Viral Populations and Pathogenesis Unit
Institut Pasteur 25-28 rue du docteur Roux, 75015 Paris
Research area of the Unit
The primary focus of this group is to study short term evolution of RNA viruses within the infected host and to probe the relative contribution of the intrinsic (viral) and extrinsic (host, environmental) factors involved. A principal research theme is uncovering the determinants of fidelity of RNA polymerases that replicate these viruses, which are major contributors to the spontaneous mutation from which adaptive mutations emerge. Fidelity variants of RNA viruses are then used as tools to examine the evolvability of viruses and their adaptability to changing conditions within the host environment. Using deep sequencing technologies, the effects of different selective pressures (different cell types, organs, hosts, etc) on the composition of the mutant population is examined and used to identify emerging adaptive mutations, with the hope to predict the evolutionary trajectory of current circulating strains towards new emerging strains with epidemic potential.
Contribution to the programme
Currently, mutations that give rise to new emergence events are not identified until after an epidemic has been declared and the evolutionary steps leading to the new viral strain are not detected. Using deep sequencing technology and controlled tissue culture infection (in different cell types) and in vivo infection (in different host organisms), the team aims to identify these early adaptive changes prior to the fixation of these mutations in the virus population and displacement of the previous master sequence. Using newly developed bioinformatics tools, the minority variants emerging within a virus population during infection will be identified and their role in increasing viral fitness or altering phenotype will be examined, when possible, by reverse genetics and molecular characterization. The long term goal is to develop a new approach coupling experimental evolution and bioinformatics to predict the emergence of new strains with epidemic potential, in particular those facilitating transmission within and between species.
References over the past 5 years
1.      Levi, L.I., Gnadig, N.F., Beaucourt, S., McPherson, M.J., Baron, B., England, P., Arnold, J.J., Vignuzzi, M. (2010) Fidelity variants of RNA dependent RNA polymerases uncover an indirect, mutagenic activity of amiloride compounds. PLOS Pathogens. 6(19): e1001163.
2.      Coffey, L.L. and Vignuzzi, M. Host alternation of chikungunya virus increases fitness while restricting population diversity and adaptability to novel selective pressures. Journal of Virology (2011) vol. 85 (2) pp. 1025-35
3.      Beaucourt, S., Bordería, A.V., Coffey, L.L., Gnädig, N.F., Sanz-Ramos, M., Beeharry, Y., and Vignuzzi, M. Isolation of Fidelity Variants of RNA Viruses and Characterization of Virus Mutation Frequency. J Vis Exp. 2011 Jun 16;(52). pii: 2953.
4.      Coffey LL, Beeharry Y, Bordería AV, Blanc H, Vignuzzi M. Arbovirus high fidelity variant loses fitness in mosquitoes and mice. Proc Natl Acad Sci U S A. 2011 Sep
5.      Bordería AV, Stapleford KA, Vignuzzi M. RNA virus population diversity: implications for inter-species transmission. Curr Opin Virol. 2011 Dec;1(6):643-8.
6.      Graci JD, Gnädig NF, Galarraga JE, Castro C, Vignuzzi M, Cameron CE.Mutational robustness of an RNA virus influences sensitivity to lethal mutagenesis. J Virol. 2012 Mar;86(5):2869-73. 
7.      Gnädig, NF, Beaucourt, S, Campagnola, G, Bordería, AV, Sanz-Ramos, M, Beeharry, Y, Gong, P, Blanc, H, Peersen, O and Vignuzzi, M. RNA virus mutator strains are attenuated in vivo. Proc Natl Acad Sci U S A. 2012, in press.