Investigation of T cell immune pressure on the influenza virus genome within a universal vaccination model

Abstract

Improved vaccination strategies are needed against influenza which affects millions of people annually and causes a substantial health burden in many countries. Current strategies are vulnerable to seasonal adaptations caused by mutations within the influenza genome which are generated in response to selection pressure and offer little to no protection against newly emerging pandemic influenza strains. Next generation vaccines aim to provide universal protection against current circulating viruses and future arising variants. Universal vaccination can be achieved through multiple approaches, but a prevailing theory is augmenting T cell responses to leverage T cell recognition of conserved viral epitopes of influenza viruses. While T cells are essential for viral clearance and reducing severity during influenza infection, they can also exert increased immunological pressure which can lead to viral variants which adapt to circumvent the immune response. The capacity of T cell-activating vaccines to inadvertently cause viral escape mutants is one of the biggest questions still facing next generation vaccine design. This study characterises mutational rates of the influenza genome and immunological responses to a next generation vaccine, Wyeth/IL-15/5Flu within a mouse challenge model. It was observed that this universal vaccine candidate leads to an increased incidence and frequency of significant mutations across multiple influenza genes when compared to mock vaccinated or seasonal inactivated influenza vaccines. However, the nature of these mutations appears to be stochastic, as few variants arose directly within T cell epitope regions. No high frequency T cell escape mutants were identified during this study, but potentially beneficial mutations were seen to arise in non-epitope regions after Wyeth/IL-15/5Flu vaccination, such as in polymerase genes and HA glycosylation positions. T cell depletion of Wyeth/IL-15/5Flu vaccinated mice reduced the incidence of significant mutations and the overall mutational frequency across multiple genes, indicating that this increased mutational rate is T cell mediated. This suggests that universal influenza vaccination may provide an increased opportunity for adaptations to arise within the influenza genome. This study also further characterised effects of mild immunopathology of increased weight loss associated with universal vaccination. Wyeth/IL-15/5Flu vaccination skewed the response to an inflammatory Th1 response compared to an anti-inflammatory Th2 response upon phylogenic HA group 2 influenza virus challenge. It is possible this occurred due to a mismatch between humoral group 1 HA phylogeny influenza-specific vaccine immunity and heterosubtypic cellular immunity during group 2 influenza infection. This study provides a novel examination of the effects of next generation T cell-activating vaccines on the influenza genome and host responses. This project used an interdisciplinary approach combining both next generation sequencing techniques and immunological approaches to determine the impact of universal vaccination against the influenza genome. These findings can help inform future vaccine design and aid in the generation of improved influenza vaccination strategies.