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Eric Delwart - One of the best experts on this subject based on the ideXlab platform.
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ICTV Virus Taxonomy Profile: Circoviridae.
Journal of General Virology, 2017Co-Authors: Mya Breitbart, Karyna Rosario, Eric Delwart, Joaquim Segalés, Arvind VarsaniAbstract:The family Circoviridae comprises viruses with small, circular, single-stranded DNA (ssDNA) genomes, including the smallest known animal viruses. Members of this family are classified into two genera, Circovirus and Cyclovirus, which are distinguished by the position of the origin of replication relative to the coding regions and the length of the intergenic regions. Within each genus, the species demarcation threshold is 80 % genome-wide nucleotide sequence identity. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Circoviridae, which is available at www.ictv.global/report/Circoviridae.
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Revisiting the Taxonomy of the Family Circoviridae: Establishment of the Genus Cyclovirus and Removal of the Genus Gyrovirus
Archives of Virology, 2017Co-Authors: Karyna Rosario, Mya Breitbart, Eric Delwart, Joaquim Segalés, Balázs Harrach, Philippe Biagini, Arvind VarsaniAbstract:The family Circoviridae contains viruses with covalently closed, circular, single-stranded DNA (ssDNA) genomes, including the smallest known autonomously replicating, capsid-encoding animal pathogens. Members of this family are known to cause fatal diseases in birds and pigs and have been historically classified in one of two genera: Circovirus, which contains avian and porcine pathogens, and Gyrovirus, which includes a single species (Chicken anemia virus). However, over the course of the past six years, viral metagenomic approaches as well as degenerate PCR detection in unconventional hosts and environmental samples have elucidated a broader host range, including fish, a diversity of mammals, and invertebrates, for members of the family Circoviridae. Notably, these methods have uncovered a distinct group of viruses that are closely related to members of the genus Circovirus and comprise a new genus, Cyclovirus. The discovery of new viruses and a re-evaluation of genomic features that characterize members of the Circoviridae prompted a revision of the classification criteria used for this family of animal viruses. Here we provide details on an updated Circoviridae taxonomy ratified by the International Committee on the Taxonomy of Viruses in 2016, which establishes the genus Cyclovirus and reassigns the genus Gyrovirus to the family Anelloviridae, a separate lineage of animal viruses that also contains circular ssDNA genomes. In addition, we provide a new species demarcation threshold of 80% genome-wide pairwise identity for members of the family Circoviridae, based on pairwise identity distribution analysis, and list guidelines to distinguish between members of this family and other eukaryotic viruses with circular, ssDNA genomes.
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Genomic characterization of novel circular ssDNA viruses from insectivorous bats in Southern Brazil.
PLOS ONE, 2015Co-Authors: Francisco Esmaile De Sales Lima, Eric Delwart, Samuel Paulo Cibulski, Helton Fernandes Dos Santos, Thais Fumaco Teixeira, Ana Paula Muterle Varela, Paulo Michel Roehe, Ana Cláudia FrancoAbstract:Circoviruses are highly prevalent porcine and avian pathogens. In recent years, novel circular ssDNA genomes have recently been detected in a variety of fecal and environmental samples using deep sequencing approaches. In this study the identification of genomes of novel circoviruses and cycloviruses in feces of insectivorous bats is reported. Pan-reactive primers were used targeting the conserved rep region of circoviruses and cycloviruses to screen DNA bat fecal samples. Using this approach, partial rep sequences were detected which formed five phylogenetic groups distributed among the Circovirus and the recently proposed Cyclovirus genera of the Circoviridae. Further analysis using inverse PCR and Sanger sequencing led to the characterization of four new putative members of the family Circoviridae with genome size ranging from 1,608 to 1,790 nt, two inversely arranged ORFs, and canonical nonamer sequences atop a stem loop.
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Faecal virome of cats in an animal shelter.
