Non-segmented negative strand RNA viruses are characterized by an intrinsic genome instability, the result of an error-prone RNA dependant RNA polymerase. To date, most viral populations have been characterized by their consensus genome sequences. As a consequence, the true extent and structure of intra-host genetic diversity have largely been ignored because of technical limitations. The question of viral selection is of critical importance. In particular, whether, upon invasion of a new organ or species, natural selection of the fittest genome routinely occurs or whether the selective process operates at the scale of the whole viral population (sometimes termed a viral ‘quasispecies’) is uncertain.
Using an optimized Next Generation Sequencing (NGS) procedure, genome-scale genetic diversity, including single nucleotide polymorphism (SNP), insertion and deletion (INDEL) events, will be determined for collections of multiple virus isolates to track the changing patterns of intra-host genetic diversity of non-segmented negative strand RNA viruses (order Mononegavirales) following the change of the host tissue and/or animal species.
Because of their complementarity in terms of available experimental and molecular tools, as well as a common replication strategy, we shall focus on two human pathogens – rabies (RABV, Genus Lyssavirus) and measles virus (MeV, genus ) – the former of zoonotic origin, and the latter being strictly confined to humans (and experimentally to some other primate species). These viruses can both invade the central nervous system (CNS) and target different organs giving rise to deadly acute or chronic diseases.
Data analysis techniques are used to identify and prioritize significant events and these changes are being compared with those occurring upon in vitro infection of cell lines representatives of the major tissue targets and in natura during change of animal hosts. Finally, hypotheses concerning the role of a given set of SNP and/or INDELs are tested in vitro by building chimeric genomes.
THis project is funded by ANR Programme Blanc 2012