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.
Highlights
Full genome sequences are increasingly used to track the geographic spread and transmission dynamics of viral pathogens
The etiological agent of the disease was identified as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)[2,3], and the disease caused by the virus was named coronavirus disease 19 (COVID-19)
We set out to sequence SARS-CoV-2 from samples across the state of Israel, with the aim of gaining a better understanding of introductions of the virus into Israel, spread of the virus inside the country, and the epidemiology of the disease, including (a) the basic reproduction number of the virus before and after social distancing measures were implemented, and (b) the extent of viral superspreading within Israel
Summary
To gain a better understanding of the dynamics of SARS-CoV-2 spread into and within Israel, we sequenced the virus from a cohort of patients representing a random sample across Israel, resulting in 212 full-genome SARS-CoV-2 sequences (Methods). We note that existing phylodynamic analyses of SARS-CoV-2, focusing on a number of different geographic regions across the world, have shown that the effective reproduction number of the virus has decreased over time, as quarantine and social distancing measures have been implemented[21,22,23]. Many of these analyses have to date modeled reductions in the reproduction number as stemming from the depletion of susceptible individuals[23], rather than from reductions in the basic reproduction number R0, the latter of which would be consistent with lowering of contact rates. Addendum September 2020: the authors would like to note that following the relaxation of social distance measures in May, case counts have substantially climbed and Israel has entered a second lockdown
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
