ebolaseq

Methodology

This document describes how ebolaseq produces the optional GP mAb escape report: from GP alignment through epitope scoring to the files written in Escape/.

Pipeline

1. Enable report → force GP protein alignment.
2. Extract GP CDS, translate, MAFFT → Alignment/MAFFT/GP/protein_aln.fasta.
3. Map epitope positions (Makona 2014 frame) to MSA columns.
4. Score isolates vs Makona; summarise per therapy (Ebanga / Inmazeb / MBP134).
5. Write Escape/ (HTML, Excel, verification files).

Makona 2014 (KJ660346.2) is the reference frame because the licensed mAbs were tested against this outbreak strain (watchlist sites match the identical UniProt Q05320 / Mayinga-76 numbering).

GP alignment (step 2)

Extract GP CDS, translate, then MAFFT all proteins into one alignment. Gaps in the MSA can shift position numbers (see step 3).

Position mapping (step 3)

Each literature epitope site has a Makona residue number (e.g. 116). Because MAFFT adds gap columns, each number is mapped to the correct MSA column via an anchor sequence. Output: gp_epitope_q05320_msa_map.tsv.

Scoring (step 4)

Per isolate at each mapped site vs Makona zaire_aa:

Status	Meaning
same	matches Makona
escape	matches a catalogued escape mutation
changed	different, not in catalogue
gap	missing or unmapped

Grantham distance for substitutions. Per therapy: contact-site conservation, epitope-change count, escape matches, max Grantham. In silico concern flags per cocktail component. Catalogue: MAB_ESCAPE_EPITOPES.md.

Outputs (step 5)

File	Content
gp_mab_escape_report.html	Interactive report
mab_escape_data.xlsx	Tables for R/Excel
gp_protein_aln.fasta	GP MSA
makona_gp_mature_reference.fasta	Makona baseline
gp_epitope_q05320_msa_map.tsv	Position ↔ column map

Limitations

• In silico only; catalogue match does not prove reduced clinical efficacy.
• Only watchlist positions in MAB_ESCAPE_EPITOPES.md; other changes appear as changed.
• MAFFT gaps and partial GP can mis-assign columns — verify with gp_epitope_q05320_msa_map.tsv.
• All isolates compared to Makona 2014 zaire_aa, including non-Zaire species, for consistent numbering.

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