SARS-CoV-2 phylodynamics differentiates the effectiveness of non-pharmaceutical interventions

Rasigade, J.-P.; Barray, A.; Shapiro, J. T.; Coquisart, C.; Vigouroux, Y.; Bal, A.; Destras, G.; Vanhems, P.; Lina, B.; Josset, L.; Wirth, T.

Quantifying the effectiveness of large-scale non-pharmaceutical interventions against COVID-19 is critical to adapting responses against future waves of the pandemic. By combining phylogenetic data of 5,198 SARS-CoV-2 genomes with the chronology of non-pharmaceutical interventions in 57 countries, we examine how interventions and combinations thereof alter the divergence rate of viral lineages, which is directly related to the epidemic reproduction number. Home containment and education lockdown had the largest independent impacts and were predicted to reduce the reproduction number by 35% and 26%, respectively. However, we find that in contexts with a reproduction number >2, no individual intervention is sufficient to stop the epidemic and increasingly stringent intervention combinations may be required. Our phylodynamic approach can complement epidemiological models to inform public health strategies against COVID-19.