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Related Experiment Video

Updated: Sep 15, 2025

Ultra-long Read Sequencing for Whole Genomic DNA Analysis

Ultra-long Read Sequencing for Whole Genomic DNA Analysis

Published on: March 15, 2019

Scalable long-read Nanopore HPV16 Amplicon-based Whole-Genome Sequencing.

Maina K Titus¹, David Giesbrecht¹, Cliff I Oduor¹

¹Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, USA.

Medrxiv : the Preprint Server for Health Sciences

|July 15, 2025

Summary

This study presents a new, affordable whole genome sequencing method for Human Papillomavirus 16 (HPV16) to track genetic diversity and cancer risk in sub-Saharan Africa.

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Last Updated: Sep 15, 2025

Ultra-long Read Sequencing for Whole Genomic DNA Analysis

Ultra-long Read Sequencing for Whole Genomic DNA Analysis

Published on: March 15, 2019

Sequencing of mRNA from Whole Blood using Nanopore Sequencing

Sequencing of mRNA from Whole Blood using Nanopore Sequencing

Published on: June 3, 2019

Validating Whole Genome Nanopore Sequencing, using Usutu Virus as an Example

Validating Whole Genome Nanopore Sequencing, using Usutu Virus as an Example

Published on: March 11, 2020

Area of Science:

Genomics
Virology
Epidemiology

Background:

Human Papillomavirus 16 (HPV16) is a key driver of cervical cancer (CC).
Genetic variations in HPV16 influence CC risk.
Sub-Saharan Africa faces a high burden of HPV-related diseases.

Purpose of the Study:

To develop an affordable, portable amplicon-based long-read whole genome sequencing (WGS) method for HPV16.
To investigate HPV16 genetic diversity in sub-Saharan Africa.
To establish a robust pipeline for HPV16 surveillance and diagnostics in low-resource settings.

Main Methods:

Utilized Oxford Nanopore Technologies (ONT) for WGS of HPV16.
Applied amplicon-based sequencing to clinical samples and a control cell line.
Employed Clair3 and PEPPER-Margin DeepVariant for variant calling and phylogenetic analysis.

Main Results:

Generated complete HPV16 genomes with high coverage (median 5,899-15,279×).
Accurately identified all four HPV16 lineages (A-D) and sublineages.
Captured comprehensive genomic variation, including lineage-informative SNPs.

Conclusions:

The developed WGS method is accurate, affordable, and portable for HPV16 analysis.
This approach is suitable for enhancing HPV16 surveillance, diagnostics, and epidemiology in resource-limited regions.