionary paths of the fox infecting clade.

Integrated Use of Molecular Techniques to Detect and Genetically Characterise DNA Viruses in Italian Wolves (Canis lupus italicus)

Simple Summary

In our study, different quantitative and qualitative molecular techniques were used to detect and genetically characterise Carnivore protoparvovirus 1, Canine adenovirus type 1 and 2 (CAdV-1 and CAdV-2), and Canine circovirus (CanineCV) in Italian wolves (Canis lupus italicus) of the Italian Apennines. Carnivore protoparvoviruses were the most frequently detected viruses, followed by CanineCV and CAdV. All the wolves tested positive for at least one of the DNA viruses screened, and 47.8% of the subjects were coinfected with two or three viruses. From viral sequences analysis, close correlations emerged between the viruses identified in the wolves and those circulating in domestic dogs, suggesting that the same viruses infect wolves and domestic dogs. Further studies are needed to investigate if pathogens are transmitted between the two species.

Abstract

In this study, internal organs (tongue, intestine, and spleen) of 23 free-ranging Italian wolves (Canis lupus italicus) found dead between 2017 and 2019 were tested for Carnivore protoparvovirus 1, Canine adenovirus (CAdV), and Canine circovirus (CanineCV) using real-time PCR assays. Genetic characterisation of the identified viruses was carried out by amplification, sequencing, and analysis of the complete viral genome or informative viral genes. All the wolves tested positive for at least one of the DNA viruses screened, and 11/23 were coinfected. Carnivore protoparvoviruses were the most frequently detected viruses (21/23), followed by CanineCV (11/23) and CAdV (4/23). From the analysis of the partial VP2 gene of 13 carnivore protoparvoviruses, 12 were canine parvovirus type 2b, closely related to the strains detected in dogs and wild carnivores from Italy, and one was a feline panleukopenia-like virus. Of the four CAdV identified, two were CAdV-1 and two were CAdV-2. The complete genome of seven CanineCVs was sequenced and related to the CanineCV identified in dogs, wolves, and foxes worldwide. Close correlations emerged between the viruses identified in wolves and those circulating in domestic dogs. Further studies are needed to investigate if these pathogens may be potentially cross-transmitted between the two species.

Molecular detection of porcine circovirus type 3 in Shanxi Province, China

Porcine circovirus type 3 (PCV3), which was first detected in the United States of America in 2015, is a potential threat to the swine industry. However, the prevalence of PCV3 in Shanxi Province, China, is unclear. In this research, the prevalence and genetic diversity of PCV3 were investigated in above area. Lung tissue samples (n = 491) from 19 pig slaughterhouses across 11 cities throughout Shanxi Province were analyzed for PCV3 infection by PCR in 2019. The results showed that PCV3 positive rates in slaughterhouses and individuals were 100% (19/19) and 86.76% (426/491), respectively. PCV2 and PCV3 double-positive rates in slaughterhouses and individuals were 100% (19/19) and 59.27% (291/491), respectively. PCR positive samples were further sequenced and 8 PCV3 isolates were identified. The nucleotide homology of these isolates with other PCV3 isolates in NCBI database was 97.45–99.90%. A phylogenetic analysis, based on the complete genomic sequence and ORF2, divided these PCV3 strains into 2 major groups. Based on A24/V and R27/K amino acid mutations of capsid protein, the 8 identified PCV3 strains were separated to 2 clades. This was the first detailed investigation into the epidemiology of PCV3 in Shanxi Province. Our findings enabled us to assess the possibility of widespread transmission from this region. Thus, current findings establish a basis for further studies of genetic variations in PCV3 strains circulating in China.

Cyclovirus detection in Chilean adults with and without community-acquired pneumonia

Cycloviruses (CyV) (genus Cyclovirus, family Circoviridae) are nonenveloped DNA viruses. The first report in humans was in 2010 and research has focused only on disease-associated human sample detection. The only HuACyV (CyCV-ChileNPA1, HuACyV10) reported in the Chilean population was in children (3.3%) with an acute respiratory infection. Its detection in respiratory samples from adults, with/without respiratory disease remains unknown. The aim of this study was to detect HuACyV10 in adults with and without respiratory disease. HuACyV10 was studied in nasopharyngeal swabs from 105 hospitalized adults with community-acquired pneumonia (CAP) and 104 adults without respiratory symptoms. Total nucleic acids were extracted, and viral rep and cp gene fragments were amplified by real-time polymerase chain reaction. HuACyV10 was detected in 19.05% adults with CAP and in 0.96% asymptomatic adults, being significantly higher in adult CAP than asymptomatic (n = 1) ones (p = 0.0001). C _t values were between 26.7 and 39.6, and the median was 34.1 for rep and 33.8 for the CAP in adults CAP (p = 0.68), and 35.7 and 36.0, respectively, in the asymptomatic case. HuACyV10 detection in CAP adults concentrated in the Autumn-Winter season of the Southern hemisphere. The only asymptomatic adult with HuACyV10 was detected in the Spring-Summer period. In this first report of HuACyV10 in respiratory samples from adults, detection was significantly higher in CAP than in asymptomatic adults. As the sensitivity of both rep and cp genes was similar, both can be applied for detecting HuACyV10. It would be advisable to investigate the pathogenic role of HuACyV10 in adult respiratory infections. ​.

Circovirus in Blood of a Febrile Horse with Hepatitis

Circoviruses infect vertebrates where they can result in a wide range of disease signs or in asymptomatic infections. Using viral metagenomics we analyzed a pool of five sera from four healthy and one sick horse. Sequences from parvovirus-H, equus anellovirus, and distantly related to mammalian circoviruses were recognized. PCR identified the circovirus reads as originating from a pregnant mare with fever and hepatitis. That horse's serum was also positive by real time PCR for equine parvovirus H and negative for the flavivirus equine hepacivirus. The complete circular genome of equine circovirus 1 strain Charaf (EqCV1-Charaf) was completed using PCR and Sanger sequencing. EqCV1 replicase showed 73-74% identity to those of their closest relatives, pig circoviruses 1/2, and elk circovirus. The closest capsid proteins were from the same ungulate circoviruses with 62-63% identity. The overall nucleotide identity of 72% to its closest relative indicates that EqCV1 is a new species in the Circovirus genus, the first reported in genus Equus. Whether EqCV1 alone or in co-infections can result in disease and its prevalence in different equine populations will require further studies now facilitated using EqCV1's genome sequence.

First detection and full genomic analysis of Canine Circovirus in CPV-2 infected dogs in Colombia, South America

Canine Circovirus (CanineCV) is an emerging virus which since its first report in USA in 2012, it has been described worldwide. It was the second mammalian circovirus species identified in dogs and its role in canine enteritis is still being uncertain as much as its association in disease with the Canine Parvovirus-2 (CPV-2). Here, we aim to confirm for the first time the presence of CanineCV in Colombia and to develop phylogenetic evolutive analyses of CanineCV in CPV-2 positive animals. DNA from samples were extracted and PCR, full genome sequencing and phylogenetic analysis was performed to detect and characterize CanineCV. From a total of 30 CPV-2 positive samples, 16.6% (n = 5) were positives for CanineCV. Sequencing analysis of Colombian CanineCV wild-type strains displayed high identity to each other (99.5–99.7% nt; 99.7% aa). The full genome phylogenetic analysis confirmed that worldwide reported CanineCV strains were separated into four distinct genotypes in addition to a European origin of the South American CanineCV strains. This study demonstrated the importance of continue surveillance of emerging viruses in canine populations and confirm for the first time the circulation and origin of CanineCV in Colombia.

Ancient origin and genetic segregation of canine circovirus infecting arctic foxes (Vulpes lagopus) in Svalbard and red foxes (Vulpes vulpes) in Northern Norway

