Ultra-rapid detection of SARS-CoV-2 in public workspace environments

Yaren, Ozlem; McCarter, Jacquelyn; Phadke, Nikhil; Bradley, Kevin M.; Overton, Benjamin; Yang, Zunyi; Ranade, Shatakshi; Patil, Kunal; Bangale, Rishikesh; Benner, Steven A.

doi:10.1371/journal.pone.0240524

Cited by 15 publications

(19 citation statements)

References 38 publications

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“…Absorbent paper is an attractive alternative to sample vials for collection, given its low cost, wide availability, and smaller environmental footprint. In fact, paper has been used as a means to isolate nucleic acid from biological samples for direct RT-PCR testing ( Glushakova et al, 2017 ) as well as RT-LAMP ( Kellner et al, 2020 ; Yaren et al, 2021 ).…”

Section: Resultsmentioning

confidence: 99%

A LAMP sequencing approach for high-throughput co-detection of SARS-CoV-2 and influenza virus in human saliva

Warneford-Thomson

Shah

Lundgren

et al. 2022

eLife

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The COVID-19 pandemic has created an urgent need for rapid, effective, and low-cost SARS-CoV-2 diagnostic testing. Here, we describe COV-ID, an approach that combines RT-LAMP with deep sequencing to detect SARS-CoV-2 in unprocessed human saliva with a low limit of detection (5–10 virions). Based on a multi-dimensional barcoding strategy, COV-ID can be used to test thousands of samples overnight in a single sequencing run with limited labor and laboratory equipment. The sequencing-based readout allows COV-ID to detect multiple amplicons simultaneously, including key controls such as host transcripts and artificial spike-ins, as well as multiple pathogens. Here, we demonstrate this flexibility by simultaneous detection of 4 amplicons in contrived saliva samples: SARS-CoV-2, influenza A, human STATHERIN, and an artificial SARS calibration standard. The approach was validated on clinical saliva samples, where it showed excellent agreement with RT-qPCR. COV-ID can also be performed directly on saliva absorbed on filter paper, simplifying collection logistics and sample handling.

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Section: Resultsmentioning

confidence: 99%

A LAMP sequencing approach for high-throughput co-detection of SARS-CoV-2 and influenza virus in human saliva

Warneford-Thomson

Shah

Lundgren

et al. 2022

eLife

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“…This decrease in sensitivity could be due to the inhibitory effect described for DARQ method, as previously observed in the amplification of several other targets [45]. To reduce inhibition in the DARQ technique, other versions of this approach have been used, moving the quencher and fluorophore to a loop primer [46,47] or incorporated into the amplification products and detected after the reaction, giving rise to the QUASR method [44].…”

Section: Discussionmentioning

confidence: 98%

Development of a Duplex LAMP Assay with Probe-Based Readout for Simultaneous Real-Time Detection of Schistosoma mansoni and Strongyloides spp. -A Laboratory Approach to Point-Of-Care

Crego-Vicente

Fernández‐Soto

Diego

et al. 2023

IJMS

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Loop-mediated isothermal amplification (LAMP) is the most popular technology for point-of-care testing applications due its rapid, sensitive and specific detection with simple instrumentation compared to PCR-based methods. Many systems for reading the results of LAMP amplifications exist, including real-time fluorescence detection using fluorophore-labelled probes attached to oligonucleotide sequences complementary to the target nucleic acid. This methodology allows the simultaneous detection of multiple targets (multiplexing) in one LAMP assay. A method for multiplexing LAMP is the amplification by release of quenching (DARQ) technique by using a 5′-quencher modified LAMP primer annealed to 3′-fluorophore-labelled acting as detection oligonucleotide. The main application of multiplex LAMP is the rapid and accurate diagnosis of infectious diseases, allowing differentiation of co-infecting pathogens in a single reaction. Schistosomiasis, caused among other species by Schistosoma mansoni and strongyloidiasis, caused by Strongyloides stercoralis, are the most common helminth-parasite infections worldwide with overlapping distribution areas and high possibility of coinfections in the human population. It would be of great interest to develop a duplex LAMP to detect both pathogens in the same reaction. In this study, we investigate the use of our two previously developed and well-stablished LAMP assays for S. mansoni and Strongyloides spp. DNA detection in a new duplex real-time eight-primer system based on a modified DARQ probe method that can be performed in a portable isothermal fluorimeter with minimal laboratory resources. We also applied a strategy to stabilize the duplexed DARQ-LAMP mixtures at room temperature for use as ready-to-use formats facilitating analysis in field settings as point-of-care diagnostics for schistosomiasis and strongyloidiasis.

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“…The question of what viral load constitutes contagiousness continues to be debated. Several groups (Dudley et al 2020, Fowler et al 2020, Mina et al 2020, Yaren et al 2021) have argued that transmission is primarily associated with an approximately 100fold higher viral loads ( ; . 100-1000 copies/lL) than the detection limit of many RT-qPCR reference assays (1 to 10 copies/lL).…”

Section: Discussionmentioning

confidence: 99%

Loop-Mediated Isothermal Amplification Detection of SARS-CoV-2 and Myriad Other Applications

Moore

Cahill²,

Aidelberg

et al. 2021

J Biomol Tech

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As the second year of the COVID-19 pandemic begins, it remains clear that a massive increase in the ability to test for SARS-CoV-2 infections in a myriad of settings is critical to controlling the pandemic and to preparing for future outbreaks. The current gold standard for molecular diagnostics is the polymerase chain reaction (PCR), but the extraordinary and unmet demand for testing in a variety of environments means that both complementary and supplementary testing solutions are still needed. This review highlights the role that loop-mediated isothermal amplification (LAMP) has had in filling this global testing need, providing a faster and easier means of testing, and what it can do for future applications, pathogens, and the preparation for future outbreaks. This review describes the current state of the art for research of LAMP-based SARS-CoV-2 testing, as well as its implications for other pathogens and testing. The authors represent the global LAMP (gLAMP) Consortium, an international research collective, which has regularly met to share their experiences on LAMP deployment and best practices; sections are devoted to all aspects of LAMP testing, including preanalytic sample processing, target amplification, and amplicon detection, then the hardware and software required for deployment are discussed, and finally, a summary of the current regulatory landscape is provided. Included as well are a series of first-person accounts of LAMP method development and deployment. The final discussion section provides the reader with a distillation of the most validated testing methods and their paths to implementation. This review also aims to provide practical information and insight for a range of audiences: for a research audience, to help accelerate research through sharing of best practices; for an implementation audience, to help get testing up and running quickly; and for a public health, clinical, and policy audience, to help convey the breadth of the effect that LAMP methods have to offer.

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Ultra-rapid detection of SARS-CoV-2 in public workspace environments

Cited by 15 publications

References 38 publications

A LAMP sequencing approach for high-throughput co-detection of SARS-CoV-2 and influenza virus in human saliva

A LAMP sequencing approach for high-throughput co-detection of SARS-CoV-2 and influenza virus in human saliva

Development of a Duplex LAMP Assay with Probe-Based Readout for Simultaneous Real-Time Detection of Schistosoma mansoni and Strongyloides spp. -A Laboratory Approach to Point-Of-Care

Loop-Mediated Isothermal Amplification Detection of SARS-CoV-2 and Myriad Other Applications

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