Final Report Summary - RNAVIRUSPOPDIVNVAX (RNA virus population diversity, virulence, attenuation and vaccine development.)
Ten years ago, the first high-fidelity variant of an RNA virus was isolated and characterized by two independent teams. Previously, it was thought that fidelity could not be altered for RNA viruses. This work provided a new study model with which to address the role of RNA quasispecies in RNA virus fitness. One of the aims of this project was to considerably build and expand on this initial observation to determine if fidelity can be altered in other viruses and to determine the role of fidelity in generating virus quasispecies. We successfully isolated and characterized over 20 high and low fidelity variants of virus from two distinct families: picornaviruses and togaviruses. Our work permitted us to confirm the theory that RNA viruses have evolved high mutation rates to facilitate rapid evolution and adaptation; but retain a certain level of fidelity so that genetic information is not completely lost. In the process, we have identified many of the structural and functional determinants in the viral polymerase (and other viral proteins) that govern replication fidelity.
In attempts to better characterize these viral populations, we developed deep sequencing and computational approaches that permit unprecedented resolution in identifying and monitoring the genetic changes occurring within viral populations, that had previously remained undetectable by more classic sequencing technologies. Using these new tools, we were able to describe how a virus population is able to adapt to a new growth condition, through the contribution of several minority variants interacting with the majority genotype. We have also characterized how viruses are able to jump to new hosts, and replicate between a set of well defined hosts. Finally, by applying our approaches to monitor the evolution of a virus in vivo, we were able to identify how a virus navigates through a host to survive genetic bottlenecks, and how monitoring viruses in the subpopulations at transmission sites can be used to predict future emergence events.
In addition to this strictly fundamental research, the expertise we acquired has permitted us to develop new antiviral approaches. Fidelity variants are now being seriously explored as methods of generating safer and more stable live attenuated vaccines (high-fidelity variants) or more diverse vaccine seeds that present broader antigenic diversity (low-fidelity variants). Fidelity variants have also proven to be good tools to identify new compounds with antiviral, mutagenic activity. Finally, by altering a virus' ability to generate mutation, or altering its ability to survive mutation, we have developed to methods of attenuating virulent strains, to create new vaccine strains.
In attempts to better characterize these viral populations, we developed deep sequencing and computational approaches that permit unprecedented resolution in identifying and monitoring the genetic changes occurring within viral populations, that had previously remained undetectable by more classic sequencing technologies. Using these new tools, we were able to describe how a virus population is able to adapt to a new growth condition, through the contribution of several minority variants interacting with the majority genotype. We have also characterized how viruses are able to jump to new hosts, and replicate between a set of well defined hosts. Finally, by applying our approaches to monitor the evolution of a virus in vivo, we were able to identify how a virus navigates through a host to survive genetic bottlenecks, and how monitoring viruses in the subpopulations at transmission sites can be used to predict future emergence events.
In addition to this strictly fundamental research, the expertise we acquired has permitted us to develop new antiviral approaches. Fidelity variants are now being seriously explored as methods of generating safer and more stable live attenuated vaccines (high-fidelity variants) or more diverse vaccine seeds that present broader antigenic diversity (low-fidelity variants). Fidelity variants have also proven to be good tools to identify new compounds with antiviral, mutagenic activity. Finally, by altering a virus' ability to generate mutation, or altering its ability to survive mutation, we have developed to methods of attenuating virulent strains, to create new vaccine strains.