Genetic Variability and Prediction of T Epitopes of the HPV16 E2 Gene in Asymptomatic Women from Cajamarca, Peru

Background: The HPV16 E2 gene plays a crucial role in viral replication and oncogene regulation. This study aimed to assess the genetic variability of the E2 gene and to identify immunogenic epitopes of the E2 protein. Methods: The E2 gene was amplified and sequenced. T-cell epitope prediction and evaluation were performed using IEDB, NetMHCpan v4.0, NetMHCIIpan v4.1, VaxiJen, ToxNet, and pLM4Alg. Results: Phylogenetic analysis of 47 E2 sequences demonstrated co-circulation of the D (n = 4) and A (n = 43) HPV16 lineages in Cajamarca. Twenty-eight Single Nucleotide Polymorphism (SNPs) were identified in E2, 21 of which were nonsynonymous. Seventeen variations were associated with positive Papanicolaou (Pap) test results. Epitope prediction identified 2 MHC class I and 27 MHC class II epitopes classified as potentially antigenic, non-toxic, and non-allergenic, with an overall global population coverage across both MHC classes of 99.78%. Conclusions: The A HPV16 lineage predominated among the women studied. The identified SNPs indicate substantial variability in the E2 gene and a relationship with endocervical lesions. In total, 29 E2-derived T-cell epitopes with immunogenic potential were identified.