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Mircea T. Sofonea

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affiliation actuelle : *Pathogenesis and Control of Chronic and Emerging Infections* (PCCEI, U1058) - Univ. Montpellier, Inserm, EFS, Univ. Antilles **postes** 2018 — maître de conférences Univ. Montpellier 2017 — 2018 chercheur post-doctorant CNRS 2014 — 2017 doctorant moniteur Univ. Montpellier **formation** 2021 DU stratégies anti-infectieuses (infectiologie hospitalière) Fac. Médecine, Univ. Montpellier 2017 doctorat en évolution des systèmes infectieux Univ. Montpellier 2014 diplôme de l'École normale supérieure Paris 2013 diplôme de l'Institut Pasteur Paris 2010 classes préparatoires Lyc. Henri-IV, Paris **concours & qualifications** 2018 Qualifications MCU biologie des populations, biologie des organismes & mathématiques appliquées 2014 Agrégation SVSTU (spécialité biologie & physiologie des organismes), CAPES mathématiques 2010 École normale supérieure de la rue d'Ulm 2009 Olympiades Internationales de Biologie 2008 Olympiades de Physique France **prix & distinctions** 2022 Prix Jean Mantz de la Société Française d’Anesthésie-Réanimation (meilleur article de l’année) 2009 Prix des Olympiades de l'Académie des Sciences
Current affiliation: *Pathogenesis and Control of Chronic and Emerging Infections* (PCCEI, U1058) - Univ. Montpellier, Inserm, EFS, Univ. Antilles **positions** 2018 — associate professor Univ. Montpellier 2017 — 2018 post-doctoral researcher CNRS 2014 — 2017 Phd student & lecturer Univ. Montpellier **responsibilities** 2023 — Member of the Steering Commitee of the TIE University-Hospital Federation University Hospital of Montpellier 2022 — Deputy Director for Research of the Exposome Institute of the University of Montpellier (ExposUM) Univ. Montpellier 2022 — Associate Editor of Anaesthesia Critical Care and Pain Medicine SFAR 2021 — Executive Member of the Modelling Coordinated Action ANRS|MIE 2021 — Member of the Air & COVID expert group ANSES 2021 — 2022 Head of the Theoretical & Experimental Evolution research group MIVEGEC 2016 — 2018 member of the organizing committee of the Evolution 2018 congress ESEB **training** 2021 University degree in anti-infective strategies (hospital infectiology) Medical school, Univ. Montpellier 2017 PhD in evolution of infectious systems Univ. Montpellier 2014 École normale supérieure diploma Paris 2013 Institut Pasteur diploma Paris 2010 classes préparatoires Lyc. Henri-IV, Paris **competitive examinations & qualifications** 2018 Associate professorship qualification in population biology, organismal biology and applied mathematics 2014 Agrégation in natural sciences (major in organismal biology & physiology), CAPES in mathematics 2010 École normale supérieure de la rue d'Ulm 2009 International Biology Olympiad 2008 France Physics Olympiad **awards & honours** 2022 Jean Mantz Prize of the French Society of Anaesthesia & Intensive Care (best article of the year) 2009 Olympiad Prize of the French Academy of Science

Publications

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Within-host evolutionary dynamics of antimicrobial quantitative resistance

Ramsès Djidjou-Demasse , Mircea T Sofonea , Marc Choisy , Samuel Alizon
Mathematical Modelling of Natural Phenomena, 2023, 18, pp.24. ⟨10.1051/mmnp/2023019⟩
Journal articles hal-03194023v4
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Epidemic models: why and how to use them

Mircea T Sofonea , Simon Cauchemez , Pierre-Yves Boëlle
Anaesthesia Critical Care & Pain Medicine, 2022, 41 (2), pp.101048. ⟨10.1016/j.accpm.2022.101048⟩
Journal articles hal-03638186v1

Corrigendum to: Analysing different exposures identifies that wearing masks and establishing COVID-19 areas reduce secondary-attack risk in aged-care facilities

Bastien Reyné , Christian Selinger , Mircea Sofonea , Stéphanie Miot , Amandine Pisoni
International Journal of Epidemiology, 2022, 51 (2), pp.689-689. ⟨10.1093/ije/dyab269⟩
Journal articles hal-04056156v1
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Epidemiological and clinical insights from SARS-CoV-2 RT-PCR crossing threshold values, France, January to November 2020

Samuel Alizon , Christian Selinger , Mircea T Sofonea , Stéphanie Haim-Boukobza , Jean-Marc Giannoli
Eurosurveillance, 2022, 27 (6), pp.2100406. ⟨10.2807/1560-7917.ES.2022.27.6.2100406⟩
Journal articles hal-03175551v3
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Non-Markovian modelling highlights the importance of age structure on Covid-19 epidemiological dynamics

