A growing number of methods are being developed and shared by the scientific community around the world for use in COVID-19-related work, some of which have been approved as FDA EUA protocols. A selection of preprints and protocols is shown below. Please note that preprints, protocols, and early access publications have not completed a peer-review process.

LAMP: Colorimetric and Fluorescence Detection Methods

 
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Development of Multiplexed RT-LAMP for Detection of SARS-CoV-2 and Influenza Viral RNA
Zhang, Y. et. al.
New England Biolabs

As the flu season arrives in the Northern Hemisphere, the ability to screen for multiple viral targets will be increasingly important, and the ability to include internal control assays in the reaction allows for decreased resource use and increased throughput. This preprint describes a multiplex RT-LAMP assay for the detection of 4 targets (SARS-CoV-2, Influenza A, Influenza B, and an internal control) in a single reaction using real-time and endpoint fluorescence detection. It utilizes the previously described Detection of Amplification by Releasing of Quenching (DARQ) method, which supplements a standard LAMP primer set with a pair of oligonucleotides containing a quencher-fluorophore duplex region that upon strand separation results in a gain of fluorescent signal.

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Rapid point‑of‑care detection of SARS‑CoV‑2 using reverse transcription loop‑mediated isothermal amplification
Mautner, L. et. al.
Bavarian Health and Food Safety Authority

This publication describes a fluorescence-based RT-LAMP assay that detects the SARS-CoV-2 genes ORF8 and N directly from pharyngeal swab samples. The assay avoids the costly and laborious RNA extraction step by using a sample pre-heating step. Pre-heating the swabs at 90 °C for 5 minutes before directly pipetting them into the RT-LAMP reaction resulted in the best combination of low detection time and specific amplification of SARS-CoV-2 positive samples. The assay is sensitive and highly specific for SARS-CoV-2 detection, showing no cross reactivity when tested on 20 other respiratory pathogens.

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SARS-CoV-2 detection using isothermal amplification and a rapid, inexpensive protocol for sample inactivation and purification
Rabe, B. et. al.
Harvard Medical School

This publication describes a rapid virion and exonuclease inactivation and sample purification protocol which, when combined with an RT-LAMP assay, brings the sensitivity to at least 1 viral RNA copy per microliter in a sample. The purification protocol involves binding nucleic acids to silica in the form of a suspension known as “glass milk”, which is readily available in large amounts. This simple inactivation and purification pipeline is inexpensive and compatible with other downstream RNA detection platforms.

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Optimizing direct RT-LAMP to detect transmissible SARS-CoV-2 from primary patient samples
Dudley, D. et. al.
University of Wisconsin-Madison, University of Wisconsin Hospitals and Clinics

This preprint describes a fluorescence-based RT-LAMP assay optimized for direct testing from nasopharyngeal swabs or saliva samples. Optimization and characterization of the direct RT-LAMP assay included the addition of guanidine hydrochloride, an alternative RNA isolation method, and testing multiple SARS-CoV-2 RT-LAMP primer sets for improved reaction efficiency. The limit of sensitivity achieved is sufficient to detect levels of virus that are necessary to culture virus from a sample, therefore representing levels where transmission is most likely. The research concludes that high-throughput RT-LAMP testing could augment RT-qPCR in SARS-CoV-2 screening programs.

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Artificial Intelligence-Assisted Loop Mediated Isothermal Amplification (AI-LAMP) for Rapid Detection of SARS-CoV-2
Rohaim, M. et. al.
The Lancaster University, University of Surrey, Brunel University London, Poole & Bournemouth Hospitals NHS Trust, University Hospitals of Morecambe Bay NHS, Foundation Trust

This publication reports the development of a high-resolution comparative genomics analysis-guided colorimetric RT-LAMP assay used in tandem with a novel hand-held smart diagnostic device. The robust, low-cost, and user-friendly diagnostic device was furnished with automated image acquisition and processing algorithms and the collated data was processed through artificial intelligence (AI) pipelines to further reduce the assay run time and the subjectivity of the colorimetric LAMP results interpretation. This advanced AI algorithm-implemented LAMP (AI-LAMP) assay, targeting the RNA-dependent RNA polymerase gene, showed high analytical sensitivity and specificity for SARS-CoV-2, with more sensitivity than RT-qPCR. The assay was validated on RNA extracted from clinical samples from SARS-CoV-2 suspected patients.

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A community-deployable SARS-CoV-2 screening test using raw saliva with 45 minutes sample-to-results turnaround
Meyerson, N. et. al.
University of Colorado Boulder

This 45-minute RT-LAMP assay targets two separate regions of the SARS-CoV-2 genome in raw saliva, providing a low-complexity, portable, and robust system for real-time community screening.

