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Journal articles

Early phylodynamics analysis of the COVID-19 epidemic in France

Gonché Danesh 1 Baptiste Elie 1 Yannis Michalakis 1 Mircea Sofonea 1 Antonin Bal 2, 3, 4, 5 Sylvie Behillil 6, 7 Grégory Destras 8, 9, 3, 4, 5 David Boutolleau 10, 11 Sonia Burrel 10, 11 Anne-Geneviève Marcelin 10, 11 Jean-Christophe Plantier 12 Vincent Thibault 13 Etienne Simon-Loriere 14 Sylvie van der Werf 6, 7 Bruno Lina 6, 7 Laurence Josset 6, 7 Vincent Enouf 15, 6, 7 Samuel Alizon 16
1 MIVEGEC - Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle
2 IAI - Institut des Agents Infectieux [Lyon]
3 Hôpital de la Croix-Rousse [CHU - HCL]
4 VirPath - Virology and human respiratory Pathologies - Virology and human respiratory Pathologies
CIRI - Centre International de Recherche en Infectiologie - UMR
5 CIRI - Centre International de Recherche en Infectiologie - UMR
6 GMV-ARN (UMR_3569 / U-Pasteur_2) - Génétique Moléculaire des Virus à ARN - Molecular Genetics of RNA Viruses
7 CNR - Centre National de Référence des virus des infections respiratoires (dont la grippe) - National Reference Center Virus Influenzae [Paris]
8 HCL - Hospices Civils de Lyon
9 CNR - Centre National de Référence des Virus des Infections Respiratoires (dont la Grippe) [Lyon]
10 iPLESP - Institut Pierre Louis d'Epidémiologie et de Santé Publique
11 CHU Pitié-Salpêtrière [AP-HP]
12 Hôpital Charles Nicolle [Rouen]
13 CHU Pontchaillou [Rennes]
14 Génomique évolutive des virus à ARN - Evolutionary genomics of RNA viruses
15 PIBNet - Pasteur International Bioresources network
16 MIVEGEC-ETE - Evolution Théorique et Expérimentale
PEV - Perturbations, Evolution, Virulence
Résumé : 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.
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Journal articles
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https://hal.archives-ouvertes.fr/hal-03001114
Contributor : Samuel Alizon Connect in order to contact the contributor
Submitted on : Thursday, December 9, 2021 - 10:18:44 AM
Last modification on : Friday, May 20, 2022 - 11:06:35 AM

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TDS-MACS | AGROPOLIS | UNIV-MONTPELLIER | B3ESTE | IRD | ANR | CNRS | INSERM | HCL | ENS-LYON | UNIV-LYON1 | IPLESP | CIRI | CIRI-B-LINA-M-ROSA-CALATRAVA-VIRPATH | UNIV-PARIS | SORBONNE-UNIVERSITE | SU-MEDECINE | UDL | SU-TI | PASTEUR | UP-SCIENCES

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Gonché Danesh, Baptiste Elie, Yannis Michalakis, Mircea Sofonea, Antonin Bal, et al.. Early phylodynamics analysis of the COVID-19 epidemic in France. Peer Community Journal, Peer Community In/Centre Mersenne, 2021, 1, pp.e45. ⟨10.24072/pcjournal.40⟩. ⟨hal-03001114v2⟩

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