Genetic Variability and Conserved T-Cell Epitope Prediction of the HPV16 E1 Protein in Cervix Samples from Peru

Background: HPV16 is the most prevalent high-risk genotype associated with cervical cancer, yet the genetic variability and immune potential of the replication protein E1 are less characterized in asymptomatic infections. We assessed HPV16 E1 diversity and predicted conserved T-cell epitopes. Methods: We conducted a descriptive cross-sectional study of cervical samples from women undergoing HPV screening. HPV was detected with universal primers and then HPV16-specific PCR. Thirty HPV16-positive samples underwent full-length E1 amplification and nanopore amplicon sequencing. Variability and phylogeny were analyzed with Clustal Omega and MEGA (maximum likelihood). MHC class I and II epitopes were predicted with the IEDB using HLA alleles representative of South American populations and evaluated for conservation, toxicity, allergenicity, and population coverage. Results: Mutations were detected in 14/30 samples, while 16 sequences matched the reference (GenBank: NC_001526.3). European lineages (A1–A3) predominated, with one sequence in the Asian-American lineage D. Seven highly conserved MHC I epitopes and 37 conserved MHC II epitopes were identified. Epitopes mapped to multiple regions across the E1 sequence. Predicted global coverage was 94.38% for MHC I, 83.75% for MHC II, and 99.09% combined. Conclusions: HPV16 E1 is highly conserved and contains candidate T-cell targets with broad predicted coverage, supporting evaluation for future vaccine or immunotherapy strategies.