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  • 1
    Keywords: CELLS ; CELL ; COMBINATION ; Germany ; GENE ; GENES ; GENOME ; PROTEINS ; COMPLEX ; COMPLEXES ; SKIN ; papillomavirus ; ACID ; EVOLUTION ; L1 ; PHYLOGENETIC ANALYSIS ; AMINO-ACID ; hair ; LONG ; adaptation ; GENOMES ; SEQUENCE DATA ; EEPV
    Abstract: Knowledge about biological diversity is the prerequisite to reliably reconstruct the evolution of pathogens such as papillomaviruses (PV). However, complete genomes of non-human PV have only been cloned and sequenced from 8 out of 18 orders within the Placentalia, although the host-specific variety of PV is considered much larger. We isolated and sequenced the complete genome of the first insectivoran PV type from hair follicle cells of the European hedgehog (Erinaceus europaeus), designated EHPV. We conducted phylogenetic analyses (maximum-likelihood criterion and Bayesian inference) with the genomic information of a systematically representative set of 67 PV types including EHPV As inferred from amino acid sequence data of the separate genes E1, E2 and L1 as well as of the gene combination E6-E7-E1-E2-L1, EHPV clustered within the beta-gamma-pi-zeta-PV supertaxon and constituted the closest relative of genus Betapapillomavirus infecting primates. Beside the typical organization of the PV genome, EHPV exhibited a 1172 lop, non-coding region between the E2 and the L2 open reading frames. This trait has been previously described for the only distantly related Lambdapapillomavirus, but a common evolutionary origin of both non-coding regions is unlikely. Our results underscore the modular organization of the PV genome and the complex natural history of PV
    Type of Publication: Journal article published
    PubMed ID: 19218207
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  • 2
    Keywords: ACID, AMINO-ACID, animals, CANCER, CELL, CELLS, cluster analysis, DNA,Viral/chemistry/genetics, Evol
    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.
    Type of Publication: Journal article published
    PubMed ID: 19605590
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  • 3
    Keywords: CANCER ; CELLS ; AGENTS ; CELL ; Germany ; CLASSIFICATION ; HYBRIDIZATION ; INFECTION ; mechanisms ; SKIN ; papillomavirus ; IN-SITU ; AMPLIFICATION ; skin cancer ; HPV ; E6 ; ONCOPROTEIN ; PREVALENCE ; papillomaviruses ; RECIPIENTS ; TRANSPLANT RECIPIENTS ; SCIENCE ; development ; Phylogeny ; SKIN-LESIONS ; human papillomavirus (HPV) ; cutaneous warts ; COMMON WARTS ; Cutaneous ; IMMUNOSUPPRESSED PATIENTS ; Organ transplant recipients (OTR)
    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. (C) 2009 Elsevier Inc. All rights reserved
    Type of Publication: Journal article published
    PubMed ID: 20096912
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  • 4
    Keywords: evaluation ; Germany ; SUPPORT ; CLONING ; DISTINCT ; GENE ; GENES ; radiation ; COMPLEX ; INFECTION ; MECHANISM ; animals ; BASE ; mechanisms ; papillomavirus ; SEQUENCE ; SEQUENCES ; TYPE-1 ; ACID ; virus ; genetics ; EVOLUTION ; BETA ; NETHERLANDS ; FRAGMENTS ; RENAL-TRANSPLANT RECIPIENTS ; heredity ; SKIN-CANCER ; molecular ; zoonosis ; LEVEL ; analysis ; methods ; EPITHELIUM ; FRAGMENT ; animal ; INFERENCE ; host ; adaptive radiation ; interspecies transmission ; BIRDS ; NUCLEOTIDE ; Co-evolution ; pathogene
