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Improving local prevalence estimates of SARS-CoV-2 infections using a causal debiasing framework

Nicholson, George; Lehmann, Brieuc; Padellini, Tullia; Pouwels, Koen B; Jersakova, Radka; Lomax, James; King, Ruairidh E; ... Holmes, Chris; + view all (2022) Improving local prevalence estimates of SARS-CoV-2 infections using a causal debiasing framework. Nature Microbiology , 7 (1) pp. 97-107. 10.1038/s41564-021-01029-0. Green open access

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Abstract

Global and national surveillance of SARS-CoV-2 epidemiology is mostly based on targeted schemes focused on testing individuals with symptoms. These tested groups are often unrepresentative of the wider population and exhibit test positivity rates that are biased upwards compared with the true population prevalence. Such data are routinely used to infer infection prevalence and the effective reproduction number, Rt, which affects public health policy. Here, we describe a causal framework that provides debiased fine-scale spatiotemporal estimates by combining targeted test counts with data from a randomized surveillance study in the United Kingdom called REACT. Our probabilistic model includes a bias parameter that captures the increased probability of an infected individual being tested, relative to a non-infected individual, and transforms observed test counts to debiased estimates of the true underlying local prevalence and Rt. We validated our approach on held-out REACT data over a 7-month period. Furthermore, our local estimates of Rt are indicative of 1-week- and 2-week-ahead changes in SARS-CoV-2-positive case numbers. We also observed increases in estimated local prevalence and Rt that reflect the spread of the Alpha and Delta variants. Our results illustrate how randomized surveys can augment targeted testing to improve statistical accuracy in monitoring the spread of emerging and ongoing infectious disease.

Type: Article
Title: Improving local prevalence estimates of SARS-CoV-2 infections using a causal debiasing framework
Location: England
Open access status: An open access version is available from UCL Discovery
DOI: 10.1038/s41564-021-01029-0
Publisher version: https://doi.org/10.1038/s41564-021-01029-0
Language: English
Additional information: © 2023 Springer Nature Limited. This article is licensed under a Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/).
UCL classification: UCL
UCL > Provost and Vice Provost Offices > UCL BEAMS
UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Maths and Physical Sciences
UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Maths and Physical Sciences > Dept of Statistical Science
URI: https://discovery.ucl.ac.uk/id/eprint/10184177
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