Full genome sequences are increasingly used to track the geographic spread and transmission dynamics of viral pathogens. Here, with a focus on Israel, we sequenced 212 SARS-CoV-2 sequences and use them to perform a comprehensive analysis to trace the origins and spread of the virus. A phylogenetic analysis including thousands of globally sampled sequences allowed us to infer multiple independent introductions into Israel, followed by local transmission. Returning travelers from the U.S. contributed dramatically more to viral spread relative to their proportion in incoming infected travelers. Using phylodynamic analysis, we estimated that the basic reproduction number of the virus was initially around ~2.0-2.6, dropping by two-thirds following the implementation of social distancing measures. A comparison between reported and model-estimated case numbers indicated high levels of transmission heterogeneity in SARS-CoV-2 spread, with between 1-10% of infected individuals resulting in 80% of secondary infections. Overall, our findings underscore the ability of this virus to efficiently transmit between and within countries, as well as demonstrate the effectiveness of social distancing measures for reducing its spread.

中文翻译：

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全基因组病毒序列为SARS-CoV-2在以色列内外传播的模式提供了信息

全基因组序列越来越多地用于跟踪病毒病原体的地理传播和传播动态。在这里，以以色列为重点，我们对212条SARS-CoV-2序列进行了测序，并使用它们进行了全面的分析，以追踪病毒的起源和传播。系统发育分析包括数千个全球采样序列，使我们可以推断出多次独立引入以色列，然后进行局部传播。从美国返回的旅行者相对于在传入的感染旅行者中所占的比例，对病毒传播的贡献更大。使用系统动力学分析，我们估计该病毒的基本繁殖数量最初约为2.0-2.6，在实施社会隔离措施后下降了三分之二。报告的病例数与模型估计的病例数之间的比较表明，SARS-CoV-2传播的传播异质性水平很高，受感染的个体中有1-10％导致了80％的继发感染。总体而言，我们的发现强调了这种病毒在国家之间和国家内部有效传播的能力，并证明了社会疏远措施对于减少其传播的有效性。