The Journal of general virology, 2014Co-Authors: Wen Zhang, Beatrix Kapusinszky, Patricia A Pesavento, Linlin Li, Xutao Deng, Eric DelwartAbstract:We describe the metagenomics-derived feline enteric virome in the faeces of 25 cats from a single shelter in California. More than 90 % of the recognizable viral reads were related to mammalian viruses and the rest to bacterial viruses. Eight viral families were detected: Astroviridae, Coronaviridae, Parvoviridae, Circoviridae, Herpesviridae, Anelloviridae, Caliciviridae and Picobirnaviridae. Six previously known viruses were also identified: feline coronavirus type 1, felid herpes 1, feline calicivirus, feline norovirus, feline panleukopenia virus and picobirnavirus. Novel species of astroviruses and bocaviruses, and the first genome of a cyclovirus in a feline were characterized. The RNA-dependent RNA polymerase region from four highly divergent partial viral genomes in the order Picornavirales were sequenced. The detection of such a diverse collection of viruses shed within a single shelter suggested that such animals experience robust viral exposures. This study increases our understanding of the viral diversity in cats, facilitating future evaluation of their pathogenic and zoonotic potentials.
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A third gyrovirus species in human faeces.
Journal of General Virology, 2012Co-Authors: Tung Gia Phan, Miguel G. O’ryan, Héctor D. Cortés, Nora Mamani, Isidore Juste O. Bonkoungou, Chunling Wang, Christian M. Leutenegger, Eric DelwartAbstract:Until 2011 the genus Gyrovirus in the family Circoviridae consisted of a single virus (Chicken anemia virus or CAV) causing a common immunosuppressive disease in chickens when a second gyrovirus (HGyV) was reported on the skin of 4 % of healthy humans. HGyV is very closely related to a recently described chicken gyrovirus, AGV2, suggesting that they belong to the same viral species. During a viral metagenomic analysis of 100 human faeces from children with diarrhoea in Chile we identified multiple known human pathogens (adenoviruses, enteroviruses, astroviruses, sapoviruses, noroviruses, parechoviruses and rotaviruses) and a novel gyrovirus species we named GyV3 sharing
Anna Marie Skalka - One of the best experts on this subject based on the ideXlab platform.
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sequences from ancestral single stranded dna viruses in vertebrate genomes the parvoviridae and Circoviridae are more than 40 to 50 million years old
Journal of Virology, 2010Co-Authors: Vladimir A Belyi, Arnold J Levine, Anna Marie SkalkaAbstract:Vertebrate genomic assemblies were analyzed for endogenous sequences related to any known viruses with single-stranded DNA genomes. Numerous high-confidence examples related to the Circoviridae and two genera in the family Parvoviridae, the parvoviruses and dependoviruses, were found and were broadly distributed among 31 of the 49 vertebrate species tested. Our analyses indicate that the ages of both virus families may exceed 40 to 50 million years. Shared features of the replication strategies of these viruses may explain the high incidence of the integrations.
Ana Paula Muterle Varela - One of the best experts on this subject based on the ideXlab platform.
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Detection of multiple viruses in oropharyngeal samples from Brazilian free-tailed bats (Tadarida brasiliensis) using viral metagenomics
Archives of Virology, 2020Co-Authors: Samuel Paulo Cibulski, Francisco Esmaile De Sales Lima, Thais Fumaco Teixeira, Ana Paula Muterle Varela, Camila Mengue Scheffer, Fabiana Quoos Mayer, André Alberto Witt, Paulo Michel RoeheAbstract:In this study, we analyzed the viral population in oropharyngeal samples from T. brasiliensis using a viral metagenomic approach. Genomes corresponding to members of the families Circoviridae, Genomoviridae, Herpesviridae, Paramyxoviridae, Coronaviridae , and Astroviridae were detected. This study provides the first preliminary understanding of the oropharyngeal virome of T. brasiliensis , which may guide the discovery and isolation of novel viruses in the future and highlights the need for continuing investigations in this regard. Graphic abstract
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Viral DNA genomes in sera of farrowing sows with or without stillbirths.
