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Buck CB, Welch N, Belford AK, Varsani A, Pastrana DV, Tisza MJ, Starrett GJ. Widespread Horizontal Gene Transfer Among Animal Viruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.25.586562. [PMID: 38712252 PMCID: PMC11071296 DOI: 10.1101/2024.03.25.586562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
The initial objective of this study was to shed light on the evolution of small DNA tumor viruses by analyzing de novo assemblies of publicly available deep sequencing datasets. The survey generated a searchable database of contig snapshots representing more than 100,000 Sequence Read Archive records. Using modern structure-aware search tools, we iteratively broadened the search to include an increasingly wide range of other virus families. The analysis revealed a surprisingly diverse range of chimeras involving different virus groups. In some instances, genes resembling known DNA-replication modules or known virion protein operons were paired with unrecognizable sequences that structural predictions suggest may represent previously unknown replicases and novel virion architectures. Discrete clades of an emerging group called adintoviruses were discovered in datasets representing humans and other primates. As a proof of concept, we show that the contig database is also useful for discovering RNA viruses and candidate archaeal phages. The ancillary searches revealed additional examples of chimerization between different virus groups. The observations support a gene-centric taxonomic framework that should be useful for future virus-hunting efforts.
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Affiliation(s)
| | - Nicole Welch
- National Cancer Institute, Bethesda, MD, USA
- current affiliation: L.E.K. Consulting, Boston, MA, USA
| | - Anna K. Belford
- National Cancer Institute, Bethesda, MD, USA
- current affiliation: University of Pittsburgh, Pittsburgh, PA, USA
| | - Arvind Varsani
- Arizona State University, Tempe, AZ, USA
- University of Cape Town, South Africa
| | | | - Michael J. Tisza
- National Cancer Institute, Bethesda, MD, USA
- current affiliation: Baylor College of Medicine, Houston, TX, USA
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Fehér E, Kaszab E, Mótyán JA, Máté D, Bali K, Hoitsy M, Sós E, Jakab F, Bányai K. Structural similarity of human papillomavirus E4 and polyomaviral VP4 exhibited by genomic analysis of the common kestrel (Falco tinnunculus) polyomavirus. Vet Res Commun 2024; 48:309-315. [PMID: 37688754 PMCID: PMC10810995 DOI: 10.1007/s11259-023-10210-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 08/28/2023] [Indexed: 09/11/2023]
Abstract
Polyomaviruses are widely distributed viruses of birds that may induce developmental deformities and internal organ disorders primarily in nestlings. In this study, polyomavirus sequence was detected in kidney and liver samples of a common kestrel (Falco tinnunculus) that succumbed at a rescue station in Hungary. The amplified 5025 nucleotide (nt) long genome contained the early (large and small T antigen, LTA and STA) and late (viral proteins, VP1, VP2, VP3) open reading frames (ORFs) typical for polyomaviruses. One of the additional putative ORFs (named VP4) showed identical localization with the VP4 and ORF-X of gammapolyomaviruses, but putative splicing sites could not be found in its sequence. Interestingly, the predicted 123 amino acid (aa) long protein sequence showed the highest similarity with human papillomavirus E4 early proteins in respect of the aa distribution and motif arrangement implying similar functions. The LTA of the kestrel polyomavirus shared <59.2% nt and aa pairwise identity with the LTA sequence of other polyomaviruses and formed a separated branch in the phylogenetic tree among gammapolyomaviruses. Accordingly, the kestrel polyomavirus may be the first member of a novel species within the Gammapolyomavirus genus, tentatively named Gammapolyomavirus faltin.
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Affiliation(s)
- Enikő Fehér
- HUN-REN Veterinary Medical Research Institute, Budapest, Hungary.
- National Laboratory for Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Budapest, Hungary.
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, Pécs, Hungary.
| | - Eszter Kaszab
- HUN-REN Veterinary Medical Research Institute, Budapest, Hungary
- National Laboratory for Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Budapest, Hungary
- Institute of Metagenomics, University of Debrecen, Debrecen, Hungary
| | - János András Mótyán
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Dóra Máté
- HUN-REN Veterinary Medical Research Institute, Budapest, Hungary
| | - Krisztina Bali
- HUN-REN Veterinary Medical Research Institute, Budapest, Hungary
- National Laboratory for Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Budapest, Hungary
| | - Márton Hoitsy
- Conservation and Veterinary Services, Budapest Zoo and Botanical Garden, Budapest, Hungary
- Department of Exotic Animal and Wildlife Medicine, University of Veterinary Medicine, Budapest, Hungary
| | - Endre Sós
- Conservation and Veterinary Services, Budapest Zoo and Botanical Garden, Budapest, Hungary
- Department of Exotic Animal and Wildlife Medicine, University of Veterinary Medicine, Budapest, Hungary
| | - Ferenc Jakab
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Krisztián Bányai
- HUN-REN Veterinary Medical Research Institute, Budapest, Hungary
- National Laboratory for Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Budapest, Hungary
- Department of Pharmacology and Toxicology, University of Veterinary Medicine, Budapest, Hungary
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3
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Harvey E, Mifsud JCO, Holmes EC, Mahar JE. Divergent hepaciviruses, delta-like viruses, and a chu-like virus in Australian marsupial carnivores (dasyurids). Virus Evol 2023; 9:vead061. [PMID: 37941997 PMCID: PMC10630069 DOI: 10.1093/ve/vead061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 10/05/2023] [Accepted: 10/12/2023] [Indexed: 11/10/2023] Open
Abstract
Although Australian marsupials are characterised by unique biology and geographic isolation, little is known about the viruses present in these iconic wildlife species. The Dasyuromorphia are an order of marsupial carnivores found only in Australia that include both the extinct Tasmanian tiger (thylacine) and the highly threatened Tasmanian devil. Several other members of the order are similarly under threat of extinction due to habitat loss, hunting, disease, and competition and predation by introduced species such as feral cats. We utilised publicly available RNA-seq data from the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database to document the viral diversity within four Dasyuromorph species. Accordingly, we identified fifteen novel virus sequences from five DNA virus families (Adenoviridae, Anelloviridae, Gammaherpesvirinae, Papillomaviridae, and Polyomaviridae) and three RNA virus taxa: the order Jingchuvirales, the genus Hepacivirus, and the delta-like virus group. Of particular note was the identification of a marsupial-specific clade of delta-like viruses that may indicate an association of deltaviruses with marsupial species. In addition, we identified a highly divergent hepacivirus in a numbat liver transcriptome that falls outside of the larger mammalian clade. We also detect what may be the first Jingchuvirales virus in a mammalian host-a chu-like virus in Tasmanian devils-thereby expanding the host range beyond invertebrates and ectothermic vertebrates. As many of these Dasyuromorphia species are currently being used in translocation efforts to reseed populations across Australia, understanding their virome is of key importance to prevent the spread of viruses to naive populations.
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Affiliation(s)
- Erin Harvey
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jonathon C O Mifsud
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jackie E Mahar
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
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Cowen S, Sims C, Ottewell K, Knox F, Friend T, Mills H, Garretson S, Rayner K, Gibson L. Return to 1616: Multispecies Fauna Reconstruction Requires Thinking Outside the Box. Animals (Basel) 2023; 13:2762. [PMID: 37685026 PMCID: PMC10486414 DOI: 10.3390/ani13172762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 08/01/2023] [Accepted: 08/03/2023] [Indexed: 09/10/2023] Open
Abstract
Conservation translocations have become increasingly popular for 'rewilding' areas that have lost their native fauna. These multispecies translocations are complex and need to consider the requirements of each individual species as well as the influence of likely interactions among them. The Dirk Hartog Island National Park Ecological Restoration Project, Return to 1616, aspires to restore ecological function to Western Australia's largest island. Since 2012, pest animals have been eradicated, and conservation translocations of seven fauna species have been undertaken, with a further six planned. Here, we present a synthesis of the innovative approaches undertaken in restoring the former faunal assemblage of Dirk Hartog Island and the key learnings gathered as the project has progressed.
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Affiliation(s)
- Saul Cowen
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Woodvale, WA 6026, Australia; (C.S.); (F.K.); (S.G.); (K.R.); (L.G.)
- School of Biological Sciences, University of Western Australia, Crawley, WA 6009, Australia
| | - Colleen Sims
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Woodvale, WA 6026, Australia; (C.S.); (F.K.); (S.G.); (K.R.); (L.G.)
| | - Kym Ottewell
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, WA 6151, Australia;
| | - Fiona Knox
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Woodvale, WA 6026, Australia; (C.S.); (F.K.); (S.G.); (K.R.); (L.G.)
- School of Veterinary Medicine, Murdoch University, Murdoch, WA 6150, Australia
| | - Tony Friend
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Albany, WA 6330, Australia;
| | - Harriet Mills
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, South Perth, WA 6951, Australia;
| | - Sean Garretson
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Woodvale, WA 6026, Australia; (C.S.); (F.K.); (S.G.); (K.R.); (L.G.)
| | - Kelly Rayner
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Woodvale, WA 6026, Australia; (C.S.); (F.K.); (S.G.); (K.R.); (L.G.)
| | - Lesley Gibson
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Woodvale, WA 6026, Australia; (C.S.); (F.K.); (S.G.); (K.R.); (L.G.)
- School of Biological Sciences, University of Western Australia, Crawley, WA 6009, Australia
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, WA 6151, Australia;
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Blois S, Goetz BM, Bull JJ, Sullivan CS. Interpreting and de-noising genetically engineered barcodes in a DNA virus. PLoS Comput Biol 2022; 18:e1010131. [PMID: 36413582 PMCID: PMC9725130 DOI: 10.1371/journal.pcbi.1010131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 12/06/2022] [Accepted: 11/08/2022] [Indexed: 11/23/2022] Open
Abstract
The concept of a nucleic acid barcode applied to pathogen genomes is easy to grasp and the many possible uses are straightforward. But implementation may not be easy, especially when growing through multiple generations or assaying the pathogen long-term. The potential problems include: the barcode might alter fitness, the barcode may accumulate mutations, and construction of the marked pathogens may result in unintended barcodes that are not as designed. Here, we generate approximately 5,000 randomized barcodes in the genome of the prototypic small DNA virus murine polyomavirus. We describe the challenges faced with interpreting the barcode sequences obtained from the library. Our Illumina NextSeq sequencing recalled much greater variation in barcode sequencing reads than the expected 5,000 barcodes-necessarily stemming from the Illumina library processing and sequencing error. Using data from defined control virus genomes cloned into plasmid backbones we develop a vetted post-sequencing method to cluster the erroneous reads around the true virus genome barcodes. These findings may foreshadow problems with randomized barcodes in other microbial systems and provide a useful approach for future work utilizing nucleic acid barcoded pathogens.
