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Shimazaki Y, Yoneya S, Fujita S, Nakashima T, Nabeshima K, Sudoh S, Matsubara K, Okumura N, Kondo H, Nishifuji K, Koba R, Tohya Y. Identification and characterization of the genome of a papillomavirus from skin lesions of four-toed hedgehogs (Atelerix albiventris). Virus Genes 2023; 59:234-239. [PMID: 36626061 DOI: 10.1007/s11262-022-01965-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 12/20/2022] [Indexed: 01/11/2023]
Abstract
The present study describes the clinical and pathological characteristics of skin lesions in two four-toed hedgehogs (Atelerix albiventris). We performed inverse PCR to identify the genome of papillomavirus (PV) in the skin lesions and subsequently sequenced the full genome of the virus, which was tentatively named Atelerix albiventris papillomavirus 1 (AalbPV1). The overall sequences of the viral genomes of both four-toed hedgehogs were identical. This study first identified the presence of a novel PV in Japanese four-toed hedgehogs and provided genetic information about this virus.
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Affiliation(s)
- Yotaro Shimazaki
- Faculty of Agriculture, Animal Medical Center, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo, 183-8509, Japan
| | - Shion Yoneya
- Laboratory of Veterinary Microbiology, Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa-shi, Kanagawa, 252-0880, Japan
| | - Shigeru Fujita
- Laboratory of Veterinary Microbiology, Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa-shi, Kanagawa, 252-0880, Japan
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Tomomi Nakashima
- IDEXX Laboratories, K.K., 5-8-18 Kajinocho, Koganei-shi, Tokyo, 184-8515, Japan
| | - Kei Nabeshima
- Ecological Risk Assessment and Control Section Center for Environmental Biology and Ecosystem, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba-shi, Ibaraki, 305-8506, Japan
| | - Sumire Sudoh
- Banquet Animal Hospital, 1-3-23 Mishuku, Setagaya-ku, Tokyo, 154-0005, Japan
| | - Katsuki Matsubara
- Banquet Animal Hospital, 1-3-23 Mishuku, Setagaya-ku, Tokyo, 154-0005, Japan
| | - Naka Okumura
- Laboratory of Veterinary Pathology, Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa-shi, Kanagawa, 252-0880, Japan
| | - Hirotaka Kondo
- Laboratory of Veterinary Pathology, Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa-shi, Kanagawa, 252-0880, Japan
| | - Koji Nishifuji
- Division of Animal Life Science, Institute of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo, 183-8509, Japan
| | - Ryota Koba
- Laboratory of Veterinary Microbiology, Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa-shi, Kanagawa, 252-0880, Japan.
| | - Yukinobu Tohya
- Laboratory of Veterinary Microbiology, Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa-shi, Kanagawa, 252-0880, Japan
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Willemsen A, van den Boom A, Dietz J, Bilge Dagalp S, Dogan F, Bravo IG, Ehrhardt A, Ehrke-Schulz E. Genomic and phylogenetic characterization of ChPV2, a novel goat PV closely related to the Xi-PV1 species infecting bovines. Virol J 2020; 17:167. [PMID: 33126890 PMCID: PMC7602357 DOI: 10.1186/s12985-020-01440-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 10/21/2020] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Papillomaviruses (PVs) infecting artiodactyls are very diverse, and only second in number to PVs infecting primates. PVs associated to lesions in economically important ruminant species have been isolated from cattle and sheep. METHODS Potential PV DNA from teat lesions of a Damascus goat was isolated, cloned and sequenced. The PV genome was analyzed using bioinformatics approaches to detect open reading frames and to predict potential features of encoded proteins as well as putative regulatory elements. Sequence comparison and phylogenetic analyses using the concatenated E1E2L2L1 nucleotide and amino acid alignments was used to reveal the relationship of the new PV to the known PV diversity and its closest relevants. RESULTS We isolated and characterized the full-genome of novel Capra hircus papillomavirus. We identified the E6, E7, E1, E2, L2, L1 open reading frames with protein coding potential and putative active elements in the ChPV2 proteins and putative regulatory genome elements. Sequence similarities of L1 and phylogenetic analyses using concatenated E1E2L2L1 nucleotide and amino acid alignments suggest the classification as a new PV type designated ChPV2 with a phylogenetic position within the XiPV genus, basal to the XiPV1 species. ChPV2 is not closely related to ChPV1, the other known goat PV isolated from healthy skin, although both of them belong confidently into a clade composed of PVs infecting cervids and bovids. Interestingly, ChPV2 contains an E6 open reading frame whereas all closely related PVs do not CONCLUSION: ChPV2 is a novel goat PV closely related to the Xi-PV1 species infecting bovines. Phylogenetic relationships and genome architecture of ChPV2 and closely related PV types suggest at least two independent E6 losses within the XiPV clade.
