Rapid-Response Viral Genome Detection using TWIST Capture and Nanopore Flongle Sequencing

The article describes a new method for rapid detection of viral pathogens by combining the TWIST Comprehensive Viral Research Panel, which covers more than 3,000 virus species, with Oxford Nanopore Flongle sequencing. This method enables unbiased detection of viruses, including uncommon or divergent species, which is advantageous compared to conventional PCR tests that detect only specifically targeted viruses. The workflow includes cDNA synthesis, dsDNA conversion, TWIST probe enrichment, and Nanopore sequencing. When tested on the QCMD 2024 Viral Metagenomics EQA panel, all expected targets were detected, with eight of thirteen viruses achieving at least 90 percent genome coverage. The method successfully resolved mixed infections of DNA and RNA viruses, and the entire workflow from nucleic acid extraction to obtaining sequence data took three days.