1. Characterising the persistence of RT-PCR positivity and incidence in a community survey of SARS-CoV-2
- Author
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Eales, O, Walters, CE, Wang, H, Haw, D, Ainslie, KEC, Atchison, CJ, Page, AJ, Prosolek, S, Trotter, AJ, Le Viet, T, Alikhan, N-F, Jackson, LM, Ludden, C, Ashby, D, Donnelly, CA, Cooke, G, Barclay, W, Ward, H, Darzi, A, Elliott, P, Riley, S, Department of Health, and The Huo Family Foundation UK Limited
- Subjects
viruses ,virus diseases ,Medicine (miscellaneous) ,biochemical phenomena, metabolism, and nutrition ,digestive system diseases ,General Biochemistry, Genetics and Molecular Biology - Abstract
Background: The REal-time Assessment of Community Transmission-1 (REACT-1) study has provided unbiased estimates of swab-positivity in England approximately monthly since May 2020 using RT-PCR testing of self-administered throat and nose swabs. However, estimating infection incidence requires an understanding of the persistence of RT-PCR swab-positivity in the community. Methods: During round 8 of REACT-1 from 6 January to 22 January 2021, we collected up to two additional swabs from 896 initially RT-PCR positive individuals approximately 6 and 9 days after their initial swab. Results: Test sensitivity and duration of positivity were estimated using an exponential decay model, for all participants and for subsets by initial N-gene cycle threshold (Ct) value, symptom status, lineage and age. A P-spline model was used to estimate infection incidence for the entire duration of the REACT-1 study. REACT-1 test sensitivity was estimated at 0.79 (0.77, 0.81) with median duration of positivity at 9.7 (8.9, 10.6) days. We found greater duration of positivity in those exhibiting symptoms, with low N-gene Ct values, or infected with the Alpha variant. Test sensitivity was found to be higher for those who were pre-symptomatic or with low N-gene Ct values. Compared to swab-positivity, our estimates of infection incidence included sharper features with evident transient increases around the time of changes in social distancing measures. Conclusions: These results validate previous efforts to estimate incidence of SARS-CoV-2 from swab-positivity data and provide a reliable means to obtain community infection estimates to inform policy response.
- Published
- 2022
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