Bastien Reyné , Quentin Richard , Christian Selinger , Mircea T Sofonea , Ramsès Djidjou-Demasse
Mathematical Modelling of Natural Phenomena, 2022, 17, pp.7. ⟨10.1051/mmnp/2022008⟩
Journal articles hal-03629334v1
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COVID-19 pandemic-associated chilblains: more links for SARS-CoV-2 and less evidence for high interferon type I systemic response

Didier Bessis , Sophie Trouillet‐Assant , Léo‐Paul Secco , Nathalie Bardin , Brigitte Blanc
British Journal of Dermatology, 2022, 187 (6), pp.1032-1035. ⟨10.1111/bjd.21820⟩
Journal articles hal-03930679v1
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Analyzing and Modeling the Spread of SARS-CoV-2 Omicron Lineages BA.1 and BA.2, France, September 2021–February 2022

Mircea Sofonea , Bénédicte Roquebert , Vincent Foulongne , David Morquin , Laura Verdurme
Emerging Infectious Diseases, 2022, 28 (7), pp.1355-1365. ⟨10.3201/eid2807.220033⟩
Journal articles hal-03714983v1

Peace, not war in Ukraine or anywhere else, please

Jean-Yves Lefrant , Romain Pirracchio , Dan Benhamou , Marc-Olivier Fischer , Rosanna Njeim
Anaesthesia Critical Care & Pain Medicine, 2022, pp.101068. ⟨10.1016/j.accpm.2022.101068⟩
Journal articles hal-03667303v1
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Variant‐specific SARS‐CoV‐2 within‐host kinetics

Baptiste Elie , Bénédicte Roquebert , Mircea T Sofonea , Sabine Trombert-Paolantoni , Vincent Foulongne
Journal of Medical Virology, 2022, 94 (8), pp.3625-3633. ⟨10.1002/jmv.27757⟩
Journal articles hal-03651890v1
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Principles of mathematical epidemiology and compartmental modelling application to COVID-19

Bastien Reyné , Nicolas Saby , Mircea T Sofonea
Anaesthesia Critical Care & Pain Medicine, 2022, 41 (1), pp.101017. ⟨10.1016/j.accpm.2021.101017⟩
Journal articles hal-03859869v1
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Detecting Rapid Spread of SARS-CoV-2 Variants, France, January 26–February 16, 2021

Stéphanie Haim-Boukobza , Bénédicte Roquebert , Sabine Trombert-Paolantoni , Emmanuel Lecorche , Laura Verdurme
Emerging Infectious Diseases, 2021, 27 (5), pp.1496-1499. ⟨10.3201/eid2705.210397⟩
Journal articles hal-03150819v3
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Estimating dates of origin and end of COVID-19 epidemics

Thomas Bénéteau , Elie ` Baptiste , Mircea T Sofonea , Samuel Alizon
Peer Community Journal, 2021, 1, pp.e70. ⟨10.24072/pcjournal.63⟩
Journal articles hal-03120811v2
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SARS-CoV-2 variants of concern are associated with lower RT-PCR amplification cycles between January and March 2021 in France

Benedicte Roquebert , Stéphanie Haim-Boukobza , Sabine Trombert-Paolantoni , Emmanuel Lecorche , Laura Verdurme
International Journal of Infectious Diseases, 2021, ⟨10.1016/j.ijid.2021.09.076⟩
Journal articles hal-03366559v1
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The SARS-CoV-2 B.1.351 lineage (VOC β) is outgrowing the B.1.1.7 lineage (VOC α) in some French regions in April 2021

Bénédicte Roquebert , Sabine Trombert-Paolantoni , Stéphanie Haim-Boukobza , Emmanuel Lecorche , Laura Verdurme
Eurosurveillance, 2021, 26 (23), ⟨10.2807/1560-7917.es.2021.26.23.2100447⟩
Journal articles hal-03289627v1
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Rapid spread of the SARS-CoV-2 Delta variant in some French regions, June 2021

Samuel Alizon , Stéphanie Haim-Boukobza , Vincent Foulongne , Laura Verdurme , Sabine Trombert-Paolantoni
Eurosurveillance, 2021, 26 (28), ⟨10.2807/1560-7917.ES.2021.26.28.2100573⟩
Journal articles hal-03289622v1
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Analysing different exposures identifies that wearing masks and establishing COVID-19 areas reduce secondary-attack risk in aged-care facilities

Bastien Reyné , Christian Selinger , Mircea T Sofonea , Stéphanie Miot , Amandine Pisoni
International Journal of Epidemiology, 2021, 50 (6), pp.1788-1794. ⟨10.1093/ije/dyab121⟩
Journal articles hal-03289625v1
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Within-host bacterial growth dynamics with both mutation and horizontal gene transfer

