# Moncla H3Nx reproduction — missing sequence accessions

For the H3Nx host-strategy paper reproduction (reviews/moncla_h3nx_hoststrategy_REVIEW).
The paper's per-host trees reference sequences not in the public repo's NCBI alignment.
Resolved 2,327 missing tree tips → accessions (2026-09-24).

## Files
- **gisaid_epi_accessions.txt** — 2,176 GISAID EPI_ISL IDs. **← THE ONE YOU NEED.**
  Log into GISAID EpiFlu, batch-search by Isolate ID (split into ~500-ID chunks if the
  UI caps the query), download FASTA + metadata, drop back into
  REPRODUCTION/data/gisaid/.
- missing_strain_accession.tsv — full tip→accession mapping (trace any strain).
- genbank_accessions.txt — 151 GenBank IDs. Already fetched by NCBI efetch
  (genbank_missing.fasta in the repro dir); listed here for completeness only.

## Coverage impact
Human host = 100% NCBI (complete already). Non-human hosts (avian/swine/equine/canine)
are ~25–55% without these — adding the 2,176 GISAID + 151 GenBank restores ~full
coverage to match the authors' trees, needed for a fair R2 clock-rate comparison.