Sample-to-answer COVID-19 nucleic acid testing using a low-cost centrifugal microfluidic platform with bead-based signal enhancement and smartphone read-out
This article has been Reviewed by the following groups
Listed in
- Evaluated articles (ScreenIT)
Abstract
LAMP-based platform for SARS-CoV-2 RNA detection incorporating beads to remove primer-dimers, enhance fluorescent signal and stop the reaction after amplification.
Article activity feed
-
-
SciScore for 10.1101/2020.11.04.20225888: (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
Software and Algorithms Sentences Resources The acquired fluorescence microscopy images were analyzed using ImageJ software (NIH, USA). 4.5. ImageJsuggested: (ImageJ, RRID:SCR_003070)For the LAMP experiments, 50 μl of each sample was heat-inactivated at 95 °C for 15 minutes and stored at −80 °C until further processing. 4.7. Detection of SARS-CoV-2 RNA using the integrated centrifugal platform: The sample containing the RNA template (in vitro synthetized RNA fragment or inactivated SARS-CoV-2) was first combined with the … SciScore for 10.1101/2020.11.04.20225888: (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
Software and Algorithms Sentences Resources The acquired fluorescence microscopy images were analyzed using ImageJ software (NIH, USA). 4.5. ImageJsuggested: (ImageJ, RRID:SCR_003070)For the LAMP experiments, 50 μl of each sample was heat-inactivated at 95 °C for 15 minutes and stored at −80 °C until further processing. 4.7. Detection of SARS-CoV-2 RNA using the integrated centrifugal platform: The sample containing the RNA template (in vitro synthetized RNA fragment or inactivated SARS-CoV-2) was first combined with the LAMP master mix at a ratio of 10% (v/v) and 10 μL were subsequently added to each of the 20 channels in the disc. LAMPsuggested: (LAMP, RRID:SCR_001740)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:Fluorescence detection using DNA intercalator dyes is an equally simple and more interference-forgiving approach but requires the tackling of two key limitations, namely (1) the relatively more complex signal transduction, particularly in miniaturized systems concerning low fluorescence signal intensities and filtering requirements 40 and (2) the high numbers (typically 6 different sequences) and design complexity of LAMP primers results very often in a variable degree of intra- (hairpins) and cross-primer hybridization (primer dimers), which result in significant non-specific fluorescence signal 41. This signal is particularly relevant at room temperature due to the lower hybridization stringency, hindering a simple, non-real-time, post-LAMP measurement. Here, the developed device incorporates an agarose bead-based strategy combined with centrifugal microfluidics to fundamentally tackle both these limitations by significantly enhancing the negative-to-positive signal ratio. Using a set of primers that we have previously developed 33 and resorting to a combination of SSIV and Bst 3.0 for LAMP and SYBR Green I for fluorescence generation, the obtained RT-LAMP results are shown in Figure 1-A. Performing a dilution series of an RNA fragment with a 226 bp sequence matching the ORF1ab of SARS-CoV-2 in water, 100 copies per 10 μL reaction could be detected within 30 min of amplification time, in agreement with the typical LoD requirements of FDA-approved COVID-19 diagnostic technol...
Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).
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.
- No protocol registration statement was detected.
-
