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

Abstract

Introduction In Marseille, France, following a first SARS-CoV-2 outbreak in March-May 2020, a second epidemic phase occurred from June, involving ten new variants. The Marseille-4 variant caused an epidemic that started in August and is still ongoing. Materials and methods The 1,038 SARS-CoV-2 whole genome sequences obtained in our laboratory by next-generation sequencing with Illumina technology were analyzed 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 Marseille-4 and earlier strains. Results Marseille-4 harbors 13 hallmark mutations. One leads to S477 N substitution in the spike receptor binding domain targeted by current vaccines. Using a specific qPCR, we observed that Marseille-4 caused 12-100% of SARS-CoV-2 infections in Marseille from September 2020, being involved in 2,106 diagnoses. This variant was more frequently associated with hypoxemia than clade 20A strains before May 2020. It caused re-infection in eleven patients SARS-CoV-2-diagnosed with different strains before June 2020, suggesting either short-term protective immunity or lack of cross-immunity. Discussion/conclusion Marseille-4 should be considered as a major SARS-CoV-2 variant. Its sudden appearance points toward an animal reservoir, possibly minks. The protective role of past-exposure and current vaccines against this variant should be evaluated.

Does SARS-CoV-2 re-infection depend on virus variant?

“…The second wave took place between mid-June 2020 and February 2021 and was linked to the Marseille-1 variant (M1V), which had an African origin, and to the Marseille-4 variant (M4V) likely originating from a mink farm in the North of France. The M1V reached a very weak peak of incidence but accounted for up to 100% of infections during part of July 2020, then disappeared after 1.5 month [ 2 ], while incidence of the M4V that appeared in July 2020 showed an atypical wave shape and continued to account for a significant proportion of the cases in February 2021, indicating a duration of seven months [ 3 ]. Finally, the third wave due to N501Y variants (N501YV) previously identified in the UK, South Africa and Brazil started in early 2021, peaked in early April 2021 and numbers of cases are now rapidly decreasing.…”

The Spike of Concern—The Novel Variants of SARS-CoV-2

“…An example of a spill over from an animal reservoir is the Marseille-4 variant (Table 1) that appeared suddenly in France at the end of the first SARS-CoV-2 wave in July 2020 (Figure 2) in an area close to a mink farm [47].…”

Rapid Isothermal Amplification for the Buccal Detection SARS-CoV-2 in the Context of Out-Patient COVID-19 Screening

“…Simultaneously, a nasopharyngeal swab was taken for each patient to perform RT-PCR analysis targeting the envelope protein (E)-encoding gene or the nucleocapsid protein (N)-encoding gene, as previously described [ 4 , 17 ]. The two technologies RT-PCR and isothermal amplification used in this study were able to detect the SARS-CoV-2 variants including the Marseille 4 variant [ 18 ] and the variant N501Y circulating in Marseille at the time of the study [ 19 ].…”