Wholegenome analysis of human papillomavirus type 16. Number indicates number of copies of hpv dna in the diluted dna specimens. Pdf human papillomavirus 16 sublineage dispersal and cervical. Papillomaviruses are epitheliotropic, circular, doublestranded dna viruses within the family papillomaviridae that are associated with benign and malignant tumors in humans and animals.
Digene hc2 test identified 11 of the 29 hpv 16 pcr. The genome sequence of human papillomavirus type 20 hpv 20. We used the agilent sureselect xt2 protocol for library preparation, illumina hiseq 2500 for sequencing, and clc. Hpv and animal pv nucleotide sequences in genbank style. Fifteen nucleic acid variations were identified in the e4 orf. Two new protein structures, hpv16 l1 vlp particles in complex with. Human papillomavirus type 16 hpv16 genomes integrated in head and neck cancers and in hpv16immortalized human keratinocyte clones express chimeric viruscell mrnas similar to those found in cervical cancers. Only the three nonsynonymous nucleotide changes differentiated epe6 and aae6 genomes. Human papillomavirus type 16 hpv 16 genomes integrated in head and neck cancers and in hpv 16 immortalized human keratinocyte clones express chimeric viruscell mrnas similar to those found in cervical cancers. Hpv can damage genes and chromosomes directly, whole.
E4 protein, the complete e4 orf was amplified by pcr in 27 hpv16positive cervical samples, and the amplicons were cloned. Moreover, a comprehensive nomenclature system for hpv variants is lacking, limiting. I am designing a panel to capture hpv, i wonder if there are big dna difference of hpv 16183. Human papillomavirus type 16 hpv16 is a major cause of cervical cancer. Human papillomavirus type 16 hpv16 genomes integrated. The organization of the region containing the integrated viral genome based on a partial restriction map of the hpv 16 integration site is shown in fig. Other hpv types are responsible for the remaining cases. Us5554538a us08222,569 us22256994a us5554538a us 5554538 a us5554538 a us 5554538a us 22256994 a us22256994 a us 22256994a us 5554538 a us5554538 a us 5554538a authority us unite. Using splinkerette amplification and comparative blast sequence analysis of the dna junctions, we detected chimeric dna consistent with templates capable of expressing the chimeric viruscellular mrna, such as in clone hfk14, which harbors an hpv 16 human chromosome 10 integration pattern, i. As different hpv types are associated with variable pathogenic potential, minor genetic variations within a given highrisk hpv type might also be associated with distinct oncogenic capacities, through variable ability of persistence or risk of.
Aims persistent infection indicated by detection of human papillomavirus 16 hpv 16 on repeat testing over a period of time poses the greatest cervical cancer risk. Peter howleys lab contains the insert hpv16 e6e7 and is published in j virol 1989 oct. Wholegenome sequencing of hpv 16 reveals new criterion. Us5554538a dna sequences derived from papillomavirus hpv33. We designed a universal human papillomavirus hpv typing assay based on target enrichment and whole genome sequencing ewgs. Plays a role in the initiation of viral dna replication.
Based on whole hpv genome sequencing, hpv type 16 can be divided into four main variant lineages abcd and nine sublineages. The 7857base pair circular genome consists of two regions coding for early e and late l genes. The complete genome is 7354 bp in length with gc content of 41. Human papillomavirus type 16 hpv16, a member of the papillomaviridae family, is the primary etiological agent of cervical cancer. Analysis of the cloned integrated viral genome by restriction analyses and hybridization with the hpv 16 probe indicated that. Genomic organization of a gamma6 papillomavirus metagenomic. Genome sequence of human papillomavirus type 20, strain hpv.
Each papillomavirus is highly tropic for a specific. Complete genome sequence of canine papillomavirus type 16. To investigate in vivo characteristics of hypermutation, differential dna denaturationpcr 3dpcr was performed using three clinical specimens obtained from. The purpose of this study was to introduce a robust laboratory procedure. E2 regulatory protein e2 human papillomavirus type 16. Pdf sequence imputation of hpv16 genomes for genetic.
Human papillomavirus type 16 variant analysis of e6, e7, and. Mut indicates a number of nucleotide substitutions that inactivated splicing silencers. Research paper analysis of the cancer genome atlas. Hpv can damage genes and chromosomes directly, wholegenome.
Investigators in the division of cancer epidemiology and genetics, national cancer institute, led by lisa mirabello, ph. The sequence alignment was converted to a consensus sequence for each hpv type in clc sequence viewer version 7. Smith b, chen z, reimers l, van doorslaer k, schiffman m, et al. The most prevalent type, hpv16, shows intratypic sequence variants that are known to differ in oncogenic potential and geographic distribution.
