Novel SARS-CoV-2 Variant Derived from Clade 19B, France

Abstract

We report a novel severe acute respiratory syndrome coronavirus 2 variant derived from clade 19B (HMN.19B variant or Henri Mondor variant). This variant is characterized by the presence of 18 amino acid substitutions, including 7-8 substitutions in the spike protein and 2 deletions. These variants actively circulate in different regions of France.

Keywords: COVID-19; France; HMN.19B variant; Henri Mondor variant; SARS-CoV-2; clade; coronavirus disease; respiratory infections; severe acute respiratory syndrome coronavirus 2; viruses; zoonoses.

Figure

Phylogenetic tree built with sequences from the 33 patients infected with the new HMN.19B or Henri Mondor variant and from 1,537 SARS-CoV-2–infected patients in France sampled during January 18–February 23, 2021, sequenced in 9 successive series. Phylogeny was performed after full-length genome alignment with Muscle 3.8.31 (maximum-likelihood model general time-reversible plus invariant sites model, 1,000 bootstrap replicates) by means of IQ-Tree 1.3.11.1 and iTOL. The HMN.19B (Henri Mondor) variant cluster is considerably different from all the others, with a 99% bootstrap value. HMN.19B sequences are colored according to the geographic origin of the patients: red, greater Paris area (IDF or HMN); blue, southeast France (ARA); green, southwest France (NAQ). *Original cluster in an occupational health unit; **cluster in the hematology department of our institution. Amino-acid substitutions and deletions detected in all sequences are described in the orange box. ARA, Auvergne-Rhône-Alpes; HMN, Henri Mondor; IDF, Ile-de-France; NAQ, Nouvelle-Aquitaine.