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Affiliation(s)
- Anouk Willemsen
- Centre National de La Recherche Scientifique (CNRS), Laboratory MIVEGEC (CNRS IRD Uni Montpellier), Montpellier, France.,Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Alexander van den Boom
- Chair for Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department for Human Medicine, Faculty of Health, Witten/Herdecke University, Stockumer Strasse 10, 58453, Witten, Germany
| | - Julienne Dietz
- Chair for Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department for Human Medicine, Faculty of Health, Witten/Herdecke University, Stockumer Strasse 10, 58453, Witten, Germany
| | - Seval Bilge Dagalp
- Faculty of Veterinary Medicine, Department of Virology, Ankara University, Ankara, Turkey
| | - Firat Dogan
- Faculty of Veterinary Medicine, Department of Virology, Hatay Mustafa Kemal University, Hatay, Turkey
| | - Ignacio G Bravo
- Centre National de La Recherche Scientifique (CNRS), Laboratory MIVEGEC (CNRS IRD Uni Montpellier), Montpellier, France.,Center for Research on the Ecology and Evolution of Diseases (CREES), Montpellier, France
| | - Anja Ehrhardt
- Chair for Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department for Human Medicine, Faculty of Health, Witten/Herdecke University, Stockumer Strasse 10, 58453, Witten, Germany
| | - Eric Ehrke-Schulz
- Chair for Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department for Human Medicine, Faculty of Health, Witten/Herdecke University, Stockumer Strasse 10, 58453, Witten, Germany.
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3
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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: 1.7] [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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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: 4.4] [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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A novel papillomavirus isolated from a nasal neoplasia in an Italian free-ranging chamois (Rupicapra r. rupicapra). Vet Microbiol 2014; 172:108-19. [PMID: 24910075 DOI: 10.1016/j.vetmic.2014.05.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Revised: 04/30/2014] [Accepted: 05/04/2014] [Indexed: 11/22/2022]
Abstract
Most amniotes are the hosts of many, distantly related papillomaviruses (PVs). Infection by PVs can be asymptomatic, or lead instead to benign or malignant lesions. However, PVs infecting animals and associated with malignancies are still largely understudied. In the present study, we communicate the complete genome of a novel PV found in a nasal neoplasia of a free-ranging alpine chamois (Rupicapra r. rupicapra) in an Italian national park. Long-PCR and cloning approaches followed for Sanger sequencing were used to identify the first PV found in chamois. The genome of the novel virus - RrupPV1 - of 7256 bp in length, presents the classical PV structure, and lacks the interE2-L2 region that hosts the E5 gene in AlphaPVs and in DeltaPVs. The nucleotide identity percentage of the L1 ORF, places RrupPV1 together with OaPV3 in the same genus. The latter is a PV isolated from a squamous cell carcinoma in sheep in Sardinia. Full-genome phylogenetic reconstructions suggest that these two viruses are sister taxa, and that both of them are very distantly related to any other known PV. Many cetartiodactyl species are infected by non-monophyletic PVs. Our results exemplify further the multiple links between the infection by certain, distantly related PVs and the development of diverse cancers in animals and highlight the need of a systematic search of oncogenic and non-oncogenic animal PVs.
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Rector A, Van Ranst M. Animal papillomaviruses. Virology 2013; 445:213-23. [PMID: 23711385 DOI: 10.1016/j.virol.2013.05.007] [Citation(s) in RCA: 167] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 04/29/2013] [Accepted: 05/03/2013] [Indexed: 11/26/2022]
Abstract
We provide an overview of the host range, taxonomic classification and genomic diversity of animal papillomaviruses. The complete genomes of 112 non-human papillomavirus types, recovered from 54 different host species, are currently available in GenBank. The recent characterizations of reptilian papillomaviruses extend the host range of the Papillomaviridae to include all amniotes. Although the genetically diverse papillomaviruses have a highly conserved genomic lay-out, deviations from this prototypic genome organization are observed in several animal papillomaviruses, and only the core ORFs E1, E2, L2 and L1 are present in all characterized papillomavirus genomes. The discovery of papilloma-polyoma hybrids BPCV1 and BPCV2, containing a papillomaviral late region but an early region encoding typical polyomaviral nonstructural proteins, and the detection of recombination breakpoints between the early and late coding regions of cetacean papillomaviruses, could indicate that early and late gene cassettes of papillomaviruses are relatively independent entities that can be interchanged by recombination.