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Affiliation(s)
- Sylvain Blois
- Department of Molecular Biosciences, LaMontagne Center for Infectious Disease, The University of Texas at Austin, Austin, Texas, United States of America
- Department of Biomedical Sciences, University of Cagliari, Monserrato, Cagliari, Italy
| | - Benjamin M. Goetz
- Center for Biomedical Research Support, The University of Texas at Austin, Austin, Texas, United States of America
| | - James J. Bull
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Christopher S. Sullivan
- Department of Molecular Biosciences, LaMontagne Center for Infectious Disease, The University of Texas at Austin, Austin, Texas, United States of America
- * E-mail:
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Dunowska M, Perrott M, Biggs P. Identification of a novel polyomavirus from a marsupial host. Virus Evol 2022; 8:veac096. [PMID: 36381233 PMCID: PMC9662318 DOI: 10.1093/ve/veac096] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 09/09/2022] [Accepted: 10/05/2022] [Indexed: 08/26/2023] Open
Abstract
We report the identification and analysis of a full sequence of a novel polyomavirus from a brushtail possum (Trichosurus vulpecula ) termed possum polyomavirus (PPyV). The sequence was obtained from the next-generation sequencing assembly during an investigation into the aetiological agent for a neurological disease of possums termed wobbly possum disease (WPD), but the virus was not aetiologically involved in WPD. The PPyV genome was 5,224 nt long with the organisation typical for polyomaviruses, including early (large and small T antigens) and late (Viral Protein 1 (VP1), VP2, and VP3) coding regions separated by the non-coding control region of 465 nt. PPyV clustered with betapolyomaviruses in the WUKI clade but showed less than 60 per cent identity to any of the members of this clade. We propose that PPyV is classified within a new species in the genus Betapolyomavirus . These data add to our limited knowledge of marsupial viruses and their evolution.
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Affiliation(s)
- Magdalena Dunowska
- School of Veterinary Science, Massey University, Palmerston North 4410, New Zealand
| | - Matthew Perrott
- School of Veterinary Science, Massey University, Palmerston North 4410, New Zealand
| | - Patrick Biggs
- School of Veterinary Science, Massey University, Palmerston North 4410, New Zealand
- School of Natural Sciences, Massey University, Palmerston North 4410, New Zealand
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7
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Quer J, Colomer-Castell S, Campos C, Andrés C, Piñana M, Cortese MF, González-Sánchez A, Garcia-Cehic D, Ibáñez M, Pumarola T, Rodríguez-Frías F, Antón A, Tabernero D. Next-Generation Sequencing for Confronting Virus Pandemics. Viruses 2022; 14:600. [PMID: 35337007 PMCID: PMC8950049 DOI: 10.3390/v14030600] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/01/2022] [Accepted: 03/10/2022] [Indexed: 02/06/2023] Open
Abstract
Virus pandemics have happened, are happening and will happen again. In recent decades, the rate of zoonotic viral spillover into humans has accelerated, mirroring the expansion of our global footprint and travel network, including the expansion of viral vectors and the destruction of natural spaces, bringing humans closer to wild animals. Once viral cross-species transmission to humans occurs, transmission cannot be stopped by cement walls but by developing barriers based on knowledge that can prevent or reduce the effects of any pandemic. Controlling a local transmission affecting few individuals is more efficient that confronting a community outbreak in which infections cannot be traced. Genetic detection, identification, and characterization of infectious agents using next-generation sequencing (NGS) has been proven to be a powerful tool allowing for the development of fast PCR-based molecular assays, the rapid development of vaccines based on mRNA and DNA, the identification of outbreaks, transmission dynamics and spill-over events, the detection of new variants and treatment of vaccine resistance mutations, the development of direct-acting antiviral drugs, the discovery of relevant minority variants to improve knowledge of the viral life cycle, strengths and weaknesses, the potential for becoming dominant to take appropriate preventive measures, and the discovery of new routes of viral transmission.
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Affiliation(s)
- Josep Quer
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (S.C.-C.); (C.C.); (D.G.-C.); (M.I.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos 3-5, 28029 Madrid, Spain; (M.F.C.); (F.R.-F.); (D.T.)
- Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona (UAB), UAB Campus, Plaça Cívica, 08193 Bellaterra, Spain
| | - Sergi Colomer-Castell
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (S.C.-C.); (C.C.); (D.G.-C.); (M.I.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos 3-5, 28029 Madrid, Spain; (M.F.C.); (F.R.-F.); (D.T.)
| | - Carolina Campos
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (S.C.-C.); (C.C.); (D.G.-C.); (M.I.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos 3-5, 28029 Madrid, Spain; (M.F.C.); (F.R.-F.); (D.T.)
| | - Cristina Andrés
- Microbiology Department, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (C.A.); (M.P.); (A.G.-S.); (T.P.)
| | - Maria Piñana
- Microbiology Department, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (C.A.); (M.P.); (A.G.-S.); (T.P.)
| | - Maria Francesca Cortese
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos 3-5, 28029 Madrid, Spain; (M.F.C.); (F.R.-F.); (D.T.)
- Clinical Biochemistry Research Group, Biochemistry Department, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
| | - Alejandra González-Sánchez
- Microbiology Department, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (C.A.); (M.P.); (A.G.-S.); (T.P.)
| | - Damir Garcia-Cehic
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (S.C.-C.); (C.C.); (D.G.-C.); (M.I.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos 3-5, 28029 Madrid, Spain; (M.F.C.); (F.R.-F.); (D.T.)
| | - Marta Ibáñez
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (S.C.-C.); (C.C.); (D.G.-C.); (M.I.)
| | - Tomàs Pumarola
- Microbiology Department, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (C.A.); (M.P.); (A.G.-S.); (T.P.)
- Microbiology Department, Universitat Autònoma de Barcelona (UAB), UAB Campus, Plaça Cívica, 08193 Bellaterra, Spain
| | - Francisco Rodríguez-Frías
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos 3-5, 28029 Madrid, Spain; (M.F.C.); (F.R.-F.); (D.T.)
- Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona (UAB), UAB Campus, Plaça Cívica, 08193 Bellaterra, Spain
- Clinical Biochemistry Research Group, Biochemistry Department, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
| | - Andrés Antón
- Microbiology Department, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (C.A.); (M.P.); (A.G.-S.); (T.P.)
- Microbiology Department, Universitat Autònoma de Barcelona (UAB), UAB Campus, Plaça Cívica, 08193 Bellaterra, Spain
| | - David Tabernero
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos 3-5, 28029 Madrid, Spain; (M.F.C.); (F.R.-F.); (D.T.)
- Microbiology Departments, Hospital Universitari Vall d’Hebron, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
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8
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Recombination in Papillomavirus: Controversy and Possibility. Virus Res 2022; 314:198756. [DOI: 10.1016/j.virusres.2022.198756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 03/20/2022] [Accepted: 03/23/2022] [Indexed: 10/18/2022]
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9
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Seal S, Dharmarajan G, Khan I. Evolution of pathogen tolerance and emerging infections: A missing experimental paradigm. eLife 2021; 10:e68874. [PMID: 34544548 PMCID: PMC8455132 DOI: 10.7554/elife.68874] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 08/23/2021] [Indexed: 12/11/2022] Open
Abstract
Researchers worldwide are repeatedly warning us against future zoonotic diseases resulting from humankind's insurgence into natural ecosystems. The same zoonotic pathogens that cause severe infections in a human host frequently fail to produce any disease outcome in their natural hosts. What precise features of the immune system enable natural reservoirs to carry these pathogens so efficiently? To understand these effects, we highlight the importance of tracing the evolutionary basis of pathogen tolerance in reservoir hosts, while drawing implications from their diverse physiological and life-history traits, and ecological contexts of host-pathogen interactions. Long-term co-evolution might allow reservoir hosts to modulate immunity and evolve tolerance to zoonotic pathogens, increasing their circulation and infectious period. Such processes can also create a genetically diverse pathogen pool by allowing more mutations and genetic exchanges between circulating strains, thereby harboring rare alive-on-arrival variants with extended infectivity to new hosts (i.e., spillover). Finally, we end by underscoring the indispensability of a large multidisciplinary empirical framework to explore the proposed link between evolved tolerance, pathogen prevalence, and spillover in the wild.
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Affiliation(s)
| | - Guha Dharmarajan
- Savannah River Ecology Laboratory, University of GeorgiaAikenUnited States
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10
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Schmidlin K, Kraberger S, Cook C, DeNardo DF, Fontenele RS, Van Doorslaer K, Martin DP, Buck CB, Varsani A. A novel lineage of polyomaviruses identified in bark scorpions. Virology 2021; 563:58-63. [PMID: 34425496 DOI: 10.1016/j.virol.2021.08.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/15/2021] [Accepted: 08/15/2021] [Indexed: 11/30/2022]
Abstract
Polyomaviruses are non-enveloped viruses with circular double-stranded DNA genomes (~4-7 kb). Initially identified in mammals, polyomaviruses have now been identified in birds and a few fish species. Although fragmentary polyomavirus-like sequences have been detected as apparent 'hitchhikers' in shotgun genomics datasets of various arthropods, the possible diversity of these viruses in invertebrates remains unclear. Scorpions are predatory arachnids that are among the oldest terrestrial animals. Using high-throughput sequencing and traditional molecular techniques we determine the genome sequences of eight novel polyomaviruses in scorpions (Centruroides sculpturatus) from the greater Phoenix area, Arizona, USA. Analysis of Centruroides transcriptomic datasets elucidated the splicing of the viral late gene array, which is more complex than that of vertebrate polyomaviruses. Phylogenetic analysis provides further evidence of co-divergence of polyomaviruses with their hosts, suggesting that at least one ancestral species of polyomaviruses was circulating amongst the primitive common ancestors of arthropods and chordates.
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Affiliation(s)
- Kara Schmidlin
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, 85287, USA; School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, 85287, USA
| | - Chelsea Cook
- Department of Biological Sciences, Marquette University, 11428 W. Clybourn St, Milwaukee, WI, 53233, USA
| | - Dale F DeNardo
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Rafaela S Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, 85287, USA; School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Koenraad Van Doorslaer
- Genetics Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ, 85719, USA; School of Animal and Comparative Biomedical Sciences, The BIO5 Institute, Department of Immunobiology, Cancer Biology Graduate Interdisciplinary Program, UA Cancer Center, University of Arizona Tucson, Tucson, AZ, 85724, USA
| | - Darren P Martin
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory, Cape Town, 7925, South Africa
| | - Christopher B Buck
- Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, 85287, USA; School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA; Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA; Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, 7925, Cape Town, South Africa.
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11
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Starrett GJ, Tisza MJ, Welch NL, Belford AK, Peretti A, Pastrana DV, Buck CB. Adintoviruses: a proposed animal-tropic family of midsize eukaryotic linear dsDNA (MELD) viruses. Virus Evol 2021; 7:veaa055. [PMID: 34646575 PMCID: PMC8502044 DOI: 10.1093/ve/veaa055] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Polintons (also known as Mavericks) were initially identified as a widespread class of eukaryotic transposons named for their hallmark type B DNA polymerase and retrovirus-like integrase genes. It has since been recognized that many polintons encode possible capsid proteins and viral genome-packaging ATPases similar to those of a diverse range of double-stranded DNA viruses. This supports the inference that at least some polintons are actually viruses capable of cell-to-cell spread. At present, there are no polinton-associated capsid protein genes annotated in public sequence databases. To rectify this deficiency, we used a data-mining approach to investigate the distribution and gene content of polinton-like elements and related DNA viruses in animal genomic and metagenomic sequence datasets. The results define a discrete family-like clade of viruses with two genus-level divisions. We propose the family name Adintoviridae, connoting similarities to adenovirus virion proteins and the presence of a retrovirus-like integrase gene. Although adintovirus-class PolB sequences were detected in datasets for fungi and various unicellular eukaryotes, sequences resembling adintovirus virion proteins and accessory genes appear to be restricted to animals. Degraded adintovirus sequences are endogenized into the germlines of a wide range of animals, including humans.
