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Ganser I, Buckeridge DL, Heffernan J, Prague M, Thiébaut R. Estimating the population effectiveness of interventions against COVID-19 in France: A modelling study. Epidemics 2024; 46:100744. [PMID: 38324970 DOI: 10.1016/j.epidem.2024.100744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 12/12/2023] [Accepted: 01/22/2024] [Indexed: 02/09/2024] Open
Abstract
BACKGROUND Non-pharmaceutical interventions (NPIs) and vaccines have been widely used to manage the COVID-19 pandemic. However, uncertainty persists regarding the effectiveness of these interventions due to data quality issues, methodological challenges, and differing contextual factors. Accurate estimation of their effects is crucial for future epidemic preparedness. METHODS To address this, we developed a population-based mechanistic model that includes the impact of NPIs and vaccines on SARS-CoV-2 transmission and hospitalization rates. Our statistical approach estimated all parameters in one step, accurately propagating uncertainty. We fitted the model to comprehensive epidemiological data in France from March 2020 to October 2021. With the same model, we simulated scenarios of vaccine rollout. RESULTS The first lockdown was the most effective, reducing transmission by 84 % (95 % confidence interval (CI) 83-85). Subsequent lockdowns had diminished effectiveness (reduction of 74 % (69-77) and 11 % (9-18), respectively). A 6 pm curfew was more effective than one at 8 pm (68 % (66-69) vs. 48 % (45-49) reduction), while school closures reduced transmission by 15 % (12-18). In a scenario without vaccines before November 2021, we predicted 159,000 or 168 % (95 % prediction interval (PI) 70-315) more deaths and 1,488,000 or 300 % (133-492) more hospitalizations. If a vaccine had been available after 100 days, over 71,000 deaths (16,507-204,249) and 384,000 (88,579-1,020,386) hospitalizations could have been averted. CONCLUSION Our results highlight the substantial impact of NPIs, including lockdowns and curfews, in controlling the COVID-19 pandemic. We also demonstrate the value of the 100 days objective of the Coalition for Epidemic Preparedness Innovations (CEPI) initiative for vaccine availability.
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Affiliation(s)
- Iris Ganser
- Univ. Bordeaux, Inserm, BPH Research Center, SISTM Team, UMR 1219 Bordeaux, France; McGill Health Informatics, School of Population and Global Health, McGill University, Montreal, Quebec, Canada
| | - David L Buckeridge
- McGill Health Informatics, School of Population and Global Health, McGill University, Montreal, Quebec, Canada
| | - Jane Heffernan
- Mathematics & Statistics, Centre for Disease Modelling, York University, Toronto, Ontario, Canada
| | - Mélanie Prague
- Univ. Bordeaux, Inserm, BPH Research Center, SISTM Team, UMR 1219 Bordeaux, France; Inria, Inria Bordeaux - Sud-Ouest, Talence, France; Vaccine Research Institute, F-94010 Creteil, France
| | - Rodolphe Thiébaut
- Univ. Bordeaux, Inserm, BPH Research Center, SISTM Team, UMR 1219 Bordeaux, France; Inria, Inria Bordeaux - Sud-Ouest, Talence, France; Vaccine Research Institute, F-94010 Creteil, France; Bordeaux University Hospital, Medical Information Department, Bordeaux, France.
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Alexandre M, Prague M, McLean C, Bockstal V, Douoguih M, Thiébaut R. Prediction of long-term humoral response induced by the two-dose heterologous Ad26.ZEBOV, MVA-BN-Filo vaccine against Ebola. NPJ Vaccines 2023; 8:174. [PMID: 37940656 PMCID: PMC10632397 DOI: 10.1038/s41541-023-00767-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 10/13/2023] [Indexed: 11/10/2023] Open
Abstract
The persistence of the long-term immune response induced by the heterologous Ad26.ZEBOV, MVA-BN-Filo two-dose vaccination regimen against Ebola has been investigated in several clinical trials. Longitudinal data on IgG-binding antibody concentrations were analyzed from 487 participants enrolled in six Phase I and Phase II clinical trials conducted by the EBOVAC1 and EBOVAC2 consortia. A model based on ordinary differential equations describing the dynamics of antibodies and short- and long-lived antibody-secreting cells (ASCs) was used to model the humoral response from 7 days after the second vaccination to a follow-up period of 2 years. Using a population-based approach, we first assessed the robustness of the model, which was originally estimated based on Phase I data, against all data. Then we assessed the longevity of the humoral response and identified factors that influence these dynamics. We estimated a half-life of the long-lived ASC of at least 15 years and found an influence of geographic region, sex, and age on the humoral response dynamics, with longer antibody persistence in Europeans and women and higher production of antibodies in younger participants.
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Affiliation(s)
- Marie Alexandre
- Department of Public Health, Bordeaux University, Inserm UMR 1219 Bordeaux Population Health Research Center, Inria SISTM, Bordeaux, France
- Vaccine Research Institute, Créteil, France
| | - Mélanie Prague
- Department of Public Health, Bordeaux University, Inserm UMR 1219 Bordeaux Population Health Research Center, Inria SISTM, Bordeaux, France
- Vaccine Research Institute, Créteil, France
| | - Chelsea McLean
- Janssen Vaccines and Prevention, Leiden, the Netherlands
| | - Viki Bockstal
- Janssen Vaccines and Prevention, Leiden, the Netherlands
- ExeVir, Ghent, Belgium
| | | | - Rodolphe Thiébaut
- Department of Public Health, Bordeaux University, Inserm UMR 1219 Bordeaux Population Health Research Center, Inria SISTM, Bordeaux, France.
- Vaccine Research Institute, Créteil, France.
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Clairon Q, Prague M, Planas D, Bruel T, Hocqueloux L, Prazuck T, Schwartz O, Thiébaut R, Guedj J. Modeling the kinetics of the neutralizing antibody response against SARS-CoV-2 variants after several administrations of Bnt162b2. PLoS Comput Biol 2023; 19:e1011282. [PMID: 37549192 PMCID: PMC10434962 DOI: 10.1371/journal.pcbi.1011282] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 08/17/2023] [Accepted: 06/20/2023] [Indexed: 08/09/2023] Open
Abstract
Because SARS-CoV-2 constantly mutates to escape from the immune response, there is a reduction of neutralizing capacity of antibodies initially targeting the historical strain against emerging Variants of Concern (VoC)s. That is why the measure of the protection conferred by vaccination cannot solely rely on the antibody levels, but also requires to measure their neutralization capacity. Here we used a mathematical model to follow the humoral response in 26 individuals that received up to three vaccination doses of Bnt162b2 vaccine, and for whom both anti-S IgG and neutralization capacity was measured longitudinally against all main VoCs. Our model could identify two independent mechanisms that led to a marked increase in measured humoral response over the successive vaccination doses. In addition to the already known increase in IgG levels after each dose, we identified that the neutralization capacity was significantly increased after the third vaccine administration against all VoCs, despite large inter-individual variability. Consequently, the model projects that the mean duration of detectable neutralizing capacity against non-Omicron VoC is between 348 days (Beta variant, 95% Prediction Intervals PI [307; 389]) and 587 days (Alpha variant, 95% PI [537; 636]). Despite the low neutralization levels after three doses, the mean duration of detectable neutralizing capacity against Omicron variants varies between 173 days (BA.5 variant, 95% PI [142; 200]) and 256 days (BA.1 variant, 95% PI [227; 286]). Our model shows the benefit of incorporating the neutralization capacity in the follow-up of patients to better inform on their level of protection against the different SARS-CoV-2 variants. Trial registration: This clinical trial is registered with ClinicalTrials.gov, Trial IDs NCT04750720 and NCT05315583.
