Design and Implementation of An Adaptive Pooling Workflow for SARS-CoV-2 Testing in an NHS Diagnostic Laboratory

18 Pages Posted: 1 Apr 2021 Last revised: 14 Apr 2021

See all articles by Michael Crone

Michael Crone

Imperial College London - Section of Structural and Synthetic Biology; Imperial College London - London Biofoundry; UK Dementia Research Institute - Care Research and Technology Centre

Paul Randell

North West London Pathology

Zoey Herm

Riffyn, Inc.

Saghar Missaghian-Cully

North West London Pathology

Loren Perelman

Riffyn, Inc.

Panagiotis Pantelidis

North West London Pathology

Paul Freemont

Imperial College London - London Biofoundry

Multiple version iconThere are 2 versions of this paper

Date Written: March 6, 2021

Abstract

Background: Diagnostic laboratories are currently required to provide routine testing of asymptomatic staff and patients as a part of their clinical screening for SARS-CoV-2 infection. However, these cohorts display very different disease prevalence from symptomatic individuals and testing capacity for asymptomatic screening is often limited. Group testing is frequently proposed as a possible solution to address this; however, proposals neglect the technical and operational feasibility of implementation in a front-line diagnostic laboratory.

Methods: Between October and December 2020, as a 7-week proof of concept, we took into account scientific, technical and operational feasibility to design and implement an adaptive pooling strategy in an NHS diagnostic laboratory in London (UK). We assessed the impact of pooling on analytical sensitivity and modelled the impact of prevalence on pooling strategy. We then considered the operational constraints to model the potential gains in capacity and the requirements for additional staff and infrastructure. Finally, we developed a LIMS-agnostic laboratory automation workflow and software solution and tested the technical feasibility of our adaptive pooling workflow.

Findings: First, we determined the analytical sensitivity of the implemented SARS-CoV-2 assay to be 250 copies/mL. We then determined that, in a setting with limited analyser capacity, the testing capacity could be increased by two-fold with pooling, however, in a setting with limited reagents, this could rise to a five-fold increase. These capacity increases could be realized with modest additional resource and staffing requirements whilst utilizing up to 76% fewer plastic consumables and 90% fewer reagents. Finally, we successfully implemented a plate-based pooling workflow and tested 920 patient samples using the reagents that would usually be required to process just 222 samples.

Interpretation: Adaptive pooled testing is a scientifically, technically and operationally feasible solution to increase testing capacity in frontline NHS diagnostic laboratories.
Funding: NHS England

Note: Funding Statement: This work was supported by funding from NHS England.

Declaration of Interests: ZH and LAP are employed by Riffyn, Inc. MAC and PSF are consultants for Analytik Jena. All the other authors declare no competing interests.

Keywords: diagnostics, SARS-CoV-2, pooling

Suggested Citation

Crone, Michael and Randell, Paul and Herm, Zoey and Missaghian-Cully, Saghar and Perelman, Loren and Pantelidis, Panagiotis and Freemont, Paul, Design and Implementation of An Adaptive Pooling Workflow for SARS-CoV-2 Testing in an NHS Diagnostic Laboratory (March 6, 2021). Available at SSRN: https://ssrn.com/abstract=3799293 or http://dx.doi.org/10.2139/ssrn.3799293

Michael Crone (Contact Author)

Imperial College London - Section of Structural and Synthetic Biology ( email )

Department of Infectious Disease
London, SW7 2AZ
United Kingdom

Imperial College London - London Biofoundry ( email )

Translation and Innovation Hub
84 Wood Lane
London, W12 0BZ
United Kingdom

UK Dementia Research Institute - Care Research and Technology Centre ( email )

Imperial College London
London
United Kingdom

Paul Randell

North West London Pathology ( email )

United Kingdom

Zoey Herm

Riffyn, Inc. ( email )

484 9th Street
Oakland, CA 94607
United States

Saghar Missaghian-Cully

North West London Pathology ( email )

United Kingdom

Loren Perelman

Riffyn, Inc. ( email )

484 9th Street
Oakland, CA 94607
United States

Panagiotis Pantelidis

North West London Pathology ( email )

United Kingdom

Paul Freemont

Imperial College London - London Biofoundry ( email )

Translation and Innovation Hub
84 Wood Lane
London, W12 0BZ
United Kingdom

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