Accessible LAMP-Enabled Rapid Test (ALERT) for Detecting SARS-CoV-2
The coronavirus disease 2019 (COVID-19) pandemic has highlighted bottlenecks in large-scale, frequent testing of populations for infections. Polymerase chain reaction (PCR)-based diagnostic tests are expensive, reliant on centralized labs, can take days to deliver results, and are prone to backlogs...
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doaj-355fa55e91b14a969e40e53977780e442021-04-23T23:05:10ZengMDPI AGViruses1999-49152021-04-011374274210.3390/v13050742Accessible LAMP-Enabled Rapid Test (ALERT) for Detecting SARS-CoV-2Ali Bektaş0Michael F. Covington1Guy Aidelberg2Anibal Arce3Tamara Matute4Isaac Núñez5Julia Walsh6David Boutboul7Constance Delaugerre8Ariel B. Lindner9Fernán Federici10Anitha D. Jayaprakash11Oakland Genomics Center, 355 30th Street, Oakland, CA 94609, USAOakland Genomics Center, 355 30th Street, Oakland, CA 94609, USACenter for Research and Interdisciplinarity (CRI), Université de Paris, INSERM U1284, F-75006 Paris, FranceInstitute for Biological and Medical Engineering, Schools of Engineering, Biology and Medicine, Pontificia Universidad Católica de Chile, Santiago 7820244, ChileInstitute for Biological and Medical Engineering, Schools of Engineering, Biology and Medicine, Pontificia Universidad Católica de Chile, Santiago 7820244, ChileInstitute for Biological and Medical Engineering, Schools of Engineering, Biology and Medicine, Pontificia Universidad Católica de Chile, Santiago 7820244, ChileSchool of Public Health, University of California Berkeley, Berkeley, CA 94720, USAClinical Immunology Department, U976 HIPI, Hôpital Saint Louis, Université de Paris, F-75006 Paris, FranceClinical Immunology Department, U976 HIPI, Hôpital Saint Louis, Université de Paris, F-75006 Paris, FranceCenter for Research and Interdisciplinarity (CRI), Université de Paris, INSERM U1284, F-75006 Paris, FranceInstitute for Biological and Medical Engineering, Schools of Engineering, Biology and Medicine, Pontificia Universidad Católica de Chile, Santiago 7820244, ChileOakland Genomics Center, 355 30th Street, Oakland, CA 94609, USAThe coronavirus disease 2019 (COVID-19) pandemic has highlighted bottlenecks in large-scale, frequent testing of populations for infections. Polymerase chain reaction (PCR)-based diagnostic tests are expensive, reliant on centralized labs, can take days to deliver results, and are prone to backlogs and supply shortages. Antigen tests that bind and detect the surface proteins of a virus are rapid and scalable but suffer from high false negative rates. To address this problem, an inexpensive, simple, and robust 60-minute do-it-yourself (DIY) workflow to detect viral RNA from nasal swabs or saliva with high sensitivity (0.1 to 2 viral particles/μL) and specificity (>97% true negative rate) utilizing reverse transcription loop-mediated isothermal amplification (RT-LAMP) was developed. ALERT (Accessible LAMP-Enabled Rapid Test) incorporates the following features: (1) increased shelf-life and ambient temperature storage, compared to liquid reaction mixes, by using wax layers to isolate enzymes from other reagents; (2) improved specificity compared to other LAMP end-point reporting methods, by using sequence-specific QUASR (quenching of unincorporated amplification signal reporters); (3) increased sensitivity, compared to methods without purification through use of a magnetic wand to enable pipette-free concentration of sample RNA and cell debris removal; (4) quality control with a nasopharyngeal-specific mRNA target; and (5) co-detection of other respiratory viruses, such as influenza B, by multiplexing QUASR-modified RT-LAMP primer sets. The flexible nature of the ALERT workflow allows easy, at-home and point-of-care testing for individuals and higher-throughput processing for labs and hospitals. With minimal effort, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific primer sets can be swapped out for other targets to repurpose ALERT to detect other viruses, microorganisms, or nucleic acid-based markers.https://www.mdpi.com/1999-4915/13/5/742RT-LAMPpoint-of-carebiodetectionSARS-CoV-2 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Ali Bektaş Michael F. Covington Guy Aidelberg Anibal Arce Tamara Matute Isaac Núñez Julia Walsh David Boutboul Constance Delaugerre Ariel B. Lindner Fernán Federici Anitha D. Jayaprakash |
