Antigen Watch
antigenic triage
Antigen Watch takes a viral isolate, aligns one of its genes against the reference
sequence for that virus, calls the amino-acid substitutions, and reports which of those
substitutions fall inside residue sets that antibodies are known to bind. The point is
triage: deciding which of a run of mutations is worth a closer look.
What it covers
- Influenza A H5N1 — HA, NA and PB2, against NC_007362.1 and its segment references.
- SARS-CoV-2 — spike (S) and nucleocapsid (N).
- Monkeypox virus — M1R and B6R.
- Dengue virus — envelope (E) and NS1, across DENV-1 to DENV-4.
What it computes
- A pairwise alignment of the isolate's gene against the curated reference, and the amino-acid mutations that follow from it.
- For each mutation, which curated epitope or antigenic sites its position falls in, if any — the sites are a deliberately small, sourced set rather than an exhaustive one.
- The position of each mutated residue on a deposited PDB structure, including the numbering offset used to get there, and an explicit "not resolved" where the structure does not model that residue.
- Where isolates carrying a given mutation have been reported from, aggregated per location, date and lineage.
What it is not
It is not a diagnostic and it does not predict outbreaks. Nothing in it substitutes for a
neutralization assay. Its optional risk-assessment panel produces an ordinal triage score
from curated lookup tables, always alongside caveats; that score is not a measurement,
carries no units, and is not comparable between viruses. Map points are administrative
centroids for the place a sample was reported from, not the place it was taken.
The interactive tool needs JavaScript and WebGL, for the structure viewer and the map.
Source, data provenance and a written inventory of the project's limitations are in its
repository.