Scalable long-read nanopore HPV16 amplicon-based whole-genome sequencing.

ABSTRACT: 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 hig

SUBMITTER: Titus MK 

PROVIDER: S-EPMC12504524 | biostudies-literature | 2025 Oct

REPOSITORIES: biostudies-literature