About: Metagenomic analysis reveals clinical SARS-CoV-2 infection and bacterial or viral superinfection and colonization

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An Entity of Type : schema:ScholarlyArticle, within Data Space : covidontheweb.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Metagenomic analysis reveals clinical SARS-CoV-2 infection and bacterial or viral superinfection and colonization
Creator	Jerome, Keith Nalla, Arun Perchetti, Garrett Huang, Meei-Li Minot, Samuel Roychoudhury, Pavitra Shean, Ryan Reinhardt, Adam Shrestha, Lasata Xie, Hong Greninger, Peddu, Vikas Phung, Quynh Reddy, Shriya
Source	Medline; PMC
abstract	BACKGROUND: More than two 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 unbiased detection of emerging pathogens, without requiring prior knowledge of the identity of the responsible agent or its genomic sequence. METHODS: To evaluate metagenomic approaches in the context of the current SARS-CoV-2 epidemic, laboratory-confirmed positive and negative samples from Seattle, Washington were evaluated by metagenomic sequencing, with comparison to a 2019 reference genomic database created before the emergence of SARS-CoV-2. RESULTS: Within 36 hours our results showed clear identification of a novel human Betacoronavirus, closely related to known Betacoronaviruses of bats, in laboratory-proven cases of SARS-CoV-2. A subset of samples also showed superinfection or colonization with human parainfluenza virus 3 or Moraxella species, highlighting the need to test directly for SARS-CoV-2 as opposed to ruling out an infection using a viral respiratory panel. Samples negative for SARS-CoV-2 by RT-PCR were also negative by metagenomic analysis, and positive for Rhinovirus A and C. Unlike targeted SARS-CoV-2 qRT-PCR testing, metagenomic analysis of these SARS-CoV-2 negative samples identified candidate etiological agents for the patients’ respiratory symptoms. CONCLUSION: Taken together, these results demonstrate the value of metagenomic analysis in the monitoring and response to this and future viral pandemics.
has issue date	2020-05-07(xsd:dateTime)
bibo:doi	10.1093/clinchem/hvaa106
bibo:pmid	32379863
has license	no-cc
sha1sum (hex)	6fca64fc4a6ac016e333ddf9fac87a1bf222917e
schema:url	https://doi.org/10.1093/clinchem/hvaa106
resource representing a document's title	Metagenomic analysis reveals clinical SARS-CoV-2 infection and bacterial or viral superinfection and colonization
has PubMed Central identifier	PMC7239240
has PubMed identifier	32379863
schema:publication	Clin Chem
resource representing a document's body	covid:6fca64fc4a6ac016e333ddf9fac87a1bf222917e#body_text
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