Abstract
We investigated SARS-CoV-2 transmission dynamics in Italy, one of the countries hit hardest by the pandemic, using phylodynamic analysis of viral genetic and epidemiological data. We observed the co-circulation of multiple SARS-CoV-2 lineages over time, which were linked to multiple importations and characterized by large transmission clusters concomitant with a high number of infections. Subsequent implementation of a three-phase nationwide lockdown strategy greatly reduced infection numbers and hospitalizations. Yet we present evidence of sustained viral spread among sporadic clusters acting as “hidden reservoirs” during summer 2020. Mathematical modelling shows that increased mobility among residents eventually catalyzed the coalescence of such clusters, thus driving up the number of infections and initiating a new epidemic wave. Our results suggest that the efficacy of public health interventions is, ultimately, limited by the size and structure of epidemic reservoirs, which may warrant prioritization during vaccine deployment.
Highlights
We investigated SARS-CoV-2 transmission dynamics in Italy, one of the countries hit hardest by the pandemic, using phylodynamic analysis of viral genetic and epidemiological data
Named nCoV-2019, the virus likely emerged from several recombination events in bats and pangolins[4], and was subsequently introduced in the human population through zoonotic transmissions[1,5]; it was later renamed SARS-CoV-2, and recognized as the etiologic agent of Coronavirus Disease 2019 (COVID-19)[6]
As the epidemic quickly spread throughout the country, establishing Italy as one of the major SARS-CoV-2 hotspots[11], the Italian government declared a Public Health Emergency of National Importance, enabling the introduction of restriction measures to limit new infections[12]
Summary
We investigated SARS-CoV-2 transmission dynamics in Italy, one of the countries hit hardest by the pandemic, using phylodynamic analysis of viral genetic and epidemiological data. As the epidemic quickly spread throughout the country, establishing Italy as one of the major SARS-CoV-2 hotspots[11], the Italian government declared a Public Health Emergency of National Importance, enabling the introduction of restriction measures to limit new infections[12].
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