c210683fd63e352426e983f869c6c9aa389da3e1
angie
  Wed Aug 26 16:59:09 2026 -0700
Add exceptions for some XFJ and XFG branches.

diff --git src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
index ca7d7436ffc..4c02deccd86 100644
--- src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
+++ src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
@@ -126,30 +126,38 @@
     reversions: [ T21711C, C22032T, A22033C, G22034A, A22770G, A23012G, G26610A,
                   # Added 2024-03-01 because they're causing reversion branches with >= 100 samples.
                   # Unfortunately 6183 and 9142 will be incorrect in XDD, XDR, XDS.
                   T2790C, T4321C, G6183A, T9142C, C13339T, A22353C, G22556A, C22577G, T22674C,
                   T22686C, G22688A, T22813G, C22895G, A22896T, A22898G, T22916C, G22917T, A22942T,
                   A23005T, C23075T, G23599T, G23604C, T24378C, T26858C,
                   # Added 2024-04-15 by request from Cornelius Roemer, doesn't affect currently
                   # designated recombinants fortunately:
                   T21941G,
                 ]
     exclusions:
       # Cornelius requested exclusion of XFJ.3.1, some of whose descendants have a real G23599T reversion.
       # https://github.com/cov-lineages/pango-designation/commit/02d2cb6aa1155e4d0473fcb1ff345f472725be27
       - site: 23599
         representative: England/CLIMB-CM7YJM45/2025
+      # Fede requested exclusion of XFJ.3 at 21617 and 21618, so XFJ.3.1 correctly shows S:I19V
+      - site: 21617
+        representative: USA/UT-UPHL-251003428161/2025
+      - site: 21618
+        representative: USA/UT-UPHL-251003428161/2025
+      # Cornelius identified real G23599T reversions in descendant sublineages of XFG (TJ.1.1 and TK.1)
+      - site: 23599
+        representative: USA/CA-CDPH-500147572/2025
 
 JN.1:
     # Inherits from BA.2.86
     representative: Denmark/DCGC-661561/2023
     ranges: [ [ 23008, 23011 ],  # https://github.com/cov-lineages/pango-designation/issues/2510
             ]
     sites: [ 1871,          # https://github.com/sars-cov-2-variants/lineage-proposals/issues/1466
              1368,          # GBW artifact, email from FedeGueli
              6569,          # ''
              17562,         # very homoplasic (or systematic error?) in JN.1, email from FedeGueli
            ]
 
 KP.1:
     # Inherits from JN.1
     representative: England/CLIMB-CM7YEN1U/2024