Ramsès Djidjou-Demasse , Samuel Alizon , Mircea T Sofonea
Journal of Mathematical Biology, 2021, ⟨10.1007/s00285-021-01571-9⟩
Journal articles hal-02500420v1
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Two waves and a high tide: the COVID-19 epidemic in France

Mircea T Sofonea , Corentin Boennec , Yannis Michalakis , Samuel Alizon
Anaesthesia Critical Care & Pain Medicine, 2021, 40 (3), pp.100881. ⟨10.1016/j.accpm.2021.100881⟩
Journal articles hal-03289626v2
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SARS‐CoV‐2 virulence evolution: Avirulence theory, immunity and trade‐offs

Samuel Alizon , Mircea T Sofonea
Journal of Evolutionary Biology, 2021, 34 (12), pp.1867 - 1877. ⟨10.1111/jeb.13896⟩
Journal articles hal-03289628v1
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Episome partitioning and symmetric cell divisions: Quantifying the role of random events in the persistence of HPV infections

Thomas Beneteau , Christian Selinger , Mircea T Sofonea , Samuel Alizon
PLoS Computational Biology, 2021, 17 (9), pp.e1009352. ⟨10.1371/journal.pcbi.1009352⟩
Journal articles hal-03357550v1
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Unresolved advantages of multipartitism in spatially structured environments

Mark P Zwart , Stéphane Blanc , Marcelle Johnson , Susanna Manrubia , Yannis Michalakis
Virus Evolution, 2021, 7 (1), ⟨10.1093/ve/veab004⟩
Journal articles hal-03219672v1
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SARS-CoV-2 viral RNA levels are not 'viral load'

Yannis Michalakis , Mircea T Sofonea , Samuel Alizon , Ignacio G. Bravo
Trends in Microbiology, 2021, 29 (11), pp.970-972. ⟨10.1016/j.tim.2021.08.008⟩
Journal articles hal-03419147v1
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Anticipating COVID-19 intensive care unit capacity strain: A look back at epidemiological projections in France

Mircea T Sofonea , Samuel Alizon
Anaesthesia Critical Care & Pain Medicine, 2021, ⟨10.1016/j.accpm.2021.100943⟩
Journal articles hal-03366541v1
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Memory is key in capturing COVID-19 epidemiological dynamics

Mircea T Sofonea , Bastien Reyné , Baptiste Elie , Ramsès Djidjou-Demasse , Christian Selinger
Epidemics, 2021, 35, pp.100459. ⟨10.1016/j.epidem.2021.100459⟩
Journal articles hal-03289624v1
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Age-structured non-pharmaceutical interventions for optimal control of COVID-19 epidemic

Quentin Richard , Samuel Alizon , Marc Choisy , Mircea T Sofonea , Ramsès Djidjou-Demasse
PLoS Computational Biology, 2021, ⟨10.1371/journal.pcbi.1008776⟩
Journal articles hal-02879512v3
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Emerging dynamics from high-resolution spatial numerical epidemics

Olivier Thomine , Samuel Alizon , Corentin Boennec , Marc Barthelemy , Mircea T Sofonea
eLife, 2021, 10, ⟨10.7554/elife.71417⟩
Journal articles hal-03415297v1
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Early phylodynamics analysis of the COVID-19 epidemic in France

Gonché Danesh , Baptiste Elie , Yannis Michalakis , Mircea T Sofonea , Antonin Bal
Peer Community Journal, 2021, 1, pp.e45. ⟨10.24072/pcjournal.40⟩
Journal articles hal-03001114v2
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A global asymptotic stability condition for a dimorphic Lotka-Volterra model with explicit indirect interactions

Mircea T Sofonea
Applicable Analysis, 2019, ⟨10.1080/00036811.2018.1437417⟩
Journal articles hal-03366505v1
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Detecting within-host interactions from genotype combination prevalence data

Samuel Alizon , Carmen Lia Murall , Emma Saulnier , Mircea T Sofonea
Epidemics, 2019, 29, pp.100349. ⟨10.1016/j.epidem.2019.100349⟩
Journal articles hal-02387765v1

Small bottleneck size in a highly multipartite virus during a complete infection cycle

Romain Gallet , Frédéric Fabre , Gael Thébaud , Mircea T Sofonea , Anne Sicard
Journal of Virology, 2018, 92 (14), pp.e00139-18. ⟨10.1128/JVI.00139-18⟩
Journal articles hal-01847886v1
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Can Ebola Virus evolve to be less virulent in humans?

