Prevaccination genomic diversity of human papillomavirus genotype 6 (HPV 6)

Kocjan, Boštjan J.; Poljak, Mario; Cimerman, Mojca; Gale, Nina; Potočnik, Marko; Bogovac, Željka; Seme, Katja

doi:10.1016/j.virol.2009.06.030

Cited by 23 publications

(38 citation statements)

References 33 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…When taking into account another 25 HPV6 isolates deposited in GenBank with sequences identical to those present in the tree, the HPV6vc-related variants were the most prevalent isolates both in genital (65% [11/17]) and oral (58% [21/36]) lesions. This common occurrence of HPV6vc-related variants is in agreement with a previous study (12). It is noteworthy that more than 30 years after the HPV6b prototype was isolated (4, 20), we have now identified an HPV6b variant (PV2702) with the 94-bp insert and only two point mutations, supporting the supposition that the original 94-bp deletion was an artifact (9).…”

supporting

confidence: 92%

Lack of Methylation in the Upstream Region of Human Papillomavirus Type 6 from Aerodigestive Tract Papillomas

Ure

Forslund

2012

J Virol

View full text Add to dashboard Cite

Methylation of the high-risk human papillomavirus type 16 (HPV16) upstream regulatory region (URR) has been described, but whether methylation is present among low-risk HPVs is unknown. The methylation status of the HPV6 URR was analyzed in papillomas from the upper aerodigestive tract of six adult patients. All CpGs in the URR were unmethylated, from both basal/ intermediate and superficial cells, suggesting that methylation is not involved in the regulation of transcription from the HPV6 URR, regardless of epithelial differentiation.

show abstract

supporting

confidence: 92%

Lack of Methylation in the Upstream Region of Human Papillomavirus Type 6 from Aerodigestive Tract Papillomas

Ure

Forslund

2012

J Virol

View full text Add to dashboard Cite

show abstract

“…In this study, the following four genomic regions were initially sequenced from 530 HPV6 isolates (collected for the purpose of this study from 15 countries on six continents): the L1 ORF, which encodes the major capsid protein and is typically used in identification of HPV types; the E5a and E5b ORFs, which have previously shown the highest diversification trend among all HPV6 coding regions (17,18); and LCR, which is considered the most variable HPV genomic region, harboring control sites for viral replication and gene expression. Following identification of the most divergent HPV6 E5a-E5b-L1-LCR genomic variants, a total of 130 HPV6 isolates were selected, completely sequenced, and phylogenetically evaluated together with 60 complete HPV6 genome sequences available in GenBank and PaVE.…”

Section: Discussionmentioning

confidence: 99%

“…The final extension step was done at 68°C for 7 min. PCR products were visualized by gel electrophoresis, purified with a QIAquick PCR purification kit (Qiagen, Hilden, Germany), and sequenced at Macrogen Europe (Amsterdam, Netherlands) or in our inhouse sequencing facility, using previously published primers (18). The in-house sequencing was performed using a BigDye Terminator sequencing kit (version 3.1; Applied Biosystems, Foster City, CA) and a sequencing protocol developed by Platt et al (20).…”

Section: Methodsmentioning

confidence: 99%

“…X00203), while lineage B was further divided into three defined sublineages (B1, B2, and B3) (19). Apart from the preliminary observation of lineage B variant predominance in HPV6-related anogenital warts and laryngeal papillomas originating from Slovenia (17), as well as the recent description of sublineage B1 predominance in anogenital lesions originating from Australia (14), no other clinical correlations for HPV6 variant groups have been observed so far (13,15,16,18).…”

mentioning

confidence: 96%

“…Two recent Slovenian studies reported a substantial genomic variability across the entire HPV6 genome and identified several novel genomic variants (17,18). The existence of two main HPV6 phylogenetic clusters and several smaller subclusters was identified recently in a study that included 43 complete HPV6 genome sequences (19).…”

mentioning

confidence: 98%

See 2 more Smart Citations

Global Genomic Diversity of Human Papillomavirus 6 Based on 724 Isolates and 190 Complete Genome Sequences

