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    April 2, 2020

    Maximizing qPCR Output During COVID-19 Pandemic

    • Diagnostic tests for COVID-19 rely on qPCR

    • There is a global need to diagnose people quicker and more extensively

    • High pressure on lab scientists creates potential for human error and misdiagnoses

    • Automating qPCR could alleviate the burden on scientists and clinicians

    • Effective use of lab automation will speed up testing and help combat the COVID-19 crisis

    As the world battles the COVID-19 pandemic and health systems face increasingly unsustainable caseloads, there is a pressing need for faster and more extensive testing. Improved testing will allow us to diagnose the infection and isolate patients sooner, reducing the spread of the virus [1, 2]. In the race to flatten the curve, every second counts.

    Here we discuss the use of quantitative PCR (qPCR) for COVID-19 diagnostics and how lab automation can help scientists and clinicians realise the full potential of this technique.

    qPCR and COVID-19 Testing

    qPCR is a powerful molecular biology technique that has a range of important applications. It has been widely used for COVID-19 testing and is considered the gold standard clinical test due to its ability to accurately detect viral RNA in patient samples [3].

    However, an average qPCR test takes around 1-2 days [3], and the availability of lab staff, qPCR equipment, and other resources is limited. This makes the scale-up of testing especially challenging. Many people experiencing COVID-19 symptoms cannot get tested, including frontline medical staff, while those who do might wait for up to a week to receive the results as their samples are in the queue [4, 5].

    Moreover, qPCR involves a lot of manual pipetting by scientists, which becomes laborious and repetitive after a long day in the lab. That, along with the pressure of testing a large number of samples very quickly, creates the potential for human error, such as inaccurate pipetting or sample contamination. These invalidate the results, and the assays need to be re-run. Contamination can also lead to false positive or false negative results and in turn misdiagnoses [6, 7]. All of this causes further delays and significant resource losses.

    How Can Lab Automation Increase qPCR Efficiency?

    One way of facilitating qPCR testing is lab automation. For example, manual pipetting can be replaced with automated liquid handling robots. This will alleviate the burden on lab staff and free them up to do other things, like sample preparation or data analysis. In addition, manual interaction will be reduced, minimizing the potential for human error.

    Automation also increases throughput and reduces the time from data to insight. Therefore, automated qPCR can speed up COVID-19 testing and enable its scale-up during the pandemic.

    However, automation has a few important challenges that limit its use in labs. Most automation devices are supported by vendor software that requires advanced coding skills and extensive training. Also, most automation protocols lack flexibility and transferability, i.e. they are specific to a single device only. If the device is in use, the protocol needs to be queued.

    Modifying the protocol for another device is no-less time-consuming due to the specificities of all the different vendor software. Yet, given how quickly things are changing, we must be able to quickly modify qPCR protocols depending on the availability of lab equipment, reagents, and other resources.

    Furthermore, labs that develop their own qPCR protocols or make significant changes to existing protocols must validate them for clinical use. But with the limited amount of viral material available, this is yet another challenge [8].

    How Can Synthace Empower the Use of Lab Automation During the COVID-19 Crisis?

    We have developed our software platform to empower biologists to use automation in their labs. Compatible with a range of devices, the Synthace platform helps overcome the aforementioned challenges and increases the efficiency of automation even further. By maximizing the efficiency of automated qPCR, it can help combat the COVID-19 crisis.

    Key benefits:

    • Transferability – Protocols can be transferred across different devices, allowing labs to quickly scale up testing

    • Flexibility – Protocols can be easily modified if there is a change in available resources

    • Robustness – Protocols are robust and maintain high assay sensitivity with effective contamination control, minimizing the chances of false positive/negative results and misdiagnoses

    • Sample provenance – Samples are tracked throughout the experiment, avoiding human error in data recording which can also lead to false positive/negative results

    • In silico simulation – Any errors in the protocol can be identified and fixed prior to execution, ensuring experimental success and saving valuable resources otherwise wasted on trial runs

    • Design of Experiments (DoE) optimization – Rapid DoE optimization of protocols helps to speed up assay validation, while reducing the amount of viral material needed

    • Cloud environment – This facilitates data sharing between groups and organizations

    • Ease of use – it does not require any coding skills or extensive training and is easy to deploy

    The Platform in Action: Synthace and Cambridge Consultants

    We have recently used the Synthace platform to execute the same automated qPCR protocol on three different liquid handling robots, manufactured by Gilson, Hamilton, and Tecan. With each device, it achieved high-fidelity consistent results, demonstrating protocol transferability and robustness [9]. Deploying the Synthace platform in labs that specialise in COVID-19 testing would enable seamless transfer of qPCR protocols across different devices, allowing for an easy and reliable process scale-up.

    Cambridge Consultants have also utilized it for automating and optimizing their qPCR assays. With the Synthace platform, they could process a 384-well plate in 2 hours, with just 25 minutes of hands-on time. That is an 81% time saving compared to manual assays. At this rate, up to four 384-well plates can be processed each day. In addition, it achieved 50% higher throughput compared to manual assays [10].

    Such increase in throughput and reduction in assay time can make COVID-19 testing more efficient, enabling us to get the results quicker and scale up the process to fit the current demand. The significant reduction in hands-on time will minimize the potential for human error and allow lab scientists to dedicate more time for things like data analysis and sample preparation.

    Cambridge Consultants also reported less background contamination and higher target DNA signals in their qPCR samples [10]. This demonstrates improved assay sensitivity that is crucial for diagnostics.

    Therefore, the Synthace platform enables flexible automation of sophisticated lab protocols, increasing their transferability, robustness and throughput, whilst simultaneously reducing hands-on time and the potential for human error. Utilising it to automate qPCR for COVID-19 diagnostics would enable faster, more reliable, and more extensive testing that would reduce the burden on health systems and help countries respond to the pandemic more effectively.

    To learn more about how the Synthace platform can empower qPCR automation by increasing its throughput, sensitivity, and robustness, request a demo.

     

    Tag(s): Lab Automation

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