Our team is interested in the role of matrix and capsid proteins as well as lipids and lipid domains in the assembly of viruses in their host cells.
We study these phenomena quantitatively at the single-molecule level in living cells and in model systems.

Our research focuses on 5 main topics (click on each to access details).

• Lipid sorting during the self-assembly of HIV-1 Gag and influenza A M1 proteins (Kerviel 2013; Saad & Muriaux, 2015; Kerviel 2016; Yandrapalli 2015, 2016; Favard 2019)
• Single molecule microscopy of HIV-1 assembly in live CD4 T cells (Mariani 2016; Mariani 2018; Inamdar 2019)
• Role of membrane co-factors and cortical actin during viral assembly. (Thomas 2015; Inamdar 2021)
• Role of M-matrix proteins and cellular cofactors in influenza virus and SARS-CoV-2 assembly. (Kerviel 2016; Bracquemond & Muriaux, 2021; Manon forthcoming)
• Atomic force microscopy (AFM) study of HIV-1, IAV and SARS-CoV-2 assembly on single virus particles. (Faivre-Moskalenko 2014; Bernaud 2015; Lyonnais 2021)

HIV-1 assembly molecular mechanism occuring at CD4 Tcells plasma membrane (Mariani et al., 2014)

1. Lipid sorting during self-assembly of HIV-1 Gag and influenza A M1 proteins

(Funding: ANR Fluobuds, CNRS, Univ Montp, GdR IMABIO, ERC Erasmus Mundus)

This project aims at deciphering the role of pre-existing or generated lipid nanodomains in the plasma membrane of the host cell during viral assembly.
In previous studies, we have shown that the interaction between the Matrix domain of the Gag protein and specific plasma membrane lipids (PS/PIP2) induces retrovirus assembly (Hamard-Péron et al., 2010 ; Hamard-Péron & Muriaux, 2011). We proposed that acidic lipid-enriched microdomains (ALEMs) are created by oligomerization of the HIV-1 Gag protein in the host cell plasma membrane during viral assembly (Kerviel et al., 2013, Yandapalli et al., 2014, Mariani et al., 2014 & Saad & Muriaux, Editorial 2015).

To show that, we first have characterized the nature and the effects of the MA domain interaction of retroviral Gag proteins (HIV-1 and MLV) with lipid membranes in silico  (Kerviel et al., 2013, Charlier et al., 2014).

In vitro, we investigated the impact of HIV-1 Gag protein self-assembly on lipid plasma membrane using model membranes with controlled molecular composition mimicking this membrane. We were able to show that, during its self-assembly, the viral Gag protein sorts membrane lipids and generates lipid nano-domains enriched in PIP2 and Cholesterol, while excluding Sphingomyelin (Yandrapalli et al., 2016).

We finally quantified this phenomenon in viral host cells (HIV-1-infected or Gag-transfected CD4 T cells) by measuring the diffusional changes of lipids (PIP2, Cholesterol, SM and PE) into and out of the viral bud on the T cell surface by sSTED-FCS (Scanning STED FCS), in collaboration with C. Eggeling (U. Oxford/ Univ Jena, UK-Germany) and J Chojnacki (U. Oxford/ IRSI Caixa, Barcelona, SP) (Favard et al., 2019). 
This work was highlighted by the Company of Biologists, by the CNRS-INSB in its monthly news as well as in its  2019 highlights and also by ANRS.