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Affiliation(s)
- Quentin Clairon
- Université de Bordeaux, Inria Bordeaux Sud-Ouest, Bordeaux, France
- Inserm, Bordeaux Population Health Research Center, SISTM Team, UMR1219, Bordeaux, France
- Vaccine Research Institute, Créteil, France
| | - Mélanie Prague
- Université de Bordeaux, Inria Bordeaux Sud-Ouest, Bordeaux, France
- Inserm, Bordeaux Population Health Research Center, SISTM Team, UMR1219, Bordeaux, France
- Vaccine Research Institute, Créteil, France
| | - Delphine Planas
- Vaccine Research Institute, Créteil, France
- Virus and Immunity Unit, Institut Pasteur, Université de Paris Cité, CNRS UMR3569, Paris, France
| | - Timothée Bruel
- Vaccine Research Institute, Créteil, France
- Virus and Immunity Unit, Institut Pasteur, Université de Paris Cité, CNRS UMR3569, Paris, France
| | - Laurent Hocqueloux
- Service des Maladies Infectieuses et Tropicales, Centre Hospitalier Régional, Orléans, France
| | - Thierry Prazuck
- Service des Maladies Infectieuses et Tropicales, Centre Hospitalier Régional, Orléans, France
| | - Olivier Schwartz
- Vaccine Research Institute, Créteil, France
- Virus and Immunity Unit, Institut Pasteur, Université de Paris Cité, CNRS UMR3569, Paris, France
| | - Rodolphe Thiébaut
- Université de Bordeaux, Inria Bordeaux Sud-Ouest, Bordeaux, France
- Inserm, Bordeaux Population Health Research Center, SISTM Team, UMR1219, Bordeaux, France
- Vaccine Research Institute, Créteil, France
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4
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Marc A, Marlin R, Donati F, Prague M, Kerioui M, Hérate C, Alexandre M, Dereuddre-bosquet N, Bertrand J, Contreras V, Behillil S, Maisonnasse P, Van Der Werf S, Le Grand R, Guedj J. Impact of variants of concern on SARS-CoV-2 viral dynamics in non-human primates. PLoS Comput Biol 2023; 19:e1010721. [PMID: 37556476 PMCID: PMC10441782 DOI: 10.1371/journal.pcbi.1010721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 08/21/2023] [Accepted: 07/12/2023] [Indexed: 08/11/2023] Open
Abstract
The impact of variants of concern (VoC) on SARS-CoV-2 viral dynamics remains poorly understood and essentially relies on observational studies subject to various sorts of biases. In contrast, experimental models of infection constitute a powerful model to perform controlled comparisons of the viral dynamics observed with VoC and better quantify how VoC escape from the immune response. Here we used molecular and infectious viral load of 78 cynomolgus macaques to characterize in detail the effects of VoC on viral dynamics. We first developed a mathematical model that recapitulate the observed dynamics, and we found that the best model describing the data assumed a rapid antigen-dependent stimulation of the immune response leading to a rapid reduction of viral infectivity. When compared with the historical variant, all VoC except beta were associated with an escape from this immune response, and this effect was particularly sensitive for delta and omicron variant (p<10-6 for both). Interestingly, delta variant was associated with a 1.8-fold increased viral production rate (p = 0.046), while conversely omicron variant was associated with a 14-fold reduction in viral production rate (p<10-6). During a natural infection, our models predict that delta variant is associated with a higher peak viral RNA than omicron variant (7.6 log10 copies/mL 95% CI 6.8-8 for delta; 5.6 log10 copies/mL 95% CI 4.8-6.3 for omicron) while having similar peak infectious titers (3.7 log10 PFU/mL 95% CI 2.4-4.6 for delta; 2.8 log10 PFU/mL 95% CI 1.9-3.8 for omicron). These results provide a detailed picture of the effects of VoC on total and infectious viral load and may help understand some differences observed in the patterns of viral transmission of these viruses.
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Affiliation(s)
| | - Romain Marlin
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses and Le Kremlin-Bicêtre, Paris, France
| | - Flora Donati
- National Reference Center for Respiratory Viruses, Institut Pasteur, Paris, France
- Molecular Genetics of RNA Viruses Unit, Institut Pasteur, UMR3569, CNRS, Université de Paris, Paris, France
| | - Mélanie Prague
- Inria Bordeaux Sud-Ouest, Inserm, Bordeaux Population Health Research Center, SISTM Team, UMR 1219, University of Bordeaux, Bordeaux, France
- Vaccine Research Institute, Créteil, France
| | | | - Cécile Hérate
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses and Le Kremlin-Bicêtre, Paris, France
| | - Marie Alexandre
- Inria Bordeaux Sud-Ouest, Inserm, Bordeaux Population Health Research Center, SISTM Team, UMR 1219, University of Bordeaux, Bordeaux, France
- Vaccine Research Institute, Créteil, France
| | - Nathalie Dereuddre-bosquet
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses and Le Kremlin-Bicêtre, Paris, France
| | | | - Vanessa Contreras
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses and Le Kremlin-Bicêtre, Paris, France
| | - Sylvie Behillil
- National Reference Center for Respiratory Viruses, Institut Pasteur, Paris, France
- Molecular Genetics of RNA Viruses Unit, Institut Pasteur, UMR3569, CNRS, Université de Paris, Paris, France
| | - Pauline Maisonnasse
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses and Le Kremlin-Bicêtre, Paris, France
| | - Sylvie Van Der Werf
- National Reference Center for Respiratory Viruses, Institut Pasteur, Paris, France
- Molecular Genetics of RNA Viruses Unit, Institut Pasteur, UMR3569, CNRS, Université de Paris, Paris, France
| | - Roger Le Grand
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses and Le Kremlin-Bicêtre, Paris, France
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5
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Hocini H, Wiedemann A, Blengio F, Lefebvre C, Cervantes-Gonzalez M, Foucat E, Tisserand P, Surenaud M, Coléon S, Prague M, Guillaumat L, Krief C, Fenwick C, Laouénan C, Bouadma L, Ghosn J, Pantaleo G, Thiébaut R, Lévy Y. Neutrophil Activation and Immune Thrombosis Profiles Persist in Convalescent COVID-19. J Clin Immunol 2023; 43:882-893. [PMID: 36943669 PMCID: PMC10029801 DOI: 10.1007/s10875-023-01459-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/24/2023] [Indexed: 03/23/2023]
Abstract
PURPOSE Following a severe COVID-19 infection, a proportion of individuals develop prolonged symptoms. We investigated the immunological dysfunction that underlies the persistence of symptoms months after the resolution of acute COVID-19. METHODS We analyzed cytokines, cell phenotypes, SARS-CoV-2 spike-specific and neutralizing antibodies, and whole blood gene expression profiles in convalescent severe COVID-19 patients 1, 3, and 6 months following hospital discharge. RESULTS We observed persistent abnormalities until month 6 marked by (i) high serum levels of monocyte/macrophage and endothelial activation markers, chemotaxis, and hematopoietic cytokines; (ii) a high frequency of central memory CD4+ and effector CD8+ T cells; (iii) a decrease in anti-SARS-CoV-2 spike and neutralizing antibodies; and (iv) an upregulation of genes related to platelet, neutrophil activation, erythrocytes, myeloid cell differentiation, and RUNX1 signaling. We identified a "core gene signature" associated with a history of thrombotic events, with upregulation of a set of genes involved in neutrophil activation, platelet, hematopoiesis, and blood coagulation. CONCLUSION The lack of restoration of gene expression to a normal profile after up to 6 months of follow-up, even in asymptomatic patients who experienced severe COVID-19, signals the need to carefully extend their clinical follow-up and propose preventive measures.
