Related Experiment Video
Updated: Jul 31, 2026
11:26
Sequencing of mRNA from Whole Blood using Nanopore Sequencing
Published on: June 3, 2019
13.7K
Nanopore adaptive sampling of a metagenomic sample derived from a human monkeypox case
Charlotte Hewel1, Hanno Schmidt2,3, Stefan Runkel2,4
1Institute of Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.
Journal of Medical Virology
|April 24, 2024
Summary
Genomic surveillance is crucial for controlling monkeypox outbreaks. Nanopore sequencing provided complete viral genome data, resolving structural variants missed by short-read sequencing, which is vital for understanding host range changes.
Area of Science:
- Genomics
- Virology
- Epidemiology
Background:
- The 2022 multi-country outbreak highlighted the need for robust genomic surveillance of monkeypox virus.
- Understanding viral evolution and host interactions is critical for outbreak control.
Purpose of the Study:
- To evaluate Nanopore and Illumina Whole Genome Sequencing (WGS) for monkeypox surveillance.
- To identify and resolve structural variants impacting monkeypox host range and evolution.
Main Methods:
- Whole Genome Sequencing (WGS) using Nanopore (PromethION P24) and Illumina (NextSeq. 2000).
- Adaptive sampling for in silico human host genome depletion and viral DNA enrichment.
- Comparative analysis of sequencing data for genome assembly and variant detection.
Main Results:
- Nanopore sequencing achieved high viral genome coverage and enabled strain determination.
- Only Nanopore data resolved two structural variants (SVs) in OPG015 and OPG208 genes, crucial for host range.
- Short-read sequencing and assembly methods frequently misassembled or misannotated these critical SVs.
Conclusions:
- Nanopore WGS is superior to standard Illumina sequencing for comprehensive monkeypox genome analysis, including SVs.
- Accurate genome assembly is essential for public databases and understanding monkeypox's host range expansion.
- Advanced genomic surveillance methods are necessary to track and control emerging infectious diseases.
