Author: Danesh, G.; Elie, B.; Michalakis, Y.; Sofonea, M. T.; Bal, A.; Behillil, S.; Destras, G.; Boutolleau, D.; Burrel, S.; Marcelin, A.-G.; Plantier, J.-C.; Thibault, V.; Simon-Loriere, E.; van der Werf, S.; Lina, B.; Josset, L.; Enouf, V.; Alizon, S.
Title: Early phylodynamics analysis of the COVID-19 epidemics in France Cord-id: 0e1wmy41 Document date: 2020_6_4
ID: 0e1wmy41
Snippet: France was one of the first countries to be reached by the COVID-19 pandemics. Here, we analyse 196 SARS-Cov-2 genomes collected between Jan 24 and Mar 24 2020, and perform a phylodynamics analysis. In particular, we analyse the doubling time, reproduction number (Rt) and infection duration associated with the epidemic wave that was detected in incidence data starting from Feb 27. We show that a slowing down of the epidemic spread can be detected in Mar, which is consistent with the implementati
Document: France was one of the first countries to be reached by the COVID-19 pandemics. Here, we analyse 196 SARS-Cov-2 genomes collected between Jan 24 and Mar 24 2020, and perform a phylodynamics analysis. In particular, we analyse the doubling time, reproduction number (Rt) and infection duration associated with the epidemic wave that was detected in incidence data starting from Feb 27. We show that a slowing down of the epidemic spread can be detected in Mar, which is consistent with the implementation of the national lock-down on Mar 17. The inferred distributions for the infection duration and Rt are in line with those estimated from contact tracing data. Overall, this analysis shows the potential to use sequence genomic data to inform public health decisions in an epidemic crisis context.
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