Scalable long-read nanopore HPV16 amplicon-based whole-genome sequencing
Human papillomavirus 16 (HPV16) drives precursor cervical lesions that often progress to cervical cancer (CC). Variation within the HPV16 genome has been associated with CC risk. Here, we developed an affordable and portable amplicon-based long-read whole genome sequencing (WGS) approach using Oxford Nanopore Technologies to investigate HPV16 genetic diversity among women in sub-Saharan African countries. Applied to a control CaSki cell line and clinical samples (n = 12), our method generated complete HPV16 genomes at high coverage (median read coverage: 5,899-15,279 ×). Benchmarking our HPV16 controls showed high accuracy for two variant calling pipelines (Clair3 and PEPPER-Margin DeepVariant). Phylogenetic analysis identified all four previously defined HPV16 lineages (A-D) and their high-risk sublineages. All lineages exhibited strong concordance across de novo assembly, reference-based phylogenetics, and unsupervised clustering. Our pipeline effectively captured the full extent of genomic variation, including putative lineage-informative SNPs. This method offers a robust amplicon-based WGS and analysis pipeline for HPV16, making it well-suited for integration into surveillance, diagnostics, and epidemiological efforts in low-resource areas.
Authors
- David Giesbrecht (ORCID: https://orcid.org/0000-0003-2498-4705)
- Karamoko Niaré (ORCID: https://orcid.org/0000-0002-7406-9508)
- Susan Cu‐Uvin (ORCID: https://orcid.org/0000-0001-5633-071X)
- Sin Ting Hui (ORCID: https://orcid.org/0000-0002-4437-4501)
- Patrick J. Loehrer (ORCID: https://orcid.org/0000-0002-1532-4660)
- Darron R. Brown (ORCID: https://orcid.org/0000-0001-5887-4382)
- Omenge Orang’o (ORCID: https://orcid.org/0000-0003-1551-244X)
- Ronald Tonui (ORCID: https://orcid.org/0000-0001-5087-1435)
- Cliff I. Oduor (ORCID: https://orcid.org/0000-0002-6914-4032)
- Rebecca Crudale (ORCID: https://orcid.org/0000-0002-0789-4196)
- Aaron Ermel (ORCID: https://orcid.org/0000-0002-1075-0126)
- Ann M. Moormann (ORCID: https://orcid.org/0000-0003-1113-2829)
- Kapten Muthoka
- Isaac E. Kim (ORCID: https://orcid.org/0000-0002-9737-8100)
- Peter Itsura (ORCID: https://orcid.org/0000-0003-2446-6393)
- Rachel A. Katzenellenbogen (ORCID: https://orcid.org/0000-0002-2597-2071)
- Abebe A. Fola (ORCID: https://orcid.org/0000-0001-5392-2859)
- Jeffrey A. Bailey
- Maina K. Titus
- Philip Tonui
Institutions
- Moi University (KE)
- University of Massachusetts Chan Medical School (US)
- Brown University (US)
- Indiana Cancer Consortium (US)
- Aga Khan University Nairobi (KE)
- AMPATH (KE)
- Indiana University School of Medicine
- Indiana University – Purdue University Indianapolis (US)
Publication Details
- Journal
- Scientific Reports
- Published
- 2025-10-07
- DOI
- https://doi.org/10.1038/s41598-025-18664-w
- Primary Topic
- Genomics and Phylogenetic Studies
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- National Institutes of Health
- National Cancer Institute