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Affiliation(s)
- Hakim Hocini
- Vaccine Research Institute, Université Paris-Est Créteil, Faculté de Médecine, INSERM U955, Team 16, Créteil, France
| | - Aurélie Wiedemann
- Vaccine Research Institute, Université Paris-Est Créteil, Faculté de Médecine, INSERM U955, Team 16, Créteil, France
| | - Fabiola Blengio
- Vaccine Research Institute, Université Paris-Est Créteil, Faculté de Médecine, INSERM U955, Team 16, Créteil, France
| | - Cécile Lefebvre
- Vaccine Research Institute, Université Paris-Est Créteil, Faculté de Médecine, INSERM U955, Team 16, Créteil, France
| | - Minerva Cervantes-Gonzalez
- Département Épidémiologie Biostatistiques Et Recherche Clinique, AP-HP, Hôpital Bichat, INSERM, Centre d'Investigation Clinique-Epidémiologie Clinique 1425, 75018, Paris, France
- UMR 1137, Université de Paris, INSERM, IAME, 75018, Paris, France
- APHP- Hôpital Bichat - Médecine Intensive et Réanimation des Maladies Infectieuses, Paris, France
| | - Emile Foucat
- Vaccine Research Institute, Université Paris-Est Créteil, Faculté de Médecine, INSERM U955, Team 16, Créteil, France
| | - Pascaline Tisserand
- Vaccine Research Institute, Université Paris-Est Créteil, Faculté de Médecine, INSERM U955, Team 16, Créteil, France
| | - Mathieu Surenaud
- Vaccine Research Institute, Université Paris-Est Créteil, Faculté de Médecine, INSERM U955, Team 16, Créteil, France
| | - Séverin Coléon
- Vaccine Research Institute, Université Paris-Est Créteil, Faculté de Médecine, INSERM U955, Team 16, Créteil, France
| | - Mélanie Prague
- Vaccine Research Institute, Université Paris-Est Créteil, Faculté de Médecine, INSERM U955, Team 16, Créteil, France
- Department of Public Health, Univ. Bordeaux, Inserm Bordeaux Population Health Research Centre, Inria SISTM, UMR 1219, Bordeaux, France
| | - Lydia Guillaumat
- Vaccine Research Institute, Université Paris-Est Créteil, Faculté de Médecine, INSERM U955, Team 16, Créteil, France
| | - Corinne Krief
- Vaccine Research Institute, Université Paris-Est Créteil, Faculté de Médecine, INSERM U955, Team 16, Créteil, France
| | - Craig Fenwick
- Service of Immunology and Allergy, Department of Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Cédric Laouénan
- Département Épidémiologie Biostatistiques Et Recherche Clinique, AP-HP, Hôpital Bichat, INSERM, Centre d'Investigation Clinique-Epidémiologie Clinique 1425, 75018, Paris, France
- UMR 1137, Université de Paris, INSERM, IAME, 75018, Paris, France
| | - Lila Bouadma
- UMR 1137, Université de Paris, INSERM, IAME, 75018, Paris, France
- APHP- Hôpital Bichat - Médecine Intensive et Réanimation des Maladies Infectieuses, Paris, France
| | - Jade Ghosn
- UMR 1137, Université de Paris, INSERM, IAME, 75018, Paris, France
- AP-HP, Hôpital Bichat, Service de Maladies Infectieuses Et Tropicales, 75018, Paris, France
| | - Giuseppe Pantaleo
- Vaccine Research Institute, Université Paris-Est Créteil, Faculté de Médecine, INSERM U955, Team 16, Créteil, France
- Swiss Vaccine Research Institute, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Rodolphe Thiébaut
- Vaccine Research Institute, Université Paris-Est Créteil, Faculté de Médecine, INSERM U955, Team 16, Créteil, France
- Department of Public Health, Univ. Bordeaux, Inserm Bordeaux Population Health Research Centre, Inria SISTM, UMR 1219, Bordeaux, France
- CHU de Bordeaux, Pôle de Santé Publique, Service d'Information Médicale, Bordeaux, France
| | - Yves Lévy
- Vaccine Research Institute, Université Paris-Est Créteil, Faculté de Médecine, INSERM U955, Team 16, Créteil, France.
- Assistance Publique-Hôpitaux de Paris, Service Immunologie Clinique, Groupe Henri-Mondor Albert-Chenevier, Créteil, France.
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Paireau J, Charpignon ML, Larrieu S, Calba C, Hozé N, Boëlle PY, Thiebaut R, Prague M, Cauchemez S. Impact of non-pharmaceutical interventions, weather, vaccination, and variants on COVID-19 transmission across departments in France. BMC Infect Dis 2023; 23:190. [PMID: 36997873 PMCID: PMC10061408 DOI: 10.1186/s12879-023-08106-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 02/20/2023] [Indexed: 04/01/2023] Open
Abstract
BACKGROUND Multiple factors shape the temporal dynamics of the COVID-19 pandemic. Quantifying their relative contributions is key to guide future control strategies. Our objective was to disentangle the individual effects of non-pharmaceutical interventions (NPIs), weather, vaccination, and variants of concern (VOC) on local SARS-CoV-2 transmission. METHODS We developed a log-linear model for the weekly reproduction number (R) of hospital admissions in 92 French metropolitan departments. We leveraged (i) the homogeneity in data collection and NPI definitions across departments, (ii) the spatial heterogeneity in the timing of NPIs, and (iii) an extensive observation period (14 months) covering different weather conditions, VOC proportions, and vaccine coverage levels. FINDINGS Three lockdowns reduced R by 72.7% (95% CI 71.3-74.1), 70.4% (69.2-71.6) and 60.7% (56.4-64.5), respectively. Curfews implemented at 6/7 pm and 8/9 pm reduced R by 34.3% (27.9-40.2) and 18.9% (12.04-25.3), respectively. School closures reduced R by only 4.9% (2.0-7.8). We estimated that vaccination of the entire population would have reduced R by 71.7% (56.4-81.6), whereas the emergence of VOC (mainly Alpha during the study period) increased transmission by 44.6% (36.1-53.6) compared with the historical variant. Winter weather conditions (lower temperature and absolute humidity) increased R by 42.2% (37.3-47.3) compared to summer weather conditions. Additionally, we explored counterfactual scenarios (absence of VOC or vaccination) to assess their impact on hospital admissions. INTERPRETATION Our study demonstrates the strong effectiveness of NPIs and vaccination and quantifies the role of weather while adjusting for other confounders. It highlights the importance of retrospective evaluation of interventions to inform future decision-making.
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Affiliation(s)
- Juliette Paireau
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, Université Paris Cité, CNRS UMR 2000, Paris, France.