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Affiliation(s)
- Annabel Rector
- Laboratory of Clinical and Epidemiological Virology, Rega Institute for Medical Research, University of Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium.
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Isolation of three novel rat and mouse papillomaviruses and their genomic characterization. PLoS One 2012; 7:e47164. [PMID: 23077564 PMCID: PMC3471917 DOI: 10.1371/journal.pone.0047164] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Accepted: 09/10/2012] [Indexed: 11/25/2022] Open
Abstract
Despite a growing knowledge about the biological diversity of papillomaviruses (PV), only little is known about non-human PV in general and about PV mice models in particular. We cloned and sequenced the complete genomes of two novel PV types from the Norway rat (Rattus norvegicus; RnPV2) and the wood mouse (Apodemus sylvaticus; AsPV1) as well as a novel variant of the recently described MmuPV1 (originally designated as MusPV) from a house mouse (Mus musculus; MmuPV1 variant). In addition, we conducted phylogenetic analyses using a systematically representative set of 79 PV types, including the novel sequences. As inferred from concatenated amino acid sequences of six proteins, MmuPV1 variant and AsPV1 nested within the Beta+Xi-PV super taxon as members of the Pi-PV. RnPV2 is a member of the Iota-PV that has a distant phylogenetic position from Pi-PV. The phylogenetic results support a complex scenario of PV diversification driven by different evolutionary forces including co-divergence with hosts and adaptive radiations to new environments. PV types particularly isolated from mice and rats are the basis for new animal models, which are valuable to study PV induced tumors and new treatment options.
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Novel animal papillomavirus sequences and accurate phylogenetic placement. Mol Phylogenet Evol 2012; 65:883-91. [PMID: 22960206 DOI: 10.1016/j.ympev.2012.08.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Revised: 07/13/2012] [Accepted: 08/14/2012] [Indexed: 01/08/2023]
Abstract
All amniotes are probably infected by specific papillomaviruses (PVs), but knowledge about PV diversity remains sparse. An insufficient taxon sampling, and a focus on humans as hosts, may perturb phylogenetic analyses leading to wrong conclusions about PV evolution. We performed a systematic approach to explore the diversity of PVs combining rolling circle amplification with the use of "universal" primers to search for the presence of novel PV sequences in animal samples. We communicate 12 sequences putatively corresponding to novel PVs gained from 10 host species in eight mammal families: Bovidae, Canidae, Cervidae, Equidae, Hominidae, Phocoenidae, Procyonidae and Pteropodidae. The phylogenetic position of the new sequences was inferred with an evolutionary placement algorithm under a Maximum Likelihood framework using a pre-computed, well-resolved tree constructed with the E1-E2-L1 gene sequences as a backbone. The new sequences were phylogenetically diverse and could be respectively placed with confidence within all four PV crown groups. The prevailing presence of sequences from the crown groups Alpha+Omikron-PVs and Beta+Xi-PVs may correspond to an increased viral diversity in these taxa, or rather reflect a combination of anthropocentric bias and preferential amplification from commonly used "universal" primers. Our results combined with literature data support the view that the number and diversity of animal PVs is overwhelmingly large.
