Mircea T. SOFONEA - epidemiology & evolution of infectious diseases

Mircea Sofonea, Simon Cauchemez, Pierre-Yves Boëlle. Epidemic models: why and how to use them. Anaesthesia Critical Care & Pain Medicine, Elsevier Masson, 2022, 41 (2), pp.101048. ⟨10.1016/j.accpm.2022.101048⟩. ⟨hal-03638186⟩

Samuel Alizon, Christian Selinger, Mircea Sofonea, Stéphanie Haim-Boukobza, Jean-Marc Giannoli, et al.. Epidemiological and clinical insights from SARS-CoV-2 RT-PCR crossing threshold values, France, January to November 2020. Eurosurveillance, European Centre for Disease Prevention and Control, 2022, 27 (6), pp.2100406. ⟨10.2807/1560-7917.ES.2022.27.6.2100406⟩. ⟨hal-03175551v3⟩

Bastien Reyné, Quentin Richard, Christian Selinger, Mircea Sofonea, Ramsès Djidjou-Demasse, et al.. Non-Markovian modelling highlights the importance of age structure on Covid-19 epidemiological dynamics. Mathematical Modelling of Natural Phenomena, EDP Sciences, 2022, 17, pp.7. ⟨10.1051/mmnp/2022008⟩. ⟨hal-03629334⟩

Baptiste Elie, Bénédicte Roquebert, Mircea Sofonea, Sabine Trombert-Paolantoni, Vincent Foulongne, et al.. Variant‐specific SARS‐CoV‐2 within‐host kinetics. Journal of Medical Virology, Wiley-Blackwell, In press, ⟨10.1002/jmv.27757⟩. ⟨hal-03651890⟩

Mark Zwart, Stéphane Blanc, Marcelle Johnson, Susanna Manrubia, Yannis Michalakis, et al.. Unresolved advantages of multipartitism in spatially structured environments. Virus Evolution, Oxford University Press, 2021, 7 (1), ⟨10.1093/ve/veab004⟩. ⟨hal-03219672⟩

Quentin Richard, Samuel Alizon, Marc Choisy, Mircea Sofonea, Ramsès Djidjou-Demasse. Age-structured non-pharmaceutical interventions for optimal control of COVID-19 epidemic. PLoS Computational Biology, Public Library of Science, 2021, ⟨10.1371/journal.pcbi.1008776⟩. ⟨hal-02879512v3⟩

Ramsès Djidjou-Demasse, Samuel Alizon, Mircea Sofonea. Within-host bacterial growth dynamics with both mutation and horizontal gene transfer. Journal of Mathematical Biology, Springer Verlag (Germany), 2021, ⟨10.1007/s00285-021-01571-9⟩. ⟨hal-02500420⟩

Thomas Beneteau, Christian Selinger, Mircea Sofonea, Samuel Alizon. Episome partitioning and symmetric cell divisions: Quantifying the role of random events in the persistence of HPV infections. PLoS Computational Biology, Public Library of Science, 2021, 17 (9), pp.e1009352. ⟨10.1371/journal.pcbi.1009352⟩. ⟨hal-03357550⟩

Bénédicte Roquebert, Sabine Trombert-Paolantoni, Stéphanie Haim-Boukobza, Emmanuel Lecorche, Laura Verdurme, et al.. 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. Eurosurveillance, European Centre for Disease Prevention and Control, 2021, 26 (23), ⟨10.2807/1560-7917.es.2021.26.23.2100447⟩. ⟨hal-03289627⟩

Stéphanie Haim-Boukobza, Bénédicte Roquebert, Sabine Trombert-Paolantoni, Emmanuel Lecorche, Laura Verdurme, et al.. Detecting Rapid Spread of SARS-CoV-2 Variants, France, January 26–February 16, 2021. Emerging Infectious Diseases, Centers for Disease Control and Prevention, 2021, 27 (5), pp.1496-1499. ⟨10.3201/eid2705.210397⟩. ⟨hal-03150819v3⟩

Bastien Reyné, Christian Selinger, Mircea Sofonea, Stéphanie Miot, Amandine Pisoni, et al.. Analysing different exposures identifies that wearing masks and establishing COVID-19 areas reduce secondary-attack risk in aged-care facilities. International Journal of Epidemiology, Oxford University Press (OUP), 2021, 50 (6), pp.1788-1794. ⟨10.1093/ije/dyab121⟩. ⟨hal-03289625⟩

Samuel Alizon, Stéphanie Haim-Boukobza, Vincent Foulongne, Laura Verdurme, Sabine Trombert-Paolantoni, et al.. Rapid spread of the SARS-CoV-2 Delta variant in some French regions, June 2021. Eurosurveillance, European Centre for Disease Prevention and Control, 2021, 26 (28), ⟨10.2807/1560-⟩. ⟨hal-03289622⟩

