2020
DOI: 10.1093/clinchem/hvaa106
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Metagenomic Analysis Reveals Clinical SARS-CoV-2 Infection and Bacterial or Viral Superinfection and Colonization

Abstract: Abstract Background More than 2 months separated the initial description of SARS-CoV-2 and discovery of its widespread dissemination in the United States. Despite this lengthy interval, implementation of specific quantitative reverse transcription (qRT)-PCR-based SARS-CoV-2 tests in the US has been slow, and testing is still not widely available. Metagenomic sequencing offers the promise of u… Show more

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Cited by 74 publications
(62 citation statements)
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“…Metagenomic next-generation sequencing (mNGS) was performed as previously described [ 17 , 56 ]. Briefly, 18 μL of extracted RNA was treated with Turbo DNAse (ThermoFisher, Waltham, MA).…”
Section: Methodsmentioning
confidence: 99%
See 1 more Smart Citation
“…Metagenomic next-generation sequencing (mNGS) was performed as previously described [ 17 , 56 ]. Briefly, 18 μL of extracted RNA was treated with Turbo DNAse (ThermoFisher, Waltham, MA).…”
Section: Methodsmentioning
confidence: 99%
“…Shotgun RNA sequencing of this material allows for simultaneous recovery of viral genomes for transmission tracking as well as understanding of in situ host response [15]. Since the first detection of SARS-CoV-2 in the US in Washington State, the University of Washington Virology Laboratory has performed shotgun RNA sequencing to recover more than 1,500 viral genomes as of August 16, 2020, to understand the evolution and molecular epidemiology of the virus [16,17]. Here, we examine host-specific gene expression differences by SARS-CoV-2 infection status, host age, sex, and viral load in NP swabs from 430 SARS-CoV-2-infected individuals and 54 negative controls.…”
Section: Introductionmentioning
confidence: 99%
“…We recovered genomes from the SARS-CoV-2 isolates from two separate patients as part of an ongoing University of Washington IRBapproved genomic surveillance project [2,3]. Sequencing libraries were generated from double-stranded cDNA [4] using Swift Biosciences' SARS-CoV-2 Normalase Amplicon Sequencing kit or the Nextera DNA Flex Pre-Enrichment kit (Illumina) followed by enrichment using a SARS-CoV-2 xGen enrichment panel (NC_045512; IDT).…”
mentioning
confidence: 99%
“… 2 However, there have been only three studies reporting the application of metagenomics to detect SARS-CoV-2 and co-infections, with a combined sample size of nine patients. 3 , 4 , 5 …”
mentioning
confidence: 99%