France: new Sars-CoV-2 variant B.1.640.2 with N501Y and E484K detected

Twelve SARS-CoV-2 positive patients living in southeastern France are infected with a variant with atypical mutations. The index case returned from travel in Cameroon.

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’.

Medrxiv preprint: 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



UPDATE 31/12/2021 – from the French Public Health Department

The B.1.640 variant is classified as a variant under investigation (VUM) by Public Health France (at 12/11/2021) as well as by WHO, ECDC and UKHSA. Since December 8, 2021, the B.1.640 lineage has been divided into two sublines: B.1.640.1 and B.1.640.2.

B.1.640.1 corresponds to the sequences of B.1.640 initially detected, and is majority. B.1.617.2* was detected within a cluster at the end of November 2021 in the Provence-Alpes-Côte region Azure.

B.1.640.2 is characterized by the presence of the E484K mutation (one of the targets of the current strategy screening), which is not present in B.1.640.1. The discrimination between these two sub-lineages is not still included in bioinformatic analysis tools. In this risk analysis, no difference is made between the two sublineages of B.1.640 and all cases are considered 20A / C variants B.1.640.

Public Health Document: Mise à jour de l’analyse de risque sur les variants émergents du SARS-CoV-2 du 01/12/2021  réalisée conjointementpar Santé publique France et le CNR des virus des infections respiratoires   (PDF download in French)

*note: we’re pretty sure they mean B.1.640.2 here, not B.1.617.2



UPDATE – 1st January 2021 – from Github

In a similar vein to the recent split of B.1.1.529(Omicron) into two sister sublineages it appears B.1.640 may also have a similar issue with a major group constating of the vast majority of sequences and a small outgroup which appears related but has a very different set of mutations (EPI_ISL_7181977; EPI_ISL_7156959; EPI_ISL_7156955; EPI_ISL_6315910; EPI_ISL_5926666) and includes sequences from France and England, indicating some degree of spread.

Defining mutations (mutations not shared between both groups shown in bold):
Major lineage:
Spike – P9L, E96Q, Δ136-144, R190S*, I210T, R346S, N394S, Y449N, F490R, N501Y, D614G, P681H, T859N, D936H
Non-spike – NSP2 – P129L, E272G; NSP3 – L1301F, A1537S; NSP4 – S386F, R401H, T492I; NSP6 – V149A; NSP12 – P323L; T32I, Q57H; M – I82T; ORF8 – Q27*STOP; N- D22Y, T205I, E378Q; S2m deletion

Minor lineage:
Spike – P9L, E96Q, Δ136-144, R190S, D215H, R346S, N394S, Y449N, E484K, F490S, N501Y, D614G, P681H, T859N, D1139H
Non-spike – NSP2 – P129L; NSP4 – D459N; NSP6 – Δ106-108, T181I; NSP12 – P323L; NSP13 – V371A; NSP14 – P46S, V437F; ORF3a – T32I, Q57H; M – I82S; ORF8 – Q27*STOP; N – D22Y, T205I

Github reportProposal to split B.1.640 into two sublineages

 









 

France: B.1.640 declared a VOI after more than 500 cases found

 

France: new coronavirus variant B.1.640 detected in Finistère, Brittany

 

Image by Rudy and Peter Skitterians from Pixabay

Europe: B.1.620 #coronavirus variant – definitely one to watch

“Last month, Gytis Dudas was tracking a concerning new coronavirus variant that had triggered an outbreak of COVID-19 in his native Lithuania and appeared sporadically elsewhere in Europe and in the United States. Exploring an international database of coronavirus genomes, Dudas found a crucial clue: One sample of the new variant came from a person who had recently flown to France from Cameroon. A collaborator, Guy Baele of KU Leuven, soon identified six more sequences from people in Europe who had traveled in Cameroon. But then their quest to pinpoint the variant’s origins hit a wall: Cameroon had uploaded a total of only 48 genomes to the global sequence repository, called GISAID. None included the variant”

Sciencemag.org report

 

B.1.620 is also listed as a Variant of Interest by the ECDC:

 

More on the B.1.620 variant traced back Cameroon by Gytis Dudas in the Pango Designation

 

 

Cameroon: travel-driven emergence and spread of SARS-CoV-2 lineage B.1.620 with multiple VOC-like mutations and deletions in Europe

 

Cameroon: travel-driven emergence and spread of SARS-CoV-2 lineage B.1.620 with multiple VOC-like mutations and deletions in Europe

“In this study we have presented evidence that a SARS-CoV-2 lineage designated B.1.620, first detected in Europe in late February, is associated with Central Africa, where it appears to circulate at very high prevalence, and has been introduced into Europe and the US on multiple occasions. A fair number of known B.1.620 genomes that were sequenced in Europe stem from travel-related cases returning from Cameroon, suggesting that it is likely to be the immediate source of this lineage.”

VOC amino acid changes lineage B.1.620 shares most in common with:

B.1.1.7 (ORF1a: SGF3675/3677Δ, S:Y144Δ, S: HV69/70Δ, S: P681H, and S: D1118H)

P.1 (ORF1a: SGF3675/3677Δ, S:P26S, S:E484K, S: T1027I) and

B.1.351 (ORF1a: SGF3675/3677Δ, S: E484K, S: LLA241/243Δ)

MedrXiv preprint Travel-driven emergence and spread of SARS-CoV-2 lineage B.1.620 with multiple VOC-like mutations and deletions in Europe

 

 

Image by rem734 from Pixabay