REACT-1 round 6 updated report: high prevalence of SARS-CoV-2 swab positivity with reduced rate of growth in England at the start of November 2020

  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

England is now in the midst of its second wave of the COVID-19 pandemic. Multiple regions of the country are at high infection prevalence and all areas experienced rapid recent growth of the epidemic during October 2020.

Methods

REACT-1 is a series of community surveys of SARS-CoV-2 RT-PCR swab-positivity in England designed to monitor the spread of the epidemic and thus increase situational awareness. Round 6 of REACT-1 commenced swab-collection on 16th October. A prior interim report included data from 16th to 25th October for 85,971 participants. Here, we report data for the entire round on 160,175 participants with swab results obtained up to 2nd November 2020.

Results

Overall weighted prevalence of infection in the community in England was 1.3% or 130 people per 10,000 infected, up from 60 people per 10,000 in the round 5 report (18th September to 5th October 2020), doubling every 24 days on average since the prior round. The corresponding R number was estimated to be 1.2. Prevalence of infection was highest in North West (2.4%, up from 1.2%), followed by Yorkshire and The Humber (2.3% up from 0.84%), West Midlands (1.6% up from 0.60%), North East (1.5% up from 1.1%), East Midlands (1.3% up from 0.56%), London (0.97%, up from 0.54%), South West (0.80% up from 0.33%), South East (0.69% up from 0.29%), and East of England (0.69% up from 0.30%). Rapid growth in the South observed in the first half of round 6 was no longer apparent in the second half of round 6. We also observed a decline in prevalence in Yorkshire and The Humber during this period. Comparing the first and second halves of round 6, there was a suggestion of decline in weighted prevalence in participants aged 5 to 12 years and in those aged 25 to 44 years. While prevalence remained high, in the second half of round 6 there was suggestion of a slight fall then rise that was seen nationally and also separately in both the North and the South.

Conclusion

The impact of the second national lockdown in England is not yet known. We provide here a detailed description of swab-positivity patterns at national, regional and local scales for the period immediately preceding lockdown, against which future trends in prevalence can be evaluated.

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    SciScore for 10.1101/2020.11.18.20233932: (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
    All computations used the PrevMap package [9] within the R computing environment [10].
    PrevMap
    suggested: None

    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 a number of limitations. In order to estimate trends over time, we assume that the individuals taking part are broadly representative of the base population by LTLA at each time point in the study. We did find evidence for limited differences in population characteristics between the first and second halves of rounds four to six, but not of sufficient size or direction to have materially affected within- or between-round trends. Also it is possible that issues with swab sample transport or changes in laboratory procedures or reagents may have affected either the integrity of the samples or the detection thresholds on RT-PCR. However, data are collected and analysed according to strict protocols and quality control (QC) procedures, and review of both the delivery chain and laboratory QC did not reveal any differences or discrepancies that might have materially affected positivity rates. Underlying the national trends, we have described a complex spatial pattern of growth and decline of the epidemic at sub-regional scales in the most recent data. Increased restrictions in west Yorkshire prior to the start of the national lockdown [8] appear to have been successful. In the North West, while there were signs of slowing of the epidemic in the worst affected areas, we did not see substantial groupings of LTLAs with lower prevalence in the second half of round 6 compared with the first. These differences suggest variation in the efficacy of the tiered local interventio...

    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.

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  2. Version published to 10.1101/2020.11.18.20233932v1 on medRxiv