Metagenomic Sequencing To Detect Respiratory Viruses in Persons under Investigation for COVID-19

Abstract

Broad testing for respiratory viruses among persons under investigation (PUIs) for SARS-CoV-2 has been performed inconsistently, limiting our understanding of alternative viral infections and coinfections in these patients. RNA metagenomic next-generation sequencing (mNGS) offers an agnostic tool for the detection of both SARS-CoV-2 and other RNA respiratory viruses in PUIs. Here, we used RNA mNGS to assess the frequencies of alternative viral infections in SARS-CoV-2 RT-PCR-negative PUIs ( n = 30) and viral coinfections in SARS-CoV-2 RT-PCR-positive PUIs ( n = 45).