Rapid Development of COVID-19 Diagnostic Assay

The Challenge

Early on during the COVID-19 pandemic, supply chain shortages were hamstringing diagnostic efforts and hindering the ability to track and curb the spread of the disease. Dr. Paul Freemont, Professor of Synthetic Biology and Co-Director of the London Biofoundry, witnessed his colleagues struggling to access reagents as early as February. Additionally, reagent allocation by the central government was limited to only 34,000 tests per week and often limited to a single reagent supplier and their specific testing platform.

Freemont decided to co-opt a diagnostic assay developed by his graduate student Michael Crone to provide what was desperately needed: a robust, validated assay agnostic to reagents and liquid handling instruments. This would allow test centers to mix and match instruments and reagents as available and relieve bottlenecks due to supply shortages.

The Outcome

Using different combinations of instruments, robots, reagents, and experiment design and analysis software, Crone and his colleagues at the London Biofoundry quickly developed several open-access high throughput workflows for testing hundreds to thousands of samples with a 24-hour turnaround.

Crone used virus-like particles (VLPs) he had previously developed and engineered them to contain RNA sequences complementary to the SARS-CoV-2 N protein primer pair sets specified by the CDC 2019-Novel Coronavirus (2019-nCoV) Real-Time RT-PCR Diagnostic Panel to test his protocols without risk of infection. The biggest hurdles faced while testing different liquid handling robots and reagents were differences in capacity on the different liquid handling robots. Crone used Riffyn Nexus and JMP software to set up and track well randomizations and plate transfers to speed up the process of testing and validating each robot and reagent combination.

Once the assays were validated using VLPs, they were validated using patient samples, accessed via a collaboration with the U.K. National Health Service (NHS). The NHS immediately added Crone’s workflow to their assay suite, rapidly scaling testing capacity one weekend when over 600 samples were run in just under 12 hours — by only two people.

Now, the NHS is in the process of buying more instrumentation so they can increase capacity to 3000 samples per day on robots running 24/7 using Crone’s assay workflow. To further raise testing capacity, the Biofoundry team is designing new workflows using Riffyn Nexus’ workflow design and sample tracking. This will facilitate the implementation of pooling approaches that will have manifold impact on testing capacity.

The results of this work were published in September in Nature Communications.

Read more of the story in this first-person account by Michael Crone.