Aim to test the hypothesis that, because the human papillomavirus hpv e2 protein represses viral early gene transcription, e2 gene sequence variation or disruption could play a part in the induction of the numerical chromosome abnormalities that have been described in squamous cervical lesions. The cobas 4500 roche, pleasanton california test detects 14 oncogenic hpv dna types and can detect individual types hpv 16 and 18, while the aptima hr hpv gen probe, san diego ca test detects 14 oncogenic hpv types of hpv mrna. We report the complete genome sequence of canine papillomavirus type 16 identified within multiple pigmented cutaneous plaques and squamous cell carcinoma from an intact female basenji dog. Aims persistent infection indicated by detection of human papillomavirus 16 hpv16 on repeat testing over a period of time poses the greatest cervical cancer risk. Several remarkable and novel observations were made following this analysis. A complete genome sequence of human papillomaviruses hpv named as hpvujs21015 was determined by viral metagenomic and pcr methods.
As different hpv types are associated with variable pathogenic potential, minor genetic variations within a given highrisk hpv type might also be associated with distinct oncogenic capacities, through variable ability. Tameseq hpv primers were designed using primer3 57 and hpv. Introduction 42 kbytes groups a1 through a9 257 kbytes hpv16 variants 158 kbytes group a10 90 kbytes group b 212 kbytes groups c, d, e, and unclassifieds 149 kbytes part ii. There are 182 types of hpv with complete genomes sequences in the. The hpv16 status test can also be performed on samples collected and placed in the thinprep solution. Human papillomavirus type 16 hpv16 genomes integrated in. Viral variants of these hpvs differ in evolutionary history and pathogenicity. For example, in the tumor 683, there was a large 6. This percentage of hpv16 prevalence is almost identical to those reported by others using mygp nested pcrdna sequencing genotyping on cervicovaginal cell suspensions, e. Map of the hpv16 genome, with genes, restriction fragments, and. Utilization of the human genome sequence localizes human. Apr 10, 2018 human papillomaviruses hpv cause infections that are responsible for diverse clinical manifestations from benign conditions to invasive cancer. Of the 53 hpv16positive samples, 51 hpv16 genomes were assembled from cin 1 n 8, cin 23 n 15, and cervical cancer group n 28.
Aug 16, 2012 the percentage of the genome sequenced ranged from 100 to 88. Of course, these data need to be confirmed and extended by wholegenome sequence analysis of hpv 16 variants and subvariants from women living in many other parts of the world. Detection of hypermutated human papillomavirus type 16 genome. The structural basis of dna target discrimination by. Complete genome sequences of eight human papillomavirus. E2 also regulates viral transcription through binding to the e2re response element 5accnnnnnnggt3 present in multiple. Analyses of the issuing cleavage patterns revealed that the highest incidence of unpaired zfabinding hpv type 16 genomic dna is situated within the first and last 1,581 bp 20% of 7,905 bp of the complete hpv type 16 genome genomic context. The major early promoter p 105 and a differentiationspecific promoter are indicated by arrows. Mrih196 expressed l1 fulllength fl but no e5 fl rna suggesting the presence of integrated hpv16 genomes with a disrupted e2 region and rearranged l1 dna sequence. Of course, these data need to be confirmed and extended by whole genome sequence analysis of hpv 16 variants and subvariants from women living in many other parts of the world.
Once the complex recognizes and binds dna at specific sites, the e2 dimer is removed from dna. Human papillomavirus genome variants and head and neck. Plays a major role in the induction and maintenance of cellular transformation. Us20120196274a1 us346,550 us2012346550a us2012196274a1 us 20120196274 a1 us20120196274 a1 us 20120196274a1 us 2012346550 a us2012346550 a us 2012346550a us 2012196274 a1 us2012196274 a1 us 2012196274a1 authority us united states prior art keywords seq id primer hpv probe identity prior art date 20110107 legal. Peter howleys lab contains the insert hpv 16 e1 and is published in j virol. Quantitative expression changes of hpv16 transcript markers correlate with the physical state of the hpv genome in hpv16 positive cervical cancer cell lines. We downloaded all 182 hpv reference genomes from pave for this study. Firstly, there are three main hpv genome states in these tumors that are split relatively evenly. A dimer of e2 interacts with a dimer of e1 in order to improve specificity of e1 dna binding activity. Mutation and phylogenetic analysis of hpv16 sequences. Us5554538a dna sequences derived from papillomavirus hpv. This percentage of hpv 16 prevalence is almost identical to those reported by others using mygp nested pcrdna sequencing genotyping on cervicovaginal cell suspensions, e. Whole genome sequencing reveals complexity in both hpv. Hpvassociated cancers and precancers 2015 std treatment.
