Genetic characterization and clinical implications of human papillomavirus type 16 (HPV16) variants from northeastern Argentina

•We sequenced 116 HPV16 LCR variants in cervical samples from Argentina.•92.1% of the samples clustered with lineage A, and 6.9% to lineage D.•We found association between lineage D variants and cancer at an OR of 13.8 (1.6–117.0).•The tMCRA of all lineages was 119,103years, in agreement with H. sapiens evolution.•HPV16 Linage D variants are a risk factor for cervical cancer in this population.