PLOS ONE, 2020Co-Authors: Caroline Tochetto, Samuel Paulo Cibulski, Ana Paula Muterle Varela, Camila Mengue Scheffer, Diane Alves De ,lima, Márcia Regina Loiko, W. P. Paim, Cristine Cerva, Candice Schmidt, Lucía Cano OrtizAbstract:A study was conducted to investigate the serum virome of sows with and without stillbirths after farrowing. Sera from sows with at least one stillbirth or with normal litters were collected immediately after farrowing. Viral DNA was extracted from serum pools and submitted to high throughput sequencing. No differences in the proportion of virus-related reads were found in both groups (p > 0.05). A variety of viral DNA genomes were identified, mostly representative of three viral families: Anelloviridae, Circoviridae and Smacoviridae. Besides, a number of novel unclassified circular Rep-encoding single stranded DNA (CRESS DNA) viruses were also identified. These findings suggest that the presence of such viral genomes in sows' sera bears no correlation with stillbirths' occurrence; it seems likely that these constitute part of the normal serum microbiome of sows at farrowing.
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Liver virome of healthy pigs reveals diverse small ssDNA viral genomes
Infection Genetics and Evolution, 2020Co-Authors: M. S. Da Silva, Ana Paula Muterle Varela, Fabiana Quoos Mayer, W. P. Paim, Renata Da Fontoura Budaszewski, M. N. Weber, Samuel Cibulski, A. C. S. Mósena, R. Canova, C.w. PereiraAbstract:Abstract Brazil is a major exporter of pork meat worldwide. Swine liver is a common ingredient in food consumed by humans, thus emphasizing the importance of evaluating the presence of associated pathogens in swine liver. To obtain knowledge, this study aimed to provide insights into the viral communities of livers collected from slaughtered pigs from southern Brazil. The 46 livers were processed and submitted for high-throughput sequencing (HTS). The sequences were most closely related to Anelloviridae, Circoviridae and Parvoviridae families. The present work also describes the first Brazilian PCV1 and the first PPV6 and PPV7 from South America. Virus frequencies revelead 63% of samples positive for TTSuV1, 71% for TTSuVk2, 10.8% for PCV, 13% for PPV and 6% for PBov. This report addresses the diversity of the liver virome of healthy pigs and expands the number of viruses detected, further characterizing their genomes to assist future studies.
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Genomic characterization of novel circular ssDNA viruses from insectivorous bats in Southern Brazil.
PLOS ONE, 2015Co-Authors: Francisco Esmaile De Sales Lima, Eric Delwart, Samuel Paulo Cibulski, Helton Fernandes Dos Santos, Thais Fumaco Teixeira, Ana Paula Muterle Varela, Paulo Michel Roehe, Ana Cláudia FrancoAbstract:Circoviruses are highly prevalent porcine and avian pathogens. In recent years, novel circular ssDNA genomes have recently been detected in a variety of fecal and environmental samples using deep sequencing approaches. In this study the identification of genomes of novel circoviruses and cycloviruses in feces of insectivorous bats is reported. Pan-reactive primers were used targeting the conserved rep region of circoviruses and cycloviruses to screen DNA bat fecal samples. Using this approach, partial rep sequences were detected which formed five phylogenetic groups distributed among the Circovirus and the recently proposed Cyclovirus genera of the Circoviridae. Further analysis using inverse PCR and Sanger sequencing led to the characterization of four new putative members of the family Circoviridae with genome size ranging from 1,608 to 1,790 nt, two inversely arranged ORFs, and canonical nonamer sequences atop a stem loop.
