Scalable and Resilient SARS-CoV-2 testing in an Academic Centre

Abstract

The emergence of the novel coronavirus SARS-CoV-2 has led to a pandemic infecting more than two million people worldwide in less than four months, posing a major threat to healthcare systems. This is compounded by the shortage of available tests causing numerous healthcare workers to unnecessarily self-isolate. We provide a roadmap instructing how a research institute can be repurposed in the midst of this crisis, in collaboration with partner hospitals and an established diagnostic laboratory, harnessing existing expertise in virus handling, robotics, PCR, and data science to derive a rapid, high throughput diagnostic testing pipeline for detecting SARS-CoV-2 in patients with suspected COVID-19. The pipeline is used to detect SARS-CoV-2 from combined nose-throat swabs and endotracheal secretions/ bronchoalveolar lavage fluid. Notably, it relies on a series of in-house buffers for virus inactivation and the extraction of viral RNA, thereby reducing the dependency on commercial suppliers at times of global shortage. We use a commercial RT-PCR assay, from BGI, and results are reported with a bespoke online web application that integrates with the healthcare digital system. This strategy facilitates the remote reporting of thousands of samples a day with a turnaround time of under 24 hours, universally applicable to laboratories worldwide.

Overcoming the bottleneck to widespread testing: a rapid review of nucleic acid testing approaches for COVID-19 detection

“…To address the dire need for increased testing, researchers across disciplines have quickly compared widely available commercial products, proposed repurposing existing reagents and infrastructure, and created novel laboratory solutions to optimize the COVID-19 testing pipeline. Academic researchers at a few institutions around the world have published detailed blueprints for establishing local pop-up testing centers, and others are likely to follow (Consortium and Doudna 2020;Sridhar et al 2020;Aitken et al 2020). A combination of testing approaches may be the most efficient way to fill the current gaps in testing.…”

“…Many protocols use commercial reagents for lysis, including DNA/RNA Shield (Zymo Research), Buffer RLT (Qiagen), and MagNA Pure External Lysis Buffer (Roche). However, multiple researchers have recently found that when compared to commercial solutions, homemade solutions containing 4M (Scallan et al 2020;Sridhar et al 2020) or 5M (Aitken et al 2020) guanidinium thiocyanate work equally well to lyse samples and recover viral RNA after purification. However, these solutions contain strong denaturants and are therefore not compatible with addition directly into amplification reactions.…”

Standard operating procedures for SARS-CoV-2 detection by a clinical diagnostic RT-LAMP assay

“…All the samples processing through the CCC pipeline was done in accordance with SOPs described recently 5 . A redefined reaction, running, and reporting SOP can be found in the Supplemental Methods.…”

“…An initial characterization of the technique was performed using 24 RNA samples purified from patient nasopharyngeal swabs, 12 of which were positive for SARS-CoV-2 as assessed by the CCC pipeline via RT-qPCR 5 . RT-LAMP could detect SARS-CoV-2 in the 12 positive samples with no amplification detected in all 12 negative samples, displaying 100% concordance to our current clinical diagnostic platform ( Figures 1C and 1E).…”

CONTAIN: An open-source shipping container laboratory optimised for automated COVID-19 diagnostics

“…The RNA extraction process employs the open-source Bio-On-Magnetic-Bead (BOMB) protocol, which uses DIY reagents and is amenable to automation 21,22 . The use of open-source hardware and reagents allow labs to navigate around limited supply chains 23 . The OT-2 liquid handling robot has a low initial cost relative to other liquid handling robots, can utilise generic plasticware and run protocols written in the coding language Python 24,25 .…”