Community prevalence of SARS-CoV-2 virus in England during May 2020: REACT study

  1. REACT Study Investigators
  2. Steven Riley
  3. Kylie E. C. Ainslie
  4. Oliver Eales
  5. Benjamin Jeffrey
  6. Caroline E. Walters
  7. Christina Atchison
  8. Peter J. Diggle
  9. Deborah Ashby
  10. Christl A. Donnelly
  11. Graham Cooke
  12. Wendy Barclay
  13. Helen Ward
  14. Graham Taylor
  15. Ara Darzi
  16. Paul Elliott

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Abstract

Background

England has experienced one of the highest rates of confirmed COVID-19 mortality in the world. SARS-CoV-2 virus has circulated in hospitals, care homes and the community since January 2020. Our current epidemiological knowledge is largely informed by clinical cases with far less understanding of community transmission.

Methods

The REal-time Assessment of Community Transmission (REACT) study is a nationally representative prevalence survey of SARS-CoV-2 virus swab-positivity in the community in England. We recruited participants regardless of symptom status.

Results

We found 159 positives from 120,610 swabs giving an average prevalence of 0.13% (95% CI: 0.11%,0.15%) from 1st May to 1st June 2020. We showed decreasing prevalence with a halving time of 8.6 (6.2, 13.6) days, implying an overall reproduction number R of 0.57 (0.45, 0.72). Adults aged 18 to 24 yrs had the highest swab-positivity rates, while those >64 yrs had the lowest. Of the 126 participants who tested positive with known symptom status in the week prior to their swab, 39 reported symptoms while 87 did not, giving an estimate that 69% (61%,76%) of people were symptom-free for the 7 days prior testing positive in our community sample. Symptoms strongly associated with swab-positivity were: nausea and/or vomiting, diarrhoea, blocked nose, loss of smell, loss of taste, headache, chills and severe fatigue. Recent contact with a known COVID-19 case was associated with odds of 24 (16, 38) for swab-positivity. Compared with non-key workers, odds of swab-positivity were 7.7 (2.4, 25) among care home (long-term care facilities) workers and 5.2 (2.9, 9.3) among health care workers. However, some of the excess risk associated with key worker status was explained by recent contact with COVID-19 cases. We found no strong evidence for geographical variability in positive swab results.

Conclusion

Our results provide a reliable baseline against which the impact of subsequent relaxation of lockdown can be assessed to inform future public health efforts to control transmission.

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  1. ScreenIT

    SciScore for 10.1101/2020.07.10.20150524: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    NIH rigor criteria are not applicable to paper type.

    Table 2: Resources

    No key resources detected.

    Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    Our study has limitations. Although we selected a representative sample of the population from the lists of patients registered with a general practitioner in England (covering almost the entire population) our response rate overall was 31% which may have affected our estimates of prevalence. Our study involved the use of self-administered nose and throat swabs to obtain evidence of infection. A number of factors need to be considered when interpreting swab-positivity prevalence. First, viral RNA may have been present but not detected during the process of swabbing, transport and analysis. Estimates of diagnostic sensitivity are in the region of 70%17–19. Therefore, our estimate of prevalence of swab positivity suggests that up to 115,000 (95% CI 99,000, 134,000) people in England may have been infected withSARS-CoV-2 virus on any given day. Second, viral RNA may persist in the nose and mouth after viable virus is no longer present20 and therefore not be indicative of active infection. Third, it is possible that self-swabbing efficacy may vary according to age and other demographic characteristics. Fourth, we had evidence to suggest that there was differential reporting of a positive result across laboratories with the commercial laboratory initially reporting a higher positivity rate than the PHE laboratories. However, we mitigated the potential impact of this difference through a calibration exercise resulting in similar swab-positivity rates between laboratories. Also, our...

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

    Results from JetFighter: We did not find any issues relating to colormaps.

    Results from rtransparent:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • No protocol registration statement was detected.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  2. ScreenIT

    SciScore for 10.1101/2020.07.10.20150524: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    NIH rigor criteria are not applicable to paper type.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    SR acknowledges support: MRC Centre for Global Infectious Disease Analysis, National Institute for Health Research (NIHR) Health Protection Research Unit (HPRU), Wellcome Trust (200861/Z/16/Z, 200187/Z/15/Z), and Centres for Disease Control and Prevention (US, U01CK0005-01-02).
    HPRU
    suggested: None

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

    • Our study has limitations.
    • Although we selected a representative sample of the population from the lists of patients registered with a general practitioner in England (covering almost the entire population) our response rate overall was 31% which may have affected our estimates of prevalence.

    Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore is not a substitute for expert review. SciScore checks for the presence and correctness of RRIDs (research resource identifiers) in the manuscript, and detects sentences that appear to be missing RRIDs. SciScore also checks to make sure that rigor criteria are addressed by authors. It does this by detecting sentences that discuss criteria such as blinding or power analysis. SciScore does not guarantee that the rigor criteria that it detects are appropriate for the particular study. Instead it assists authors, editors, and reviewers by drawing attention to sections of the manuscript that contain or should contain various rigor criteria and key resources. For details on the results shown here, including references cited, please follow this link.

  3. Version published to 10.1101/2020.07.10.20150524 on medRxiv