Immune dysregulation through longitudinal lymphocyte trajectories and their clinical determinants in hospitalized COVID-19 patients José Pedro Cidade, Fabio Silvio Taccone, Luis Felipe Reyes, Laura Merson, Benjamin Lefevre, et al. Intensive Care Medicine Experimental, 2026 Objective Immune dysregulation plays a pivotal role in the pathophysiology of sepsis and COVID-19, with lymphopenia emerging as a consistent marker of severity and poor prognosis. However, most existing studies have assessed lymphocyte counts at isolated time points, limiting insights into their temporal behavior and prognostic value. The dynamics of lymphocyte recovery or persistence of lymphopenia remain largely unexplored in large populations, as well as the impact of adjunctive therapies such as corticosteroids. We hypothesized that the persistence or recovery of lymphopenia may be key to understanding disease progression and predicting outcomes. Using the multinational ISARIC cohort, we investigated longitudinal lymphocyte trajectories in hospitalized patients and the clinical determinants associated with their evolution over time. Methods We conducted a multinational prospective observational cohort study using data from the ISARIC-WHO Clinical Characterization Protocol. Patients with confirmed SARS-CoV-2 infection and at least four lymphocyte measurements during the first 28 days of hospitalization were included. We analyzed lymphocyte trajectories, Cox regression survival analyses and multivariable linear regression modelling. We also applied multistate models and joint modeling to assess the association between lymphocyte trajectories and 28-day mortality, incorporating corticosteroid use as a time-varying covariate. Results Of 945,317 screened patients, 231,933 hospitalized adults with confirmed COVID-19 and sufficient lymphocyte data were included, with 56.6% classified as lymphopenic. Lymphopenia was independently associated with higher rates of ICU admission, organ support, and in-hospital mortality (OR = 1.52, 95% CI 1.48–1.55), and lower absolute lymphocyte counts were strongly linked to worse survival in adjusted Cox models (HR = 1.33 per 1 × 10⁹ cells/L decrease, 95% CI 1.28–1.38). Multistate modeling revealed that lymphopenic patients had a significantly higher daily transition rate to death and a shorter duration in that immune state, while corticosteroid exposure was associated with an increased likelihood of entering and remaining in lymphopenia. Joint modeling identified age, sex, and corticosteroid use as significant predictors of lower lymphocyte trajectories over time, with distinct dynamics between survivors and non-survivors. Conclusion Lymphopenia was common and strongly associated with worse outcomes in hospitalized COVID-19 patients, with impaired recovery particularly evident in those receiving corticosteroids. These findings highlight the value of lymphocyte monitoring to inform tailored immunomodulatory strategies in sepsis and severe viral infections.
Defective RNA Polymerase III sensing of mitochondrial DNA in pulmonary epithelial cells impairs type I IFN immunity to SARS-CoV-2 Michelle Møhlenberg, Sofie Eg Jørgensen, Renée Marije van der Sluis, Thomas Zillinger, Daniëla Maria Hinke, et al. Proceedings of the National Academy of Sciences of the United States of America, 2026 The clinical spectrum of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection ranges from asymptomatic cases to critical COVID-19 pneumonia. To investigate the role of host genetics in susceptibility to critical COVID-19 and identify pathophysiological mechanisms and pathways, we analyzed whole-exome and whole-genome sequencing data from the COVID Human Genetic Effort. We identified 10 rare, monoallelic predicted loss-of-function variants in 18 patients in POLR3A and POLR3C encoding two subunits of RNA polymerase III (POL III), a nuclear multisubunit enzyme, which has been implicated in cytosolic DNA sensing. These variants were deleterious for expression of full-length POLR3A and POLR3C proteins. We demonstrate that human pulmonary A549-hACE2 cells with reduced POLR3A or POLR3C expression exhibit impaired type I IFN responses to transfected mitochondrial DNA (mtDNA) or SARS-CoV-2 infection, together with increased viral replication. Mechanistically, we show that SARS-CoV-2 induces cellular mtDNA release via oligomerization of the mitochondrial voltage-dependent anion channel under virus-induced oxidative stress, enabling POL III–mtDNA interaction. These findings establish POL III as a sensor of endogenous mtDNA released during viral infection and indicate that autosomal dominant POL III haploinsufficiency may predispose individuals to critical COVID-19.
