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Michael Novakhov – SharedNewsLinks℠: Introductions and early spread of SARS-CoV-2 in France | bioRxiv



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Introductions and early spread of SARS-CoV-2 in France

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, Etienne Simon-Loriere
Sylvie Behillil

2National Reference Center for Respiratory Viruses, Institut Pasteur, Paris, France
3Molecular Genetics of RNA Viruses, CNRS – UMR 3569, University of Paris, Institut Pasteur, Paris, France

Artem Baidaliuk

1Evolutionary genomics of RNA viruses, Institut Pasteur, Paris, France

Flora Donati

2National Reference Center for Respiratory Viruses, Institut Pasteur, Paris, France
3Molecular Genetics of RNA Viruses, CNRS – UMR 3569, University of Paris, Institut Pasteur, Paris, France

Mélanie Albert

2National Reference Center for Respiratory Viruses, Institut Pasteur, Paris, France
3Molecular Genetics of RNA Viruses, CNRS – UMR 3569, University of Paris, Institut Pasteur, Paris, France

Andreea Alexandru

4Mutualized Platform of Microbiology, Pasteur International Bioresources Network, Institut Pasteur, Paris, France

Maud Vanpeene

4Mutualized Platform of Microbiology, Pasteur International Bioresources Network, Institut Pasteur, Paris, France

Angela Brisebarre

2National Reference Center for Respiratory Viruses, Institut Pasteur, Paris, France
3Molecular Genetics of RNA Viruses, CNRS – UMR 3569, University of Paris, Institut Pasteur, Paris, France

Marion Barbet

2National Reference Center for Respiratory Viruses, Institut Pasteur, Paris, France
3Molecular Genetics of RNA Viruses, CNRS – UMR 3569, University of Paris, Institut Pasteur, Paris, France

Fawzi Derrar

5National Influenza Centre, Viral Respiratory Laboratory, Algiers, Algeria

Sylvie van der Werf

2National Reference Center for Respiratory Viruses, Institut Pasteur, Paris, France
3Molecular Genetics of RNA Viruses, CNRS – UMR 3569, University of Paris, Institut Pasteur, Paris, France

Vincent Enouf

2National Reference Center for Respiratory Viruses, Institut Pasteur, Paris, France
3Molecular Genetics of RNA Viruses, CNRS – UMR 3569, University of Paris, Institut Pasteur, Paris, France
4Mutualized Platform of Microbiology, Pasteur International Bioresources Network, Institut Pasteur, Paris, France

Abstract

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.

Michael Novakhov – SharedNewsLinks℠