Merge pull request #90 from nextstrain/james/cattle-outliers

cattle-flu updates
nextstrain · Aug 29, 2024 · 0ddee36 · 0ddee36
2 parents 0984ad8 + 5d6291d
commit 0ddee36
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diff --git a/config/h5n1-cattle-outbreak/dropped_strains_h5n1-cattle-outbreak.txt b/config/h5n1-cattle-outbreak/dropped_strains_h5n1-cattle-outbreak.txt
@@ -17,6 +17,12 @@ A/domesticcat/NewMexico/24-009116-001/2024
 # These strains are basal to the outbreak and we exclude them to avoid low-confidence DTA reconstruction.
 A/Peregrinefalcon/California/24-005915-001/2024
 
+# These three cattle strains are hundreds of mutations diverged from the outbreak - perhaps due to poor sequencing?
+# Perhaps they are another introduction? Dropping for now
+A/CATTLE/USA/24-022332-005/2024
+A/CATTLE/USA/24-015672-001/2024
+A/CATTLE/USA/24-022332-007/2024
+
 # These strains represent diversity that's significantly outgrouped relative to cattle outbreak
 A/americancrow/Iowa/24-006634-001/2024
 A/AmericanCrow/USA/24-004479-001-original/2024

diff --git a/ingest/build-configs/ncbi/defaults/host-map.tsv b/ingest/build-configs/ncbi/defaults/host-map.tsv
@@ -1,8 +1,10 @@
 # Check for bird codes in https://www.carolinabirdclub.org/bandcodes.html
+# Note that the first column in this TSV is case insensitive
 Accipitridae	Avian
 alpaca	Nonhuman Mammal
 american crow	Avian
 AMERICAN ROBIN	Avian
+Turdus migratorius	Avian
 american wigeon	Avian
 Anas platyrhynchos	Avian
 Anatidae	Avian