Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2025 Jan;30(1):2400293.
doi: 10.2807/1560-7917.ES.2025.30.1.2400293.

Monitoring SARS-CoV-2 variants with complementary surveillance systems: risk evaluation of the Omicron JN.1 variant in France, August 2023 to January 2024

Adriana Traore  1 , Kelly Charniga  2 , Sophie Grellet  3   4 , Garance Terpant  3   4 , Héléna Da Cruz  3   4 , Anais Lamy  3   4 , Nathalie Thomas  3   4 , Gwladys Gbaguidi  3   4 , Alizé Mercier  3   4 , Julie Prudhomme  3   4 , Benoit Visseaux  5 , Vincent Vieillefond  6 , Stéphanie Haim-Boukobza  7 , Jean-Marc Giannoli  8 ; RELAB Study Group  9 ; Laboratory group  10 ; Javier Castro-Alvarez  1 , Alain-Claude Kouamen  1 , Marie-Anne Rameix-Welti  11   12 , Samar Beirrera-Ibraim  11 , Gregory Destras  13 , Laurence Josset  13 , Simon Cauchemez  2 , Bruno Lina  13 , Bruno Coignard  1 , Justine Schaeffer  1 , Vincent Enouf  11 , Antonin Bal  13 ; Members of the Laboratory Group; Members of the RELAB Study Group
Collaborators, Affiliations

Monitoring SARS-CoV-2 variants with complementary surveillance systems: risk evaluation of the Omicron JN.1 variant in France, August 2023 to January 2024

Adriana Traore et al. Euro Surveill. 2025 Jan.

Abstract

BackgroundEarly detection and characterisation of SARS-CoV-2 variants have been and continue to be essential for assessing their public health impact. In August 2023, Santé publique France implemented enhanced surveillance for BA.2.86 and sub-lineage JN.1 because of their genetic divergence from other variants and increased prevalence.AimTo detail how combining epidemiological and laboratory data sources, targeted investigations and modelling enabled comprehensive characterisation of sub-lineage JN.1.MethodsData were collected from epidemiological investigations using a standardised questionnaire and from routine and novel (RELAB network) surveillance systems. JN.1 cases were compared with cases infected with previously circulating variants, such as EG.5, BA.4/BA.5 and other BA.2.86 sub-lineages. The growth rate and doubling time of JN.1 were estimated.ResultsJN.1 was first detected in September 2023 in the Île-de-France region, France, and spread widely across the country. By late November, doubling time was estimated to be 8.6 to 26.4 days depending on the region. For all data sources, cases infected by JN.1 showed similar demographics, rates of hospitalisation and RT-PCR cycle threshold values compared with those infected by previous variants. JN.1 cases also had older median age (54 years; 40-71 vs 47 years; 30-59), more frequent reports of feverish feeling and less frequent cough or nausea compared with BA.4/BA.5 cases. JN.1 cases had significantly higher frequency of anosmia compared with other BA.2.86 cases.ConclusionCombining different data sources played a key role in detecting emerging variant JN.1, for which no evidence of increased public health impact was found despite its genetic divergence.

Keywords: BA.2.86; COVID-19; JN.1; SARS-CoV-2 variant; genomic surveillance; laboratory network.

PubMed Disclaimer

Conflict of interest statement

Conflict of interest: None declared.

Figures

Figure 1
Figure 1
Schematic illustration of the genetic lineage of SARS-CoV-2 Omicron variants, December 2021–September 2023
Figure 2
Figure 2
Flowchart of the generation of each dataset used in this study, France, February 2024
Figure 3
Figure 3
Weekly estimated number of COVID-19 cases for mainland Francea, weeks 36–47 2023
Figure 4
Figure 4
Proportion of symptoms (A) and risk factors (B) reported by JN.1§ cases (n = 70) compared with previously investigated other BA.2.86§ cases (n = 71), and BA.4/BA.5§ (n = 266) cases, France, 2022–2023
Figure 5
Figure 5
Number of cases by week of sampling (A) and distribution of Ct values (B) for variants EG.5§ (n = 133) and JN.1§ (n = 493), RELAB network, France, up to epidemiological week 3 of 2024
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

References

    1. Santé publique France (SpF). Consortium EMERGEN 2023. Paris: SpF. [Accessed: 18 May 2024]. French. Available from: https://www.santepubliquefrance.fr/dossiers/coronavirus-covid-19/consort...
    1. Rasmussen M, Møller FT, Gunalan V, Baig S, Bennedbæk M, Christiansen LE, et al. First cases of SARS-CoV-2 BA.2.86 in Denmark, 2023. Euro Surveill. 2023;28(36):2300460. 10.2807/1560-7917.ES.2023.28.36.2300460 - DOI - PMC - PubMed
    1. World Health Organization (WHO). BA.2.86 initial risk evaluation of BA.2.86 and its sublineages, 21 November 2023. Geneva: WHO; 2023. Available from: https://www.who.int/docs/default-source/coronaviruse/21112023_ba.2.86_ir...
    1. World Health Organization (WHO). JN.1 Initial Risk Evaluation of JN.1, 19 December 2023. Geneva: WHO; 2023. Available from: https://www.who.int/docs/default-source/coronaviruse/18122023_jn.1_ire_c...
    1. Kaku Y, Okumura K, Padilla-Blanco M, Kosugi Y, Uriu K, Hinay AA, Jr, et al. Virological characteristics of the SARS-CoV-2 JN.1 variant. Lancet Infect Dis. 2024;24(2):e82. 10.1016/S1473-3099(23)00813-7 - DOI - PubMed

Supplementary concepts

LinkOut - more resources