High-risk human papillomavirus (HPV) drives cervical cancer and a subset of head and neck cancers. HPV integration is associated with structural variation (SV) and dysregulation of both the HPV and human genomes, both of which have been difficult to resolve using short-read sequencing. We recently reported distinct patterns of genomic regulation around HPV integration events in cervical cancer using Oxford Nanopore Technologies (ONT) long-read sequencing in a paper published in Genome Research (Porter et al. 2024, doi:10.1101/gr.279041.124). We profiled 72 tumors from the HIV+ Tumor Molecular Characterization Project (HTMCP) and categorized HPV integration events based on patterns of HPV / human genome rearrangements. We observed complex HPV integration structures, in some cases involving heterologous amplifications of HPV-human concatemers, and methylation and gene expression changes in cis with the HPV-integrated allele. We are continuing this work in cervical cancer and in head and neck cancer as part of the personalized approaches in the treatment of head and neck cancers (PATH) study, the latter of which a subset of samples are driven by Epstein-barr virus (EBV) in addition to HPV+ and virus-negative cases (see PATH study page).