Open AccessMetagenomic Sequencing To Detect Respiratory Viruses in Persons under Investigation for COVID-19
Author(s) -
Ahmed Babiker,
Heath L. Bradley,
Victoria Stittleburg,
Jessica Ingersoll,
Autum Key,
Colleen S. Kraft,
Jesse J. Waggoner,
Anne Piantadosi
Publication year - 2020
Publication title -
journal of clinical microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.349
H-Index - 255
eISSN - 1070-633X
pISSN - 0095-1137
DOI - 10.1128/jcm.02142-20
Subject(s) - metagenomics , virology , biology , covid-19 , respiratory system , limiting , rna , coinfection , virus , medicine , gene , genetics , outbreak , pathology , infectious disease (medical specialty) , mechanical engineering , disease , engineering , anatomy
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.