Canine circovirus (CanineCV) is a relatively new viral species, belonging to the family Circoviridae, whose pathogenic role is still uncertain. Since its first description in one domestic dog in 2011 from the USA, several reports have been documenting its distribution worldwide. Recently, CanineCV was also detected in wild animals such as wolves, foxes and badgers. In order to investigate the presence and the genetic characteristics of CanineCV in foxes of Arctic and Sub-Arctic regions, the presence of CanineCV DNA in internal organs (liver and spleen) of 51 arctic foxes (Vulpes lagopus) from Svalbard archipelago and 59 red foxes (Vulpes vulpes) from Northern Norway, sampled from 1996 to 2001 and from 2014 to 2018, respectively, was screened by real-time PCR. CanineCV was detected in 11/51 arctic foxes and in 10/59 red foxes, backdating the circulation of the virus at least to 1996 in the arctic fox population. The complete genome of 14 identified CanineCV was sequenced and analysed showing an identity higher than 80.8% with the reference strains available to date. According to the species demarcation threshold of 80% genome-wide nucleotide sequence identity for members of the family Circoviridae provided by International Committee on Taxonomy of Viruses (ICTV), all the CanineCV belong to a single species. Phylogenetic analysis revealed that all the CanineCV were subdivided into five main clusters with one including only CanineCV identified in foxes. Furthermore, CanineCV identified in arctic foxes and red foxes formed two distinct lineages. From these data, we hypothesize that the viral transmission did not occur between the two species of foxes as a consequence of the lack of contact between the two hosts or that the virus acquired mutations in the time elapsed between the samplings.

Development of a recombinase-aided amplification assay for rapid and sensitive detection of porcine circovirus 3

Porcine circovirus type 3 (PCV3) is a novel member of the genus Circovirus, first detected in the United States in 2016, with subsequent reports in many countries. PCV3 infections have caused serious economic losses in the pig industry. Alternative rapid and sensitive assays for PCV3 detection are needed for clinical diagnosis, especially in laboratories not equipped with more sophisticated equipment. Here, a real-time recombinase-aided amplification assay (RAA) was developed for PCV3 detection. Specific primers and probes targeting the conserved region of the capsid gene of PCV3 were designed. The assay was performed at 39 °C for 30 min using specialized equipment. Furthermore, 36 clinical samples were used to evaluate the RAA. The analytical sensitivity of the RAA for PCV3 was 38 copies per reaction at 95% probability level, using a probit regression model. There was no cross-reactivity with other DNA viruses belonging to the Circoviridae and Parvoviridae families. The detection rate agreed with that obtained by an established real-time PCR assay with a kappa value of 1.0. Our results demonstrated that this new RAA could be used for the rapid, accurate, and sensitive detection of PCV3.

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.

Infectious Causation of Abnormal Host Behavior: Toxoplasma gondii and Its Potential Association With Dopey Fox Syndrome

The apicomplexan parasite Toxoplasma gondii, the causative agent of toxoplasmosis, can infect all warm-blooded animals. T. gondii can subtly alter host behaviors-either through manipulation to enhance transmission to the feline definitive host or as a side-effect, or "constraint," of infection. In humans, T. gondii infection, either alone or in association with other co-infecting neurotropic agents, has been reliably associated with both subtle behavioral changes and, in some cases, severe neuropsychiatric disorders, including schizophrenia. Research on the potential impact of T. gondii on the behavior of other long-lived naturally infected hosts is lacking. Recent studies reported a large number of wild red foxes exhibiting a range of aberrant behavioral traits, subsequently classified as Dopey Fox Syndrome (DFS). Here we assessed the potential association between T. gondii and/or other neurotropic agents with DFS. Live, captive foxes within welfare centers were serologically tested for T. gondii and, if they died naturally, PCR-tested for vulpine circovirus (FoxCV). Post-mortem pseudo-control wild foxes, obtained from pest management companies, were PCR-tested for T. gondii, FoxCV, canine distemper virus (CDV), canine adenovirus type (CAV)-1 and CAV-2. We also assessed, using non-invasive assays, whether T. gondii-infected foxes showed subtle behavioral alterations as observed among infected rodent (and other) hosts, including altered activity, risk, and stress levels. All foxes tested negative for CAV, CDV, CHV, and DogCV. DFS was found to be associated with singular T. gondii infection (captives vs. pseudo-controls, 33.3% (3/9) vs. 6.8% (5/74)) and singular FoxCV infection (66.7% (6/9) vs. 11.1% (1/9)) and with T. gondii/FoxCV co-infection (33.3% (3/9) vs. 11.1% (1/9)). Overall, a higher proportion of captive foxes had signs of neuroinflammation compared to pseudo-controls (66.7% (4/6) vs. 11.1% (1/9)). Consistent with behavioral changes seen in infected rodents, T. gondii-infected foxes displayed increased attraction toward feline odor (n=6 foxes). These preliminary results suggest that wild foxes with DFS are infected with T. gondii and likely co-infected with FoxCV and/or another co-infecting neurotropic agent. Our findings using this novel system have important implications for our understanding of both the impact of parasites on mammalian host behavior in general and, potentially, of the infectious causation of certain neuropsychiatric disorders.

