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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
Human papillomavirus type 16 genetic variants: Phylogeny and Classification Based on E6 and LCR
Journal of Virology, Volume 86, No. 12, Year 2012
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Description
Naturally occurring genetic variants of human papillomavirus type 16 (HPV16) are common and have previously been classified into 4 major lineages; European-Asian (EAS), including the sublineages European (EUR) and Asian (As), African 1 (AFR1), African 2 (AFR2), and North-American/Asian-American (NA/AA).Weaimed to improve the classification of HPV16 variant lineages by using a large resource of HPV16-positive cervical samples collected from geographically diverse populations in studies onHPVand/or cervical cancer undertaken by the International Agency for Research on Cancer. In total, we sequenced the entire E6 genes and long control regions (LCRs) of 953 HPV16 isolates from 27 different countries worldwide. Phylogenetic analyses confirmed previously described variant lineages and subclassifications.Wecharacterized two new sublineages within each of the lineages AFR1 and AFR2 that are robustly classified using E6 and/or the LCR.Wecould differentiate previously identified AA1, AA2, andNAsublineages, although they could not be distinguished by E6 alone, requiring the LCR for correct phylogenetic classification.Wethus provide a classification system for HPV16 genomes based on 13 and 32 phylogenetically distinguishing positions in E6 and the LCR, respectively, that distinguish nine HPV16 variant sublineages (EUR, As, AFR1a, AFR1b, AFR2a, AFR2b, NA, AA1, and AA2). Ninety-seven percent of all 953 samples fitted this classification perfectly. Other positions were frequently polymorphic within one or more lineages but did not define phylogenetic subgroups. Such a standardized classification of HPV16 variants is important for future epidemiological and biological studies of the carcinogenic potential of HPV16 variant lineages. © 2012, American Society for Microbiology.
Authors & Co-Authors
Gheit, Tarik
France, Lyon
Centre International de Recherche Sur le Cancer
Franceschi, Silvia F.
France, Lyon
Centre International de Recherche Sur le Cancer
Vignat, Jérôme
France, Lyon
Centre International de Recherche Sur le Cancer
Burk, Robert David
United States, New York
Albert Einstein College of Medicine of Yeshiva University
Sylla, Bakary Sidiki
France, Lyon
Centre International de Recherche Sur le Cancer
Tommasino, Massimo
France, Lyon
Centre International de Recherche Sur le Cancer
Clifford, Gary M.
France, Lyon
Centre International de Recherche Sur le Cancer
Hammouda, Doudja
Unknown Affiliation
Loria, Dora Ida
Unknown Affiliation
Matos, Elena Lina
Unknown Affiliation
Eluf-Neto, Jose E.
Unknown Affiliation
Ghadirian, Parviz
Unknown Affiliation
Ferreccio, Catterina R.
Unknown Affiliation
Luzoro, Amaranta V.
Unknown Affiliation
Ojeda, José Manuel
Unknown Affiliation
Prado, Rodrigo B.
Unknown Affiliation
Aristizabal, Nubia
Unknown Affiliation
Molano, Mónica
Unknown Affiliation
Posso, Héctor V.
Unknown Affiliation
Torroella-Kouri, Marta
Unknown Affiliation
Kordzaia, Dimitri D.
Unknown Affiliation
Keïta, Namory
Unknown Affiliation
Koulibaly, Moussa
Unknown Affiliation
Rajkumar, Thangarajan
Unknown Affiliation
Rajkumar, Rajamanickam
Unknown Affiliation
Lee, Dukhee
Unknown Affiliation
Shin, Hairim
Unknown Affiliation
Bayo, Siné
Unknown Affiliation
Chaouki, Noureddine
Unknown Affiliation
Thomas, Jaiyeola O.
Unknown Affiliation
Okolo, Clement Abu
Unknown Affiliation
Adewole, Isaac Folorunso A.
Unknown Affiliation
Meijer, Chris J.L.M.
Unknown Affiliation
Snijders, Peter Jf
Unknown Affiliation
Rolón, Pedro Anibal
Unknown Affiliation
Caceres, Eduardo
Unknown Affiliation
Santos, Carlos L.
Unknown Affiliation
Ngelangel, Corazon A.
Unknown Affiliation
Zaton´ski, Witold A.
Unknown Affiliation
Gichangi, Peter B.
Unknown Affiliation
de Vuyst, Hugo
Unknown Affiliation
de Sanjosé, Sílvia
Unknown Affiliation
Castellsagué, X.
Unknown Affiliation
Kitinya, James N.
Unknown Affiliation
Chichareon, Saibua Bunnag
Unknown Affiliation
Sukvirach, Sukhon
Unknown Affiliation
Tunsakul, Sirirat
Unknown Affiliation
Wabinga, Henry R.
Unknown Affiliation
Statistics
Citations: 129
Authors: 48
Affiliations: 2
Identifiers
Doi:
10.1128/JVI.00483-12
ISSN:
10985514
Research Areas
Cancer
Genetics And Genomics