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Kocjan BJ, Jelen MM, Maver PJ, Seme K, Poljak M. Pre-vaccination genomic diversity of human papillomavirus genotype 6 (HPV 6): A comparative analysis of 21 full-length genome sequences. INFECTION GENETICS AND EVOLUTION 2011; 11:1805-10. [DOI: 10.1016/j.meegid.2011.06.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Revised: 06/08/2011] [Accepted: 06/27/2011] [Indexed: 11/26/2022]
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Köhler A, Gottschling M, Manning K, Lehmann MD, Schulz E, Krüger-Corcoran D, Stockfleth E, Nindl I. Genomic characterization of ten novel cutaneous human papillomaviruses from keratotic lesions of immunosuppressed patients. J Gen Virol 2011; 92:1585-1594. [PMID: 21471318 DOI: 10.1099/vir.0.030593-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Viral warts from immunosuppressed organ transplant recipients (OTR) persist over years and may progress into non-melanoma skin cancer. The types of human papillomaviruses (HPV) in such lesions are different from that seen in the general population. A subset of these lesions is not infected with the classical wart-associated HPV types. In order to gain a better understanding of the HPV types in those lesions, we isolated ten novel HPVs from persisting keratotic lesions of immunosuppressed OTRs by rolling circle amplification and subsequent long-template PCR. Additionally, we sequenced and characterized the whole genome of the ten novel HPV types. Phylogenetic analyses revealed that nine HPV types belonged to the genus Gammapapillomavirus (γ-PV) and one to the genus Betapapillomavirus. In a phylogenetic analysis using L1 fragments of human and non-human PV types, primate papillomaviruses and our novel HPV types nested within the genus γ-PV in a highly polyphyletic pattern. This study significantly broadens the knowledge concerning the diversity and evolution of the poorly known γ-PV types.
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Affiliation(s)
- Anja Köhler
- Charité, Department of Dermatology, Venereology and Allergy, Skin Cancer Center Charité, University Hospital of Berlin, Berlin, Germany
| | - Marc Gottschling
- Department of Biology, Systematic Botany and Mycology, Geo Bio-Center Ludwig-Maximilians-Universität München, Munich, Germany
| | - Kizzie Manning
- Charité, Department of Dermatology, Venereology and Allergy, Skin Cancer Center Charité, University Hospital of Berlin, Berlin, Germany
| | - Mandy D Lehmann
- Charité, Department of Dermatology, Venereology and Allergy, Skin Cancer Center Charité, University Hospital of Berlin, Berlin, Germany
| | - Eric Schulz
- Charité, Department of Dermatology, Venereology and Allergy, Skin Cancer Center Charité, University Hospital of Berlin, Berlin, Germany
| | - Daniela Krüger-Corcoran
- Charité, Department of Dermatology, Venereology and Allergy, Skin Cancer Center Charité, University Hospital of Berlin, Berlin, Germany
| | - Eggert Stockfleth
- Charité, Department of Dermatology, Venereology and Allergy, Skin Cancer Center Charité, University Hospital of Berlin, Berlin, Germany
| | - Ingo Nindl
- Charité, Department of Dermatology, Venereology and Allergy, Skin Cancer Center Charité, University Hospital of Berlin, Berlin, Germany
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Modular organizations of novel cetacean papillomaviruses. Mol Phylogenet Evol 2011; 59:34-42. [DOI: 10.1016/j.ympev.2010.12.013] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Revised: 12/02/2010] [Accepted: 12/22/2010] [Indexed: 11/20/2022]
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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: 1138] [Impact Index Per Article: 75.9] [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: 1.4] [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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Köhler A, Gottschling M, Förster J, Röwert-Huber J, Stockfleth E, Nindl I. Genomic characterization of a novel human papillomavirus (HPV-117) with a high viral load in a persisting wart. Virology 2010; 399:129-133. [PMID: 20096912 DOI: 10.1016/j.virol.2009.12.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2009] [Revised: 11/24/2009] [Accepted: 12/17/2009] [Indexed: 11/27/2022]
Abstract
Warts from immunosuppressed organ transplant recipients (OTR) persist over years and may progress into non-melanoma skin cancer. Human papillomaviruses (HPV) are considered the causal agents for the development of such warts. We isolated the novel type HPV-117 from a persisting wart by rolling circle amplification. One hundred eighteen warts from immunocompetent patients (IC) and 49 warts from OTR were analyzed by HPV-117 E6 type-specific PCR. As inferred from a phylogenetic analysis, the new type HPV-117 belonged to alpha-PV species 2, including the most similar types HPV-10 and HPV-94. The general prevalence of HPV-117 in warts was 2% in IC (2/118), and 12% in OTR (6/49). The high viral load in dysplastic cells of a Verruca vulgaris was shown by in situ hybridization. Our results suggest an active role of the novel type in the development of cutaneous warts of OTR.