Molecular characterization of canine astrovirus, vesivirus and circovirus, isolated from diarrheic dogs in Turkey

BACKGROUND

Canine astrovirus (CAstV) has been considered the primary cause of gastroenteritis in young animals worldwide, while canine vesivirus (CVeV) and canine circovirus (CCiV) are occasionally reported.

AIMS

This study aimed to investigate the existence and molecular characteristics for these three viruses in Turkey. Methods: Faecal samples from 150 shelter dogs with gastrointestinal problems (127 adults and 23 puppies) were collected and examined by reverse transcription-polymerase chain reaction (RT-PCR) analysis based on the partial sequence of RdRp gene (ORF1b) for CAstV, ORF2 gene of CVeV and capsid protein (Cap) and replication associated protein (Rep) gene of CCiV. Randomly selected positive samples were submitted to sequencing and molecular analyses were conducted based on partial sequences.

RESULTS

It was found that 66% (99/150) of diarrhoeic dogs were positive for CAstV, 3.33% (5/150) for CVeV, and 6% (9/150) for CCiV. Four sub-genotypes for CAstV and two sub-genotypes for CVeV were suggested according to molecular analyses. The phylogenetic relationship of CCiV with other strains obtained from various areas was further demonstrated.

CONCLUSION

This study emphasizes the importance of emerging viruses for canids, classification of them and their proportional contribution in gastroenteritis cases. We concluded that astrovirus infection must be considered as the major cause of diarrhea in dogs; However, the prevalences of vesivirus and circovirus were relatively low in cases makes them less important in Turkey.

Does porcine circovirus type 3 (PCV3) interfere with porcine circovirus type 2 (PCV2) vaccine efficacy?

PCV2 is globally spread pathogen involved in a number of diseases (PCVD). Commonly used vaccines against PCV2 are proved to be highly efficacious. The role of recently discovered PCV3 for pig health and interference with PCV2 remains unknown. The study performed on serum samples from seven farms vaccinated against PCV2 and four non-vaccinated showed very low prevalence of PCV2 viremia in the former (3 out of 106 positive serum pools) and high prevalence of PCV2 viremia in the latter (35 out of 60 positive pools). Mean log₁₀ PCV2 genome equivalents were lower in vaccinated farms (4.8 ± 0.6 log₁₀  copies/ml) than in non-vaccinated farms (6.3 ± 1.3 log₁₀  copies/ml). PCV3 was detected in 31 out of 106 and 12 out of 60 serum pools from vaccinated and non-vaccinated farms, respectively. Mean log₁₀ PCV3 genome equivalents were significantly (p < 0.05) lower in vaccinated farms (3.9 ± 0.8 log₁₀  copies/ml) than in non-vaccinated farms (4.4 ± 0.6 log₁₀  copies/ml). Concurrent PCV2 and PCV3 infection was rare and found only in 1 out of 529 and 4 out of 292 individual serum samples from vaccinated and non-vaccinated farms, respectively. Our results showed lack of impact of PCV3 circulation on PCV2 vaccine efficacy. On the other hand, intensive PCV2 circulation and high viremia detected in non-vaccinated farms did not seem to increase the level of PCV3 infection.

Development of a droplet digital polymerase chain reaction for sensitive and simultaneous identification of porcine circovirus type 2 and 3

In this study, a sensitive assay for simultaneous detection of porcine circovirus type 2 (PCV2) and type 3 (PCV3) was established using droplet digital PCR (ddPCR). Pairs of primers and probes were specifically designed to amplify PCV2 and PCV3. Specificity of the assay was confirmed by the failure of amplification of DNA of other relevant viruses. The detection limit for ddPCR was 2 copies/μL for PCV2 and 1 copy/μL for PCV3, a 3- and 10-fold greater sensitivity than TaqMan real-time PCR, respectively. Both methods showed a high degree of linearity, although TaqMan real-time PCR showed less sensitivity than ddPCR for clinical detection. In summary, the results demonstrated that the established ddPCR is an effective alternative method for the precise simultaneous quantification of PCV2 and PCV3 in clinical samples, especially in detecting lower concentrations of co-infected samples.

