A framework for reconstructing SARS-CoV-2 transmission dynamics using excess mortality data

  1. Mahan Ghafari
  2. Oliver J. Watson
  3. Ariel Karlinsky
  4. Luca Ferretti
  5. Aris Katzourakis

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Abstract

The transmission dynamics and burden of SARS-CoV-2 in many regions of the world is still largely unknown due to the scarcity of epidemiological analyses and lack of testing to assess the prevalence of disease. In this work, we develop a quantitative framework based on excess mortality data to reconstruct SARS-CoV-2 transmission dynamics and assess the level of underreporting in infections and deaths. Using weekly all-cause mortality data from Iran, we are able to show a strong agreement between our attack rate estimates and seroprevalence measurements in each province and find significant heterogeneity in the level of exposure across the country with 11 provinces reaching near 100% attack rates. Despite having a young population, our analysis reveals that incorporating limited access to medical services in our model, coupled with undercounting of COVID-19-related deaths, leads to estimates of infection fatality rate in most provinces of Iran that are comparable to high-income countries.

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  1. Version published to 10.1038/s41467-022-30711-y
  2. Version published to 10.1101/2021.10.04.21264540v2 on medRxiv
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    SciScore for 10.1101/2021.10.04.21264540: (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

    Experimental Models: Cell Lines
    SentencesResources
    By weighting the known age-stratified IFR estimates for COVID-19 [29], IFRi, by the fraction of the population in each age-group, , we can account for the non-uniform attack rate per age group and find an average province-level IFR, ⟨IFR⟩, which we then use to estimate the attack rates.
    COVID-19
    suggested: None
    Software and Algorithms
    SentencesResources
    We use the data from the beginning of year 1394 to the end of summer 1398 in Solar Hijri calendar (SH) (from 2015-03-15 to 2019-09-22 in Common Era) to calculate background mortality.
    Solar
    suggested: (SOLAR, RRID:SCR_000850)

    Results from OddPub: Thank you for sharing your code and data.

    Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

    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.

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

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  4. Version published to 10.1101/2021.10.04.21264540v1 on medRxiv