A role for Biofoundries in rapid development and validation of automated SARS-CoV-2 clinical diagnostics

Michael A Crone,Kirsten Jensen,Miles Priestman,Marko Storch,Arthi Anand,David J Sharp,Paul Randell,Marta Ciechonska,Paul S Freemont

doi:10.1038/s41467-020-18130-3

Abstract

The SARS-CoV-2 pandemic has shown how a rapid rise in demand for patient and community sample testing can quickly overwhelm testing capability globally. With most diagnostic infrastructure dependent on specialized instruments, their exclusive reagent supplies quickly become bottlenecks, creating an urgent need for approaches to boost testing capacity. We address this challenge by refocusing the London Biofoundry onto the development of alternative testing pipelines. Here, we present a reagent-agnostic automated SARS-CoV-2 testing platform that can be quickly deployed and scaled. Using an in-house-generated, open-source, MS2-virus-like particle (VLP) SARS-CoV-2 standard, we validate RNA extraction and RT-qPCR workflows as well as two detection assays based on CRISPR-Cas13a and RT-loop-mediated isothermal amplification (RT-LAMP). In collaboration with an NHS diagnostic testing lab, we report the performance of the overall workflow and detection of SARS-CoV-2 in patient samples using RT-qPCR, CRISPR-Cas13a, and RT-LAMP. The validated RNA extraction and RT-qPCR platform has been installed in NHS diagnostic labs, increasing testing capacity by 1000 samples per day.

Highlights

The severe acute respiratory syndrome (SARS)-CoV-2 pandemic has shown how a rapid rise in demand for patient and community sample testing can quickly overwhelm testing capability globally
We have been able to quickly repurpose automated liquid-handling infrastructure in the London Biofoundry to establish two frontline SARS-CoV-2 testing platforms, which are operational in two London hospitals with a testing capacity of 2000 samples per day
We have developed CRISPR and colorimetric LAMP-based workflows and have established a SARS-CoV-2 virus-like particle (VLP) standard, which has allowed us to validate the workflows within our biofoundry before implementation

Summary

Introduction

The SARS-CoV-2 pandemic has shown how a rapid rise in demand for patient and community sample testing can quickly overwhelm testing capability globally. With most diagnostic infrastructure dependent on specialized instruments, their exclusive reagent supplies quickly become bottlenecks, creating an urgent need for approaches to boost testing capacity We address this challenge by refocusing the London Biofoundry onto the development of alternative testing pipelines. Many research institutions around the world have established non-commercial Biofoundries, which offer integrated infrastructure including state-of-the-art automated high-throughput (HT) equipment to enable the design-build-test cycle for largescale experimental designs in synthetic biology[4] This infrastructure, in combination with technical expertise in molecular biology, analytics, automation, engineering, and software development, provides an excellent, self-sufficient, and agile capability to quickly establish platforms for prototyping biological testing standards and developing liquid-handling workflows, such as those needed for automated diagnostic testing of SARS-CoV-2. The particles contain the genomic RNA segment encoding the full-length N protein for validation using the N1, N2, and N3 primer–probe sets specified by the Centers for Disease Control and Prevention (CDC) 2019-Novel Coronavirus (2019-nCoV) real-time RT-PCR Diagnostic Panel[8,9]

Methods

Results

Conclusion