Implementation of an open-source robotic platform for SARS-CoV-2 testing by real-time RT-PCR
Open Access
- 14 July 2021
- journal article
- research article
- Published by Public Library of Science (PLoS) in PLOS ONE
- Vol. 16 (7), e0252509
- https://doi.org/10.1371/journal.pone.0252509
Abstract
The current global pandemic due to the SARS-CoV-2 has pushed the limits of global health systems across all aspects of clinical care, including laboratory diagnostics. Supply chain disruptions and rapidly-shifting markets have resulted in flash-scarcity of commercial laboratory reagents; this has motivated health care providers to search for alternative workflows to cope with the international increase in demand for SARS-CoV-2 testing. The aim of this study is to present a reproducible workflow for real time RT-PCR SARS-CoV-2 testing using OT-2 open-source liquid-handling robots (Opentrons, NY). We have developed a framework that includes a code template which is helpful for building different stand-alone robotic stations, capable of performing specific protocols. Such stations can be combined together to create a complex multi-stage workflow, from sample setup to real time RT-PCR. Using our open-source code, it is easy to create new stations or workflows from scratch, adapt existing templates to update the experimental protocols, or to fine-tune the code to fit specific needs. Using this framework, we developed the code for two different workflows and evaluated them using external quality assessment (EQA) samples from the European Molecular Genetics Quality Network (EMQN). The affordability of this platform makes automated SARS-CoV-2 PCR testing accessible for most laboratories and hospitals with qualified bioinformatics personnel. This platform also allows for flexibility, as it is not dependent on any specific commercial kit, and thus it can be quickly adapted to protocol changes, reagent, consumable shortages, or any other temporary material constraints.This publication has 10 references indexed in Scilit:
- Evaluation of two automated low-cost RNA extraction protocols for SARS-CoV-2 detectionPLOS ONE, 2021
- Optimización y adecuación de la capacidad diagnóstica para la realización de grandes volúmenes de RT-PCR de SARS-CoV-2Enfermedades Infecciosas y Microbiología Clínica, 2021
- Scalable and robust SARS-CoV-2 testing in an academic centerNature Biotechnology, 2020
- Presymptomatic SARS-CoV-2 Infections and Transmission in a Skilled Nursing FacilityThe New England Journal of Medicine, 2020
- Asymptomatic Transmission, the Achilles’ Heel of Current Strategies to Control Covid-19The New England Journal of Medicine, 2020
- Leveraging open hardware to alleviate the burden of COVID-19 on global health systemsPLoS Biology, 2020
- In Vitro Diagnostic Assays for COVID-19: Recent Advances and Emerging TrendsDiagnostics, 2020
- Evaluation of a quantitative RT-PCR assay for the detection of the emerging coronavirus SARS-CoV-2 using a high throughput systemEurosurveillance, 2020
- A new coronavirus associated with human respiratory disease in ChinaNature, 2020
- Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCREurosurveillance, 2020