Clinical phenotypes and outcomes associated with SARS-CoV-2 variant Omicron in critically ill French patients with COVID-19

Nicolas de Prost (1) , Etienne Audureau (2, 3) , Nicholas Heming (4, 5) , Elyanne Gault (4, 6) , Tài Pham (7, 8, 9) , Amal Chaghouri (10) , Nina de Montmollin (11) , Guillaume Voiriot (12) , Laurence Morand-Joubert (13, 14) , Adrien Joseph (15) , Marie-Laure Chaix (16, 17) , Sébastien Préau (18, 19) , Raphaël Favory (20) , Aurélie Guigon (21) , Charles-Edouard Luyt (22, 23) , Sonia Burrel (13, 24) , Julien Mayaux (24) , Stéphane Marot (13, 25) , Damien Roux (26, 27) , Diane Descamps (28, 29) , Sylvie Meireles , Frédéric Pène (30) , Flore Rozenberg (31) , Damien Contou (32) , Amandine Henry (33) , Stéphane Gaudry (34) , Ségolène Brichler (34) , Jean-François Timsit (29, 28) , Antoine Kimmoun (35, 36, 37) , Cédric Hartard (38, 39) , Louise-Marie Jandeaux , Samira Fafi-Kremer (40) , Paul Gabarre (41) , Malo Emery (42) , Claudio Garcia-Sanchez , Sébastien Jochmans (43) , Aurélia Pitsch (44) , Djillali Annane , Elie Azoulay , Armand Mekontso Dessap , Christophe Rodriguez , Jean-Michel Pawlotsky , Slim Fourati

1 CHU Henri Mondor [Créteil]
2 IMRB - Institut Mondor de Recherche Biomédicale
3 Hôpital Henri Mondor
4 2I - Infection et inflammation
5 Hôpital Raymond Poincaré [Garches]
6 Hôpital Ambroise Paré [AP-HP]
7 CESP - Centre de recherche en épidémiologie et santé des populations
8 Hôpital Bicêtre
9 CARMAS - Groupe de recherche clinique CARMAS (Cardiovascular and Respiratory Manifestations of Acute lung injury and Sepsis)
10 Hôpital Paul Brousse
11 Département des maladies respiratoires [CHU Cochin]
12 CHU Tenon [AP-HP]
13 iPLESP - Institut Pierre Louis d'Epidémiologie et de Santé Publique
14 CHU Saint-Antoine [AP-HP]
15 CRC (UMR_S_1138 / U1138) - Centre de Recherche des Cordeliers
16 GenCellDi (U944 / UMR7212) - Génomes, biologie cellulaire et thérapeutiques
17 Laboratoire de Virologie [CHU Saint-Louis]
18 RID-AGE - Facteurs de Risque et Déterminants Moléculaires des Maladies liées au Vieillissement - U 1167
19 CHU Lille
20 Hôpital Roger Salengro [Lille]
21 CHRO - Centre Hospitalier Régional d'Orléans
22 Service de Médecine Intensive et Réanimation - R3S [CHU Pitié-Salpêtrière]
23 ICAN - Unité de Recherche sur les Maladies Cardiovasculaires, du Métabolisme et de la Nutrition = Research Unit on Cardiovascular and Metabolic Diseases
24 CHU Pitié-Salpêtrière [AP-HP]
25 Service de Virologie [CHU Pitié-Salpêtrière]
26 DMU Esprit - Département Médico-Universitaire Épidémiologie et biostatistique, Santé publique, Pharmacie, Pharmacologie, Recherche, Information médicale, Thérapeutique et médicaments)
27 INEM - UM 111 (UMR 8253 / U1151) - Institut Necker Enfants-Malades
28 IAME (UMR_S_1137 / U1137) - Infection, Anti-microbiens, Modélisation, Evolution
29 AP-HP - Hôpital Bichat - Claude Bernard [Paris]
30 AP-HP. Nord - Université Paris Cité
31 GHU AP-HP Centre Université de Paris
32 Centre Hospitalier Victor Dupouy
33 CeRéMAIA - Hôpital André Mignot - Centre de Référence des Maladies Auto-Inflammatoires et des Amyloses [CH Versailles]
34 Hôpital Avicenne [AP-HP]
35 DCAC - Défaillance Cardiovasculaire Aiguë et Chronique
36 INI-CRCT - Cardiovascular and Renal Clinical Trialists [Vandoeuvre-les-Nancy]
37 CHRU Nancy - Centre Hospitalier Régional Universitaire de Nancy
38 LCPME - Laboratoire de Chimie Physique et Microbiologie pour les Matériaux et l'Environnement
39 Service de Virologie [CHRU Nancy]
40 Immuno-Rhumatologie Moléculaire
41 Service de Réanimation Médicale [CHU Saint-Antoine]
42 Réanimation Polyvalente [Saint-Denis, La Réunion]
43 Service de Médecine intensive [CH de Melun]
44 CHM - Centre Hospitalier de Melun

Infection with SARS-CoV-2 variant Omicron is considered to be less severe than infection with variant Delta, with rarer occurrence of severe disease requiring intensive care. Little information is available on comorbid factors, clinical conditions and specific viral mutational patterns associated with the severity of variant Omicron infection. In this multicenter prospective cohort study, patients consecutively admitted for severe COVID-19 in 20 intensive care units in France between December 7th 2021 and May 1st 2022 were included. Among 259 patients, we show that the clinical phenotype of patients infected with variant Omicron (n = 148) is different from that in those infected with variant Delta (n = 111). We observe no significant relationship between Delta and Omicron variant lineages/sublineages and 28-day mortality (adjusted odds ratio [95% confidence interval] = 0.68 [0.35-1.32]; p = 0.253). Among Omicroninfected patients, 43.2% are immunocompromised, most of whom have received two doses of vaccine or more (85.9%) but display a poor humoral response to vaccination. The mortality rate of immunocompromised patients infected with variant Omicron is significantly higher than that of nonimmunocompromised patients (46.9% vs 26.2%; p = 0.009). In patients infected with variant Omicron, there is no association between specific sublineages (BA.1/BA.1.1 (n = 109) and BA.2 (n = 21)) or any viral genome polymorphisms/ mutational profile and 28-day mortality.

Domains: Life Sciences [q-bio]

Nicolas de Prost, Etienne Audureau, Nicholas Heming, Elyanne Gault, Tài Pham, et al.. Clinical phenotypes and outcomes associated with SARS-CoV-2 variant Omicron in critically ill French patients with COVID-19. Nature Communications, 2022, 13 (1), pp.6025. ⟨10.1038/s41467-022-33801-z⟩. ⟨hal-03947764⟩