The Crick COVID-19 Consortium

A partnership between The Francis Crick Institute, Health Services Laboratory (HSL), Institute of Cancer Research and University College London Hospital NHS Trust.

Last updated

1 July 2020

The Crick COVID-19 Operations Team: a team of NHS virologists from University College London Hospital NHS Foundation Trust (UCLH), the NHS trust diagnostic laboratory (Health Services Laboratories), clinician scientists working at both UCLH and the Crick, Crick scientists, and Crick leadership.

Introduction

The Crick COVID-19 Consortium commenced on 19 March 2020 in response to the emerging COVID-19 pandemic in a collaboration between University College London Hospitals NHS Foundation Trust, Health Services Laboratories (HSL), the Institute of Cancer Research and the Francis Crick Institute.

Over two weeks, the consortium set up a high throughput RT-PCR COVID-19 diagnostics assay in an academic environment. The work is conducted at the Francis Crick Institute as an extension of the accredited laboratories at HSL. The aim was to been to minimise dependencies on reagents, in short supply globally, to provide resilience to the pipeline and provide a scaleable platform to screen hundreds to thousands of healthcare workers and patients per day.

The downloadable Standard Operating Procedures (SOPs) provide a step-by-step approach to set up a diagnostic pipeline in an academic institute in collaboration with partner laboratories and hospital trusts.

COVID-19 testing approach

The COVID-19 testing approach was developed from the outset as a partnership, and all processes were established in the Crick COVID-19 diagnostic testing pipeline through close coordination with the NHS trust diagnostic laboratory. 

The Crick approach was based on five main workstreams, that were developed and tested independently, and are therefore largely standalone. The approach relies on highly trained research staff to support a semi-automated, but not highly integrated, pathway. The advantage is that the approach is agile and can make use of lab-space distributed across a research institution. Such a set-up is highly dependent on shift-work to maximise sample throughput, particularly with respect to sample reception, tracking and viral inactivation.

Download the SOPs

COVID testing pipeline workflow

Sample reception

  • Method 1 Registration of WINPATH recorded samples to internal LIMS (Added 27 April) 

Viral inactivation

  • Method 2 Swab inactivation using 5 M Guanidinium thiocyanate (Added 09 April, Updated 27 April)

Sample plating

  • Method 3 Automated transfer from individual 2ml tubes to 96-well plate (Added 09 April, Updated 27 April)

RNA extraction

  • Method 4 Kit free method automated on Biomek FX (Added 09 April, Updated 27 April)

RT-PCR: SARS-CoV-2 detection using BGI kit

  • Method 5 Master-mix plate preparation (Added 09 April, Updated 27 April)
  • Method 6 RNA transfer (Added 09 April, Updated 27 April)
  • Method 7 RT-PCR setup (Added 27 April)

Reporting

  • Method 8 Analysis and reporting of RT-PCR results (Added 09 April, Updated 27 April, 11 May)

Further SOPs

Buffers

  • Method 9 Binding Buffer (Added 9 April 2020; updated 27 April 2020)
  • Method 10 TET Buffer (Added 9 April 2020; updated 27 April 2020)
  • Method 11 L6 Inactivation Buffer (Added 9 April 2020; updated 27 April, 11 May)
  • Method 12 0.1 M Tris HCl (Added 9 April 2020; updated 27 April 2020, 11 May 2020)
  • Method 13 5M NaOH (Added 9 April 2020; updated 27 April 2020, 11 May 2020, 29 May 2020)
  • Method 14 0.2 M EDTA (Added 9 April 2020; updated 27 April 2020, 11 May 2020)

Procedure for virus inactivation being performed in a Category 2 facility

  • Method 15 (Added 9 April 2020, updated 27 April 2020, 11 May 2020)

Procedure for sample tracking pipeline

  • Method 16 Sample Tracking Pipeline (Added 29 May 2020)

Download all SOPs

Download all SOPs (Added 9 April 2020; updated 27 April 2020, 8 June 2020)

RT-LAMP SOPs