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Affiliation(s)
- Anja Köhler
- Charité, Department of Dermatology, Venereology and Allergy, Skin Cancer Center Charité, University Hospital of Berlin, Berlin, Germany
| | - Marc Gottschling
- Department of Biology, Systematic Botany and Mycology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Jana Förster
- Charité, Department of Dermatology, Venereology and Allergy, Skin Cancer Center Charité, University Hospital of Berlin, Berlin, Germany
| | - Joachim Röwert-Huber
- Charité, Department of Dermatology, Venereology and Allergy, Skin Cancer Center Charité, University Hospital of Berlin, Berlin, Germany
| | - Eggert Stockfleth
- Charité, Department of Dermatology, Venereology and Allergy, Skin Cancer Center Charité, University Hospital of Berlin, Berlin, Germany
| | - Ingo Nindl
- Charité, Department of Dermatology, Venereology and Allergy, Skin Cancer Center Charité, University Hospital of Berlin, Berlin, Germany.
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Schulz E, Gottschling M, Wibbelt G, Stockfleth E, Nindl I. Isolation and genomic characterization of the first Norway rat (Rattus norvegicus) papillomavirus and its phylogenetic position within Pipapillomavirus, primarily infecting rodents. J Gen Virol 2009; 90:2609-2614. [PMID: 19605590 DOI: 10.1099/vir.0.012583-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
A series of papillomavirus (PV) types have been isolated from different rodent species, and most of them belong to the genus Pipapillomavirus. We isolated and sequenced the complete genome of a novel PV type (designated RnPV) from the oral cavity of the Norway rat (Rattus norvegicus), as well as an L1 gene fragment from hair-follicle cells of the European beaver (Castor fiber). As inferred from amino acid sequence data, RnPV clustered within the beta+gamma+pi+Xi-PV supertaxon as a member of the genus Pipapillomavirus. The closest relatives of RnPV were McPV-2 and MmPV, and time estimates indicated that the genus Pipapillomavirus originated in the late Cenozoic era. The close relationship of RnPV to other murid PV types supports the hypothesis of co-divergence between members of the genus Pipapillomavirus and their hosts. However, the derived Neogene origin of the genus Pipapillomavirus is much younger than has been considered for the Rodentia as the primary hosts, indicating that alternative interpretations of the phylogenetic trees should be conceived.
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Affiliation(s)
- Eric Schulz
- Clinic for Dermatology, Venereology and Allergology, Skin Cancer Center Charité (HTCC), Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Marc Gottschling
- Department of Biology, Systematic Botany, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Gudrun Wibbelt
- Institut für Zoo- und Wildtierforschung, Berlin, Germany
| | - Eggert Stockfleth
- Clinic for Dermatology, Venereology and Allergology, Skin Cancer Center Charité (HTCC), Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Ingo Nindl
- DKFZ - Charité, Viral Transformation Mechanisms, German Cancer Research Center, Heidelberg, Germany.,Clinic for Dermatology, Venereology and Allergology, Skin Cancer Center Charité (HTCC), Charité - Universitätsmedizin Berlin, Berlin, Germany
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Li L, Barry P, Yeh E, Glaser C, Schnurr D, Delwart E. Identification of a novel human gammapapillomavirus species. J Gen Virol 2009; 90:2413-2417. [PMID: 19570953 DOI: 10.1099/vir.0.012344-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
By using random PCR amplification, shotgun sequencing and sequence similarity searches, we analysed nucleic acids present in cell cultures inoculated with samples from unexplained cases of encephalitis. We identified a divergent human papillomavirus (HPV) sequence originating from a rectal swab. The full genome was amplified by inverse PCR and sequenced. The prototype of the sixth gammapapillomavirus species, HPV116, was not found in the patient's cerebrospinal fluid or respiratory secretions, nor in culture supernatants from other unexplained cases of encephalitis, indicating that its identification in an encephalitis patient was accidental.
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Affiliation(s)
- Linlin Li
- Department of Laboratory Medicine, University of California, San Francisco, CA 94118, USA
- Blood Systems Research Institute, San Francisco, CA 94118, USA
| | - Pennan Barry
- Department of Medicine, University of California, San Francisco, CA 94143, USA
| | - Elaine Yeh
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA 94804, USA
| | - Carol Glaser
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA 94804, USA
| | - David Schnurr
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA 94804, USA
| | - Eric Delwart
- Department of Laboratory Medicine, University of California, San Francisco, CA 94118, USA
- Blood Systems Research Institute, San Francisco, CA 94118, USA
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