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2. Single molecule microscopy of HIV-1 assembly in living CD4 T cells

(Funding : ANR Fluobuds, CNRS, Univ Montp, GdR IMABIO, Erasmus Mundus)

In parallel, we have studied the dynamics of capsid protein assembly in the cell using super-resolution optical microscopy methods (Live PALM, spt-PALM), in collaboration with the teams of JB Sibarita (IINS, Bordeaux) and M. Dahan (Institut Curie, Paris).
We followed the Gag self-assembly, molecule by molecule, at a resolution of a tenths of nanometers, generating billions of individual trajectories. (Mariani et al., 2016, Journal Cover)

We rely on methods from Big Data, for the automatic analysis of these trajectories using Bayesian inferences. In collaboration with J.B. Masson (Institut Pasteur), M. El Beheiry and M. Dahan (I. Curie), we were able to follow, during 25 minutes, molecules after molecules, the self-assembly of Gag during the formation of a VLP of HIV-1 in a T lymphocyte. This was done by measuring both the changes in the diffusion of these molecules (left part of the movie) but also in the attraction energy (right part of the movie) that is sensed by each Gag in the viccinity of the assembly site. (Mariani et al., 2018)

Our work on the study of HIV-1 assembly using super-resolution microscopies of the living has resulted in 2 general interest reviews (Inamdar et al., 2019 et Arone et al., 2021).

 
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3. Role of membrane co-factors and cortical actin during viral assembly .

(Funding : ANRS, Sidaction, FRM)

This project aims to undesrtand the role of filamentous cortical actin (F-actin) and newly identified cellular co-factors from HIV-1 host cells (T-CD4+ lymphocytes) in the modulation of the dynamics and organization of membrane domains as well as in the membrane curvature generation during HIV-1 assembly as well as filamentous cortical actin (F-actin).



In our previous research, we have shown that CD81 tetraspanin is a host cell transmembrane protein involved in HIV-1 assembly in CD4 (Grigorov et al., 2009) and that the clathrin-dynamin endocytosis pathway was involved in the transmission of HIV-1 from CD4 T cells to CD4 T cells (Bosch et al., 2008). We are now interested in studying the role of these tetraspanins in the assembly of another human retrovirus HTLV-1 chronically infecting T cells in collaboration with Hélène Dutartre (CIRI,ENS Lyon)
In parallel, we also studied the role of a major regulator of the cortical actin network regulated by the Rac1/IRSp53/Wave2/arp2/3 activation pathway in the assembly of the HIV-1 Gag protein and the release of the viral particle in CD4 T cells, the main hosts of HIV-1. (Thomas et al., 2015).

We recently showed that the membrane bending factor IRSp53 was indeed involved in the assembly and budding of the HIV-1 Gag viral particle (Inamdar et al., 2021). During the reduction of IRSp53 expression by interfering RNA in HIV-1 Gag particle-producing cells, we observe a blockage of virus assembly at midstream (Figure A). IRSp53 is found at the site of virus assembly, as observed by PALM (Gag)/STORM (IRSp53) microscopy (Figure B) and quantified by correlating experimental single molecule coordinate based colocalization (CBC) measurements with those obtained by numerical simulations on pre-defined models (Figure C). The cellular protein IRSp53 assists in membrane bending during HIV-1 particle formation to finalize HIV-1 assembly and budding.


From Inamdar et al., 2021.

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4. Role of M-matrix proteins and cellular cofactors in the assembly of influenza virus and SARS-CoV-2.

We are currently studying other enveloped RNA viruses. The influenza virus, A (H1N1) pdm09, still circulating, which caused the first pandemic of the 21st century. We are interested in the role of the matrix protein M1 (and M2) in the membrane assembly of this virus. M1 is the most abundant viral protein and is essential for influenza virus assembly. We have recently shown that the arginine triplet (R76/77/78) located on helix 5 of M1, a highly conserved motif among influenza A subtypes, is essential for its localization to the cell plasma membrane, for the membrane attachment of M1, for its incorporation into viral particles and for its infectivity (in collaboration with O.Moncorgé, IRIM CNRS Montpellier and P. Roingeard, University of Tours). Its mutation completely abolishes the production of infectious virus. This study also allowed us to develop a minimal system for the production of non-infectious influenza A VLP-M (Kerviel, Dash et al., 2016).

We are now interested in the role of cortical actin and its dynamic regulators in the assembly and budding of influenza A virus and SARS-CoV-2 (Bracquemond & Muriaux, 2021), that we explore using RNA interference, infection, and cell biology techniques coupled with advanced photonic microscopies.

