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Early phylodynamics analysis of the COVID-19 epidemic in France
- Source :
- Peer Community Journal, Peer Community Journal, Peer Community In/Centre Mersenne, 2021, ⟨10.1101/2020.06.03.20119925⟩, Peer Community Journal, 2021, 1, pp.e45. ⟨10.24072/pcjournal.40⟩, Peer Community Journal, Peer Community In/Centre Mersenne, 2021, 1, pp.e45. ⟨10.24072/pcjournal.40⟩
- Publication Year :
- 2021
- Publisher :
- HAL CCSD, 2021.
-
Abstract
- 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 andℛtare 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.
- Subjects :
- 0106 biological sciences
Coronavirus disease 2019 (COVID-19)
Genomic data
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
Context (language use)
[SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy
010603 evolutionary biology
01 natural sciences
03 medical and health sciences
[SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems
Incidence data
Pandemic
[SDV.BID.SPT] Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy
[SDV.BID.EVO] Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE]
[SDV.EE.ECO] Life Sciences [q-bio]/Ecology, environment/Ecosystems
[SDV.EE.SANT] Life Sciences [q-bio]/Ecology, environment/Health
030304 developmental biology
[SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology
[SDV.EE.SANT]Life Sciences [q-bio]/Ecology, environment/Health
0303 health sciences
[SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]
[SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE]
[SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE]
[SDV.EE.IEO] Life Sciences [q-bio]/Ecology, environment/Symbiosis
[INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation
[SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]
3. Good health
[SDE.BE] Environmental Sciences/Biodiversity and Ecology
Geography
Viral phylodynamics
[SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie
[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology
[SDV.GEN.GPO] Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE]
[SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie
[INFO.INFO-MO] Computer Science [cs]/Modeling and Simulation
[SDE.BE]Environmental Sciences/Biodiversity and Ecology
Contact tracing
Demography
[SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Subjects
Details
- Language :
- English
- ISSN :
- 28043871
- Database :
- OpenAIRE
- Journal :
- Peer Community Journal, Peer Community Journal, Peer Community In/Centre Mersenne, 2021, ⟨10.1101/2020.06.03.20119925⟩, Peer Community Journal, 2021, 1, pp.e45. ⟨10.24072/pcjournal.40⟩, Peer Community Journal, Peer Community In/Centre Mersenne, 2021, 1, pp.e45. ⟨10.24072/pcjournal.40⟩
- Accession number :
- edsair.doi.dedup.....d5802e688eb048c11621aa454ab6af7b