Fourteen months in and on the pandemic: questions, tools and insights

 

SARS-CoV-2 virus has spread over the world rapidly creating one of the largest pandemics ever. The absence of immunity, presymptomatic transmission, and the relatively high level of virulence of the COVID-19 infection led to a massive flow of patients in intensive care units (ICU). This un-precedented situation called for rapid quantitative analyses and robust modelling projections to best inform the general public, the care staff and the public health policy makers, in a context of lack of data and hindsight.

In this presentation, we discuss several aspects of the SARS-CoV-2 infection, spreading and evolu-tion tackled by the ETE modelling team using diverse methodologies from statistical modelling, phylodynamics and mathematical epidemiology. We address questions such as the early inference of key epidemiological parameters (reproduction numbers, wave initiation date, lockdown efficien-cies), the optimization of non-pharmaceutical control strategies, the epidemiological implications of spatial and transmission heterogeneity, how to anticipate short, medium-term dynamics, not forget-ting perspectives related to vaccine rollout and variants.

 

 

Recent publications:

Mircea T. Sofonea, Bastien Reyné, Baptiste Elie, Ramsès Djidjou-Demasse, Christian Selinger, Yannis Michalakis, Samuel Alizon (2021, Epidemics) Memory is key in capturing COVID-19 epidemiological dynamics [PDF]

Bénédicte Roquebert, Stéphanie Haim-Boukobza, Sabine Trombert-Paolantoni, Emmanuel Lecorche, Laura Verdurme, Vincent Foulongne, Christian Selinger, Yannis Michalakis, Samuel Alizon, Mircea T Sofonea, (2021, medRxiv) SARS-CoV-2 variants of concern are associated with lower RT-PCR amplification cycles between January and March 2021 in France 

Bastien Reyné, Gonché Danesh, Samuel Alizon, Mircea T. Sofonea (2020, medRxiv) Rt2: computing and visualising COVID-19 epidemics temporal reproduction number