Full genome viral sequences inform patterns of SARS-CoV-2 spread into and within Israel
Authors: Nadav Sorek
Sharon Amit
Talia Kustin
Danielle Miller
Amit Huppert
Moran Meir
Adi Stern
Avi Peretz
Shiraz Gefen-Halevi
Katia Koelle
Dana Wolf
Diana Roif-Kaminsky
Michael A Martin
Avraham Shaag
Noam Harel
Yonat Shemer-Avni
Naama M Kopelman
Olesya Vorontsov
Omer Tirosh
Journal: Nature Communications (2020)
Discipline: Multidisciplinary
Keywords: genome sequences; SARS-CoV-2; viral spread; travelers; United States of America
Affiliations: The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel., Department of Biology, Emory University, Atlanta, GA, USA., Population Biology, Ecology, and Evolution Graduate Program, Laney Graduate School, Emory University, Atlanta, GA, USA., Microbiology Laboratory, Assuta Ashdod University-Affiliated Hospital, Ashdod, Israel., Clinical Microbiology Laboratory, Sheba Medical Center, Ramat-Gan, Israel., Clinical Virology Unit, Hadassah Hebrew University Medical Center, Jerusalem, Israel., The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel., Clinical Microbiology Laboratory, The Baruch Padeh Medical Center, Poriya, Tiberias, Israel., Clinical Virology Laboratory, Soroka Medical Center and the Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel., Microbiology Division, Barzilai University Medical Center, Ashkelon, Israel., Department of Computer Science, Holon Institute of Technology, Holon, Israel., Bio-statistical and Bio-mathematical Unit, The Gertner Institute for Epidemiology and Health Policy Research, Chaim Sheba Medical Center, 52621, Tel Hashomer, Israel., School of Public Health, The Sackler Faculty of Medicine, Tel-Aviv University, 69978, Tel Aviv, Israel., Emory-UGA Center of Excellence of Influenza Research and Surveillance (CEIRS), Atlanta, GA, USA., The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel. ., Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, Israel. .

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. 

Retracted: No

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 This article has a corrigendum:  In the above-mentioned article, it has come to the authorsu2019 attention that, during the preparation of Figure 5C and Supplemental Figure S2C for the final version of this article, the authors unintentionally assembled incorrect tubulin immunoblots due to similarities in the markings or names, such as FLT3 versus FT, between two similar experiments. The amended versions of these figures are shown below. Neither the quantitative determinations nor the conclusions of this article are altered. The authors apologize for these errors. http: genesdev.cshlp.org content 30 7 870.full **The corrigendum did not clarify the similarities between Fig. S4B and Fig.S4E** Could authors check it please and provide an explanation? ,