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infectious diseases modelling


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My research aims to improve the understanding and the anticipation of the epidemiological and evolutionary dynamics of infectious diseases by integrating sources of heterogeneity (polymorphism, spatial structuring, anti-infective treatments, health policies) in the multi-level quantitative analysis (from intra-host to public health via transmission) of pathogens such as Ebola virus, human papillomaviruses, multidrug-resistant bacteria, and more recently SARS-CoV-2.


► Research work

   peer-reviewed international publications

• Bénéteau T, Elie B, Sofonea MT, Alizon S. (2021) Estimating dates of origin and end of COVID-19 epidemics. PCI Math Comp Biol [pdf]

• Alizon S, Haim-Boukobza S, Foulongne V, Verdurme L, Trombert-Paolantoni S, , Lecorche E, Roquebert B, Sofonea MT. (2021) Rapid spread of the SARS-CoV-2 delta variant in French regions in June 2021. Eurosurveillance [link]

• Bénéteau T, Selinger C=, Sofonea MT=, Alizon S=. (2021) Episome partitioning and symmetric cell divisions: quantifying the role of random events in the persistence of HPV infections. PLoS Comput Biol [in press]

• Alizon S & Sofonea MT. (2021) SARS-CoV-2 virulence evolution: avirulence theory, immunity, and trade-offs. J Evol Biol [pdf]

• Reyné B, Selinger C, Sofonea MT, Miot S, Pisoni A, Tuaillon E, Bousquet J, Blain H, Alizon S. (2021) Analysing different exposures identifies that wearing masks and establishing COVID-19 areas reduce secondary attack risk in aged care facilities. Int J Epidemiol [pdf]

• Roquebert B, Trombert-Paolantoni S, Haim-Boukobza S, Lecorche E, Verdurme L, Foulongne V, Sofonea MT=, Alizon S=. (2021)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 [pdf]

Sofonea MT, Boennec C, Michalakis Y, Alizon S. (2021) Two waves and a high tide: the COVID-19 epidemic in France. Anaesth Crit Care Pain Med [link]

Sofonea MT, Reyné B, Elie B, Djidjou-Demasse R, Selinger C, Michalakis Y, Alizon S. (2021) Memory is key in capturing COVID-19 epidemiological dynamics. Epidemics [lien]

• Haim-Boukobza S, Roquebert B, Trombert-Paolantoni S, Lecorche E, Verdurme L, Foulongne V, Selinger C, Michalakis Y, Sofonea MT=, Alizon S=. (2021) Detecting Rapid Spread of SARS-CoV-2 Variants, France, January 26–February 16, 2021. Emerg Infect Dis 10.3201/eid2705.210397 [pdf]

• Richard Q, Alizon S, Choisy M, Sofonea MT, Djidjou-Demasse R. (2021) Age-structured non-pharmaceutical interventions for optimal control of COVID-19 epidemic. PLoS Comput Biol 17(3):e1008776 [link]

• Djidjou-Demasse R, Alizon S, Sofonea MT. (2021) Within-host bacterial growth dynamics with both mutation and horizontal gene transfer. J Math Biol 82, 16. [pdf]

• Zwart MP, Blanc S, Johnson M, Manrubia S, Michalakis Y, Sofonea MT. (2021) Unresolved advantages of multipartitism in spatially structured environments. Virus Evol 7(1): veab004. [link]

• Danesh G, Elie B, Michalakis Y, Sofonea MT, Bal A, Behillil S, Destras G, Boutolleau D, Burrel S, Marcelin A-G, Plantier J-C, Thibault V, Simon-Loriere E, van der Werf S, Lina B, Josset L, Enouf V, Alizon S. (2020) Early phylodynamics analysis of the COVID-19 epidemics in France. PCI Evol Biol [pdf]

Alizon S, Murall C-L, Saulnier E, Sofonea MT. (2019) Detecting within-host interactions from genotype combination prevalence data. Epidemics 29: 100349 [pdf]

Sofonea MT. (2019) A global asymptotic stability condition for a Lotka-Volterra model with indirect interactions. Applicable Analysis 98(9), 1636-1645 [pdf]

• Gallet R, Fabre F, Thébaud G, Sofonea MT, Sicard A, Blanc S, Michalakis Y. (2018) Small bottleneck size in a highly multipartite virus during a complete infectious cycle. J Virol 92(14) [pdf]

Sofonea MT, Aldakak L, Boullosa LF VV, Alizon S. (2018) Can Ebola Virus evolve to be less virulent in humans? J Evol Biol 31 (3), 382-392 [pdf] [sm]

Sofonea MT, Alizon S, Michalakis Y. (2017) Exposing the diversity of multiple infection patterns. J Theor Biol 419: 278--289. [pdf] [sm]

Sofonea MT, Alizon S, Michalakis Y. (2015) From within-host interactions to epidemiological competition: a general model for multiple infections. Phil Trans R Soc B 370(1675): 20140303. [pdf] [sm]

   preprints

• Elie B, Lecorche E, Sofonea MT, Trombert-Paolantoni S, Foulongne V, Guedj J, Haim-Boukobza S, Roquebert B, Alizon S. (2021) Inferring SARS-CoV-2 variant within-host kinetics. medRxiv [pdf

• Thomine O, Alizon S, Barthelemy M, Boennec C, Sofonea MT. (2021) Emerging dynamics from high-resolution spatial numerical epidemics. Zenodo [pdf]

• Alizon S & Sofonea MT. (2021) SARS-CoV-2 virulence evolution: avirulence theory, immunity, and trade-offs. Zenodo [pdf]

