Molecular archeological evidence in support of the repeated loss of a papillomavirus gene

Doorslaer, Koenraad Van; McBride, Alison A.

doi:10.1038/srep33028

Cited by 40 publications

(49 citation statements)

References 52 publications

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“…Interestingly, none of them were identified in a variety of 653 cutaneous samples with the same testing approach [21]. These results, together with previously published findings [13,17,26,28,[40][41][42][43], suggest the possible adaptation of the mentioned HPV types to the mucosal epithelium [44].…”

Section: Discussionsupporting

confidence: 57%

Assessing Gammapapillomavirus infections of mucosal epithelia with two broad-spectrum PCR protocols

et al. 2020

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Background: Human papillomaviruses (HPVs) have been divided into mucosal and cutaneous types according to their primary epithelial tissue tropism. However, recent studies showed the presence of several cutaneous types in mucosal lesions and healthy mucosa from different anatomical sites. Methods: Here, the HPV prevalence and type-specific distribution were assessed in a variety of mucosal samples from 435 individuals using a combination of two established broad-spectrum primer systems: Gamma-PV PCR and CUT PCR.Results: Overall HPV prevalence in anal canal swabs, cervical cancer biopsies, genital warts and oral swabs was 85, 47, 62 and 4%, respectively. In anal canal swabs, Alpha-PVs were most frequently found (59%), followed by Gamma-(37%) and Beta-PVs (4%). The prevalence and persistence of HPV infection in the anal canal of 226 individuals were further explored. Overall HPV, Gamma-PVs and multiple HPV infections were significantly higher in men vs. women (p = 0.034, p = 0.027 and p = 0.003, respectively); multiple HPV infections were more common in individuals ≤40 years (p = 0.05), and significantly higher prevalence of Gamma-PVs and multiple HPV infections was observed in HIV-1-positive vs. HIV-1-negative individuals (p = 0.003 and p = 0.04, respectively). Out of 21 patients with follow-up anal swabs, only one persistent infection with the same type (HPV58) was detected. Conclusions: Our findings suggest that Gamma-PVs (except species Gamma-6) are ubiquitous viruses with dual muco-cutaneous tissue tropism. Anal canal Gamma-PV infections may be associated with sexual behavior and the host immune status. This study expands the knowledge on Gamma-PVs' tissue tropism, providing valuable data on the characteristics of HPV infection in the anal canal.

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Section: Discussionsupporting

confidence: 57%

Assessing Gammapapillomavirus infections of mucosal epithelia with two broad-spectrum PCR protocols

et al. 2020

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“…SfPV1 contains an ORF within E6 that is similar to the HPV and BPV1 E5 proteins and was previously designated E8 (29); it is also renamed E10. Finally, members of Gammapapillomavirus species 6 (HPV101, 103 and 108) lack a canonical E6 ORF, but potentially encode a highly hydrophobic (E5-like) protein from an overlapping open reading frame, now also designated E10 (9). …”

Section: Improvementsmentioning

confidence: 99%

“…In addition to this core set of proteins, most viruses encode for E6 and E7 proteins, which optimize the cellular milieu for the viral life cycle (6,7). Certain viruses also express small, hydrophobic proteins that are designated E5 (8) or E10 (9). The highly divergent, yet highly expressed, E4 protein is imprinted within the E2 open reading frame (ORF) (10).…”

Section: Introductionmentioning

confidence: 99%

The Papillomavirus Episteme: a major update to the papillomavirus sequence database

et al. 2016

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The Papillomavirus Episteme (PaVE) is a database of curated papillomavirus genomic sequences, accompanied by web-based sequence analysis tools. This update describes the addition of major new features. The papillomavirus genomes within PaVE have been further annotated, and now includes the major spliced mRNA transcripts. Viral genes and transcripts can be visualized on both linear and circular genome browsers. Evolutionary relationships among PaVE reference protein sequences can be analysed using multiple sequence alignments and phylogenetic trees. To assist in viral discovery, PaVE offers a typing tool; a simplified algorithm to determine whether a newly sequenced virus is novel. PaVE also now contains an image library containing gross clinical and histopathological images of papillomavirus infected lesions. Database URL: https://pave.niaid.nih.gov/.

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“…The pattern of presence/absence of E6 and E7 in extant PVs demands an evolutionary explanation. One hypothesis proposes that the MRCA of all PVs already contained these ORFs and invokes six independent repeated loss events for E6 in different PV lineages (Van Doorslaer and McBride, 2016), including in the lineage leading to extant fish PVs, and one gene loss event for E7 in another PV lineage. An alternative hypothesis, more parsimonious with the absence of E6 and E7 in fish PVs, proposes an ancestral PV genome spanning only the minimal arrangement E1-E2-L2-L1, the gain of the ancestral E6 and E7 genes in the lineage of amniote PVs, at least 184 Ma, followed by five independent loss events for E6 and one loss event for E7.…”

Section: Inconsistencies Of the Current Scenario Of Pvs Evolutionmentioning

confidence: 99%

Origin and evolution of papillomavirus (onco)genes and genomes

Willemsen

Bravo

2018

Preprint

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Papillomaviruses (PVs) are ancient viruses infecting vertebrates, from fish to mammals. Although the genomes of PVs are small and show conserved synteny, PVs display large genotypic diversity and ample variation in the phenotypic presentation of the infection. Most PVs genomes contain two small early genes E6 and E7. In a bunch of closely related human PVs, the E6 and E7 proteins provide the viruses with oncogenic potential. The recent discoveries of PVs without E6 and E7 in different fish species place a new root on the PV tree, and suggest that the ancestral PV consisted of the minimal PV backbone E1-E2-L2-L1. Bayesian phylogenetic analyses date the most recent common ancestor of the PV backbone to 424 million years ago (Ma). Common ancestry tests on extant E6 and E7 genes indicate that they share respectively a common ancestor dating back to at least 184 Ma. In AlphaPVs infecting primates, the appearance of the E5 oncogene 53-58 Ma concurred with i) a significant increase in substitution rate, ii) a basal radiation, and iii) key gain of functions in E6 and E7. This series of events was instrumental to build the extant phenotype of oncogenic human PVs. Our results assemble the current knowledge on PV diversity and present an ancient evolutionary timeline punctuated by evolutionary innovations in the history of this successful viral family.

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Molecular archeological evidence in support of the repeated loss of a papillomavirus gene

Cited by 40 publications

References 52 publications

Assessing Gammapapillomavirus infections of mucosal epithelia with two broad-spectrum PCR protocols

Assessing Gammapapillomavirus infections of mucosal epithelia with two broad-spectrum PCR protocols

The Papillomavirus Episteme: a major update to the papillomavirus sequence database

Origin and evolution of papillomavirus (onco)genes and genomes

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