Clinical phenotypes and outcomes associated with SARS-CoV-2 Omicron variant JN.1 in critically ill COVID-19 patients: a prospective, multicenter cohort study

de Prost, Nicolas; Audureau, Etienne; Guillon, Antoine; Handala, Lynda; Préau, Sébastien; Guigon, Aurélie; Uhel, Fabrice; Hingrat, Quentin Le; Delamaire, Flora; Grolhier, Claire; Tamion, Fabienne; Moisan, Alice; Darreau, Cédric; Thomin, Jean; Contou, Damien; Henry, Amandine; Daix, Thomas; Hantz, Sébastien; Saccheri, Clément; Giordanengo, Valérie; Pham, Tài; Chaghouri, Amal; Bay, Pierre; Pawlotsky, Jean-Michel; Fourati, Slim

doi:10.1101/2024.03.11.24304075

Cited by 3 publications

(3 citation statements)

References 20 publications

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“…However, the high heterogeneity of T cell responses within vaccinated individuals, with an average individual targeting a median of 11 CD4+ and 10 CD8+ S-specific epitopes [ 39 ], makes widespread T cell escape in the population unlikely. Thus, T cell responses are expected to protect against severe disease from BA.2.86 and JN.1 infections, consistent with a recent clinical study conducted on JN.1 infected patients in a French cohort [ 41 ]. T cell recognition of BA.2.86 and JN.1 is also expected to be enhanced with the XBB.1.5 BNT162b2 booster vaccine currently recommended by the US CDC.…”

Section: Discussionsupporting

confidence: 86%

Cross-Reactivity Assessment of Vaccine-Derived SARS-CoV-2 T Cell Responses against BA.2.86 and JN.1

Sohail,

Ahmed,

Quadeer

et al. 2024

Viruses

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The SARS-CoV-2 Omicron sub-variants BA.2.86 and JN.1 contain multiple mutations in the spike protein that were not present in previous variants of concern and Omicron sub-variants. Preliminary research suggests that these variants reduce the neutralizing capability of antibodies induced by vaccines, which is particularly significant for JN.1. This raises concern as many widely deployed COVID-19 vaccines are based on the spike protein of the ancestral Wuhan strain of SARS-CoV-2. While T cell responses have been shown to be robust against previous SARS-CoV-2 variants, less is known about the impact of mutations in BA.2.86 and JN.1 on T cell responses. We evaluate the effect of mutations specific to BA.2.86 and JN.1 on experimentally determined T cell epitopes derived from the spike protein of the ancestral Wuhan strain and the spike protein of the XBB.1.5 strain that has been recommended as a booster vaccine. Our data suggest that BA.2.86 and JN.1 affect numerous T cell epitopes in spike compared to previous variants; however, the widespread loss of T cell recognition against these variants is unlikely.

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Section: Discussionsupporting

confidence: 86%

Cross-Reactivity Assessment of Vaccine-Derived SARS-CoV-2 T Cell Responses against BA.2.86 and JN.1

Sohail,

Ahmed,

Quadeer

et al. 2024

Viruses

View full text Add to dashboard Cite

show abstract

“…Our results also expand upon the limited data available on clinical severity of JN lineage infection. Analyses of data from 40 ICUs in France and national surveillance from Denmark found no differences between JN lineages and co-circulating variants on ICU outcomes and ICU/hospitalization risk, respectively [ 17 , 21 ]. A study conducted in an integrated healthcare system in the US found evidence of decreased clinical severity of JN lineage infection for some outcomes, including emergency department visits and hospital admission [ 18 ].…”

Section: Discussionmentioning

confidence: 99%

“…Early evidence indicated that BA.2.86 and JN.1 infections may be associated with a modest degree of immune escape from updated COVID-19 vaccines [14][15][16][17][18][19][20], but were not associated with more severe clinical outcomes compared to previously co-circulating XBB lineages [17,18,21]. Additional estimates of lineage-specific VE and severity are needed given limited evaluations that use whole-genome sequencing in their assessments.…”

Section: Introductionmentioning

confidence: 99%

Effectiveness of Updated 2023–2024 (Monovalent XBB.1.5) COVID-19 Vaccination Against SARS-CoV-2 Omicron XBB and BA.2.86/JN.1 Lineage Hospitalization and a Comparison of Clinical Severity — IVY Network, 26 Hospitals, October 18, 2023–March 9, 2024