Community and Hospital-Based Laboratory Surveillance for Influenza, Respiratory Syncytial Virus, and SARS-CoV-2 During the 2023–2024 Season, Lyon, France Cécile Chauvel, Jean‐Sébastien Casalegno, Benoit Visseaux, Vincent Vieillefond, Stéphanie Haim‐Boukozba, et al. Journal of Medical Virology, 2025 Influenza, respiratory syncytial virus (RSV) and SARS‐CoV‐2 are among the main respiratory viruses circulating in the population, with a significant burden on public health. While individuals at higher risk are more likely to develop severe symptoms leading to hospitalization, viral circulation in the community remains less extensively monitored. This study compared viral circulation between RELAB, a recently established community‐based laboratory surveillance network (n = 22 843 tested patients) and hospital surveillance at the Hospices Civils de Lyon, France (n = 23 046 tested patients), for the season 2023–2024. For influenza and SARS‐CoV‐2, similar trends were observed in at‐risk populations (children under 5 years and adults over 65 years) in both settings. Circulation of these two viruses was first detected in the community and insights from the young adult population (19–64 years) were only captured in the community network. Circulation of RSV was more intense in terms of number of cases and started in the pediatric population, and consequently was more represented in the hospital setting. In conclusion, this study highlighted the complementarity between community and hospital surveillance, as different populations and periods of viral circulation were observed.
Clinical Characterization and Outcomes of Human Clade IIb Mpox Virus Disease: A European Multicenter Mpox Observational Cohort Study (MOSAIC) Elise Pesonel, Cédric Laouénan, Laetitia Guiraud, Josephine Bourner, Isabelle Hoffmann, et al. Clinical Infectious Diseases, 2025 Background The global mpox outbreak that started in May 2022 was caused by a novel clade IIb variant of the mpox virus (Orthopoxvirus monkeypox, MPXV). It differed from the traditional Western and Central Africa disease in transmission patterns and clinical presentation. Methods To address the need for detailed clinical and virologic data, we conducted an observational cohort study (MOSAIC) during May 2022–July 2023 in individuals with confirmed MPXV infection enrolled in 6 European countries. Case management decisions were left to the attending physician. Participants were monitored for up to 6 months for clinical signs/symptoms and clinical and virologic outcomes through hospital visits, phone interviews, and self-administered questionnaires. Outcomes included time to lesion resolution, clinical status, and virus clearance. Results The 518 participants not receiving any specific treatment (“untreated”) were diagnosed a median 5 days from symptom onset; 90% were managed as outpatients. Lesions were mostly cutaneous (88%) and perigenital (74%). By day 14 from the first polymerase chain reaction (PCR)–positive sample, 39% had resolved lesions. Time to 95% unculturable virus was longest in cutaneous lesions (52 days). A putative systemic antiviral was available for 57 participants, 44% as inpatients; 34% and 58% had resolved lesions by day 14 from the first PCR-positive sample and from treatment start, respectively. Time to 95% unculturable virus was 60 days in skin and oropharynx. No death or recrudescence occurred by day 180. Conclusions MOSAIC provides comprehensive insights into the clinical and virologic characteristics of mpox caused by the clade IIb variant. The study forms the basis of clinical characterization for ongoing mpox outbreaks.