    Abstract: The diversity of papillomaviruses (PVes) infecting stratified squamous epithelia of warm-blooded animals, such as birds and mammals, is only fragmentarily documented. The PV types are sequenced from 9 of 18 placental taxa at the order level to date. Current phylogenetic analyses of PV sequences frequently do not consider evolutionary polarity and statistical evaluation of internal nodes, that are required for robust evolutionary conclusions. In this study, we isolated and characterized three putatively novel animal PV types from hair follicles comprising the first known insectivoran PV and two cervid PVes. With the help of the primer pair FAP59/FAP64, we amplified L1 gene fragments consisting of approximately 470 base pairs. Phylogenetic analyses were performed with a representative set of 73 PV sequences that included the three novel PVes using Maximum Likelihood, Bayesian inference, Maximum Parsimony, and distance-based methods on amino acid alignments. The three novel PVes appear to be components of the beta+gamma+pi+xi-PV supertaxon, within which the insectivoran PV has an isolated phylogenetic position. The two cervid PVes constitute a distinct group that is only distantly related to the core cervid PVes of the delta-PVes. The molecular data supports a complex evolutionary scenario for PVes which is driven by multiple mechanisms comprising host-linked evolution, adaptive radiation establishing different ecological niches, and multiple infections across species borders
    Type of Publication: Journal article published
    PubMed ID: 18210195
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  • 5
    Keywords: radiation ; SEQUENCE ; virus ; INFECTIOUS-DISEASES ; PHYLOGENETIC TREES ; COTTONTAIL RABBIT PAPILLOMAVIRUS ; DIVERSIFICATION ; HOST-PARASITE ASSOCIATIONS ; GENOMIC CHARACTERIZATION ; TYPE-1 DNA
    Abstract: The associations between pathogens and their hosts are complex and can result from a variety of evolutionary processes including codivergence, lateral transfer, or duplication. Papillomaviruses (PVs) are double-stranded DNA viruses ubiquitously present in mammals and are a suitable target for rigorous statistical tests of potential virus-host codivergence. We analyze the evolutionary dynamics of PV diversification by comparing robust phylogenies of PVs and their respective hosts using different statistical approaches to assess topological and branch-length congruence. Mammalian PVs segregated into four diverse major clades that overlapped to varying degrees in terms of their mammalian host lineages. The hypothesis that PVs and hosts evolved independently was globally rejected (P = 0.0001), although only 90 of 207 virus-host associations (43%) were significant in individual tests. Virus-host codivergence accounted roughly for one-third of the evolutionary events required to reconcile PV-host evolutionary histories. When virus-host associations were analyzed locally within each of the four viral clades, numerous independent topological congruencies were identified that were incompatible with respect to the global trees. These results support an evolutionary scenario in which early PV radiation was followed by independent codivergence between viruses within each of the major clades and their hosts. Moreover, heterogeneous groups of closely related PVs infecting non-related hosts suggest several interspecies transmission events. Our results argue thus for the importance of alternative events in PV evolution, in contrast to the prevailing opinion that these viruses show a high degree of host specificity and codivergence
    Type of Publication: Journal article published
    PubMed ID: 21285031
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  • 6
    Keywords: CLASSIFICATION ; recombination ; HIGH-THROUGHPUT ; ROLLING-CIRCLE AMPLIFICATION ; HEALTHY SKIN ; MAXIMUM-LIKELIHOOD ; GENOMIC CHARACTERIZATION ; Betapapillomavirus ; CETACEAN PAPILLOMAVIRUSES ; ALIGNMENTS
    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.