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Affiliation(s)
| | - Michael J Tisza
- Laboratory of Cellular Oncology, NCI, NIH, Bethesda, MD 20892, USA
| | - Nicole L Welch
- Laboratory of Cellular Oncology, NCI, NIH, Bethesda, MD 20892, USA
| | - Anna K Belford
- Laboratory of Cellular Oncology, NCI, NIH, Bethesda, MD 20892, USA
| | - Alberto Peretti
- Laboratory of Cellular Oncology, NCI, NIH, Bethesda, MD 20892, USA
| | - Diana V Pastrana
- Laboratory of Cellular Oncology, NCI, NIH, Bethesda, MD 20892, USA
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12
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Ortiz-Baez AS, Cousins K, Eden JS, Chang WS, Harvey E, Pettersson JHO, Carver S, Polkinghorne A, Šlapeta J, Rose K, Holmes EC. Meta-transcriptomic identification of Trypanosoma spp. in native wildlife species from Australia. Parasit Vectors 2020; 13:447. [PMID: 32891158 PMCID: PMC7487544 DOI: 10.1186/s13071-020-04325-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 08/30/2020] [Indexed: 12/31/2022] Open
Abstract
Background Wildlife species carry a remarkable diversity of trypanosomes. The detection of trypanosome infection in native Australian fauna is central to understanding their diversity and host-parasite associations. The implementation of total RNA sequencing (meta-transcriptomics) in trypanosome surveillance and diagnosis provides a powerful methodological approach to better understand the host species distribution of this important group of parasites. Methods We implemented a meta-transcriptomic approach to detect trypanosomes in a variety of tissues (brain, liver, lung, skin, gonads) sampled from native Australian wildlife, comprising four marsupials (koala, Phascolarctos cinereus; southern brown bandicoot, Isoodon obesulus; swamp wallaby, Wallabia bicolor; bare-nosed wombat, Vombatus ursinus), one bird (regent honeyeater, Anthochaera phrygia) and one amphibian (eastern dwarf tree frog, Litoria fallax). Samples corresponded to both clinically healthy and diseased individuals. Sequencing reads were de novo assembled into contigs and annotated. The evolutionary relationships among the trypanosomatid sequences identified were determined through phylogenetic analysis of 18S rRNA sequences. Results We detected trypanosome sequences in all six species of vertebrates sampled, with positive samples in multiple organs and tissues confirmed by PCR. Phylogenetic analysis indicated that the trypanosomes infecting marsupials were related to those previously detected in placental and marsupial mammals, while the trypanosome in the regent honeyeater grouped with avian trypanosomes. In contrast, we provide the first evidence for a trypanosome in the eastern dwarf tree frog that was phylogenetically distinct from those described in other amphibians. Conclusions To our knowledge, this is the first meta-transcriptomic analysis of trypanosomes in native Australian wildlife, expanding the known genetic diversity of these important parasites. We demonstrated that RNA sequencing is sufficiently sensitive to detect low numbers of Trypanosoma transcripts and from diverse hosts and tissues types, thereby representing an effective means to detect trypanosomes that are divergent in genome sequence.![]()
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Affiliation(s)
- Ayda Susana Ortiz-Baez
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life & Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Kate Cousins
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life & Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia
| | - John-Sebastian Eden
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life & Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia.,Centre for Virus Research, Westmead Institute for Medical Research, Westmead, NSW, Australia
| | - Wei-Shan Chang
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life & Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Erin Harvey
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life & Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia
| | - John H-O Pettersson
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life & Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia.,Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Scott Carver
- Department of Biological Sciences, University of Tasmania, Hobart, TAS, Australia
| | - Adam Polkinghorne
- Department of Microbiology and Infectious Diseases, NSW Health Pathology, Nepean Hospital, Penrith, NSW, Australia.,The University of Sydney Medical School, Nepean Clinical School, Faculty of Medicine and Health, University of Sydney, Penrith, NSW, Australia
| | - Jan Šlapeta
- Laboratory of Veterinary Parasitology, Sydney School of Veterinary Science, The University of Sydney, Sydney, NSW, Australia
| | - Karrie Rose
- Australian Registry of Wildlife Health, Taronga Conservation Society Australia, Mosman, NSW, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life & Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia.
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13
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Borvető F, Bravo IG, Willemsen A. Papillomaviruses infecting cetaceans exhibit signs of genome adaptation following a recombination event. Virus Evol 2020; 6:veaa038. [PMID: 32665861 PMCID: PMC7326301 DOI: 10.1093/ve/veaa038] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Papillomaviruses (PVs) have evolved through a complex evolutionary scenario where virus-host co-evolution alone is not enough to explain the phenotypic and genotypic PV diversity observed today. Other evolutionary processes, such as host switch and recombination, also appear to play an important role in PV evolution. In this study, we have examined the genomic impact of a recombination event between distantly related PVs infecting Cetartiodactyla (even-toed ungulates and cetaceans). Our phylogenetic analyses suggest that one single recombination was responsible for the generation of extant 'chimeric' PV genomes infecting cetaceans. By correlating the phylogenetic relationships to the genomic content, we observed important differences between the recombinant and non-recombinant cetartiodactyle PV genomes. Notably, recombinant PVs contain a unique set of conserved motifs in the upstream regulatory region (URR). We interpret these regulatory changes as an adaptive response to drastic changes in the PV genome. In terms of codon usage preferences (CUPrefs), we did not detect any particular differences between orthologous open reading frames in recombinant and non-recombinant PVs. Instead, our results are in line with previous observations suggesting that CUPrefs in PVs are rather linked to gene expression patterns as well as to gene function. We show that the non-coding URR of PVs infecting cetaceans, the central regulatory element in these viruses, exhibits signs of adaptation following a recombination event. Our results suggest that also in PVs, the evolution of gene regulation can play an important role in speciation and adaptation to novel environments.
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Affiliation(s)
- Fanni Borvető
- Centre National de la Recherche Scientifique (CNRS), Laboratory MIVEGEC (CNRS IRD Univ, Montpellier), 911 Avenue Agropolis, BP 64501, 34394 Montpellier, France
| | - Ignacio G Bravo
- Centre National de la Recherche Scientifique (CNRS), Laboratory MIVEGEC (CNRS IRD Univ, Montpellier), 911 Avenue Agropolis, BP 64501, 34394 Montpellier, France
| | - Anouk Willemsen
- Centre National de la Recherche Scientifique (CNRS), Laboratory MIVEGEC (CNRS IRD Univ, Montpellier), 911 Avenue Agropolis, BP 64501, 34394 Montpellier, France
- Corresponding author: E-mail:
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14
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Evolution and molecular epidemiology of polyomaviruses. INFECTION GENETICS AND EVOLUTION 2019; 79:104150. [PMID: 31870972 DOI: 10.1016/j.meegid.2019.104150] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 12/17/2019] [Accepted: 12/19/2019] [Indexed: 02/08/2023]
Abstract
Polyomaviruses (PyVs) are small DNA viruses that infect several species, including mammals, birds and fishes. Their study gained momentum after the report of previously unidentified viral species in the past decade, and especially, since the description of the first polyomavirus clearly oncogenic for humans. The aim of this work was to review the most relevant aspects of the evolution and molecular epidemiology of polyomaviruses, allowing to reveal general evolutionary patterns and to identify some unaddressed issues and future challenges. The main points analysed included: 1) the species and genera assignation criteria; 2) the hypotheses, mechanisms and timescale of the ancient and recent evolutionary history of polyomaviruses; and 3) the molecular epidemiology of human viruses, with special attention to JC, BK and Merkel cell polyomaviruses.
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15
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Willemsen A, Félez-Sánchez M, Bravo IG. Genome Plasticity in Papillomaviruses and De Novo Emergence of E5 Oncogenes. Genome Biol Evol 2019; 11:1602-1617. [PMID: 31076746 PMCID: PMC6557308 DOI: 10.1093/gbe/evz095] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/29/2019] [Indexed: 02/06/2023] Open
Abstract
The clinical presentations of papillomavirus (PV) infections come in many different flavors. While most PVs are part of a healthy skin microbiota and are not associated to physical lesions, other PVs cause benign lesions, and only a handful of PVs are associated to malignant transformations linked to the specific activities of the E5, E6, and E7 oncogenes. The functions and origin of E5 remain to be elucidated. These E5 open reading frames (ORFs) are present in the genomes of a few polyphyletic PV lineages, located between the early and the late viral gene cassettes. We have computationally assessed whether these E5 ORFs have a common origin and whether they display the properties of a genuine gene. Our results suggest that during the evolution of Papillomaviridae, at least four events lead to the presence of a long noncoding DNA stretch between the E2 and the L2 genes. In three of these events, the novel regions evolved coding capacity, becoming the extant E5 ORFs. We then focused on the evolution of the E5 genes in AlphaPVs infecting primates. The sharp match between the type of E5 protein encoded in AlphaPVs and the infection phenotype (cutaneous warts, genital warts, or anogenital cancers) supports the role of E5 in the differential oncogenic potential of these PVs. In our analyses, the best-supported scenario is that the five types of extant E5 proteins within the AlphaPV genomes may not have a common ancestor. However, the chemical similarities between E5s regarding amino acid composition prevent us from confidently rejecting the model of a common origin. Our evolutionary interpretation is that an originally noncoding region entered the genome of the ancestral AlphaPVs. This genetic novelty allowed to explore novel transcription potential, triggering an adaptive radiation that yielded three main viral lineages encoding for different E5 proteins, displaying distinct infection phenotypes. Overall, our results provide an evolutionary scenario for the de novo emergence of viral genes and illustrate the impact of such genotypic novelty in the phenotypic diversity of the viral infections.
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Affiliation(s)
- Anouk Willemsen
- Laboratory MIVEGEC (UMR CNRS IRD Uni Montpellier), Centre National de la Recherche Scientique (CNRS), Montpellier, France
| | - Marta Félez-Sánchez
- Infections and Cancer Laboratory, Catalan Institute of Oncology (ICO), Barcelona, Spain
| | - Ignacio G Bravo
- Laboratory MIVEGEC (UMR CNRS IRD Uni Montpellier), Centre National de la Recherche Scientique (CNRS), Montpellier, France
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16
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Abstract
Cancer is ubiquitous in wildlife, affecting animals from bivalves to pachyderms and cetaceans. Reports of increasing frequency demonstrate that neoplasia is associated with substantial mortality in wildlife species. Anthropogenic activities and global weather changes are shaping new geographical limitations for many species, and alterations in living niches are associated with visible examples of genetic bottlenecks, toxin exposures, oncogenic pathogens, stress and immunosuppression, which can all contribute to cancers in wild species. Nations that devote resources to monitoring the health of wildlife often do so for human-centric reasons, including for the prediction of the potential for zoonotic disease, shared contaminants, chemicals and medications, and for observing the effect of exposure from crowding and loss of habitat. Given the increasing human footprint on land and in the sea, wildlife conservation should also become a more important motivating factor. Greater attention to the patterns of the emergence of wildlife cancer is imperative because growing numbers of species are existing at the interface between humans and the environment, making wildlife sentinels for both animal and human health. Therefore, monitoring wildlife cancers could offer interesting and novel insights into potentially unique non-age-related mechanisms of carcinogenesis across species.