Ma,

Surie,

Lauring

et al. 2024

Preprint

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BackgroundAssessing COVID-19 vaccine effectiveness (VE) and severity of SARS-CoV-2 variants can inform public health risk assessments and decisions about vaccine composition. BA.2.86 and its descendants, including JN.1 (referred to collectively as “JN lineages”), emerged in late 2023 and exhibited substantial genomic divergence from co-circulating XBB lineages.MethodsWe analyzed patients hospitalized with COVID-19–like illness at 26 hospitals in 20 U.S. states admitted October 18, 2023–March 9, 2024. Using a test-negative, case-control design, we estimated the effectiveness of an updated 2023–2024 (Monovalent XBB.1.5) COVID-19 vaccine dose against sequence-confirmed XBB and JN lineage hospitalization using logistic regression. Odds of severe outcomes, including intensive care unit (ICU) admission and invasive mechanical ventilation (IMV) or death, were compared for JN versus XBB lineage hospitalizations using logistic regression.Results585 case-patients with XBB lineages, 397 case-patients with JN lineages, and 4,580 control-patients were included. VE in the first 7–89 days after receipt of an updated dose was 54.2% (95% CI = 36.1%–67.1%) against XBB lineage hospitalization and 32.7% (95% CI = 1.9%–53.8%) against JN lineage hospitalization. Odds of ICU admission (adjusted odds ratio [aOR] 0.80; 95% CI = 0.46–1.38) and IMV or death (aOR 0.69; 95% CI = 0.34–1.40) were not significantly different among JN compared to XBB lineage hospitalizations.ConclusionsUpdated 2023–2024 COVID-19 vaccination provided protection against both XBB and JN lineage hospitalization, but protection against the latter may be attenuated by immune escape. Clinical severity of JN lineage hospitalizations was not higher relative to XBB lineage hospitalizations.

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Effectiveness of Updated 2023–2024 (Monovalent XBB.1.5) COVID-19 Vaccination Against SARS-CoV-2 Omicron XBB and BA.2.86/JN.1 Lineage Hospitalization and a Comparison of Clinical Severity—IVY Network, 26 Hospitals, 18 October 2023–9 March 2024

Ma,

Surie,

Lauring

et al. 2024

Clinical Infectious Diseases

View full text Add to dashboard Cite

Background Assessing variant-specific COVID-19 vaccine effectiveness (VE) and severity can inform public health risk assessments and decisions about vaccine composition. BA.2.86 and its descendants, including JN.1 (referred to collectively as “JN lineages”), emerged in late 2023 and exhibited substantial divergence from co-circulating XBB lineages. Methods We analyzed patients hospitalized with COVID-19–like illness at 26 hospitals in 20 U.S. states admitted October 18, 2023–March 9, 2024. Using a test-negative, case-control design, we estimated effectiveness of an updated 2023–2024 (Monovalent XBB.1.5) COVID-19 vaccine dose against sequence-confirmed XBB and JN lineage hospitalization using logistic regression. Odds of severe outcomes, including intensive care unit (ICU) admission and invasive mechanical ventilation (IMV) or death, were compared for JN versus XBB lineage hospitalizations using logistic regression. Results 585 case-patients with XBB lineages, 397 case-patients with JN lineages, and 4,580 control-patients were included. VE in the first 7–89 days after receipt of an updated dose was 54.2% (95% CI = 36.1%–67.1%) against XBB lineage hospitalization and 32.7% (95% CI = 1.9%–53.8%) against JN lineage hospitalization. Odds of ICU admission (adjusted odds ratio [aOR] 0.80; 95% CI = 0.46–1.38) and IMV or death (aOR 0.69; 95% CI = 0.34–1.40) were not significantly different among JN compared to XBB lineage hospitalizations. Conclusions Updated 2023–2024 COVID-19 vaccination provided protection against both XBB and JN lineage hospitalization, but protection against the latter may be attenuated by immune escape. Clinical severity of JN lineage hospitalizations was not higher relative to XBB.

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Clinical phenotypes and outcomes associated with SARS-CoV-2 Omicron variant JN.1 in critically ill COVID-19 patients: a prospective, multicenter cohort study

Cited by 3 publications

References 20 publications

Cross-Reactivity Assessment of Vaccine-Derived SARS-CoV-2 T Cell Responses against BA.2.86 and JN.1

Cross-Reactivity Assessment of Vaccine-Derived SARS-CoV-2 T Cell Responses against BA.2.86 and JN.1

Effectiveness of Updated 2023–2024 (Monovalent XBB.1.5) COVID-19 Vaccination Against SARS-CoV-2 Omicron XBB and BA.2.86/JN.1 Lineage Hospitalization and a Comparison of Clinical Severity — IVY Network, 26 Hospitals, October 18, 2023–March 9, 2024

Effectiveness of Updated 2023–2024 (Monovalent XBB.1.5) COVID-19 Vaccination Against SARS-CoV-2 Omicron XBB and BA.2.86/JN.1 Lineage Hospitalization and a Comparison of Clinical Severity—IVY Network, 26 Hospitals, 18 October 2023–9 March 2024

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