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

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.Fil: Jelen, Mateja M. University of Ljubljana; EsloveniaFil: Chen, Zigui. Albert Einstein College of Medicine. New York; Estados UnidosFil: Kocjan, Botjan J.. University of Ljubljana; EsloveniaFil: Burt, Felicity J.. University of the Free State. Bloemfontein; SudáfricaFil: Chan, Paul K.S.. Chinese University of Hong Kong; ChinaFil: Chouhy, Diego. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; ArgentinaFil: Combrinck, Catharina E.. University of the Free State. Bloemfontein; SudáfricaFil: Coutlee, Francois. Hôpital Notre-Dame-Pavillon Deschamps. Montréal; CanadáFil: Estrade, Christine. Lausanne University Hospital; SuizaFil: Ferenczy, Alex. McGill University and Jewish General Hospital. Montreal; CanadáFil: Fiander, Alison. Institute of Cancer and Genetics. Cardiff; Reino UnidoFil: Franco, Eduardo L.. McGill University. Montreal; CanadáFil: Garland, Suzanne M.. The Royal Women's Hospital. Parkville; Australia. The University of Melbourne; Australia. Murdoch Children's Research Institute. Victoria; AustraliaFil: Giri, Adriana Angelica. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; ArgentinaFil: González, Joaquín Víctor. Dirección Nacional de Instituto de Investigación. Administración Nacional de Laboratorio e Instituto de Salud; ArgentinaFil: Gröning, Arndt. Medizinisches Versorgungszentrum wagnerstibbe für Laboratoriumsmedizin und Pathologie GmbH. Hannover; AlemaniaFil: Heidrich, Kerstin. Medizinisches Versorgungszentrum wagnerstibbe für Laboratoriumsmedizin und Pathologie GmbH. Hannover; AlemaniaFil: Hibbitts, Sam. Institute of Cancer and Genetics. Cardiff; Reino UnidoFil: Hosnjak, Lea. University of Ljubljana; EsloveniaFil: Luk, Tommy N.M. The Chinese University of Hong Kong; China. Hong Kong Special Administrative Region; ChinaFil: Marinic, Karina. Hospital Dr. Julio C. Perrando. Chaco; ArgentinaFil: Matsukura, Toshihiko. National Institute of Health. Tokyo; JapónFil: Neumann, Anna. The University of Melbourne; Australia. Medizinisches Versorgungszentrum wagnerstibbe für Laboratoriumsmedizin und Pathologie GmbH. Hannover; AlemaniaFil: Oštrbenk, Anja. University of Ljubljana; EsloveniaFil: Picconi, Maria Alejandra. Dirección Nacional de Instituto de Investigación. Administración Nacional de Laboratorio e Instituto de Salud; ArgentinaFil: Richardson, Harriet. Queen's University. Ontario; CanadáFil: Sagadin, Martin. University of Ljubljana; EsloveniaFil: Sahli, Roland. Lausanne University Hospital; SuizaFil: Seedat, Riaz Y.. University of the Free State. Bloemfontein; SudáfricaFil: Seme, Katja. University of Ljubljana; EsloveniaFil: Severini, Alberto. Public Health Agency of Canada. Winnipeg; CanadáFil: Sinchi, Jessica L. Hospital Dr. Julio C. Perrando. Chaco; ArgentinaFil: Smahelova, Jana. Institute of Hematology and Blood Transfusion. Praga; República ChecaFil: Tabrizi, Sepehr N.. The University of Melbourne; Australia. Murdoch Children's Research Institute. Victoria; Australia. The Royal Women's Hospital. Parkville; AustraliaFil: Tachezy, Ruth. Institute of Hematology and Blood Transfusion. Praga; República ChecaFil: Tohme, Sarah. Public Health Agency of Canada. Winnipeg; CanadáFil: Uloza, Virgilijus. Lithuanian University of Health Sciences. Kaunas; LituaniaFil: Vitkauskiene, Astra. Lithuanian University of Health Sciences. Kaunas; LituaniaFil: Wong, Yong Wee. Universti Kebangsaan Malaysia. Bangi; MalasiaFil: Lepeja, Snježana Židovec. University Hospital for Infectious Diseases Dr. Fran Mihaljević. Zagreb; CroaciaFil: Burk, Robert D.. Albert Einstein College of Medicine.New York; Estados UnidosFil: Poljak, Mario. Albert Einstein College of Medicine. New York; Estados Unido