IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v12y2021i1d10.1038_s41467-021-26267-y.html
   My bibliography  Save this article

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
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-021-26267-y
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-021-26267-y?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    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.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Imelda Trejo & Nicolas W Hengartner, 2022. "A modified Susceptible-Infected-Recovered model for observed under-reported incidence data," PLOS ONE, Public Library of Science, vol. 17(2), pages 1-23, February.
    2. Martin Hellwig & Viola Priesemann & Guntram B. Wolff, 2021. "Reducing the Mobility of SARS-CoV-2 Variants to Safeguard Containments," Intereconomics: Review of European Economic Policy, Springer;ZBW - Leibniz Information Centre for Economics;Centre for European Policy Studies (CEPS), vol. 56(4), pages 234-236, July.
    3. Clara S. Grønkjær & Rune H. B. Christensen & Daniel Kondziella & Michael E. Benros, 2023. "Long-term neurological outcome after COVID-19 using all SARS-CoV-2 test results and hospitalisations in Denmark with 22-month follow-up," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
    4. Bello, Piera & Rocco, Lorenzo, 2022. "Education and COVID-19 excess mortality," Economics & Human Biology, Elsevier, vol. 47(C).
    5. Elina Lampi & Daniel Carelli & Jon Pierre & Björn Rönnerstrand, 2023. "Two pandemics: the COVID-19 pandemic’s impact on future AMR collaboration in Europe," Palgrave Communications, Palgrave Macmillan, vol. 10(1), pages 1-10, December.
    6. Mutahhar A. Dar & Bartlomiej Gladysz & Aleksander Buczacki, 2021. "Impact of COVID19 on Operational Activities of Manufacturing Organizations—A Case Study and Industry 4.0-Based Survive-Stabilise-Sustainability (3S) Framework," Energies, MDPI, vol. 14(7), pages 1-28, March.
    7. Shakhany, Mohammad Qaleh & Salimifard, Khodakaram, 2021. "Predicting the dynamical behavior of COVID-19 epidemic and the effect of control strategies," Chaos, Solitons & Fractals, Elsevier, vol. 146(C).
    8. Patrick Mellacher, 2022. "Endogenous viral mutations, evolutionary selection, and containment policy design," Journal of Economic Interaction and Coordination, Springer;Society for Economic Science with Heterogeneous Interacting Agents, vol. 17(3), pages 801-825, July.
    9. Carlo Corradini & Jesse Matheson & Enrico Vanino, 2024. "Neighbourhood labour structure, lockdown policies, and the uneven spread of COVID‐19: within‐city evidence from England," Economica, London School of Economics and Political Science, vol. 91(363), pages 944-979, July.
    10. Mario Morvan & Anna Lo Jacomo & Celia Souque & Matthew J. Wade & Till Hoffmann & Koen Pouwels & Chris Lilley & Andrew C. Singer & Jonathan Porter & Nicholas P. Evens & David I. Walker & Joshua T. Bunc, 2022. "An analysis of 45 large-scale wastewater sites in England to estimate SARS-CoV-2 community prevalence," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
    11. Kang, Yong Joo & Park, Dojoon & Eom, Young Ho, 2024. "Global contagion of US COVID-19 panic news," Emerging Markets Review, Elsevier, vol. 59(C).
    12. Kelsey M. Haas & Michael J. McGregor & Mehdi Bouhaddou & Benjamin J. Polacco & Eun-Young Kim & Thong T. Nguyen & Billy W. Newton & Matthew Urbanowski & Heejin Kim & Michael A. P. Williams & Veronica V, 2023. "Proteomic and genetic analyses of influenza A viruses identify pan-viral host targets," Nature Communications, Nature, vol. 14(1), pages 1-27, December.
    13. Teixeira, João Filipe & Silva, Cecília & Moura e Sá, Frederico, 2022. "The strengths and weaknesses of bike sharing as an alternative mode during disruptive public health crisis: A qualitative analysis on the users’ motivations during COVID-19," Transport Policy, Elsevier, vol. 129(C), pages 24-37.
    14. Shameena Gill & Alia Maisara Adenan & Adli Ali & Noor Akmal Shareela Ismail, 2022. "Living through the COVID-19 Pandemic: Impact and Lessons on Dietary Behavior and Physical Well-Being," IJERPH, MDPI, vol. 19(2), pages 1-23, January.
    15. Grégory Claeys & Zsolt Darvas & Maria Demertzis & Guntram B. Wolff, 2021. "The Great COVID-19 Divergence: Managing a Sustainable and Equitable Recovery in the EU," Intereconomics: Review of European Economic Policy, Springer;ZBW - Leibniz Information Centre for Economics;Centre for European Policy Studies (CEPS), vol. 56(4), pages 211-219, July.
    16. Holger Strulik & Volker Grossmann, 2022. "Life Cycle Economics with Infectious and Chronic Diseases," CESifo Working Paper Series 10141, CESifo.
    17. Carol Nash, 2022. "Enhancing Hopeful Resilience Regarding Depression and Anxiety with a Narrative Method of Ordering Memory Effective in Researchers Experiencing Burnout," Challenges, MDPI, vol. 13(2), pages 1-15, June.
    18. Bradley, Jake & Ruggieri, Alessandro & Spencer, Adam Hal, 2021. "Twin Peaks: Covid-19 and the labor market," European Economic Review, Elsevier, vol. 138(C).
    19. Spyros Niavis & Dimitris Kallioras & George Vlontzos & Marie-Noelle Duquenne, 2021. "COVID-19 Pandemic and Lockdown Fine Optimality," Economies, MDPI, vol. 9(1), pages 1-26, March.
    20. Weichen Wang & Andrea Gurgone & Humberto Martínez & Maria Cristina Barbieri Góes & Ettore Gallo & Ádam Kerényi & Enrico Maria Turco & Carla Coburger & Pêdra D. S. Andrade, 2022. "COVID-19 Mortality and Economic Losses: The Role of Policies and Structural Conditions," JRFM, MDPI, vol. 15(8), pages 1-28, August.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-26267-y. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.