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Affiliation(s)
- Patricia A Pesavento
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California, Davis, CA, USA.
| | - Dalen Agnew
- Veterinary Diagnostic Laboratory, Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, MI, USA
| | - Michael K Keel
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Kevin D Woolard
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California, Davis, CA, USA
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17
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Van Doorslaer K, Kraberger S, Austin C, Farkas K, Bergeman M, Paunil E, Davison W, Varsani A. Fish polyomaviruses belong to two distinct evolutionary lineages. J Gen Virol 2018. [PMID: 29517483 PMCID: PMC5982132 DOI: 10.1099/jgv.0.001041] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The Polyomaviridae is a diverse family of circular double-stranded DNA viruses. Polyomaviruses have been isolated from a wide array of animal hosts. An understanding of the evolutionary and ecological dynamics of these viruses is essential to understanding the pathogenicity of polyomaviruses. Using a high throughput sequencing approach, we identified a novel polyomavirus in an emerald notothen (Trematomus bernacchii) sampled in the Ross sea (Antarctica), expanding the known number of fish-associated polyomaviruses. Our analysis suggests that polyomaviruses belong to three main evolutionary clades; the first clade is made up of all recognized terrestrial polyomaviruses. The fish-associated polyomaviruses are not monophyletic, and belong to two divergent evolutionary lineages. The fish viruses provide evidence that the evolution of the key viral large T protein involves gain and loss of distinct domains.
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Affiliation(s)
- Koenraad Van Doorslaer
- Cancer Biology Graduate Interdisciplinary Program, Genetics Graduate Interdisciplinary Program, Bio5 Institute, and the University of Arizona Cancer Center University of Arizona, 1657 E Helen St., Tucson, AZ 85721, USA.,School of Animal and Comparative Biomedical Sciences, University of Arizona, 1657 E Helen St., Tucson, AZ 85721, USA
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Charlotte Austin
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Kata Farkas
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.,School of Environment, Natural Resources and Geography Bangor University Bangor, LL57 2UW, UK
| | - Melissa Bergeman
- School of Animal and Comparative Biomedical Sciences, University of Arizona, 1657 E Helen St., Tucson, AZ 85721, USA
| | - Emma Paunil
- School of Animal and Comparative Biomedical Sciences, University of Arizona, 1657 E Helen St., Tucson, AZ 85721, USA
| | - William Davison
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA.,School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.,Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town, 7925, South Africa
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18
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Transcriptome sequencing of the long-nosed bandicoot (Perameles nasuta) reveals conservation and innovation of immune genes in the marsupial order Peramelemorphia. Immunogenetics 2017; 70:327-336. [PMID: 29159447 DOI: 10.1007/s00251-017-1043-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 10/30/2017] [Indexed: 12/22/2022]
Abstract
Bandicoots are omnivorous marsupials of the order Peramelemorphia. Conservation concerns and their unique biological characteristics suggest peramelomorphs are worthy research subjects, but knowledge of their genetics and immunology has lagged behind that of other high-profile marsupials. Here, we characterise the transcriptome of the long-nose bandicoot (Perameles nasuta), the first high-throughput data set from any peramelomorph. We investigate the immune gene repertoire of the bandicoot, with a focus on key immune gene families, and compare to previously characterised marsupial and mammalian species. We find that the immune gene complement in bandicoot is often conserved with respect to other marsupials; however, the diversity of expressed transcripts in several key families, such as major histocompatibility complex, T cell receptor μ and natural killer cell receptors, appears greater in the bandicoot than other Australian marsupials, including devil and koala. This transcriptome is an important first step for future studies of bandicoots and the bilby, allowing for population level analysis and construction of bandicoot-specific immunological reagents and assays. Such studies will be critical to understanding the immunology and physiology of Peramelemorphia and to inform the conservation of these unique marsupials.
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19
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Beck AP, Shima AL, Bennett MD, Johnson LK. Metastatic Squamous Cell Carcinoma in a Northern Brown Bandicoot (Isoodon macrourus). Vet Sci 2017; 4:vetsci4010010. [PMID: 29056669 PMCID: PMC5606615 DOI: 10.3390/vetsci4010010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 01/23/2017] [Accepted: 02/09/2017] [Indexed: 11/16/2022] Open
Abstract
Aside from a handful of notable exceptions, neoplasia is not reported as a major cause of mortality in wild animal populations and often goes undetected. For northern brown bandicoots specifically, there are few reported tumors in the literature and on file in the Australian Registry of Wildlife Health. This report describes a case of squamous cell carcinoma in a northern brown bandicoot (Isoodon macrourus), with metastases to the draining lymph nodes and lung. This neoplasm consisted predominantly of well-differentiated squamous cells and multifocal keratin pearls, with areas possibly consistent with epithelial to mesenchymal transition, as identified by positive immunohistochemical staining by both pancytokeratin (AE1/AE3) and vimentin. Additional investigations were negative for bandicoot papillomatosis carcinomatosis viruses.
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Affiliation(s)
- Amanda P Beck
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville 4811, Queensland, Australia.
| | - Amy L Shima
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville 4811, Queensland, Australia.
| | - Mark D Bennett
- School of Veterinary and Life Sciences, Murdoch University, South Street Campus, Murdoch 6150, Western Australia, Australia.
| | - Linda K Johnson
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville 4811, Queensland, Australia.
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20
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Huang C, Liu WJ, Xu W, Jin T, Zhao Y, Song J, Shi Y, Ji W, Jia H, Zhou Y, Wen H, Zhao H, Liu H, Li H, Wang Q, Wu Y, Wang L, Liu D, Liu G, Yu H, Holmes EC, Lu L, Gao GF. A Bat-Derived Putative Cross-Family Recombinant Coronavirus with a Reovirus Gene. PLoS Pathog 2016; 12:e1005883. [PMID: 27676249 PMCID: PMC5038965 DOI: 10.1371/journal.ppat.1005883] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Accepted: 08/19/2016] [Indexed: 12/21/2022] Open
Abstract
The emergence of severe acute respiratory syndrome coronavirus (SARS-CoV) in 2002 and Middle East respiratory syndrome coronavirus (MERS-CoV) in 2012 has generated enormous interest in the biodiversity, genomics and cross-species transmission potential of coronaviruses, especially those from bats, the second most speciose order of mammals. Herein, we identified a novel coronavirus, provisionally designated Rousettus bat coronavirus GCCDC1 (Ro-BatCoV GCCDC1), in the rectal swab samples of Rousettus leschenaulti bats by using pan-coronavirus RT-PCR and next-generation sequencing. Although the virus is similar to Rousettus bat coronavirus HKU9 (Ro-BatCoV HKU9) in genome characteristics, it is sufficiently distinct to be classified as a new species according to the criteria defined by the International Committee of Taxonomy of Viruses (ICTV). More striking was that Ro-BatCoV GCCDC1 contained a unique gene integrated into the 3'-end of the genome that has no homologs in any known coronavirus, but which sequence and phylogeny analyses indicated most likely originated from the p10 gene of a bat orthoreovirus. Subgenomic mRNA and cellular-level observations demonstrated that the p10 gene is functional and induces the formation of cell syncytia. Therefore, here we report a putative heterologous inter-family recombination event between a single-stranded, positive-sense RNA virus and a double-stranded segmented RNA virus, providing insights into the fundamental mechanisms of viral evolution.
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Affiliation(s)
- Canping Huang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - William J. Liu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
- College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Wen Xu
- Yunnan Provincial Center for Disease Control and Prevention, Kunming Yunnan, China
| | - Tao Jin
- China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Yingze Zhao
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Jingdong Song
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Yi Shi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Wei Ji
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Hao Jia
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
- College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Yongming Zhou
- Yunnan Provincial Center for Disease Control and Prevention, Kunming Yunnan, China
| | - Honghua Wen
- Center for Disease Control and Prevention of Mengla County, Mengla Yunnan, China
| | - Honglan Zhao
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Huaxing Liu
- Center for Disease Control and Prevention of Mengla County, Mengla Yunnan, China
| | - Hong Li
- Yunnan Provincial Center for Disease Control and Prevention, Kunming Yunnan, China
| | - Qihui Wang
- CAS Key Laboratory of Microbial and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Ying Wu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Liang Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Di Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Network Information Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Guang Liu
- China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Hongjie Yu
- Division of Infectious Disease, Key Laboratory of Surveillance and Early-warning on Infectious Disease, Chinese Centre for Disease Control and Prevention, Beijing, China
| | - Edward C. Holmes
- Marie Bashir Institute of Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Lin Lu
- Yunnan Provincial Center for Disease Control and Prevention, Kunming Yunnan, China
| | - George F. Gao
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
- College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Laboratory of Protein Engineering and Vaccines, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
- Office of Director-General, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
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21
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Bolatti EM, Chouhy D, Casal PE, Pérez GR, Stella EJ, Sanchez A, Gorosito M, Bussy RF, Giri AA. Characterization of novel human papillomavirus types 157, 158 and 205 from healthy skin and recombination analysis in genus γ-Papillomavirus. INFECTION GENETICS AND EVOLUTION 2016; 42:20-9. [PMID: 27108808 DOI: 10.1016/j.meegid.2016.04.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 04/14/2016] [Accepted: 04/15/2016] [Indexed: 01/17/2023]
Abstract
Gammapapillomavirus (γ-PV) is a diverse and rapidly expanding genus, currently consisting of 79 fully characterized human PV (HPV) types. In this study, three novel types, HPV157, HPV158 and HPV205, obtained from healthy sun-exposed skin of two immunocompetent individuals, were amplified by the "Hanging droplet" long PCR technique, cloned, sequenced and characterized. HPV157, HPV158 and HPV205 genomes comprise 7154-bp, 7192-bp and 7298-bp, respectively, and contain four early (E1, E2, E6 and E7) and two late genes (L1 and L2). Phylogenetic analysis of the L1 ORF placed all novel types within the γ-PV genus: HPV157 was classified as a new member of species γ-12 while HPV158 and HPV205 belong to species γ-1. We then explored potential recombination events in genus γ-PV with the RDP4 program in a dataset of 74 viruses (71 HPV types with available full-length genomes and the 3 novel types). Two events, both located in the E1 ORF, met the inclusion criterion (p-values <0.05 with at least four methods) and persisted in different ORF combinations: an inter-species recombination in species γ-8 (major and minor parents: species γ-24 and γ-11, respectively), and an intra-species recombination in species γ-7 (recombinant strain: HPV170; major and minor parents: HPV-109 and HPV-149, respectively). These findings were confirmed by phylogenetic tree incongruence analysis. An additional incongruence was found in members of species γ-9 but it was not detected by the RDP4. This report expands our knowledge of the family Papillomaviridae and provides for the first time in silico evidence of recombination in genus γ-PV.