Insights into the genetic and host adaptability of emerging porcine circovirus 3

Porcine circovirus 3 (PCV3) was found to be associated with reproductive disease in pigs, and since its first identification in the United States, it subsequently spread worldwide, especially in China, where it might pose a potential threat to the porcine industry. However, no exhaustive analysis was performed to understand its evolution in the prospect of codon usage pattern. Here, we performed a deep codon usage analysis of PCV3. PCV3 sequences were classified into two clades: PCV3a and PCV3b, confirmed by principal component analysis. Additionally, the degree of codon usage bias of PCV3 was slightly low as inferred from the analysis of the effective number of codons. The codon usage pattern was mainly affected by natural selection, but there was a co-effect of mutation pressure and dinucleotide frequency. Moreover, based on similarity index analysis, codon adaptation index analysis and relative codon deoptimization index analysis, we found that PCV3 might pose a potential risk to public health though with unknow pathogenicity. In conclusion, this work reinforces the systematic understanding of the evolution of PCV3, which was reflected by the codon usage patterns and fitness of this novel emergent virus.

Detection and sequencing of porcine circovirus 3 in commercially sourced laboratory mice

Porcine circovirus 3 (PCV3), a recently discovered virus, has spread widely in pigs throughout the world. In order to investigate the possibility of mice used to study the infection of PCV3, commercially sourced Balb/C and ICR mice were screened for PCV3 infection. Blood samples were collected from 20 mice (10 each of Balb/c and ICR), DNA was extracted, and subjected to PCR with PCV3 specific primers. We found all 20 serum samples tested positive for PCV3 DNA. From four mice, the complete genomes of PCV3 were amplified and sequenced, and a phylogenetic tree was constructed. The results showed that the amplified genome was 2000 bp, and sequence comparison showed that the homology of the complete genome and ORF2 gene with those of porcine PCV3 are 97.9%-98.8% and 96.9%-98.3%, respectively. Amino acids alignment results showed that the Cap protein of the mouse PCV3 isolates share 90.7%-96.3% amino acid homology with that of the references strains derived from pigs. Phylogenetic analysis based on ORF2 sequences showed that all PCV3 strains clustered together and were clearly separate from other circovirus species. We detected PCV3 in experimental mice in China for the first time, which is an opportunity to use mice to study the infection of PCV3 and a potential hazard to swine industry.

Molecular detection and genomic characterization of porcine circovirus 3 in pigs from Northeast China

Background

First identified in the United States in 2016, porcine circovirus type 3 (PCV3) is a newly emerging porcine circovirus exhibiting a wide range of clinical syndromes, which may be associated with the pathogenicity observed in pigs.

Results

The aim of this study was to identify and characterize the full genome sequence of PCV3 strains circulating in Northeast China. Herein, 105 lung samples isolated from sick pigs in Northeast China during 2018 were analyzed for PCV3. Using PCR, the total PCV3-positive rate was 33.3% (35/105), with rates of 17.8% (8/45), 66.7% (10/15), and 37.8% (17/45) in Heilongjiang, Jilin, and Liaoning province, respectively. Additionally, our findings showed that PCV3-positive samples had a high rate of co-infection with PCV2, PPV6, and PPV7. To study the evolution of the PCV3 in Northeast China, we sequenced the entire genome of 13 strains of PCV3. The results of phylogenetic analyses revealed that PCV3 could be divided into two clades, PCV3a and PCV3b. Interestingly, a G deletion at position 1072 was found in the 1999 nt genome of PCV3-CN2018LN-4 (MH277118). The G deletion terminated replicase protein translation and induced a truncated replicase protein.

Conclusion

These results contribute to the understanding of PCV3 molecular epidemiology and evolution in Northeast China. A new strain of PCV3 with truncated replicase protein was identified.

