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

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, Yonat Shemer-Avni, Diana Roif-Kaminsky, Naama M. Kopelman, Amit Huppert, Katia Koelle and Adi Stern ()
Additional contact information
Danielle Miller: Tel Aviv University
Michael A. Martin: 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
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
Katia Koelle: Emory University
Adi Stern: Tel Aviv University

Nature Communications, 2020, vol. 11, issue 1, 1-10

Abstract: 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.

Date: 2020
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DOI: 10.1038/s41467-020-19248-0

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