7e6a7ad1f3194e32d9af0a87aff074aa01a859d3
angie
  Mon Apr 22 14:16:28 2024 -0700
Added more sites by request, including new branch GE.1.2.1.

diff --git src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
index 116f1a6..41ac597 100644
--- src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
+++ src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
@@ -112,37 +112,41 @@
               [ 21539, 21542 ],  # run of muts, France/...-HCL, makes a mini-JN.1
               [ 21765, 21770 ],  # https://github.com/sars-cov-2-variants/lineage-proposals/issues/606
               [ 21610, 21624 ],  # https://github.com/sars-cov-2-variants/lineage-proposals/issues/1347
               [ 21625, 21631 ],  # https://github.com/sars-cov-2-variants/lineage-proposals/issues/1380
               [ 22194, 22196 ] ] # https://github.com/sars-cov-2-variants/lineage-proposals/issues/1380
     sites: [ 58, 59,   # https://github.com/sars-cov-2-variants/lineage-proposals/issues/1089
              13427,    # https://github.com/sars-cov-2-variants/lineage-proposals/issues/1313
              21302, 21304, 21305, # https://github.com/sars-cov-2-variants/lineage-proposals/issues/1190
            ]
     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,
                 ]
 
 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
 
 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
     # simultaneous Delta/Omicron and the noise from false reversions is so intolerable that we'll
     # just have to watch out for missing reversions when working with recombinants.
     # False muts in recombinants that were later re-placed in BA.2.75:
     # XBD: G12160A, T22917G, T23018G
@@ -185,30 +189,36 @@
                   C23013A, C23019T, C23031T, T24424A, A24469T, T25000C, T26060C, G26577C, A26709G,
                   T26858C, T27807C ]
 XBB.1:
     # Inherits from XBB
     # Here I'm going a bit past the technical start of XBB.1, to include G27915T to be more sure
     # that it's XBB.1 before we mask out the defining mutation of XBB.1
     representative: England/LSPA-32578111/2022
     reversions: [ T22317G ]
 
 XBB.1.5:
     # Inherits from XBB.1
     # Don't believe reversions on 27915 once we're as far as XBB.1.*
     representative: England/BRBR-32671539/2022
     reversions: [ T27915G ]
 
+GE.1.2.1:
+    # Inherits from XBB (GE is XBB.2.3.10).
+    # https://github.com/cov-lineages/pango-designation/commit/cb172ab49c31a1a12f774ddf00247e8c8e6985f3
+    representative: Netherlands/NH-RIVM-135739/2023
+    sites: [ 27383, 27384, 27385, 27395, 27431, 27688, 27810, 28218 ]
+
 XBC:
     # Inherits nothing!  Should find out its deletions.
     # Deletion 22289-22294 pointed out in #2405.
     # Cornelius Roemer requested to mask several reversions in
     # https://github.com/cov-lineages/pango-designation/issues/1100#issuecomment-1426502678
     representative: Philippines/PH-VUI-142736/2022
     ranges: [ [ 22289, 22294 ] ]
     reversions: [ G5584A, T13019C, T22329C, T25000C, C27718T, T28271A ]
 
 XCK:
     # Inherits from XBB.1.5
     # @FedeGueli pointed out that the usher tree had a very flaky 29729. TL;DR mafft is counfounding
     # two nearby deletions, a new 29726 and the old 29734-29759, and making a false subst by getting
     # the deletion boundaries wrong.  Mask 29729 here.
     representative: USA/TX-CDC-QDX84451512/2023