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COVID-19 epidemic severity is associated with timing of non-pharmaceutical interventions

By Manon Ragonnet-Cronin, Olivia Boyd, Lily Geidelberg, David Jorgensen, Fabricia F Nascimento, Igor Siveroni, Robert Johnson, Marc Baguelin, Zulma M Cucunuba, Elita Jauneikaite, Swapnil Mishra, Hayley A Thompson, Oliver John Watson, Neil Ferguson, Christl A. Donnelly, Erik Volz

Posted 18 Sep 2020
medRxiv DOI: 10.1101/2020.09.15.20194258

Background: 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. International comparisons are hampered by highly variable conditions under which epidemics spread and differences in the timing and scale of interventions. Cumulative COVID-19 morbidity and mortality are functions of both the rate of epidemic growth and the duration of uninhibited growth before interventions were implemented. Incomplete and sporadic testing during the early COVID-19 epidemic makes it difficult to identify how long SARS-CoV-2 was circulating in different places. SARS-CoV-2 genetic sequences can be analyzed to provide an estimate of both the time of epidemic origin and the rate of early epidemic growth in different settings. Methods: 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 cross-referenced with dates of the most stringent interventions in each location as well as the number of cumulative COVID-19 deaths following maximum intervention. Phylodynamic methods were used to estimate the rate of early epidemic growth and proxy estimates of epidemic size. Findings: The time elapsed between epidemic origin and maximum intervention is strongly associated with different measures of epidemic severity and explains 46% of variance in numbers infected at time of maximum intervention. The reproduction number is independently associated with epidemic severity. In multivariable regression models, epidemic severity was not associated with census population size. The time elapsed between detection of initial COVID-19 cases to interventions was not associated with epidemic severity, indicating that many locations experienced long periods of cryptic transmission. Interpretation: Locations where strong non-pharmaceutical interventions were implemented earlier experienced much less severe COVID-19 morbidity and mortality during the period of study.

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