REACT-1 round 12 report: resurgence of SARS-CoV-2 infections in England associated with increased frequency of the Delta variant

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

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Abstract

Background

England entered a third national lockdown from 6 January 2021 due to the COVID-19 pandemic. Despite a successful vaccine rollout during the first half of 2021, cases and hospitalisations have started to increase since the end of May as the SARS-CoV-2 Delta (B.1.617.2) variant increases in frequency. The final step of relaxation of COVID-19 restrictions in England has been delayed from 21 June to 19 July 2021.

Methods

The REal-time Assessment of Community Transmision-1 (REACT-1) study measures the prevalence of swab-positivity among random samples of the population of England. Round 12 of REACT-1 obtained self-administered swab collections from participants from 20 May 2021 to 7 June 2021; results are compared with those for round 11, in which swabs were collected from 15 April to 3 May 2021.

Results

Between rounds 11 and 12, national prevalence increased from 0.10% (0.08%, 0.13%) to 0.15% (0.12%, 0.18%). During round 12, we detected exponential growth with a doubling time of 11 (7.1, 23) days and an R number of 1.44 (1.20, 1.73). The highest prevalence was found in the North West at 0.26% (0.16%, 0.41%) compared to 0.05% (0.02%, 0.12%) in the South West. In the North West, the locations of positive samples suggested a cluster in Greater Manchester and the east Lancashire area. Prevalence in those aged 5-49 was 2.5 times higher at 0.20% (0.16%, 0.26%) compared with those aged 50 years and above at 0.08% (0.06%, 0.11%). At the beginning of February 2021, the link between infection rates and hospitalisations and deaths started to weaken, although in late April 2021, infection rates and hospital admissions started to reconverge. When split by age, the weakened link between infection rates and hospitalisations at ages 65 years and above was maintained, while the trends converged below the age of 65 years. The majority of the infections in the younger group occurred in the unvaccinated population or those without a stated vaccine history. We observed the rapid replacement of the Alpha (B.1.1.7) variant of SARS-CoV-2 with the Delta variant during the period covered by rounds 11 and 12 of the study.

Discussion

The extent to which exponential growth continues, or slows down as a consequence of the continued rapid roll-out of the vaccination programme, including to young adults, requires close monitoring. Data on community prevalence are vital to track the course of the epidemic and inform ongoing decisions about the timing of further lifting of restrictions in England.

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    SciScore for 10.1101/2021.06.17.21259103: (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: Thank you for sharing your code and data.

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    There are a number of limitations to our study. We changed our sampling strategy in round 12 in order to improve precision of prevalence estimates in more urban and deprived areas, especially at relatively low prevalence: rather than aiming to achieve similar sample sizes by lower-tier local authority (LTLA), as in previous rounds, we selected our sample to be proportionate to population by LTLA. This had the effect of increasing the numbers sampled in urban areas and decreasing those in rural areas. Although this may have affected comparison of unweighted prevalence across rounds, it should not affect comparisons of weighted estimates, since, in each round, we use weighting to correct our prevalence estimates to be representative of England as a whole. Nonetheless, the change in sampling strategy will affect participation rates since participation is higher in more affluent rural areas (which have been down-sampled) than in more deprived urban areas (up-sampled). Here we report an overall response rate of 13.4% compared with 15.5% at the previous round [12]. Participation rates may also have been affected by the availability of ‘surge’ testing (including among non-symptomatic people) in areas of high prevalence. In addition, willingness to take part in a national surveillance programme such as REACT-1 may have reduced as lockdown eases and individuals are less likely to be available at home, e.g. for courier pick-up of the completed swab. Notwithstanding these limitations we...

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

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

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    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
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