Emergence in Southern France of a new SARS-CoV-2 variant of probably Cameroonian origin

 Philippe Colson, Jérémy Delerce, Emilie Burel, Jordan Dahan, Agnès Jouffret, Florence Fenollar, Nouara Yahi, Jacques Fantini, Bernard La Scola, Didier Raoult

doi: https://doi.org/10.1101/2021.12.24.21268174

This article is a preprint and has not been peer-reviewed [what does this mean?]. It reports new medical research that has yet to be evaluated and so should not be used to guide clinical practice.

PDF: https://www.medrxiv.org/content/10.1101/2021.12.24.21268174v1.full.pdf

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.

Competing Interest Statement

DR has a conflict of interest being a consultant for Hitachi High-Technologies Corporation, Tokyo, Japan from 2018 to 2020. All other authors have no conflicts of interest to declare. Funding sources had no role in the design and conduct of the study; collection, management, analysis, and interpretation of the data; and preparation, review, or approval of the manuscript.

Funding Statement

This work was supported by the French Government under the Investments for the Future program managed by the National Agency for Research (ANR), no. Mediterranee-Infection 10-IAHU-03 Region Provence Alpes Cote d Azur and European funding FEDER PRIMMI (Fonds Europeen de Developpement Regional-Plateformes de Recherche et d Innovation Mutualisees Mediterranee Infection), no. FEDER PA 0000320 PRIMMI Hitachi High-Technologies Corporation, Tokyo, Japan.

https://www.medrxiv.org/content/10.1101/2021.12.24.21268174v1