Jelen

Chen

Kocjan

et al. 2014

J Virol

Self Cite

View full text Add to dashboard Cite

Human papillomavirus type 6 (HPV6) is the major etiological agent of anogenital warts and laryngeal papillomas and has been included in both the quadrivalent and nonavalent prophylactic HPV vaccines. This study investigated the global genomic diversity of HPV6, using 724 isolates and 190 complete genomes from six continents, and the association of HPV6 genomic variants with geographical location, anatomical site of infection/disease, and gender. Initially, a 2,800-bp E5a-E5b-L1-LCR fragment was sequenced from 492/530 (92.8%) HPV6-positive samples collected for this study. Among them, 130 exhibited at least one single nucleotide polymorphism (SNP), indel, or amino acid change in the E5a-E5b-L1-LCR fragment and were sequenced in full. A global alignment and maximum likelihood tree of 190 complete HPV6 genomes (130 fully sequenced in this study and 60 obtained from sequence repositories) revealed two variant lineages, A and B, and five B sublineages: B1, B2, B3, B4, and B5. HPV6 (sub)lineage-specific SNPs and a 960-bp representative region for whole-genome-based phylogenetic clustering within the L2 open reading frame were identified. Multivariate logistic regression analysis revealed that lineage B predominated globally. Sublineage B3 was more common in Africa and North and South America, and lineage A was more common in Asia. Sublineages B1 and B3 were associated with anogenital infections, indicating a potential lesion-specific predilection of some HPV6 sublineages. Females had higher odds for infection with sublineage B3 than males. In conclusion, a global HPV6 phylogenetic analysis revealed the existence of two variant lineages and five sublineages, showing some degree of ethnogeographic, gender, and/or disease predilection in their distribution. IMPORTANCEThis study established the largest database of globally circulating HPV6 genomic variants and contributed a total of 130 new, complete HPV6 genome sequences to available sequence repositories. Two HPV6 variant lineages and five sublineages were identified and showed some degree of association with geographical location, anatomical site of infection/disease, and/or gender. We additionally identified several HPV6 lineage-and sublineage-specific SNPs to facilitate the identification of HPV6 variants and determined a representative region within the L2 gene that is suitable for HPV6 whole-genome-based phylogenetic analysis. This study complements and significantly expands the current knowledge of HPV6 genetic diversity and forms a comprehensive basis for future epidemiological, evolutionary, functional, pathogenicity, vaccination, and molecular assay development studies.

show abstract

Prevaccination genomic diversity of human papillomavirus genotype 11: A study on 63 clinical isolates and 10 full‐length genome sequences

Maver

Kocjan

Seme

et al. 2011

Journal of Medical Virology

Self Cite

View full text Add to dashboard Cite

Prevaccination genomic diversity of human papillomavirus genotype 11 (HPV 11) was established by sequencing 40% of the genome of 63 clinical isolates obtained from an ethnogeographically closed Caucasian cohort, and full‐length genome sequencing of the ten most divergent isolates. In the study, which included the largest number of isolates to date, by analyzing pooled L1, LCR, E6, E5a, and E5b sequences (3,217 bp) of an individual isolate, a total of 23 genomic variants were identified, of which three (5 isolates) and twenty (58 isolates) corresponded to prototypic and non‐prototypic variant groups, respectively. Several novel, potentially important mutations are described. Full‐length genome sequences of ten isolates revealed more than 99% similarity to the HPV 11 prototype isolate. The minimum genomic distance between the full‐length sequences of genomic variants and the prototype was 3 point mutations and 2 inserts and the maximum distance 31 point mutations, one insertion and one deletion. Within the ethnogeographically closed cohort investigated in this study, HPV 11 was shown to be less polymorphic in comparison to the majority of HPV genotypes studied to date. J. Med. Virol. 83:461–470, 2011. © 2011 Wiley‐Liss, Inc.

show abstract

Prevaccination genomic diversity of human papillomavirus genotype 6 (HPV 6)

Cited by 23 publications

References 33 publications

Lack of Methylation in the Upstream Region of Human Papillomavirus Type 6 from Aerodigestive Tract Papillomas

Lack of Methylation in the Upstream Region of Human Papillomavirus Type 6 from Aerodigestive Tract Papillomas

Global Genomic Diversity of Human Papillomavirus 6 Based on 724 Isolates and 190 Complete Genome Sequences

Prevaccination genomic diversity of human papillomavirus genotype 11: A study on 63 clinical isolates and 10 full‐length genome sequences

Contact Info

Product

Resources

About