Metagenomic sequencing to detect respiratory viruses in persons under investigation for COVID-19.

Babiker, Ahmed; Bradley, Heath L; Stittleburg, Victoria D; Ingersoll, Jessica M; Key, Autum; Kraft, Colleen S; Waggoner, Jesse J; Piantadosi, Anne

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 co-infections 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. Herein, we used RNA mNGS to assess the frequencies of alternative viral infections in SARS-CoV-2 RT-PCR negative PUIs (n=30) and viral co-infections 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), Human coronavirus OC43 (N=2) and Human coronavirus HKU1(N=1)). mNGS also identified both co-infections (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), Human coronavirus NL63 (N=1)). Among SARS-CoV-2 RT-PCR positive PUIs, lower cycle threshold (CT) values correlated with greater SARS-CoV-2 read recovery by mNGS (R2: 0.65, p-value: <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.