Surveillance Open Access
Like 0



Successive epidemic waves of COVID-19 illustrated the potential of SARS-CoV-2 variants to reshape the pandemic. Detecting and characterising emerging variants is essential to evaluate their public health impact and guide implementation of adapted control measures.


To describe the detection of emerging variant, B.1.640, in France through genomic surveillance and present investigations performed to inform public health decisions.


Identification and monitoring of SARS-CoV-2 variant B.1.640 was achieved through the French genomic surveillance system, producing 1,009 sequences. Additional investigation of 272 B.1.640-infected cases was performed between October 2021 and January 2022 using a standardised questionnaire and comparing with Omicron variant-infected cases.


B.1.640 was identified in early October 2021 in a school cluster in Bretagne, later spreading throughout France. B.1.640 was detected at low levels at the end of SARS-CoV-2 Delta variant’s dominance and progressively disappeared after the emergence of the Omicron (BA.1) variant. A high proportion of investigated B.1.640 cases were children aged under 14 (14%) and people over 60 (27%) years, because of large clusters in these age groups. B.1.640 cases reported previous SARS-CoV-2 infection (4%), anosmia (32%) and ageusia (34%), consistent with data on pre-Omicron SARS-CoV-2 variants. Eight percent of investigated B.1.640 cases were hospitalised, with an overrepresentation of individuals aged over 60 years and with risk factors.


Even though B.1.640 did not outcompete the Delta variant, its importation and continuous low-level spread raised concerns regarding its public health impact. The investigations informed public health decisions during the time that B.1.640 was circulating.


Article metrics loading...

Loading full text...

Full text loading...



