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Full genome viral sequences inform patterns of SARS-CoV-2 spread into and within Israel

Author

Listed:
  • Danielle Miller

    (Tel Aviv University)

  • Michael A. Martin

    (Emory University
    Emory University)

  • Noam Harel

    (Tel Aviv University)

  • Omer Tirosh

    (Tel Aviv University)

  • Talia Kustin

    (Tel Aviv University)

  • Moran Meir

    (Tel Aviv University)

  • Nadav Sorek

    (Assuta Ashdod University-Affiliated Hospital)

  • Shiraz Gefen-Halevi

    (Sheba Medical Center)

  • Sharon Amit

    (Sheba Medical Center)

  • Olesya Vorontsov

    (Hadassah Hebrew University Medical Center)

  • Avraham Shaag

    (Hadassah Hebrew University Medical Center)

  • Dana Wolf

    (Hadassah Hebrew University Medical Center)

  • Avi Peretz

    (Bar-Ilan University
    The Baruch Padeh Medical Center)

  • Yonat Shemer-Avni

    (Ben-Gurion University of the Negev)

  • Diana Roif-Kaminsky

    (Barzilai University Medical Center)

  • Naama M. Kopelman

    (Holon Institute of Technology)

  • Amit Huppert

    (Bio‐statistical and Bio‐mathematical Unit, The Gertner Institute for Epidemiology and Health Policy Research, Chaim Sheba Medical Center
    Tel‐Aviv University)

  • Katia Koelle

    (Emory University
    Emory-UGA Center of Excellence of Influenza Research and Surveillance (CEIRS))

  • Adi Stern

    (Tel Aviv University
    Tel Aviv University)

Abstract

Full genome sequences are increasingly used to track the geographic spread and transmission dynamics of viral pathogens. Here, with a focus on Israel, we sequence 212 SARS-CoV-2 sequences and use them to perform a comprehensive analysis to trace the origins and spread of the virus. We find that travelers returning from the United States of America significantly contributed to viral spread in Israel, more than their proportion in incoming infected travelers. Using phylodynamic analysis, we estimate that the basic reproduction number of the virus was initially around 2.5, dropping by more than two-thirds following the implementation of social distancing measures. We further report high levels of transmission heterogeneity in SARS-CoV-2 spread, with between 2-10% of infected individuals resulting in 80% of secondary infections. Overall, our findings demonstrate the effectiveness of social distancing measures for reducing viral spread.

Suggested Citation

  • Danielle Miller & Michael A. Martin & Noam Harel & Omer Tirosh & Talia Kustin & Moran Meir & Nadav Sorek & Shiraz Gefen-Halevi & Sharon Amit & Olesya Vorontsov & Avraham Shaag & Dana Wolf & Avi Peretz, 2020. "Full genome viral sequences inform patterns of SARS-CoV-2 spread into and within Israel," Nature Communications, Nature, vol. 11(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-19248-0
    DOI: 10.1038/s41467-020-19248-0
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    Cited by:

    1. Edyth Parker & Catelyn Anderson & Mark Zeller & Ahmad Tibi & Jennifer L. Havens & Geneviève Laroche & Mehdi Benlarbi & Ardeshir Ariana & Refugio Robles-Sikisaka & Alaa Abdel Latif & Alexander Watts & , 2022. "Regional connectivity drove bidirectional transmission of SARS-CoV-2 in the Middle East during travel restrictions," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    2. Shenoy, Ajay & Sharma, Bhavyaa & Xu, Guanghong & Kapoor, Rolly & Rho, Haedong Aiden & Sangha, Kinpritma, 2022. "God is in the rain: The impact of rainfall-induced early social distancing on COVID-19 outbreaks," Journal of Health Economics, Elsevier, vol. 81(C).
    3. Bjarke Frost Nielsen & Kim Sneppen & Lone Simonsen & Joachim Mathiesen, 2021. "Differences in social activity increase efficiency of contact tracing," The European Physical Journal B: Condensed Matter and Complex Systems, Springer;EDP Sciences, vol. 94(10), pages 1-11, October.

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