Project

rhinovirus; respiratory enterovirus; adaptation; innate immunity; reverse genetics; enterovirus; variants; genotype; phenotype; adaptations; epidemiology

Lead
Lay summary
Human rhinoviruses (HRV) and enteroviruses (HEV) are the most frequent causes of respiratory infections. These viruses are characterized by a huge diversity and frequent discovery of new strains such as the HRV-C lineage identified recently.HRVs and HEVs share identical genome organization. However significant phenotypic characteristics differentiate them. In vivo, rhinoviruses are restricted to the respiratory tract, whereas enteroviruses infect the gastrointestinal tract and can spread to other sites such as the central nervous system. In vitro, HRVs and HEVs differ by their optimal growth temperature, acid tolerance and cell tropism. Our previous investigations revealed that some HRVs are more related to enteroviruses than to other HRV at the genome level, which is surprising given the different phenotypes. The basis underlying these contradictory observations is not fully understood. Our goals is to define the genomic regions supporting these differences. Using representative rhino- and enteroviral strains with distinct phenotypes, we will characterize features such as temperature, acid sensitivity, and interferon induction/sensitivity. We also plan to construct an HRV-C infectious clone to characterize this newly discovered virus.This part of the project will be complemented by a molecular epidemiology survey of circulating rhino- and enteroviruses. This approach has allowed us to identify an previously unknown enterovirus genotype (EV104) adapted to the respiratory tract. We plan to genotype circulating strains, to assess the incidence of EV104 and to identify other new variants. Through different collaborations, we have access to specimens collected from transplant recipients chronically infected with rhinoviruses. We will sequence the genomes of such samples collected at different times and from different sites to study in-host adaptation. We will then compare viral adaptation in immunocompromised versus immunocompetent patients. Comparison with viral adaptation under in vitro conditions, such as cell cultures, will also be performed. These investigations will shed some light on the diversity of HRV and HEV genomes and could highlight key features shaping the phenotypes of these viruses. This is of importance since HRVs and HEVs have a high propensity to mutate and could generate new genotypes with phenotypes of unexpected severity. A better understanding of the regions defining phenotypic features and of those implicated in viral adaptation may help to anticipate the phenotype of new variants and to develop antivirals targeting areas less prone to generate resistant mutants.

Direct link to Lay Summary

Last update: 21.02.2013

Active participation

Number	Title	Start	Funding scheme

Human rhinoviruses (HRV) and enteroviruses (HEV) are the most frequent causes of respiratory infections. These two picornaviruses are characterized by the existence of approximately 100 serotypes, but their diversity expands well beyond these predefined serotypes and encompasses also previously unrecognized genotypes. As an example, a new HRV lineage named HRV-C was recently identified.HRVs and HEVs share an identical genome organization, have similar functional RNA secondary structures, and are classified within the same genus because of their high sequence homology. Despite their common genomic features, significant phenotypic characteristics differentiate these two groups of viruses. In vivo, rhinoviruses are restricted to the respiratory tract, whereas enteroviruses infect primarily the gastrointestinal tract and can spread to other sites such as the central nervous system. In vitro, most HRVs and HEVs differ by their optimal growth temperature, acid tolerance, receptor usage and cell tropism. In addition, some HRV and HEV serotypes cannot be grown in cell culture. Our previous investigations revealed that HRV-B are more related to enteroviruses than to HRV-A at the global genome level, which is surprising given the different phenotypes. The genomic basis underlying these different and apparently contradictory observations is not yet fully understood. One of our goals is to define more precisely the genomic regions supporting these differences. Using a panel of representative rhino- and enteroviral strains with distinct phenotypes, we will first characterize features such as temperature and acid sensitivity, as well as interferon induction/sensitivity. The latter assessment may explain why some strains can be isolated in cell culture whereas others cannot, such as the HRV-C viruses. We plan to construct an infectious clone from an HRV-C strain to better characterize its replicative ability in vitro including its interferon susceptibility and, potentially, to determine its receptor usage.This part of the project will be complemented by a molecular epidemiology survey of circulating rhino- and enteroviruses using strains routinely identified in our clinical laboratory or within cohort studies conducted by our group. This approach has allowed us to identify a previously unknown enterovirus genotype (EV104) adapted to the respiratory tract. We plan to conduct this systematic genotyping of circulating strains over several years, first to assess the incidence of this newly discovered EV104, and second to identify other potential new variants. Through different established collaborations, we have access to precious samples such as specimens collected from transplant recipients chronically infected with rhinoviruses. Whenever possible, we will systematically complete the genomes of such samples collected at different times and from different sites to study in-host genome adaptation. We will then compare viral adaptation in immunocompromised patients versus immunocompetent volunteers experimentally infected with HRVs. Comparison with viral adaptation under in vitro conditions, such as cell cultures, will also be performed. Taken together, these investigations will shed some light on the diversity of HRV and HEV genomes and could highlight the key genomic features shaping the phenotypes of these viruses. This is likely of importance since HRVs and HEVs have a high propensity to mutate and could thus generate new genotypes with phenotypes of unexpected severity. A better understanding of the regions defining phenotypic features and of those implicated in viral adaptation may help first to anticipate the phenotype of new variants and second, to develop potent antivirals targeting areas less prone to generate resistant mutants.