- Infectious Diseases Department, Santé Publique France, Saint Maurice, France.
| | - Marie-Laure Charpignon
- Institute for Data, Systems, and Society (IDSS), Cambridge, MA, USA
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
- University of Bordeaux, Inria Bordeaux Sud-Ouest, Inserm, Bordeaux Population Health Research Center, SISTM Team, UMR1219, Bordeaux, France
| | - Sophie Larrieu
- Regions Department, Regional Office Nouvelle-Aquitaine, Santé publique France, Bordeaux, France
| | - Clémentine Calba
- Regions Department, Regional Office Provence-Alps-French Riviera and Corsica, Santé Publique France, Marseille, France
| | - Nathanaël Hozé
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, Université Paris Cité, CNRS UMR 2000, Paris, France
| | - Pierre-Yves Boëlle
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Paris, France
| | - Rodolphe Thiebaut
- University of Bordeaux, Inria Bordeaux Sud-Ouest, Inserm, Bordeaux Population Health Research Center, SISTM Team, UMR1219, Bordeaux, France
| | - Mélanie Prague
- University of Bordeaux, Inria Bordeaux Sud-Ouest, Inserm, Bordeaux Population Health Research Center, SISTM Team, UMR1219, Bordeaux, France
| | - Simon Cauchemez
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, Université Paris Cité, CNRS UMR 2000, Paris, France
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7
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Hocini H, Wiedemann A, Blengio F, Lefebvre C, Cervantes-Gonzalez M, Foucat E, Tisserand P, Surenaud M, Coléon S, Prague M, Guillaumat L, Krief C, Fenwick C, Laouénan C, Bouadma L, Ghosn J, Pantaleo G, Thiébaut R, Lévy Y. Correction to: Neutrophil Activation and Immune Thrombosis Profiles Persist in Convalescent COVID‑19. J Clin Immunol 2023:10.1007/s10875-023-01477-9. [PMID: 36991251 PMCID: PMC10060908 DOI: 10.1007/s10875-023-01477-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Affiliation(s)
- Hakim Hocini
- Vaccine Research Institute, Université Paris-Est Créteil, Faculté de Médecine, INSERM U955, Team 16, Créteil, France
| | - Aurélie Wiedemann
- Vaccine Research Institute, Université Paris-Est Créteil, Faculté de Médecine, INSERM U955, Team 16, Créteil, France
| | - Fabiola Blengio
- Vaccine Research Institute, Université Paris-Est Créteil, Faculté de Médecine, INSERM U955, Team 16, Créteil, France
| | - Cécile Lefebvre
- Vaccine Research Institute, Université Paris-Est Créteil, Faculté de Médecine, INSERM U955, Team 16, Créteil, France
| | - Minerva Cervantes-Gonzalez
- Département Épidémiologie Biostatistiques Et Recherche Clinique, AP-HP, Hôpital Bichat, INSERM, Centre d'Investigation Clinique‑Epidemiologie Clinique 1425, 75018, Paris, France
- UMR 1137, Université de Paris, INSERM, IAME, 75018, Paris, France
- APHP- Hôpital Bichat - Médecine Intensive et Réanimation des Maladies Infectieuses, Paris, France
| | - Emile Foucat
- Vaccine Research Institute, Université Paris-Est Créteil, Faculté de Médecine, INSERM U955, Team 16, Créteil, France
| | - Pascaline Tisserand
- Vaccine Research Institute, Université Paris-Est Créteil, Faculté de Médecine, INSERM U955, Team 16, Créteil, France
| | - Mathieu Surenaud
- Vaccine Research Institute, Université Paris-Est Créteil, Faculté de Médecine, INSERM U955, Team 16, Créteil, France
| | - Séverin Coléon
- Vaccine Research Institute, Université Paris-Est Créteil, Faculté de Médecine, INSERM U955, Team 16, Créteil, France
| | - Mélanie Prague
- Vaccine Research Institute, Université Paris-Est Créteil, Faculté de Médecine, INSERM U955, Team 16, Créteil, France
- Department of Public Health, Univ. Bordeaux, Inserm Bordeaux Population Health Research Centre, Inria SISTM, UMR 1219, Bordeaux, France
| | - Lydia Guillaumat
- Vaccine Research Institute, Université Paris-Est Créteil, Faculté de Médecine, INSERM U955, Team 16, Créteil, France
| | - Corinne Krief
- Vaccine Research Institute, Université Paris-Est Créteil, Faculté de Médecine, INSERM U955, Team 16, Créteil, France
| | - Craig Fenwick
- Service of Immunology and Allergy, Department of Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Cédric Laouénan
- Département Épidémiologie Biostatistiques Et Recherche Clinique, AP-HP, Hôpital Bichat, INSERM, Centre d'Investigation Clinique‑Epidemiologie Clinique 1425, 75018, Paris, France
- UMR 1137, Université de Paris, INSERM, IAME, 75018, Paris, France
| | - Lila Bouadma
- UMR 1137, Université de Paris, INSERM, IAME, 75018, Paris, France
- APHP- Hôpital Bichat - Médecine Intensive et Réanimation des Maladies Infectieuses, Paris, France
| | - Jade Ghosn
- UMR 1137, Université de Paris, INSERM, IAME, 75018, Paris, France
- AP-HP, Hôpital Bichat, Service de Maladies Infectieuses Et Tropicales, 75018, Paris, France
| | - Giuseppe Pantaleo
- Vaccine Research Institute, Université Paris-Est Créteil, Faculté de Médecine, INSERM U955, Team 16, Créteil, France
- Swiss Vaccine Research Institute, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Rodolphe Thiébaut
- Vaccine Research Institute, Université Paris-Est Créteil, Faculté de Médecine, INSERM U955, Team 16, Créteil, France
- Department of Public Health, Univ. Bordeaux, Inserm Bordeaux Population Health Research Centre, Inria SISTM, UMR 1219, Bordeaux, France
- CHU de Bordeaux, Pôle de Santé Publique, Service d'Information Médicale, Bordeaux, France
| | - Yves Lévy
- Vaccine Research Institute, Université Paris-Est Créteil, Faculté de Médecine, INSERM U955, Team 16, Créteil, France.
- Assistance Publique‑Hopitaux de Paris, Service Immunologie Clinique, Groupe Henri-Mondor Albert-Chenevier, Créteil, France.
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8
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Collin A, Hejblum BP, Vignals C, Lehot L, Thiébaut R, Moireau P, Prague M. Using a population-based Kalman estimator to model the COVID-19 epidemic in France: estimating associations between disease transmission and non-pharmaceutical interventions. Int J Biostat 2023; 0:ijb-2022-0087. [PMID: 36607837 DOI: 10.1515/ijb-2022-0087] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 11/08/2022] [Indexed: 01/07/2023]
Abstract
In response to the COVID-19 pandemic caused by SARS-CoV-2, governments have adopted a wide range of non-pharmaceutical interventions (NPI). These include stringent measures such as strict lockdowns, closing schools, bars and restaurants, curfews, and barrier gestures such as mask-wearing and social distancing. Deciphering the effectiveness of each NPI is critical to responding to future waves and outbreaks. To this end, we first develop a dynamic model of the French COVID-19 epidemics over a one-year period. We rely on a global extended Susceptible-Infectious-Recovered (SIR) mechanistic model of infection that includes a dynamic transmission rate over time. Multilevel data across French regions are integrated using random effects on the parameters of the mechanistic model, boosting statistical power by multiplying integrated observation series. We estimate the parameters using a new population-based statistical approach based on a Kalman filter, used for the first time in analysing real-world data. We then fit the estimated time-varying transmission rate using a regression model that depends on the NPIs while accounting for vaccination coverage, the occurrence of variants of concern (VoC), and seasonal weather conditions. We show that all NPIs considered have an independent significant association with transmission rates. In addition, we show a strong association between weather conditions that reduces transmission in summer, and we also estimate increased transmissibility of VoC.
