High-throughput technologies have the potential to improve our understanding of the interaction between microbes, hosts and the environment. Nevertheless, the benefits of these technologies must be assessed before they can be transformed from research tools to routine public health practices. In this context, next-generation sequencing and whole genome sequencing will be set up, validated and applied to improve the tools used for the genetic characterisation of influenza virus strains, the detection of new subtypes of influenza viruses as well as other respiratory viruses.
Influenza viruses evolve very rapidly, leading to the emergence of mutants that escape immunity and that are antigenically different from vaccine strains. This is due to small mutations in the hemagglutinin (HA) and neuraminidase (NA) genes that make the protein unrecognizable to pre-existing host immunity. This is the reason why people can be infected several times by influenza viruses and why the vaccine has to be adapted every season.
The widely and currently used antivirals are neuraminidase inhibitors (NAI) which are active against influenza A and B. The development and dissemination of drug resistance is a significant threat to the clinical utility of these antivirals. Influenza viruses with reduced sensitivity to NAI typically contain mutations in the NA which directly or indirectly alter the shape of the NA catalytic site, thus reducing the inhibitor binding ability. For example, the Y275H mutation in N1 is associated with Influenza strains which may develop phenotypic resistance to these antivirals, and thus become less susceptible to their inhibitory activity. The emergence and worldwide spread of oseltamivir-resistant seasonal A(H1N1) viruses during the 2007-2009 seasons emphasize the need for continuous monitoring of antiviral drug susceptibilities. Other mutations associated with resistance to antivirals have also been described for A(H3N2) and influenza B.
We evaluate the use of next-generation sequencing (NGS) for influenza virus whole genome or targeted (e.g. HA, NA) sequencing, including the analysis of minor genetic variants in the viral RNA quasispecies population, for high resolution characterisation of influenza strains and identification of genetic drift variants of influenza viruses throughout and especially early in the influenza season and to monitor potential mutations associated with resistance to neuraminidase inhibitors.
We will also evaluate the use of NGS for viral metagenomics as an open and untargeted detection tool that allows identification of any virus, including emerging (ex. new subtypes of Influenza virus A) or new pathogens and unexpected viruses in respiratory samples.