Emergence in Southern France of a new SARS-CoV-2 variant of probably Cameroonian origin harbouring both substitutions N501Y and E484K in the spike protein

ABSTRACTSARS-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.</jats:p

Emergence in southern France of a new SARS-CoV-2 variant harbouring both N501Y and E484K substitutions in the spike protein

International audienceAbstract 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, with the index case returning from travel in Cameroon. For 13 SARS-CoV-2-positive patients living in the same geographical area of southeastern France, a qPCR test for screening variant-associated mutations showed an atypical combination. The genome sequences were obtained by next-generation sequencing with Oxford Nanopore Technologies on GridION instruments within about 8 h. Analysis revealed 46 nucleotide substitutions and 37 deletions, resulting in 30 amino acid substitutions and 12 deletions. Fourteen of the amino acid substitutions, including N501Y and E484K, and nine deletions are located in the spike protein. This genotype pattern led to the establishment of a new Pangolin lineage, named B.1.640.2, that is a phylogenetic sister group to the old B.1.640 lineage, which has now been renamed B.1.640.1. The lineages differ by 25 nucleotide substitutions and 33 deletions. The combination of mutations in these isolates and their phylogenetic position indicate, based on our previous definition, that they represent a new variant, which we have named “IHU”. These data are a further example of the unpredictability of the emergence of SARS-CoV-2 variants, and of their possible introduction into a given geographical area from abroad

Emergence in southern France of a new SARS-CoV-2 variant harbouring both N501Y and E484K substitutions in the spike protein

AbstractSARS-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, with the index case returning from travel in Cameroon. For 13 SARS-CoV-2-positive patients living in the same geographical area of southeastern France, a qPCR test for screening variant-associated mutations showed an atypical combination. The genome sequences were obtained by next-generation sequencing with Oxford Nanopore Technologies on GridION instruments within about 8 h. Analysis revealed 46 nucleotide substitutions and 37 deletions, resulting in 30 amino acid substitutions and 12 deletions. Fourteen of the amino acid substitutions, including N501Y and E484K, and nine deletions are located in the spike protein. This genotype pattern led to the establishment of a new Pangolin lineage, named B.1.640.2, that is a phylogenetic sister group to the old B.1.640 lineage, which has now been renamed B.1.640.1. The lineages differ by 25 nucleotide substitutions and 33 deletions. The combination of mutations in these isolates and their phylogenetic position indicate, based on our previous definition, that they represent a new variant, which we have named “IHU”. These data are a further example of the unpredictability of the emergence of SARS-CoV-2 variants, and of their possible introduction into a given geographical area from abroad.</jats:p

De la mer du Nord à la mer Baltique. Identités, contacts et communications au Moyen Âge

Au Moyen Âge, la mer du Nord a permis les contacts entre les populations de ses régions riveraines: les eaux séparant les îles Britanniques, le continent et la Scandinavie ne voyaient pas seulement se déplacer des missionnaires et des marchands, car c'est également de la mer que l'on vit arriver les vikings. La mer Baltique était en revanche beaucoup moins connue des auteurs occidentaux, qui étaient frappés par la multiplicité des peuples et des cultures qui en occupaient les rives : on mentionnait des ports de traite, des voyages de marchands, des populations aux coutumes étranges. Comparer les espaces de la mer du Nord et de la mer Baltique en tant que zones de contacts au Moyen Âge est une tâche difficile : non seulement les spécialistes ne prennent que trop rarement connaissance de leurs recherches respectives, mais l'horizon international nécessite la prise en compte de traditions historiographiques dans une multitude de langues nationales. Ce volume présente les résultats d'un atelier interdisciplinaire tenu à Boulogne-sur-Mer en octobre 2009, qui a réuni des chercheurs d'Europe du Nord-Ouest (Belgique, France, Luxembourg, Royaume-Uni) et du Centre-Est (Pologne et République tchèque) en soulignant les apports d'une nouvelle génération d'historiens et d'archéologues dans un domaine qui s'est radicalement transformé depuis une quinzaine d'années