ROBOCOV: An affordable open-source robotic platform for SARS-CoV-2 testing by RT-qPCR

Abstract

Current global pandemic due to the SARS-CoV-2 has struggled and pushed the limits of global health systems. Supply chain disruptions and scarce availability of commercial laboratory reagents have motivated worldwide actors to search for alternative workflows to cope with the demand.We have used the OT-2 open-source liquid-handling robots (Opentrons, NY), RNA extraction and RT-qPCR reagents to set-up a reproducible workflow for RT-qPCR SARS-CoV-2 testing. We developed a framework with a template and several functions and classes that allow the creation of customized RT-qPCR automated circuits. As a proof of concept, we provide data obtained by a fully-functional tested code using the MagMax™ Pathogen RNA/DNA kit and the MagMax™ Viral/Pathogen II kit (Thermo Fisher Scientific, MA) on the Kingfisher™ Flex instrument (Thermo Fisher Scientific, MA). With these codes available is easy to create new stations or circuits from scratch, adapt existing ones to changes in the experimental protocol, or perform fine adjustments to fulfil special needs.The affordability of this platform makes it accessible for most laboratories and hospitals with a bioinformatician, democratising automated SARS-CoV-2 PCR testing and increasing, temporarily or not, the capacity of carrying out tests. It also confers flexibility, as this platform is not dependant on any particular commercial kit and can be quickly adapted to protocol changes or other special needs.

Robots Under COVID-19 Pandemic: A Comprehensive Survey

“…An ultra-high-throughput Mass Spectrometry (MS) platform [60] was developed for Clinical Proteomics; by conducting the sample pipetting and mixing with liquid handling robots, the workflow can handle up to 180 samples per day. In [61] , researchers used liquid-handling robots, RNA extraction and quantitative reverse transcription PCR (RT-qPCR) reagents to set-up a reproducible workflow for RT-qPCR SARS-CoV-2 testing. With automated SARS-CoV-2 PCR testing, increases in capacity and improvement in testing flexibility can be better adapted to future protocol changes.…”

Tracking SARS-CoV-2: Novel Trends and Diagnostic Strategies

“…The OT-2 has gained popularity in the scientific community day by day, thanks to its flexibility and affordability [280]. While the Felix and Echo 525 cost are in the order of hundreds of thousands of pounds, the customizable OT-2 costs between 5 and 15 thousand, depending on the selected configuration.…”

“…Researchers at the Biomedical Diagnostic Center (CBD) of the Hospital Clinic of Barcelona have developed an automated COVID-19 screening circuit named ROBOCOV, using four OT-2 robots from Opentrons, a KingFisher Flex extraction instrument from ThermoFisher, and an ABI 7500 qPCR device [280]. In this circuit, the initial setup, sample preparation, plate filling for RNA extraction, and qPCR mix preparation steps were carried out by four OT-2 robots while RNA extraction was performed by the KingFisher Flex and real-time qPCR process was done by the ABI 7500 qPCR device, as shown in Figure 6.…”

“…Initial sample setup, sample preparation, and plate filling are performed by OT-2 Station A, B1, and B2, respectively. RNA extraction is processed by KingFisher Flex [280]. Then, qPCR mic preparation is done by OT-2 Station C, and, finally, the qPCR process is run by ABI 7500 [280].…”

“…RNA extraction is processed by KingFisher Flex [280]. Then, qPCR mic preparation is done by OT-2 Station C, and, finally, the qPCR process is run by ABI 7500 [280]. The analysis results are exported as a user-friendly R file.…”