Peter howleys lab contains the insert hpv16 e1 and is published in j virol. Routine human papillomavirus genotyping by dna sequencing in. Genome sequence of human papillomavirus type 20, strain. We previously demonstrated that ctot and gtoa hypermutations accumulated in the hpv16 genome by apobec3 expression in vitro. The hpv transcriptome in hpv16 positive cell lines. Searchable database of papilloma genomes with visualization and. Here, we report the complete genome sequences of four hpv16 asian american variants and four european variants, isolated from cervical biopsies and scrapings in india. The coverage for types 39, 40, 16, 74, 56, 30, 71, 90, 86 and 81 remained equal or close to that observed when reads were. Hpv type is defined as a complete genome whose l1 gene sequence is at least 10% dissimilar to that of any other hpv type 3. Although the data presented on these web pages is outdated, it is still useful as.
Hpv16 status test for integration, viral load, and e6 variant the sample is collected from the endocervix and ectocervix using the oneswab specimen collection platform. The human papillomavirus type 16 w12e isolate genome genbank. Zinc finger arrays binding human papillomavirus types 16. Hi, most of hpv infections are cleared by the body within 2 years. The genome sequence of human papillomavirus type 20 hpv20. In multivariate analysis, the rr of death conferred by hpv18 was 2. The open reading frames orfs open boxes are diagramed above the bracket and the numbers above each orf are the nucleotide. Signature sequence validation of human papillomavirus type 16. We report the complete genome sequence of canine papillomavirus type 16 identified within multiple pigmented cutaneous plaques and squamous cell carcinoma from an intact. Functional variants of human papillomavirus type 16. Source human papillomavirus type 16 organism human papillomavirus type. An 800base pair noncoding region is present upstream of the e6 gene and is called the long control region lcr.
Apr 11, 2019 for example, in the tumor 683, there was a large 6. Highrisk human papillomaviruses hpvs, particularly hpv types 16 and 18 hpv 16 and hpv 18, respectively, play a cardinal role in the etiology of cervical cancer. However, variants of hpv 16, hpv 31 and hpv 33 may share several short sequence homologies in the hypervariable l1 gene commonly targeted for hpv genotyping. Detection of hypermutated human papillomavirus type 16. Absence of human papillomavirus16 and 18 dna and epstein. The e6e7 promoter of human papillomavirus type 16 is activated in the absence of e2 proteins by a sequenceaberrant sp1 distal. E4 protein is thought to contribute to the release of newly formed viral particles from infected epithelia. We wholegenome sequenced 796 hpv16positive exfoliated cervical cell specimens from the kaiser permanente. Nov 07, 20 the virus that causes cervical, head and neck, anal and other cancers can damage chromosomes and genes where it inserts its dna into human dna, according to a new study led by researchers at the. Download scientific diagram map of the hpv16 genome, with genes, restriction fragments, and pcrgenerated subclones that were examined for attachment. Doctors give trusted, helpful answers on causes, diagnosis, symptoms, treatment, and more. Human papillomaviruses hpv cause infections that are responsible for diverse clinical manifestations from benign conditions to invasive cancer. Are there big dna difference of hpv 16 1832 and other hpvs.
We designed a universal human papillomavirus hpv typing assay based on target enrichment and wholegenome sequencing ewgs. Mdl offers the hpv16 status test as a reflexfor hpv. The hpv 16 genome contains the viral oncogenes e6 and e7, which encode proteins capable of immortalizing and transforming normal cells. Introduction, glossary, and landmarks of the genome. Disvhpv16, versatile and powerful software to detect hpv in rna. Peter howleys lab contains the insert hpv 16 e6e7 and is published in j virol 1989 oct. Mar 31, 2020 a complete genome sequence of human papillomaviruses hpv named as hpv ujs21015 was determined by viral metagenomic and pcr methods. Acts mainly as an oncoprotein by stimulating the destruction of many host cell key regulatory proteins. In order to investigate amino acid mutations in the hpv16 e1. Wholegenome analysis of human papillomavirus types 16, 18. Complete genome sequences of eight human papillomavirus type. But there is vaccine approved for use in women and men to prevent the high risk hpvs.