5. HIV-1, IAV and SARS-CoV-2 assembly visualized by Atomic force microscopy (AFM) on single virus particles.

(Funding : ANRS 2015, ANRS 2019, MUSE)

We have shown using atomic force microscopy at the level of single virus particles that genomic RNA is a polydispersity factor in the morphology of HIV-1 (Faivre-Moskalenko et al.,2014). In collaboration with the physicists C. Moskalenko and M. Castelnovo at ENS Lyon, atomic force microscopy is used to quantitatively study the variation of the size of viral particles and cores produced by host cells, as a function of various microenvironments (Bernaud et al., 2015). This polydispersity is an estimator of the self-assembly efficiency of the HIV-1 Gag protein.
We have recently imaged the infectious and the inactivated SARS-CoV2 virus by AFM in collaboration with Sébastien Lyon and the Cemipai team (Lyonnais et al., 2021).

We continue to analyze all types of VLPs derived from HIV-1, IAV and SARS-CoV-2 viruses by these fluorescence techniques, which represent wonderful tools to study the assembly or the entry of viruses into their host cell (outside a BSL3).

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*Co-last and/or corresponding, # Co first, In Bold, team members

Publication Year : 2023

• Quantifying membrane binding and diffusion with Fluorescence Correlation Spectroscopy diffusion laws. Mouttou A#, Bremaud E#, Noero J, Dibsy R, Arone C, Mak J, Muriaux D, Berry H*, Favard C*. Biophysical Journal.
  
• Virus Detection and Identification in Minutes Using Single-Particle Imaging and Deep Learning. Shiaelis N, Tometzki A, Peto L, McMahon A, Hepp C, Bickerton E, Favard C, Muriaux D, Andersson M, Oakley S, Vaughan A, Matthews PC, Stoesser N, Crook DW, Kapanidis AN, Robb NC. ACS Nano.
  
• Optimization of resonant dielectric multilayer for enhanced fluorescence imaging, A. Mouttou, F. Lemarchand, C. Koc, A. Moreau, J. Lumeau, C. Favard*, A.L. Lereu*. Optical Materials: X

• The FDA-approved drug Auranofin has a dual inhibitory effect on SARS-CoV-2 entry and NF-κB signaling. Laplantine E, Chable-Bessia C, Oudin A, Swain J, Soria A, Merida P, Gourdelier M, Mestiri S, Besseghe I, Bremaud E, Neyret A, Lyonnais S, Favard C, Benaroch P, Hubert M, Schwartz O, Guerin M, Danckaert A, Del Nery E, Muriaux D,* Weil R.*. iScience.
  
• Optimized production and fluorescent labeling of SARS-CoV-2 virus-like particles. Gourdelier M, Swain J, Arone C, Mouttou A, Bracquemond D, Merida P, Saffarian S, Lyonnais S, Favard C, Muriaux D. Scientific Reports
• Antibody response after first and second BNT162b2 vaccination to predict the need for subsequent injections in nursing home residents.Tuaillon E, Pisoni A, Veyrenche N, Rafasse S, Niel C, Gros N, Muriaux D, Picot MC, Aouinti S, Van de Perre P, Bousquet J, Blain H. Scientific Reports
• Specific intracellular signature of SARS-CoV-2 infection using confocal Raman microscopy. Salehi H, Ramoji A, Mougari S, Merida P, Neyret A, Popp J, Horvat B, Muriaux D, Cuisinier F. Communication Chemistry
• Extracellular vesicles containing the I-BAR protein IRSp53 are released from the cell plasma membrane in an Arp2/3 dependent manner. de Poret A, Dibsy R, Merida P, Trausch A, Inamdar K, Muriaux D. Biology of the Cell
• Resonant dielectric multilayer with controlled absorption for enhanced total internal reflection fluorescence microscopy. Mouttou A, Lemarchand F, Koc C, Moreau A, Lumeau J, Favard C, Lereu AL. Optics Express
• The control of transcriptional memory by stable mitotic bookmarking. Bellec M, Dufourt J, Hunt G, Lenden-Hasse H, Trullo A, Zine El Aabidine A, Lamarque M, Gaskill MM, Faure-Gautron H, Mannervik M, Harrison MM, Andrau JC, Favard C, Radulescu O, Lagha M. Nature Communication
• Deciphering the Assembly of Enveloped Viruses Using Model Lipid Membranes. Brémaud E, Favard C, Muriaux D. Membranes
• Low selectivity index of ivermectin and macrocyclic lactones on SARS-CoV2 replication in vitro argues against their therapeutic use for COVID-19 Chable-Bessia C., Boullé A., J. Swain, M. Hénaut, P. Merida, N. Gros, A. Makinson, S. Lyonnais, C.B. Chesnais, D.Muriaux. COVID
• Role of the membrane curvature factor IRSp53 in HIV-1 particle assembly and budding. Muriaux D. Medecine Science 

