BREAKING! Southern France Reports Spread Of New SARS-CoV-2 Variant B.1.640.2 With 46 Mutations And 37 Deletions Originating From Cameroon!
French health authorities have reported the spread of a new SARS-CoV-2 variant B.1.640.2 that possess 46 mutations and 37 deletions including the N501Y and E484K mutations.
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As of press time, a total of 67 patients all displaying moderate and severe conditions of the disease and requiring hospitalization have been identified having been infected with the new SARS-Cov-2 variant
B.1.640.2 which was first detected in late November 2021 in Southern France. Experts are warning that more cases could be in existence but doctors and experts could be assuming that is its due to Delta variant or sub-variants as not all hospitalized patients get genomic sequencings done.
Initially only 12 patients were identified as having been infected with the new variant in late November and early December by researchers from IHU Méditerranée Infection-France and the Aix-Marseille University-France. The researchers believed that the variant came from a traveler returning from Cameroon, Africa.
The researchers published their initial findings of the variant in on a preprint server.
https://www.medrxiv.org/content/10.1101/2021.12.24.21268174v1
For the initial first 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 approximately 8 h.
The study team’s preliminary analysis revealed 46 mutations and 37 deletions resulting in 30 amino acid substitutions and 12 deletions.
Importantly 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.
Substitutions N501Y and E484K are combined as in the Beta, Gamma, Theta and Omicron variants. Substitution F490S is present as in the Lambda variant, and substitution P681H is present as in the Lambda and Omicron variants.
In other structural proteins than the spike, amino acid changes include two substitutions in the nucleocapsid protein and one in the membrane protein. In non-structural proteins, amino acid changes include one substitution in proteins Nsp2, Nsp3, Nsp4, Nsp6, Nsp12 (RNA dependent RNA polymerase), and Nsp13 (helicase); two substitutions in Nsp14 (3’- 5’exonuclease); four substitutions in Nsp8 (which is part of the replication complex with Nsp7 and Nsp12); and three deletions in Nsp6.
Finally, in regulatory proteins, amino acid changes include four substitutions in ORF3a, one in ORF9b and one in ORF8. In addition, codon 27 of ORF8 gene is changed into a stop codon, as in the Alpha variant; some members of the Marseille-4 variant (B.1.160) that predominated in the geographical area between August 2020 and February 2021 also exhibit a stop codon in ORF8 gene but at
another position.
Detailed studies are still underway and the researchers are concerned that the new variant besides possibly being immune and vaccine evasive and but having the same infectious and transmissibility potential as the Delta could be far more virulent and cause disease severity based on the fact that it has been identified in only hospitalized cases to date.
The WHO, ECDC and the U.S. CDC along with numerous other entities have been reported on this new variant emergence and studies are currently underway. It is still too early to predict whether this new variant will become dominant in circulation and become another global threat or whether it will simply fizzle out in France itself.
The report and these study findings 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.
Thailand Medical News will continue to report on developments of this new B.1.640.2 variant as it continues to spread.
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