Genetic variability in the major capsid L1 protein of human papillomavirus type 16 (HPV-16) and 18 (HPV-18).

HPV-16 and HPV-18 infections result in nearly 73% of cervical cancers worldwide. The L1 protein comprising HPV vaccine formulations elicit high-titre neutralizing antibodies. The aim of this study was to detect L1 HPV-16 and HPV-18 gene polymorphisms and analyze intratypic variations. HPV-16 (n = 29) and HPV-18 (n = 5) L1 gene sequences were obtained from cervical samples harvested from Italian women. Phylogenetic trees were constructed using the Neighbor-Joining and the Kimura 2-parameters methods (MEGA software). To estimate selection pressures acting on the L1 gene, codon-specific non-synonymous (d(N)) and synonymous (d(S)) substitutions were inferred using the Nei-Gojobori method and Jukes-Cantor model (MEGA software) and integrated analyses carried out using SLAC, FEL and REL methodologies. All the HPV-16 L1 sequences analyzed fell into the European branch (99.4-99.7% similarity). Thirty-four single nucleotide changes were observed and 18 (52.9%) were non-synonymous mutations (7/18 were identified in sequences encoding an immunodominant loop and one occurred in the sequence encoding the α-4 domain associated with VLP conformation). There was no evidence of positive selection in the sequence alignment of L1 HPV-16 genes (P-value < 0.1). One mutation was identified in a negatively selected codon. HPV-18 L1 analyzed sequences fell into two phylogenetic branches: the HPV-18 European branch (99.5-100% similarity) and the HPV-18 African branch (99.8% similarity). Nine single nucleotide changes were observed and 4/9 (44.5%) of these nucleotide mutations were non-synonymous and one was present in a sequence encoding the immunodominant FG loop. There was no evidence of positive selection in the sequence alignment of L1 HPV-18 genes (P-value < 0.1). This study identified polymorphisms of undefined biological activity in HPV-16 and HPV-18 L1 sequences. Information regarding the genetic diversity of HPV-16 and HPV-18 L1 gene sequences may help define the oncogenic potential of respective strains and to better understand immune escape mechanisms.