Publication Year : 2021

• Imaging translation dynamics in live embryos reveals spatial heterogeneities. Dufourt J.,Bellec M., Trullo A., Dejean M., De Rossi S., Favard C. & Lagha M., Science
• Receptor binding domain-IgG levels correlate with protection in residents facing SARS-CoV-2 B.1.1.7 outbreaks. Blain H, Tuaillon E, Gamon L, Pisoni A, Miot S, Delpui V, Si-Mohamed N, Niel C, Rolland Y, Montes B, Groc S, Rafasse S, Dupuy AM, Gros N, Muriaux D, Picot MC, Bousquet J. Allergy
• Full assembly of HIV-1 particles requires assistance of the membrane curvature factor IRSp53. K. Inamdar, F-C. Tsai, A. de Poret, R. Dibsy, J. Manzi, P. Merida, R. Muller, P. Lappalainen, P. Roingeard, J. Mak, P. Bassereau, C. Favard, D. Muriaux*. eLife
• Betacoronavirus Assembly: Clues and Perspectives for Elucidating SARS-CoV-2 Particle Formation and Egress. Bracquemond D, Muriaux D., mBio
• SARS-CoV-2 Poorly Replicates in Cells of the Human Blood-Brain Barrier Without Associated Deleterious Effects Constant O, Barthelemy J, Bolloré K, Tuaillon E, Gosselet F, Chable-Bessia C, Merida P, Muriaux D, Van de Perre P, Salinas S and Simonin Y. Frontiers Immunology
• Illuminating the nanoscopic world of viruses by fluorescence super-resolution microscopy. Arone C, Dibsy R, Inamdar K, Lyonnais S, Arhel NJ, Favard C*, Muriaux D*. Virologie
• Atomic force microscopy analysis of native infectious and inactivated SARS-CoV-2 virions. S Lyonnais, M Henaut, A Neyret, P Merida, C. Cazevieille, N Gros, C Chable-Bessia, D Muriaux. Scientific Reports
• Fluorescence recovery after photobleaching. Sibarita, J.-B. & Favard, C., in Imaging Modalities for Biological and Preclinical Research: A Compendium, Volume 1, Institute Of Physics Publishing
  

Publication Year : 2020

• Enhanced total internal reflection fluorescence imaging based on dielectric resonant multilayers for multimodal fluorescence microscopy, A.L. Lereu*, A. Mouttou, F. Le Marchand, T. Begou, A. Moreau, D. Muriaux, J. Lumeau, C. Favard*, Proceedings SPIE 11461
• Statistical Tests for Force Inference in Heterogeneous Environments. Serov AS, Laurent F, Floderer C, Perronet K, Favard C, Muriaux D, Westbrook N, Vestergaard CL, Masson JB., Scientific Reports
  
• Mapping spatio-temporal dynamics of single biomolecules in living cells F. Laurent, C. Floderer, C. Favard, D. Muriaux, J-B. Masson, C.L. Vestergaard, Physical Biology
  
