Query live pathogen genomic surveillance through the GenSpectrum LAPIS
API: which viral lineages are circulating now, how fast they are
growing, and what mutations they carry. Covers 15 instances spanning
SARS-CoV-2, influenza A (including H5N1 and the seasonal H3N2/H1N1pdm
clades), and the Pathoplexus organisms.
This is a class of question large models answer confidently and wrongly.
Lineage names post-date training; the nomenclature is a live data
structure rather than a convention (XFG only resolves through
alias_key.json); and 294 of the ~6,230 designated names have been
withdrawn or redesignated, so remembered facts are not merely stale.
Four standard-library CLIs, no API key:
resolve_lineage.py is this name still valid, what does it expand
to, what is it descended from
lineage_prevalence.py discover the top lineages in a window, then
weekly prevalence with Wilson intervals,
coverage flags, and a guarded growth fit
mutation_profile.py defining mutations, or a diff between two
lineages, for assay-match questions
reporting_lag.py measure how long sequences take to arrive and
derive a trust cutoff
Nothing hardcodes a field name. Schemas differ materially between
instances -- dateFrom is correct on SARS-CoV-2 and a hard 400 on H5N1 --
so every script reads /sample/databaseConfig and picks the collection,
submission, and lineage columns from what the instance declares.
The API traps documented in references/lapis-api.md were all verified
against the live services. The sharpest: a trailing '*' expands to
descendants only where the column carries a lineage index. pangoLineage=
XFG returns 4 and XFG* returns 640; on H5N1, clade=2.3.4.4b returns
62413 and clade=2.3.4.4b* returns 0. Silently wrong in both directions,
so lineage_filter() refuses to build the query that lies.
Two statistical guards, both prompted by wrong output during testing.
A lineage observed zero times in every week produced a confident
+0.105/week slope from the continuity correction alone as the
denominator shrank; growth fits now require real observations. And the
quasi-binomial dispersion is floored at 1, since an estimate below the
model's own scale reports an interval narrower than binomial sampling
allows.
117 tests, including live checks gated behind LAPIS_LIVE_TESTS=1 that
document the API behaviour the scripts were built against.
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