Resurgence of SARS-CoV-2: Detection by community viral surveillance

  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

Even highly effective vaccines will not save us from the need to monitor severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) activity, perhaps for years to come. Public health institutions will need early warning of any uptick in cases to prepare and deploy interventions as required. Riley et al. developed a community-wide program that was designed to detect resurgence at low prevalence and has been used to track SARS-CoV-2 virus across England. In the four rounds of sampling from May to September 2020, almost 600,000 people representative of all communities were monitored. The results revealed the greatest prevalence among 18- to 24-year-olds, with increasing incidence among older age groups and elevated odds of infection among some communities. This testing approach offers a model for the type of real-time, country-wide population-based surveillance work that needs to be conducted to monitor SARS-CoV-2.

Science , abf0874, this issue p. 990

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  1. Version published to 10.1126/science.abf0874
  2. ScreenIT

    SciScore for 10.1101/2020.09.11.20192492: (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

    Antibodies
    SentencesResources
    The protocol of the REACT suite of studies describes REACT-1 (antigen) and REACT-2 (antibody) [8].
    REACT-1 (antigen)
    suggested: None
    REACT-2
    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 limitations. First, although we aimed to be representative of the population of England by inviting a random sample of people on the NHS patient register, differential response by e.g. age, sex, ethnicity may have distorted our findings. For overall estimates of prevalence we reweighted our sample to be representative of England taking into account sample design and non-response. Prevalence estimates for subgroups were not reweighted because of low numbers of swab-positive participants. Second, we relied on self-swabbing to obtain estimates of swab positivity. A throat and nose swab is estimated to have 70% to 80% sensitivity [16], so we are likely to have underestimated true prevalence, although, this would not be expected to have affected trend analysis or estimation of the R value. Third, it is possible that at least part of the trends we observe in swab positivity during our study may have been the result of changing availability symptom-driven test capacity. We mitigated this potential bias by monitoring the proportion of swab-positive participants who were asymptomatic (overall 72%, ranging by round from 65% to 81%) and by repeating R estimates for the subset of asymptomatic individuals in each round. Our findings have implications for control of the COVID-19 pandemic. Until effective vaccines are available and widely disseminated, control of the SARS-CoV-2 virus must rely on established public health measures [17] including social distancing, frequent han...

    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.

    About SciScore

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  3. Version published to 10.1101/2020.09.11.20192492v2 on medRxiv
  4. Version published to 10.1101/2020.09.11.20192492v1 on medRxiv