Olivier Thomine, Samuel Alizon, Corentin Boennec, Marc Barthelemy, Mircea Sofonea. Emerging dynamics from high-resolution spatial numerical epidemics. eLife, eLife Sciences Publication, 2021, 10, ⟨10.7554/elife.71417⟩. ⟨hal-03415297⟩

Samuel Alizon, Mircea Sofonea. SARS‐CoV‐2 virulence evolution: Avirulence theory, immunity and trade‐offs. Journal of Evolutionary Biology, Wiley, 2021, 34 (12), pp.1867 - 1877. ⟨10.1111/jeb.13896⟩. ⟨hal-03289628⟩

Mircea Sofonea, Bastien Reyné, Baptiste Elie, Ramsès Djidjou-Demasse, Christian Selinger, et al.. Memory is key in capturing COVID-19 epidemiological dynamics. Epidemics, Elsevier, 2021, 35, pp.100459. ⟨10.1016/j.epidem.2021.100459⟩. ⟨hal-03289624⟩

Mircea Sofonea, Corentin Boennec, Yannis Michalakis, Samuel Alizon. Two waves and a high tide: the COVID-19 epidemic in France. Anaesthesia Critical Care & Pain Medicine, Elsevier Masson, 2021, 40 (3), pp.100881. ⟨10.1016/j.accpm.2021.100881⟩. ⟨hal-03289626⟩

Benedicte Roquebert, Stéphanie Haim-Boukobza, Sabine Trombert-Paolantoni, Emmanuel Lecorche, Laura Verdurme, et al.. SARS-CoV-2 variants of concern are associated with lower RT-PCR amplification cycles between January and March 2021 in France. International Journal of Infectious Diseases, Elsevier, 2021, ⟨10.1016/j.ijid.2021.09.076⟩. ⟨hal-03366559⟩

Yannis Michalakis, Mircea Sofonea, Samuel Alizon, Ignacio G. Bravo. SARS-CoV-2 viral RNA levels are not 'viral load'. Trends in Microbiology, Elsevier, 2021, 29 (11), pp.970-972. ⟨10.1016/j.tim.2021.08.008⟩. ⟨hal-03419147⟩

Mircea Sofonea, Samuel Alizon. Anticipating COVID-19 intensive care unit capacity strain: A look back at epidemiological projections in France. Anaesthesia Critical Care & Pain Medicine, Elsevier Masson, 2021, ⟨10.1016/j.accpm.2021.100943⟩. ⟨hal-03366541⟩

Gonché Danesh, Baptiste Elie, Yannis Michalakis, Mircea Sofonea, Antonin Bal, et al.. Early phylodynamics analysis of the COVID-19 epidemic in France. Peer Community Journal, Peer Community In/Centre Mersenne, 2021, 1, pp.e45. ⟨10.24072/pcjournal.40⟩. ⟨hal-03001114v2⟩

Mircea Sofonea. A global asymptotic stability condition for a dimorphic Lotka-Volterra model with explicit indirect interactions. Applicable Analysis, Taylor & Francis, 2019, ⟨10.1080/00036811.2018.1437417⟩. ⟨hal-03366505⟩

Samuel Alizon, Carmen Lia Murall, Emma Saulnier, Mircea Sofonea. Detecting within-host interactions from genotype combination prevalence data. Epidemics, Elsevier, 2019, 29, pp.100349. ⟨10.1016/j.epidem.2019.100349⟩. ⟨hal-02387765⟩

Romain Gallet, Frédéric Fabre, Gael Thébaud, Mircea Sofonea, Anne Sicard, et al.. Small bottleneck size in a highly multipartite virus during a complete infection cycle. Journal of Virology, American Society for Microbiology, 2018, 92 (14), pp.e00139-18. ⟨10.1128/JVI.00139-18⟩. ⟨hal-01847886⟩

Mircea Sofonea, L. Aldakak, Luis F. V. V. Boullosa, Samuel Alizon. Can Ebola Virus evolve to be less virulent in humans?. Journal of Evolutionary Biology, Wiley, 2018, 31 (3), pp.382 - 392. ⟨10.1111/jeb.13229⟩. ⟨hal-01897077⟩

Mircea Sofonea, Samuel Alizon, Yannis Michalakis. Exposing the diversity of multiple infection patterns. Journal of Theoretical Biology, Elsevier, 2017, 419, pp.278 - 289. ⟨10.1016/j.jtbi.2017.02.011⟩. ⟨hal-01567902⟩

Mircea Sofonea, Samuel Alizon, Yannis Michalakis. From within-host interactions to epidemiological competition: a general model for multiple infections. Philosophical Transactions of the Royal Society B: Biological Sciences, Royal Society, The, 2015, 370 (1675), pp.20140303. ⟨10.1098/rstb.2014.0303⟩. ⟨hal-01571806⟩

