2c7413be1d0412785eb7238454dacefc57de05bc
angie
  Tue Mar 10 15:53:08 2026 -0700
Mask reversions caused by dropout in BA.3.2

diff --git src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
index 5737b7d37ce..ca7d7436ffc 100644
--- src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
+++ src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
@@ -153,32 +153,39 @@
 KP.1:
     # Inherits from JN.1
     representative: England/CLIMB-CM7YEN1U/2024
     reversions: [ T17334G        # Reversion of JN.1.11.1 mutation, email from FedeGueli
                 ]
 
 KP.3.1.1:
     # Inherits from JN.1
     representative: England/CLIMB-CM7YJCHG/2024
     reversions: [ C22926T,  # https://github.com/sars-cov-2-variants/lineage-proposals/issues/1914
                   C22928T,  # ''
                   # Others I noticed while looking at the above:
                   G7842A, T23948G, C3565T, T17334G, G19722A, G23055A, T28271A, T23063A, G22910A
                 ]
 
+BA.3.2:
+    # No inheritance
+    representative: SouthAfrica/NICD-N58822/2024
+    representativeBacktrack: 2
+    reversions: [ C27382G, A27395T, T27807C # dropout in Netherlands sequences
+                ]
+
 RE.1.1:
-    # No inheritance -- BA.3.2 descendant with lots of dropout in Australia/WA sequences
+    # Inherits from BA.3.2; lots of dropout in Australia/WA sequences
     # https://github.com/sars-cov-2-variants/lineage-proposals/issues/3093#issuecomment-3508425340
     representative: Australia/WA17392/2025
     reversions: [ A336G, C13375T, C22629A, T28996A ]
     sites: [ 28254 ]
 
 BA.4:
     # BA.4 is placed on the BA.2 branch so it inherits all the BA.2 sites.
     representative: SouthAfrica/NICD-N41664/2022
     ranges: [ [ 686, 694 ], [ 21765, 21770 ] ]
 
 BA.5:
     # BA.5 is placed on the BA.2 branch so it inherits all the BA.2 sites.
     representative: England/PHEP-YYFJPAM/2022
     ranges: [ [ 21765, 21770 ] ]
     # Some of these should be reverted in recombinants, but we're pretty much past the point of