Evaluating an Upper Respiratory Disease Panel on the Portable MinION Sequencer

Wanda J. Lyon; Zachary K. Smith; Brian Grier; James Baldwin; Clarise R. Starr

Oxford Nanopore's MinION may therefore provide us with new opportunities to track infectious disease, for example, rapid sequencing of viral genomes in response to the early phase of influenza pandemics, or for determination of coronavirus virus genotypes during outbreaks. In addition, sequencing will allow for rapid sequencing of viral genomes and provides an opportunity to gain insight into viral genetic drift (single nucleotide polymorphism), emergence of new strains such as SARS-like coronavirus or MERS-CoV, and transmission. To date, a limited number of pathogenic viral studies have been done with the MinION, and all of the published results have focused on sequencing DNA rather than RNA, which is the focus of this The purpose of this study is to examine the efficacy of using the MinION to sequence URD organisms present in clinical nasal washes using targeted amplification, WGA and whole transcriptome amplification (WTA) of low titer URD samples.