Application of Oxford Nanopore Technology to Plant Virus Detection

• Published in: Viruses Vol. 13; no. 8; p. 1424
• Main Authors: Liefting, Lia W, Waite, David W, Thompson, Jeremy R
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 22.07.2021; MDPI
• Subjects: Accuracy; Agricultural production; biosecurity; Capital costs; Datasets; diagnostics; Genomes; Germplasm; High-Throughput Nucleotide Sequencing; high-throughput sequencing; Methods; MinION; Nanopore Sequencing; Next-generation sequencing; ONT; Pathogens; Plant Diseases - virology; Plant viruses; Plant Viruses - genetics; Plant Viruses - isolation & purification; Protocol; Quarantine; Reagents; Sequence Analysis, DNA - methods; Viruses; biosecurity; diagnostics; ONT; rRNA depletion; MinION; plant viruses; high-throughput sequencing
• ISSN: 1999-4915; 1999-4915
• DOI: 10.3390/v13081424

The adoption of Oxford Nanopore Technologies (ONT) sequencing as a tool in plant virology has been relatively slow despite its promise in more recent years to yield large quantities of long nucleotide sequences in real time without the need for prior amplification. The portability of the MinION and Flongle platforms combined with lowering costs and continued improvements in read accuracy make ONT an attractive method for both low- and high-scale virus diagnostics. Here, we provide a detailed step-by-step protocol using the ONT Flongle platform that we have developed for the routine application on a range of symptomatic post-entry quarantine and domestic surveillance plant samples. The aim of this methods paper is to highlight ONT's feasibility as a valuable component to the diagnostician's toolkit and to hopefully stimulate other laboratories towards the eventual goal of integrating high-throughput sequencing technologies as validated plant virus diagnostic methods in their own right.