Improving the efficiency and effectiveness of an industrial SARS-CoV-2 diagnostic facility

Julie A Douthwaite,Fred Kuenzi,David J Nicholls,Paula M Allen,David G Tew,Roger Clark,Abigail Marklew,Charlotte A Ashby,Penny A Smee,Abhishek Upadhyay,Anna Cuthbert,Christopher Brankin,Simon Fish,Patrick H Maxwell,Craig Hewitt,Oona Delpuech,Shane Weaver,Ruud M Dewildt,Matthieu Chodorge,Julian D Phipps,John R Ferdinand,Menelas N Pangalos,Ian Richards,Joost Van Kempen,Stuart M Baddeley,Jon G Bartlett,Chris Abell,Steve Rees,Jane Elliott,Molly A Taylor,Alexandra L Orton,Rob Howes,Nalini Mehta,Andy Neely,Hannah Duvoisin,David Brierley ,Ian Goodfellow ,Giles S Ratcliffe ,Emma Koppe ,Christopher Brown ,Douglas Ross‐Thriepland ,Gareth J Browne ,Ian D Waddell ,Thomas M Hill ,Melanie Leveridge ,Palwinder K Mander,Haidee Pitt,Rahul Sharma,Nancy T Malintan,Clive Green

doi:10.1038/s41598-022-06873-6

Abstract

On 11th March 2020, the UK government announced plans for the scaling of COVID-19 testing, and on 27th March 2020 it was announced that a new alliance of private sector and academic collaborative laboratories were being created to generate the testing capacity required. The Cambridge COVID-19 Testing Centre (CCTC) was established during April 2020 through collaboration between AstraZeneca, GlaxoSmithKline, and the University of Cambridge, with Charles River Laboratories joining the collaboration at the end of July 2020. The CCTC lab operation focussed on the optimised use of automation, introduction of novel technologies and process modelling to enable a testing capacity of 22,000 tests per day. Here we describe the optimisation of the laboratory process through the continued exploitation of internal performance metrics, while introducing new technologies including the Heat Inactivation of clinical samples upon receipt into the laboratory and a Direct to PCR protocol that removed the requirement for the RNA extraction step. We anticipate that these methods will have value in driving continued efficiency and effectiveness within all large scale viral diagnostic testing laboratories.

Highlights

Following the declaration of SARS-CoV-2 as a pandemic by the World Health Organisation on 11th March 20201, governments across the world announced unprecedented measures to mitigate the spread of the virus through their populations
The Cambridge COVID-19 Testing Centre (CCTC) is unique in many ways to other local and national COVID-19 diagnostic laboratories, as in addition to processing the normal single swab samples, the centre evolved a process for pooled patient swab samples from the University of Cambridge Asymptomatic Testing Programme for its s tudents[13,14] and testing of staff samples from the local NHS Trust hospital (Addenbrooke’s Hospital—the largest in the East of England)
The critical first step in this journey was to establish and agree Key Performance Indicators (KPI) setting a baseline against which to measure performance. These KPI focused on four areas: 1. Quality In-Process (IP) void rate ≤ 0.5% of samples voided through process errors in the laboratory 2

Summary

Introduction

Following the declaration of SARS-CoV-2 as a pandemic by the World Health Organisation on 11th March 20201, governments across the world announced unprecedented measures to mitigate the spread of the virus through their populations. Initial deployment with a focus on rapidly expanding capacity meant that the CCTC adopted the standard RT-qPCR process already established in many facilities, but from the outset condensed the PCR reaction into a 384-well format, thereby reducing the PCR machine requirement by fourfold. Whilst this assay process delivered high quality in a robust manner there was still room for continued optimisation in terms of efficiency. All partners worked together thereafter to further develop technologies and iteratively improve performance as an analytical facility

Methods

Results

Conclusion