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Initial evaluation of a mobile SARS-CoV-2 RT-LAMP testing strategy
Newman, C. et. al.
University of Wisconsin-Madison

This preprint describes a simple, outdoor, mobile RT-LAMP assay workflow where self-collected saliva for 494 volunteers was tested for SARS-CoV-2 RNA.

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A colorimetric RT-LAMP assay and LAMP-sequencing for detecting SARS-CoV-2 RNA in clinical samples
Dao Thi et. al.
Heidelberg University, Center for Molecular Biology of Heidelberg University, German Center for Infection Research (DZIF), German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance

Researchers at Heidelberg University tested an RT-LAMP assay on several hundred clinical RNA samples isolated from pharyngeal swabs collected from individuals being tested for COVID-19, confirming that the RT-LAMP assay was a simpler albeit less sensitive option compared to RT-qPCR for large-scale testing for SARS-CoV-2 RNA. The investigators also developed a simplified version of this method (direct swab-to-RT-LAMP assay) that did not require a prior RNA isolation step as well as a method for highly multiplexed sequencing of RT-LAMP reactions (LAMP-sequencing).

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LamPORE: rapid, accurate and highly scalable molecular screening for SARS-CoV-2 infection, based on nanopore sequencing
James, P. et al.
Oxford Nanopore Technologies

This fast, scalable method has testing and screening applications, employing LAMP-based amplification followed by library construction and nanopore sequencing. 

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Standard operating procedures for SARS-CoV-2 detection by a clinical diagnostic RT-LAMP assay
Buck, M. et. al.
The Francis Crick Institute, University College London, Health Services Laboratories, The Royal Marsden Hospital, The Institute of Cancer Research, The Royal Free Hospital

This preprint, from the Crick COVID-19 Consortium, presents a clinically-validated standard operating procedure (SOP) for high-throughput SARS-CoV-2 detection by RT-LAMP in 25 minutes that is robust, reliable, repeatable, sensitive, specific, and inexpensive. Compared to RT-qPCR, RT-LAMP translates into a ten-fold decrease in total reagent cost and a potential four-fold increase in pipeline output. Additionally, preliminary data is provided suggesting that RT-LAMP can be performed without prior RNA extraction, allowing rapid and cost-effective testing that could potentially be extended to point-of-care.

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Rapid SARS-CoV-2 testing in primary material based on a novel multiplex LAMP assay
Schermer, M. et. al.
University of Cologne, Howard Hughes Medical Institute, Broad Institute, MIT, McGovern Institute, Massachusetts Consortium for Pathogen Readiness, German Center for Infection Research

This preprint describes the use of PCR-independent methods for detection of SARS-CoV-2 RNA from nasopharyngeal swabs, including LAMP and specific high-sensitivity enzymatic reporter unlocking (SHERLOCK). The research includes a novel multiplexed LAMP approach to detect SARS-CoV-2 RNA, with the assay targeting the Orf3a and Orf7a regions. Inactivation of the sample by a brief heat step, primer optimization, guanidine hydrochloride addition, and multiplexing helped to increase the sensitivity of the reaction.

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Clinical assessment and validation of a rapid and sensitive SARS-CoV-2 test using reverse-transcription loop-mediated isothermal amplification
Anahtar, M. et. al.
Massachusetts General Hospital, Harvard Medical School, New England Biolabs, Howard Hughes Medical Institute, Blavatnik Institute

This preprint presents a simple clinical workflow that utilizes a sensitive and highly specific colorimetric RT-LAMP assay to detect SARS-CoV-2 in a 40-minute protocol.

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Rapid and extraction-free detection of SARS-CoV-2 from saliva with colorimetric LAMP
Lalli, M. et. al.
Washington University School of Medicine

This preprint outlines development of a rapid colorimetric assay using RT-LAMP optimized on human saliva samples without an RNA purification step.

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Host, Viral, and Environmental Transcriptome Profiles of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)
Butler, D.J. et al.
Weill Cornell Medicine, Baylor College of Medicine, Hudson Alpha Discovery Institute, University Hospital Tuebingen, Columbia University, New England Biolabs

This preprint outlines the design of a 30-minute colorimetric LAMP test to identify SARS-CoV-2 infection and development of a large-scale shotgun metatranscriptomic profiling platform for nasopharyngeal swabs.

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Direct on-the-spot detection of SARS-CoV-2 in patients
Nadav, B. et. al.
Technion – Israel Institute of Technology, Meir Medical Center, Tel-Aviv University, Canadian Institute for Advanced Research

This publication describes development of a protocol based on RT-LAMP for direct detection of SARS-CoV-2 on nose and throat swabs, with no RNA purification step required.The direct RT-LAMP method was applied to over 180 different patient samples and successfully detected patients with medium to high viral loads, while yielding very few false positives.

