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

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Title

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

Subject

Description

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.

Date Last Updated (Year-Month-Day)

2020-10-16

Citation

Babiker, A., H. L. Bradley, V. D. Stittleburg, J. M. Ingersoll, A. Key, C. S. Kraft, J. J. Waggoner, and A. Piantadosi. 2020. "Metagenomic sequencing to detect respiratory viruses in persons under investigation for COVID-19." Journal of clinical microbiology.

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 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.

Accessibility

Available free online. This article is made available via the PMC Open Access Subset for unrestricted noncommercial re-use and secondary analysis in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic.