biostudies-literatureNkone PPoliomyelitis Research FoundationUniversity of PretoriaDiscovery FoundationSouth African Department of Science and InnovationSouth African Medical Research CouncilNational Research FoundationDivision of Intramural Research, National Institute of Allergy and Infectious DiseasesNational Health Laboratory Service56https://www.ebi.ac.uk/biostudies/studies/S-EPMC8959563biostudies-literatureUnknown19(1)<h4>Background</h4>Despite multiple attempts, there is still no effective HIV-1 vaccine available. The HIV-1 polymerase (pol) gene is highly conserved and encodes cytotoxic T-lymphocyte (CTL) epitopes. The aim of the study was to characterise HIV-1 Pol CTL epitopes in mostly sample pairs obtained during early and chronic stages of infection.<h4>Methods</h4>Illumina deep sequencing was performed for all samples while Sanger sequencing was only performed on baseline samples. Codons under immune selection pressure were assessed by computing nonsynonymous to synonymous mutation ratios using MEGA. Minority CTL epitope variants occurring at [Formula: see text] 5% were detected using low-frequency variant tool in CLC Genomics. Los Alamos HIV database was used for mapping mutations to known HIV-1 Virology journalDeep sequencing of the HIV-1 polymerase gene for characterisation of cytotoxic T-lymphocyte epitopes during early and chronic disease stages.PMC8959563PRF 20/22Nkone PTiemessen CTRedd ADLoubser SIsmail AMayaphi SHQuinn TCfalseDeep sequencing of the HIV-1 polymerase gene for characterisation of cytotoxic T-lymphocyte epitopes during early and chronic disease stages.<h4>Background</h4>Despite multiple attempts, there is still no effective HIV-1 vaccine available. The HIV-1 polymerase (pol) gene is highly conserved and encodes cytotoxic T-lymphocyte (CTL) epitopes. The aim of the study was to characterise HIV-1 Pol CTL epitopes in mostly sample pairs obtained during early and chronic stages of infection.<h4>Methods</h4>Illumina deep sequencing was performed for all samples while Sanger sequencing was only performed on baseline samples. Codons under immune selection pressure were assessed by computing nonsynonymous to synonymous mutation ratios using MEGA. Minority CTL epitope variants occurring at [Formula: see text] 5% were detected using low-frequency variant tool in CLC Genomics. Los Alamos HIV database was used for mapping mutations to known HIV-1 2022-01-01T00:00:00Z2022 Mar2026-05-31T06:01:08.284Z2025-02-19T01:54:43.396ZS-EPMC89595633534625910.1186/s12985-022-01772-8