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Affiliation(s)
- Annabelle Collin
- Inria, Inria Bordeaux - Sud-Ouest, Bordeaux INP, IMB UMR 5251, Université Bordeaux, Talence, France
| | - Boris P Hejblum
- Inria, Inria Bordeaux - Sud-Ouest, Talence, Univ. Bordeaux, Inserm, Bordeaux Population Health Research Center, SISTM Team, UMR 1219, F-33000 Bordeaux, France
- Vaccine Research Institute, F-94000 Créteil, France
| | - Carole Vignals
- Inria, Inria Bordeaux - Sud-Ouest, Talence, Univ. Bordeaux, Inserm, Bordeaux Population Health Research Center, SISTM Team, UMR 1219, F-33000 Bordeaux, France
- Vaccine Research Institute, F-94000 Créteil, France
- CHU Pellegrin, F-33000 Bordeaux, France
| | - Laurent Lehot
- Inria, Inria Bordeaux - Sud-Ouest, Talence, Univ. Bordeaux, Inserm, Bordeaux Population Health Research Center, SISTM Team, UMR 1219, F-33000 Bordeaux, France
- Vaccine Research Institute, F-94000 Créteil, France
| | - Rodolphe Thiébaut
- Inria, Inria Bordeaux - Sud-Ouest, Talence, Univ. Bordeaux, Inserm, Bordeaux Population Health Research Center, SISTM Team, UMR 1219, F-33000 Bordeaux, France
- Vaccine Research Institute, F-94000 Créteil, France
- CHU Pellegrin, F-33000 Bordeaux, France
| | - Philippe Moireau
- ISPED Inserm U1219 Bordeaux Population Health Bureau 23 146 rue Leo Saignat CS 61292 33076 Bordeaux Cedex, France
| | - Mélanie Prague
- Inria, Inria Saclay-Ile de France, France and LMS, CNRS UMR 7649, Ecole Polytechnique, Institut Polytechnique de Paris, Palaiseau, France
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9
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Wang MH, Staples P, Prague M, Goyal R, DeGruttola V, Onnela JP. Leveraging Contact Network Information in Clustered Randomized Studies of Contagion Processes. Obs Stud 2023; 9:157-175. [PMID: 37325081 PMCID: PMC10270696 DOI: 10.1353/obs.2023.0021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
In a randomized study, leveraging covariates related to the outcome (e.g. disease status) may produce less variable estimates of the effect of exposure. For contagion processes operating on a contact network, transmission can only occur through ties that connect affected and unaffected individuals; the outcome of such a process is known to depend intimately on the structure of the network. In this paper, we investigate the use of contact network features as efficiency covariates in exposure effect estimation. Using augmented generalized estimating equations (GEE), we estimate how gains in efficiency depend on the network structure and spread of the contagious agent or behavior. We apply this approach to simulated randomized trials using a stochastic compartmental contagion model on a collection of model-based contact networks and compare the bias, power, and variance of the estimated exposure effects using an assortment of network covariate adjustment strategies. We also demonstrate the use of network-augmented GEEs on a clustered randomized trial evaluating the effects of wastewater monitoring on COVID-19 cases in residential buildings at the the University of California San Diego.
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10
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Alexandre M, Marlin R, Prague M, Coleon S, Kahlaoui N, Cardinaud S, Naninck T, Delache B, Surenaud M, Galhaut M, Dereuddre-Bosquet N, Cavarelli M, Maisonnasse P, Centlivre M, Lacabaratz C, Wiedemann A, Zurawski S, Zurawski G, Schwartz O, Sanders RW, Le Grand R, Levy Y, Thiébaut R. Modelling the response to vaccine in non-human primates to define SARS-CoV-2 mechanistic correlates of protection. eLife 2022; 11:75427. [PMID: 35801637 PMCID: PMC9282856 DOI: 10.7554/elife.75427] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 06/22/2022] [Indexed: 11/29/2022] Open
Abstract
The definition of correlates of protection is critical for the development of next-generation SARS-CoV-2 vaccine platforms. Here, we propose a model-based approach for identifying mechanistic correlates of protection based on mathematical modelling of viral dynamics and data mining of immunological markers. The application to three different studies in non-human primates evaluating SARS-CoV-2 vaccines based on CD40-targeting, two-component spike nanoparticle and mRNA 1273 identifies and quantifies two main mechanisms that are a decrease of rate of cell infection and an increase in clearance of infected cells. Inhibition of RBD binding to ACE2 appears to be a robust mechanistic correlate of protection across the three vaccine platforms although not capturing the whole biological vaccine effect. The model shows that RBD/ACE2 binding inhibition represents a strong mechanism of protection which required significant reduction in blocking potency to effectively compromise the control of viral replication.
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Affiliation(s)
- Marie Alexandre
- Department of Public Health, Inserm Bordeaux Population Health Research Centre, University of Bordeaux, Inria SISTM, UMR 1219, Bordeaux, France
| | - Romain Marlin
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | - Mélanie Prague
- Department of Public Health, Inserm Bordeaux Population Health Research Centre, University of Bordeaux, Inria SISTM, UMR 1219, Bordeaux, France
| | - Severin Coleon
- Vaccine Research Institute, Inserm U955, Créteil, France
| | - Nidhal Kahlaoui
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | | | - Thibaut Naninck
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | - Benoit Delache
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | | | - Mathilde Galhaut
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | - Nathalie Dereuddre-Bosquet
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | - Mariangela Cavarelli
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | - Pauline Maisonnasse
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | | | | | | | - Sandra Zurawski
- Baylor Scott and White Research Institute, Dallas, United States
| | - Gerard Zurawski
- Baylor Scott and White Research Institute, Dallas, United States
| | | | - Rogier W Sanders
- Department of Medical Microbiology, University of Amsterdam, Amsterdam, Netherlands
| | - Roger Le Grand
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | - Yves Levy
- Vaccine Research Institute, Inserm U955, Créteil, France
| | - Rodolphe Thiébaut
- Department of Public Health, Inserm Bordeaux Population Health Research Centre, University of Bordeaux, Inria SISTM, UMR 1219, Bordeaux, France
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11
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Prague M, Lavielle M. SAMBA: A novel method for fast automatic model building in nonlinear mixed-effects models. CPT Pharmacometrics Syst Pharmacol 2022; 11:161-172. [PMID: 35104058 PMCID: PMC8846636 DOI: 10.1002/psp4.12742] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 10/15/2021] [Accepted: 10/28/2021] [Indexed: 11/30/2022] Open
Abstract
The success of correctly identifying all the components of a nonlinear mixed-effects model is far from straightforward: it is a question of finding the best structural model, determining the type of relationship between covariates and individual parameters, detecting possible correlations between random effects, or also modeling residual errors. We present the Stochastic Approximation for Model Building Algorithm (SAMBA) procedure and show how this algorithm can be used to speed up this process of model building by identifying at each step how best to improve some of the model components. The principle of this algorithm basically consists in "learning something" about the "best model," even when a "poor model" is used to fit the data. A comparison study of the SAMBA procedure with Stepwise Covariate Modeling (SCM) and COnditional Sampling use for Stepwise Approach (COSSAC) show similar performances on several real data examples but with a much reduced computing time. This algorithm is now implemented in Monolix and in the R package Rsmlx.
