"Within-host rhinovirus evolution in upper and lower respiratory tract highlights capsid variability and mutation-independent compartmentalization"

Supplemental Material of the article published at The Journal of Infectious Diseases, February 2024

Figure_Generation.Rmd Scripts to generate analysis and figures for most of paper: Figure 1, 2, S3, S5, S7, S8

1_AYM_All_Dataframes Script to combine all dataframes to generate Table S2

Alignments Fasta allignments done through HHpred of RV A, B, and C and epitopes

Deep_Mutation Deep mutational script for alligning fastas and mapping deep mutational 4GB3 to 1AYMN capsid.

Epitopes Contains dataframes and maps epitope positions to each RV capsid.

Interpentamer_Sites Maps interpentameter positions to each RV capsid.

MAF_vs_SASA Maps surface area accessibility to RV A to generate surface area analysis and Figure 3. All pymol files are contained in directory.

mNGS_PCR Script to combine and reformate data to generate figure S1.

RV_LAVA_DATAFRAMES Combines all lava output dataframes together.

Structure_Protein Annotates structure of iSNVs within the capside using EMBOSS

Surface_Exposure Annotates position of iSNVs within the capside using viperDB

viperdb_info viperDB dataframes

Microbiome_analysis Microbiome characterization in upper and lower respiratory tract samples from immunocompromised patients during HRV infection to evaluate cross-contamination.

Revica-Coinfection Detailed summary of the metagenomic analysis performed with Revica (https://github.com/greninger-lab/revica).