Vaccine induced selection pressure on seasonal influenza virus in mice

Abstract

Influenza viruses are characterised by their ability to overcome species barriers and evade host immunity, at times with devastating consequences. Within individuals, influenza virus populations exist as a closely related quasispecies that may evolve to exhibit diverse antigenicity. Protection conferred by seasonal influenza vaccines against disease is punctuated by rapid accumulation of genetic changes in the surface antigens that leads to emergence of novel subtypes disparate to the vaccine seed strains. Next generation universal vaccines designed to target conserved viral epitopes can potentially offer broad protection against diverse circulating and emerging subtypes. Host immune pressure resulting from widespread vaccine usage on a population wide level has been implied to accelerate the process of antigenic diversification, leading to inherent concern for the emergence of escape phenotypes that can circumvent universal protection.

This study characterises temporal genome wide evolution of influenza viruses as a function of intra-host adaptation, and further defines the impact of heterosubtypic immune pressure in driving variant formation within a mouse model. Mapping of minor variant landscape over distal timepoints revealed both transient and fixed changes in the consensus sequence. Fixation events of functional variants were found to be accelerated by vaccine induced heterosubtypic immune selection, although inherent drift occurring within major immunodominant regions was not dependent on the immune status of the host. Emergence of escape phenotypes that encompassed the ability to ablate vaccine mediated protection from mortality and exhibited a high level of host directed virulence was associated with sustained adaptation under heterosubtypic immune selection, of which productive display of virulent characteristics was attributed to polygenic alterations. Importantly, genotypic markers associated with host-specific virulence unique to heterosubtypic immune escape phenotypes were identified within the polymerase encoding segments. Using structural based approaches, a functional residue involved in mediating template directed nucleotide addition that exhibited distinctive side chain flexibility was identified in the polymerase active site. Alterations at the residue was found to impact transcription fidelity of the RdRp machinery. Preliminary investigations on approaches to engineer attenuated vaccines by structural manipulation within the RdRp were explored at this residue.

This study addresses the impact of broadly protective vaccines on short-term viral evolution within the context of natural infection using a combination of molecular, virological and deep sequencing approaches, which contributes to defining larger evolutionary patterns of influenza virus under selection pressure. Findings from this study provide a basis for informing the design of next generation vaccines that can confer broad, cross-subtype protection and impart preliminary assessments of the potential of universal vaccine driven escape. Importantly, results from this study can serve as a mechanistic framework for future generation of assessment platforms that can be used for efficient identification of emerging antigenically novel viral subtypes that pose inherent threats to the greater population.