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Designate 4 new clades: CH.1.1 -> 23C, XBB.1.9 -> 23D, XBB.2.3 -> 23E, EG.5.1 (XBB.1.9.2.5.1) -> 23F #1078

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merged 3 commits into from
Aug 9, 2023
Merged

Designate 4 new clades: CH.1.1 -> 23C, XBB.1.9 -> 23D, XBB.2.3 -> 23E, EG.5.1 (XBB.1.9.2.5.1) -> 23F #1078

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69345ba
Add five new clades
corneliusroemer Jul 31, 2023
f745a10
Remove XBC from list of new clades
corneliusroemer Aug 7, 2023
168c6c0
Add 52H as required mutation for 23F (EG.5.1)
corneliusroemer Aug 7, 2023
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4 changes: 4 additions & 0 deletions defaults/clade_display_names.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -31,3 +31,7 @@
22F: 22F (XBB)
23A: 23A (XBB.1.5)
23B: 23B (XBB.1.16)
23C: 23C (CH.1.1)
23D: 23D (XBB.1.9)
23E: 23E (XBB.2.3)
23F: 23F (EG.5.1)
6 changes: 5 additions & 1 deletion defaults/clade_emergence_dates.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -30,6 +30,10 @@ Nextstrain_clade first_sequence
22C 2021-12-01
22D 2022-04-01
22E 2022-07-10
22F 2022-08-01
22F 2022-07-01
23A 2022-10-01
23B 2022-11-01
23C 2022-06-01
23D 2022-08-01
23E 2022-10-01
23F 2023-01-01
4 changes: 4 additions & 0 deletions defaults/clade_hierarchy.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -31,3 +31,7 @@ clade parent WHO
22F 21L Omicron
23A 22F Omicron
23B 22F Omicron
23C 22D Omicron
23D 22F Omicron
23E 22F Omicron
23F 23D Omicron
27 changes: 26 additions & 1 deletion defaults/clades.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -179,4 +179,29 @@ clade gene site alt
23B nuc 12730 A
23B nuc 14856 G
23B nuc 18703 T
23B nuc 28447 G
23B nuc 28447 G

23C clade 22D
23C nuc 3857 A
23C nuc 20741 G
23C nuc 22599 C
23C nuc 22917 G
23C nuc 22893 C
23C nuc 23019 C

23D clade 22F
23D nuc 5720 A
23D nuc 12789 T
23D nuc 28297 C

23E clade 22F
23E nuc 4234 T
23E nuc 23123 T
23E nuc 27431 T

23F clade 23D
23F nuc 2334 T
23F nuc 9693 T
23F nuc 21718 T
23F nuc 22480 T
23F nuc 22930 A
9 changes: 4 additions & 5 deletions defaults/color_ordering.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -34031,25 +34031,24 @@ clade_membership 22E (BQ.1)
clade_membership 22F (XBB)
clade_membership 23A (XBB.1.5)
clade_membership 23B (XBB.1.16)
clade_membership 23C (CH.1.1)
clade_membership 23D (XBB.1.9)
clade_membership 23E (XBB.2.3)
clade_membership 23F (EG.5.1)

################


emerging_lineage BA.2.3.20
emerging_lineage BN.1
emerging_lineage CH.1.1
emerging_lineage XAY
emerging_lineage XBC
emerging_lineage XBB.1.9
emerging_lineage XBB.1.9.1
emerging_lineage XBB.1.9.2
emerging_lineage EG.5
emerging_lineage XBB.1.42
emerging_lineage XBB.1.22.1
emerging_lineage XBB.1.19
emerging_lineage XBB.1.17.1
emerging_lineage FE.1
emerging_lineage XBB.2.3

################

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57 changes: 27 additions & 30 deletions defaults/emerging_lineages.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -181,6 +181,32 @@ clade gene site alt
23B nuc 18703 T
23B nuc 28447 G


23C clade 22D
23C nuc 3857 A
23C nuc 20741 G
23C nuc 22599 C
23C nuc 22917 G
23C nuc 22893 C
23C nuc 23019 C

23D clade 22F
23D nuc 5720 A
23D nuc 12789 T
23D nuc 28297 C

23E clade 22F
23E nuc 4234 T
23E nuc 23123 T
23E nuc 27431 T

23F clade 23D
23F nuc 2334 T
23F nuc 9693 T
23F nuc 22480 T
23F nuc 22930 A


BA.2.3.20 clade 21L
BA.2.3.20 nuc 6770 G
BA.2.3.20 nuc 22332 A
Expand All @@ -207,38 +233,15 @@ XAY nuc 22899 A
XAY nuc 23679 T
XAY nuc 27575 G

CH.1.1 clade 22D
CH.1.1 nuc 3857 A
CH.1.1 nuc 23019 C
CH.1.1 nuc 22599 C
CH.1.1 nuc 20741 G
CH.1.1 nuc 22893 C
CH.1.1 nuc 22917 G

FE.1 clade 22F
FE.1 nuc 3662 G
FE.1 nuc 8001 G
FE.1 nuc 26012 G

XBB.1.9 clade 22F
XBB.1.9 nuc 5720 A
XBB.1.9 nuc 12789 T
XBB.1.9 nuc 28297 C

XBB.1.9.1 clade XBB.1.9
XBB.1.9.1 clade 23D
XBB.1.9.1 nuc 11956 T
XBB.1.9.1 nuc 23018 C

XBB.1.9.2 clade XBB.1.9
XBB.1.9.2 nuc 16878 T
XBB.1.9.2 nuc 23018 C
XBB.1.9.2 nuc 27507 C

XBB.2.3 clade 22F
XBB.2.3 nuc 4234 T
XBB.2.3 nuc 23123 T
XBB.2.3 nuc 27431 T

XBB.1.22.1 clade 22F
XBB.1.22.1 nuc 22161 G
XBB.1.22.1 nuc 23018 C
Expand All @@ -262,9 +265,3 @@ XBB.1.19 nuc 10042 G
XBB.1.19 nuc 21363 T
XBB.1.19 nuc 23018 C
XBB.1.19 nuc 27915 G

EG.5 clade XBB.1.9.2
EG.5 nuc 2334 T
EG.5 nuc 9693 T
EG.5 nuc 22480 T
EG.5 nuc 22930 A
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