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epidemiology & evolution of infectious diseases


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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

   international publications

• Bessis D, Trouillet-Assant S, Secco LP, Bardin N, Blanc B, Blatière V, Chable-Bessia C, Delfour C, Girard C, Gros N, Le Moing V, Molinari N, Pallure V, Pisoni A, Raison-Peyron N, Reynaud E, Schwob E, Pescarmona R, Samaran Q, Willems M, Vincent T, Sofonea MT, Belot A, Tuaillon E. (2022) COVID-19 pandemic associated chilblains. More link for SARS-CoV-2 and less evidence for high interferon type-1 systemic response. Br J Dermatol.

Sofonea MT, Roquebert B, Foulongne V, Morquin D, Verdurme L, Trombert-Paolantoni S, Roussel M, Bonetti JC, Zerah J, Haim-Boukobza S, Alizon S. (2022) Analyzing and modeling the spread of SARS-CoV-2 Omicron lineages BA.1 and BA.2 in France (September 1, 2021, to February 28, 2022). Emerg Infect Dis.

• 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. J Med Virol.

Sofonea MT, Cauchemez S, Boëlle PY. (2022) Epidemic models: why and how to use them. Anaesth Crit Care Pain Med.

• Reyné B, Richard Q, Noûs C, Selinger C=, Sofonea MT=, Djidjou-Demasse R=, Alizon S=. (2022) Non-Markovian modelling highlights the importance of age structure on Covid-19 epidemiological dynamics. Math Model Nat Phenom.

• 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. (2022) Epidemiological and clinical insights from SARS-CoV-2 RT-PCR cycle amplification values. Eurosurveillance.

• Reyné B, Saby N, Sofonea MT. (2022) Principles of mathematical epidemiology and compartmental modelling application to COVID-19. Anaesth Crit Care Pain Med.

• Bénéteau T, Elie B, Sofonea MT, Alizon S. (2021) Estimating dates of origin and end of COVID-19 epidemics. Peer Community Journal.

• Djidjou-Demasse R=, Sofonea MT=, Choisy M, Alizon S. (2021) Within-host evolutionary dynamics of antimicrobial quantitative resistance. PCI Math Comp Biol.

• 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. (2021) Early phylodynamics analysis of the COVID-19 epidemics in France. Peer Community Journal.

• Kuschmierz P and 60 others. (2021) European first-year university students accept evolution but lack substantial knowledge about it: a standardized European cross-country assessment. Evo Edu Outreach.

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

• 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. Int J Infect Dis.

• Michalakis Y, Sofonea MT, Alizon S, Bravo IG. (2021) SARS-CoV-2 viral RNA levels are not “viral load”. Trends Microbiol.

Sofonea MT & Alizon S (2021) Anticipating COVID-19 intensive care unit capacity strain: A look back at epidemiological projections in France. Anaesth Crit Care Pain Med.

• 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.

• 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.

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

• 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.

• 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.

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.

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.

• 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.

• 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.

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

• Zwart MP, Blanc S, Johnson M, Manrubia S, Michalakis Y, Sofonea MT. (2021) Unresolved advantages of multipartitism in spatially structured environments. Virus Evol.

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

Sofonea MT. (2019) A global asymptotic stability condition for a Lotka-Volterra model with indirect interactions. Applicable Analysis.

• 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.

Sofonea MT, Aldakak L, Boullosa LF VV, Alizon S. (2018) Can Ebola Virus evolve to be less virulent in humans? J Evol Biol.

Sofonea MT, Alizon S, Michalakis Y. (2017) Exposing the diversity of multiple infection patterns. J Theor Biol.

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.

   preprints

• Reyné B, Sofonea MT, Alizon S. (2022) Modelling long-term COVID-19 hospital admission dynamics using immune protection waning data. medRxiv.

• Kamiya T, Alvarez-Iglesias A, Ferguson J, Sofonea MT, Fitz-Simon N. (2022) Estimating time-dependent infectious contact: a multi-strain epidemiological model of SARS-CoV-2 on the island of Ireland. medRxiv.

• Fitz-Simon N, Ferguson J, Alvarez-Iglesias A, Sofonea MT, Kamiya T. (2022) Understanding the role of mask-wearing during COVID-19 on the island of Ireland. medRxiv.

• Verdume L, Danesh G, Trombert S, Sofonea MT, Noel V, Foulongne V, Montès B, Tuaillon E, Haim-Boukobza S, Roquebert B, Alizon S. (2021) Spread of SARS-CoV-2 Delta variant infections bearing the S:E484Q and S:T95I mutations in July and August 2021 in France. medRxiv.

• Boennec C, Alizon S, Sofonea MT. Anticipating the hospital burden of future COVID-19 epidemic waves. medRxiv.

Sofonea MT, Boennec C, Fontalirant A, Regnat M, Lefrant JY, Alizon S, Fischer MO. (2021) Quantifying the real-life impacts of vaccination on critical COVID-19. OSF.

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

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.

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

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

   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.

   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.

   books

• Collective work (edited by Boudeau D, Caudron N, Delorme L, Fabre P, Godard F, Rilhac M, Sicard M, Sofonea MT). (2021) Du labo à la classe : l’évolution en action. APBG.

Collective work (edited by Gibert P). (2021) Regards croisés sur les pandémies. CNRS Éditions.

   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.

   thesis

Sofonea MT (2017) Virulence evolution and multiple infections. PhD thesis in evolution of infectious systems. Univ. Montpellier.


► 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.

• 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.

• 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.

• Boennec C, Sofonea MT, Alizon S. (2021) COVimpact – Estimating the residual hospital impact of COVID-19 in France. France Bioinformatique.

► Responsibilities

• Deputy Director for Research of the Exposome Institute of the University of Montpellier (ExposUM) (since 2022)
• Guest Editor of Anaesthesia Critical Care and Pain Medicine (since 2021)
• Member of the Modelling Coordinated Action of the ANRS|MIE (since 2021)
• Member of the Air & COVID expert group of the ANSES (since 2021)
• 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)


► Co-supervision of Phd theses

• Thomas Beneteau (Ligue nationale contre le Cancer grant, 2019 - 2023)
• Bastien Reyné (French Doctoral School grant, 2020 - 2023)
• Olivier Supplisson (ANRS|MIE grant, 2022 - 2025)
• Morgana D'Ottavi (INSERM grant, 2022 - 2025)


► 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

7 invitations, 9 selected talks