1. Medicine
  2. Microbiology and Infectious Disease
Download icon

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

  1. A Sarah Walker  Is a corresponding author
  2. Emma Pritchard
  3. Thomas House
  4. Julie V Robotham
  5. Paul J Birrell
  6. Iain Bell
  7. John Bell
  8. John Newton
  9. Jeremy Farrar
  10. Ian Diamond
  11. Ruth Studley
  12. Jodie Hay
  13. Karina-Doris Vihta
  14. Timothy EA Peto
  15. Nicole Stoesser
  16. Philippa C Matthews
  17. David W Eyre
  18. Koen Pouwels
  19. COVID-19 Infection Survey team
  1. University of Oxford, United Kingdom
  2. University of Manchester, United Kingdom
  3. Public Health England, United Kingdom
  4. Office for National Statistics, United Kingdom
  5. The Wellcome Trust, United Kingdom
  6. University of Glasgow, United Kingdom
Research Article
  • Cited 3
  • Views 1,627
  • Annotations
Cite this article as: eLife 2021;10:e64683 doi: 10.7554/eLife.64683

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 6,550(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 6,189 participants with IgG S-antibody tests post-first RT-PCR-positive, 4,808(78%) were ever antibody-positive; Cts were significantly higher in those remaining antibody-negative.

Conclusions: Marked variation in community SARS-CoV-2 Ct values suggest 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.

Data availability

De-identified study data are available for access by accredited researchers in the ONS Secure Research Service (SRS) for accredited research purposes under part 5, chapter 5 of the Digital Economy Act 2017. Individuals can apply to be an accredited researcher using the short form on https://researchaccreditationservice.ons.gov.uk/ons/ONS_registration.ofml. Accreditation requires completion of a short free course on accessing the SRS. To request access to data in the SRS, researchers must submit a research project application for accreditation in the Research Accreditation Service (RAS). Research project applications are considered by the project team and the Research Accreditation Panel (RAP) established by the UK Statistics Authority. Project application example guidance and an exemplar of a research project application are available. A complete record of accredited researchers and their projects is published on the UK Statistics Authority website to ensure transparency of access to research data. For further information about accreditation, contact Research.Support@ons.gov.uk or visit the SRS website.Data points underlying Figures are provided in Supplementary File 4 and Stata code in Supplementary File 3.

Article and author information

Author details

  1. A Sarah Walker

    Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
    For correspondence
    sarah.walker@ndm.ox.ac.uk
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0412-8509
  2. Emma Pritchard

    Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
    Competing interests
    No competing interests declared.
  3. Thomas House

    University of Manchester, Manchester, United Kingdom
    Competing interests
    No competing interests declared.
  4. Julie V Robotham

    Modelling and Economics Unit, Public Health England, London, United Kingdom
    Competing interests
    No competing interests declared.
  5. Paul J Birrell

    Modelling and Economics Unit, Public Health England, London, United Kingdom
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8131-4893
  6. Iain Bell

    Office for National Statistics, Office for National Statistics, London, United Kingdom
    Competing interests
    No competing interests declared.
  7. John Bell

    Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
    Competing interests
    No competing interests declared.
  8. John Newton

    Public Health England, Public Health England, London, United Kingdom
    Competing interests
    No competing interests declared.
  9. Jeremy Farrar

    The Wellcome Trust, London, United Kingdom
    Competing interests
    No competing interests declared.
  10. Ian Diamond

    Office for National Statistics, Office for National Statistics, London, United Kingdom
    Competing interests
    No competing interests declared.
  11. Ruth Studley

    Office for National Statistics, Office for National Statistics, London, United Kingdom
    Competing interests
    No competing interests declared.
  12. Jodie Hay

    Virology, University of Glasgow, Glasgow, United Kingdom
    Competing interests
    No competing interests declared.
  13. Karina-Doris Vihta

    Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
    Competing interests
    No competing interests declared.
  14. Timothy EA Peto

    Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
    Competing interests
    No competing interests declared.
  15. Nicole Stoesser

    Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4508-7969
  16. Philippa C Matthews

    Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4036-4269
  17. David W Eyre

    Big Data Institute, University of Oxford, Oxford, United Kingdom
    Competing interests
    David W Eyre, declares lecture fees from Gilead, outside the submitted work..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5095-6367
  18. Koen Pouwels

    Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7097-8950
  19. COVID-19 Infection Survey team

Funding

Department of Health and Social Care (-)

  • A Sarah Walker
  • Emma Pritchard
  • Thomas House
  • Iain Bell
  • Ian Diamond
  • Ruth Studley
  • Jodie Hay
  • Karina-Doris Vihta
  • Koen Pouwels

National Institutes of Health Research (NIHR200915)

  • A Sarah Walker
  • Emma Pritchard
  • Julie V Robotham
  • Karina-Doris Vihta
  • Timothy EA Peto
  • Nicole Stoesser
  • David W Eyre
  • Koen Pouwels

Huo Family Foundation

  • Emma Pritchard
  • Koen Pouwels

Medical Research Council (MC_UU_12023/22)

  • A Sarah Walker

Wellcome Trust (110110/Z/15/Z)

  • Philippa C Matthews

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Ethics

Human subjects: Written informed consent was obtained from participants aged 16 years and older, and from parents/carers for those aged 2-15 years; those aged 10-15 years provided written assent. The study received ethical approval from the South Central Berkshire B Research Ethics Committee (20/SC/0195).

