Rt2: computing and visualising COVID-19 epidemics temporal reproduction number

Bastien Reyné (1) , Gonché Danesh (1) , Samuel Alizon (2, 3) , Mircea T Sofonea (1)

1 MIVEGEC-ETE - Evolution Théorique et Expérimentale
2 MIVEGEC - Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle
3 CIRB - Centre interdisciplinaire de recherche en biologie

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 reproduction number (R t), which corresponds to the average number of secondary infections caused by an infected person. This number is computed with the R0 package, which better captures past variations, and the EpiEstim package, which provides a more accurate estimate of current values. R t can be computed in different countries using either the daily number of new cases or of deaths. For France, these numbers can also be computed at the regional and departmental level using also daily numbers of hospital and ICU admissions. Finally, in addition to R t , we represent the incidence using a one-week sliding window to buffer daily variations. Overall, Rt2 provides an accurate and timely overview of the state and speed of spread of COVID-19 epidemics at different scales, using different metrics. Context Monitoring the state and speed of spread of COVID-19 epidemics at the national and regional levels is crucial to implement non-pharmaceutical interventions (Flaxman et al., 2020). Every day, public health agencies communicate key figures to monitor the epidemic, especially incidences, which correspond to the number of new cases detected. These incidences are typically related to four variables, which are PCR-based detection, deaths, hospitalisations, and ICU admissions. The statistical analysis of time variations in these time series can inform us about epidemiological dynamics.

Domaines: Modélisation et simulation; Biodiversité et Ecologie; Santé publique et épidémiologie; Bio-Informatique, Biologie Systémique [q-bio.QM]; Evolution [q-bio.PE]; Systématique, phylogénie et taxonomie; Ecosystèmes; Interactions entre organismes; Santé; Génétique des populations [q-bio.PE]; Virologie

Bastien Reyné, Gonché Danesh, Samuel Alizon, Mircea T Sofonea. Rt2: computing and visualising COVID-19 epidemics temporal reproduction number. 2020. ⟨hal-03045490⟩