First name: Francois
  Last name: Blanquart
  Position: Chargé de Recherche CNRS
  Email: francois.blanquart

Research interest

I work in evolutionary biology with a focus on the evolution of human pathogens.



2009-2013: PhD in « Evolution, Ecologie, Ressources génétiques, Paléontologie ». PhD under the direction of Dr. Sylvain Gandon, CNRS, Université Montpellier 2.

Academic positions

2017-present: Chargé de Recherche CNRS

2014-2017: Postdoctoral researcher and Marie Skłodowska-Curie fellow, Department of Infectious Disease Epidemiology, Imperial College London and University of Oxford, United Kingdom.

List of the main publications

Exhaustive list of publications


Royer G, Clermont O, Marin J, Condamine B, Dion S, Blanquart F, Galardini M, Denamur E
Epistatic interactions between the high pathogenicity island and other iron uptake systems shape Escherichia coli extra-intestinal virulence.
Nature Communications 2023, 14, 3667.

Cotto O, Armand-Lefèvre L, Matheron S, Ruppé E, Blanquart F
Within-Host Dynamics and Duration of Colonization of Travel-Acquired Multidrug-Resistant Enterobacterales in Untreated Individuals.
Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America 2023, 77, 934-936.

Burgaya J, Marin J, Royer G, Condamine B, Gachet B, Clermont O, Jaureguy F, Burdet C, Lefort A, de Lastours V, Denamur E, Galardini M, Blanquart F, Colibafi/Septicoli & Coliville groups
The bacterial genetic determinants of Escherichia coli capacity to cause bloodstream infections in humans.
PLoS genetics 2023, 19, e1010842.

Coppée R, Blanquart F, Jary A, Leducq V, Ferré VM, Franco Yusti AM, Daniel L, Charpentier C, Lebourgeois S, Zafilaza K, Calvez V, Descamps D, Marcelin AG, Visseaux B, Bridier-Nahmias A
Phylodynamics of SARS-CoV-2 in France, Europe, and the world in 2020.
eLife 2023, 12, e82538.


Foutel-Rodier F, Blanquart F, Courau P, Czuppon P, Duchamps JJ, Gamblin J, Kerdoncuff É, Kulathinal R, Régnier L, Vuduc L, Lambert A, Schertzer E
From individual-based epidemic models to McKendrick-von Foerster PDEs: a guide to modeling and inferring COVID-19 dynamics.
Journal of Mathematical Biology 2022, 85, 43.

Cosentino G, Bernard M, Ambroise J, Giannoli JM, Guedj J, Débarre F, Blanquart F
SARS-CoV-2 viral dynamics in infections with Alpha and Beta variants of concern in the French community.
The Journal of Infection 2022, 84, 94-118.

Piel D, Bruto M, Labreuche Y, Blanquart F, Goudenège D, Barcia-Cruz R, Chenivesse S, Le Panse S, James A, Dubert J, Petton B, Lieberman E, Wegner KM, Hussain FA, Kauffman KM, Polz MF, Bikard D, Gandon S, Rocha EPC, Le Roux F
Phage-host coevolution in natural populations.
Nature Microbiology 2022, 7, 1075-1086.

Leducq V, Jary A, Bridier-Nahmias A, Daniel L, Zafilaza K, Damond F, Goldstein V, Duval A, Blanquart F, Calvez V, Descamps D, Marcelin AG, Visseaux B
Nosocomial transmission clusters and lineage diversity characterized by SARS-CoV-2 genomes from two large hospitals in Paris, France, in 2020.
Scientific Reports 2022, 12, 1094.

Zhao L, Wymant C, Blanquart F, Golubchik T, Gall A, Bakker M, Bezemer D, Hall M, Ong SH, Albert J, Bannert N, Fellay J, Grabowski MK, Gunsenheimer-Bartmeyer B, Günthard HF, Kivelä P, Kouyos RD, Laeyendecker O, Meyer L, Porter K, van Sighem A, van der Valk M, Berkhout B, Kellam P, Cornelissen M, Reiss P, Fraser C, Ferretti L
Phylogenetic estimation of the viral fitness landscape of HIV-1 set-point viral load.
Virus Evolution 2022, 8, veac022.

Lehtinen S, Croucher NJ, Blanquart F, Fraser C
Epidemiological dynamics of bacteriocin competition and antibiotic resistance.
Proceedings. Biological Sciences 2022, 289, 20221197.

Wymant C, Bezemer D, Blanquart F, Ferretti L, Gall A, Hall M, Golubchik T, Bakker M, Ong SH, Zhao L, Bonsall D, de Cesare M, MacIntyre-Cockett G, Abeler-Dörner L, Albert J, Bannert N, Fellay J, Grabowski MK, Gunsenheimer-Bartmeyer B, Günthard HF, Kivelä P, Kouyos RD, Laeyendecker O, Meyer L, Porter K, Ristola M, van Sighem A, Berkhout B, Kellam P, Cornelissen M, Reiss P, Fraser C, Netherlands ATHENA HIV Observational Cohort†, BEEHIVE Collaboration†
A highly virulent variant of HIV-1 circulating in the Netherlands.
Science (New York, N.Y.) 2022, 375, 540-545.

