A high-throughput strategy for COVID-19 testing based on next-generation sequencing
This article has been Reviewed by the following groups
Listed in
- Evaluated articles (ScreenIT)
Abstract
COVID-19 testing as sufficient as needed is essential for healthcare workers, patients, and authorities to make informed decisions to confront and eventually defeat severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Currently, diagnosis of COVID-19 relies on quantitative reverse-transcription PCR, which is low-throughput, laborious, and often false-negative, making it overwhelmingly challenging to meet testing needs even in industrialized countries. Here we propose a new strategy, which employs a modified loop-mediated isothermal amplification (LAMP) assay, a simple procedure requiring no sophisticated instruments, to index and amplify viral genes from individual specimens, of which the products are readily available for construction of multiplexed libraries for next-generation sequencing. Our strategy would allow precise diagnosis of thousands of specimens in 1-2 days with significantly lower operating expenses. Furthermore, this strategy will make it possible for patients to collect, process, and mail their own samples to facilities for a quick, reliable diagnosis at a population scale.
Article activity feed
-
SciScore for 10.1101/2020.06.12.20129718: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization The primer sequences for LAMP reaction were designed using PrimerExplorer V5 (https://primerexplorer.jp) to target the same area in the N gene of SARS-CoV-2 targeted by the CDC-designed N2 RT-PCR assay, with the introduction of PstI or HindIII sites and randomized six bases (Supplemental Figure 1). Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources LAMP reactions: LAMP reactions were performed using the WarmStart LAMP Kit (DNA & RNA) (New England Biolabs, E1700S) according to the manufacturer’s instruction. LAMPsuggested: (LAMP, RRID:SCR_0017…SciScore for 10.1101/2020.06.12.20129718: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization The primer sequences for LAMP reaction were designed using PrimerExplorer V5 (https://primerexplorer.jp) to target the same area in the N gene of SARS-CoV-2 targeted by the CDC-designed N2 RT-PCR assay, with the introduction of PstI or HindIII sites and randomized six bases (Supplemental Figure 1). Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources LAMP reactions: LAMP reactions were performed using the WarmStart LAMP Kit (DNA & RNA) (New England Biolabs, E1700S) according to the manufacturer’s instruction. 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: 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.
-
