Colorimetric loop-mediated isothermal amplification (LAMP) for cost-effective and quantitative detection of SARS-CoV-2: the change in color in LAMP-based assays quantitatively correlates with viral copy number

Gonzalez‐González, Everardo; Lara-Mayorga, Itzel Montserrat; Rodríguez‐Sánchez, Iram P.; Zhang, Yu Shrike; Martínez-Chapa, Sergio O.; Santiago, Grissel Trujillo‐de; Álvarez, Mario Moisés

doi:10.1039/d0ay01658f

Cited by 44 publications

(42 citation statements)

References 45 publications

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“…Due to its simplicity, accuracy comparable with RT-qPCR to detect SARS-CoV-2 RNA, does not require PCR machine and naked eye readable colorimetric output, RT-LAMP was the focus of massive testing campaigns (14,16,28). This screening strategy is compatible with: home, primary care clinics, point of entry Upon RNA extraction from nasopharyngeal swab-derived clinical samples we found a LoD of 20 viral genomic copies/µL, confirming previous studies based on N SARS-CoV-2 target (9,30,43). It is worth noting that when using non-clinical SARS-CoV-2 extracted RNA or synthetic target, the LoD reaches less than 0.5 cps/µL.…”

Section: Discussionsupporting

confidence: 84%

Clinical validation of colorimetric RT-LAMP, a fast, highly sensitive and specific COVID-19 molecular diagnostic tool that is robust to detect SARS-CoV-2 variants of concern

Alves

Oliveira

Franco-Luiz

et al. 2021

Preprint

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The COVID-19 pandemics unfolded due to the widespread SARS-CoV-2 transmission reinforced the urgent need for affordable molecular diagnostic alternative methods for massive testing screening. We present the clinical validation of a pH-dependent colorimetric RT-LAMP (reverse transcription loop-mediated isothermal amplification) for SARS-CoV-2 detection. The method revealed a limit of detection of 19.3 viral genomic copies/uL when using RNA extracted samples obtained from nasopharyngeal swabs collected in guanidine-containing viral transport medium. Typical RT-LAMP reactions were performed at 65 C for 30 min. When compared to RT-qPCR, up to Ct value 32, RT-LAMP presented 97% (87.4-99.4% 95% CI) sensitivity and 100% (86.2-100%) specificity for SARS-CoV-2 RNA detection targeting N gene. No cross-reactivity was detected when testing other non-SARS-CoV virus, confirming high specificity. The test is compatible with primary RNA extraction free samples. We also demonstrated that colorimetric RT-LAMP can detect SARS-CoV-2 variants of concern (VOC) and variants of interest (VOI), such as variants occurring in Brazil named P.1, P.2, B.1.1.374 and B.1.1.371. The method meets point-of-care requirements and can be deployed in the field for high-throughput COVID-19 testing campaigns, especially in countries where COVID-19 testing efforts are far from ideal to tackle the pandemics. Although RT-qPCR is considered the gold standard for SARS-CoV-2 RNA detection, it requires expensive equipments, infrastructure and highly trained personnel. In contrast, RT-LAMP emerges as an affordable, inexpensive and simple alternative for SARS-CoV-2 molecular detection that can be applied to massive COVID-19 testing campaigns and save lives.

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Section: Discussionsupporting

confidence: 84%

Clinical validation of colorimetric RT-LAMP, a fast, highly sensitive and specific COVID-19 molecular diagnostic tool that is robust to detect SARS-CoV-2 variants of concern

Alves

Oliveira

Franco-Luiz

et al. 2021

Preprint

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“…Some RT-LAMP tests use end-point lateral flow strips for detection (Table S1), which adds a user step, but more importantly, should not be done at the POC because it exposes the testing site to amplicons that will give false positive results in subsequent tests. Others use in-tube detection by eye (30) or a cell phone (31) which increases the user burden and could introduce additional sources of error. Real-time detection used in Harmony COVID-19 removes the need for extra detection steps or user interpretation.…”

Section: Discussionmentioning

confidence: 99%

Harmony COVID-19: a ready-to-use kit, low-cost detector, and smartphone app for point-of-care SARS-CoV-2 RNA detection