  1. World Health Organization (WHO). Weekly epidemiological update on COVID-19 - 4 January 2023, edition 124. Geneva: WHO; 2022. Available from: https://www.who.int/publications/m/item/weekly-epidemiological-update-on-covid-19---4-january-2023
  2. Bouvet M, Imbert I, Subissi L, Gluais L, Canard B, Decroly E. RNA 3′-end mismatch excision by the severe acute respiratory syndrome coronavirus nonstructural protein nsp10/nsp14 exoribonuclease complex. Proc Natl Acad Sci USA. 2012;109(24):9372-7.  https://doi.org/10.1073/pnas.1201130109  PMID: 22635272 
  3. Harvey WT, Carabelli AM, Jackson B, Gupta RK, Thomson EC, Harrison EM, et al. SARS-CoV-2 variants, spike mutations and immune escape. Nat Rev Microbiol. 2021;19(7):409-24.  https://doi.org/10.1038/s41579-021-00573-0  PMID: 34075212 
  4. Rambaut A, Holmes EC, O’Toole Á, Hill V, McCrone JT, Ruis C, et al. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol. 2020;5(11):1403-7.  https://doi.org/10.1038/s41564-020-0770-5  PMID: 32669681 
  5. Markov PV, Katzourakis A, Stilianakis NI. Antigenic evolution will lead to new SARS-CoV-2 variants with unpredictable severity. Nat Rev Microbiol. 2022;20(5):251-2.  https://doi.org/10.1038/s41579-022-00722-z  PMID: 35288685 
  6. Davies NG, Abbott S, Barnard RC, Jarvis CI, Kucharski AJ, Munday JD, et al. Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England. Science. 2021;372(6538):eabg3055.  https://doi.org/10.1126/science.abg3055  PMID: 33658326 
  7. World Health Organization (WHO). Tracking SARS-CoV-2 variants. Geneva: WHO; 2022. Available from: https://www.who.int/en/activities/tracking-SARS-CoV-2-variants
  8. Santé publique France. Consortium EMERGEN. Saint-Maurice: Santé publique France; 2022. Available from: https://www.santepubliquefrance.fr/emergen
  9. European Centre for Disease Prevention and Control (ECDC). Guidance for representative and targeted genomic SARS-CoV-2 monitoring. Stockholm: ECDC; 3 May 2021. Available from: https://www.ecdc.europa.eu/en/publications-data/guidance-representative-and-targeted-genomic-sars-cov-2-monitoring
  10. Aksamentov I, Roemer C, Hodcroft E, Neher R. Nextclade: clade assignment, mutation calling and quality control for viral genomes. J Open Source Softw. 2021;6(67):3773.  https://doi.org/10.21105/joss.03773 
  11. Rambaut A, Holmes EC, O’Toole Á, Hill V, McCrone JT, Ruis C, et al. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol. 2020;5(11):1403-7.  https://doi.org/10.1038/s41564-020-0770-5  PMID: 32669681 
  12. Github. Emerging B.1.X variant lineage in Europe and Africa with conserved Spike mutations: P9L, E96Q, R346S, Y449N, P681H and T859N - issue 297. 2021. Available from: https://github.com/cov-lineages/pango-designation/issues/297
  13. Maisa A, Spaccaferri G, Fournier L, Schaeffer J, Deniau J, Rolland P, et al. First cases of Omicron in France are exhibiting mild symptoms, November 2021-January 2022. Infect Dis Now. 2022;52(3):160-4.  https://doi.org/10.1016/j.idnow.2022.02.003  PMID: 35167979 
  14. R Core Team. R: A language and environment for statistical computing. Vienna: R Foundation for Statistical Computing; 2022. Available from: https://www.R-project.org
  15. Wickman H. ggplot2: Elegant graphics for data analysis. Second edition. New York: Springer; 2016.
  16. Santé publique France. Analyse de risque sur les variants émergents du SARS-CoV-2 - Analyse préliminaire du 12/11/2021 concernant le variant B.1.640. [Risk analysis on emerging variants of SARS-CoV-2 - Preliminary analysis of 12/11/2021 concerning variant B.1.640.] Saint-Maurice: Santé publique France; 2021. French. Available from: https://www.santepubliquefrance.fr/media/files/01-maladies-et-traumatismes/maladies-et-infections-respiratoires/infection-a-coronavirus/analyse-de-risque-des-variants-emergents-de-sars-cov-2-12-11-21
  17. Mastrovito B, Naimi C, Kouam L, Naudot X, Fournier L, Spaccaferri G, et al. Investigation of outbreak cases infected with the SARS-CoV-2 B.1.640 variant in a fully vaccinated elderly population, Normandy, France, November to December 2021. Euro Surveill. 2022;27(6):2200078.  https://doi.org/10.2807/1560-7917.ES.2022.27.6.2200078  PMID: 35144722 
  18. Gómez-Carballa A, Bello X, Pardo-Seco J, Martinón-Torres F, Salas A. Mapping genome variation of SARS-CoV-2 worldwide highlights the impact of COVID-19 super-spreaders. Genome Res. 2020;30(10):1434-48.  https://doi.org/10.1101/gr.266221.120  PMID: 32878977 
  19. Eales O, Page AJ, de Oliveira Martins L, Wang H, Bodinier B, Haw D, et al. SARS-CoV-2 lineage dynamics in England from September to November 2021: high diversity of Delta sub-lineages and increased transmissibility of AY.4.2. BMC Infect Dis. 2022;22(1):647.  https://doi.org/10.1186/s12879-022-07628-4  PMID: 35896970 
  20. Leung K, Shum MH, Leung GM, Lam TT, Wu JT. Early transmissibility assessment of the N501Y mutant strains of SARS-CoV-2 in the United Kingdom, October to November 2020. Euro Surveill. 2021;26(1):2002106.  https://doi.org/10.2807/1560-7917.ES.2020.26.1.2002106  PMID: 33413740 
  21. Ramanathan M, Ferguson ID, Miao W, Khavari PA. SARS-CoV-2 B.1.1.7 and B.1.351 spike variants bind human ACE2 with increased affinity. Lancet Infect Dis. 2021;21(8):1070.  https://doi.org/10.1016/S1473-3099(21)00262-0  PMID: 34022142 
  22. Faria NR, Mellan TA, Whittaker C, Claro IM, Candido DDS, Mishra S, et al. Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil. Science. 2021;372(6544):815-21.  https://doi.org/10.1126/science.abh2644  PMID: 33853970 
  23. Tegally H, Wilkinson E, Giovanetti M, Iranzadeh A, Fonseca V, Giandhari J, et al. Detection of a SARS-CoV-2 variant of concern in South Africa. Nature. 2021;592(7854):438-43.  https://doi.org/10.1038/s41586-021-03402-9  PMID: 33690265 
  24. Lubinski B, Fernandes MHV, Frazier L, Tang T, Daniel S, Diel DG, et al. Functional evaluation of the P681H mutation on the proteolytic activation of the SARS-CoV-2 variant B.1.1.7 (Alpha) spike. iScience. 2022;25(1):103589.  https://doi.org/10.1016/j.isci.2021.103589  PMID: 34909610 
  25. Liu Y, Liu J, Johnson BA, Xia H, Ku Z, Schindewolf C, et al. Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. Cell Rep. 2022;39(7):110829.  https://doi.org/10.1016/j.celrep.2022.110829  PMID: 35550680 
  26. Weisblum Y, Schmidt F, Zhang F, DaSilva J, Poston D, Lorenzi JC, et al. Escape from neutralizing antibodies by SARS-CoV-2 spike protein variants. eLife. 2020;9:9.  https://doi.org/10.7554/eLife.61312  PMID: 33112236 
  27. Santé publique France. Analyse de risque sur les variants émergents du SARS-CoV-2 au 05/01/2022. [Risk analysis on emerging variants of SARS-CoV-2 as of 05/01/2022]. Saint-Maurice: Santé publique France; 2022. French. Available from: https://www.santepubliquefrance.fr/media/files/01-maladies-et-traumatismes/maladies-et-infections-respiratoires/infection-a-coronavirus/analyse-de-risque-des-variants-emergents-de-sars-cov-2-05-01-22
  28. Bastard J, Taisne B, Figoni J, Mailles A, Durand J, Fayad M, et al. Impact of the Omicron variant on SARS-CoV-2 reinfections in France, March 2021 to February 2022. Euro Surveill. 2022;27(13):2200247.  https://doi.org/10.2807/1560-7917.ES.2022.27.13.2200247  PMID: 35362406 
  29. Vihta KD, Pouwels KB, Peto TE, Pritchard E, House T, Studley R, et al. , COVID-19 Infection Survey team. Omicron-associated changes in SARS-CoV-2 symptoms in the United Kingdom. Clin Infect Dis. 2022;76(3):e133-41. . Epub ahead of print. https://doi.org/10.1093/cid/ciac613  PMID: 35917440 

Data & Media loading...

Supplementary data

Submit comment
Comment moderation successfully completed
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error