Multiplex Target-Redundant RT-LAMP for Robust Detection of SARS-CoV-2 Using Fluorescent Universal Displacement Probes
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Abstract
The COVID-19 pandemic has had tremendous impact, and the ability to perform molecular diagnostics in resource limited settings has emerged as a key resource for mitigating spread of the disease. One challenge in COVID-19 diagnosis, as well as other viruses, is ongoing mutation that can allow viruses to evade detection by diagnostic tests.
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SciScore for 10.1101/2021.08.13.21261995: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics Field Sample Permit: Specimens were collected and tested for SARS-CoV-2 infection as part of the Seattle Flu Study, as approved by the Institutional Review Board at the University of Washington (IRB#: STUDY0006181).
IRB: Specimens were collected and tested for SARS-CoV-2 infection as part of the Seattle Flu Study, as approved by the Institutional Review Board at the University of Washington (IRB#: STUDY0006181).
Consent: Informed consent was obtained for all participant samples, including for use of de-identified, remnant specimens.Sex as a biological variable not detected. Randomization Probe adapters and universal displacement probe sequences were generated from randomized sequence and … SciScore for 10.1101/2021.08.13.21261995: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics Field Sample Permit: Specimens were collected and tested for SARS-CoV-2 infection as part of the Seattle Flu Study, as approved by the Institutional Review Board at the University of Washington (IRB#: STUDY0006181).
IRB: Specimens were collected and tested for SARS-CoV-2 infection as part of the Seattle Flu Study, as approved by the Institutional Review Board at the University of Washington (IRB#: STUDY0006181).
Consent: Informed consent was obtained for all participant samples, including for use of de-identified, remnant specimens.Sex as a biological variable not detected. Randomization Probe adapters and universal displacement probe sequences were generated from randomized sequence and manually modified in Geneious, using OligoAnalyzer and NUPACK as secondary analysis tools, to minimize dimer and hairpin structures within and between the probes and adapted loop primers. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources Primer and IAC design: Three sets of LAMP primers (Table 1) targeting different regions of the SARS-CoV-2 nucleocapsid phosphoprotein were designed manually using the primer design feature of Geneious 8.1.9 (14) against the SARS-CoV-2 reference sequence (GenBank accession number: NC_045512). Geneioussuggested: (Geneious, RRID:SCR_010519)The IAC was designed using a composite primer technique (18) for LAMP. LAMPsuggested: (LAMP, RRID:SCR_001740)5µL of extracted RNA was added to the 15µL RT-PCR reaction mixture and subjected to 5 minutes at 55°C, 1 minutes of 94°C and 45 cycles of 1 second 94°C and 30 seconds at 57°C and read using FAM channel on a CFX96 (Bio-Rad Laboratories, Hercules, California). Bio-Rad Laboratoriessuggested: (Bio-Rad Laboratories, RRID:SCR_008426)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: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.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.
- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
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