Evaluating metagenomics and targeted approaches for diagnosis and surveillance of viruses.

ABSTRACT:

Background

Metagenomics is a powerful approach for the detection of unknown and novel pathogens. Workflows based on Illumina short-read sequencing are becoming established in diagnostic laboratories. However, high sequencing depth requirements, long turnaround times, and limited sensitivity hinder broader adoption. We investigated whether we could overcome these limitations using protocols based on untargeted sequencing with Oxford Nanopore Technologies (ONT), which offers real-time data acquisition and analysis, or a targeted panel approach, which allows the selective sequencing of known pathogens and could improve sensitivity.

Methods

We evaluated detection of viruses with readily available untargeted metagenomic workflows using Illumina and ONT, and an Illumina-based enri

SUBMITTER: Buddle S 

PROVIDER: S-EPMC11382446 | biostudies-literature | 2024 Sep

REPOSITORIES: biostudies-literature