Limited spread of a rare spike E484K-harboring SARS-CoV-2 in Marseille, France

Philippe Colson (1, 2, 3) , Jacques Fantini (4) , Nouara Yahi (4) , Jeremy Delerce (2) , Anthony Levasseur (1, 2, 3) , Pierre-Edouard Fournier (2, 5, 3) , Jean-Christophe Lagier (1, 2, 3) , Didier Raoult (1, 2, 3) , Bernard La Scola (1, 2, 3)

1 MEPHI - Microbes évolution phylogénie et infections
2 IHU Marseille - Institut Hospitalier Universitaire Méditerranée Infection
3 APHM - Assistance Publique - Hôpitaux de Marseille
4 UNIS - Inserm U1072 - Unité de Neurobiologie des canaux Ioniques et de la Synapse
5 VITROME - Vecteurs - Infections tropicales et méditerranéennes

We detected SARS-CoV-2 of PANGO lineage R.1 with the spike substitution E484K in three patients. Eleven other sequences in France and 8,831 worldwide were available from GISAID, 92% originating from Japan. The three genome sequences from our institute were phylogenetically closest to another from Guinea-Conakry, where one of the patients had travelled. These viruses did not exhibit any unusual features in cell culture. Spike structural predictions indicated a 1.3-time higher transmissibility index than for the globally spread B.1.1.7 variant but also an affinity loss for gangliosides that might have slowed dissemination. The spread of new SARS-CoV-2 mutants/variants is still not well understood and therefore difficult to predict, and this hinders implementation of effective preventive measures, including adapted vaccines.

Domaines: Bactériologie; Cardiologie et système cardiovasculaire; Maladies émergentes; Maladies infectieuses; Parasitologie; Virologie

Philippe Colson, Jacques Fantini, Nouara Yahi, Jeremy Delerce, Anthony Levasseur, et al.. Limited spread of a rare spike E484K-harboring SARS-CoV-2 in Marseille, France. Archives of Virology, 2022, 167 (2), pp.583-589. ⟨10.1007/s00705-021-05331-4⟩. ⟨hal-03663685⟩