Mircea T Sofonea , L. Aldakak , Luis F. V. V. Boullosa , Samuel Alizon
Journal of Evolutionary Biology, 2018, 31 (3), pp.382 - 392. ⟨10.1111/jeb.13229⟩
Journal articles hal-01897077v1
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Exposing the diversity of multiple infection patterns

Mircea T Sofonea , Samuel Alizon , Yannis Michalakis
Journal of Theoretical Biology, 2017, 419, pp.278 - 289. ⟨10.1016/j.jtbi.2017.02.011⟩
Journal articles hal-01567902v1

From within-host interactions to epidemiological competition: a general model for multiple infections

Mircea T Sofonea , Samuel Alizon , Yannis Michalakis
Philosophical Transactions of the Royal Society B: Biological Sciences, 2015, 370 (1675), pp.20140303. ⟨10.1098/rstb.2014.0303⟩
Journal articles hal-01571806v1
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Épidémiologie et évolution du SARS-CoV-2

Samuel Alizon , Mircea T Sofonea
Les années COVID : comment y survivre, , pp.65-74, 2023, 978-2-493270-69-6
Book sections hal-04184205v1
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De Delta à Omicron, scénarios de tendances hospitalières pour l'hiver 2021-2022

Samuel Alizon , Mircea T Sofonea
[Rapport de recherche] 16, CNRS - Centre National de la Recherche Scientifique; IRD - Institut de recherche pour le developpement; Université de Montpellier. 2021
Reports hal-03502127v1

Note d’appui scientifique et technique de l’Anses relatif à la viabilité dans l’air et la dose infectante du virus SARS-COV-2

Pierre Le Cann , Christophe Batéjat , Benoit Delache , Ignacio Garcia-Verdugo , Thi Lan Ha
Saisine n°2021-SA-0018, Anses. 2021, 101 p
Reports anses-03898683v1
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Évolution de la virulence et COVID-19

Samuel Alizon , Yannis Michalakis , Mircea T Sofonea
[Rapport de recherche] 12, Centre National de la Recherche Scientifique (CNRS); Institut de recherche pour le développement (IRD); Université de Montpellier (UM), FRA. 2020
Reports hal-02950712v1
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Modéliser l'épidémie de COVID-19 (résumé)

Samuel Alizon , Mircea T Sofonea , Yannis Michalakis
[Rapport de recherche] 7, Centre National de la Recherche Scientifique (CNRS); Institut de recherche pour le développement (IRD); Université de Montpellier (UM), FRA. 2020
Reports hal-02950651v1
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Les effets sexe spécifiques de COVID-19 en France et l’implication potentielle des déficits en G6PD

Yannis Michalakis , Mircea T Sofonea , Samuel Alizon
[Rapport de recherche] 11, Centre National de la Recherche Scientifique (CNRS); Institut de recherche pour le développement (IRD); Université de Montpellier (UM), FRA. 2020
Reports hal-02950702v1
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Analyse de l’épidémie de COVID-19 en France et scénarios de contrôle

Samuel Alizon , Mircea T Sofonea
[Rapport de recherche] 9, Centre National de la Recherche Scientifique (CNRS); Institut de recherche pour le développement (IRD); Université de Montpellier (UM), FRA. 2020
Reports hal-02950665v1
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Les effets sexe spécifiques de COVID-19 en France pourraient-ils être expliqués par des comorbidités ?

Yannis Michalakis , Mircea T Sofonea , Samuel Alizon
[Rapport de recherche] 10, Centre National de la Recherche Scientifique (CNRS); Institut de recherche pour le développement (IRD); Université de Montpellier (UM), FRA. 2020
Reports hal-02950676v1
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Limites et délais dans l’estimation du nombre de reproduction

Samuel Alizon , Bastien Reyné , Mircea T Sofonea
[Rapport de recherche] 5, Centre National de la Recherche Scientifique (CNRS); Institut de recherche pour le développement (IRD); Université de Montpellier (UM), FRA. 2020
Reports hal-02882697v1
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Immunité de groupe et contrôle de l’épidémie de COVID-19

Mircea T Sofonea , Samuel Alizon
[Rapport Technique] 2, Centre National de la Recherche Scientifique (CNRS); Institut de Recherche pour le Développement (IRD); Université de Montpellier (UM), FRA. 2020
Reports hal-02882682v1
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Stochasticité et épidémie de COVID-19

Thomas Bénéteau , Baptiste Elie , Samuel Alizon , Mircea T Sofonea
[Rapport de recherche] 8, Centre National de la Recherche Scientifique (CNRS); Institut de Recherche pour le Développement (IRD); Université de Montpellier (UM), FRA. 2020
Reports hal-02950660v1