RT-PCR genotyping assays to identify SARS-CoV-2 variants in England in 2021: A design and retrospective evaluation study

Bray, Neil, Sopwith, Will, Edmunds, Matt, Vansteenhouse, Harper, Feenstra, Jelena D. M., Jacobs, Peter, Rajput, Kamal, O'Connell, Anne Marie, Smith, Melanie L., Blomquist, Paula, Hatziioanou, Diane, Elson, Richard ORCID: https://orcid.org/0000-0001-6350-5274, Vivancos, Roberto, Gallagher, Eileen, Wigglesworth, Mark J., Dominiczak, Anna, Hopkins, Susan and Lake, Iain R. ORCID: https://orcid.org/0000-0003-4407-5357 (2024) RT-PCR genotyping assays to identify SARS-CoV-2 variants in England in 2021: A design and retrospective evaluation study. The Lancet Microbe, 5 (2). e173-e180. ISSN 2666-5247

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Background: Whole-genome sequencing (WGS) is the gold standard diagnostic tool to identify and genetically characterise emerging pathogen mutations (variants), but cost, capacity, and timeliness limit its use when large populations need rapidly assessing. We assessed the potential of genotyping assays to provide accurate and timely variant information at scale by retrospectively examining surveillance for SARS-CoV-2 variants in England between March and September, 2021, when genotyping assays were used widely for variant detection. Methods: We chose a panel of four RT-PCR genotyping assays to detect circulating variants of SARS-COV-2 in England and developed a decision algorithm to assign a probable SARS-CoV-2 variant to samples using the assay results. We extracted surveillance data from the UK Health Security Agency databases for 115 934 SARS-CoV-2-positive samples (March 1–Sept 6, 2021) when variant information was available from both genotyping and WGS. By comparing the genotyping and WGS variant result, we calculated accuracy metrics (ie, sensitivity, specificity, and positive predictive value [PPV]) and the time difference between the sample collection date and the availability of variant information. We assessed the number of samples with a variant assigned from genotyping or WGS, or both, over time. Findings: Genotyping and an initial decision algorithm (April 10–May 11, 2021 data) were accurate for key variant assignment: sensitivities and PPVs were 0·99 (95% CI 0·99–0·99) for the alpha, 1·00 (1·00–1·00) for the beta, and 0·91 (0·80–1·00) for the gamma variants; specificities were 0·97 (0·96–0·98), 1·00 (1·00–1·00), and 1·00 (1·00–1·00), respectively. A subsequent decision algorithm over a longer time period (May 27–Sept 6, 2021 data) remained accurate for key variant assignment: sensitivities were 0·91 (95% CI 0·74–1·00) for the beta, 0·98 (0·98–0·99) for the delta, and 0·93 (0·81–1·00) for the gamma variants; specificities were 1·00 (1·00–1·00), 0·96 (0·96–0·97), and 1·00 (1·00–1·00), respectively; and PPVs were 0·83 (0·62–1·00), 1·00 (1·00–1·00), and 0·78 (0·59–0·97), respectively. Genotyping produced variant information a median of 3 days (IQR 2–4) after the sample collection date, which was faster than with WGS (9 days [8–11]). The flexibility of genotyping enabled a nine-times increase in the quantity of samples tested for variants by this method (from 5000 to 45 000). Interpretation: RT-PCR genotyping assays are suitable for high-throughput variant surveillance and could complement WGS, enabling larger scale testing for known variants and timelier results, with important implications for effective public health responses and disease control globally, especially in settings with low WGS capacity. However, the choice of panels of RT-PCR assays is highly dependent on database information on circulating variants generated by WGS, which could limit the use of genotyping assays when new variants are emerging and spreading rapidly. Funding: UK Health Security Agency and National Institute for Health Research Health Protection Research Unit in Emergency Preparedness and Response.

Item Type: Article
Additional Information: Data sharing: The UKHSA welcomes applications from organisations looking to use these data, and all applications will be rigorously reviewed using an objective, standards-based process. Potential applicants should contact DataAccess@ukhsa.gov.uk. Acknowledgments: This work was made possible by the UK Lighthouse Laboratories, their staff members (>6000 people), and Department of Health and Social Care (DHSC) funding between 2020 and 2021. We thank all members of the UKHSA Outbreak Surveillance Team who acted as a central information point to produce timely, accurate, and detailed surveillance reports to support the UK’s COVID-19 response and were central to much of the data used in this paper. We acknowledge the University of Glasgow for supporting in cash and kind the Glasgow Lighthouse Laboratory, which piloted the genotyping assays. RV is affiliated to the National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Emerging and Zoonotic Infections and the NIHR HPRU in Gastrointestinal Infections. SH is affiliated to the NIHR HPRU in Health Care Acquired Infections and Antimicrobial Resistance. IRL is funded by the NIHR HPRU in Emergency Preparedness and Response. AD was Director of the Lighthouse Laboratories and was co-funded by the DHSC then UKHSA and the University of Glasgow. The views expressed in this article are those of the author(s) and are not necessarily those of UK Health Security Agency, the Department of Health and Social Care, the National Health Service, or the National Institute for Health Research.
Uncontrolled Keywords: microbiology (medical),infectious diseases,virology,microbiology,sdg 3 - good health and well-being,4* ,/dk/atira/pure/subjectarea/asjc/2700/2726
Faculty \ School: Faculty of Science > School of Environmental Sciences
University of East Anglia Research Groups/Centres > Theme - ClimateUEA
UEA Research Groups: Faculty of Science > Research Groups > Environmental Social Sciences
University of East Anglia Schools > Faculty of Science > Tyndall Centre for Climate Change Research
Faculty of Science > Research Centres > Tyndall Centre for Climate Change Research
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Depositing User: LivePure Connector
Date Deposited: 02 Dec 2023 03:32
Last Modified: 04 Mar 2024 18:20
URI: https://ueaeprints.uea.ac.uk/id/eprint/93849
DOI: 10.1016/S2666-5247(23)00320-8


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