8206caf3deee5603597c6fdbcae1320afc37281a angie Sat Dec 23 18:25:37 2023 -0800 Additional sites/ranges for BA.2.86 and XBC. diff --git src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml index 1a51e1c..8fc850b 100644 --- src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml +++ src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml @@ -1,193 +1,198 @@ # Trying out a more data-driven approach to identifying nodes, sites and specific mutations # for branch-specific masking. version: 0 B.1.1.7: representative: Italy/TAA-1900553896/2021 representativeBacktrack: 1 # use the parent node of representative's node ranges: [ [ 11288, 11296] ] # recurring deletion found in many VoCs B.1.351: representative: SouthAfrica/CERI-KRISP-K012031/2021 ranges: [ [ 11288, 11296] ] P.1: representative: FRA/IHUCOVID-005193-N1/2021 ranges: [ [ 11288, 11296] ] B.1.617.2: representative: IND/GBRC714b/2021 # Deletions at S:157-158 (22029-22034), ORF8:119-120 (28248-28253); mask adjacent noisy bases too ranges: [ [ 22027, 22034], [28246, 28254] ] sites: [ 21302, 21304, 21305, # https://github.com/cov-lineages/pango-designation/issues/398 21846, # S:95 noisy -- caused split AY.100 28461, # https://github.com/cov-lineages/pango-designation/issues/435 28271 ] # deletion BA.1: representative: England/DHSC-CYBJ4Y8/2022 ranges: [ [ 6513, 6515 ], [ 11283, 11291 ], # https://github.com/cov-lineages/pango-designation/issues/361 [ 21765, 21770 ], [ 21988, 21995 ], [ 22194, 22217 ], # deletion 22194-22196, insertion after 22204, big mess after that [ 28362, 28370 ] ] sites: [ 203, 22813, 22898, 22882, 23854 ] BA.1.1: # On the BA.1 branch, so it inherits BA.1 masking. representative: England/ALDP-2BEB0A0/2021 ranges: [ [ 76, 77 ] ] reversions: [ G26530A ] # false reversions on this really messed up the BA.1.1.1 branch. # XD should have this reversion, oh well. BA.2: # I'm including some 5' UTR and 3' UTR sites now; in retrospect could have started earlier. # I would mask 210 too but it's useful for finding breakpoints of Delta/BA.2 recombinants. # 212 is also noisy but I'm leaving it in as a red flag for 210 mutations that might be noise. representative: England/DHSC-CYBAB7G/2022 representativeBacktrack: 1 ranges: [ # 5' UTR [ 76, 81 ], [83, 86 ], [ 88, 89 ], [ 91, 94 ], [ 96, 101 ], [ 105, 106 ], [ 123, 124 ], [ 126, 127 ], [ 129, 136 ], [ 139, 141 ], [ 143, 148 ], [ 151, 152 ], [ 157, 159 ], [ 179, 180 ], [ 197, 201 ], [ 203, 204], [ 206, 207 ], [ 216, 219 ], [ 221, 225 ], [ 230, 233 ], [ 241, 243 ], [ 245, 246 ], # deletions [ 11288, 11296 ], [ 21633, 21641 ], [ 28361, 28371 ], [ 29734, 29759 ], # 28877 and 28878 together are highly homoplasic in all of B.1.1 (28881-28883). # They seem to be found very consistently in P.1*, but pop up in many places in Alpha # and Omicrons. I haven't looked closely at the Alpha instances but they caused # some mini-Omicrons (https://github.com/cov-lineages/pango-designation/issues/988). # Possibly could also mask in B.1.1.7 and BA.1 but those are old news. [ 28877, 28878 ], # 3'UTR [ 29769, 29779 ], [ 29781, 29782 ] ] sites: [ # 5'UTR 103, 110, 119, 121, 154, 162, 164, 214, 228, 239, # amplicon dropout (there are so many more; omitting to avoid recombinant trouble) 22786, 22882, 23854, # Recurrent multi-muts / misaligned insertions # https://github.com/cov-lineages/pango-designation/issues/2327#issuecomment-1763481773 28245, 28251, 28254, # 3' UTR 29760, 29762, 29764, 29766, # only Luxembourg, made a mini-BA.2 29767, 29784, 29786, 29793, 29800, 29803 ] BA.2.75: # Inherits BA.2 masking but has so many problems with false reversions I'm adding a ton here. representative: India/WB-INSACOG-1931503209307/2022 