About: Preliminary optimisation of a simplified sample preparation method to permit direct detection of SARS-CoV-2 within saliva samples using reverse-transcription loop-mediated isothermal amplification (RT-LAMP)

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About: Preliminary optimisation of a simplified sample preparation method to permit direct detection of SARS-CoV-2 within saliva samples using reverse-transcription loop-mediated isothermal amplification (RT-LAMP) Goto Sponge NotDistinct Permalink

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	Preliminary optimisation of a simplified sample preparation method to permit direct detection of SARS-CoV-2 within saliva samples using reverse-transcription loop-mediated isothermal amplification (RT-LAMP)
Creator	Anderson, Paul Banyard, Ashley Brown, Ian Kidd, Stephen Andreou, Michael Clark, Duncan Cortes, Nicholas Howson, Emma Laxman, Shailen Morant, Nick Walsh, Charlotte Cassar, Claire Cawthraw, Saira Costello, Paula Cross, David Hockey, Jess Houghton, Lewis, Tom Rahou, Sabah Rivers, Samantha Sawyer, Jason Slater-Jefferies, Joanne
Source	MedRxiv
abstract	We describe the optimization of a simplified sample preparation method which permits rapid and direct detection of SARS-CoV-2 RNA within saliva using reverse-transcription loop-mediated isothermal amplification (RT-LAMP). Treatment of saliva samples prior to RT-LAMP by dilution 1:1 in MucolyseTM, followed by dilution (within the range of 1 in 5 to 1 in 40) in 10% (w/v) Chelex 100 Resin and a 98oC heat step for 2 minutes enabled detection of SARS-CoV-2 RNA in all positive saliva samples tested, with no amplification detected in pooled negative saliva. The time to positivity for which SARS-CoV-2 RNA was detected in these positive saliva samples was proportional to the real-time reverse-transcriptase PCR cycle threshold (CT), with SARS-CoV-2 RNA detected in as little as 05:43 (CT 21.08), 07:59 (CT 24.47) and 08:35 (CT 25.27) minutes, respectively. The highest CT where direct RT-LAMP detected SARS-CoV-2 RNA was 31.39 corresponding to a 1 in 40 dilution of a positive saliva sample (1:1 in MucolyseTM) with a starting CT of 25.27. When RT-LAMP was performed on pools of SARS-CoV-2 negative saliva samples spiked with whole inactivated SARS-CoV-2 virus, RNA was detected at dilutions spanning 1 in 5 to 1 in 160 representing CTs spanning 22.49-26.43. Here we describe a simple but critical rapid sample preparation method which can be used up front of RT-LAMP to permit direct detection of SARS-CoV-2 within saliva samples. Saliva is a sample which can be collected non-invasively without the use of highly skilled staff and critically can be obtained from both healthcare and home settings. Critically, this approach overcomes both the requirement and validation of different swabs and the global bottleneck in obtaining RNA extraction robots and reagents to enable molecular testing by PCR. Such testing opens the possibility of public health approaches for effective intervention to control the COVID-19 pandemic through regular SARS-CoV-2 testing at a population scale, combined with isolation and contact tracing for positive cases.
has issue date	2020-07-21(xsd:dateTime)
bibo:doi	10.1101/2020.07.16.20155168
has license	medrxiv
sha1sum (hex)	974834a78b23cbf923b1f6069a264ab23b451cd1
schema:url	https://doi.org/10.1101/2020.07.16.20155168
resource representing a document's title	Preliminary optimisation of a simplified sample preparation method to permit direct detection of SARS-CoV-2 within saliva samples using reverse-transcription loop-mediated isothermal amplification (RT-LAMP)
resource representing a document's body	covid:974834a78b23cbf923b1f6069a264ab23b451cd1#body_text
is schema:about of	named entity 'time' named entity 'rapid' named entity 'detected' named entity 'positivity' named entity 'detection' named entity 'When' named entity 'describe' named entity 'samples' named entity 'loop-mediated isothermal amplification' named entity 'OPTIMIZATION' named entity 'CRITICAL' named entity 'LOOP' named entity 'SAMPLES' named entity '3 4' named entity 'TRANSCRIPTION' covid:arg/974834a78b23cbf923b1f6069a264ab23b451cd1 named entity 'describe' named entity 'PCR' named entity 'direct' named entity 'RNA' named entity 'saliva' named entity 'direct' named entity 'w/v' named entity 'RNA' named entity 'RNA' named entity 'SARS-CoV' named entity 'saliva samples' named entity 'RNA' named entity 'saliva' named entity 'PCR' named entity 'RNA' named entity 'saliva samples' named entity 'saliva samples' named entity 'reverse-transcription' named entity 'SARS-CoV-2' named entity 'saliva samples' named entity 'UHS' named entity 'University Hospital Southampton' named entity 'SARS-CoV2' named entity 'RNA' named entity 'SARS-CoV-2' named entity 'CC-BY-ND' named entity 'rRT-PCR' named entity 'virus' named entity 'lysis' named entity 'qPCR' named entity 'RNA' named entity 'transcription' named entity 'medRxiv' named entity 'UHS' named entity 'SARS-CoV-2' named entity 'SARS-CoV-2' named entity 'rRT-PCR' named entity 'UHS' named entity 'COVID-19' named entity 'assay' named entity 'SARS-CoV-2' named entity 'saliva' named entity 'saliva' named entity 'UHS' named entity 'Agilent' named entity 'hot-start' named entity 'saliva' named entity 'RNA'

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