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A simple direct RT-LAMP SARS-CoV-2 saliva diagnostic

Flynn, Michael J. and Snitser, Olga and Flynn, James and Green, Samantha and Yelin, Idan and Szwarcwort-Cohen, Moran and Kishony, Roy and Elowitz, Michael B. (2020) A simple direct RT-LAMP SARS-CoV-2 saliva diagnostic. . (Unpublished) https://resolver.caltech.edu/CaltechAUTHORS:20201123-140413855

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Abstract

Widespread, frequent testing is essential for curbing the ongoing COVID-19 pandemic. Because its simplicity makes it ideal for widely distributed, high throughput testing, RT-LAMP provides an attractive alternative to RT-qPCR. However, most RT-LAMP protocols require the purification of RNA, a complex and low-throughput bottleneck that has often been subject to reagent supply shortages. Here, we report an optimized RT-LAMP-based SARS-CoV-2 diagnostic protocol for saliva and swab samples. In the protocol we replace RNA purification with a simple sample preparation step using a widely available chelating agent, as well as optimize key protocol parameters. When tested on clinical swab and saliva samples, this assay achieves a limit of detection of 105 viral genomes per ml, with sensitivity close to 90% and specificity close to 100%, and takes 45 minutes from sample collection to result, making it well suited for a COVID-19 surveillance program.


Item Type:Report or Paper (Discussion Paper)
Related URLs:
URLURL TypeDescription
https://doi.org/10.1101/2020.11.19.20234948DOIDiscussion Paper
ORCID:
AuthorORCID
Yelin, Idan0000-0003-2515-4113
Elowitz, Michael B.0000-0002-1221-0967
Additional Information:The copyright holder for this preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license. This version posted November 22, 2020. This project was supported by the Caltech Merkin Institute for Translational Research and the Israel Science Foundation (grant No. 3633/19) within the KillCorona Curbing Coronavirus Research Program. James Flynn provided his own funds to conduct the study at Catholic Medical Center. Data Availability: All data from this study can be obtained by emailing the first author. The authors have declared no competing interest. Author Declarations: I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes. The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The IRB of the Technion at Israel Institute of Technology gave approval for Olga Snitser to collect anonymized SARS-CoV-2 swab samples and assay them with RT-qPCR and the RT-LAMP protocol developed in this paper. The IRB of Catholic Medical Center in Manchester, New Hampshire gave approval for James Flynn to collect patient saliva samples and assay them with the RT-LAMP diagnostic developed in this paper. All necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived. Yes. I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes. I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes.
Group:Richard N. Merkin Institute for Translational Research, COVID-19
Funders:
Funding AgencyGrant Number
Caltech Merkin Institute for Translational ResearchUNSPECIFIED
Israel Science Foundation3633/19
James FlynnUNSPECIFIED
Record Number:CaltechAUTHORS:20201123-140413855
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20201123-140413855
Official Citation:A simple direct RT-LAMP SARS-CoV-2 saliva diagnostic. Michael J. Flynn, Olga Snitser, Idan Yelin, James Flynn, Samantha Green, Moran Szwarcwort, Roy Kishony, Michael B. Elowitz. medRxiv 2020.11.19.20234948; doi: https://doi.org/10.1101/2020.11.19.20234948
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:106792
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:23 Nov 2020 22:20
Last Modified:02 Feb 2021 19:43

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