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Abstract

Background

Early 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.

Aim

To detail how combining epidemiological and laboratory data sources, targeted investigations and modelling enabled comprehensive characterisation of sub-lineage JN.1.

Methods

Data 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.

Results

JN.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.

Conclusion

Combining 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.

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This work is licensed under a Creative Commons Attribution 4.0 International License.
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2025-01-09
2025-01-15
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Monitoring SARS-CoV-2 variants with complementary surveillance systems: risk evaluation of the Omicron JN.1 variant in France, August 2023 to January 2024
<p class="citation"> <span>Citation style for this article:</span> <span class="meta-value authors"> <a href="/search?value1=Adriana+Traore&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Traore Adriana</a>, <a href="/search?value1=Kelly+Charniga&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Charniga Kelly</a>, <a href="/search?value1=Sophie+Grellet&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Grellet Sophie</a>, <a href="/search?value1=Garance+Terpant&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Terpant Garance</a>, <a href="/search?value1=H%C3%A9l%C3%A9na+Da+Cruz&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Da Cruz Héléna</a>, <a href="/search?value1=Anais+Lamy&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Lamy Anais</a>, <a href="/search?value1=Nathalie+Thomas&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Thomas Nathalie</a>, <a href="/search?value1=Gwladys+Gbaguidi&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Gbaguidi Gwladys</a>, <a href="/search?value1=Aliz%C3%A9+Mercier&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Mercier Alizé</a>, <a href="/search?value1=Julie+Prudhomme&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Prudhomme Julie</a>, <a href="/search?value1=Benoit+Visseaux&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Visseaux Benoit</a>, <a href="/search?value1=Vincent+Vieillefond&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Vieillefond Vincent</a>, <a href="/search?value1=St%C3%A9phanie+Haim-Boukobza&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Haim-Boukobza Stéphanie</a>, <a href="/search?value1=Jean-Marc+Giannoli&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Giannoli Jean-Marc</a>, <a href="/search?value1=RELAB+Study+Group&option1=author&noRedirect=true" class="nonDisambigAuthorLink">RELAB Study Group</a>, <a href="/search?value1=Laboratory+group&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Laboratory group</a>, <a href="/search?value1=Javier+Castro-Alvarez&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Castro-Alvarez Javier</a>, <a href="/search?value1=Alain-Claude+Kouamen&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Kouamen Alain-Claude</a>, <a href="/search?value1=Marie-Anne+Rameix-Welti&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Rameix-Welti Marie-Anne</a>, <a href="/search?value1=Samar+Beirrera-Ibraim&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Beirrera-Ibraim Samar</a>, <a href="/search?value1=Gregory+Destras&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Destras Gregory</a>, <a href="/search?value1=Laurence+Josset&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Josset Laurence</a>, <a href="/search?value1=Simon+Cauchemez&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Cauchemez Simon</a>, <a href="/search?value1=Bruno+Lina&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Lina Bruno</a>, <a href="/search?value1=Bruno+Coignard&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Coignard Bruno</a>, <a href="/search?value1=Justine+Schaeffer&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Schaeffer Justine</a>, <a href="/search?value1=Vincent+Enouf&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Enouf Vincent</a>, <a href="/search?value1=Antonin+Bal&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Bal Antonin</a></span>. Monitoring SARS-CoV-2 variants with complementary surveillance systems: risk evaluation of the Omicron JN.1 variant in France, August 2023 to January 2024. <a href="/content/ecdc">Euro Surveill.</a> 2025;30(1):pii=2400293. <a href="https://doi.org/10.2807/1560-7917.ES.2025.30.1.2400293" title="doi link" target="_blank">https://doi.org/10.2807/1560-7917.ES.2025.30.1.2400293</a> <span class="ES_Article_citation"> <span class="generated">Received</span>: 13 May 2024;&nbsp;&nbsp; <span class="generated">Accepted</span>: 19 Sept 2024 </span> </p>
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