Nanopore metagenomic sequencing for detection and characterization of SARS-CoV-2

Metagenomic Next-Generation Sequencing (mNGS) may allow for the detection of pathogens that can be missed in targeted assays. The goal of this study was to assess the performance of nanopore-based Sequence-Independent Single Primer Amplification for the detection and characterization of SARS-CoV-2. We report 100% specificity overall and 95.2% sensitivity for specimens with a RT-PCR cycle threshold value less than 30. We assembled high-quality SARS-CoV-2 genomes and found 100% concordance with variant of concern PCR results. This study supports future work examining the broader feasibility of nanopore mNGS as a diagnostic strategy for the detection and characterization of viral pathogens.

BC CDC Presenters

10/21/2021 7:05:00 PM