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Affiliation(s)
- Elisa M Bolatti
- Instituto de Biología Molecular y Celular de Rosario (CONICET), Suipacha 590, 2000 Rosario, Argentina.
| | - Diego Chouhy
- Instituto de Biología Molecular y Celular de Rosario (CONICET), Suipacha 590, 2000 Rosario, Argentina; Area Virología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina.
| | - Pablo E Casal
- Area Virología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina.
| | - Germán R Pérez
- Area Virología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina.
| | - Emma J Stella
- Instituto de Biología Molecular y Celular de Rosario (CONICET), Suipacha 590, 2000 Rosario, Argentina.
| | - Adriana Sanchez
- División de Dermatología, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Santa Fe 3100, 2000 Rosario, Argentina.
| | - Mario Gorosito
- División de Anatomía Patológica, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Santa Fe 3100, 2000 Rosario, Argentina.
| | - Ramón Fernandez Bussy
- División de Dermatología, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Santa Fe 3100, 2000 Rosario, Argentina.
| | - Adriana A Giri
- Instituto de Biología Molecular y Celular de Rosario (CONICET), Suipacha 590, 2000 Rosario, Argentina; Area Virología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina.
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22
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Buck CB, Van Doorslaer K, Peretti A, Geoghegan EM, Tisza MJ, An P, Katz JP, Pipas JM, McBride AA, Camus AC, McDermott AJ, Dill JA, Delwart E, Ng TFF, Farkas K, Austin C, Kraberger S, Davison W, Pastrana DV, Varsani A. The Ancient Evolutionary History of Polyomaviruses. PLoS Pathog 2016; 12:e1005574. [PMID: 27093155 PMCID: PMC4836724 DOI: 10.1371/journal.ppat.1005574] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 03/23/2016] [Indexed: 12/21/2022] Open
Abstract
Polyomaviruses are a family of DNA tumor viruses that are known to infect mammals and birds. To investigate the deeper evolutionary history of the family, we used a combination of viral metagenomics, bioinformatics, and structural modeling approaches to identify and characterize polyomavirus sequences associated with fish and arthropods. Analyses drawing upon the divergent new sequences indicate that polyomaviruses have been gradually co-evolving with their animal hosts for at least half a billion years. Phylogenetic analyses of individual polyomavirus genes suggest that some modern polyomavirus species arose after ancient recombination events involving distantly related polyomavirus lineages. The improved evolutionary model provides a useful platform for developing a more accurate taxonomic classification system for the viral family Polyomaviridae. Polyomaviruses are a family of DNA-based viruses that are known to infect various terrestrial vertebrates, including humans. In this report, we describe our discovery of highly divergent polyomaviruses associated with various marine fish. Searches of public deep sequencing databases unexpectedly revealed the existence of polyomavirus-like sequences in scorpion and spider datasets. Our analysis of these new sequences suggests that polyomaviruses have slowly co-evolved with individual host animal lineages through an established mechanism known as intrahost divergence. The proposed model is similar to the mechanisms through with other DNA viruses, such as papillomaviruses, are thought to have evolved. Our analysis also suggests that distantly related polyomaviruses sometimes recombine to produce new chimeric lineages. We propose a possible taxonomic scheme that can account for these inferred ancient recombination events.
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Affiliation(s)
- Christopher B. Buck
- Lab of Cellular Oncology, NCI, NIH, Bethesda, Maryland, United States of America
- * E-mail:
| | | | - Alberto Peretti
- Lab of Cellular Oncology, NCI, NIH, Bethesda, Maryland, United States of America
| | - Eileen M. Geoghegan
- Lab of Cellular Oncology, NCI, NIH, Bethesda, Maryland, United States of America
| | - Michael J. Tisza
- Lab of Cellular Oncology, NCI, NIH, Bethesda, Maryland, United States of America
| | - Ping An
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Joshua P. Katz
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - James M. Pipas
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Alison A. McBride
- Lab of Viral Diseases, NIAID, NIH, Bethesda, Maryland, United States of America
| | - Alvin C. Camus
- Department of Pathology, University of Georgia, Athens, Georgia, United States of America
| | - Alexa J. McDermott
- Animal Health Department, Georgia Aquarium, Inc., Atlanta, Georgia, United States of America
| | - Jennifer A. Dill
- Department of Pathology, University of Georgia, Athens, Georgia, United States of America
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, California, United States of America
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, United States of America
| | - Terry F. F. Ng
- Blood Systems Research Institute, San Francisco, California, United States of America
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, United States of America
| | - Kata Farkas
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Charlotte Austin
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Simona Kraberger
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - William Davison
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Diana V. Pastrana
- Lab of Cellular Oncology, NCI, NIH, Bethesda, Maryland, United States of America
| | - Arvind Varsani
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town, South Africa
- Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
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23
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A taxonomy update for the family Polyomaviridae. Arch Virol 2016; 161:1739-50. [PMID: 26923930 DOI: 10.1007/s00705-016-2794-y] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Accepted: 02/12/2016] [Indexed: 12/16/2022]
Abstract
Many distinct polyomaviruses infecting a variety of vertebrate hosts have recently been discovered, and their complete genome sequence could often be determined. To accommodate this fast-growing diversity, the International Committee on Taxonomy of Viruses (ICTV) Polyomaviridae Study Group designed a host- and sequence-based rationale for an updated taxonomy of the family Polyomaviridae. Applying this resulted in numerous recommendations of taxonomical revisions, which were accepted by the Executive Committee of the ICTV in December 2015. New criteria for definition and creation of polyomavirus species were established that were based on the observed distance between large T antigen coding sequences. Four genera (Alpha-, Beta, Gamma- and Deltapolyomavirus) were delineated that together include 73 species. Species naming was made as systematic as possible - most species names now consist of the binomial name of the host species followed by polyomavirus and a number reflecting the order of discovery. It is hoped that this important update of the family taxonomy will serve as a stable basis for future taxonomical developments.
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Mengual-Chuliá B, Bedhomme S, Lafforgue G, Elena SF, Bravo IG. Assessing parallel gene histories in viral genomes. BMC Evol Biol 2016; 16:32. [PMID: 26847371 PMCID: PMC4743424 DOI: 10.1186/s12862-016-0605-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 01/29/2016] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND The increasing abundance of sequence data has exacerbated a long known problem: gene trees and species trees for the same terminal taxa are often incongruent. Indeed, genes within a genome have not all followed the same evolutionary path due to events such as incomplete lineage sorting, horizontal gene transfer, gene duplication and deletion, or recombination. Considering conflicts between gene trees as an obstacle, numerous methods have been developed to deal with these incongruences and to reconstruct consensus evolutionary histories of species despite the heterogeneity in the history of their genes. However, inconsistencies can also be seen as a source of information about the specific evolutionary processes that have shaped genomes. RESULTS The goal of the approach here proposed is to exploit this conflicting information: we have compiled eleven variables describing phylogenetic relationships and evolutionary pressures and submitted them to dimensionality reduction techniques to identify genes with similar evolutionary histories. To illustrate the applicability of the method, we have chosen two viral datasets, namely papillomaviruses and Turnip mosaic virus (TuMV) isolates, largely dissimilar in genome, evolutionary distance and biology. Our method pinpoints viral genes with common evolutionary patterns. In the case of papillomaviruses, gene clusters match well our knowledge on viral biology and life cycle, illustrating the potential of our approach. For the less known TuMV, our results trigger new hypotheses about viral evolution and gene interaction. CONCLUSIONS The approach here presented allows turning phylogenetic inconsistencies into evolutionary information, detecting gene assemblies with similar histories, and could be a powerful tool for comparative pathogenomics.
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Affiliation(s)
- Beatriz Mengual-Chuliá
- Infections and Cancer Laboratory, Catalan Institute of Oncology (ICO), Barcelona, Spain.,Bellvitge Institute of Biomedical Research (IDIBELL), Barcelona, Spain
| | - Stéphanie Bedhomme
- Infections and Cancer Laboratory, Catalan Institute of Oncology (ICO), Barcelona, Spain.,Bellvitge Institute of Biomedical Research (IDIBELL), Barcelona, Spain.,Centre d'Ecologie Fonctionnelle et Evolutive, UMR CNRS 5175, Montpellier, France
| | - Guillaume Lafforgue
- Centre d'Ecologie Fonctionnelle et Evolutive, UMR CNRS 5175, Montpellier, France.,Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, València, Spain
| | - Santiago F Elena
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, València, Spain.,I2SysBio, Consejo Superior de Investigaciones Científicas-Universitat de València, València, Spain.,The Santa Fe Institute, Santa Fe, NM, USA
| | - Ignacio G Bravo
- Infections and Cancer Laboratory, Catalan Institute of Oncology (ICO), Barcelona, Spain. .,MIVEGEC (UMR CNRS 5290, IRD 224, UM), National Center for Scientific Research (CNRS), Montpellier, France. .,National Center for Scientific Research (CNRS), Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle (MIVEGEC), UMR CNRS 5290, IRD 224, UM, 911 Avenue Agropolis, BP 64501, 34394, Montpellier, Cedex 5, France.
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25
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Theiss JM, Günther T, Alawi M, Neumann F, Tessmer U, Fischer N, Grundhoff A. A Comprehensive Analysis of Replicating Merkel Cell Polyomavirus Genomes Delineates the Viral Transcription Program and Suggests a Role for mcv-miR-M1 in Episomal Persistence. PLoS Pathog 2015. [PMID: 26218535 PMCID: PMC4517807 DOI: 10.1371/journal.ppat.1004974] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Merkel cell polyomavirus (MCPyV) is considered the etiological agent of Merkel cell carcinoma and persists asymptomatically in the majority of its healthy hosts. Largely due to the lack of appropriate model systems, the mechanisms of viral replication and MCPyV persistence remain poorly understood. Using a semi-permissive replication system, we here report a comprehensive analysis of the role of the MCPyV-encoded microRNA (miRNA) mcv-miR-M1 during short and long-term replication of authentic MCPyV episomes. We demonstrate that cells harboring intact episomes express high levels of the viral miRNA, and that expression of mcv-miR-M1 limits DNA replication. Furthermore, we present RACE, RNA-seq and ChIP-seq studies which allow insight in the viral transcription program and mechanisms of miRNA expression. While our data suggest that mcv-miR-M1 can be expressed from canonical late strand transcripts, we also present evidence for the existence of an independent miRNA promoter that is embedded within early strand coding sequences. We also report that MCPyV genomes can establish episomal persistence in a small number of cells for several months, a time period during which viral DNA as well as LT-Ag and viral miRNA expression can be detected via western blotting, FISH, qPCR and southern blot analyses. Strikingly, despite enhanced replication in short term DNA replication assays, a mutant unable to express the viral miRNA was severely limited in its ability to establish long-term persistence. Our data suggest that MCPyV may have evolved strategies to enter a non- or low level vegetative stage of infection which could aid the virus in establishing and maintaining a lifelong persistence.