• Stick-slip dynamics of cell adhesion triggers spontaneous symmetry breaking and directional migration. K. Hennig, I. Wang, P. Moreau, L. Valon, S De Beco, M Coppey, Y. Miroshnikova, C. Albiges Rizo, C. Favard, R. Voituriez, M.Balland, Science Advances

Publication Year : 2019

• HIV-1 Gag specifically restricts PI(4,5)P₂ and cholesterol mobility in living cells creating a nanodomain platform for virus assembly. C. Favard#, J Chojnacki#, P. Merida, N. Yandrapalli, J. Mak, C. Eggeling*, D. Muriaux*, Science Advances
  
• Monitoring HIV-1 Assembly in Living Cells: Insights from Dynamic and Single Molecule Microscopy. K Inamdar , C Floderer , C Favard * and D Muriaux*,Viruses
  
• Zelda, le maestro du réveil du génome zygotique J. Dufourt, M. Bellec, O. Messina, A. Trullo, C. Favard, O. Radulescu, M. Lagha., Medecines & Sciences
  

Publication Year : 2018

• Single molecule localisation microscopy reveals how HIV-1 Gag proteins sense membrane virus assembly sites in living host CD4 T cells. Floderer C., Masson JB., Boilley E., Georgeault S., Merida P., El Beheiry M., Dahan M., Roingeard P., Sibarita JB., Favard C.* Muriaux D*. Scientific Reports
  
• Numerical Simulation and FRAP Experiments Show that the Plasma Membrane Binding Protein PH-EFA6 does not Exhibit Anomalous Sub-Diffusion in Cells. C. Favard*, Biomolecules
  
• The NC domain of HIV-1 Gag contributes to the interaction of Gag with TSG101. S.E. El Meshri, E. Boutant, A. Mouhand, A. Thomas, V. Larue, L. Richert, V. Vivet-Boudou, Y. Mély, C. Tisné*, D. Muriaux*, H. de Rocquigny*, Biochemical Biophysical Acta
• Temporal Control of Transcription by Zelda in living Drosophila embryos. J. Dufourt, A. Trullo, J. Hunter, C. Fernandez, J. Lazaro, M. Dejean, L. Morales, K.N. Schulz, M. M. Harrison, C. Favard, O. Radulescu, M. Lagha, Nature Communication

Publication Year : 2016

Current Team Members (2020-2021)

• Delphine Muriaux – Research Director, PI CNRS, Virology.
• Cyril Favard – PI CNRS, Biophysics.
• Peggy Merida - Lab Manager Permanent Staff CNRS, Cell Biology

• Jittendriya Swain - Post Doc Membrane Biophysics and Virology
• Rayane Dibsy - Ph.D. Student CBS2 Montpellier.
• Manon Gourdelier - Ph.D. Student  CBS2 Montpellier.
• Anita Mouttou - Ph.D. Student CBS2 Montpellier.
• Coline Arone - Ph.D. Student CBS2 Montpellier.
• Erwan Bremaud - Chemical Engineer.

Alumni

2020

• Aurore de Poret  CIFRE-CILOA. Now working for Bayer.
• Kaushik Inamdar, ANRS, starting his post-doc at MPI for Biophysical Chemistry (S. Jakobs group) in Goettingen, Germany. 
• David Bracquemond, Chemical Engineer for CEMIPAI.
• Aurélie Favarin (w/L. Picas) - Infectious disease master student , Univ. Montp. Now doing a Ph.D. in Paris
  

2019 

• Noémie Oziol - Master Infectious Disease, Univ Montpellier.
• Favarin Aurélie - Master Infectious Disease , Univ Montpellier
• Alice Trausch - Biotechnology Technician, CNRS

2018

• Rayane Dibsy - Master Infectious Disease, NUM Montpellier
• Paul Lambert - Master Physics of Living Systems, NUM Montpellier
• Mathilde Henaut - Engineer School Last year Student ENSAIA Nancy
• Lisa Morichon - Biotechnology Technician, CNRS

