Characterising the persistence of RT-PCR positivity and incidence in a community survey of SARS-CoV-2
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.
Citation
Eales O, Walters CE, Wang H et al. Characterising the persistence of RT-PCR positivity and incidence in a community survey of SARS-CoV-2 [version 1; peer review: 2 approved with reservations]. Wellcome Open Res 2022, 7:102. [DOI]