Imperial College London
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Professor Christl Donnelly CBE FMedSci FRS

Faculty of Medicine, School of Public Health

Visiting Professor
 
 
 
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Contact

 

c.donnelly Website

 
 
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Location

 

School of Public HealthWhite City Campus

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Summary

 

Publications

Citation

BibTex format

@unpublished{Eales:2021,
author = {Eales, O and Walters, C and Wang, H and Haw, D and Ainslie, K and Atchison, C and Page, A and Prosolek, S and Trotter, A and Viet, TL and Alikhan, N-F and Jackson, LM and Ludden, C and COG, UK TCGUKC and Ashby, D and Donnelly, C and Cooke, G and Barclay, W and Ward, H and Darzi, A and Elliott, P and Riley, S},
title = {Characterising the persistence of RT-PCR positivity and incidence in a community survey of SARS-CoV-2},
url = {http://hdl.handle.net/10044/1/91056},
year = {2021}
}
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RIS format (EndNote, RefMan)

TY  - UNPB
AB  - BackgroundCommunity 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-administeredthroat 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.MethodsDuring 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.ResultsWe 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 proportionof positive individuals detected on first swab, was found to be higher  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 socialdistancing measures.DiscussionHome self-swabbing for RT-PCR based on a single swab, as implemented in REACT-1, has hig
AU  - Eales,O
AU  - Walters,C
AU  - Wang,H
AU  - Haw,D
AU  - Ainslie,K
AU  - Atchison,C
AU  - Page,A
AU  - Prosolek,S
AU  - Trotter,A
AU  - Viet,TL
AU  - Alikhan,N-F
AU  - Jackson,LM
AU  - Ludden,C
AU  - COG,UK TCGUKC
AU  - Ashby,D
AU  - Donnelly,C
AU  - Cooke,G
AU  - Barclay,W
AU  - Ward,H
AU  - Darzi,A
AU  - Elliott,P
AU  - Riley,S
PY  - 2021///
TI  - Characterising the persistence of RT-PCR positivity and incidence in a community survey of SARS-CoV-2
UR  - http://hdl.handle.net/10044/1/91056
ER  -
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