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discovery of a genome of a distant relative of chicken anemia virus reveals a new member of the genus gyrovirus
Archives of Virology, 2011Co-Authors: Franciscus Antonius Maria Rijsewijk, Samuel Paulo Cibulski, Helton Fernandes Dos Santos, Thais Fumaco Teixeira, Ana Paula Muterle Varela, Ana Cláudia Franco, Diogenes Dezen, Paulo Michel RoeheAbstract:A 2.4-kb phi29 polymerase amplification product from serum of a diseased chicken was cloned and sequenced. The 2383-nucleotide sequence showed about 40% identity to a representative genome of chicken anemia virus (CAV), the only member of the genus Gyrovirus, family Circoviridae. The new genome had an organization similar to that of CAV: a putative 5′ untranscribed region of about 400 nt followed by three partially overlapping open reading frames encoding VP1, VP2 and VP3 homologs. The amino acid identities between these homologs and those of CAV were 38.8%, 40.3%, and 32.2%, respectively. Based on these limited similarities, it is proposed that the newly identified virus is a member of a new species in the genus Gyrovirus. For this new species, the name Avian gyrovirus 2 (AGV2) is proposed.
Mart Krupovic - One of the best experts on this subject based on the ideXlab platform.
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Chimeric viruses blur the borders between the major groups of eukaryotic single-stranded DNA viruses
Nature Communications, 2013Co-Authors: Simon Roux, François Enault, Gisèle Bronner, Daniel Vaulot, Patrick Forterre, Mart KrupovicAbstract:Metagenomic studies have uncovered an astonishing diversity of ssDNA viruses encoding replication proteins (Reps) related to those of eukaryotic Circoviridae, Geminiviridae or Nanoviridae; however, exact evolutionary relationships among these viruses remain obscure. Recently, a unique chimeric virus (CHIV) genome, which has apparently emerged via recombination between ssRNA and ssDNA viruses, has been discovered. Here we report on the assembly of 13 new CHIV genomes recovered from various environments. Our results indicate a single event of capsid protein (CP) gene capture from an RNA virus in the history of this virus group. The domestication of the CP gene was followed by an unprecedented recurrent replacement of the Rep genes in CHIVs with distant counterparts from diverse ssDNA viruses. We suggest that parasitic and symbiotic interactions between unicellular eukaryotes were central for the emergence of CHIVs and that such turbulent evolution was primarily dictated by incongruence between the CP and Rep proteins.
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Networks of evolutionary interactions underlying the polyphyletic origin of ssDNA viruses
Current Opinion in Virology, 2013Co-Authors: Mart KrupovicAbstract:Viruses with single-stranded (ss) DNA genomes infect hosts from all three domains of life and are present in all imaginable environments. Many new ssDNA viruses have been recently isolated, including those infecting algae, fungi, insects and even archaea. In parallel, culture-independent metagenomic approaches have illuminated the tremendous genetic diversity of these viruses, yielding valuable insights into their evolution. Here, I integrate this knowledge to propose a scenario in which certain groups of ssDNA viruses (including Geminiviridae, Circoviridae, Parvoviridae and Microviridae) have originated from plasmids via acquisition of jelly-roll capsid protein genes from ssRNA viruses. This scenario places structurally related viruses with DNA and RNA genomes into an evolutionary continuum and highlights general evolutionary trends in the virosphere.
Arvind Varsani - One of the best experts on this subject based on the ideXlab platform.
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ICTV Virus Taxonomy Profile: Circoviridae.
Journal of General Virology, 2017Co-Authors: Mya Breitbart, Karyna Rosario, Eric Delwart, Joaquim Segalés, Arvind VarsaniAbstract:The family Circoviridae comprises viruses with small, circular, single-stranded DNA (ssDNA) genomes, including the smallest known animal viruses. Members of this family are classified into two genera, Circovirus and Cyclovirus, which are distinguished by the position of the origin of replication relative to the coding regions and the length of the intergenic regions. Within each genus, the species demarcation threshold is 80 % genome-wide nucleotide sequence identity. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Circoviridae, which is available at www.ictv.global/report/Circoviridae.
