Characterization of sequence variations within HPV16 isolates among Indian women: Prediction of causal role of rare non-synonymous variations within intact isolates in cervical cancer pathogenesis

We re-sequenced HPV16 genome (~ 6 kb) implicated in cervical carcinogenesis (LCR, E2, E5, E6, E7, L1, L2) to prioritize sequence variants for functional validation as biomarkers, using CaCx cases (n = 74) and asymptomatic controls (n = 24). Of the nucleotide variations recorded (n = 271), non-synonymous changes in L2 region were significantly higher (p = 0.005) among cases (2.67%) compared to controls (1.27%). Using SIFT database, 29 non-synonymous changes (frequency = 0.01–0.03) predicted as deleterious to protein functions were identified. Haplotype analysis considering 110 polymorphic variations (frequency ≥ 0.05) within intact viral isolates (53 CaCx cases and 21 controls) using NETWORK software, confirmed Asian–American (AA, 14.86%) and European (E, 85.14%) variants, differing at 78 positions. The E-variants portrayed thirty-six haplotypes, of which, E-12 was most prevalent within cases (38.1%; 16 / 42) and controls (28.57%; 6 / 21) harboring polymorphic variations at 10 positions, in contrast to HPV16R. Cases of the E-12 haplotype harbored 7 deleterious mutations distributed within L1 (n = 1), E2 (n = 1), E5 (n = 1), and L2 (n = 4), while none within similar controls. Thus rare deleterious variations within genes implicated in productive infection over the E-12 haplotype background of intact HPV16 isolates might be of causal relevance for CaCx development.