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Point-of-care testing for COVID-19 using SHERLOCK diagnostics
Joung, J. et. al.
Howard Hughes Medical Institute, Broad Institute, MIT, McGovern Institute, Massachusetts General Hospital, Brigham and Women’s Hospital, Ragon Institute, University of Washington, Fred Hutchinson Cancer Research Center

The preprint outlines a simple test chemistry called STOP (SHERLOCK Testing in One Pot) for detecting SARS-CoV-2 in one hour that is suitable for point-of-care use. This simplified test, STOPCovid, provides sensitivity comparable to RT-qPCR-based SARS-CoV-2 tests and has a limit of detection of 100 copies of viral genome input in saliva or nasopharyngeal swabs per reaction.

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EasyCOV : LAMP based rapid detection of SARS‐CoV‐2 in saliva
L’Helgouach et. al.
Sys2Diag, Montpellier University Hospital

This preprint describes a direct saliva RT-LAMP based virus detection assay called EasyCOV that utilizes a colorimetric readout of test results.

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FDA EUA: Color Genomics, Inc. SARS CoV-2 Diagnostic Assay



Luna RT-qPCR

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SalivaDirect: Simple and sensitive molecular diagnostic test for SARS-CoV-2 surveillance
Vogels, C. et. al.
Yale School of Public Health, Connecticut Agricultural Experimental Station, Yale University School of Medicine

SalivaDirect is an extraction-free, dualplex RT-qPCR laboratory developed test consisting of three steps: (1) collecting saliva without preservative buffers, (2) proteinase K treatment and heat inactivation, and (3) dualplex RT-qPCR virus detection.

Guidance and an interactive version of this protocol can be found here.

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A direct RT-qPCR approach to test large numbers of individuals for SARS-CoV-2
Maricic, T. et. al.
Max Planck Institute for Evolutionary Anthropology, Hospital St. Georg, Karolinska Institutet, ImmunoDeficiencyCenter Leipzig (IDCL) at Hospital St. Georg Leipzig

This preprint present a safe, cheap and fast PCR-based approach to detect individuals with high levels of SARS-CoV-2 in single or pooled gargle lavages (“mouthwashes”), without the need for nasopharyngeal swabs or RNA extraction. It describes the use of daily tests of all staff and residents of a local nursing home previously affected by COVID-19. The authors suggest that this approach could be scaled-up to test all staff members and visitors of retirement homes and other institutions in an entire city or region.

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Direct RT-qPCR Detection of SARS-CoV-2 RNA From Patient Nasopharyngeal Swabs Without an RNA Extraction Step
Bruce, E. et. al.
University of Vermont, University of Washington, Fred Hutchinson Cancer Research Center, IXIS LLC

This preprint describes a direct RT-qPCR detection assay that omits the RNA extraction step. In a blinded study, the direct assay correctly identified 92% of nasopharyngeal samples demonstrated to be positive for SARS-CoV-2 RNA by traditional methods that included RNA extraction.

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A blueprint for the implementation of a validated approach for the detection of SARS-Cov2 in clinical samples in academic facilities
Sridhar, S. et. al.
University of Cambridge, Wellcome Sanger institute, Addenbrookes Hospital

This preprint describes the process of developing a SARS-CoV-2 diagnostic workflow in a conventional academic Containment Level 2 (CL2) laboratory using RT-qPCR detection.

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Optimized qRT-PCR approach for the detection of intra- and extra-cellular SARS-CoV-2 RNAs
Toptan, T. et. al.
Goethe University, GenXPro Gmbh

This preprint outlines SARS-CoV-2 detection that can be accomplished with either probe or dye-based RT-qPCR approaches.

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Triplex Real-Time RT-PCR for Severe Acute Respiratory Syndrome Coronavirus 2
Waggoner, JJ. et. al.
Emory University, Stanford University

This research letter describes development of a triplex assay for streamlined detection of the N2, E, and RNase P targets in SARS-CoV-2 RNA.

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FDA EUA: Diatherix Eurofins Laboratory SARS-CoV-2 PCR Test

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FDA EUA: InBios Smart Detect SARS-CoV-2 rRT-PCR Kit

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FDA EUA: Solaris Multiplex SARS-CoV-2 Assay

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FDA EUA: Yale School of Public Health, Department of Epidemiology of Microbial Diseases SalivaDirect

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FDA EUA: Guardant Health, Inc., Guardant-19

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FDA EUA: BilliontoOne, Inc. qSanger-COVID-19 Assay

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