A circovirus and cycloviruses identified in feces of bobcats (Lynx rufus) in California

2024 taxonomy update for the family Circoviridae

Circovirids have a circular single-stranded DNA genome packed into a small icosahedral capsid. They are classified within two genera, Circovirus and Cyclovirus, in the family Circoviridae (phylum Cressdnaviricota, class Arfiviricetes, order Cirlivirales). Over the last five years, a number of new circovirids have been identified, and, as a result, 54 new species have been created for their classification based on the previously established species demarcation criterion, namely, that viruses classified into different species share less than 80% genome-wide pairwise sequence identity. Of note, one of the newly created species includes a circovirus that was identified in human hepatocytes and suspected of causing liver damage. Furthermore, to comply with binomial species nomenclature, all new and previously recognized species have been (re)named in binomial format with a freeform epithet. Here, we provide a summary of the properties of circovirid genomes and their classification as of June 2024 (65 species in the genus Circovirus and 90 species in the genus Cyclovirus). Finally, we provide reference datasets of the nucleotide and amino acid sequences representing each of the officially recognized circovirid species to facilitate further classification of newly discovered members of the Circoviridae.

Identification and characterization of a novel circovirus in Iberian lynx in Spain

Circoviruses cause severe disease in pigs and birds. Canine circovirus has thus far only been associated with respiratory and gastrointestinal disorders and systemic disease in dogs. The Iberian lynx (Lynx pardinus) is one of the most endangered carnivores in Europe and the most endangered felid worldwide. Exploring the virome of these animals may be important in terms of virus discovery and assessing the interspecies-circulation of viruses from related carnivores. In this study, 162 spleen samples from Iberian lynx were screened for CRESS DNA viruses. Overall, 11 (6.8%) of 162 samples tested positive using a consensus PCR. Partial rep sequences were tightly related to each other (96.6-100%). Specific molecular protocols were designed on the partial rep sequences of the novel virus, Iberian lynx-associated circovirus-1 (ILCV-1). By screening a subset of 45 spleen samples, the infection rate of ILCV-1 in Iberian lynxes was 57.8% (26/45). ILCV-1 strains formed a separate cluster intermingled with bat, rodent, mongoose, and felid circoviruses. The genome of the novel virus displayed the highest nucleotide identity (64.3-65.3%) to mongoose circoviruses, thus representing a novel candidate circovirus species. The detection of these viruses in the spleen tissues could suggest systemic infection in the animal host. Overall, these findings suggest that this novel circovirus is common in the Iberian lynx. Further studies are warranted to assess the possible health implications of ILCV-1 in this endangered species.

A panoramic view of the virosphere in three wastewater treatment plants by integrating viral-like particle-concentrated and traditional non-concentrated metagenomic approaches

Wastewater biotreatment systems harbor a rich diversity of microorganisms, and the effectiveness of biotreatment systems largely depends on the activity of these microorganisms. Specifically, viruses play a crucial role in altering microbial behavior and metabolic processes throughout their infection phases, an aspect that has recently attracted considerable interest. Two metagenomic approaches, viral-like particle-concentrated (VPC, representing free viral-like particles) and non-concentrated (NC, representing the cellular fraction), were employed to assess their efficacy in revealing virome characteristics, including taxonomy, diversity, host interactions, lifestyle, dynamics, and functional genes across processing units of three wastewater treatment plants (WWTPs). Our findings indicate that each approach offers unique insights into the viral community and functional composition. Their combined use proved effective in elucidating WWTP viromes. We identified nearly 50,000 viral contigs, with Cressdnaviricota and Uroviricota being the predominant phyla in the VPC and NC fractions, respectively. Notably, two pathogenic viral families, Asfarviridae and Adenoviridae, were commonly found in these WWTPs. We also observed significant differences in the viromes of WWTPs processing different types of wastewater. Additionally, various phage-derived auxiliary metabolic genes (AMGs) were active at the RNA level, contributing to the metabolism of the microbial community, particularly in carbon, sulfur, and phosphorus cycling. Moreover, we identified 29 virus-carried antibiotic resistance genes (ARGs) with potential for host transfer, highlighting the role of viruses in spreading ARGs in the environment. Overall, this study provides a detailed and integrated view of the virosphere in three WWTPs through the application of VPC and NC metagenomic approaches. Our findings enhance the understanding of viral communities, offering valuable insights for optimizing the operation and regulation of wastewater treatment systems.

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.

Identification of small circular DNA viruses in coyote fecal samples from Arizona (USA)

Coyotes (Canis latrans) have a broad geographic distribution across North and Central America. Despite their widespread presence in urban environments in the USA, there is limited information regarding viruses associated with coyotes in the USA and in particular the state of Arizona. To explore viruses associated with coyotes, particularly small DNA viruses, 44 scat samples were collected (April-June 2021 and November 2021-January 2022) along the Salt River near Phoenix, Arizona (USA), along 43 transects (500 m). From these samples, we identified 11 viral genomes: two novel circoviruses, six unclassified cressdnaviruses, and two anelloviruses. One of the circoviruses is most closely related to a circovirus sequence identified from an aerosolized dust sample in Arizona, USA. The second circovirus is most closely related to a rodent-associated circovirus and canine circovirus. Of the unclassified cressdnaviruses, three encode replication-associated proteins that are similar to those found in protists (Histomonas meleagridis and Monocercomonoides exilis), implying an evolutionary relationship with or a connection to similar unidentified protist hosts. The two anelloviruses are most closely related to those found in rodents, and this suggests a diet-related identification.

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.

Using archived and biocollection samples towards deciphering the DNA virus diversity associated with rodent species in the families cricetidae and heteromyidae

Rodentia is the most speciose order of mammals, and they are known to harbor a wide range of viruses. Although there has been significant research on zoonotic viruses in rodents, research on the diversity of other viruses has been limited, especially for rodents in the families Cricetidae and Heteromyidae. In fecal and liver samples of nine species of rodents, we identify 346 distinct circular DNA viral genomes. Of these, a large portion are circular, single-stranded DNA viruses in the families Anelloviridae (n = 3), Circoviridae (n = 5), Genomoviridae (n = 7), Microviridae (n = 297), Naryaviridae (n = 4), Vilyaviridae (n = 15) and in the phylum Cressdnaviricota (n = 13) that cannot be assigned established families. We also identified two large bacteriophages of 36 and 50 kb that are part of the class Caudoviricetes. Some of these viruses are clearly those that infect rodents, however, most of these likely infect various organisms associated with rodents, their environment or their diet.