Corona Detective: a simple, scalable, and robust SARS-CoV-2 detection method based on reverse transcription loop-mediated isothermal amplification

Abstract

Surveillance screening at scale to identify people infected by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) prior to extensive transmission is key to bringing an end to the coronavirus disease 2019 (COVID-19) pandemic, even though vaccinations have already begun. Here we describe Corona Detective, a sensitive and rapid molecular test to detect the virus, based on loop-mediated isothermal amplification, which could be applied anywhere at low cost. Critically, the method uses freeze-dried reagents, readily shipped without coldchain dependence. The reaction detects the viral nucleocapsid gene through a sequence-specific quenched-fluorescence readout, which avoids false positives and also allows multiplex detection with an internal control cellular RNA. Corona Detective can be used in 8-tube strips to be read with a simple open-design fluorescence detector. Other methods to use and produce Corona Detective locally in a variety of formats are possible and already openly shared. Detection specificity is ensured through inclusion of positive and negative control reactions to run in parallel with the diagnostic reactions. A simple user protocol, including sample preparation, and a bioinformatics pipeline to ensure that viral variants will still be detectable with SARS-CoV-2 primer sets complete the method. Through rapid production and distribution of Corona Detective reactions, quite inexpensive at scale, daily or weekly surveillance testing of large populations, without waiting for symptoms to develop, is anticipated, in combination with vaccination campaigns, to finally control this pandemic.

Community review: a robust and scalable selection system for resource allocation within open science and innovation communities

“…The speed and cost-efficiency of the community review process has allowed for a reactive response to the high-pressure environment created by the pandemic. This agility has meant that within the short time frame given, projects have been able to produce literature, methods and hardware and put them to use (21)(22)(23)(24)(25)(26). Overall, the community review system allows for a rapid, agile, iterative, distributed and scalable review process for volunteer action and micro-grant attribution.…”

Community review: a robust and scalable selection system for resource allocation within open science and innovation communities

“…This agility has meant that within the short time frame given, projects have been able to produce literature, methods and hardware and put them to use. [23][24][25][26][27][28] Overall, the community review system allows for a rapid, agile, iterative, distributed and scalable review process for volunteer action and micro-grant attribution. It is particularly suited for open research and innovation communities collaborating in a decentralized manner and looking for ways to distribute common resources fairly and swiftly.…”

Open Educational Resources for distributed hands-on teaching in molecular biology

“…This open hardware device facilitates PCR reactions through precise, easily adjustable temperature cycles, and can be powered by a standard USB/USB-C charger, making it ideal for use outside traditional laboratory settings. Concurrently, better access to public domain DNA plasmids encoding for diagnostic enzymes has surged during the pandemic [30][31][32][33][34]. For instance, the FreeGenes project and ReClone network have engaged researchers around the globe who share DNA plasmids encoding these off-patent enzymes and protocols for their local production [35].…”

“…We focus on detecting the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) for two main reasons: first, the students' motivation for learning about the virus causing the COVID19 pandemic; and second, the availability of low-cost and open-access RT-PCR reagents for SARS-CoV-2 detection, a result of ongoing local initiatives (e.g. [30][31][32][33][34]). The crucial role of SARS-CoV-2 RNA detection in COVID-19 diagnostics has underscored the relevance of this technique.…”