What role do host genes have in driving vaccine virus evolution in vivo?

Evaluating host gene expression in virus infected tissues to make predictions on virus subtypes based on host transcriptomic response

We will investigate the direct impact of virus upon host gene expression using the 10X Visium Spatial transcriptomics platform. This cutting-edge protocol, combining IF microscopy and Illumina based RNA-Seq, will identify direct overlaps with host cellular gene expression and virus localisation in host tissues. When combined with ultra-deep transcriptomic datasets will create a multi-layered map of spatial gene expression which will help us to understand both the pathological disease process in hosts and the selective forces that drive the evolution of LAVs post-vaccination. 

We hypothesise that differences in gene expression between pathogenic/non-disease infected groups will inform about protective correlates of host-pathogen interactions, whilst characterising host cellular pressures upon both pathogenic and attenuated viruses. We will use DL protocols with spatial transcriptomics data to predict labels for different biological processes i.e., pathogenic vs attenuation. 

Anticipated outcomes

This objective will classify images based on infection with pathogenic or non-diseases causing viruses using host transcriptomic responses.