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Rapid incidence estimation from SARS-CoV-2 genomes reveals decreased case detection in Europe during summer 2020

Author

Listed:
  • Maureen Rebecca Smith

    (Robert Koch Institute
    Robert Koch Institute)

  • Maria Trofimova

    (Robert Koch Institute
    Robert Koch Institute)

  • Ariane Weber

    (Max-Planck Institute for the Science of Human History)

  • Yannick Duport

    (Robert Koch Institute
    Robert Koch Institute)

  • Denise Kühnert

    (Max-Planck Institute for the Science of Human History
    German COVID Omics Initiative (deCOI))

  • Max von Kleist

    (Robert Koch Institute
    Robert Koch Institute
    German COVID Omics Initiative (deCOI))

Abstract

By October 2021, 230 million SARS-CoV-2 diagnoses have been reported. Yet, a considerable proportion of cases remains undetected. Here, we propose GInPipe, a method that rapidly reconstructs SARS-CoV-2 incidence profiles solely from publicly available, time-stamped viral genomes. We validate GInPipe against simulated outbreaks and elaborate phylodynamic analyses. Using available sequence data, we reconstruct incidence histories for Denmark, Scotland, Switzerland, and Victoria (Australia) and demonstrate, how to use the method to investigate the effects of changing testing policies on case ascertainment. Specifically, we find that under-reporting was highest during summer 2020 in Europe, coinciding with more liberal testing policies at times of low testing capacities. Due to the increased use of real-time sequencing, it is envisaged that GInPipe can complement established surveillance tools to monitor the SARS-CoV-2 pandemic. In post-pandemic times, when diagnostic efforts are decreasing, GInPipe may facilitate the detection of hidden infection dynamics.

Suggested Citation

  • Maureen Rebecca Smith & Maria Trofimova & Ariane Weber & Yannick Duport & Denise Kühnert & Max von Kleist, 2021. "Rapid incidence estimation from SARS-CoV-2 genomes reveals decreased case detection in Europe during summer 2020," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-26267-y
    DOI: 10.1038/s41467-021-26267-y
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    References listed on IDEAS

    as
    1. Nicky Phillips, 2021. "The coronavirus is here to stay — here’s what that means," Nature, Nature, vol. 590(7846), pages 382-384, February.
    2. Sean L. Wu & Andrew N. Mertens & Yoshika S. Crider & Anna Nguyen & Nolan N. Pokpongkiat & Stephanie Djajadi & Anmol Seth & Michelle S. Hsiang & John M. Colford & Art Reingold & Benjamin F. Arnold & Al, 2020. "Substantial underestimation of SARS-CoV-2 infection in the United States," Nature Communications, Nature, vol. 11(1), pages 1-10, December.
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