Detecting SARS-CoV-2 at point of care: preliminary data comparing loop-mediated isothermal amplification (LAMP) to polymerase chain reaction (PCR)
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Abstract
Background
A cost effective and efficient diagnostic tool for COVID-19 as near to the point of care (PoC) as possible would be a game changer in the current pandemic. We tested reverse transcription loop mediated isothermal amplification (RT-LAMP), a method which can produce results in under 30 min, alongside standard methods in a real-life clinical setting.
Methods
This prospective service improvement project piloted an RT-LAMP method on nasal and pharyngeal swabs on 21 residents of a high dependency care home, with two index COVID-19 cases, and compared it to multiplex tandem reverse transcription polymerase chain reaction (RT-PCR). We recorded vital signs of patients to correlate clinical and laboratory information and calculated the sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of a single swab using RT-LAMP compared with the current standard, RT-PCR, as per Standards for Reporting Diagnostic Accuracy Studies (STARD) guidelines.
Results
The novel method accurately detected 8/10 RT-PCR positive cases and identified a further 3 positive cases. Eight further cases were negative using both methods. Using repeated RT-PCR as a “gold standard”, the sensitivity and specificity of a single novel test were 80 and 73% respectively. PPV was 73% and NPV was 83%. Incorporating retesting of low signal RT-LAMP positives improved the specificity to 100%. We also speculate that hypothermia may be a significant early clinical sign of COVID-19.
Conclusions
RT-LAMP testing for SARS-CoV-2 was found to be promising, fast and to work equivalently to RT-PCR methods. RT-LAMP has the potential to transform COVID-19 detection, bringing rapid and accurate testing to the PoC. RT-LAMP could be deployed in mobile community testing units, care homes and hospitals to detect disease early and prevent spread.
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SciScore for 10.1101/2020.04.01.20047357: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
No key resources detected.
Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:Strengths + Limitations: We have been able to perform these tests quickly in a group at high risk for severe disease, and a setting where early identification of infected patients is key to preventing further spread. Many other …
SciScore for 10.1101/2020.04.01.20047357: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
No key resources detected.
Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:Strengths + Limitations: We have been able to perform these tests quickly in a group at high risk for severe disease, and a setting where early identification of infected patients is key to preventing further spread. Many other studies so far have used laboratory samples to estimate efficacy but have been unable to estimate the clinical utility. Swabs were taken by the same clinician, minimising the risk of technical error or observer biases. All RT-LAMP samples were tested in the MicrosensDx laboratory, and RT-PCR in the hospital laboratory, and there was no viral transport medium on the RT-LAMP swabs. Actual Point of Care testing, and or viral medium could be used to optimise performance further but use of dry swabs could ease issues with supply of viral transport media. We are limited by a small sample size, so our estimates have wide confidence intervals. However, they appear to be concordant with other (pre-print) studies on RT-LAMP performed purely on laboratory samples. A further possible limitation of our study is that only upper respiratory samples were used. Additional work is needed to test this method with sputum or bronchiolar lavage specimens, which may improve sensitivity for hospitalised patients. We are also aware that sampling sites were different on Day 3 and 4, however discordant patients had deep nasal samples on Day 4, and this does not appear to have affected our results. Generalisability, Implications & Future Research: Use of this rapid test, for exam...
Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a protocol registration statement.
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