Nanopore metagenomic sequencing for detection and characterization of SARS-CoV-2 in clinical samples.

ABSTRACT:

Objectives

The COVID-19 pandemic has underscored the need for rapid novel diagnostic strategies. 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 (SISPA) for the detection and characterization of SARS-CoV-2.

Methods

We performed mNGS on clinical samples and designed a diagnostic classifier that corrects for barcode crosstalk between specimens. Phylogenetic analysis was performed on genome assemblies.

Results

Our assay yielded 100% specificity overall and 95.2% sensitivity for specimens with a RT-PCR cycle threshold value less than 30. We assembled 10 complete, and one near-c

SUBMITTER: Gauthier NPG 

PROVIDER: S-EPMC8601544 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature