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Characterising the persistence of RT-PCR positivity and incidence in a community survey of SARS-CoV-2
File | Description | Size | Format | |
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shedding_binary.pdf | Working paper | 1.29 MB | Adobe PDF | View/Open |
Title: | Characterising the persistence of RT-PCR positivity and incidence in a community survey of SARS-CoV-2 |
Authors: | Eales, O Walters, C Wang, H Haw, D Ainslie, K Atchison, C Page, A Prosolek, S Trotter, A Viet, TL Alikhan, N-F Jackson, LM Ludden, C (COG UK), TCGUKC Ashby, D Donnelly, C Cooke, G Barclay, W Ward, H Darzi, A Elliott, P Riley, S |
Item Type: | Working Paper |
Abstract: | Background Community surveys of SARS-CoV-2 RT-PCR swab-positivity provide prevalence estimates largely unaffected by biases from who presents for routine case testing. The REal-time Assessment of Community Transmission-1 (REACT-1) has estimated swab-positivity approximately monthly since May 2020 in England from RT-PCR testing of self-administered throat and nose swabs in random non-overlapping cross-sectional community samples. Estimating infection incidence from swab-positivity 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, of the 2,282 participants who tested RT-PCR positive, we recruited 896 (39%) from whom we collected up to two additional swabs for RT-PCR approximately 6 and 9 days after the initial swab. We estimated sensitivity and duration of positivity using an exponential model of positivity decay, for all participants and for subsets by initial N-gene cycle threshold (Ct) value, symptom status, lineage and age. Estimates of infection incidence were obtained for the entire duration of the REACT-1 study using P-splines. Results We estimated the overall sensitivity of REACT-1 to detect virus on a single swab as 0.79 (0.77, 0.81) and median duration of positivity following a positive test as 9.7 (8.9, 10.6) days. We found greater median duration of positivity where there was a low N-gene Ct value, in those exhibiting symptoms, or for infection with the Alpha variant. The estimated proportion of positive individuals detected on first swab, was found to be higher 𝑃 for those with an 0 initially low N-gene Ct value and those who were pre-symptomatic. When compared to swab-positivity, estimates of infection incidence over the duration of REACT-1 included sharper features with evident transient increases around the time of key changes in social distancing measures. Discussion Home self-swabbing for RT-PCR based on a single swab, as implemented in REACT-1, has high overall sensitivity. However, participants' time-since-infection, symptom status and viral lineage affect the probability of detection and the duration of positivity. 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. |
Issue Date: | 13-Aug-2021 |
URI: | http://hdl.handle.net/10044/1/91056 |
Copyright Statement: | © 2021 The Author(s). |
Keywords: | SARS-CoV-2 coronavirus research |
Appears in Collections: | Faculty of Medicine Institute of Global Health Innovation |