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Revisiting the Taxonomy of the Family Circoviridae: Establishment of the Genus Cyclovirus and Removal of the Genus Gyrovirus
Archives of Virology, 2017Co-Authors: Karyna Rosario, Mya Breitbart, Eric Delwart, Joaquim Segalés, Balázs Harrach, Philippe Biagini, Arvind VarsaniAbstract:The family Circoviridae contains viruses with covalently closed, circular, single-stranded DNA (ssDNA) genomes, including the smallest known autonomously replicating, capsid-encoding animal pathogens. Members of this family are known to cause fatal diseases in birds and pigs and have been historically classified in one of two genera: Circovirus, which contains avian and porcine pathogens, and Gyrovirus, which includes a single species (Chicken anemia virus). However, over the course of the past six years, viral metagenomic approaches as well as degenerate PCR detection in unconventional hosts and environmental samples have elucidated a broader host range, including fish, a diversity of mammals, and invertebrates, for members of the family Circoviridae. Notably, these methods have uncovered a distinct group of viruses that are closely related to members of the genus Circovirus and comprise a new genus, Cyclovirus. The discovery of new viruses and a re-evaluation of genomic features that characterize members of the Circoviridae prompted a revision of the classification criteria used for this family of animal viruses. Here we provide details on an updated Circoviridae taxonomy ratified by the International Committee on the Taxonomy of Viruses in 2016, which establishes the genus Cyclovirus and reassigns the genus Gyrovirus to the family Anelloviridae, a separate lineage of animal viruses that also contains circular ssDNA genomes. In addition, we provide a new species demarcation threshold of 80% genome-wide pairwise identity for members of the family Circoviridae, based on pairwise identity distribution analysis, and list guidelines to distinguish between members of this family and other eukaryotic viruses with circular, ssDNA genomes.
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Discovery of a novel circular DNA virus in the Forbes sea star, Asterias forbesi
Archives of Virology, 2015Co-Authors: Elizabeth Fahsbender, Karyna Rosario, Arvind Varsani, Ian Hewson, Allison D. Tuttle, Mya BreitbartAbstract:A single-stranded DNA (ssDNA) virus, Asterias forbesi-associated circular virus (AfaCV), was discovered in a Forbes sea star displaying symptoms of sea star wasting disease (SSWD). The AfaCV genome organization is typical of circular Rep-encoding ssDNA (CRESS-DNA) viruses and is similar to that of members of the family Circoviridae. PCR-based surveys indicate that AfaCV is not clearly associated with SSWD, whereas the sea star-associated densovirus (SSaDV), recently implicated in SSWD in the Pacific, was prevalent in symptomatic specimens. AfaCV represents the first CRESS-DNA virus detected in echinoderms, adding to the growing diversity of these viruses recently recovered from invertebrates.
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Dragonfly cyclovirus, a novel single-stranded DNA virus discovered in dragonflies (Odonata: Anisoptera)
Journal of General Virology, 2011Co-Authors: Karyna Rosario, Elizabeth J. Wiltshire, Daisy Stainton, Simona Kraberger, Milen Marinov, Matthew Walters, Douglas A. Collings, Darren P. Martin, Mya Breitbart, Arvind VarsaniAbstract:Dragonfly cyclovirus (DfCyV), a new species of ssDNA virus discovered using viral metagenomics in dragonflies (familyLibellulidae) from the Kingdom of Tonga. Metagenomic sequences of DfCyV were similar to viruses of the recently proposed genus Cyclovirus within the family Circoviridae. Specific PCRs resulted in the recovery of 21 DfCyV genomes from three dragonfly species (Pantala flavescens, Tholymis tillarga and Diplacodes bipunctata). The 1741 nt DfCyV genomes share >95 % nucleotide identity and are classified into 11 subtypes representing a single strain. The DfCyV genomes share 48–63 % genome-wide nucleotide identity with cycloviruses identified in human faecal samples. Recombination analysis revealed three recombinant DfCyV genomes, suggesting that recombination plays an important role in cyclovirus evolution. To our knowledge, this is the first report of a circular ssDNA virus identified in insects, and the data may help elucidate evolutionary links among novel Circoviridae recently identified in animals and environmental samples.