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Affiliation(s)
- Mélanie Prague
- Inria Bordeaux Sud‐Ouest, Inserm, Bordeaux Population Health Research CenterSISTM TeamUMR 1219University of BordeauxBordeauxFrance
- Vaccine Research InstituteCréteilFrance
| | - Marc Lavielle
- Inria & CMAP, Ecole PolytechniqueCNRSInstitut Polytechnique de ParisParisFrance
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12
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Colas C, Hejblum B, Rouillon S, Thiébaut R, Oudeyer PY, Moulin-Frier C, Prague M. EpidemiOptim: A Toolbox for the Optimization of Control Policies in Epidemiological Models. J ARTIF INTELL RES 2021. [DOI: 10.1613/jair.1.12588] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Modeling the dynamics of epidemics helps to propose control strategies based on pharmaceuticaland non-pharmaceutical interventions (contact limitation, lockdown, vaccination,etc). Hand-designing such strategies is not trivial because of the number of possibleinterventions and the difficulty to predict long-term effects. This task can be cast as an optimization problem where state-of-the-art machine learning methods such as deep reinforcement learning might bring significant value. However, the specificity of each domain|epidemic modeling or solving optimization problems|requires strong collaborationsbetween researchers from different fields of expertise. This is why we introduce EpidemiOptim, a Python toolbox that facilitates collaborations between researchers inepidemiology and optimization. EpidemiOptim turns epidemiological models and cost functions into optimization problems via a standard interface commonly used by optimization practitioners (OpenAI Gym). Reinforcement learning algorithms based on QLearning with deep neural networks (DQN) and evolutionary algorithms (NSGA-II) are already implemented. We illustrate the use of EpidemiOptim to find optimal policies fordynamical on-o lockdown control under the optimization of the death toll and economic recess using a Susceptible-Exposed-Infectious-Removed (SEIR) model for COVID-19. Using EpidemiOptim and its interactive visualization platform in Jupyter notebooks, epidemiologists, optimization practitioners and others (e.g. economists) can easily compare epidemiological models, costs functions and optimization algorithms to address important choicesto be made by health decision-makers. Trained models can be explored by experts and non-experts via a web interface.
This article is part of the special track on AI and COVID-19.
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13
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Alexandre M, Prague M, Thiébaut R. Between-group comparison of area under the curve in clinical trials with censored follow-up: Application to HIV therapeutic vaccines. Stat Methods Med Res 2021; 30:2130-2147. [PMID: 34218746 DOI: 10.1177/09622802211023963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In clinical trials, longitudinal data are commonly analyzed and compared between groups using a single summary statistic such as area under the outcome versus time curve (AUC). However, incomplete data, arising from censoring due to a limit of detection or missing data, can bias these analyses. In this article, we present a statistical test based on splines-based mixed-model accounting for both the censoring and missingness mechanisms in the AUC estimation. Inferential properties of the proposed method were evaluated and compared to ad hoc approaches and to a non-parametric method through a simulation study based on two-armed trial where trajectories and the proportion of missing data were varied. Simulation results highlight that our approach has significant advantages over the other methods. A real working example from two HIV therapeutic vaccine trials is presented to illustrate the applicability of our approach.
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Affiliation(s)
- Marie Alexandre
- University of Bordeaux, Inria Bordeaux Sud-Ouest, Inserm, Bordeaux Population Health Research Center, SISTM Team, France.,Data Science Division, Vaccine Research Institute (VRI), Créteil, France
| | - Mélanie Prague
- University of Bordeaux, Inria Bordeaux Sud-Ouest, Inserm, Bordeaux Population Health Research Center, SISTM Team, France.,Data Science Division, Vaccine Research Institute (VRI), Créteil, France
| | - Rodolphe Thiébaut
- University of Bordeaux, Inria Bordeaux Sud-Ouest, Inserm, Bordeaux Population Health Research Center, SISTM Team, France.,Data Science Division, Vaccine Research Institute (VRI), Créteil, France
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14
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Villain L, Commenges D, Pasin C, Prague M, Thiébaut R. Adaptive protocols based on predictions from a mechanistic model of the effect of IL7 on CD4 counts. Stat Med 2018; 38:221-235. [PMID: 30259533 DOI: 10.1002/sim.7957] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 07/05/2018] [Accepted: 08/18/2018] [Indexed: 12/16/2022]
Abstract
In human immunodeficiency virus-infected patients, antiretroviral therapy suppresses the viral replication, which is followed in most patients by a restoration of CD4+ T cells pool. For patients who fail to do so, repeated injections of exogenous interleukin 7 (IL7) are experimented. The IL7 is a cytokine that is involved in the T cell homeostasis and the INSPIRE study has shown that injections of IL7 induced a proliferation of CD4+ T cells. Phase I/II INSPIRE 2 and 3 studies have evaluated a protocol in which a first cycle of three IL7 injections is followed by a new cycle at each visit when the patient has less than 550 CD4 cells/μL. Restoration of the CD4 concentration has been demonstrated, but the long-term best adaptive protocol is yet to be determined. A mechanistic model of the evolution of CD4 after IL7 injections has been developed, which is based on a system of ordinary differential equations and includes random effects. Based on the estimation of this model, we use a Bayesian approach to forecast the dynamics of CD4 in new patients. We propose four prediction-based adaptive protocols of injections to minimize the time spent under 500 CD4 cells/μL for each patient, without increasing the number of injections received too much. We show that our protocols significantly reduce the time spent under 500 CD4 over a period of two years, without increasing the number of injections. These protocols have the potential to increase the efficiency of this therapy.
