Supplemental files for: Xiao and Dolan, et al., "Poliovirus intrahost evolution is required to overcome tissue-specific innate immune responses."

"RNA viruses have a great evolutionary capacity, allowing them to quickly adapt and overcome challenges encountered during infection. Here we show that poliovirus infection requires adaptation to tissue-specific innate immune microenvironments. The virus’ ability to establish robust infection and virulence correlates with its evolutionary capacity. We further identified a region in the multi-functional poliovirus protein 2B as a hotspot for the accumulation of minor alleles that facilitate a more effective suppression of the interferon response. We propose that population genetic dynamics enables poliovirus spread between tissues through optimization of the genetic composition of low frequency variants, which together cooperate to circumvent tissue-specific challenges. Thus, intrahost virus evolution determines pathogenesis, allowing a dynamic regulation of viral functions required to overcome barriers to infection."

The data set deposited here includes the following:
1. Gene expression
2. Viral allele fitness values computed from in vitro passaged populations. "FitnessValues.csv"
3. Host gene expression values computed by TopHat/CuffDiff pipeline. "hostgeneexpressionvalues_PVinfection.csv"
4. Genetic composition data for in vivo poliovirus populations determined by RNAseq. "InVivoPVRNAseq.zip"
5. Mus musculus GO annotation db Rdata structure. "mmusAnnots.Rdata"
5. Analysis data for clustering of significant DEGs. "PV_mmus_cluster_MDS_FCdata.txt"
6. Raw CuffDiff output "RawCuffDiffData.zip"