REACT-1 round 15 interim report: High and rising prevalence of SARS-CoV-2 infection in England from end of September 2021 followed by a fall in late October 2021

  1. Marc Chadeau-Hyam
  2. Oliver Eales
  3. Barbara Bodinier
  4. Haowei Wang
  5. David Haw
  6. Matthew Whitaker
  7. Caroline E. Walters
  8. Christina Atchison
  9. Peter J. Diggle
  10. Andrew J. Page
  11. Deborah Ashby
  12. Wendy Barclay
  13. Graham Taylor
  14. Graham Cooke
  15. Helen Ward
  16. Ara Darzi
  17. Christl A. Donnelly
  18. Paul Elliott

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Abstract

Background

The third wave of COVID-19 in England coincided with the rapid spread of the Delta variant of SARS-CoV-2 from the end of May 2021. Case incidence data from the national testing programme (Pillar 2) in England may be affected by changes in testing behaviour and other biases. Community surveys may provide important contextual information to inform policy and the public health response.

Methods

We estimated patterns of community prevalence of SARS-CoV-2 infection in England using RT-PCR swab-positivity, demographic and other risk factor data from round 15 (interim) of the REal-time Assessment of Community Transmission-1 (REACT-1) study (round 15a, carried out from 19 to 29 October 2021). We compared these findings with those from round 14 (9 to 27 September 2021).

Results

During mid- to late-October 2021 (round 15a) weighted prevalence was 1.72% (1.61%, 1.84%) compared to 0.83% (0.76%, 0.89%) in September 2021 (round 14). The overall reproduction number (R) from round 14 to round 15a was 1.12 (1.11, 1.14) with increases in prevalence over this period (September to October) across age groups and regions except Yorkshire and The Humber. However, within round 15a (mid- to late-October) there was evidence of a fall in prevalence with R of 0.76 (0.65, 0.88). The highest weighted prevalence was observed among children aged 5 to 12 years at 5.85% (5.10%, 6.70%) and 13 to 17 years at 5.75% (5.02%, 6.57%). At regional level, there was an almost four-fold increase in weighted prevalence in South West from round 14 at 0.59% (0.43%,0.80%) to round 15a at 2.18% (1.84%, 2.58%), with highest smoothed prevalence at subregional level also found in South West in round 15a. Age, sex, key worker status, and presence of children in the home jointly contributed to the risk of swab-positivity. Among the 126 sequenced positive swabs obtained up until 23 October, all were Delta variant; 13 (10.3%) were identified as the AY.4.2 sub-lineage.

Discussion

We observed the highest overall prevalence of swab-positivity seen in the REACT-1 study in England to date in round 15a (October 2021), with a two-fold rise in swab-positivity from round 14 (September 2021). Despite evidence of a fall in prevalence from mid- to late-October 2021, prevalence remains high, particularly in school-aged children, with evidence also of higher prevalence in households with one or more children. Thus, vaccination of children aged 12 and over remains a high priority (with possible extension to children aged 5-12) to help reduce within-household transmission and disruptions to education, as well as among adults, to lessen the risk of serious disease among those infected.

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    SciScore for 10.1101/2021.11.03.21265877: (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.

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    As with any study, the REACT-1 study has limitations. We cannot meaningfully calculate a response rate for round 15 since it is not yet complete, but between rounds 1 (May 2020) and 14 (September 2021) the response rate declined from approximately 30% to approximately 12%. Although we used rim weighting to adjust our prevalence estimates for differential response by age, sex, deprivation, LTLA counts and ethnicity, it remains possible that our estimates are not fully representative of the population as a whole. The data on participants who consented for their REACT-1 data to be linked to their NHS records which include data from the COVID-19 immunisation programme are not yet available for round 15. Surveillance in England indicates that influenza incidence was low up to 26 October 2021 (the most recent data reported by UKHSA [19]), although it will almost certainly increase in coming weeks unless strict social distancing were to be reinstated. For viral infections, co-infections with other bacterial and viral pathogens can increase the risks of complications and mortality. The combined effects of SARS-CoV-2 and influenza co-infections are not well understood [20]. Even if co-infected individuals do not experience increased risks of serious disease, the dual demands on the NHS of caring for COVID-19 and influenza patients is likely to put its resources under pressure. It is therefore essential to monitor ongoing infection risks of both SARS-CoV-2 and influenza so that appropr...

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