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Affiliation(s)
- Laura Villain
- University of Bordeaux, Inserm, Bordeaux, Population Health Research Center, Team SISTM, Bordeaux, France.,INRIA Bordeaux Sud Ouest, Talence, France.,Vaccine Research Institute (VRI), Hôpital Henri Mondor, Créteil, France
| | - Daniel Commenges
- University of Bordeaux, Inserm, Bordeaux, Population Health Research Center, Team SISTM, Bordeaux, France.,INRIA Bordeaux Sud Ouest, Talence, France.,Vaccine Research Institute (VRI), Hôpital Henri Mondor, Créteil, France
| | - Chloé Pasin
- University of Bordeaux, Inserm, Bordeaux, Population Health Research Center, Team SISTM, Bordeaux, France.,INRIA Bordeaux Sud Ouest, Talence, France.,Vaccine Research Institute (VRI), Hôpital Henri Mondor, Créteil, France
| | - Mélanie Prague
- University of Bordeaux, Inserm, Bordeaux, Population Health Research Center, Team SISTM, Bordeaux, France.,INRIA Bordeaux Sud Ouest, Talence, France.,Vaccine Research Institute (VRI), Hôpital Henri Mondor, Créteil, France
| | - Rodolphe Thiébaut
- University of Bordeaux, Inserm, Bordeaux, Population Health Research Center, Team SISTM, Bordeaux, France.,INRIA Bordeaux Sud Ouest, Talence, France.,Vaccine Research Institute (VRI), Hôpital Henri Mondor, Créteil, France
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15
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Jarne A, Commenges D, Villain L, Prague M, Lévy Y, Thiébaut R. Modeling $\mathrm{CD4}^{+}$ T cells dynamics in HIV-infected patients receiving repeated cycles of exogenous Interleukin 7. Ann Appl Stat 2017. [DOI: 10.1214/17-aoas1047] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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16
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Prague M, Commenges D, Gran JM, Ledergerber B, Young J, Furrer H, Thiébaut R. Dynamic models for estimating the effect of HAART on CD4 in observational studies: Application to the Aquitaine Cohort and the Swiss HIV Cohort Study. Biometrics 2016; 73:294-304. [PMID: 27461460 DOI: 10.1111/biom.12564] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 05/01/2016] [Accepted: 06/01/2016] [Indexed: 11/29/2022]
Abstract
Highly active antiretroviral therapy (HAART) has proved efficient in increasing CD4 counts in many randomized clinical trials. Because randomized trials have some limitations (e.g., short duration, highly selected subjects), it is interesting to assess the effect of treatments using observational studies. This is challenging because treatment is started preferentially in subjects with severe conditions. This general problem had been treated using Marginal Structural Models (MSM) relying on the counterfactual formulation. Another approach to causality is based on dynamical models. We present three discrete-time dynamic models based on linear increments models (LIM): the first one based on one difference equation for CD4 counts, the second with an equilibrium point, and the third based on a system of two difference equations, which allows jointly modeling CD4 counts and viral load. We also consider continuous-time models based on ordinary differential equations with non-linear mixed effects (ODE-NLME). These mechanistic models allow incorporating biological knowledge when available, which leads to increased statistical evidence for detecting treatment effect. Because inference in ODE-NLME is numerically challenging and requires specific methods and softwares, LIM are a valuable intermediary option in terms of consistency, precision, and complexity. We compare the different approaches in simulation and in illustration on the ANRS CO3 Aquitaine Cohort and the Swiss HIV Cohort Study.
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Affiliation(s)
- Mélanie Prague
- Harvard T.H. Chan School of Public Health, Biostatistics Department, Boston, U.S.A
| | - Daniel Commenges
- University of Bordeaux, ISPED, F-33000 Bordeaux, France.,INSERM, U1219 Bordeaux Population Health Research Centre, F-33000, Bordeaux, France.,INRIA (SISTM) Centre Recherche Bordeaux Sud-Ouest, University of Bordeaux, Talence, France
| | - Jon Michael Gran
- Oslo Center for Biostatistics and Epidemiology, Oslo University Hospital and University of Oslo, Norway
| | - Bruno Ledergerber
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, Switzerland
| | - Jim Young
- Basel Institute for Clinical Epidemiology and Biostatistics, University Hospital of Basel, Switzerland
| | - Hansjakob Furrer
- Department of Infectious Diseases Bern University Hospital, University of Bern, Switzerland
| | - Rodolphe Thiébaut
- University of Bordeaux, ISPED, F-33000 Bordeaux, France.,INSERM, U1219 Bordeaux Population Health Research Centre, F-33000, Bordeaux, France.,INRIA (SISTM) Centre Recherche Bordeaux Sud-Ouest, University of Bordeaux, Talence, France
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17
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Thiébaut R, Prague M, Commenges D. [Mathematical dynamical models for personalized medicine]. Med Sci (Paris) 2014; 30 Spec No 2:23-6. [PMID: 25407454 DOI: 10.1051/medsci/201430s205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
One of the necessary conditions to perform any personalized medicine is to obtain good individual predictions. In addition to the numerous markers available (omics data), the methods used to analyze the data are very important too. We are presenting an example of mathematical dynamical mechanistic model that could be used for adapting the antiretroviral treatment in patients infected by the human immunodeficiency virus. The interest of this type of approach is to build a model based on biological knowledge about the interaction between markers and therefore to allow for a better predictive power.
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Affiliation(s)
- Rodolphe Thiébaut
- Inserm U897, INRIA SISTM (statistics in systems biology and translational medicine), université de Bordeaux, ISPED (institut de santé publique, d'épidémiologie et de développement), CHU de Bordeaux, unité de soutien méthodologique à la recherche clinique et épidémiologique, Bordeaux, France; institut de recherche vaccinale (Labex) UPEC, Créteil, France
| | - Mélanie Prague
- Inserm U897, INRIA SISTM (statistics in systems biology and translational medicine), université de Bordeaux, ISPED (institut de santé publique, d'épidémiologie et de développement), CHU de Bordeaux, unité de soutien méthodologique à la recherche clinique et épidémiologique, Bordeaux, France; institut de recherche vaccinale (Labex) UPEC, Créteil, France
| | - Daniel Commenges
- Inserm U897, INRIA SISTM (statistics in systems biology and translational medicine), université de Bordeaux, ISPED (institut de santé publique, d'épidémiologie et de développement), CHU de Bordeaux, unité de soutien méthodologique à la recherche clinique et épidémiologique, Bordeaux, France; institut de recherche vaccinale (Labex) UPEC, Créteil, France
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18
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Thiébaut R, Drylewicz J, Prague M, Lacabaratz C, Beq S, Jarne A, Croughs T, Sekaly RP, Lederman MM, Sereti I, Commenges D, Lévy Y. Quantifying and predicting the effect of exogenous interleukin-7 on CD4+ T cells in HIV-1 infection. PLoS Comput Biol 2014; 10:e1003630. [PMID: 24853554 PMCID: PMC4031052 DOI: 10.1371/journal.pcbi.1003630] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 04/03/2014] [Indexed: 12/22/2022] Open
Abstract
Exogenous Interleukin-7 (IL-7), in supplement to antiretroviral therapy, leads to a substantial increase of all CD4+ T cell subsets in HIV-1 infected patients. However, the quantitative contribution of the several potential mechanisms of action of IL-7 is unknown. We have performed a mathematical analysis of repeated measurements of total and naive CD4+ T cells and their Ki67 expression from HIV-1 infected patients involved in three phase I/II studies (N = 53 patients). We show that, besides a transient increase of peripheral proliferation, IL-7 exerts additional effects that play a significant role in CD4+ T cell dynamics up to 52 weeks. A decrease of the loss rate of the total CD4+ T cell is the most probable explanation. If this effect could be maintained during repeated administration of IL-7, our simulation study shows that such a strategy may allow maintaining CD4+ T cell counts above 500 cells/µL with 4 cycles or fewer over a period of two years. This in-depth analysis of clinical data revealed the potential for IL-7 to achieve sustained CD4+ T cell restoration with limited IL-7 exposure in HIV-1 infected patients with immune failure despite antiretroviral therapy. HIV infection is characterized by a decrease of CD4+ T-lymphocytes in the blood. Whereas antiretroviral treatment succeeds to control viral replication, some patients fail to reconstitute their CD4+ T cell count to normal value. IL-7 is a promising cytokine under evaluation for its use in HIV infection, in supplement to antiretroviral therapy, as it increases cell proliferation and survival. Here, we use data from three clinical trials testing the effect of IL-7 on CD4+ T-cell recovery in treated HIV-infected individuals and use a simple mathematical model to quantify IL-7 effects by estimating the biological parameters of the model. We show that the increase of peripheral proliferation could not explain alone the long-term dynamics of T cells after IL-7 injections underlining other important effects such as the improvement of cell survival. We also investigate the feasibility and the efficiency of repetitions of IL-7 cycles and argue for further evaluation through clinical trials.