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Affiliation(s)
- Juliane Marie Theiss
- Research Group Virus Genomics, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Thomas Günther
- Research Group Virus Genomics, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Malik Alawi
- Research Group Virus Genomics, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
- Bioinformatics Service Facility, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Friederike Neumann
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Uwe Tessmer
- Research Group Virus Genomics, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Nicole Fischer
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- * E-mail: (NF); (AG)
| | - Adam Grundhoff
- Research Group Virus Genomics, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
- * E-mail: (NF); (AG)
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26
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Bravo IG, Félez-Sánchez M. Papillomaviruses: Viral evolution, cancer and evolutionary medicine. EVOLUTION MEDICINE AND PUBLIC HEALTH 2015; 2015:32-51. [PMID: 25634317 PMCID: PMC4356112 DOI: 10.1093/emph/eov003] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Papillomaviruses (PVs) are a numerous family of small dsDNA viruses infecting virtually all mammals. PVs cause infections without triggering a strong immune response, and natural infection provides only limited protection against reinfection. Most PVs are part and parcel of the skin microbiota. In some cases, infections by certain PVs take diverse clinical presentations from highly productive self-limited warts to invasive cancers. We propose PVs as an excellent model system to study the evolutionary interactions between the immune system and pathogens causing chronic infections: genotypically, PVs are very diverse, with hundreds of different genotypes infecting skin and mucosa; phenotypically, they display extremely broad gradients and trade-offs between key phenotypic traits, namely productivity, immunogenicity, prevalence, oncogenicity and clinical presentation. Public health interventions have been launched to decrease the burden of PV-associated cancers, including massive vaccination against the most oncogenic human PVs, as well as systematic screening for PV chronic anogenital infections. Anti-PVs vaccines elicit protection against infection, induce cross-protection against closely related viruses and result in herd immunity. However, our knowledge on the ecological and intrapatient dynamics of PV infections remains fragmentary. We still need to understand how the novel anthropogenic selection pressures posed by vaccination and screening will affect viral circulation and epidemiology. We present here an overview of PV evolution and the connection between PV genotypes and the phenotypic, clinical manifestations of the diseases they cause. This differential link between viral evolution and the gradient cancer-warts-asymptomatic infections makes PVs a privileged playground for evolutionary medicine research.
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Affiliation(s)
- Ignacio G Bravo
- Infections and Cancer Laboratory, Catalan Institute of Oncology (ICO), Barcelona, Spain; Bellvitge Institute of Biomedical Research (IDIBELL), Barcelona, Spain Infections and Cancer Laboratory, Catalan Institute of Oncology (ICO), Barcelona, Spain; Bellvitge Institute of Biomedical Research (IDIBELL), Barcelona, Spain Infections and Cancer Laboratory, Catalan Institute of Oncology (ICO), Barcelona, Spain; Bellvitge Institute of Biomedical Research (IDIBELL), Barcelona, Spain
| | - Marta Félez-Sánchez
- Infections and Cancer Laboratory, Catalan Institute of Oncology (ICO), Barcelona, Spain; Bellvitge Institute of Biomedical Research (IDIBELL), Barcelona, Spain Infections and Cancer Laboratory, Catalan Institute of Oncology (ICO), Barcelona, Spain; Bellvitge Institute of Biomedical Research (IDIBELL), Barcelona, Spain
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27
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Varsani A, Porzig EL, Jennings S, Kraberger S, Farkas K, Julian L, Massaro M, Ballard G, Ainley DG. Identification of an avian polyomavirus associated with Adélie penguins (Pygoscelis adeliae). J Gen Virol 2014; 96:851-857. [PMID: 25537375 DOI: 10.1099/vir.0.000038] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Little is known about viruses associated with Antarctic animals, although they are probably widespread. We recovered a novel polyomavirus from Adélie penguin (Pygoscelis adeliae) faecal matter sampled in a subcolony at Cape Royds, Ross Island, Antarctica. The 4988 nt Adélie penguin polyomavirus (AdPyV) has a typical polyomavirus genome organization with three ORFs that encoded capsid proteins on the one strand and two non-structural protein-coding ORFs on the complementary strand. The genome of AdPyV shared ~60 % pairwise identity with all avipolyomaviruses. Maximum-likelihood phylogenetic analysis of the large T-antigen (T-Ag) amino acid sequences showed that the T-Ag of AdPyV clustered with those of avipolyomaviruses, sharing between 48 and 52 % identities. Only three viruses associated with Adélie penguins have been identified at a genomic level, avian influenza virus subtype H11N2 from the Antarctic Peninsula and, respectively, Pygoscelis adeliae papillomavirus and AdPyV from capes Crozier and Royds on Ross Island.
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Affiliation(s)
- Arvind Varsani
- Electron Microscope Unit, Division of Medical Biochemistry, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory, 7700, South Africa.,Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.,School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
| | | | - Scott Jennings
- Department of Fisheries and Wildlife, Oregon Cooperative Fish and Wildlife Research Unit, US Geological Survey, Oregon State University, Corvallis, OR, USA
| | - Simona Kraberger
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
| | - Kata Farkas
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
| | - Laurel Julian
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
| | - Melanie Massaro
- School of Environmental Sciences, Charles Sturt University, Albury, NSW, Australia
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García-Pérez R, Ibáñez C, Godínez JM, Aréchiga N, Garin I, Pérez-Suárez G, de Paz O, Juste J, Echevarría JE, Bravo IG. Novel papillomaviruses in free-ranging Iberian bats: no virus-host co-evolution, no strict host specificity, and hints for recombination. Genome Biol Evol 2014; 6:94-104. [PMID: 24391150 PMCID: PMC3914694 DOI: 10.1093/gbe/evt211] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Papillomaviruses (PVs) are widespread pathogens. However, the extent of PV infections in bats remains largely unknown. This work represents the first comprehensive study of PVs in Iberian bats. We identified four novel PVs in the mucosa of free-ranging Eptesicus serotinus (EserPV1, EserPV2, and EserPV3) and Rhinolophus ferrumequinum (RferPV1) individuals and analyzed their phylogenetic relationships within the viral family. We further assessed their prevalence in different populations of E. serotinus and its close relative E. isabellinus. Although it is frequent to read that PVs co-evolve with their host, that PVs are highly species-specific, and that PVs do not usually recombine, our results suggest otherwise. First, strict virus–host co-evolution is rejected by the existence of five, distantly related bat PV lineages and by the lack of congruence between bats and bat PVs phylogenies. Second, the ability of EserPV2 and EserPV3 to infect two different bat species (E. serotinus and E. isabellinus) argues against strict host specificity. Finally, the description of a second noncoding region in the RferPV1 genome reinforces the view of an increased susceptibility to recombination in the E2-L2 genomic region. These findings prompt the question of whether the prevailing paradigms regarding PVs evolution should be reconsidered.
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Affiliation(s)
- Raquel García-Pérez
- Infections and Cancer Laboratory, Catalan Institute of Oncology (ICO), Barcelona, Spain
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29
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Varsani A, Kraberger S, Jennings S, Porzig EL, Julian L, Massaro M, Pollard A, Ballard G, Ainley DG. A novel papillomavirus in Adélie penguin (Pygoscelis adeliae) faeces sampled at the Cape Crozier colony, Antarctica. J Gen Virol 2014; 95:1352-1365. [PMID: 24686913 DOI: 10.1099/vir.0.064436-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Papillomaviruses are epitheliotropic viruses that have circular dsDNA genomes encapsidated in non-enveloped virions. They have been found to infect a variety of mammals, reptiles and birds, but so far they have not been found in amphibians. Using a next-generation sequencing de novo assembly contig-informed recovery, we cloned and Sanger sequenced the complete genome of a novel papillomavirus from the faecal matter of Adélie penguins (Pygoscelis adeliae) nesting on Ross Island, Antarctica. The genome had all the usual features of a papillomavirus and an E9 ORF encoding a protein of unknown function that is found in all avian papillomaviruses to date. This novel papillomavirus genome shared ~60 % pairwise identity with the genomes of the other three known avian papillomaviruses: Fringilla coelebs papillomavirus 1 (FcPV1), Francolinus leucoscepus papillomavirus 1 (FlPV1) and Psittacus erithacus papillomavirus 1. Pairwise identity analysis and phylogenetic analysis of the major capsid protein gene clearly indicated that it represents a novel species, which we named Pygoscelis adeliae papillomavirus 1 (PaCV1). No evidence of recombination was detected in the genome of PaCV1, but we did detect a recombinant region (119 nt) in the E6 gene of FlPV1 with the recombinant region being derived from ancestral FcPV1-like sequences. Previously only paramyxoviruses, orthomyxoviruses and avian pox viruses have been genetically identified in penguins; however, the majority of penguin viral identifications have been based on serology or histology. This is the first report, to our knowledge, of a papillomavirus associated with a penguin species.
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Affiliation(s)
- Arvind Varsani
- Electron Microscope Unit, Division of Medical Biochemistry, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory, 7700, South Africa.,Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA.,School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Simona Kraberger
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Scott Jennings
- Department of Fisheries and Wildlife, Oregon Cooperative Fish and Wildlife Research Unit, US Geological Survey, Oregon State University, Corvallis, OR, USA
| | | | - Laurel Julian
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Melanie Massaro
- School of Environmental Sciences, Charles Sturt University, Albury, NSW 2640, Australia
| | | | - Grant Ballard
- Point Blue Conservation Science, Petaluma, CA 94954, USA
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31
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Wain-Hobson S. Pandemic influenza viruses: time to recognize our inability to predict the unpredictable and stop dangerous gain-of-function experiments. EMBO Mol Med 2013; 5:1637-41. [PMID: 24186378 PMCID: PMC3840482 DOI: 10.1002/emmm.201303475] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Simon Wain-Hobson
- Institut PasteurParis, France
- The Foundation for Vaccine ResearchWashington, DC, USA
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32
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Lagatie O, Tritsmans L, Stuyver LJ. The miRNA world of polyomaviruses. Virol J 2013; 10:268. [PMID: 23984639 PMCID: PMC3765807 DOI: 10.1186/1743-422x-10-268] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 08/27/2013] [Indexed: 12/20/2022] Open
Abstract
Polyomaviruses are a family of non-enveloped DNA viruses infecting several species, including humans, primates, birds, rodents, bats, horse, cattle, raccoon and sea lion. They typically cause asymptomatic infection and establish latency but can be reactivated under certain conditions causing severe diseases. MicroRNAs (miRNAs) are small non-coding RNAs that play important roles in several cellular processes by binding to and inhibiting the translation of specific mRNA transcripts. In this review, we summarize the current knowledge of microRNAs involved in polyomavirus infection. We review in detail the different viral miRNAs that have been discovered and the role they play in controlling both host and viral protein expression. We also give an overview of the current understanding on how host miRNAs may function in controlling polyomavirus replication, immune evasion and pathogenesis.
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Affiliation(s)
- Ole Lagatie
- Janssen Diagnostics, Turnhoutseweg 30, Beerse 2340, Belgium.
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Van Doorslaer K. Evolution of the papillomaviridae. Virology 2013; 445:11-20. [PMID: 23769415 DOI: 10.1016/j.virol.2013.05.012] [Citation(s) in RCA: 163] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Revised: 04/02/2013] [Accepted: 05/09/2013] [Indexed: 02/08/2023]
Abstract
Viruses belonging to the Papillomaviridae family have been isolated from a variety of mammals, birds and non-avian reptiles. It is likely that most, if not all, amniotes carry a broad array of viral types. To date, the complete genomic sequence of more than 240 distinct viral types has been characterized at the nucleotide level. The analysis of this sequence information has begun to shed light on the evolutionary history of this important virus family. The available data suggests that many different evolutionary mechanisms have influenced the papillomavirus phylogenetic tree. Increasing evidence supports that the ancestral papillomavirus initially specialized to infect different ecological niches on the host. This episode of niche sorting was followed by extensive episodes of co-speciation with the host. This review attempts to summarize our current understanding of the papillomavirus evolution.
