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Timing the SARS-CoV-2 Index Case in Hubei Province

View ORCID ProfileJonathan Pekar, Michael Worobey, Niema Moshiri, Konrad Scheffler, Joel O. Wertheim
doi: https://doi.org/10.1101/2020.11.20.392126
Jonathan Pekar
1Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA 92093, USA
2Department of Biomedical Informatics, University of California San Diego, La Jolla, CA 92093, USA
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Michael Worobey
3Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
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  • For correspondence: worobey@arizona.edu jwertheim@health.ucsd.edu
Niema Moshiri
4Department Computer Science & Engineering, University of California San Diego, La Jolla, CA 92093, USA
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Konrad Scheffler
5Illumina, Inc., San Diego, CA 92122, USA
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Joel O. Wertheim
6Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
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  • For correspondence: worobey@arizona.edu jwertheim@health.ucsd.edu
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Abstract

Understanding when SARS-CoV-2 emerged is critical to evaluating our current approach to monitoring novel zoonotic pathogens and understanding the failure of early containment and mitigation efforts for COVID-19. We employed a coalescent framework to combine retrospective molecular clock inference with forward epidemiological simulations to determine how long SARS-CoV-2 could have circulated prior to the time of the most recent common ancestor. Our results define the period between mid-October and mid-November 2019 as the plausible interval when the first case of SARS-CoV-2 emerged in Hubei province. By characterizing the likely dynamics of the virus before it was discovered, we show that over two-thirds of SARS-CoV-2-like zoonotic events would be self-limited, dying out without igniting a pandemic. Our findings highlight the shortcomings of zoonosis surveillance approaches for detecting highly contagious pathogens with moderate mortality rates.

Competing Interest Statement

JOW has received funding from Gilead Sciences, LLC (completed) and the CDC (ongoing) via grants and contracts to his institution unrelated to this research.

Footnotes

  • https://github.com/pekarj/SC2_Index_Case

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted November 24, 2020.
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Timing the SARS-CoV-2 Index Case in Hubei Province
Jonathan Pekar, Michael Worobey, Niema Moshiri, Konrad Scheffler, Joel O. Wertheim
bioRxiv 2020.11.20.392126; doi: https://doi.org/10.1101/2020.11.20.392126
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Timing the SARS-CoV-2 Index Case in Hubei Province
Jonathan Pekar, Michael Worobey, Niema Moshiri, Konrad Scheffler, Joel O. Wertheim
bioRxiv 2020.11.20.392126; doi: https://doi.org/10.1101/2020.11.20.392126

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