Abstract
Following SARS-CoV-2 emergence in China, a specific surveillance was implemented in France. Phylogenetic analysis of sequences retrieved through this surveillance suggests that detected initial introductions, involving non-clade G viruses, did not seed local transmission. Nevertheless, identification of clade G variants subsequently circulating in the country, with the earliest from a patient who neither travelled to risk areas nor had contact with travellers, suggests that SARS-CoV-2 might have been present before the first recorded local cases.
Highlights
Following SARS-CoV-2 emergence in China, a specific surveillance was implemented in France
Identification of clade G variants subsequently circulating in the country, with the earliest from a patient who neither travelled to risk areas nor had contact with travellers, suggests that SARS-CoV-2 might have been present before the first recorded local cases
As the COVID-19 epidemic progressed in the country, the task of identifying SARS-CoV-2 infections was shared with the National Reference Center for Respiratory Viruses (NRC)-associated laboratory in Lyon and extended to first line hospital laboratories in the whole country, with the NRC at Institut Pasteur focusing on the northern part of France, including the densely populated capital
Summary
Samples used in this study were collected as part of approved ongoing surveillance conducted by the NRC at Institut Pasteur (WHO reference laboratory providing confirmatory testing for COVID-19). The first European cases, who were originally in Île-de-France (IDF) and who were previously described elsewhere [6], were direct imports from Hubei, China They were sampled on 24 January 2020 and the two derived respective viral genomes, IDF0372 and IDF0373, fall near the base of the tree, within clade V, according to GISAID nomenclature (Figure 2, Figure 3A). Several genomes correspond to patients in GE, Normandie (N), IDF, Hauts-de-France (HF) and B with recent history of travel in Europe (GE3067, N1620, IDF2792), United Arab Emirates (IDF2936), Madagascar (HF1993), Egypt (B1623, B2330) or linked to Paris airports (IDF1980) These genomes might represent additional introductions of the same clade, since the respective cases tested positive for the virus when other local G-clade-virus infections had already been detected in the north of France. It is impossible to infer with confidence how the virus was introduced to France from the epicentre of the outbreak, and multiple routes are possible
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