Ramsès Djidjou-Demasse, Mircea Sofonea, Marc Choisy, Samuel Alizon. Within-host evolutionary dynamics of antimicrobial quantitative resistance. 2021. ⟨hal-03194023v4⟩

Mircea Sofonea, Corentin Boennec, Yannis Michalakis, Samuel Alizon. Two waves and a high tide: the COVID-19 epidemic in France. 2021. ⟨hal-03322646⟩

Thomas Bénéteau, Elie Baptiste, Mircea Sofonea, Samuel Alizon. Estimating dates of origin and end of COVID-19 epidemics. 2021. ⟨hal-03120811⟩

Ramsès Djidjou-Demasse, Christian Selinger, Mircea Sofonea. Épidémiologie mathématique & modélisation de la pandémie de COVID-19 : enjeux et diversité. 2020. ⟨hal-02924338⟩

Bastien Reyné, Gonché Danesh, Samuel Alizon, Mircea Sofonea. Rt2: computing and visualising COVID-19 epidemics temporal reproduction number. 2020. ⟨hal-03045490⟩

Mircea Sofonea, Bastien Reyné, Baptiste Elie, Ramsès Djidjou-Demasse, Christian Selinger, et al.. Epidemiological monitoring and control perspectives: application of a parsimonious modelling framework to the COVID-19 dynamics in France. 2020. ⟨hal-02619546⟩

Samuel Alizon, Mircea Sofonea. De Delta à Omicron, scénarios de tendances hospitalières pour l'hiver 2021-2022. [Rapport de recherche] 16, CNRS - Centre National de la Recherche Scientifique; IRD - Institut de recherche pour le developpement; Université de Montpellier. 2021. ⟨hal-03502127⟩

Yannis Michalakis, Mircea Sofonea, Samuel Alizon. Les effets sexe spécifiques de COVID-19 en France et l’implication potentielle des déficits en G6PD. [Rapport de recherche] 11, Centre National de la Recherche Scientifique (CNRS); Institut de recherche pour le développement (IRD); Université de Montpellier (UM), FRA. 2020. ⟨hal-02950702⟩

Samuel Alizon, Mircea Sofonea, Yannis Michalakis. Modéliser l'épidémie de COVID-19 (résumé). [Rapport de recherche] 7, Centre National de la Recherche Scientifique (CNRS); Institut de recherche pour le développement (IRD); Université de Montpellier (UM), FRA. 2020. ⟨hal-02950651⟩

Yannis Michalakis, Mircea Sofonea, Samuel Alizon. Les effets sexe spécifiques de COVID-19 en France pourraient-ils être expliqués par des comorbidités ?. [Rapport de recherche] 10, Centre National de la Recherche Scientifique (CNRS); Institut de recherche pour le développement (IRD); Université de Montpellier (UM), FRA. 2020. ⟨hal-02950676⟩

Samuel Alizon, Yannis Michalakis, Mircea Sofonea. Évolution de la virulence et COVID-19. [Rapport de recherche] 12, Centre National de la Recherche Scientifique (CNRS); Institut de recherche pour le développement (IRD); Université de Montpellier (UM), FRA. 2020. ⟨hal-02950712⟩

Mircea Sofonea, Samuel Alizon. Immunité de groupe et contrôle de l’épidémie de COVID-19. [Rapport Technique] 2, Centre National de la Recherche Scientifique (CNRS); Institut de Recherche pour le Développement (IRD); Université de Montpellier (UM), FRA. 2020. ⟨hal-02882682⟩

Thomas Bénéteau, Baptiste Elie, Samuel Alizon, Mircea Sofonea. Stochasticité et épidémie de COVID-19. [Rapport de recherche] 8, Centre National de la Recherche Scientifique (CNRS); Institut de Recherche pour le Développement (IRD); Université de Montpellier (UM), FRA. 2020. ⟨hal-02950660⟩

Samuel Alizon, Mircea Sofonea. Analyse de l’épidémie de COVID-19 en France et scénarios de contrôle. [Rapport de recherche] 9, Centre National de la Recherche Scientifique (CNRS); Institut de recherche pour le développement (IRD); Université de Montpellier (UM), FRA. 2020. ⟨hal-02950665⟩

Samuel Alizon, Bastien Reyné, Mircea Sofonea. Limites et délais dans l’estimation du nombre de reproduction. [Rapport de recherche] 5, Centre National de la Recherche Scientifique (CNRS); Institut de recherche pour le développement (IRD); Université de Montpellier (UM), FRA. 2020. ⟨hal-02882697⟩

Mircea Sofonea. Évolution de la virulence et infections multiples. Biologie animale. Université Montpellier, 2017. Français. ⟨NNT : 2017MONTT114⟩. ⟨tel-01704686⟩