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Unprecedented public health interventions including travel restrictions and national lockdowns have been implemented to stem the COVID-19 epidemic, but the effectiveness of non-pharmaceutical interventions is still debated. We carried out a phylogenetic analysis of more than 29,000 publicly available whole genome SARS-CoV-2 sequences from 57 locations to estimate the time that the epidemic originated in different places. These estimates were examined in relation to the dates of the most stringent interventions in each location as well as to the number of cumulative COVID-19 deaths and phylodynamic estimates of epidemic size. Here we report that the time elapsed between epidemic origin and maximum intervention is associated with different measures of epidemic severity and explains 11% of the variance in reported deaths one month after the most stringent intervention. Locations where strong non-pharmaceutical interventions were implemented earlier experienced much less severe COVID-19 morbidity and mortality during the period of study.

Original publication




Journal article


Nature communications

Publication Date





MRC Centre for Global Infectious Disease Analysis and the Department of Infectious Disease Epidemiology, Imperial College London, London, UK.


Humans, Severity of Illness Index, Public Health, Communicable Disease Control, Phylogeny, Epidemics, Phylogeography, COVID-19, SARS-CoV-2