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Published in BioRxiv - 04/29/2020
Fabiana Gámbaro, Sylvie Behillil, Artem Baidaliuk, Flora Donati, Mélanie Albert, Andreea Alexandru, Maud Vanpeene, Méline Bizard, Angela Brisebarre, Marion Barbet, Fawzi Derrar, Sylvie van der Werf, Vincent Enouf, View ORCID ProfileEtienne Simon-Loriere

Following the emergence of coronavirus disease (COVID-19) in Wuhan, China in December 2019, specific COVID-19 surveillance was launched in France on January 10, 2020. Two weeks later, the first three imported cases of COVID-19 into Europe were diagnosed in France. We sequenced 97 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes from samples collected between January 24 and March 24, 2020 from infected patients in France. Phylogenetic analysis identified several early independent SARS-CoV-2 introductions without local transmission, highlighting the efficacy of the measures taken to prevent virus spread from symptomatic cases. In parallel, our genomic data reveals the later predominant circulation of a major clade in many French regions, and implies local circulation of the virus in undocumented infections prior to the wave of COVID-19 cases. This study emphasizes the importance of continuous and geographically broad genomic sequencing and calls for further efforts with inclusion of asymptomatic infections.