Diversity and Evolution of Computationally Predicted T cell Epitopes against Human Respiratory Syncytial Virus

Data_collection

HRSV_0622.gb/ HRSV_0622.fasta file were downoladed form NCBI Genbank 'nucleotide database' with searching term "HRSV" 25790 records were get there

metadata

1. Metadata was download from NCBI virus with Virus search "Human orthopneumovirus (HRSV), taxid 11250", saved in "HRSV_0622.csv"
2. genotype refernce were get with the note features from gb file using customized Gbmunge package, subtype information were collected with Blastn tool with cutomized HRSV_ref (n=2) database blastn -query /Users/jianichen1/Dropbox/RSV-genotyping_20/RSV_epitope/HRSV_0622.fasta -db HRSV_ref -outfmt "6 qseqid stitle sseqid" -max_target_seqs 1 >> HRSV_subtype.txt

Vaccine strain

1. artificial strain were saved under the dirctory "Artificial"
2. vaccine combinnant mutant strain: recombinant mutant rA2cp mutant cp-RSV mutant cpts-248 cp52, cold passaged deletion mutant mutant cpts-248/404 recombinant D46/D53 strain

Eptiope identification

Eitopes information collect from iVAX tool kits were cleaned up

1. Class II: Binding potential score top 5%, Binding alleles >3 for class II

Class I: Bind to any HLA allele top 1% binding prbablity

2. Conservation
3. tolerate epitope: cross-conserved to human protein
4. cross-conserved for both type A and type B

Epitope distribution

1. Epitope heatbar, compare with other pathogen
2. distribution map to 3D structure using pymol

Epitope landscape

1. Epitope distance algorithm with cross-conseved epitope T cell epitope immune distance (D) between two wild circulating strains (w(1 )and w(2 )) can be defined as the sum of Z-scaled binding probabilities of paired epitopes that are unable to induce cross-reactivity (non-cross conserved epitopes) within two protein sequences using equations (1.1 and 1.2). d is the T cell immunity distance between a pair of epitopes, i and j are the non-cross conserved T cell epitopes from two protein sequences, a is a class I or class II allele, p is the predicted binding probability against allele a, A is a set of alleles.

2. MDS + k-means cluster
3. validate with IEDB results

Vaccine strain evaluation

calculate share epitope propotion

Phylogenetic analysis

1. ML with Raxml
2. Ancestral sequence recosntruction "Treetime"