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Affiliation(s)
- Rodolphe Thiébaut
- INSERM, ISPED, Centre INSERM U897-Epidemiologie-Biostatistique, Bordeaux, France
- Univ. Bordeaux, ISPED, Centre INSERM U897-Epidemiologie-Biostatistique, Bordeaux, France
- INRIA, SISTM team, Bordeaux, France
- * E-mail:
| | - Julia Drylewicz
- Laboratory for Translational Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Mélanie Prague
- INSERM, ISPED, Centre INSERM U897-Epidemiologie-Biostatistique, Bordeaux, France
- Univ. Bordeaux, ISPED, Centre INSERM U897-Epidemiologie-Biostatistique, Bordeaux, France
- INRIA, SISTM team, Bordeaux, France
| | - Christine Lacabaratz
- INSERM, Unité U955, Créteil, France
- Université Paris-Est, Faculté de Médecine, UMR-S955 Creteil, France
| | | | - Ana Jarne
- INSERM, ISPED, Centre INSERM U897-Epidemiologie-Biostatistique, Bordeaux, France
- Univ. Bordeaux, ISPED, Centre INSERM U897-Epidemiologie-Biostatistique, Bordeaux, France
- INRIA, SISTM team, Bordeaux, France
| | | | - Rafick-Pierre Sekaly
- Vaccine and Gene Therapy Institute-Florida, Port St. Lucie, Florida, United States of America
| | - Michael M. Lederman
- Case Western Reserve University/University Hospitals/Case Medical Center, Cleveland, Ohio, United States of America
| | - Irini Sereti
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Daniel Commenges
- INSERM, ISPED, Centre INSERM U897-Epidemiologie-Biostatistique, Bordeaux, France
- Univ. Bordeaux, ISPED, Centre INSERM U897-Epidemiologie-Biostatistique, Bordeaux, France
- INRIA, SISTM team, Bordeaux, France
| | - Yves Lévy
- INSERM, Unité U955, Créteil, France
- Université Paris-Est, Faculté de Médecine, UMR-S955 Creteil, France
- AP-HP, Groupe Henri-Mondor Albert-Chenevier, Immunologie Clinique, Creteil, France
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Prague M, Commenges D, Guedj J, Drylewicz J, Thiébaut R. NIMROD: a program for inference via a normal approximation of the posterior in models with random effects based on ordinary differential equations. Comput Methods Programs Biomed 2013; 111:447-458. [PMID: 23764196 DOI: 10.1016/j.cmpb.2013.04.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 03/04/2013] [Accepted: 04/23/2013] [Indexed: 06/02/2023]
Abstract
Models based on ordinary differential equations (ODE) are widespread tools for describing dynamical systems. In biomedical sciences, data from each subject can be sparse making difficult to precisely estimate individual parameters by standard non-linear regression but information can often be gained from between-subjects variability. This makes natural the use of mixed-effects models to estimate population parameters. Although the maximum likelihood approach is a valuable option, identifiability issues favour Bayesian approaches which can incorporate prior knowledge in a flexible way. However, the combination of difficulties coming from the ODE system and from the presence of random effects raises a major numerical challenge. Computations can be simplified by making a normal approximation of the posterior to find the maximum of the posterior distribution (MAP). Here we present the NIMROD program (normal approximation inference in models with random effects based on ordinary differential equations) devoted to the MAP estimation in ODE models. We describe the specific implemented features such as convergence criteria and an approximation of the leave-one-out cross-validation to assess the model quality of fit. In pharmacokinetics models, first, we evaluate the properties of this algorithm and compare it with FOCE and MCMC algorithms in simulations. Then, we illustrate NIMROD use on Amprenavir pharmacokinetics data from the PUZZLE clinical trial in HIV infected patients.
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Affiliation(s)
- Mélanie Prague
- Univ. Bordeaux, ISPED, Centre INSERM U897-Epidemiologie-Biostatistique, F-33000 Bordeaux, France.
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Prague M, Commenges D, Thiébaut R. Dynamical models of biomarkers and clinical progression for personalized medicine: the HIV context. Adv Drug Deliv Rev 2013; 65:954-65. [PMID: 23603207 DOI: 10.1016/j.addr.2013.04.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2012] [Revised: 02/15/2013] [Accepted: 04/10/2013] [Indexed: 01/11/2023]
Abstract
Mechanistic models, based on ordinary differential equation systems, can exhibit very good predictive abilities that will be useful to build treatment monitoring strategies. In this review, we present the potential and the limitations of such models for guiding treatment (monitoring and optimizing) in HIV-infected patients. In the context of antiretroviral therapy, several biological processes should be considered in addition to the interaction between viruses and the host immune system: the mechanisms of action of the drugs, their pharmacokinetics and pharmacodynamics, as well as the viral and host characteristics. Another important aspect to take into account is clinical progression, although its implementation in such modelling approaches is not easy. Finally, the control theory and the use of intrinsic properties of mechanistic models make them very relevant for dynamic treatment adaptation. Their implementation would nevertheless require their evaluation through clinical trials.
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Philip P, Sagaspe P, Prague M, Tassi P, Capelli A, Bioulac B, Commenges D, Taillard J. Acute versus chronic partial sleep deprivation in middle-aged people: differential effect on performance and sleepiness. Sleep 2012; 35:997-1002. [PMID: 22754046 PMCID: PMC3369235 DOI: 10.5665/sleep.1968] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
STUDY OBJECTIVE To evaluate the effects of acute sleep deprivation and chronic sleep restriction on vigilance, performance, and self-perception of sleepiness. DESIGN Habitual night followed by 1 night of total sleep loss (acute sleep deprivation) or 5 consecutive nights of 4 hr of sleep (chronic sleep restriction) and recovery night. PARTICIPANTS Eighteen healthy middle-aged male participants (age [(± standard deviation] = 49.7 ± 2.6 yr, range 46-55 yr). MEASUREMENTS Multiple sleep latency test trials, Karolinska Sleepiness Scale scores, simple reaction time test (lapses and 10% fastest reaction times), and nocturnal polysomnography data were recorded. RESULTS Objective and subjective sleepiness increased immediately in response to sleep restriction. Sleep latencies after the second and third nights of sleep restriction reached levels equivalent to those observed after acute sleep deprivation, whereas Karolinska Sleepiness Scale scores did not reach these levels. Lapse occurrence increased after the second day of sleep restriction and reached levels equivalent to those observed after acute sleep deprivation. A statistical model revealed that sleepiness and lapses did not progressively worsen across days of sleep restriction. Ten percent fastest reaction times (i.e., optimal alertness) were not affected by acute or chronic sleep deprivation. Recovery to baseline levels of alertness and performance occurred after 8-hr recovery night. CONCLUSIONS In middle-aged study participants, sleep restriction induced a high increase in sleep propensity but adaptation to chronic sleep restriction occurred beyond day 3 of restriction. This sleepiness attenuation was underestimated by the participants. One recovery night restores daytime sleepiness and cognitive performance deficits induced by acute or chronic sleep deprivation. CITATION Philip P; Sagaspe P; Prague M; Tassi P; Capelli A; Bioulac B; Commenges D; Taillard J. Acute versus chronic partial sleep deprivation in middle-aged people: differential effect on performance and sleepiness. SLEEP 2012;35(7):997-1002.
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Affiliation(s)
- Pierre Philip
- Université de Bordeaux, Sommeil, Attention et Neuropsychiatrie, USR 3413, F-33000 Bordeaux, France.
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