reversions: [ # BA.2-level but not masked BA.2-wide to avoid messing up recombinants: G670T, T2790C, T3037C, T4321C, G9424A, T9534C, T9866C, T10029C, T10198C, G18163A, T19955C, G20055A, T21618C, G22200T, A22578G, T22674C, C22679T, T22686C, G22688A, A22775G, T22813G, A22992G, A22995C, C23013A, G23055A, T23063A, C23075T, G23403A, T23525C, G23599T, A23604C, T23948G, T24424A, A24469T, T25000C, T26270C, G26577C, T27807C, T28271A, C29510A, # BA.2.75-defining, very dropout-prone: T4586C, G22001A, C22016T, A22033C, G22190A, C22577G, G26275A, # BA.2.75-defining, bad but maybe not quite as bad: T3796C, T3927C, T5183C, G12444A, A15451G, G22190A, A22331G, A22898G, G22942T, C23013A ] # False muts in re-placed (from BA.5) recombinants: # XBD: A26275G # XBP: G22331A, G22577C, G22898A, A26275G # XBR: A22190G, G22331A, G22577C, G22898A, A26275G # XBS: A22190G, G22331A, G22577C, G22898A, A26275G BN.1.2.3: # Inherits from BA.2.75 representative: England/QEUH-326228D4/2022 sites: [ 337 # https://github.com/cov-lineages/pango-designation/issues/2016#issuecomment-1626159006 ] BA.2.86: # Inherits from BA.2 # @Over-There-Is requested 21610 - very messy indeed. # https://github.com/sars-cov-2-variants/lineage-proposals/issues/606#issuecomment-1801095482 # @aviczhl2 pointed out some recurring reversions: # https://github.com/sars-cov-2-variants/lineage-proposals/issues/1072 representative: OY747147.1 - sites: [ 21610 ] + ranges: [ [ 21765, 21770 ] ] # https://github.com/sars-cov-2-variants/lineage-proposals/issues/606 + sites: [ 21610, + 21302, 21304, 21305, # https://github.com/sars-cov-2-variants/lineage-proposals/issues/1190 + ] reversions: [ T21711C, C22032T, A22033C, G22034A, A23012G, G26610A ] 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 # XBP: G12160A, # XBR: G12160A # XBS: G12160A reversions: [ G670T, T2790C, T3037C, A4184G, T4321C, G9424A, T9534C, T10198C, A12160G, T15714C, T17410C, G18163A, T19955C, G20055A, T21618C, G22200T, A22578G, T22674C, C22679T, T22686C, G22688A, A22775G, T22813G, G22882T, G22917T, A22992G, A22995C, C23013A, G23018T, G23055A, T23063A, C23075T, G23403A, T23525C, G23599T, A23604C, T25000C, A26529G, G26577C, A26709G, T27807C, T27889C, T28271A, C29510A ] BQ.1: # Inherits from BA.5 # Mask some suspicious run-of-nearby-site mutations that cause a mini-BQ.1 branch and # caused trouble when minimizing the tree for pango-designation v1.18.1 pangolin-data release. representative: England/PHEP-YYGYEQS/2022 sites: [ 114, 117, 244, 256, 258, 261, 264 ] BQ.1.1: # Inherits from BQ.1 representative: England/DHSC-CYF1KSU/2022 reversions: [ C22893A, A22942T ] XBB: # Inherits from BA.2 # Lots of false reversions; I would also mask G405A except that would be wrong for XBN. representative: BGD/icddrb_TND_06_1053/2022 # Homopolymer run 21999-22005 causes big trouble for Ion Torrent & nanopore, leading to false # substitutions in 21994, 21995 and 21998 as discussed in pango-designation issues 1882, 1503, # 1999, 1918. 21998 in particular crops up a lot, all over XBB, interfering with many sublins. # Also, XBB.1.9, XBB.1.16 and XBB.2.3 sequences all seem to have del21991-21993 though very few # XBB.1.5 polytomy sequences seem to have it. Mask anyway, causing trouble. ranges: [ [ 21991, 21995 ] ] sites: [ 21998 ] reversions: [ T2790C, T3037C, A4184G, T4321C, T9344C, G9424A, T10198C, C17859T, G19326A, T21618C, C21810T, A22000C, G22109C, C22577G, A22578G, C22599G, A22664C, C22679T, T22686C, G22688A, T22813G, C22895G, C22896T, A22898G, G22942T, A22992G, A22995C, 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 ] 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 representativeBacktrack: 2 sites: [ 29729 ]