Performance of Subgenomic RT-PCR for Predicting SARS-CoV-2 Infectivity Compared to Genomic RT-PCR and Culture Isolation Célia Sentis, Delphine Parraud, Geneviève Billaud, Martine Valette, Maude Bouscambert‐Duchamp, et al. Journal of Medical Virology, 2025 SARS‐CoV‐2 clinical samples can be detected as positive for a long period of time using real‐time RT‐PCR, even when patients are no longer infectious. Viral culture is the gold standard for assessing a patient's infectivity, but it is a time‐consuming technique and lacks sensitivity. SARS‐CoV‐2 subgenomic RNA (sgRNA) detection has been used as a proxy for assessing the infectivity but only a limited number of studies have described its use in vitro and in clinical samples. This study aimed to evaluate the correlation between results from viral culture, genomic RT‐PCR (gRT‐PCR), and subgenomic RT‐PCR (sgRT‐PCR) during in vitro infection and in clinical samples. In vitro viral replication kinetics showed that both genomic RNA (gRNA) and subgenomic RNA (sgRNA) levels remained stable up to 21 days in the absence of replication‐competent virus. Using clinical samples, sgRNA was detected in 87.5% of culture‐positive samples, demonstrating better performances than gRT‐PCR (Positive predictive value (PPV) 93.3% and Negative predictive value (NPV) of 87.5%) and an almost perfect agreement with culture results (Cohen κ = 0.81 [95% CI: 0.66–0.95]). These findings suggest that testing for sgRNA and/or using a gRNA Ct cut‐off of 21.2 could be used as a proxy to determine the presence of SARS‐CoV‐2 replication‐competent virus.
High Nasopharyngeal SARS-CoV-2 Load and Delayed Clearance in Hospitalized Patients With Blood Autoantibodies Neutralizing Type I Interferons A Marchal, T Kerdiles, A Perrin, A Gervais, P Bastard, L Bizien, G Lingas, ... The Journal of Infectious Diseases, jiag172 , 2026 2026
Efficacy, safety, pharmacokinetics, immunogenicity, and serum neutralizing activity of AZD7442 (tixagevimab-cilgavimab) in patients hospitalized with COVID-19: long-term … CR Massonnaud, N Peiffer-Smadja, P Poignard, S Jamard, F Goehringer, ... Clinical Microbiology and Infection 32 (4), 618-628 , 2026 2026 Citations: 1
Efficacy, safety, pharmacokinetics, immunogenicity, and serum neutralizing activity of AZD7442 (tixagevimab-cilgavimab) in patients hospitalized with COVID-19: long-term … CR Massonnaud, N Peiffer-Smadja, P Poignard, S Jamard, F Goehringer, ... Clinical Microbiology and Infection , 2025 2025
Community and Hospital‐Based Laboratory Surveillance for Influenza, Respiratory Syncytial Virus, and SARS‐CoV‐2 During the 2023–2024 Season, Lyon, France C Chauvel, JS Casalegno, B Visseaux, V Vieillefond, S Haim‐Boukozba, ... Journal of Medical Virology 97 (9), e70549 , 2025 2025 Citations: 2
Clinical research in rapid sequence during a pandemic: Lessons learned and the way forward F Ader, É Aubret, N Bergaud, M Bouscambert-Duchamp, S Circosta, ... Infectious Diseases Now, 105135 , 2025 2025
Performance of Subgenomic RT‐PCR for Predicting SARS‐CoV‐2 Infectivity Compared to Genomic RT‐PCR and Culture Isolation C Sentis, D Parraud, G Billaud, M Valette, M Bouscambert‐Duchamp, ... Journal of Medical Virology 97 (5), e70363 , 2025 2025
sST2 is a key outcome biomarker in COVID-19: insights from discovery randomized trial DM Smadja, CR Massonnaud, A Philippe, M Rosa, S Luneau, A Rauch, ... Scientific Reports 15 (1), 14348 , 2025 2025 Citations: 4
Performance of whole genome sequencing for respiratory syncytial virus: insights from the first external quality assessment, France, 2024 A Moisan, H Regue, Y Rahou, A Gaymard, A Oblette, L Avon, N Bergaud, ... Clinical Microbiology and Infection 31 (4), 647-650 , 2025 2025
