Characterising the persistence of RT-PCR positivity and incidence in a community survey of SARS-CoV-2

• Published in: Wellcome open research Vol. 7; p. 102
• Main Authors: Eales, Oliver, Walters, Caroline E., Wang, Haowei, Haw, David, Ainslie, Kylie E. C., Atchison, Christina J., Page, Andrew J., Prosolek, Sophie, Trotter, Alexander J., Le Viet, Thanh, Alikhan, Nabil-Fareed, Jackson, Leigh M., Ludden, Catherine, Ashby, Deborah, Donnelly, Christl A., Cooke, Graham, Barclay, Wendy, Ward, Helen, Darzi, Ara, Elliott, Paul, Riley, Steven
• Format: Journal Article
• Language: English
• Published: 2022
• ISSN: 2398-502X; 2398-502X
• DOI: 10.12688/wellcomeopenres.17723.1

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.