Section: Evolutionary Biology
Topic: Evolution, Health sciences, Population biology

Early phylodynamics analysis of the COVID-19 epidemic in France

Danesh, Gonché1 ; Elie, Baptiste1; Michalakis, Yannis1 ; Sofonea, Mircea T1 ; Bal, Antonin2, 3; Behillil, Sylvie4; Destras, Grégory2, 3; Boutolleau, David5; Burrel, Sonia5; Marcelin, Anne-Geneviève5; Plantier, Jean-Christophe6; Thibault, Vincent7; Simon-Loriere, Etienne8; van der Werf, Sylvie4; Lina, Bruno4; Josset, Laurence4  ; Enouf, Vincent9, 4  ; Alizon, Samuel10, 1  
1 MIVEGEC, CNRS, IRD, Université de Montpellier, France
2 CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
3 Laboratoire de Virologie des HCL, Institut des agents Infectieux, Centre National de Référence des virus des infections respiratoires (dont la grippe), Hôpital de la Croix-Rousse, Lyon, France
4 National Reference Center for Respiratory Viruses, Molecular Genetics of RNA Viruses, CNRS-UMR 3569, The Institut Pasteur, Paris, France
5 Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique (iPLESP), AP-HP, Pitié Salpêtrière Hospital, Department of Virology, Paris, France
6 Laboratoire de Virologie, CHU Charles Nicolle, Rouen, France
7 Laboratoire de Virologie, CHU de Rennes, Rennes, France
8 Evolutionary genomics of RNA viruses, Institut Pasteur, Paris, France
9 Mutualized Platform of Microbiology, Pasteur International Bioresources Network, The Institut Pasteur, Paris, France
10 Center for Interdisciplinary Research in Biology (CIRB), College de France, CNRS, INSERM, Université PSL, Paris, France

Corresponding author(s): Josset, Laurence (laurence.josset@chu-lyon.fr); Enouf, Vincent (vincent.enouf@pasteur.fr); Alizon, Samuel (samuel.alizon@cnrs.fr)

10.24072/pcjournal.40 - Peer Community Journal, Volume 1 (2021), article no. e45.

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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.
Published online:
DOI: 10.24072/pcjournal.40
Type: Research article

Danesh, Gonché 1; Elie, Baptiste 1; Michalakis, Yannis 1; Sofonea, Mircea T 1; Bal, Antonin 2, 3; Behillil, Sylvie 4; Destras, Grégory 2, 3; Boutolleau, David 5; Burrel, Sonia 5; Marcelin, Anne-Geneviève 5; Plantier, Jean-Christophe 6; Thibault, Vincent 7; Simon-Loriere, Etienne 8; van der Werf, Sylvie 4; Lina, Bruno 4; Josset, Laurence 4; Enouf, Vincent 9, 4; Alizon, Samuel 10, 1

1 MIVEGEC, CNRS, IRD, Université de Montpellier, France
2 CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
3 Laboratoire de Virologie des HCL, Institut des agents Infectieux, Centre National de Référence des virus des infections respiratoires (dont la grippe), Hôpital de la Croix-Rousse, Lyon, France
4 National Reference Center for Respiratory Viruses, Molecular Genetics of RNA Viruses, CNRS-UMR 3569, The Institut Pasteur, Paris, France
5 Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique (iPLESP), AP-HP, Pitié Salpêtrière Hospital, Department of Virology, Paris, France
6 Laboratoire de Virologie, CHU Charles Nicolle, Rouen, France
7 Laboratoire de Virologie, CHU de Rennes, Rennes, France
8 Evolutionary genomics of RNA viruses, Institut Pasteur, Paris, France
9 Mutualized Platform of Microbiology, Pasteur International Bioresources Network, The Institut Pasteur, Paris, France
10 Center for Interdisciplinary Research in Biology (CIRB), College de France, CNRS, INSERM, Université PSL, Paris, France
License: CC-BY 4.0
Copyrights: The authors retain unrestricted copyrights and publishing rights 
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     author = {Danesh, Gonch\'e and Elie, Baptiste and Michalakis, Yannis and Sofonea, Mircea T and Bal, Antonin and Behillil, Sylvie and Destras, Gr\'egory and Boutolleau, David and Burrel, Sonia and Marcelin, Anne-Genevi\`eve and Plantier, Jean-Christophe and Thibault, Vincent and Simon-Loriere, Etienne and van der Werf, Sylvie and Lina, Bruno and Josset, Laurence and Enouf, Vincent and Alizon, Samuel},
     title = {Early phylodynamics analysis of the {COVID-19} epidemic in {France}},
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%A Boutolleau, David
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Danesh, Gonché; Elie, Baptiste; Michalakis, Yannis; Sofonea, Mircea T; Bal, Antonin; Behillil, Sylvie; Destras, Grégory; Boutolleau, David; Burrel, Sonia; Marcelin, Anne-Geneviève; Plantier, Jean-Christophe; Thibault, Vincent; Simon-Loriere, Etienne; van der Werf, Sylvie; Lina, Bruno; Josset, Laurence; Enouf, Vincent; Alizon, Samuel. Early phylodynamics analysis of the COVID-19 epidemic in France. Peer Community Journal, Volume 1 (2021), article  no. e45. doi : 10.24072/pcjournal.40. https://peercommunityjournal.org/articles/10.24072/pcjournal.40/

PCI peer reviews and recommendation, and links to data, scripts, code and supplementary information: 10.24072/pci.evolbiol.100107

Conflict of interest of the recommender and peer reviewers:
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article.

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