Ct threshold values, a proxy for viral load in community SARS-CoV-2 cases, demonstrate wide variation across populations and over time.
Published version
Peer-reviewed
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Repository DOI
Change log
Authors
Pritchard, Emma
House, Thomas
Robotham, Julie V
Abstract
Background
Information on SARS-CoV-2 in representative community surveillance is limited, particularly cycle threshold (Ct) values (a proxy for viral load).Methods
We included all positive nose and throat swabs 26 April 2020 to 13 March 2021 from the UK's national COVID-19 Infection Survey, tested by RT-PCR for the N, S, and ORF1ab genes. We investigated predictors of median Ct value using quantile regression.Results
Of 3,312,159 nose and throat swabs, 27,902 (0.83%) were RT-PCR-positive, 10,317 (37%), 11,012 (40%), and 6550 (23%) for 3, 2, or 1 of the N, S, and ORF1ab genes, respectively, with median Ct = 29.2 (~215 copies/ml; IQR Ct = 21.9-32.8, 14-56,400 copies/ml). Independent predictors of lower Cts (i.e. higher viral load) included self-reported symptoms and more genes detected, with at most small effects of sex, ethnicity, and age. Single-gene positives almost invariably had Ct > 30, but Cts varied widely in triple-gene positives, including without symptoms. Population-level Cts changed over time, with declining Ct preceding increasing SARS-CoV-2 positivity. Of 6189 participants with IgG S-antibody tests post-first RT-PCR-positive, 4808 (78%) were ever antibody-positive; Cts were significantly higher in those remaining antibody negative.Conclusions
Marked variation in community SARS-CoV-2 Ct values suggests that they could be a useful epidemiological early-warning indicator.Funding
Department of Health and Social Care, National Institutes of Health Research, Huo Family Foundation, Medical Research Council UK; Wellcome Trust.Description
Funder: Department of Health
Funder: Department of Health & Social Care
Keywords
Microbiology, Community, Infectious disease, Medicine, Viral load, Symptoms, Sars-cov-2, Humans, Viral Load, COVID-19, SARS-CoV-2, COVID-19 Testing
Journal Title
eLife
Conference Name
Journal ISSN
2050-084X
Volume Title
10
Publisher
Publisher DOI
Sponsorship
Medical Research Council (MC_UU_12023/22)
NIH HHS (NIHR200915)
National Institutes of Health Research (NIHR200915)
Wellcome Trust (110110/Z/15/Z)
NIH HHS (NIHR200915)
National Institutes of Health Research (NIHR200915)
Wellcome Trust (110110/Z/15/Z)