Characterization of dog serum virome from Northeastern Brazil

Domestic dogs share habitats with human, a fact that makes them a potential source of zoonotic viruses. Moreover, knowledge regarding possible bloodborne pathogens is important due to the increasing application of blood transfusion in dogs. In the present study, we evaluated the serum virome of 520 dogs using throughput sequencing (HTS). The serum samples were pooled and sequenced using an Illumina MiSeq platform. Our unbiased method identified prevalent canine pathogens as canine protoparvovirus 1 (canine parvovirus 2), undersearched agents as canine bocaparvovirus 1 (minute virus of canines) and canine circovirus, circular viruses closely related to viruses recently found in human samples, and new parvovirus and anelloviruses. The dog virome described in the present work furthers the knowledge concerning the viral population in domestic animals. The present data includes information regarding viral agents that are potentially transmitted through blood transfusion among dogs.

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.

New viruses associated with canine gastroenteritis

A number of novel viruses have been associated with canine gastroenteritis in recent years, from viral families as diverse as Caliciviridae and Picornaviridae to Parvoviridae and Circoviridae. The ability of many of these viruses to cause disease is uncertain, but epidemiological studies are continually adding to our knowledge of these potential pathogens. This review presents a summary of the latest research and current understanding of novel viruses associated with canine gastroenteritis.

Goose Parvovirus and Circovirus Coinfections in Ornamental Ducks

Clinical observations and diagnostic procedures carried out to elucidate the cause of high mortality in 2-8-wk-old ornamental ducks (mandarin, wood, falcated, and silver teal ducks) are described. At necropsy, ducklings showed general pallor of skeletal and heart muscles, subcutaneous gelatinous transudates, pericarditis, ascites, and severe edema and hyperemia of lungs. Histopathologic examination revealed that the most important changes were located in the crop, bursa of Fabricius, and lungs with presence of amorphic basic intracytoplasmic inclusions. No bacteria or fungi could be detected from affected organs and ascitic fluid. Viral diagnosis included molecular detection for the presence of goose parvovirus (GPV), circovirus, avian influenza, herpesviruses, paramyxovirus, reovirus, and polyomavirus. Both GPV and circovirus could be detected by real-time PCR and nested broad-spectrum PCR, respectively. Phylogenetically, full-length nucleotide sequence of GPV showed a close similarity ranging from 95.6% to 97.9% with European and Asian pathogenic GPV. On the other hand, the detected circovirus showed nucleotide identity of 90% to 98% with goose circoviruses (GoCVs). This is the first report of GoCVs and GPV in ornamental ducks. The concurrence of GPV and GoCV infections is thought to contribute to the high mortality.

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.

Pathological findings in the red fox (Vulpes vulpes), stone marten (Martes foina) and raccoon dog (Nyctereutes procyonoides), with special emphasis on infectious and zoonotic agents in Northern Germany

Anthropogenic landscape changes contributed to the reduction of availability of habitats to wild animals. Hence, the presence of wild terrestrial carnivores in urban and peri-urban sites has increased considerably over the years implying an increased risk of interspecies spillover of infectious diseases and the transmission of zoonoses. The present study provides a detailed characterisation of the health status of the red fox (Vulpes vulpes), stone marten (Martes foina) and raccoon dog (Nyctereutes procyonoides) in their natural rural and peri-urban habitats in Schleswig-Holstein, Germany between November 2013 and January 2016 with focus on zoonoses and infectious diseases that are potentially threatening to other wildlife or domestic animal species. 79 red foxes, 17 stone martens and 10 raccoon dogs were collected from traps or hunts. In order to detect morphological changes and potential infectious diseases, necropsy and pathohistological work-up was performed. Additionally, in selected animals immunohistochemistry (influenza A virus, parvovirus, feline leukemia virus, Borna disease virus, tick-borne encephalitis, canine adenovirus, Neospora caninum, Toxoplasma gondii and Listeria monocytogenes), next-generation sequencing, polymerase chain reaction (fox circovirus) and serum-neutralisation analysis (canine distemper virus) were performed. Furthermore, all animals were screened for fox rabies virus (immunofluorescence), canine distemper virus (immunohistochemistry) and Aujeszky's disease (virus cultivation). The most important findings included encephalitis (n = 16) and pneumonia (n = 20). None of the investigations revealed a specific cause for the observed morphological alterations except for one animal with an elevated serum titer of 1:160 for canine distemper. Animals displayed macroscopically and/or histopathologically detectable infections with parasites, including Taenia sp., Toxocara sp. and Alaria alata. In summary, wildlife predators carry zoonotic parasitic disease and suffer from inflammatory diseases of yet unknown etiology, possibly bearing infectious potential for other animal species and humans. This study highlights the value of monitoring terrestrial wildlife following the "One Health" notion, to estimate the incidence and the possible spread of zoonotic pathogens and to avoid animal to animal spillover as well as transmission to humans.

