Use of the variplex™ SARS-CoV-2 RT-LAMP as a rapid molecular assay to complement RT-PCR for COVID-19 diagnosis

Rödel, Jürgen; Egerer, Renate; Suleyman, Aynur; Sommer-Schmid, Beatrice; Baier, Michael; Henke, Andreas; Edel, Birgit; Löffler, Bettina

doi:10.1016/j.jcv.2020.104616

Cited by 63 publications

(60 citation statements)

References 20 publications

(41 reference statements)

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“…If (as suggested in the United Kingdom strategy) a test is used to move people from being isolated back into a situation where they may infect others, then sensitivity is important – and with an estimated test sensitivity around 70% [22] , it appears prima facie that current test sensitivities may make this strategy risky; however, as sensitivity will correlate with degree of viral shedding and therefore infectivity, this theoretical risk is reduced in practice. (Sensitivity estimates in the literature are highly variable [23] , [24] , [25] , measures are sometimes used to detect false negative results caused by inadequate sampling [26] , and new tests with different performance characteristics are being introduced [ 27 , 28 ], meaning the interactions between test sensitivity and public health response need to be re-evaluated for each test whose deployment is considered.) Nevertheless, when a test is being used to identify and isolate asymptomatic infectious individuals who would otherwise have been free to infect others, any sensitivity that results in a clinically significant reduction in disease spread is useful (and a small percentage reduction in disease spread may be sufficient in populations where the virus effective reproduction number R eff is just above 1).…”

Section: Not All Positive Tests Reflect Infectionmentioning

confidence: 99%

Diagnostic tool or screening programme? Asymptomatic testing for SARS-CoV-2 needs clear goals and protocols

Skittrall¹,

Fortune²,

Jalal³

et al. 2021

The Lancet Regional Health - Europe

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Section: Not All Positive Tests Reflect Infectionmentioning

confidence: 99%

Diagnostic tool or screening programme? Asymptomatic testing for SARS-CoV-2 needs clear goals and protocols

Skittrall¹,

Fortune²,

Jalal³

et al. 2021

The Lancet Regional Health - Europe

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“…As a result, some samples might give a positive result to the antibody test but www.nature.com/scientificreports/ provide a negative result to the LAMP test. Buck et al (2020), Thi et al (2020) and Rodel et al (2020) are also studies with sensitivity below 80% 34,39,72 . These studies also reported quantity of viral RNA (as Ct value of RT-qPCR) in purified RNA sample.…”

Section: Sensitivity Specificity and Diagnostic Odd Ratio (Dor) Of Nmentioning

confidence: 99%

The diagnostic accuracy of isothermal nucleic acid point-of-care tests for human coronaviruses: A systematic review and meta-analysis

Subsoontorn

Lohitnavy

Kongkaew

2020

Sci Rep

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Many recent studies reported coronavirus point-of-care tests (POCTs) based on isothermal amplification. However, the performances of these tests have not been systematically evaluated. Cochrane Handbook for Systematic Reviews of Diagnostic Test Accuracy was used as a guideline for conducting this systematic review. We searched peer-reviewed and preprint articles in PubMed, BioRxiv and MedRxiv up to 28 September 2020 to identify studies that provide data to calculate sensitivity, specificity and diagnostic odds ratio (DOR). Quality Assessment of Diagnostic Accuracy Studies 2 (QUADAS-2) was applied for assessing quality of included studies and Preferred Reporting Items for a Systematic Review and Meta-analysis of Diagnostic Test Accuracy Studies (PRISMA-DTA) was followed for reporting. We included 81 studies from 65 research articles on POCTs of SARS, MERS and COVID-19. Most studies had high risk of patient selection and index test bias but low risk in other domains. Diagnostic specificities were high (> 0.95) for included studies while sensitivities varied depending on type of assays and sample used. Most studies (n = 51) used reverse transcription loop-mediated isothermal amplification (RT-LAMP) to diagnose coronaviruses. RT-LAMP of RNA purified from COVID-19 patient samples had pooled sensitivity at 0.94 (95% CI: 0.90–0.96). RT-LAMP of crude samples had substantially lower sensitivity at 0.78 (95% CI: 0.65–0.87). Abbott ID Now performance was similar to RT-LAMP of crude samples. Diagnostic performances by CRISPR and RT-LAMP on purified RNA were similar. Other diagnostic platforms including RT- recombinase assisted amplification (RT-RAA) and SAMBA-II also offered high sensitivity (> 0.95). Future studies should focus on the use of un-bias patient cohorts, double-blinded index test and detection assays that do not require RNA extraction.