Community and hospital-based laboratory surveillance for influenza, RSV, and SARS-CoV-2 during the 2023-2024 season, Lyon, France C Chauvel, JS Casalegno, B VISSEAUX, V Vieillefond, S Haim-Boukozba, ... Authorea Preprints , 2025 2025
Genotypic and phenotypic characterisation of respiratory syncytial virus after nirsevimab breakthrough infections: a large, multicentre, observational, real-world study S Fourati, A Reslan, J Bourret, JS Casalegno, Y Rahou, L Chollet, S Pillet, ... The Lancet Infectious Diseases 25 (3), 301-311 , 2025 2025 Citations: 71
Advancing respiratory virus diagnostics: integrating the nasal IFN-I score for improved viral detection M Mommert-Tripon, D Parraud, C Grosbois, A Gaymard, V Cheynet, ... EBioMedicine 110 , 2024 2024 Citations: 3
Antiviral effect of Evusheld in COVID-19 hospitalized patients infected with pre-Omicron or Omicron variants: a modelling analysis of the randomized DisCoVeRy trial M Beaulieu, A Gaymard, C Massonnaud, N Peiffer-Smadja, ... Journal of Antimicrobial Chemotherapy 79 (11), 2887-2895 , 2024 2024 Citations: 6
Lack of association between classical HLA genes and asymptomatic SARS-CoV-2 infection A Marchal, ET Cirulli, I Neveux, E Bellos, RS Thwaites, KMS Barrett, ... Human Genetics and Genomics Advances 5 (3) , 2024 2024 Citations: 9
Characteristics and outcomes of COVID-19 patients admitted to hospital with and without respiratory symptoms BW Citarella, C Kartsonaki, ED Ibáñez-Prada, BP Gonçalves, J Baruch, ... Heliyon 10 (10) , 2024 2024 Citations: 2
Impact of the H274Y Substitution on N1, N4, N5, and N8 Neuraminidase Enzymatic Properties and Expression in Reverse Genetic Influenza A Viruses A Gaymard, C Picard, G Vazzoler, P Massin, E Frobert, M Sabatier, ... Viruses 16 (3), 388 , 2024 2024 Citations: 2
Immunomodulators for immunocompromised patients hospitalized for COVID-19: a meta-analysis of randomized controlled trials II Siempos, AC Kalil, D Belhadi, VC Veiga, AB Cavalcanti, ... EClinicalMedicine 69 , 2024 2024 Citations: 8
Tixagevimab-cilgavimab (AZD7442) for the treatment of patients hospitalized with COVID-19 (DisCoVeRy): a phase 3, randomized, double-blind, placebo-controlled trial M Hites, CR Massonnaud, EL Lapique, D Belhadi, S Jamard, ... Journal of Infection 88 (3) , 2024 2024 Citations: 9
Gestion des prélèvements biologiques d’un patient suspect ou confirmé d’infection par le virus monkeypox (MPV) M Bouscambert, S Burrel, O Ferraris, N Lemaitre, S Allix, A Merens, B Lina, ... Revue de biologie médicale 381 (6), 73-77 , 2024 2024
Implementation of Recommendations on the Use of Corticosteroids in Severe COVID-19 F Camirand-Lemyre, L Merson, BKT Vijayaraghavan, AJC Burrell, ... JAMA network open 6 (12), e2346502-e2346502 , 2023 2023 Citations: 10
Association between SARS‐CoV‐2 viral kinetics and clinical score evolution in hospitalized patients N Néant, G Lingas, A Gaymard, D Belhadi, M Hites, T Staub, R Greil, ... CPT: Pharmacometrics & Systems Pharmacology , 2023 2023 Citations: 5
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First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020 G Spiteri, J Fielding, M Diercke, C Campese, V Enouf, A Gaymard, A Bella, ... Eurosurveillance 25 (9), 2000178 , 2020 2020 Citations: 861
Autoantibodies neutralizing type I IFNs are present in~ 4% of uninfected individuals over 70 years old and account for~ 20% of COVID-19 deaths P Bastard, A Gervais, T Le Voyer, J Rosain, Q Philippot, J Manry, ... Science immunology 6 (62), eabl4340 , 2021 2021 Citations: 674
X-linked recessive TLR7 deficiency in~ 1% of men under 60 years old with life-threatening COVID-19 T Asano, B Boisson, F Onodi, D Matuozzo, M Moncada-Velez, ... Science immunology 6 (62), eabl4348 , 2021 2021 Citations: 460
