Introduction and initial circulation of SARS-CoV-2 in France

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Following the emergence of COVID-19 disease in Wuhan in December 2019, syndromic surveillance was implemented in France from January 10, 2020. Two weeks later, the first three imported cases of COVID-19 in Europe were diagnosed in France.

The National Reference Center for Respiratory Viruses has been contributing to the genomic surveillance of SARS-CoV-2 for northern France since the first cases were identified.

A phylogenetic analysis of around a hundred genomes from samples collected from patients in France between January 24 and March 24, 2020 revealed several early introductions of SARS-CoV-2 without local transmission, emphasizing the efficacy of the measures taken to prevent the spread of the virus from symptomatic cases.

At the same time, these genomic data also confirmed the predominant circulation of viruses from the same clade in several French regions, which is compatible with multiple introductions in the country. The earliest sequence in this clade, dating from February 19, 2020, corresponds to a case without any travel history, suggesting that the virus had been circulating silently before the wave of COVID-19 cases.

The study also highlights the low genetic diversity of the virus and points to a lack of representativeness of the viruses sequenced in some regions. This makes it impossible to estimate the exact timing of the introduction of the virus or to pinpoint its source (whether imported directly from China or from an intermediate country), given the still incomplete sampling in many countries.

This research provides clues as to the origin of the epidemic in France and emphasizes the challenges involved in containing the spread of a virus when a proportion of the cases are asymptomatic.

"Sequencing the SARS-CoV-2 genome is vital to help us understand the evolution and spread of the virus in a given population. Thanks to the active efforts of the National Reference Center from the outset, even before the emergence of the first cases in France, we now know that the first imported, symptomatic cases did not lead to large-scale transmission of the virus across France," explains Professor Sylvie Van der Werf, Director of the National Reference Center (CNR) for Respiratory Viruses at the Institut Pasteur and joint last author of the study.

As Etienne Simon-Lorière, Head of the Evolutionary Genomics of RNA Viruses group at Institut Pasteur and joint last author of the study, points out, "Based on our initial observations, in light of the sequenced strains, the spread of the virus in France is associated with asymptomatic cases. We now need to sequence new strains in different regions to gain a better understanding of the spread of the virus through France."



Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020, Eurosurveillance, 13 août 2020

Fabiana Gambaro, Artem Baidaliuk, Sylvie Behillil, Flora Donati, Melanie Albert, Andreea Alexandru, Maud Vanpeene, Meline Bizard, Angela Brisebarre, Marion Barbet, Fawzi Derrar, Sylvie van der Werf, Vincent Enouf, Etienne Simon-Loriere

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