244

Title *

Early phylodynamics analysis of the COVID-19 epidemics in Franceuse asterix (*) to get italics

Authors *

Gonché Danesh, Baptiste Elie,Yannis Michalakis, Mircea T. Sofonea, Antonin Bal, Sylvie Behillil, Grégory Destras, David Boutolleau, Sonia Burrel, Anne-Geneviève Marcelin, Jean-Christophe Plantier, Vincent Thibault, Etienne Simon-Loriere, Sylvie van der Werf, Bruno Lina, Laurence Josset, Vincent Enouf, Samuel Alizon and the COVID SMIT PSL groupPlease use the format "First name initials family name" as in "Marie S. Curie, Niels H. D. Bohr, Albert Einstein, John R. R. Tolkien, Donna T. Strickland"

Year *

2020

Picture *

Abstract *

<p>France was one of the first countries to be reached by the COVID-19 pandemic. 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. Different models suggest a slowing down of the epidemic in Mar, which would be consistent with the implementation of the national lock-down on Mar 17. The inferred distributions for the effective infection duration and Rt are in line with those estimated from contact tracing data. Finally, based on the available sequence data, we estimate that the French epidemic wave originated between mid-Jan and early Feb. Overall, this analysis shows the potential to use sequence genomic data to inform public health decisions in an epidemic crisis context and calls for further analyses with denser sampling.</p>

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https://platform.gisaid.org/You should fill this box only if you chose 'All or part of the results presented in this preprint are based on data'. URL must start with http:// or https://

Indicate the full web address (DOI or URL) giving public access to these scripts (if you have any problems with the deposit of your scripts, please contact contact@evolbiol.peercommunityin.org). In case all raw scripts are included in the preprint, indicate the DOI or URL of the preprint. *

https://www.medrxiv.org/content/10.1101/2020.06.03.20119925v3.supplementary-materialYou should fill this box only if you chose 'Scripts were used to obtain or analyze the results'. URL must start with http:// or https://

Indicate the full web address (DOI, SWHID or URL) giving public access to these codes (if you have any problems with the deposit of your codes, please contact contact@evolbiol.peercommunityin.org). In case all raw codes are included in the preprint, indicate the DOI or URL of the preprint. *

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Keywords (optional)

phylodynamics, SARS-Cov-2, virus, France, outbreak

Methods that require specific expertise (optional)

NonePlease indicate the methods that may require specialised expertise during the peer review process (use a comma to separate various required expertises).

Thematic fields *

Evolutionary Epidemiology, Molecular Evolution, Phylogenetics / Phylogenomics

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Submission date

2020-06-04 13:13:57

Recommender

B. Jesse Shapiro

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