Methods the integrity and sequence of the e2 gene from 11. The rna bait included 23,941 probes targeting 191 hpv types and 12 probes targeting betaglobin as a control. Future studies may also investigate whether similar hpv 16 variantspecific associations will be observed in hpv 16 associated cancers at other anatomical locations eg. Aptima hpv 16 1845 test is also fdacleared to triage its pooled aptima hr hpv test further, although there are. During its normal life cycle, the hpv 16 genome exists in a circular, or episomal state and upon infection of the basal cells of the squamous epithelium, remains distinct from the host genomic dna.
This study was designed to analyze sequence variations in e6, e7, and l1 genes and. Future studies may also investigate whether similar hpv 16 variantspecific associations will be observed in hpv 16associated cancers at other anatomical locations eg. The aptima hpv 16 1845 genotype assay is an in vitro nucleic acid amplification test for the qualitative detection of e6e7 viral messenger rna mrna of human papillomavirus hpv types 16, 18, and 45 in cervical specimens from women with aptima hpv assay positive. In adult women, hpv 16 and hpv 18 cause 60% to 70% of cervical cancers worldwide. E6 associates with host ube3ae6ap ubiquitinprotein ligase, and inactivates tumor suppressors tp53 and tp73 by targeting them to the 26s proteasome for degradation. Furthermore, persistent hpv infection is necessary for clinical progression to cin 3 24. The hpv16 genome contains the viral oncogenes e6 and e7, which encode proteins capable of immortalizing and transforming normal cells. Pdf mutations in the hpv16 genome induced by apobec3 are.
Whole viral genome sequences from 7116 hpv16positive. The most prevalent type, hpv 16, shows intratypic sequence variants that are known to differ in oncogenic potential and geographic distribution. Human papillomavirus type 16 variant analysis of e6, e7. Us20120196274a1 materials and methods for genotyping and. These hpvs account for 75% of invasive cervical cancers worldwide. Over 80 types of hpv have now been described and are categorised as low risk for example, hpv 6 and hpv 11, intermediate risk for example, hpv 31 and hpv 33, and high risk for example, hpv 16 and hpv 18, based on their association with clinical disease. Signature sequence validation of human papillomavirus type. A file containing the entire genome sequence of hpv16, interrupted at. Epidemiology of acquisition and clearance of cervical human papillomavirus infection in women from a highrisk area for cervical cancer. Jan 24, 2019 the sequence alignment was converted to a consensus sequence for each hpv type in clc sequence viewer version 7. This study was designed to analyze sequence variations. Af125673 54, 99 was used as a viral reference sequence since it was the parental sequence modified by sitedirected mutagenesis to generate the epe6 and aae6 viral genomes used in this study.
Routine human papillomavirus genotyping by dna sequencing. The epidemiology of anogenital hpv infections in children is less welldelineated at the population. The 7,908 bp circular, doublestranded dna genome of the hpv16 reference sequence is illustrated. The reference mapping to the hpv genomes was additionally performed using all the reference genome sequences in a single mapping table 2, simultaneous mapping, with random assignment of reads mapping to more than one genome. May 03, 2020 the human papillomavirus hpv 16 genome, showing open reading frames gray rectangles containing gene names, splice donor 5 and splice acceptor 3 splice sites black arrows. Molecular and phylogenetic analysis of the hpv 16 e4 gene. However, variants of hpv16, hpv31 and hpv33 may share several short sequence homologies in the hypervariable l1 gene commonly targeted for hpv genotyping. Genome sequence data from the cancer genome atlas hnc samples were analyzed to gain a full understanding of the hpv genome status for these tumors. The virus that causes cervical, head and neck, anal and other cancers can damage chromosomes and genes where it inserts its dna into human dna, according to a new study led by researchers at the. The human papillomavirus hpv16 genome, showing open reading frames gray rectangles containing gene names, splice donor 5 and. Sequence imputation of hpv16 genomes for genetic association. Highrisk human papillomaviruses hpvs, particularly hpv types 16 and 18 hpv16 and hpv18, respectively, play a cardinal role in the etiology of cervical cancer. Mar 21, 2017 mutation and phylogenetic analysis of hpv16 sequences. Background human papillomavirus 16 hpv16 species group alpha9 of the alphapapillomavirus genus contains hpv16, hpv31, hpv33, hpv35, hpv52, hpv58 and hpv67.
The bracket line in the middle of the panel represents a linear form of the virus genome for better presentation of headtotail junction, promoters arrows, and early a e and late a l polyadenylation sites. Their genomes are circular and approximately 8 kilobase pairs in size. In the tree of hpv 16 apart from the variants found in this study we have used variants of hpv 16 retrieved from genbank. Are there big dna difference of hpv 161832 and other hpvs.
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