As of 01/21/2022, 10 sequences that may correspond to a Delta/Omicron recombinant have been identified in France… this recombinant has potentially already been circulating at very low levels since mid-January.
On 02/16/2022, a discussion thread was opened on the Github bioinformatics forum of the Pangolin nomenclature tool about a Delta/Omicron recombinant potential in France.
Performed from the GISAID database, these analyzes had identified four sequences from France, four sequences from Denmark and one sequence from the Netherlands which form a separate phylogenetic branch.
This signal was investigated by the Respiratory Infections Virus CNR and the RNA Virus Evolutionary Genomics Laboratory at the Institut Pasteur, which confirmed that the four sequences from France did indeed correspond to a recombinant.
The majority of the genome of this recombinant corresponds to the AY.4 sublineage of the VOC Delta, and a large portion of the S gene (coding for the Spike protein) corresponds to the BA.1 sublineage of the VOC Omicron. A request to assign a specific lineage has been made.
Additional analyzes were carried out on the EMERGEN database, using three mutations which seem to characterize the sequences of this recombinant: ORF1a:E352D, S:A27S, S:N764K. This “proxy mutation” is not 100% specific and sensitive in identifying this recombinant, and work is in progress to refine it.
As of 02/21/2022, 10 sequences in the EMERGEN database carried these three mutations, 9 of which were sequenced during Flash surveys. These samples come from different regions and the oldest dates back to 17/01. The detection during Flash surveys and the geographic dispersion of the cases suggest that this recombinant has potentially already been circulating at very low levels since mid-January. Additional analyzes are underway to confirm these results, and this signal is being closely monitored by the CNR, the laboratories of the EMERGEN consortium and Public Health France.
As of 02/21/2021, 59 probable Delta/Omicron co-infections have been identified in France (source: EMERGEN
From French Health Department document: Risk analysis on emerging variants of SARS-CoV-2 carried out jointly by Public Health France and the CNR for respiratory infection viruses – machine translated into English below:analyse_risque_variants_20220223 – English