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Affiliation(s)
- Koenraad Van Doorslaer
- DNA Tumor Virus Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 209892, USA.
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Abstract
During the past 6 years, focused virus hunting has led to the discovery of nine new human polyomaviruses, including Merkel cell polyomavirus, which has been linked to Merkel cell carcinoma, a lethal skin cell cancer. The discovery of so many new and highly divergent human polyomaviruses raises key questions regarding their evolution, tropism, latency, reactivation, immune evasion and contribution to disease. This Review describes the similarities and differences among the new human polyomaviruses and discusses how these viruses might interact with their human host.
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Affiliation(s)
- James A DeCaprio
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.
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Lim ES, Reyes A, Antonio M, Saha D, Ikumapayi UN, Adeyemi M, Stine OC, Skelton R, Brennan DC, Mkakosya RS, Manary MJ, Gordon JI, Wang D. Discovery of STL polyomavirus, a polyomavirus of ancestral recombinant origin that encodes a unique T antigen by alternative splicing. Virology 2013; 436:295-303. [PMID: 23276405 PMCID: PMC3693558 DOI: 10.1016/j.virol.2012.12.005] [Citation(s) in RCA: 140] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Revised: 10/08/2012] [Accepted: 12/05/2012] [Indexed: 12/12/2022]
Abstract
The family Polyomaviridae is comprised of circular double-stranded DNA viruses, several of which are associated with diseases, including cancer, in immunocompromised patients. Here we describe a novel polyomavirus recovered from the fecal microbiota of a child in Malawi, provisionally named STL polyomavirus (STLPyV). We detected STLPyV in clinical stool specimens from USA and The Gambia at up to 1% frequency. Complete genome comparisons of two STLPyV strains demonstrated 5.2% nucleotide divergence. Alternative splicing of the STLPyV early region yielded a unique form of T antigen, which we named 229T, in addition to the expected large and small T antigens. STLPyV has a mosaic genome and shares an ancestral recombinant origin with MWPyV. The discovery of STLPyV highlights a novel alternative splicing strategy and advances our understanding of the complex evolutionary history of polyomaviruses.
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MESH Headings
- Adolescent
- Adult
- Alternative Splicing
- Antigens, Viral, Tumor/genetics
- Child
- Child, Preschool
- Cluster Analysis
- DNA, Viral/chemistry
- DNA, Viral/genetics
- Evolution, Molecular
- Feces/virology
- Female
- Gambia
- Gene Expression Regulation, Viral
- Genome, Viral
- Humans
- Infant
- Malawi
- Male
- Molecular Sequence Data
- Phylogeny
- Polyomavirus/classification
- Polyomavirus/genetics
- Polyomavirus/isolation & purification
- Polyomavirus Infections/epidemiology
- Polyomavirus Infections/virology
- Prevalence
- Recombination, Genetic
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- United States
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Affiliation(s)
- Efrem S. Lim
- Departments of Molecular Microbiology and Pathology & Immunology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, Missouri, USA
| | - Alejandro Reyes
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, Missouri, USA
| | - Martin Antonio
- Medical Research Council Unit, PO Box 273, Banjul, The Gambia
| | - Debasish Saha
- Medical Research Council Unit, PO Box 273, Banjul, The Gambia
| | | | | | - O. Colin Stine
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, 660 W Redwood St., Baltimore, Maryland, USA
| | - Rebecca Skelton
- Department of Internal Medicine, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, Missouri, USA
| | - Daniel C. Brennan
- Department of Internal Medicine, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, Missouri, USA
| | - Rajhab S. Mkakosya
- Department of Pathology, University of Malawi College of Medicine, Private Bag 360, Chichiri, Blantyre 3, Malawi
| | - Mark J. Manary
- Department of Pediatrics, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, Missouri, USA
- Department of Community Health, University of Malawi College of Medicine, Private Bag 360, Chichiri, Blantyre 3, Malawi
| | - Jeffrey I. Gordon
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, Missouri, USA
| | - David Wang
- Departments of Molecular Microbiology and Pathology & Immunology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, Missouri, USA
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Cui J, Holmes EC. Evidence for an endogenous papillomavirus-like element in the platypus genome. J Gen Virol 2012; 93:1362-1366. [PMID: 22422067 DOI: 10.1099/vir.0.041483-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Papillomaviruses (PVs) infect a wide range of vertebrates and have diversified into multiple genetic types, some of which have serious consequences for human health. Although PVs have to date only been characterized as exogenous viral forms, here we report the observation of an endogenous viral element (EPVLoa) in the genome of the platypus (Ornithorhynchus anatinus) that is related to PVs. Further data mining for endogenous PV-like elements is therefore warranted.
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Affiliation(s)
- Jie Cui
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Edward C Holmes
- Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA.,Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
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37
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Rivera R, Robles-Sikisaka R, Hoffman EM, Stacy BA, Jensen ED, Nollens HH, Wellehan JFX. Characterization of a novel papillomavirus species (ZcPV1) from two California sea lions (Zalophus californianus). Vet Microbiol 2011; 155:257-66. [PMID: 22005176 DOI: 10.1016/j.vetmic.2011.09.027] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Revised: 09/16/2011] [Accepted: 09/23/2011] [Indexed: 12/24/2022]
Abstract
A seven-year old California sea lion (Zalophus californianus) presented with focally extensive, bilaterally symmetric, proliferative axillary skin lesions and preputial lesions. A second California sea lion in the same population presented with similar proliferative lesions on the underside of the tail. Histopathology revealed epidermal hyperplasia with severe hyperkeratosis, with proliferating keratinocytes forming broad, branching pegs that extended into the dermis. Pan-papillomaviral consensus PCR was used to obtain initial E1 sequence template and the complete genome was determined using a combination of rolling circle amplification and specific-primer PCR. Analysis revealed a novel papillomavirus, Zalophus californianus papillomavirus 1 (ZcPV1), with seven open reading frames encoding five early proteins (E6, E7, E1, E2 and E4) and two late proteins (L1 and L2). Phylogenetic analysis revealed that (ZcPV1) is most closely related to Equine papillomavirus 1 (EcPV1) in the genus Zetapapillomavirus, and Canine papillomaviruses 3 and 4 (CPV3, CPV4) in the genus Chipapillomavirus. The lesions regressed without intervention over a period of several months.
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Affiliation(s)
- Rebecca Rivera
- Hubbs-SeaWorld Research Institute, Center for Marine Veterinary Virology, 2595 Ingraham St., San Diego, CA 92109, USA.
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Wellehan JF, Rivera R, Archer LL, Benham C, Muller JK, Colegrove KM, Gulland FM, St. Leger JA, Venn-Watson SK, Nollens HH. Characterization of California sea lion polyomavirus 1: Expansion of the known host range of the Polyomaviridae to Carnivora. INFECTION GENETICS AND EVOLUTION 2011; 11:987-96. [DOI: 10.1016/j.meegid.2011.03.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2010] [Revised: 02/11/2011] [Accepted: 03/17/2011] [Indexed: 11/29/2022]
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Evolution and taxonomic classification of human papillomavirus 16 (HPV16)-related variant genomes: HPV31, HPV33, HPV35, HPV52, HPV58 and HPV67. PLoS One 2011; 6:e20183. [PMID: 21673791 PMCID: PMC3103539 DOI: 10.1371/journal.pone.0020183] [Citation(s) in RCA: 123] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Accepted: 04/23/2011] [Indexed: 11/19/2022] Open
Abstract
Background Human papillomavirus 16 (HPV16) species group (alpha-9) of the Alphapapillomavirus genus contains HPV16, HPV31, HPV33, HPV35, HPV52, HPV58 and HPV67. These HPVs account for 75% of invasive cervical cancers worldwide. Viral variants of these HPVs differ in evolutionary history and pathogenicity. Moreover, a comprehensive nomenclature system for HPV variants is lacking, limiting comparisons between studies. Methods DNA from cervical samples previously characterized for HPV type were obtained from multiple geographic regions to screen for novel variants. The complete 8 kb genomes of 120 variants representing the major and minor lineages of the HPV16-related alpha-9 HPV types were sequenced to capture maximum viral heterogeneity. Viral evolution was characterized by constructing phylogenic trees based on complete genomes using multiple algorithms. Maximal and viral region specific divergence was calculated by global and pairwise alignments. Variant lineages were classified and named using an alphanumeric system; the prototype genome was assigned to the A lineage for all types. Results The range of genome-genome sequence heterogeneity varied from 0.6% for HPV35 to 2.2% for HPV52 and included 1.4% for HPV31, 1.1% for HPV33, 1.7% for HPV58 and 1.1% for HPV67. Nucleotide differences of approximately 1.0% - 10.0% and 0.5%–1.0% of the complete genomes were used to define variant lineages and sublineages, respectively. Each gene/region differs in sequence diversity, from most variable to least variable: noncoding region 1 (NCR1) /noncoding region 2 (NCR2) >upstream regulatory region (URR)> E6/E7 > E2/L2 > E1/L1. Conclusions These data define maximum viral genomic heterogeneity of HPV16-related alpha-9 HPV variants. The proposed nomenclature system facilitates the comparison of variants across epidemiological studies. Sequence diversity and phylogenies of this clinically important group of HPVs provides the basis for further studies of discrete viral evolution, epidemiology, pathogenesis and preventative/therapeutic interventions.
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40
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Taxonomical developments in the family Polyomaviridae. Arch Virol 2011; 156:1627-34. [PMID: 21562881 DOI: 10.1007/s00705-011-1008-x] [Citation(s) in RCA: 141] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Accepted: 04/20/2011] [Indexed: 01/01/2023]
Abstract
The Polyomaviridae Study Group of the International Committee on Taxonomy of Viruses (ICTV) has recommended several taxonomical revisions, as follows: The family Polyomaviridae, which is currently constituted as a single genus (Polyomavirus), will be comprised of three genera: two containing mammalian viruses and one containing avian viruses. The two mammalian genera will be designated Orthopolyomavirus and Wukipolyomavirus, and the avian genus will be named Avipolyomavirus. These genera will be created by the redistribution of species from the current single genus (Polyomavirus) and by the inclusion of several new species. In addition, the names of several species will be changed to reflect current usage.
