Early phylodynamics analysis of the COVID-19 epidemic in France
Peer Community Journal
; 1(e45), 2021.
Article
in English
| CAB Abstracts | ID: covidwho-1893604
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 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.
Prion, Viral, Bacterial and Fungal Pathogens of Humans [VV210]; Molecular Biology and Molecular Genetics [ZZ360]; Genetics and Molecular Biology of Microorganisms [ZZ395]; human diseases; coronavirus disease 2019; viral diseases; public health; epidemics; molecular epidemiology; genomes; phylogenetics; disease incidence; detection; contact tracing; estimation; nucleotide sequences; genetic sequencing; genomics; man; Severe acute respiratory syndrome coronavirus 2; France; Homo; Hominidae; primates; mammals; vertebrates; Chordata; animals; eukaryotes; Severe acute respiratory syndrome-related coronavirus; Betacoronavirus; Coronavirinae; Coronaviridae; Nidovirales; positive-sense ssRNA Viruses; ssRNA Viruses; RNA Viruses; viruses; European Union Countries; high income countries; Mediterranean Region; OECD Countries; very high Human Development Index countries; Western Europe; Europe; SARS-CoV-2; viral infections; DNA sequences
Full text:
Available
Collection:
Databases of international organizations
Database:
CAB Abstracts
Language:
English
Journal:
Peer Community Journal
Year:
2021
Document Type:
Article
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