Author/Editor     Jelen, Mateja; Chen, Zigui; Kocjan, Boštjan; Hošnjak, Lea; Oštrbenk, Anja; Sagadin, Martin; Seme, Katja; Židovec-Lepej, Snježana; Poljak, Mario
Title     Global genomic diversity of human papillomavirus type 11 (HPV11) based on 433 isolates and 78 complete genome sequences
Type     članek
Publication year     2016
ISSN     0022-538X - Journal of virology
Language     eng
Abstract     Human papillomavirus type 11 (HPV11) is an etiological agent of anogenital warts and laryngeal papillomas, and is included in the 4-valent and 9-valent prophylactic HPV vaccines. We established the largest collection of globally circulating HPV11 isolates to date and examined their genomic diversity among 433 isolates and 78 complete genomes (CGs) from six continents. The HPV11 genomic variation was initially studied within the 2,800 bp E5a-E5b-L1-URR region, in 181/207 (87.4%) isolates collected for this study. Of these, 30 HPV11 variants containing unique single nucleotide polymorphisms (SNPs), indels (insertions or deletions), or amino acid changes were fully sequenced. A maximum likelihood tree based on the global alignment of 78 HPV11 CGs (30 CGs from our study and 48 CGs from GenBank) revealed two HPV11 lineages (A and B) and four sublineages (A1, A2, A3, and A4). HPV11 (sub)lineage-specific SNPs within the CG were identified, as well as the 208 bp representative region for CG-based phylogenetic clustering within the partial E2 open reading frame and the non-coding region 2. Globally sublineage A2 was most prevalent, followed by sublineages A1, A3, and A4 and lineage B. IMPORTANCE: This collaborative international study defined the global HPV11 heterogeneity and established the largest collection of globally circulating HPV11 genomic variants to date. Thirty novel complete HPV11 genomes were determined and submitted to the available sequence repositories. Global phylogenetic analysis revealed two HPV11 variant lineages and four sublineages. The HPV11 (sub)lineage-specific SNPs and the identified representative region within the partial genomic region E2/NCR2 will enable simpler identification and comparison of HPV11 variants worldwide. This study provides an important knowledge base of HPV11 for future studies in HPV epidemiology, evolution, pathogenicity, prevention, and molecular assay development.
Keywords     human papillomavirus
genomic diversity
genomes
človeški papiloma virus
genomske raznolikosti
genom