Maximising 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, minimising 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 Antha Empower the Use of Lab Automation During the COVID-19 Crisis?

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

Key benefits of Antha:

  • 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, minimising 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) optimisation – Rapid DoE optimisation 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 organisations

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

Antha in Action: Synthace and Cambridge Consultants

We have recently used Antha to execute the same automated qPCR protocol on three different liquid handling robots, manufactured by Gilson, Hamilton, and Tecan. With each device, Antha achieved high-fidelity consistent results, demonstrating protocol transferability and robustness [9]. Deploying Antha 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 utilised Antha for automating and optimising their qPCR assays. With Antha 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, Antha 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 minimise 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, Antha 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 Antha 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 Antha can empower qPCR automation by increasing its throughput, sensitivity, and robustness, join us for our live group demo on 3rd April (on demand recording coming soon).

To learn more about how Antha facilitated Cambridge Consultants’ work, check out our joint case study and register for our joint webinar on 14th April.

Synthace’s Response to COVID-19

Synthace is currently offering Antha pro bono to any teams and organisations working on COVID-19 therapeutics, diagnostics, and process scale-up. For more information, please read the message from our CEO and contact us at covid@synthace.com.

Antha is now available for remote/virtual deployment at our client companies. This minimises the need for site visits and face-to-face interactions, without bringing science to a halt. If you think you and your team could benefit from Antha, contact us to book a tailored demo at demo@synthace.com.

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