Panpradist

Kline

Atkinson

et al. 2021

Preprint

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RNA amplification tests sensitively detect SARS-CoV-2 infection, but their complexity and cost are prohibitive for expanding COVID-19 testing. We developed Harmony COVID-19, a point-of-care test using inexpensive consumables, ready-to-use reagents, and a simple device accommodating up to 4 samples simultaneously. Our ready-to-use, 4-plex reverse-transcription, loop-mediated isothermal amplification (RT-LAMP) can detect down to 0.38 SARS-CoV-2 RNA copies/μL and can report in 17 min for high viral load samples (5,000 copies/μL). Harmony detected 97% or 83% of contrived samples with ≥0.5 viral particles/μL in nasal matrix or saliva, respectively. Evaluation in clinical nasal specimens in viral transport media (VTM, n=101) showed 100% detection of RNA extracted from specimens with ≥0.5 SARS-CoV-2 RNA copies/μL, with 100% specificity in specimens positive for other respiratory pathogens. VTM is non-ideal for Harmony system, yet extraction-free analysis of VTM specimens (n=29) had 95% success in specimens with ≥1 RNA copies/μL. Usability testing performed first-time by healthcare workers showed 95% accuracy

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“…According to the study, when compared to RT-PCR, which is less sensitive, loop-based isothermal amplification has a sensitivity of more than 97% to the target open reading frame (ORF 1ab) gene. Another study found that loop-mediated isothermal amplification is precise, owing to the use of six to eight primers to determine the eight various sections of the target DNA [ 59 , 60 ].…”

Section: Ongoing Diagnostic Techniques For Sars-cov-2mentioning

confidence: 99%

Nanotechnology Integration for SARS-CoV-2 Diagnosis and Treatment: An Approach to Preventing Pandemic

Asdaq¹,

Ikbal

Sahu

et al. 2021

Nanomaterials

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The SARS-CoV-2 outbreak is the COVID-19 disease, which has caused massive health devastation, prompting the World Health Organization to declare a worldwide health emergency. The corona virus infected millions of people worldwide, and many died as a result of a lack of particular medications. The current emergency necessitates extensive therapy in order to stop the spread of the coronavirus. There are various vaccinations available, but no validated COVID-19 treatments. Since its outbreak, many therapeutics have been tested, including the use of repurposed medications, nucleoside inhibitors, protease inhibitors, broad spectrum antivirals, convalescence plasma therapies, immune-modulators, and monoclonal antibodies. However, these approaches have not yielded any outcomes and are mostly used to alleviate symptoms associated with potentially fatal adverse drug reactions. Nanoparticles, on the other hand, may prove to be an effective treatment for COVID-19. They can be designed to boost the efficacy of currently available antiviral medications or to trigger a rapid immune response against COVID-19. In the last decade, there has been significant progress in nanotechnology. This review focuses on the virus’s basic structure, pathogenesis, and current treatment options for COVID-19. This study addresses nanotechnology and its applications in diagnosis, prevention, treatment, and targeted vaccine delivery, laying the groundwork for a successful pandemic fight.

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Colorimetric loop-mediated isothermal amplification (LAMP) for cost-effective and quantitative detection of SARS-CoV-2: the change in color in LAMP-based assays quantitatively correlates with viral copy number

Abstract: Colorimetric LAMP for COVID-19 intensified diagnostics: a simple and quantitative method comparable in diagnostic performance to RT-qPCR.

Cited by 44 publications

References 45 publications

Clinical validation of colorimetric RT-LAMP, a fast, highly sensitive and specific COVID-19 molecular diagnostic tool that is robust to detect SARS-CoV-2 variants of concern

Clinical validation of colorimetric RT-LAMP, a fast, highly sensitive and specific COVID-19 molecular diagnostic tool that is robust to detect SARS-CoV-2 variants of concern

Harmony COVID-19: a ready-to-use kit, low-cost detector, and smartphone app for point-of-care SARS-CoV-2 RNA detection

Nanotechnology Integration for SARS-CoV-2 Diagnosis and Treatment: An Approach to Preventing Pandemic

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