Remdesivir plus standard of care versus standard of care alone for the treatment of patients admitted to hospital with COVID-19 (DisCoVeRy): a phase 3, randomised, controlled … F Ader, M Bouscambert-Duchamp, M Hites, N Peiffer-Smadja, J Poissy, ... The Lancet Infectious Diseases 22 (2), 209-221 , 2022 2022 Citations: 447
Cluster of coronavirus disease 2019 (COVID-19) in the French Alps, February 2020 K Danis, O Epaulard, T Bénet, A Gaymard, S Campoy, E Botelho-Nevers, ... Clinical Infectious Diseases 71 (15), 825-832 , 2020 2020 Citations: 365
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Characterization and treatment of SARS-CoV-2 in nasal and bronchial human airway epithelia A Pizzorno, B Padey, T Julien, S Trouillet-Assant, A Traversier, ... Cell Reports Medicine 1 (4) , 2020 2020 Citations: 276
Two-step strategy for the identification of SARS-CoV-2 variant of concern 202012/01 and other variants with spike deletion H69–V70, France, August to December 2020 A Bal, G Destras, A Gaymard, K Stefic, J Marlet, S Eymieux, H Regue, ... Eurosurveillance 26 (3), 2100008 , 2021 2021 Citations: 274
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Modeling SARS-CoV-2 viral kinetics and association with mortality in hospitalized patients from the French COVID cohort N Néant, G Lingas, Q Le Hingrat, J Ghosn, I Engelmann, Q Lepiller, ... Proceedings of the National Academy of Sciences 118 (8), e2017962118 , 2021 2021 Citations: 253
The risk of COVID-19 death is much greater and age dependent with type I IFN autoantibodies J Manry, P Bastard, A Gervais, T Le Voyer, J Rosain, Q Philippot, ... Proceedings of the National Academy of Sciences 119 (21) , 2022 2022 Citations: 217
Functional balance between Neuraminidase and Hemagglutinin in influenza viruses A Gaymard, N Le Briand, E Frobert, B Lina, V Escuret Clinical Microbiology and Infection , 2016 2016 Citations: 214
Characteristics of the delayed respiratory syncytial virus epidemic, 2020/2021, Rhône Loire, France JS Casalegno, D Ploin, A Cantais, E Masson, E Bard, M Valette, R Fanget, ... Eurosurveillance 26 (29), 2100630 , 2021 2021 Citations: 121
Performance Assessment of SARS-CoV-2 PCR Assays Developed by WHO Referral Laboratories S Etievant, A Bal, V Escuret, K Brengel-Pesce, M Bouscambert, V Cheynet, ... Journal of Clinical Medicine 9 (6), 1871 , 2020 2020 Citations: 111
COVID-19 symptoms at hospital admission vary with age and sex: results from the ISARIC prospective multinational observational study Infection 49 (5), 889-905 , 2021 2021 Citations: 106
Impact of original, B. 1.1. 7, and B. 1.351/P. 1 SARS-CoV-2 lineages on vaccine effectiveness of two doses of COVID-19 mRNA vaccines: Results from a nationwide case-control … T Charmet, L Schaeffer, R Grant, S Galmiche, O Chény, C Von Platen, ... The Lancet Regional Health–Europe 8 , 2021 2021 Citations: 103
Early assessment of diffusion and possible expansion of SARS-CoV-2 Lineage 20I/501Y. V1 (B. 1.1. 7, variant of concern 202012/01) in France, January to March 2021 A Gaymard, P Bosetti, A Feri, G Destras, V Enouf, A Andronico, S Burrel, ... Eurosurveillance 26 (9), 2100133 , 2021 2021 Citations: 86
Molecular characterization of SARS-CoV-2 in the first COVID-19 cluster in France reveals an amino acid deletion in nsp2 (Asp268del) A Bal, G Destras, A Gaymard, M Bouscambert-Duchamp, M Valette, ... Clinical Microbiology and Infection 26 (7), 960-962 , 2020 2020 Citations: 83
Clinical characteristics, risk factors and outcomes in patients with severe COVID-19 registered in the International Severe Acute Respiratory and Emerging Infection Consortium … LF Reyes, S Murthy, E Garcia-Gallo, M Irvine, L Merson, I Martin-Loeches, ... ERJ Open Research 8 (1) , 2022 2022 Citations: 80