Global genomic diversity of human papillomavirus type 6 (HPV6): a comparative analysis of 724 isolates and 190 complete genome sequences.

MATEJA M JELEN; ZIGUI CHEN; BOSTJAN J. KOCJAN; KATJA SEME; FELICITY J. BURT; PAUL K. S. CHAN; DIEGO CHOUHY; CATHARINA E. COMBRINCK; FRANÇOIS COUTLÉE; CHRISTINE ESTRADE; ALEX FERENCZY; ALISON FIANDER; EDUARDO L. FRANCO; SUZANNE M. GARLAND; ADRIANA A. GIRI; JOAQUÍN VÍCTOR GONZÁLEZ; ARNDT GRÖNING; KERSTIN HEIDRICH; SAM HIBBITTS; LEA HONJAK; TOMMY N. M. LUK; KARINA MARINIC; TOSHIHIKO MATSUKURA; ANNA NEUMANN; ANJA OSTRBENK; MARIA ALEJANDRA PICCONI; HARRIET RICHARDSON; MARTIN SAGADIN; ROLAND SAHLI; RIAZ Y. SEEDAT; ALBERTO SEVERINI; JESSICA L. SINCHI; JANA SMAHELOVA; SEPEHR N. TABRIZI; RUTH TACHEZY; SARAH TOHME; VIRGILIJUS ULOZA; ASTRA VITKAUSKIENE; YONG WEE WONG; SNJEZANA ZIDOVEC LEPEJ; ROBERT D. BURK; MARIO POLJAK

Seattle

Conferencia; 29th International Papillomavirus Conference and Public Health & Clinical Workshops.; 2014

International Society on Papillomavirus

Abstract CS.PP02.13 pp. 130 BACKGROUND: HPV6 is the major etiological agent of anogenital warts and laryngeal papillomas. Geographical and clinical associations of globally circulating HPV6 variants have never been clearly evaluated. OBJECTIVES: To characterize the global genomic diversity of HPV6 and explore geographical and clinical associations of HPV6 genome variants. METHODS: A total of 530 HPV6 isolates from anogenital region (179 anogenital warts, 186 cervical swabs, 35 unspecified), head and neck region (83 laryngeal papillomas, 1 nasal papilloma) and 46 isolates from unspecified anatomical site from 14 countries (six continents) were sequenced in 4 regions: E5a-E5b-L1-LCR. Isolates with unique single nucleotide polymorphisms (SNPs), indels and amino acid changes were fully sequenced. Global and pairwise alignments were used for nucleotide difference calculation, maximum likelihood (RAxML) phylogenetic tree construction, lineage/sublineage assignment and identification of (sub)lineage specific SNPs. Geographical and clinical associations were statistically evaluated on 724 HPV6 isolates obtained from our study and GenBank.  RESULTS: 492/530 HPV6 isolates were successfully sequenced in E5a-E5b-L1-LCR regions; of them, 130 were fully sequenced. Pairwise heterogeneity of 190 HPV6 complete genomes (130 from our study, 60 from GenBank) was 1.6%. Open reading frames (ORFs) differed in nucleotide diversity, from 13.2% (E5b) to least 3.4% (E7). Global phylogenetic tree revealed two lineages (A and B) and five B sublineages: B1-B5. A 960-bp region within L2 ORF was designated as the representative region for complete-genome-based phylogenetic clustering. Significant (p