Identification and genetic characterization of porcine circovirus type 3 in China

A novel circovirus called porcine circovirus type 3 (PCV3) was recently reported to exist in the USA. This circovirus is associated with porcine dermatitis, nephropathy syndrome and reproductive failure. This study reports on the first identification, widely epidemic, different phylogenetic clusters, potential role in sow reproductive failure and possible origins of PCV3 in China.

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.

Screening red foxes (Vulpes vulpes) for possible viral causes of encephalitis

Background

Next to various known infectious and non-infectious causes, the aetiology of non-suppurative encephalitis in red foxes (Vulpes vulpes) often remains unclear. Known causes in foxes imply rabies, canine distemper, toxoplasmosis, Aujeszky’s disease, as well as parvovirus, adenovirus, circovirus and flavivirus infections. In this study, particular attention was paid on bornaviruses, since red foxes are predators of bicoloured white-toothed shrews, a reservoir of Borna disease virus 1 (BoDV-1). In addition, foxes are known to be highly susceptible for viruses of the order Mononegavirales.

Methods

Analyses for the presence of anti-BoDV-1 antibodies, BoDV-1-RNA and antigen were performed on 225 blood and 59 brain samples, from a total of 232 red foxes. Foxes originated from BoDV-1 endemic and non-endemic German areas. Additional investigations for the presence of rabies, canine distemper, toxoplasmosis, Aujeszky’s disease, parvovirus, adenovirus and flavivirus infections were carried out on 16 red foxes with non-suppurative (meningo-) encephalitis. A metagenomic analysis was used on three representative brain samples displaying encephalitis.

Results

Among 225 foxes, 37 displayed anti-BoDV-1 antibodies with titres ranging between 1:40 and 1:2560, regardless of geographic origin. In 6 out of 16 foxes with encephalitis, canine distemper virus was detected. No evidence of any of the other investigated agents was found in the 16 fox brains with encephalitis. Metagenomics revealed no infectious agents, except for one already known canine distemper case.

Conclusion

Red foxes can exhibit BoDV-1 specific antibodies without association with geographic origin or encephalitis due to bornavirus infection. The encephalitis pattern was highly conspicuous for a viral infection, but remained unclear in 10 out of 16 foxes. Thus, presently unknown infectious and non-infectious causes need to be considered and further investigated, especially since foxes also tend to occur in human proximity.

WITHDRAWN: Clinical Signs, Neuroanatomical Distribution and Histopathological Characterisation of Meningoencephalitis in Wild Red Foxes (Vulpes vulpes) Associated with a Novel fox Circovirus

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Specific Detection of Two Divergent Simian Arteriviruses Using RNAscope In Situ Hybridization

Simian hemorrhagic fever (SHF) is an often lethal disease of Asian macaques. Simian hemorrhagic fever virus (SHFV) is one of at least three distinct simian arteriviruses that can cause SHF, but pathogenesis studies using modern methods have been scarce. Even seemingly straightforward studies, such as examining viral tissue and cell tropism in vivo, have been difficult to conduct due to the absence of standardized SHFV-specific reagents. Here we report the establishment of an in situ hybridization assay for the detection of SHFV and distantly related Kibale red colobus virus 1 (KRCV-1) RNA in cell culture. In addition, we detected SHFV RNA in formalin-fixed, paraffin-embedded tissues from an infected rhesus monkey (Macaca mulatta). The assay is easily performed and can clearly distinguish between SHFV and KRCV-1. Thus, if further developed, this assay may be useful during future studies evaluating the mechanisms by which a simian arterivirus with a restricted cell tropism can cause a lethal nonhuman primate disease similar in clinical presentation to human viral hemorrhagic fevers.

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.