EDIDPasteur/madagascar_influenza

Characterize influenza sequences from Madagascar and Africa available in GISAID # Madagascar Influenza *Last updated: 2026-04-23* **Report:** ## Contents - Goal - Data - Alignment pipeline - Phylogenetic tree pipeline - Reproducing the analysis - Progress ## Goal Do Malagasy influenza viruses form distinct local lineages (monophyletic clades), or are they sporadic importations from the broader African gene pool? This determines whether sustained in-country surveillance in Madagascar is justified from a genomic-epidemiology perspective. ## Data ### GISAID (downloaded 16 March 2026) **30,065 isolates** (all Africa, all hosts, after deduplication) — **1,849 from Madagascar (6.1%)**. Raw GISAID files are not tracked by git; derived outputs (`combined_metadata.tsv`) are. | Tag | Description | Isolates | Sequences | |-----|-------------|----------|-----------| | `a_human_africa` | Flu A human Africa | 19,902 | 110,901 | | `b_human_africa` | Flu B human Africa | 5,081 | 27,900 | | `animal_environmental_africa` | All animal/env Africa | 5,160 | 22,314 | | **Total** | after deduplication | **30,065** | **161,143** | **782 / 1,849 Madagascar isolates (42.3%) are analysis-ready** (complete 8-segment genome + known location + known date). ### Norosoa Razanajatovo (unpublished avian, 2021–2023) 109 avian isolates, 830 segment sequences from Institut Pasteur de Madagascar. Files in `data/norosoa_avian_*.fasta` — not tracked by git. | Subtypes | Isolates | |----------|----------| | H9N2 | 55 | | H4 (partial) | 14 | | H6N2, H6N8 | 13 | | H1N2 | 8 | | other | 19 | Notes: 3 isolates already in GISAID (partial); 1 confirmed co-infection (H1N2/H6N1); 1 confirmed import from Brazil (H4N6). ## Alignment pipeline **358 MAFFT alignments** — one per segment × subtype × scope (Africa / Madagascar), filtered to ≥ 3 sequences. Input: 161,143 GISAID + 830 Norosoa sequences. Outputs: `alignments/aligned/`. ```bash bash scripts/align_segments.sh # submits SLURM jobs (resumable) squeue -u $USER # monitor ``` | Script | Purpo …