High prevalence of SARS-CoV-2 swab positivity and increasing R number in England during October 2020: REACT-1 round 6 interim report

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

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Abstract

Background

REACT-1 measures prevalence of SARS-CoV-2 infection in representative samples of the population in England using PCR testing from self-administered nose and throat swabs. Here we report interim results for round 6 of observations for swabs collected from the 16th to 25th October 2020 inclusive.

Methods

REACT-1 round 6 aims to collect data and swab results from 160,000 people aged 5 and above. Here we report results from the first 86,000 individuals. We estimate prevalence of PCR-confirmed SARS-CoV-2 infection, reproduction numbers (R) and temporal trends using exponential growth or decay models. Prevalence estimates are presented both unweighted and weighted to be representative of the population of England, accounting for response rate, region, deprivation and ethnicity. We compare these interim results with data from round 5, based on swabs collected from 18th September to 5th October 2020 inclusive.

Results

Overall prevalence of infection in the community in England was 1.28% or 128 people per 10,000, up from 60 per 10,000 in the previous round. Infections were doubling every 9.0 (6.1, 18) days with a national reproduction number (R) estimated at 1.56 (1.27, 1.88) compared to 1.16 (1.05, 1.27) in the previous round. Prevalence of infection was highest in Yorkshire and The Humber at 2.72% (2.12%, 3.50%), up from 0.84% (0.60%, 1.17%), and the North West at 2.27% (1.90%, 2.72%), up from 1.21% (1.01%, 1.46%), and lowest in South East at 0.55% (0.45%, 0.68%), up from 0.29% (0.23%, 0.37%). Clustering of cases was more prevalent in Lancashire, Manchester, Liverpool and West Yorkshire, West Midlands and East Midlands. Interim estimates of R were above 2 in the South East, East of England, London and South West, but with wide confidence intervals. Nationally, prevalence increased across all age groups with the greatest increase in those aged 55-64 at 1.20% (0.99%, 1.46%), up 3-fold from 0.37% (0.30%, 0.46%). In those aged over 65, prevalence was 0.81% (0.58%, 0.96%) up 2-fold from 0.35% (0.28%, 0.43%). Prevalence remained highest in 18 to 24-year olds at 2.25% (1.47%, 3.42%).

Conclusion

The co-occurrence of high prevalence and rapid growth means that the second wave of the epidemic in England has now reached a critical stage. Whether via regional or national measures, it is now time-critical to control the virus and turn R below one if further hospital admissions and deaths from COVID-19 are to be avoided.

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  1. ScreenIT

    SciScore for 10.1101/2020.10.30.20223123: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: We obtained research ethics approval from the South Central-Berkshire B Research Ethics Committee (IRAS ID: 283787).
    RandomizationIn brief, we obtain a nose and throat swab from non-overlapping random samples of the population of England (stratified by the 315 lower-tier local authorities) at ages five years and above, using the National Health Service (NHS) list of GP registered patients as the sampling frame.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    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. We assume that across each round the individuals taking part have similar characteristics including propensity to test positive or negative given the levels of circulating virus at the time. It is possible that symptomatic individuals may choose instead to be tested through the national “Test and Trace” system or alternatively may be more likely to participate in our study in order to obtain a test result. While both sources of bias are possible, we have no reason to believe they are operating to any large extent, and in any case would be unlikely to explain trends in our data within any one round. We also weight the data to be representative of England as a whole, which should correct for under- or over-representation of any particular group. Also, we rely on self-administered nose and throat swabs which may miss virus (if present) in 20% to 30% of people [6]. In addition, any changes in laboratory procedures may affect positivity rates. However, we have been using the same methods across all rounds of the study, and same laboratory and protocols (with strict quality control), which should minimise any such errors. The co-occurrence of high prevalence and rapid growth means that the second wave of the epidemic in England has now reached a critical stage. While it is possible that some of the current control measures may be too recent to have fed through to the data reported here, the high prevalence already reached and the rapid acceleration mean t...

    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.
    • Thank you for including a protocol registration statement.

    About SciScore

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  2. Version published to 10.1101/2020.10.30.20223123 on medRxiv