2017

• Shantoshini Dash - Ph.D. CBS2 Montpellier, Now Post-Doc Pennsylvania University
• Elise Boilley - Master EPHE Paris Sorbonne. Consultant for Efor Lyon
• Salma Guerfallah - Master Infectious Disease, Univ. Montpellier
• Aida Houhou - Master Biopysics Univ. Montpellier
• Sarah Hadouch - B. Sc. Chemistry
• Mélanie Amigues - Biotechnology Technician, CNRS

2016

• Charlotte Mariani, Ph.D. "Quantifying the nano-dynamic of HIV-1 Gag protein on the plasma membrane of T-Cells during viral assembly." Now Bioprocess Validation Specialist @ Merck Inc.
• Naresh Yandrapalli, Ph.D., "Role of HIV-1 Gag protein multimerization in the generation of nanodomains in lipid membranes", Now Post-Doc at Max Planck Institute Postdam.
• Julien Noero, Master Biophysics NUM
• Lisa Morichon, Biotechnology Technician Student

2015 

• Nathalie Gros, Lab Manager, Now CNRS Permanent position at CNRS at Cemipai.
• Alexis Chesseron, Master Physics of the living systems, NUM
• Jordan Tremoulet, Biotechnology Technician Student

2014

• Adeline Kerviel - Ph.D. Now Post Doc at NIH Bethesda.
• Jan Prchal - Visiting Scientist - Sanofi Price - Institute of Chemical Technology - Prague (CZ)
• Emmanuel Aurouet - Master EPHE Now @ Beckman Coulter
• Rony Midahuen - Master Biotechnology.

2013

• Audrey Thomas - Ph.D. Student.
• Sophie Guillaume - B Sc Chemistry
• Alexandre Pasquiou – Master Biological Imaging (Nice, Zeiss Fellowship) - Now @ Amplitech
• Taoufik Lahdidioui - Master Software Engineering (Montpellier)

2012

•  Charlotte Berliat –Engineer Chemistry/Physics/Electronics Lyon - Now @ Laboratoire Aguettant
• Fatimata Diagne – Master EPHE.
• Stéphane Pelletier - BSc Cell Biology
• Elise Faye - BSc Chemistry

Past and present in pictures

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ACADEMICS COLLABORATORS

INTERNATIONAL

• J. Mak, Melbourne, Australia.
• C. Eggeling, Leibniz-Institute of Photonic Technology, Jena, Germany
• A. Rein, NIH, Fredericks, USA
• J. Saad, University Alabama, USA
• J.Chojnacki, IrsiCaixa AIDS Research Institute, Barcelona, Spain
• A.Kapanidis & N. Robb Oxford University & Warwick University, UK
• S. Saffarian, University of Utah, USA
• D.V. Nicolau, Mc Gill University, Canada

NATIONAL

• J.B. Sibarita, IINS, Bordeaux.
• J.B. Masson, Institut Pasteur, Paris.
• P. Bassereau, Institut Curie, Paris.
• C. Picart, CEA, Grenoble.
• P. Roingeard, INSERM U966, Tours.
• H. Berry, INRIA, Lyon
• M. Balland, LiPhy, Grenoble
• A.Cimarelli, CIRI, ENS Lyon
• H.Dutartre, CIRI, ENS Lyon
• R.Weil, Institut Pasteur & UPMC, Paris
• A. Lereu & J.Lumeau, Institut Fresnel, Marseille.

LOCAL/IN HOUSE

• L. Chaloin, IRIM.
• M. Bonazzi, IRIM.
• O. Moncorgé, C. Goujon, IRIM.
• L. Picas, IRIM.
• S. Lyonnais, CEMIPAI.
• M. Lagha/J. Dufourt, IGMM.
• C.Mathé, IBMM.

INDUSTRIAL COLLABORATORS

• Myriade, Paris.
• Idylle, Paris.
• OTR3, Paris.
• Flash Therapeutics, Toulouse.
• AI BioPharma, Montpellier.