Reviewing Editor

  1. M Dawn Teare, Newcastle University, United Kingdom

Publication history

  1. Received: November 6, 2020
  2. Accepted: July 6, 2021
  3. Accepted Manuscript published: July 12, 2021 (version 1)
  4. Version of Record published: July 15, 2021 (version 2)

Copyright

© 2021, Walker et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 1,627
    Page views
  • 156
    Downloads
  • 3
    Citations

Article citation count generated by polling the highest count across the following sources: Crossref, PubMed Central, Scopus.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Download citations (links to download the citations from this article in formats compatible with various reference manager tools)

Open citations (links to open the citations from this article in various online reference manager services)

  1. Further reading

Further reading

    1. Medicine
    Mieradilijiang Abudupataer et al.
    Research Article Updated

    Background:

    Bicuspid aortic valve (BAV) is the most common congenital cardiovascular disease in general population and is frequently associated with the development of thoracic aortic aneurysm (TAA). There is no effective strategy to intervene with TAA progression due to an incomplete understanding of the pathogenesis. Insufficiency of NOTCH1 expression is highly related to BAV-TAA, but the underlying mechanism remains to be clarified.

    Methods:

    A comparative proteomics analysis was used to explore the biological differences between non-diseased and BAV-TAA aortic tissues. A microfluidics-based aorta smooth muscle-on-a-chip model was constructed to evaluate the effect of NOTCH1 deficiency on contractile phenotype and mitochondrial dynamics of human aortic smooth muscle cells (HAoSMCs).

    Results:

    Protein analyses of human aortic tissues showed the insufficient expression of NOTCH1 and impaired mitochondrial dynamics in BAV-TAA. HAoSMCs with NOTCH1-knockdown exhibited reduced contractile phenotype and were accompanied by attenuated mitochondrial fusion. Furthermore, we identified that mitochondrial fusion activators (leflunomide and teriflunomide) or mitochondrial fission inhibitor (Mdivi-1) partially rescued the disorders of mitochondrial dynamics in HAoSMCs derived from BAV-TAA patients.

    Conclusions:

    The aorta smooth muscle-on-a-chip model simulates the human pathophysiological parameters of aorta biomechanics and provides a platform for molecular mechanism studies of aortic disease and related drug screening. This aorta smooth muscle-on-a-chip model and human tissue proteomic analysis revealed that impaired mitochondrial dynamics could be a potential therapeutic target for BAV-TAA.

    Funding:

    National Key R and D Program of China, National Natural Science Foundation of China, Shanghai Municipal Science and Technology Major Project, Shanghai Science and Technology Commission, and Shanghai Municipal Education Commission.

    1. Medicine
    Elisabeth Gludovacz et al.
    Research Article Updated

    Background:

    Excessive plasma histamine concentrations cause symptoms in mast cell activation syndrome, mastocytosis, or anaphylaxis. Anti-histamines are often insufficiently efficacious. Human diamine oxidase (hDAO) can rapidly degrade histamine and therefore represents a promising new treatment strategy for conditions with pathological histamine concentrations.

    Methods:

    Positively charged amino acids of the heparin-binding motif of hDAO were replaced with polar serine or threonine residues. Binding to heparin and heparan sulfate, cellular internalization and clearance in rodents were examined.

    Results:

    Recombinant hDAO is rapidly cleared from the circulation in rats and mice. After mutation of the heparin-binding motif, binding to heparin and heparan sulfate was strongly reduced. The double mutant rhDAO-R568S/R571T showed minimal cellular uptake. The short α-distribution half-life of the wildtype protein was eliminated, and the clearance was significantly reduced in rodents.

    Conclusions:

    The successful decrease in plasma clearance of rhDAO by mutations of the heparin-binding motif with unchanged histamine-degrading activity represents the first step towards the development of rhDAO as a first-in-class biopharmaceutical to effectively treat diseases characterized by excessive histamine concentrations in plasma and tissues.

    Funding:

    Austrian Science Fund (FWF) Hertha Firnberg program grant T1135 (EG); Sigrid Juselius Foundation, Medicinska Understödsförening Liv och Hälsa rft (TAS and SeV).