Fig. 1.

Virological features and scanning electron microscopy image of the SARS-CoV-2 IHU variant. (a) Map of the IHU variant genome showing amino acid substitutions and deletions. (b) Phylogeny reconstruction based on genome sequences of Pangolin lineage B.1.640.2 (available from the GISAID sequence database as of December 31, 2021). Phylogenetic analysis was performed using the nextstrain/ncov tool (https://github.com/nextstrain/ncov) and visualized using Auspice (https://docs.nextstrain.org/projects/auspice/en/stable/). The x-axis shows time. This figure is adapted from screenshots of the nextclade web application (https://clades.nextstrain.org) [9, 10]. Sequences are labelled with the GISAID identifier ((https://www.gisaid.org/) [12]), the country and region of origin, and the date of the patient’s sampling. ARA, Auvergne-Rhône-Alpes (French region); IDF, Ile-de-France (French region); IHU-MI, University Hospital Institute Méditerranée Infection (Marseille, France); PACA, Provence-Alpes-Côte d’Azur (French region). Sequences from France are shown in blue. Sequences obtained in our laboratory (IHU Méditerranée Infection, Marseille, France) are indicated by a pale blue background. (c) Representation of the spike of the IHU variant showing the location of all of its amino acid substitutions and deletions. N-terminal domain (NTD) mutations are in blue, receptor binding domain (RBD) mutations are in red, mutations involved in ACE-2 unmasking are in yellow, mutations at the S1-S2 cleavage site are in green, and mutations in the fusion region are in cyan. (d) Scanning electron microscopy image of a respiratory sample positive for the SARS-CoV-2 IHU variant, obtained using a SUV 5000 microscope (Hitachi High-Technologies Corporation, Tokyo, Japan)