The 1st year of the COVID-19 epidemic in Estonia: an interrupted time series of population based nationwide cross-sectional studies

  1. Anneli Uusküla
  2. Ruth Kalda
  3. Mihkel Solvak
  4. Mikk Jürisson
  5. Meelis Käärik
  6. Krista Fischer
  7. Aime Keis
  8. Uku Raudvere
  9. Jaak Vilo
  10. Hedi Peterson
  11. Ene Käärik
  12. Mait Metspalu
  13. Tuuli Jürgenson
  14. Lili Milani
  15. Liis Kolberg
  16. Ene-Margit Tiit
  17. Kristjan Vassil

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Abstract

Background

Decisions about the continued need for control measures and the effect of introducing COVID-19 vaccinations rely on accurate and population-based data on SARS-CoV-2 positivity and risk factors for testing positive.

Methods

In this interrupted time series of population-based nationwide cross-sectional studies, data from nasopharyngeal testing and questionnaires were used to estimate the SARS-CoV-2 RNA prevalence and factors associated with test positivity over the 1 st year of the COVID-19 epidemic.

The study is registered with the ISRCTN Registry, ISRCTN10182320 .

Results

Between April 23, 2020 and February 2, 2021, results were available from 34,915 individuals and 27,870 samples from 11 consecutive studies. The percentage of people testing positive for SARS-CoV-2 decreased from 0.27% (95% CI 0.10% - 0.59%) in April to 0.04% (95% CI 0.00% - 0.22%) by the end of May and remained very low (0.01%, 95% CI 0.00% - 0.17%) until the end of August, followed by an increase since November (0.37%, 95% CI 0.18% - 0.68%) that escalated to 2.69% (95% CI 2.08% - 2.69%) in January 2021. In addition to substantial change in time, an increasing number of household members (for one additional OR 1.15, 95% CI 1.02-1.29), reporting current symptoms of COVID-19 (OR 2.21, 95% CI 1.59-3.09), and completing questionnaire in the Russian language (OR 1.85, 95% CI 1.15-2.99) were associated with increased odds for SARS-CoV-2 RNA positivity.

Conclusions

SARS-CoV-2 population prevalence needs to be carefully monitored as vaccine programmes are rolled out in order to inform containment decisions.

Strengths and limitations of this study

  • Our study relies upon nation-wide and population-based data on SARS-CoV-2 prevalence, and presents changes in prevalence over the whole 1st year of the Covid-19 epidemic.

  • Our analysis of SARS-CoV-2 infection risk factors is not limited to notification or health care-based case data.

  • Selection bias may have been introduced as a result of low response rate. The direction of bias is unclear, but most likely operates rather uniformly over the period of observation, though this presents less of a threat to the SARS-CoV-2 prevalence trend analysis.

  • Our data could be used to adequately project the future course of the SARS-CoV-2 epidemic and the effect of control measures.

Article activity feed

  1. ScreenIT

    SciScore for 10.1101/2021.09.06.21263154: (What is this?)

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

    Table 1: Rigor

    EthicsField Sample Permit: Using standardised methodology (population-based, random stratified sampling) 11 cross-sectional studies were conducted with data collection during April 23-29, April 30 – May 6, May 22-31, June 11-22, August 6-25, September 21 – October 3, November 11-19, November 26 – December 6, December 11-20 in 2020, and January 7-18, January 21 – February 2 in 2021.
    Sex as a biological variablenot detected.
    RandomizationUsing standardised methodology (population-based, random stratified sampling) 11 cross-sectional studies were conducted with data collection during April 23-29, April 30 – May 6, May 22-31, June 11-22, August 6-25, September 21 – October 3, November 11-19, November 26 – December 6, December 11-20 in 2020, and January 7-18, January 21 – February 2 in 2021.
    Blindingnot detected.
    Power Analysisnot 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 several limitations. The degree to which the study is representative of the larger population is influenced by the low response rate and potential selective factors associated with responses. To minimise non-response bias, the prevalence estimates were weighted (age, gender, and region) to ensure representativeness of the source population. Yet, there could be other factors for which we did not have detailed information about population distributions which are also associated with testing positive for SARS-CoV-2. The number of people testing SARS-CoV-2 RNA positive in the cross-sectional studies is low leading to relatively large uncertainty around estimates. We see the long period of observation and population-based nationwide study design as strengths of our work. Interpretation of changes in SARS-CoV-2 incidence and positivity rates originating from case notification or clinical cases is likely to be confounded by substantial changes in testing practice over time. Our study is based on a series of cross-sectional studies with a standardised methodology, and is thereby very unlikely to be influenced by the testing practice. As this evaluation is based upon observing a single population over time, we speculate that selection bias or unmeasured confounders would operate rather uniformly over the period of observation, though presenting a less threatening trend of SARS-CoV-2 prevalence and analysis of factors associated with SARS-CoV-2 positivity.

    Results from TrialIdentifier: We found the following clinical trial numbers in your paper:

    IdentifierStatusTitle
    ISRCTN10182320NANA

    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.

    Results from scite Reference Check: We found no unreliable references.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  2. Version published to 10.1101/2021.09.06.21263154 on medRxiv