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“…Testing for infection with SARS-CoV-2 followed by contact tracing is instrumental in controlling spread, but is seriously hampered by diagnostic delays inherent to the use of high-throughput RT-PCR [Kretzschmar et al (2020)]. Novel rapid testing technologies, such as antigen-based tests and LAMP, can reduce diagnostic delays to several minutes [Rödel et al (2020)]. Moreover, such tests can identify symptomatic and asymptomatically infected subjects with high Yet, compared to PCR-based testing, test sensitivity of rapid tests ranges from 70% to 90%, with false-negative results reported mainly in samples with low viral loads (i.e., high CT values), that may reflect subjects with low likelihood of being infectious [Gremmels et al (2020)].…”

Section: Introductionmentioning

confidence: 99%

Regular universal screening for SARS-CoV-2 infection may not allow reopening of society after controlling a pandemic wave

Bootsma

Kretzschmar

Rozhnova

et al. 2020

Preprint

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BackgroundTo limit societal and economic costs of lockdown measures, public health strategies are needed that control the spread of SARS-CoV-2 and simultaneously allow lifting of disruptive measures. Regular universal random screening of large proportions of the population regardless of symptoms has been proposed as a possible control strategy.MethodsWe developed a mathematical model that includes test sensitivity depending on infectiousness for PCR-based and antigen-based tests, and different levels of onward transmission for testing and non-testing parts of the population. Only testing individuals participate in high-risk transmission events, allowing more transmission in case of unnoticed infection. We calculated the required testing interval and coverage to bring the effective reproduction number due to universal random testing (Rrt) below 1, for different scenarios of risk behavior of testing and non-testing individuals.FindingsWith R0 = 2.5, lifting all control measures for tested subjects with negative test results would require 100% of the population being tested every three days with a rapid test method with similar sensitivity as PCR-based tests. With remaining measures in place reflecting Re = 1.3, 80% of the population would need to be tested once a week to bring Rrt below 1. With lower proportions tested and with lower test sensitivity, testing frequency should increase further to bring Rrt below 1. With similar Re values for tested and non-tested subjects, and with tested subjects not allowed to engage in higher risk events, at least 80% of the populations needs to test every five days to bring Rrt below. The impact of the test-sensitivity on the reproduction number is far less than the frequency of testing.InterpretationRegular universal random screening followed by isolation of infectious individuals is not a viable strategy to reopen society after controlling a pandemic wave of SARS-CoV-2. More targeted screening approaches are needed to better use rapid testing such that it can effectively complement other control measures.FundingRECOVER (H2020-101003589) (MJMB), ZonMw project 10430022010001 (MK, HH), FCT project 131_596787873 (GR). ZonMw project 91216062 (MK)

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Use of the variplex™ SARS-CoV-2 RT-LAMP as a rapid molecular assay to complement RT-PCR for COVID-19 diagnosis

Abstract: Highlights Rapid detection of SARS-CoV-2 by variplex™ RT-LAMP from respiratory samples. Homogenization of samples using SL solution for testing without RNA elution. Combination of RT-LAMP and RT-PCR increases diagnostic accuracy.

Cited by 63 publications

References 20 publications

Diagnostic tool or screening programme? Asymptomatic testing for SARS-CoV-2 needs clear goals and protocols

Diagnostic tool or screening programme? Asymptomatic testing for SARS-CoV-2 needs clear goals and protocols

The diagnostic accuracy of isothermal nucleic acid point-of-care tests for human coronaviruses: A systematic review and meta-analysis

Regular universal screening for SARS-CoV-2 infection may not allow reopening of society after controlling a pandemic wave

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