Background: HPV 11 is classified taxonomically in alpha-papillomavirus genus - species 10. Next to HPV 6, HPV 11 is the most important low-risk HPV, involved in the etiology of genital warts and laryngeal papillomas. HPV 11 is one of four primary targets included in quadrivalent HPV vaccine. Currently, knowledge about HPV 11 genomic variation and its impact on viral characteristics is rather limited.

Objectives: To investigate genomic diversity of HPV 11 within 5 different genomic regions on the largest number of HPV 11 isolates to date.

Methods: A total of 63 HPV 11 isolates were sequenced across approximately 40% (3217 base pairs) of the HPV 11 genome. The identification and characterization of HPV 11 variants was based on analysis of L1, LCR, E6, E5a and E5b genomic regions. All coding regions were analyzed to identify amino acid changes that could have an impact on biological properties and structure of viral proteins. Selected representatives of HPV 11 variants containing specific amino acid changes in analyzed coding regions (8 isolates) were sequenced across the whole genome and phylogenetic analysis was performed.

Results: After combining nucleotide data in all 5 genomic regions for each of 63 HPV 11 isolates, a total of 23 HPV 11 genomic variants, composed of 11 L1, 12 LCR, 6 E6, 4 E5a and 4 E5b genomic variants were identified. Several newly identified, potentially important mutations were described. Eight complete HPV 11 genome sequences determined in our study and 2 complete HPV 11 genomes obtained from sequence repositories were included in phylogenetic analysis that showed distribution of HPV 11 variants in two closely related clusters.

Conclusions: The present study, carried out on the largest number of HPV 11 isolates to date, provides important data on HPV 11 genomic diversity for future molecular, diagnostic and vaccination studies.