Gonché Danesh

Gonché Danesh
French National Centre for Scientific Research | CNRS · Maladies Infectieuses et Vecteurs Ecologie, Génétique, Evolution et Contrôle (MIVEGEC)

About

10
Publications
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29
Citations

Publications

Publications (10)
Preprint
Phylodynamic analyses generate important and timely data to optimise public health response to SARS-CoV-2 outbreaks and epidemics. However, their implementation is hampered by the massive amount of sequence data and the difficulty to parameterise dedicated software packages. We introduce the COVFlow pipeline, accessible at https://gitlab.in2p3.fr/e...
Article
Full-text available
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 inci...
Preprint
Analysing 92,598 variant screening tests performed on SARS-CoV-2 positive samples collected in France between 1 July and 31 August 2021 shows an increase of Kappa-like infections. Full genome sequencing reveals that these correspond to Delta variants bearing the S:E484Q mutation. Most of these sequences belong to a phylogenetic cluster and also bea...
Article
Full-text available
Opioid substitution and syringes exchange programs have drastically reduced hepatitis C virus (HCV) spread in France but HCV sexual transmission in men having sex with men (MSM) has recently arisen as a significant public health concern. The fact that the virus is transmitting in a heterogeneous population, with different transmission routes, makes...
Thesis
Full-text available
Le contrôle des maladies infectieuses est un enjeu majeur en santé publique humaine, animale et végétale. Aux données épidémiologiques classiques telles que l'incidence ou la prévalence, se sont ajoutées des données génétiques issues des progrès des techniques de séquençage. L’abondance de ces données associée à l’évolution rapide des pathogènes, e...
Preprint
Analysing the spread of COVID-19 epidemics in a timely manner is essential for public health authorities. However, raw numbers may be misleading because of spatial and temporal variations. We introduce Rt2, an R-program with a shiny interface, which uses incidence data, i.e. number of new cases per day, to compute variations in the temporal reprodu...
Preprint
Full-text available
We introduce TiPS, an R-based simulation software to generate time series and genealogies associated with a population dynamics model. The approach is flexible since it can capture any model defined with a set of ordinary differential equations (ODE), and allow parameter values to vary over time periods. Computational time is minimal thanks to the...
Preprint
Full-text available
France was one of the first countries to be reached by the COVID-19 pandemics. 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 (R t) and infection duration associated with the epidemic wave that was detected in in...
Article
Full-text available
Natural transformation is the acquisition, controlled by bacteria, of extracellular DNA and is one of the most common mechanisms of horizontal gene transfer, promoting the spread of resistance genes. However, its evolutionary function remains elusive, and two main roles have been proposed: (i) the new gene acquisition and genetic mixing within bact...
Preprint
Full-text available
Opioid substitution and syringes exchange programs have drastically reduced hepatitis C virus (HCV) spread in France but HCV sexual transmission in men having sex with men (MSM) has recently arose as a significant public health concern. The fact that the virus is transmitting in a heterogeneous population, with 'new' and 'classical' hosts, makes pr...

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Projects

Project (1)
Project
Studying the spread and the evolution of SARS-CoV-2 at the within- and between-host levels using various type of data (incidence, sequences, Ct).