Marin J, Clermont O, Royer G, Mercier-Darty M, Decousser JW, Tenaillon O, Denamur E, Blanquart F
The Population Genomics of Increased Virulence and Antibiotic Resistance in Human Commensal Escherichia coli over 30 Years in France.
Applied and Environmental Microbiology 2022, 88, e0066422.

Blanquart F, Hozé N, Cowling BJ, Débarre F, Cauchemez S
Selection for infectivity profiles in slow and fast epidemics, and the rise of SARS-CoV-2 variants.
eLife 2022, 11, e75791.


Belloir A, Blanquart F
Estimating the global reduction in transmission and rise in detection capacity of the novel coronavirus SARS-CoV-2 in early 2020.
Epidemics 2021, 35, 100445.

Tubiana S, Burdet C, Houhou N, Thy M, Manchon P, Blanquart F, Charpentier C, Guedj J, Alavoine L, Behillil S, Leclercq A, Lucet JC, Yazdanpanah Y, Attia M, Demeret C, Rose T, Bielicki JA, Bruijning-Verhagen P, Goossens H, Descamps D, van der Werf S, Lina B, Duval X, CoVCONTACT study group, Principal investigator, Sponsor: Inserm
High-risk exposure without personal protective equipment and infection with SARS-CoV-2 in-hospital workers - The CoV-CONTACT cohort.
The Journal of Infection 2021, 82, 186-230.

Czuppon P, Blanquart F, Uecker H, Débarre F
The Effect of Habitat Choice on Evolutionary Rescue in Subdivided Populations.
The American Naturalist 2021, 197, 625-643.

Czuppon P, Schertzer E, Blanquart F, Débarre F
The stochastic dynamics of early epidemics: probability of establishment, initial growth rate, and infection cluster size at first detection.
Journal of the Royal Society, Interface 2021, 18, 20210575.

Czuppon P, Débarre F, Gonçalves A, Tenaillon O, Perelson AS, Guedj J, Blanquart F
Success of prophylactic antiviral therapy for SARS-CoV-2: Predicted critical efficacies and impact of different drug-specific mechanisms of action.
PLoS computational biology 2021, 17, e1008752.

Blanquart F, Abad C, Ambroise J, Bernard M, Cosentino G, Giannoli JM, Débarre F
Characterisation of vaccine breakthrough infections of SARS-CoV-2 Delta and Alpha variants and within-host viral load dynamics in the community, France, June to July 2021.
Euro Surveillance: Bulletin Europeen Sur Les Maladies Transmissibles = European Communicable Disease Bulletin 2021, 26, 2100824.

Gaymard A, Bosetti P, Feri A, Destras G, Enouf V, Andronico A, Burrel S, Behillil S, Sauvage C, Bal A, Morfin F, Van Der Werf S, Josset L, ANRS MIE AC43 COVID-19, French viro COVID group, Blanquart F, Coignard B, Cauchemez S, Lina B
Early assessment of diffusion and possible expansion of SARS-CoV-2 Lineage 20I/501Y.V1 (B.1.1.7, variant of concern 202012/01) in France, January to March 2021.
Euro Surveillance: Bulletin Europeen Sur Les Maladies Transmissibles = European Communicable Disease Bulletin 2021, 26, 2100133.

Marc A, Kerioui M, Blanquart F, Bertrand J, Mitjà O, Corbacho-Monné M, Marks M, Guedj J
Quantifying the relationship between SARS-CoV-2 viral load and infectiousness.
eLife 2021, 10, e69302.


Wan C, Bachmann N, Mitov V, Blanquart F, Céspedes SP, Turk T, Neumann K, Beerenwinkel N, Bogojeska J, Fellay J, Roth V, Böni J, Perreau M, Klimkait T, Yerly S, Battegay M, Walti L, Calmy A, Vernazza P, Bernasconi E, Cavassini M, Metzner KJ, Günthard HF, Kouyos RD, Swiss HIV Cohort Study
Heritability of the HIV-1 reservoir size and decay under long-term suppressive ART.
Nature Communications 2020, 11, 5542.

Duprilot M, Baron A, Blanquart F, Dion S, Pouget C, Lettéron P, Flament-Simon SC, Clermont O, Denamur E, Nicolas-Chanoine MH
Success of Escherichia coli O25b:H4 Sequence Type 131 Clade C Associated with a Decrease in Virulence.
Infection and Immunity 2020, 88, e00576-20.


Lehtinen S, Blanquart F, Lipsitch M, Fraser C, with the Maela Pneumococcal Collaboration
On the evolutionary ecology of multidrug resistance in bacteria.
PLoS pathogens 2019, 15, e1007763.