Emergence and outcomes of the SARS-CoV-2 'Marseille-4' variant

Abstract

Background: In Marseille, France, following a first severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak in March-May 2020, a second epidemic phase occurred from June, involving 10 new variants. The Marseille-4 variant caused an epidemic that started in August and is still ongoing.

Methods: The 1038 SARS-CoV-2 whole genome sequences obtained in our laboratory by next-generation sequencing with Illumina technology were analysed using Nextclade and nextstrain/ncov pipelines and IQ-TREE. A Marseille-4-specific qPCR assay was implemented. Demographic and clinical features were compared between patients with the Marseille-4 variant and those with earlier strains.

Results: Marseille-4 harbours 13 hallmark mutations. One leads to an S477N substitution in the receptor binding domain of the spike protein targeted by current vaccines. Using a specific qPCR, it was observed that Marseille-4 caused 12-100% of SARS-CoV-2 infections in Marseille from September 2020, being involved in 2106 diagnoses. This variant was more frequently associated with hypoxemia than were clade 20A strains before May 2020. It caused a re-infection in 11 patients diagnosed with different SARS-CoV-2 strains before June 2020, suggesting either short-term protective immunity or a lack of cross-immunity.

Conclusions: Marseille-4 should be considered as a major SARS-CoV-2 variant. Its sudden appearance points towards an animal reservoir, possibly mink. The protective role of past exposure and current vaccines against this variant should be evaluated.

Keywords: COVID-19; Marseille-4; Molecular epidemiology; Mutations; SARS-CoV-2; Spike; Variant.

Figure 1

Schematic diagram of the evolution of the SARS-CoV-2 Marseille-4 variant in Europe.

Figure 2

Evolution of the Marseille-4 variant over time. (a) Weekly number of genomes of the Marseille-4 variant worldwide. (b) Weekly frequency normalized to 100% of the countries where genomes of the Marseille-4 variant were obtained. (c) Time distribution of the daily number of genomes of the Marseille-4 variant per country. (d) Weekly number of genomes of the Marseille-4 variant in French regions. (e) Weekly frequency normalized to 100% of the French regions where genomes of the Marseille-4 variant were obtained.

Figure 3

Genome sequence-based phylogenetic trees showing the evolution of SARS-CoV-2 Marseille-4 variant strains. (a) Time-scale phylogenetic tree. (b) Phylogenetic tree based on mutational events. Full-length genome sequences obtained in this study were compared to those available in the GISAID database (https://www.gisaid.org/). Phylogenetic trees were reconstructed and visualized using the Nextstrain pipeline (https://github.com/nextstrain/ncov/) (Hadfield et al., 2018).

Figure 4

Three-dimensional structure of the spike protein showing the amino acid substitutions in the receptor-binding motif of the Marseille-4 variant and of other variants detected in humans and/or mink. The structure was predicted using the Phyre2 web portal (http://www.sbg.bio.ic.ac.uk/∼phyre2/html/page.cgi?id=index) (Kelley et al., 2015) and visualized using the Pymol tool v.1.8 (https://pymol.org/2/) (Janson and Paiardini, 2020). Amino acids where a substitution was observed in humans are shown in red, those where a substitution was observed in mink are shown in yellow, and those where a substitution was observed in humans and mink are shown in orange.

Figure 5

Phylogenetic tree based on SARS-CoV-2 full-length genomes. A total of 744 genomes of SARS-CoV-2 were integrated in a phylogenetic analysis. All genomes were aligned using MAFFT version 7 (Katoh and Standley, 2013). The phylogenetic tree was reconstructed using IQ-TREE with the GTR model, with 1000 ultrafast bootstrap repetitions (Minh et al., 2020), and was visualized with iTOL (Interactive Tree Of Life; https://itol.embl.de/) (Letunic and Bork, 2016). DK, Denmark; NTH, The Netherlands.