A picture of the inside of the Crick during the COVID-19 crisis, emptied of researchers.

The Crick COVID19 Consortium

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

Intro

Last updated

27 April 2020

Welcome to the CRICK COVID19 Operations Team, a team of NHS trust virologists (University College London Hospitals), the NHS trust diagnostic laboratory (HSL), clinician scientists working at the both University College London Hospital NHS trust and the Crick, Crick scientists and Crick leadership.

Introduction

The CRICK COVID19 Consortium commenced on 19 March 2020 in response to the emerging COVID19 pandemic in a collaboration between University College London Hospitals, Health Services Laboratory (HSL), the Institute of Cancer Research and the Francis Crick Institute.

Over 2 weeks, the consortium has set up a high throughput RTPCR COVID19 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 has been to minimise dependencies on reagents, in short supply globally, to provide resilience to the pipeline and provide a scale-able platform to screen hundreds to thousands of healthcare workers and patients per day.

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

COVID19 testing approach

The COVID19 testing approach was developed from the outset as a partnership, and all processes have been established in the CRICK COVID19 diagnostic testing pipeline through close coordination with the NHS trust diagnostic laboratory. 

The Crick approach is based on five main work-streams, 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.

Columns

The Crick COVID19 testing pipeline

Method 16 Sample Tracking Pipeline (Added 29 May)

  • Sample reception

    Registration of WINPATH recorded samples to internal LIMS

     

  • Viral inactivation

    Swab inactivation using 5 M Guanidinium thiocyanate

    • Method 2 (Added 09 April, Updated 27 April)
  • Sample plating

    Automated transfer from individual 2ml tubes to 96-well plate

  • RNA Extraction

    Kit free method automated on Biomek FX

  • 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

    Analysis and reporting of RT-PCR results

    • Method 8 (Added 09 April, Updated 27 April, 11 May)

Download all SOPs

Download all available Standard Operating Procedures (16.86MB, pdf) (Added 09 April, Updated 27 April).

Download all SOPs

Further SOPs

Buffers
  • Method 9 Binding Buffer (Added 09 April, Updated 27 April)
  • Method 10 TET Buffer (Added 09 April, Updated 27 April)
  • Method 11 L6 Inactivation Buffer (Added 09 April, Updated 27 April, 11 May)
  • Method 12 0.1 M Tris HCl (Added 09 April, Updated 27 April, 11 May)
  • Method 13 5M NaOH (Added 09 April, Updated 27 April, 11 May, 29 May)
  • Method 14 0.2 M EDTA (Added 09 April, Updated 27 April, 11 May)
Procedure for virus inactivation being performed in a Category 2 facility
  • Method 15 (Added 09 April, Updated 27 April,11 May)

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