REACT-1 round 11 report: low prevalence of SARS-CoV-2 infection in the community prior to the third step of the English roadmap out of lockdown

  1. Steven Riley
  2. David Haw
  3. Caroline E. Walters
  4. Haowei Wang
  5. Oliver Eales
  6. Kylie E. C. Ainslie
  7. Christina Atchison
  8. Claudio Fronterre
  9. Peter J. Diggle
  10. Andrew J. Page
  11. Alexander J. Trotter
  12. Thanh Le Viet
  13. Nabil-Fareed Alikhan
  14. Justin O’Grady
  15. The COVID-19 Genomics UK (COG-UK) Consortium
  16. Deborah Ashby
  17. Christl A. Donnelly
  18. Graham Cooke
  19. Wendy Barclay
  20. Helen Ward
  21. Ara Darzi
  22. Paul Elliott

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Abstract

Background

National epidemic dynamics of SARS-CoV-2 infections are being driven by: the degree of recent indoor mixing (both social and workplace), vaccine coverage, intrinsic properties of the circulating lineages, and prior history of infection (via natural immunity). In England, infections, hospitalisations and deaths fell during the first two steps of the “roadmap” for exiting the third national lockdown. The third step of the roadmap in England takes place on 17 May 2021.

Methods

We report the most recent findings on community infections from the REal-time Assessment of Community Transmission-1 (REACT-1) study in which a swab is obtained from a representative cross-sectional sample of the population in England and tested using PCR. Round 11 of REACT-1 commenced self-administered swab-collection on 15 April 2021 and completed collections on 3 May 2021. We compare the results of REACT-1 round 11 to round 10, in which swabs were collected from 11 to 30 March 2021.

Results

Between rounds 10 and 11, prevalence of swab-positivity dropped by 50% in England from 0.20% (0.17%, 0.23%) to 0.10% (0.08%, 0.13%), with a corresponding R estimate of 0.90 (0.87, 0.94). Rates of swab-positivity fell in the 55 to 64 year old group from 0.17% (0.12%, 0.25%) in round 10 to 0.06% (0.04%, 0.11%) in round 11. Prevalence in round 11 was higher in the 25 to 34 year old group at 0.21% (0.12%, 0.38%) than in the 55 to 64 year olds and also higher in participants of Asian ethnicity at 0.31% (0.16%, 0.60%) compared with white participants at 0.09% (0.07%, 0.11%). Based on sequence data for positive samples for which a lineage could be identified, we estimate that 92.3% (75.9%, 97.9%, n=24) of infections were from the B.1.1.7 lineage compared to 7.7% (2.1%, 24.1%, n=2) from the B.1.617.2 lineage. Both samples from the B.1.617.2 lineage were detected in London from participants not reporting travel in the previous two weeks. Also, allowing for suitable lag periods, the prior close alignment between prevalence of infections and hospitalisations and deaths nationally has diverged.

Discussion

We observed marked reductions in prevalence from March to April and early May 2021 in England reflecting the success of the vaccination programme and despite easing of restrictions during lockdown. However, there is potential upwards pressure on prevalence from the further easing of lockdown regulations and presence of the B.1.617.2 lineage. If prevalence rises in the coming weeks, policy-makers will need to assess the possible impact on hospitalisations and deaths. In addition, consideration should be given to other health and economic impacts if increased levels of community transmission occur.

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    SciScore for 10.1101/2021.05.13.21257144: (What is this?)

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

    Table 1: Rigor

    EthicsIRB: Research ethics approval was obtained from the South Central-Berkshire B Research Ethics Committee (IRAS ID: 283787).
    Sex as a biological variablenot detected.
    RandomizationIn REACT-1 we collect a self-administered throat and nose swab sample and questionnaire data from a random sample of the population in England at ages 5 years and above (parent/guardian administered at ages 5 to 12) [7].
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    No key resources detected.

    Results from OddPub: Thank you for sharing your code and data.

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    Our study has limitations. Our sampling may not be fully representative of the population of England, despite attempts to correct for this using weighting. There is now widespread availability of testing in England, including for non-symptomatic people through either ‘surge’ testing in areas of high prevalence or where there are variants of concerns (VOCs), or on demand using lateral flow tests. We have seen a moderate fall in response rate during the course of the study (currently 15% of people to whom we send invite letters provide a viable swab), which may reflect lower levels of public concern in recent weeks. Nonetheless, we believe that our estimates of prevalence and R are broadly representative of the population, and likely less affected by these changes in testing behaviour than routine surveillance data [6]. Reliable sequencing data were only obtained for 20% of the positive samples, since at higher Ct values (when there is less virus present) good sequence coverage is difficult to obtain. If prevalence rises in the coming weeks, policy-makers will need to assess the possible impact on hospitalisations and deaths. In addition, consideration should be given to other health and economic impacts if increased levels of community transmission occur.

    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.

    Results from scite Reference Check: We found no unreliable references.

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  2. Version published to 10.1101/2021.05.13.21257144v1 on medRxiv