spellingShingle |
Ali Bektaş Michael F. Covington Guy Aidelberg Anibal Arce Tamara Matute Isaac Núñez Julia Walsh David Boutboul Constance Delaugerre Ariel B. Lindner Fernán Federici Anitha D. Jayaprakash Accessible LAMP-Enabled Rapid Test (ALERT) for Detecting SARS-CoV-2 Viruses RT-LAMP point-of-care biodetection SARS-CoV-2 |
author_facet |
Ali Bektaş Michael F. Covington Guy Aidelberg Anibal Arce Tamara Matute Isaac Núñez Julia Walsh David Boutboul Constance Delaugerre Ariel B. Lindner Fernán Federici Anitha D. Jayaprakash |
author_sort |
Ali Bektaş |
title |
Accessible LAMP-Enabled Rapid Test (ALERT) for Detecting SARS-CoV-2 |
title_short |
Accessible LAMP-Enabled Rapid Test (ALERT) for Detecting SARS-CoV-2 |
title_full |
Accessible LAMP-Enabled Rapid Test (ALERT) for Detecting SARS-CoV-2 |
title_fullStr |
Accessible LAMP-Enabled Rapid Test (ALERT) for Detecting SARS-CoV-2 |
title_full_unstemmed |
Accessible LAMP-Enabled Rapid Test (ALERT) for Detecting SARS-CoV-2 |
title_sort |
accessible lamp-enabled rapid test (alert) for detecting sars-cov-2 |
publisher |
MDPI AG |
series |
Viruses |
issn |
1999-4915 |
publishDate |
2021-04-01 |
description |
The coronavirus disease 2019 (COVID-19) pandemic has highlighted bottlenecks in large-scale, frequent testing of populations for infections. Polymerase chain reaction (PCR)-based diagnostic tests are expensive, reliant on centralized labs, can take days to deliver results, and are prone to backlogs and supply shortages. Antigen tests that bind and detect the surface proteins of a virus are rapid and scalable but suffer from high false negative rates. To address this problem, an inexpensive, simple, and robust 60-minute do-it-yourself (DIY) workflow to detect viral RNA from nasal swabs or saliva with high sensitivity (0.1 to 2 viral particles/μL) and specificity (>97% true negative rate) utilizing reverse transcription loop-mediated isothermal amplification (RT-LAMP) was developed. ALERT (Accessible LAMP-Enabled Rapid Test) incorporates the following features: (1) increased shelf-life and ambient temperature storage, compared to liquid reaction mixes, by using wax layers to isolate enzymes from other reagents; (2) improved specificity compared to other LAMP end-point reporting methods, by using sequence-specific QUASR (quenching of unincorporated amplification signal reporters); (3) increased sensitivity, compared to methods without purification through use of a magnetic wand to enable pipette-free concentration of sample RNA and cell debris removal; (4) quality control with a nasopharyngeal-specific mRNA target; and (5) co-detection of other respiratory viruses, such as influenza B, by multiplexing QUASR-modified RT-LAMP primer sets. The flexible nature of the ALERT workflow allows easy, at-home and point-of-care testing for individuals and higher-throughput processing for labs and hospitals. With minimal effort, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific primer sets can be swapped out for other targets to repurpose ALERT to detect other viruses, microorganisms, or nucleic acid-based markers. |
topic |
RT-LAMP point-of-care biodetection SARS-CoV-2 |
url |
https://www.mdpi.com/1999-4915/13/5/742 |
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