Ubiquiter circovirus sequences raise challenges in laboratory diagnosis: the case of honey bee and bee mite, reptiles, and free living amoebae

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

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

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

Genomic Diversity of CRESS DNA Viruses in the Eukaryotic Virome of Swine Feces

Replication-associated protein (Rep)-encoding single-stranded DNA (CRESS DNA) viruses are a diverse group of viruses, and their persistence in the environment has been studied for over a decade. However, the persistence of CRESS DNA viruses in herds of domestic animals has, in some cases, serious economic consequence. In this study, we describe the diversity of CRESS DNA viruses identified during the metagenomics analysis of fecal samples collected from a single swine herd with apparently healthy animals. A total of nine genome sequences were assembled and classified into two different groups (CRESSV1 and CRESSV2) of the Cirlivirales order (Cressdnaviricota phylum). The novel CRESS DNA viral sequences shared 85.8–96.8% and 38.1–94.3% amino acid sequence identities for the Rep and putative capsid protein sequences compared to their respective counterparts with extant GenBank record. Data presented here show evidence for simultaneous infection of swine herds with multiple novel CRESS DNA viruses, including po-circo-like viruses and fur seal feces-associated circular DNA viruses. Given that viral genomes with similar sequence and structure have been detected in swine fecal viromes from independent studies, investigation of the association between presence of CRESS DNA viruses and swine health conditions seems to be justified.

Meta-Transcriptomic Discovery of a Divergent Circovirus and a Chaphamaparvovirus in Captive Reptiles with Proliferative Respiratory Syndrome

Viral pathogens are being increasingly described in association with mass morbidity and mortality events in reptiles. However, our knowledge of reptile viruses remains limited. Herein, we describe the meta-transcriptomic investigation of a mass morbidity and mortality event in a colony of central bearded dragons (Pogona vitticeps) in 2014. Severe, extensive proliferation of the respiratory epithelium was consistently found in affected dragons. Similar proliferative lung lesions were identified in bearded dragons from the same colony in 2020 in association with increased intermittent mortality. Total RNA sequencing identified two divergent DNA viruses: a reptile-infecting circovirus, denoted bearded dragon circovirus (BDCV), and the first exogeneous reptilian chaphamaparvovirus—bearded dragon chaphamaparvovirus (BDchPV). Phylogenetic analysis revealed that BDCV was most closely related to bat-associated circoviruses, exhibiting 70% amino acid sequence identity in the Replicase (Rep) protein. In contrast, in the nonstructural (NS) protein, the newly discovered BDchPV showed approximately 31%–35% identity to parvoviruses obtained from tilapia fish and crocodiles in China. Subsequent specific PCR assays revealed BDCV and BDchPV in both diseased and apparently normal captive reptiles, although only BDCV was found in those animals with proliferative pulmonary lesions and respiratory disease. This study expands our understanding of viral diversity in captive reptiles.

Occurrence and genetic diversity of CRESS DNA viruses in wild birds: a Hungarian study

Circoviruses, cycloviruses and other circular, replication-associated protein-encoding single stranded (CRESS) DNA viruses have been detected in a variety of animal taxa. In this study, cloacal swab samples (n = 90) were examined for CRESS DNA viruses from 31 wild bird species living at various aquatic sites in Hungary to identify possible reservoirs of viruses pathogenic to domestic poultry. A total of 30 (33.3%) specimens tested positive with pan-CRESS DNA virus specific PCR. Goose circovirus (GoCV), Duck associated cyclovirus 1 (DuACyV-1) and Garrulus glandarius associated circular virus 1 (GgaCV-1) were detected in nine, three and two different bird species, respectively. Selected specimens were subjected to whole genome sequencing. The obtained sequence data revealed conserved gene structure within the identified virus species and detected homologous (within GoCV) and possible heterologous recombination (within DuACyV-1) events. Results presented here provide new information on the genomic diversity and evolution of selected CRESS DNA viruses.

Blind Trading: A Literature Review of Research Addressing the Welfare of Ball Pythons in the Exotic Pet Trade

Simple Summary

The Ball python is a small species that is commonly kept as an exotic pet across the world. Despite huge numbers of these snakes being kept and traded in the pet industry, there is very little information available about how catching, breeding, transporting and housing them in captivity could impact their welfare. Our study reviewed the published literature for this species and found 88 relevant peer-reviewed scientific papers. Physical health was the predominant focus of research, with numerous studies reporting on disease, injury or clinical treatments. Far fewer papers focused on other aspects of Ball python wellbeing, including behaviour, nutrition, environment or mental condition. We also found that very few studies focused on wellbeing prior to pet ownership, i.e., during the early stages of the trade chain when they are caught from the wild, transported, or bred in captivity. We recommend that more research is needed to assess the impact of the exotic pet trade on this species’ welfare. In particular, research on welfare conditions during capture and transportation of wild Ball pythons, and the potential effects of captive breeding, could help reduce suffering throughout the trade.

Abstract

Extensive numbers of Ball pythons are caught, bred, traded and subsequently kept in captivity across the world as part of the exotic pet industry. Despite their widespread availability as pets, relatively little is known about the potential welfare challenges affecting them. We reviewed the literature for research focused on the health and welfare of Ball pythons in the international pet trade. From a total of 88 articles returned from the search criteria, our analysis showed that very few actually focused on trade (10%) or animal welfare (17%). Instead, the majority (64%) of articles focused on veterinary science. There was a considerable bias towards physical health, with most studies neglecting the four other domains of animal welfare (behaviour, nutrition, environment and mental health). Furthermore, very few studies considered Ball pythons prior to resulting pet ownership, during wild capture and transportation or captive breeding operations. Our review demonstrates that our current understanding of welfare for Ball pythons traded as exotic pets is limited. We recommend that future research should focus on aspects of the industry that are currently overlooked, including the potential consequences of genetic selection during captive-breeding and the conditions provided for snakes prior to and during international transportation.

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.

Characterization of the genomic sequence of a novel CRESS DNA virus identified in Eurasian jay (Garrulus glandarius)

Circular replication associated protein (Rep)-encoding ssDNA (CRESS DNA) viruses have diverse genomic architecture and are widely distributed in different ecosystems. In this study we characterized the complete genomic sequence of a novel circovirus-like virus, Garrulus glandarius associated circular virus-1 (GgaCV-1). The genome size (1971 nt) and other features (the nonanucleotide, rolling circle replication motif and SF3 helicase motif) are also reminiscent of circoviruses. Similar genomes with uni-directionally localized and overlapping rep and cap genes are typical of type V CRESS DNA viruses that were identified in invertebrates and environmental samples of aquatic ecosystems. GgaCV-1 showed the highest aa identity with partial rep sequences detected in bat feces (77%) and with the rep (54%) and cap (42%) of Lake Sarah-associated circular virus-23 of New Zealand freshwater mussel origin. A dietary origin for GgaCV-1 could not be excluded as the virus was detected in the cloacal swab specimen of an Eurasian jay. Further studies may help to reveal the linkage among variable organisms regarding virus transmission.