PHYLODYNAMIC of SARS-CoV-2 TRANSMISSION in FRANCE: 2020

ABSTRACT

Background: In 2020, France reported 2.7 million cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), making it the second most affected European country by the COVID-19 pandemic after the United Kingdom. However, dynamics of SARS-CoV-2 transmissions within France or between France and other countries remains partially characterized. We propose an analysis of these dynamics on multiple scales, from the continents to the French administrative regions. Methods: We produced 736 SARS-CoV-2 sequences from Ile-de-France (Paris area, France) and analyzed them concomitantly with GISAID deposited sequences to elucidate the origins and spread of the virus from January 2020 to December 2020. A total of 4,571 worldwide sequences, including 1,652 French sequences, constituted the final dataset. All sequences were selected to be representative of each country temporal distribution of SARS-CoV-2 to the week resolution. We used a maximum likelihood phylogenetic framework to estimate the most probable temporal and geographic spread of SARS-CoV-2 within France and worldwide. Depending on the geographical focus (France, Europe or worldwide), we pruned the tree accordingly in 1,000 independent replicates. Results: Phylogenetic analysis revealed that, during the 1st French epidemic wave (from March to May), the majority of viruses introduced to France came from North America (USA) and Europe (Spain, Italy, ?). France regularly transmitted to neighboring European countries Belgium, Germany, Italy and United Kingdom. Contrary to the 1st wave, inter-country transmission events were limited to neighboring countries and intercontinental transmission were almost absent during the French 2nd wave (from September to November). At the French regions-scale, we observed that Ile-de-France (IDF) was the main source of infections for all other French regions during the 1st epidemic wave, with a minor participation of Provence-Alpes-Côte d'Azur (PACA). For the 2nd epidemic wave, PACA was the main source of infections for all other French regions, with a lower participation of IDF and other regions. Conclusion: Overall, our findings allow a more comprehensive representation of SARS-CoV-2 transmission chains related to and within France and the global temporal distribution of those events, in link with control measures applied during the whole 2020 period. IDF and PACA were the main hubs of transmissions in France for the 1st and the 2nd epidemic waves, respectively.