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Insights into Polyomaviridae microRNA function derived from study of the bandicoot papillomatosis carcinomatosis viruses. J Virol 2011; 85:4487-500. [PMID: 21345962 DOI: 10.1128/jvi.02557-10] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Several different members of the Polyomaviridae, including some human pathogens, encode microRNAs (miRNAs) that lie antisense with respect to the early gene products, the tumor (T) antigens. These miRNAs negatively regulate T antigen expression by directing small interfering RNA (siRNA)-like cleavage of the early transcripts. miRNA mutant viruses of some members of the Polyomaviridae express increased levels of early proteins during lytic infection. However, the importance of miRNA-mediated negative regulation of the T antigens remains uncertain. Bandicoot papillomatosis carcinomatosis virus type 1 (BPCV1) is associated with papillomas and carcinomas in the endangered marsupial the western barred bandicoot (Perameles bougainville). BPCV1 is the founding member of a new group of viruses that remarkably share distinct properties in common with both the polyomavirus and papillomavirus families. Here, we show that BPCV1 encodes, in the same orientation as the papillomavirus-like transcripts, a miRNA located within a long noncoding region (NCR) of the genome. Furthermore, this NCR serves the function of both promoter and template for the primary transcript that gives rise to the miRNA. Unlike the polyomavirus miRNAs, the BPCV1 miRNA is not encoded antisense to the T antigen transcripts but rather lies in a separate, proximal region of the genome. We have mapped the 3' untranslated region (UTR) of the BPCV1 large T antigen early transcript and identified a functional miRNA target site that is imperfectly complementary to the BPCV1 miRNA. Chimeric reporters containing the entire BPCV1 T antigen 3' UTR undergo negative regulation when coexpressed with the BPCV1 miRNA. Notably, the degree of negative regulation observed is equivalent to that of an identical reporter that is engineered to bind to the BPCV1 miRNA with perfect complementarity. We also show that this miRNA and this novel mode of early gene regulation are conserved with the related BPCV2. Finally, papillomatous lesions from a western barred bandicoot express readily detectable levels of this miRNA, stressing its likely importance in vivo. Combined, the alternative mechanisms of negative regulation of T antigen expression between the BPCVs and the polyomaviruses support the importance of miRNA-mediated autoregulation in the life cycles of some divergent polyomaviruses and polyomavirus-like viruses.
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Mizutani T, Sayama Y, Nakanishi A, Ochiai H, Sakai K, Wakabayashi K, Tanaka N, Miura E, Oba M, Kurane I, Saijo M, Morikawa S, Ono SI. Novel DNA virus isolated from samples showing endothelial cell necrosis in the Japanese eel, Anguilla japonica. Virology 2011; 412:179-87. [PMID: 21277610 DOI: 10.1016/j.virol.2010.12.057] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Revised: 12/06/2010] [Accepted: 12/28/2010] [Indexed: 11/25/2022]
Abstract
Economic loss due to viral endothelial cell necrosis of eel (VECNE) of Anguilla japonica is a serious problem for the cultured Japanese eel market. However, the viral genome responsible for VECNE is unknown. We recently developed a rapid determination system for viral nucleic acid sequences (RDV) to determine viral genome sequences. In this study, viral DNA fragments were obtained using RDV, and approximately 15-kbp circular full genome sequences were determined using a next-generation sequencing system, overlapping PCR, and Southern blot analysis. One open reading frame (ORF) was homologous to the large T-antigen of polyomavirus; other ORFs have no homology with any nucleic or amino acid sequences of polyomavirus. Therefore, as this DNA virus might comprise a novel virus family, we provisionally named it Japanese eel endothelial cells-infecting virus (JEECV). JEECV was detected in both naturally and experimentally infected eels, suggesting that JEECV potentially causes VECNE.
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Affiliation(s)
- Tetsuya Mizutani
- Virology 1, National Institute of Infectious Diseases, Gakuen 4-7-1, Musashimurayama, Tokyo, Japan.
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43
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Bravo IG, de Sanjosé S, Gottschling M. The clinical importance of understanding the evolution of papillomaviruses. Trends Microbiol 2010; 18:432-8. [DOI: 10.1016/j.tim.2010.07.008] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2010] [Revised: 07/27/2010] [Accepted: 07/29/2010] [Indexed: 12/26/2022]
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Schowalter RM, Pastrana DV, Pumphrey KA, Moyer AL, Buck CB. Merkel cell polyomavirus and two previously unknown polyomaviruses are chronically shed from human skin. Cell Host Microbe 2010; 7:509-15. [PMID: 20542254 DOI: 10.1016/j.chom.2010.05.006] [Citation(s) in RCA: 430] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2010] [Revised: 03/16/2010] [Accepted: 05/03/2010] [Indexed: 12/16/2022]
Abstract
Mounting evidence indicates that Merkel cell polyomavirus (MCV), a circular double-stranded DNA virus, is a causal factor underlying a highly lethal form of skin cancer known as Merkel cell carcinoma. To explore the possibility that MCV and other polyomaviruses commonly inhabit healthy human skin, we developed an improved rolling circle amplification (RCA) technique to isolate circular DNA viral genomes from human skin swabs. Complete MCV genomes were recovered from 40% of healthy adult volunteers tested, providing full-length, apparently wild-type cloned MCV genomes. RCA analysis also identified two previously unknown polyomavirus species that we name human polyomavirus-6 (HPyV6) and HPyV7. Biochemical experiments show that polyomavirus DNA is shed from the skin in the form of assembled virions. A pilot serological study indicates that infection or coinfection with these three skin-tropic polyomaviruses is very common. Thus, at least three polyomavirus species are constituents of the human skin microbiome.
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Affiliation(s)
- Rachel M Schowalter
- Tumor Virus Molecular Biology Section, Laboratory of Cellular Oncology, National Cancer Institute, Bethesda, MD 20892-4263, USA
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Stevens H, Rector A, Van Ranst M. Multiply primed rolling-circle amplification method for the amplification of circular DNA viruses. Cold Spring Harb Protoc 2010; 2010:pdb.prot5415. [PMID: 20360369 DOI: 10.1101/pdb.prot5415] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The use of whole genome amplification and analysis of viruses is of increasing importance, as data generated using these methods are currently used for clinical diagnostics, epidemiological studies, phylogenetic analyses, and studies of genome organization and evolution. The best known amplification method for DNA is the polymerase chain reaction (PCR). This technique, however, has drawbacks: PCR produces relatively small amplicons and also requires prior knowledge of sequence data for the construction of the required consensus or degenerate primers. For circular DNA templates, it is possible to overcome these drawbacks by using the multiply primed rolling-circle amplification (RCA) technique, which mimics the rolling-circle mechanism that occurs in nature for replication of circular DNA molecules, e.g., plasmids. The RCA protocol described here is optimized for the amplification of circular DNA virus genomes.
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Affiliation(s)
- Hans Stevens
- Laboratory of Clinical and Epidemiological Virology, Rega Institute, University of Leuven, B-3000 Leuven, Belgium.
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Classification of papillomaviruses (PVs) based on 189 PV types and proposal of taxonomic amendments. Virology 2010; 401:70-9. [PMID: 20206957 DOI: 10.1016/j.virol.2010.02.002] [Citation(s) in RCA: 1098] [Impact Index Per Article: 78.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2009] [Revised: 01/27/2010] [Accepted: 02/03/2010] [Indexed: 10/19/2022]
Abstract
We present an expansion of the classification of the family Papillomaviridae, which now contains 29 genera formed by 189 papillomavirus (PV) types isolated from humans (120 types), non-human mammals, birds and reptiles (64, 3 and 2 types, respectively). To accommodate the number of PV genera exceeding the Greek alphabet, the prefix "dyo" is used, continuing after the Omega-PVs with Dyodelta-PVs. The current set of human PVs is contained within five genera, whereas mammalian, avian and reptile PVs are contained within 20, 3 and 1 genera, respectively. We propose standardizations to the names of a number of animal PVs. As prerequisite for a coherent nomenclature of animal PVs, we propose founding a reference center for animal PVs. We discuss that based on emerging species concepts derived from genome sequences, PV types could be promoted to the taxonomic level of species, but we do not recommend implementing this change at the current time.
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The first complete papillomavirus genome characterized from a marsupial host: a novel isolate from Bettongia penicillata. J Virol 2010; 84:5448-53. [PMID: 20200246 DOI: 10.1128/jvi.02635-09] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The first fully sequenced papillomavirus (PV) of marsupials, tentatively named Bettongia penicillata papillomavirus type 1 (BpPV1), was detected in papillomas from a woylie (Bettongia penicillata ogilbyi). The circular, double-stranded DNA genome contains 7,737 bp and encodes 7 open reading frames (ORFs), E6, E7, E1, E2, E4, L2, and L1, in typical PV conformation. BpPV1 is a close-to-root PV with L1 and L2 ORFs most similar to European hedgehog PV and bandicoot papillomatosis carcinomatosis virus types 1 and 2 (BPCV1 and -2). It appears that the BPCVs arose by recombination between an ancient PV and an ancient polyomavirus more than 10 million years ago.
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Abstract
For humans, strong evidence indicates that some mucosal papillomavirus (PV) types cause genital and oral neoplasia, and weaker evidence suggests that some cutaneous PVs may cause cutaneous squamous cell carcinomas (SCC). For nonhuman species, strong evidence supports a causal role of PVs in the development of feline and equine sarcoids. Likewise, PVs are believed to cause cutaneous SCCs in rabbits, western barred bandicoots, and some rodents. Furthermore, some evidence suggests that PVs may influence the development of both feline and canine cutaneous SCCs. This review discusses the evidence that PVs cause human cutaneous SCCs and the proposed mechanisms for this action. It then reviews preneoplastic and neoplastic skin diseases that are associated with PV infection in nonhuman mammals.
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Affiliation(s)
- J. S. Munday
- Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand
| | - M. Kiupel
- Diagnostic Center for Population and Animal Health, Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, MI
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Woolford L, Bennett MD, Sims C, Thomas N, Friend JA, Nicholls PK, Warren KS, O'Hara AJ. Prevalence, emergence, and factors associated with a viral papillomatosis and carcinomatosis syndrome in wild, reintroduced, and captive western barred bandicoots (Perameles bougainville). ECOHEALTH 2009; 6:414-425. [PMID: 19898897 DOI: 10.1007/s10393-009-0258-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2008] [Revised: 07/23/2009] [Accepted: 09/14/2009] [Indexed: 05/28/2023]
Abstract
Once widespread across western and southern Australia, wild populations of the western barred bandicoot (WBB) are now only found on Bernier and Dorre Islands, Western Australia. Conservation efforts to prevent the extinction of the WBB are presently hampered by a papillomatosis and carcinomatosis syndrome identified in captive and wild bandicoots, associated with infection with the bandicoot papillomatosis carcinomatosis virus type 1 (BPCV1). This study examined the prevalence and distribution of BPCV1 and the associated syndrome in two island and four mainland (reintroduced and captive) WBB populations in Western Australia, and factors that may be associated with susceptibility to this syndrome. BPCV1 and the syndrome were found in the wild WBB population at Red Cliff on Bernier Island, and in mainland populations established from all or a proportion of founder WBBs from Red Cliff. BPCV1 and the syndrome were not found in the wild population on Dorre Island or in the mainland population founded by animals exclusively from Dorre Island. Findings suggested that BPCV1 and the syndrome were disseminated into mainland WBB populations through the introduction of affected WBBs from Red Cliff. No difference in susceptibility to the syndrome was found between Dorre Island, Bernier Island, and island-cross individuals. Severity of lesions and the number of affected animals observed in captivity was greater than that observed in wild populations. This study provided epidemiological evidence to support the pathological and molecular association between BPCV1 infection and the papillomatosis and carcinomatosis syndrome and revealed increasing age as an additional risk factor for this disease.
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Affiliation(s)
- Lucy Woolford
- School of Veterinary and Biomedical Sciences, Murdoch University, South Street, Murdoch, WA, Australia.
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50
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Johne R, Müller H, Rector A, van Ranst M, Stevens H. Rolling-circle amplification of viral DNA genomes using phi29 polymerase. Trends Microbiol 2009; 17:205-11. [DOI: 10.1016/j.tim.2009.02.004] [Citation(s) in RCA: 143] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2008] [Revised: 01/16/2009] [Accepted: 02/25/2009] [Indexed: 12/01/2022]
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