    Type of Publication: Journal article published
    PubMed ID: 22960206
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  • 7
    Keywords: CELLS ; carcinoma ; CELL ; Germany ; human ; DNA ; INFECTION ; MECHANISM ; FAMILY ; mechanisms ; SKIN ; MEMBERS ; papillomavirus ; PATTERNS ; AGE ; PCR ; human papillomavirus ; HPV ; HUMAN-PAPILLOMAVIRUS ; SQUAMOUS-CELL CARCINOMA ; squamous cell carcinoma ; INDIVIDUALS ; CHILDREN ; PREVALENCE ; REGRESSION ; FAMILIES ; EPIDERMODYSPLASIA-VERRUCIFORMIS ; LIFE ; hair ; HIGH-THROUGHPUT ; ACTINIC KERATOSES ; NONMELANOMA SKIN-CANCER ; USA ; ONSET ; TRANSMISSION ; Phylogeny ; SQUAMOUS-CELL ; HPV types ; CUTANEOUS HUMAN PAPILLOMAVIRUSES ; PARENTS ; MOTHER ; HISTORICAL ASSOCIATIONS ; LINE-BLOTTING SYSTEM
    Abstract: Several cutaneotropic human papillomavirus (HPV) types seem to be involved in the early onset of cutaneous squamous-cell carcinoma. To test the hypothesis that cutaneotropic HPV infections are facilitated because of close and frequent skin contact (for example, between child and mother), we examined HPV prevalence in hair follicle cells from 134 volunteers (1-89 years of age, median 42 years) from 13 families. We used a high-throughput HPV-typing approach with a sensitive beta-/gamma-cutaneous PCR method, followed by reverse line blotting, to detect 30 cutaneotropic HPV types. HPV prevalence in all individuals was 42% and increased with age from 5% at 〈= 20 years to 27% at 21-40 years, 53% at 41-60 years, and 76% at 460 years. The effect of life age was significant, independent of couples and family members shown by regression analyses (P 〈= 10(-8)). A higher similarity of HPV infection patterns was observed in couples versus two randomly chosen individuals (P 〈= 0.05). However, the same specific HPV type was rarely found within couples or between children and their parents. Cutaneotropic HPV types are occasionally exchanged between family members during the entire lifetime, but other donors should also be considered in viral transmission
    Type of Publication: Journal article published
    PubMed ID: 19516265
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  • 8
  • 9
    Keywords: CELLS ; CELL ; COMBINATION ; Germany ; human ; GENE ; GENES ; GENOME ; RESOLUTION ; radiation ; COMPLEX ; COMPLEXES ; DNA ; INFECTION ; MECHANISM ; recombination ; animals ; mechanisms ; SKIN ; BIOLOGY ; BOVINE PAPILLOMAVIRUS ; OPEN READING FRAME ; papillomavirus ; ACID ; HUMANS ; genetics ; EVOLUTION ; BETA ; L1 ; INFECTIONS ; RECONSTRUCTION ; heredity ; MOLECULAR-CLONING ; review ; ALIGNMENT ; EPIDERMODYSPLASIA-VERRUCIFORMIS ; GENOME ORGANIZATION ; NUCLEOTIDE-SEQUENCE ; zoonosis ; LEVEL ; methods ; TESTS ; EVENTS ; ROLLING-CIRCLE AMPLIFICATION ; animal ; host ; virology ; TOPOLOGY ; E2 ; adaptive radiation ; coevolution ; COTTONTAIL RABBIT PAPILLOMAVIRUS ; EQUINE SARCOIDS ; high performance computing ; interspecies transmission ; ORAL PAPILLOMAVIRUS
    Abstract: The circular, double-stranded 8-kb DNA genome of papillomaviruses (PVes) consists mainly of 4 large genes, E1, E2, L2, and L1. Approximately 150 papillomavirus genomes have been sequenced to date. We analyzed a representative sample of 53 PVes genomes using maximum likelihood, Bayesian inference, maximum parsimony, and distance-based methods both on nucleotide (nt) and on amino acid (aa) alignments. When the 4 genes were analyzed separately, aa-inferred phylogenies contradicted each other less than nt-inferred trees (judged by partition homogeneity tests). In particular, gene combinations including the L2 gene generated significant incongruence (P 〈 0.001). Combined analyses of the remaining genes E1-E2-L1 produced a well-supported phylogeny including supertaxon beta + gamma + pi + xi-PVes (infecting Artiodactyla, Carnivora, Primates, and Rodentia) and supertaxon K + lambda + mu + nu + sigma-PVes (infecting Carnivora, Lagomorpha, Primates, and Rodentia). Based on the tree topology, host-linked evolution appears plausible at shallow, rather than deeper, taxonomic levels. Diversification within PVes may also involve adaptive radiation establishing different niches (within a single-host species) and recombination events (within single-host cells). Heterogeneous groups of closely related PVes infecting, for example, humans and domestic animals such as hamster, dog, and cattle suggest multiple infections across species borders. Additional evolutionary phenomena such as strong codon usage preferences, and computational biases including reconstruction artifacts and insufficient taxon sampling, may contribute to the incomplete resolution of deep phylogenetic nodes. The molecular data globally supports a complex evolutionary scenario for PVes, which is driven by multiple mechanisms but not exclusively by coevolution with corresponding hosts
    Type of Publication: Journal article published
    PubMed ID: 17344207
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