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Global genomic diversity of human papillomavirus 6 based on 724 isolates and 190 complete genome sequences
MM. Jelen, Z. Chen, BJ. Kocjan, FJ. Burt, PK. Chan, D. Chouhy, CE. Combrinck, F. Coutlée, C. Estrade, A. Ferenczy, A. Fiander, EL. Franco, SM. Garland, AA. Giri, JV. González, A. Gröning, K. Heidrich, S. Hibbitts, L. Hošnjak, TN. Luk, K. Marinic,...
Language English Country United States
Document type Journal Article, Research Support, N.I.H., Extramural, Research Support, Non-U.S. Gov't
NLK
Free Medical Journals
from 1967 to 6 months ago
Freely Accessible Science Journals
from 1967 to 6 months ago
PubMed Central
from 1967 to 1 year ago
Europe PubMed Central
from 1967 to 6 months ago
Open Access Digital Library
from 1967-02-01
Open Access Digital Library
from 1967-02-01
PubMed
24741079
DOI
10.1128/jvi.00621-14
Knihovny.cz E-resources
- MeSH
- Biological Evolution MeSH
- Cell Lineage MeSH
- Phylogeny MeSH
- Genetic Variation genetics MeSH
- Genome, Viral genetics MeSH
- Genomics methods MeSH
- Genotype MeSH
- Papillomavirus Infections complications genetics virology MeSH
- Humans MeSH
- Human papillomavirus 6 genetics isolation & purification MeSH
- Anus Neoplasms complications genetics virology MeSH
- Uterine Cervical Neoplasms complications genetics virology MeSH
- Head and Neck Neoplasms complications genetics virology MeSH
- Check Tag
- Humans MeSH
- Male MeSH
- Female MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Research Support, N.I.H., Extramural MeSH
UNLABELLED: 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. IMPORTANCE: This 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.
Department of Oncology Division of Cancer Epidemiology McGill University Montréal Québec Canada
Department of Pathology McGill University and Jewish General Hospital Montréal Québec Canada
Department of Pediatrics Albert Einstein College of Medicine New York New York USA
DNA Laboratories Sdn Bhd UKM MTDC Technology Centre Universti Kebangsaan Malaysia Bangi Malaysia
Ganshintetsu Memorial Laboratory Department of Virology 2 National Institute of Health Tokyo Japan
Lausanne University Hospital Institute of Microbiology Lausanne Switzerland
Queen's Cancer Research Institute Queen's University Kingston Ontario Canada
References provided by Crossref.org
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