Ct threshold values, a proxy for viral load in community SARS-CoV-2 cases, demonstrate wide variation across populations and over time

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.

Keywords: SARS-CoV-2; community; infectious disease; medicine; microbiology; symptoms; viral load.

Figure 1.. Distribution of Ct values at each positive test by genes detected and self-reported symptoms.

Note: Points show the median and boxes the interquartile range. OR=ORF1ab. Positives where only the ORF1ab+N genes were detected are split by whether the swab was taken before or after 16 November 2020, reflecting the expansion of B.1.1.7 (which has S-gene target failure on the assay used in the survey).

Figure 2.. Percentage reporting symptoms by Ct value.

Note: Points show the percentage of positive tests with each rounded Ct value reporting any symptoms or cough, fever, anosmia/ageusia at each test or around each test (see Materials and methods for symptoms collection and definitions). Ct values under 11 and over 36 grouped with 11 and 36, respectively.

Figure 3.. Variation over calendar time in the distribution of Ct values in the UK (A) and England (B) together with percentage positivity in England (B), and in self-reported symptoms (C) and evidence supporting positives (D).

Note: Panel (A) shows the distribution of Ct values each week including all positives across the UK. Panel (B) is restricted to England shown together with the official estimates of positivity as reported by the Office for National Statistics (black line) and periods of national ‘stay-at-home’ restrictions (schools shut in dark grey, schools open in light gray). Panels (C) and (D) show the proportions reporting symptoms and with different levels of evidence supporting the positive test, respectively. Variation in the width of 95% CI reflects the increase in size of the survey from mid August (Supplementary file 1).

Figure 4.. Ct values (A) and percentage positive of all tests (B) by level of evidence and time.

Note: Panel (A) shows median Ct values according to level of evidence and panel (B) percentage of all swab tests positive according to level of evidence over calendar time. The early part of the study is grouped into 3 week periods due to lower numbers of positives.

Figure 5.. Percentage of positive antibody tests over time from first positive swab.

Note: showing the percentage of participants with S-antibody positive or negative tests according to days from their first positive swab, separately for those with and without any antibody results prior to their first positive swab.

Appendix 1—figure 1.. Relationship between Ct values and viral load.

Appendix 1—figure 2.. Directed acyclic graph of potential relationships between factors.

*May also depend on factors which effect self-swabbing efficiency, e.g., demographics.