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Characterising the Persistence of RT-PCR Positivity and Incidence in a Community Survey of SARS-CoV-2
Eales et al. (2022) Wellcome Open Research 7102
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Authors:
O Eales, CE Walters, H Wang, D Haw, KEC Ainslie, CJ Atchison, AJ Page, S Prosolek, AJ Trotter, T Le Viet, NF Alikhan, LM Jackson, C Ludden, COVID-19 Genomics UK Consortium, D Ashby, CA Donnelly, G Cooke, W Barclay, H Ward, A Darzi, P Elliott, S Riley
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.