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

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). mNGS identified all viruses detected by routine clinical testing (influenza A [ n  = 3], human metapneumovirus [ n =  2], and human coronavirus OC43 [ n =  2], and human coronavirus HKU1 [ n =  1]). mNGS also identified both coinfections (1, 2.2%) and alternative viral infections (4, 13.3%) that were not detected by routine clinical workup (respiratory syncytial virus [ n =  3], human metapneumovirus [ n =  1], and human coronavirus NL63 [ n =  1]). Among SARS-CoV-2 RT-PCR-positive PUIs, lower cycle threshold ( C T ) values correlated with greater SARS-CoV-2 read recovery by mNGS ( R 2 , 0.65; P < 0.001). Our results suggest that current broad-spectrum molecular testing algorithms identify most respiratory viral infections among SARS-CoV-2 PUIs, when available and implemented consistently.