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

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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