Genomic characterization of ten novel cutaneous human papillomaviruses from keratotic lesions of immunosuppressed patients

Köhler, Annette G.; Gottschling, Marc; Manning, Kizzie; Lehmann, Malte; Schulz, Eric; Krüger-Corcoran, D.; Stockfleth, Eggert; Nindl, Ingo

doi:10.1099/vir.0.030593-0

Cited by 48 publications

(44 citation statements)

References 38 publications

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“…In fact, the intratype heterogeneity of HPVs from the genera Betapapillomavirus and Gammapapillomavirus has remained basically unexplored, and there is currently a significant effort to characterize novel types from these genera (Bottalico et al, 2011; Kohler et al, 2011; Li et al, 2012). With implementation of Next-Gen sequencing (Barzon et al, 2011; Ekstrom et al, 2011), it is anticipated that there will be rapid advances in studying these genome variants (Bernard, 2013), particularly if associated with pathologic lesions.…”

Section: Introductionmentioning

confidence: 99%

Human papillomavirus genome variants

2013

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Amongst the human papillomaviruses (HPVs), the genus Alphapapillomavirus contains HPV types that are uniquely pathogenic. They can be classified into species and types based on genetic distances between viral genomes. Current circulating infectious HPVs constitute a set of viral genomes that have evolved with the rapid expansion of the human population. Viral variants were initially identified through restriction enzyme polymorphisms and more recently through sequence determination of viral fragments. Using partial sequence information, the history of variants, and the association of HPV variants with disease will be discussed with the main focus on the recent utilization of full genome sequence information for variant analyses. The use of multiple sequence alignments of complete viral genomes and phylogenetic analyses have begun to define variant lineages and sublineages using empirically defined differences of 1.0–10.0% and 0.5–1.0%, respectively. These studies provide the basis to define the genetics of HPV pathogenesis.

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Section: Introductionmentioning

confidence: 99%

Human papillomavirus genome variants

2013

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“…The validity of this concept was extensively demonstrated for cutaneous beta and gamma human papillomaviruses (β and γ-HPVs) that are commonly present on the superficial layers of the skin in most individuals [3]–[5]. Indeed, in this setting, several studies have reported the genetic diversity of cutaneous human papillomaviruses using consensus PCR targeting L1 gene [6] or more recently through sequencing rolling circle products [7], [8]. Furthermore, functional metagenomic methods were recently applied to cutaneous samples and led to the description of new human virus species belonging to the Polyomaviridae family.…”

Section: Introductionmentioning

confidence: 99%

Human Skin Microbiota: High Diversity of DNA Viruses Identified on the Human Skin by High Throughput Sequencing

et al. 2012

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The human skin is a complex ecosystem that hosts a heterogeneous flora. Until recently, the diversity of the cutaneous microbiota was mainly investigated for bacteria through culture based assays subsequently confirmed by molecular techniques. There are now many evidences that viruses represent a significant part of the cutaneous flora as demonstrated by the asymptomatic carriage of beta and gamma-human papillomaviruses on the healthy skin. Furthermore, it has been recently suggested that some representatives of the Polyomavirus genus might share a similar feature. In the present study, the cutaneous virome of the surface of the normal-appearing skin from five healthy individuals and one patient with Merkel cell carcinoma was investigated through a high throughput metagenomic sequencing approach in an attempt to provide a thorough description of the cutaneous flora, with a particular focus on its viral component. The results emphasize the high diversity of the viral cutaneous flora with multiple polyomaviruses, papillomaviruses and circoviruses being detected on normal-appearing skin. Moreover, this approach resulted in the identification of new Papillomavirus and Circovirus genomes and confirmed a very low level of genetic diversity within human polyomavirus species. Although viruses are generally considered as pathogen agents, our findings support the existence of a complex viral flora present at the surface of healthy-appearing human skin in various individuals. The dynamics and anatomical variations of this skin virome and its variations according to pathological conditions remain to be further studied. The potential involvement of these viruses, alone or in combination, in skin proliferative disorders and oncogenesis is another crucial issue to be elucidated.

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“…Their prevalence and natural history, for example acquisition soon after birth, reflects a commensalic interaction with the immunocompetent host [8]–[10]. Historically, several cutaneous papillomaviruses have been isolated from patients with the genetic disease epidermodysplasia verruciformis [11], [12], and from immunosuppressed patients [13], probably due to higher viral loads among these patient groups [14]. As a consequence of improved methods, several PVs have been characterized, and the number of HPV types of the γ-PV genus has been expanded from 16 HPV types in 2010 [7] to 62 representative HPV types in 2013 (retrieved from GenBank, September 2013).…”

Section: Introductionmentioning

confidence: 99%

Characterization of Human Papillomavirus Type 154 and Tissue Tropism of Gammapapillomaviruses

Ure

Forslund

2014

PLoS ONE

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The novel human papillomavirus type 154 (HPV154) was characterized from a wart on the crena ani of a three-year-old boy. It was previously designated as the putative HPV type FADI3 by sequencing of a subgenomic FAP amplicon. We obtained the complete genome by combined methods including rolling circle amplification (RCA), genome walking through an adapted method for detection of integrated papillomavirus sequences by ligation-mediated PCR (DIPS-PCR), long-range PCR, and finally by cloning of four overlapping amplicons. Phylogenetically, the HPV154 genome clustered together with members of the proposed species Gammapapillomavirus 11, and demonstrated the highest identity in L1 to HPV136 (68.6%). The HPV154 was detected in 3% (2/62) of forehead skin swabs from healthy children. In addition, the different detection sites of 62 gammapapillomaviruses were summarized in order to analyze their tissue tropism. Several of these HPV types have been detected from multiple sources such as skin, oral, nasal, and genital sites, suggesting that the gammapapillomaviruses are generalists with a broader tissue tropism than previously appreciated. The study expands current knowledge concerning genetic diversity and tropism among HPV types in the rapidly growing gammapapillomavirus genus.

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Genomic characterization of ten novel cutaneous human papillomaviruses from keratotic lesions of immunosuppressed patients

Cited by 48 publications

References 38 publications

Human papillomavirus genome variants

Human papillomavirus genome variants

Human Skin Microbiota: High Diversity of DNA Viruses Identified on the Human Skin by High Throughput Sequencing

Characterization of Human Papillomavirus Type 154 and Tissue Tropism of Gammapapillomaviruses

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