id	author	title	date	pages	extension	mime	words	sentences	flesch	summary	cache	txt
cord-330287-bkqjkhwu	Miller, Danielle	Full genome viral sequences inform patterns of SARS-CoV-2 spread into and within Israel	2020-11-02		.txt	text/plain	6758	329	49	So-called genomic epidemiology allows for effective reconstruction of viral geographical spread as well as estimation of key epidemiological quantities such as the basic reproduction number of a virus, its growth rate and doubling time, and patterns of disease incidence and prevalence. Here, 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. To estimate the basic reproduction number of SARS-CoV-2 in Israel initially and then following the implementation of social distancing measures, we performed coalescent-based phylodynamic inference using the PhyDyn program implemented in BEAST2 (Methods). Our phylodynamic analysis assumes an underlying susceptibleexposed-infected-recovered (SEIR)-type epidemiological model for SARS-CoV-2 transmission dynamics and explicitly incorporates transmission heterogeneity ( Supplementary Fig. 4 , Methods).	./cache/cord-330287-bkqjkhwu.txt	./txt/cord-330287-bkqjkhwu.txt