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About:
Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment
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An Entity of Type :
schema:ScholarlyArticle
, within Data Space :
covidontheweb.inria.fr
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document(s)
Type:
Academic Article
research paper
schema:ScholarlyArticle
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type
Academic Article
research paper
schema:ScholarlyArticle
isDefinedBy
Covid-on-the-Web dataset
has title
Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment
Creator
Gilbert, Jack
Ali, Farhana
Allard, Sarah
Allen, Eric
Belda-Ferre, Pedro
Carpenter, Carolina
Chiang, Leslie
Knight, Rob
Marotz, Clarisse
Mcdonald, Daniel
Minich, Jeremiah
Shaffer, Justin
Swafford, Austin
Sweeney, Daniel
Source
Medline; PMC
abstract
Background: Determining the role of fomites in the transmission of SARS-CoV-2 is essential in the hospital setting and will likely be important outside of medical facilities as governments around the world make plans to ease COVID-19 public health restrictions and attempt to safely reopen economies. Expanding COVID-19 testing to include environmental surfaces would ideally be performed with inexpensive swabs that could be transported safely without concern of being a source of new infections. However, CDC-approved clinical-grade sampling supplies and techniques using a synthetic swab are expensive, potentially expose laboratory workers to viable virus and prohibit analysis of the microbiome due to the presence of antibiotics in viral transport media (VTM). To this end, we performed a series of experiments comparing the diagnostic yield using five consumer-grade swabs (including plastic and wood shafts and various head materials including cotton, synthetic, and foam) and one clinical grade swab for inhibition to RNA. For three of these swabs, we evaluated performance to detect SARS-CoV-2 in twenty intensive care unit (ICU) hospital rooms of patients with 16 COVID-19+. All swabs were placed in 95% ethanol and further evaluated in terms of RNase activity. SARS-CoV-2 was measured both directly from the swab and from the swab eluent. Results: Compared to samples collected in VTM, 95% ethanol demonstrated significant inhibition properties against RNases. When extracting directly from the swab head as opposed to the eluent, RNA recovery was approximately 2-4x higher from all six swab types tested as compared to the clinical standard of testing the eluent from a CDC-approved synthetic swab. The limit of detection (LoD) of SARs-CoV-2 from floor samples collected using the CGp or TMI swabs was similar or better than the CDC standard, further suggesting that swab type does not impact RNA recovery as measured by SARs-CoV-2. The LoD for TMI was between 0-362.5 viral particles while SYN and CGp were both between 725–1450 particles. Lastly microbiome analyses (16S rRNA) of paired samples (e.g., environment to host) collected using different swab types in triplicate indicated that microbial communities were not impacted by swab type but instead driven by the patient and sample type (floor or nasal). Conclusions: Compared to using a clinical-grade synthetic swab, detection of SARS-CoV-2 from environmental samples collected from ICU rooms of patients with COVID was similar using consumer grade swabs, stored in 95% ethanol. The yield was best from the swab head rather than the eluent and the low level of RNase activity in these samples makes it possible to perform concomitant microbiome analysis.
has issue date
2020-08-18
(
xsd:dateTime
)
bibo:doi
10.21203/rs.3.rs-56028/v1
bibo:pmid
32839765
has license
cc-by
sha1sum (hex)
9fe1b3d9feca1bca4daa727cc233d99e3ef78d9b
schema:url
https://doi.org/10.21203/rs.3.rs-56028/v1
resource representing a document's title
Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment
has PubMed Central identifier
PMC7444291
has PubMed identifier
32839765
schema:publication
Res Sq
resource representing a document's body
covid:9fe1b3d9feca1bca4daa727cc233d99e3ef78d9b#body_text
is
schema:about
of
named entity 'restrictions'
named entity 'SARS-CoV-2'
named entity 'VTM'
named entity 'ethanol'
named entity 'EtOH'
named entity 'positive swab'
named entity 'speci'
named entity 'RNA'
named entity 'virus'
named entity 'EtOH'
named entity 'Speci'
named entity 'eluent'
named entity 'isopropanol'
named entity 'metabolomics'
named entity 'diagnostic testing'
named entity 'alcohol'
named entity 'Marine Biology'
named entity 'RNA'
named entity 'RNase'
named entity 'Mann-Whitney'
named entity 'spacecraft assembly clean rooms'
named entity 'polymerase chain reactions'
named entity 'Severe acute respiratory syndrome coronavirus 2'
named entity 'Speci'
named entity 'RT-qPCR'
named entity 'PERMANOVA'
named entity 'CDC'
named entity 'viral particles'
named entity 'eluent'
named entity 'EtOH'
named entity 'eluent'
named entity 'SARS-CoV-2'
named entity 'CDC'
named entity 'SARS-CoV-2'
named entity 'RNA'
named entity 'EMP'
named entity 'speci'
named entity 'viral particles'
named entity 'COVID-19'
named entity 'Secondary infections'
named entity 'RT-qPCR'
named entity 'gene'
named entity 'SARS-CoV-2'
named entity 'biosafety level'
named entity 'Real-Time PCR'
named entity 'eluent'
named entity 'RNA'
named entity 'COVID'
named entity 'adsorbed'
named entity 'alternative medical'
named entity 'SARS-CoV-2'
named entity 'microbiome'
named entity 'SARS-CoV-2'
named entity 'microbiome'
named entity 'eluent'
named entity 'Speci'
named entity 'RNA'
named entity 'microbiome'
named entity 'RNA'
named entity 'RT-qPCR'
named entity 'Becton, Dickinson and Company'
named entity 'biomass'
named entity 'JPL'
named entity 'SARS-CoV-2'
named entity 'public health policy'
named entity 'EtOH'
named entity 'one-way ANOVA'
named entity 'antimicrobial agents'
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