The new variant was detected in early December in a traveler who returned to France from Cameroon, the hospital IHU Mediterrannee in Marseille announced.
The returnee from Cameroon reportedly infected 12 people in southern France.
This new mutant, called B.1.640.2, has 46 mutations in an “atypical combination,” according to a preprint study that has not yet been peer-reviewed.
The report posted on the preprint repository MedRxiv on December 29, revealed that IHU has 46 mutations and 37 deletions resulting in 30 amino acid substitutions and 12 deletions.
According to this study, the two already known spike protein mutations N501Y and E484K are also found in the new coronavirus variant. The N501Y mutation, for example, was detected very early in the alpha variant. It causes the pathogen to bind more strongly to human cells and thus to spread more easily in the body.
E484K is one of the escape mutations located directly in the spike protein and thus possibly reduces the effectiveness of COVID-19 vaccines.
ABSTRACT:
SARS-CoV-2 variants have become a major virological, epidemiological and clinical concern, particularly with regard to the risk of escape from vaccine-induced immunity. Here we describe the emergence of a new variant. For twelve SARS-CoV-positive patients living in the same geographical area of southeastern France, qPCR testing that screen for variant-associated mutations showed an atypical combination. The index case returned from a travel in Cameroon. The genomes were obtained by next-generation sequencing with Oxford Nanopore Technologies on GridION instruments within ≈8 h. Their analysis revealed 46 mutations and 37 deletions resulting in 30 amino acid substitutions and 12 deletions. Fourteen amino acid substitutions, including N501Y and E484K, and 9 deletions are located in the spike protein. This genotype pattern led to create a new Pangolin lineage named B.1.640.2, which is a phylogenetic sister group to the old B.1.640 lineage renamed B.1.640.1. Both lineages differ by 25 nucleotide substitutions and 33 deletions. The mutation set and phylogenetic position of the genomes obtained here indicate based on our previous definition a new variant we named “IHU”. These data are another example of the unpredictability of the emergence of SARS-CoV-2 variants, and of their introduction in a given geographical area from abroad.
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