• Djidjou-Demasse R=, Sofonea MT=, Choisy M, Alizon S. (2021) Within-host evolutionary dynamics of antimicrobial quantitative resistance. HAL []

• Roquebert B, Haim-Boukobza S, Trombert-Paolantoni S, Lecorche E, Verdurme L, Foulongne V, Burrel S, Alizon S=, Sofonea MT=. (2021) SARS-CoV-2 variants of concern are associated with lower RT-PCR amplification cycles between January and March 2021 in France. medRxiv [pdf]

• Alizon S, Selinger C=, Sofonea MT=, Haim-Boukobza S, Giannoli JM, Ninove L, Pillet S, Vincent T, de Rougemont A, Tumiotto C, Sollis M, Stephan R, Bressolette-Bodin C, Salmona M, L'Honneur AS, Behillil S, Lefeuvre C, Dina J, Hantz S, Hartard C, Veyer D, Delagreverie HM, Fourati S, Visseaux B, Henquell C, Lina B, Foulongne V, Burrel S (2021) Epidemiological and clinical insights from SARS-CoV-2 RT-PCR cycle amplification values. medRxiv [pdf]

• Michalakis Y, Sofonea MT=, Alizon S.= (2021) SARS-CoV-2 viral RNA is not viral load. osf [pdf]

• Bénéteau T, Elie B, Sofonea MT, Alizon S. (2021) Estimating dates of origin and end of COVID-19 epidemics. medRxiv [pdf]

• Reyné B, Danesh G, Alizon S, Sofonea MT. (2020) Rt2: computing and visualising COVID-19 epidemics temporal reproduction number. medRxiv [pdf]

Sofonea MT, Reyné B, Elie B, Djidjou-Demasse R, Selinger C, Michalakis Y, Alizon S. (2020) Epidemiological monitoring and control perspectives: application of a parsimonious modelling framework to the COVID-19 dynamics in France. medRxiv [pdf]

• Djidjou-Demasse R, Michalakis Y, Choisy M, Sofonea MT, Alizon S. (2020) Optimal COVID-19 epidemic control until vaccine deployment. medRxiv [pdf]

Sofonea MT, Alizon S, Michalakis Y. (2018) Why multiple infections favour virulent parasites. bioRxiv [pdf][som]

   French publications

• Djidjou-Demasse R, Selinger C, Sofonea MT. (2020) Épidémiologie mathématique et modélisation de la pandémie de Covid-19 : enjeux et diversité. Revue Francophone des Laboratoires [lien]

   expert report

Anses. (2021) Note d'appui scientifique et technique relative à la viabilité dans l'air et la dose infectante du virus SARS-CoV-2. (saisine 2021-SA-0018). Maisons-Alfort : Anses, 101 p [pdf] (in French)

   books

Collective work (edited by P. Gibert). (2021) Regards croisés sur les pandémies. CNRS Éditions [link] (in French)

   protocoles

• Beniermann A, Kuschmierz P, Pinxten R, Aivelao T, Bohlin G, Brennecke JS, Cebesoy UB, Cvetković D, Đorđević M, Dvořáková RM, Futo M, Geamana N, Korfiatis K, Lendvai A, Mogias A, Paolucci S, Ptersson M, Pietrzak B, Porozovs J, Realdon G, Savković U, Sofonea MT, Šorgo A, Stermin AN, Torkar G, Uitto A, Vázquez BL, Graf D. (2021) Evolution Education Questionnaire on Acceptance and Knowledge (EEQ) - Standardised and ready-to-use protocols to measure acceptance of evolution and knowledge about evolution in an international context Zenodo [link]

   thesis

Sofonea MT (2017) Virulence evolution and multiple infections. PhD thesis in evolution of infectious systems. [pdf]


► Softwares

Sofonea MT, Reyné B, Alizon S. (2020) COVIDSIM – Combining statistical analysis of hospital data and parsimonious non Markovian modelling for infering epidemiological parameters and simulating NPI of the COVID-19 epidemic in France. i-Trop bioinformatics [link]

• Reyné B, Danesh G, Alizon S, Sofonea MT. (2020) Rt2 – Estimating the reproduction number of COVID-19 epidemics in different countries and, for France, in regions and departments using incidence, hosptialisation, and mortality data. France Bioinformatique [link]

• Boennec C, Alizon S, Sofonea MT. (2021) COVIDici – Visualization & projection tool of the COVID-19 populational data in France at national, regional and departmental levels. France Bioinformatique [link]

► Responsibilities

• Head of the Theoretical & Experimental Evolution research group (MIVEGEC - Univ. Montpellier, CNRS, IRD - since 2021)
• Member of the modelling & evolutionary ecology expert panel of Arbo-France (French network for the study of arboviroses) (since 2020)
• PhD grant reviewer (ENS, Paris, since 2019)
• member of the organizing committee of the Evolution 2018 congress (Montpellier, 2016 - 2018)
• organizer of the weekly MIVEGEC lab seminar (Montpellier, 2015)


► Co-supervision of Phd theses

• Thomas Beneteau (Ligue nationale contre le Cancer grant, 2019 - )

• Bastien Reyné (French Doctoral School grant, 2020 - )


► Co-supervision of Master internships

• Thomas Beneteau (M2 AgroParisTech, 2019)
• Julien Lombard (M1 Rennes, 2019)
• Luis F.V.V. Boullosa (M1 international MEME 2016)
• Lafi Aldakak (M1 international MEME, 2015)


► International communications

3 invitations, 9 selected talks