From 6736a50cfbe080f06bc0d0698278e674f3dc794e Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Thu, 27 Jul 2023 15:02:04 +0200 Subject: [PATCH] Add new lineages to emerging_lineages.tsv and color_ordering.tsv --- defaults/color_ordering.tsv | 9 +- defaults/emerging_lineages.tsv | 327 +++++++++++++++++++-------------- 2 files changed, 194 insertions(+), 142 deletions(-) diff --git a/defaults/color_ordering.tsv b/defaults/color_ordering.tsv index ddf558f1d..b2244e86e 100644 --- a/defaults/color_ordering.tsv +++ b/defaults/color_ordering.tsv @@ -34040,8 +34040,15 @@ emerging_lineage BN.1 emerging_lineage CH.1.1 emerging_lineage XAY emerging_lineage XBC -emerging_lineage FE.1 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 ################ diff --git a/defaults/emerging_lineages.tsv b/defaults/emerging_lineages.tsv index 3b55c4407..d10b40f13 100644 --- a/defaults/emerging_lineages.tsv +++ b/defaults/emerging_lineages.tsv @@ -24,10 +24,10 @@ clade gene site alt 20D nuc 13536 T 20D nuc 23731 T -20E (EU1) clade 20A -20E (EU1) nuc 22227 T -20E (EU1) nuc 28932 T -20E (EU1) nuc 29645 T +20E clade 20A +20E nuc 22227 T +20E nuc 28932 T +20E nuc 29645 T 20F clade 20B 20F nuc 1163 T @@ -45,143 +45,149 @@ clade gene site alt 20G nuc 28472 T 20G nuc 28869 T -20H (Beta, V2) clade 20C -20H (Beta, V2) nuc 23012 A -20H (Beta, V2) nuc 23063 T -20H (Beta, V2) nuc 23403 G -20H (Beta, V2) nuc 26456 T - -20I (Alpha, V1) clade 20B -20I (Alpha, V1) nuc 14676 T -20I (Alpha, V1) nuc 15279 T -20I (Alpha, V1) nuc 23063 T - -20J (Gamma, V3) clade 20B -20J (Gamma, V3) nuc 733 C -20J (Gamma, V3) nuc 2749 T -20J (Gamma, V3) nuc 3828 T -20J (Gamma, V3) nuc 5648 C -20J (Gamma, V3) nuc 12778 T -20J (Gamma, V3) nuc 13860 T - -21A (Delta) clade 20A -21A (Delta) nuc 21618 G -21A (Delta) nuc 26767 C -21A (Delta) nuc 28461 G - -21B (Kappa) clade 20A -21B (Kappa) nuc 17523 T -21B (Kappa) nuc 22917 G -21B (Kappa) nuc 23012 C -21B (Kappa) nuc 27638 C -21B (Kappa) nuc 28881 T -21B (Kappa) nuc 29402 T - -21C (Epsilon) clade 20C -21C (Epsilon) nuc 17014 T -21C (Epsilon) nuc 21600 T -21C (Epsilon) nuc 22018 T -21C (Epsilon) nuc 22917 G - -21D (Eta) clade 20A -21D (Eta) nuc 14407 T -21D (Eta) nuc 20724 G -21D (Eta) nuc 23593 C -21D (Eta) nuc 24224 C -21D (Eta) nuc 24748 T - -21E (Theta) clade 20B -21E (Theta) nuc 12049 T -21E (Theta) nuc 23341 C -21E (Theta) nuc 23604 A -21E (Theta) nuc 24187 A -21E (Theta) nuc 24836 A - -21F (Iota) clade 20C -21F (Iota) nuc 16500 C -21F (Iota) nuc 20262 G -21F (Iota) nuc 21575 T -21F (Iota) nuc 22320 G - -21G (Lambda) clade 20D -21G (Lambda) nuc 21786 T -21G (Lambda) nuc 21789 T -21G (Lambda) nuc 22917 A -21G (Lambda) nuc 23031 C - -21H (Mu) clade 20A -21H (Mu) nuc 3428 G -21H (Mu) nuc 4878 T -21H (Mu) nuc 11451 G -21H (Mu) nuc 13057 T -21H (Mu) nuc 17491 T -21H (Mu) nuc 27925 A - -21I (Delta) clade 21A (Delta) -21I (Delta) nuc 5184 T -21I (Delta) nuc 9891 T -21I (Delta) nuc 22227 T - -21J (Delta) clade 21A (Delta) -21J (Delta) nuc 11332 G -21J (Delta) nuc 19220 T - -21K (Omicron) clade 21M (Omicron) -21K (Omicron) nuc 15240 T -21K (Omicron) nuc 23202 A -21K (Omicron) nuc 23525 T -21K (Omicron) nuc 27259 C - -21L (Omicron) clade 21M (Omicron) -21L (Omicron) nuc 21618 T -21L (Omicron) nuc 22775 A - -21M (Omicron) clade 20B -21M (Omicron) nuc 18163 G -21M (Omicron) nuc 23599 G - -22A (Omicron) clade 21L (Omicron) -22A (Omicron) nuc 12160 A -22A (Omicron) nuc 9866 C -22A (Omicron) nuc 28724 T - -22B (Omicron) clade 21L (Omicron) -22B (Omicron) nuc 12160 A -22B (Omicron) nuc 9866 C -22B (Omicron) nuc 27259 A - -22C (Omicron) clade 21L (Omicron) -22C (Omicron) nuc 22917 A -22C (Omicron) nuc 23673 T - -22D (Omicron) clade 21L (Omicron) -22D (Omicron) nuc 3796 T -22D (Omicron) nuc 26275 G - -22E (Omicron) clade 22B (Omicron) -22E (Omicron) nuc 14257 C -22E (Omicron) nuc 16935 A -22E (Omicron) nuc 28312 T -22E (Omicron) nuc 22942 A - -22F (Omicron) clade 21L (Omicron) -22F (Omicron) nuc 15461 A -22F (Omicron) nuc 17859 C -22F (Omicron) nuc 23019 C -22F (Omicron) nuc 26275 G - -23A (Omicron) clade 22F (Omicron) -23A (Omicron) nuc 22317 T -23A (Omicron) nuc 23018 C -23A (Omicron) nuc 27915 T - -BA.2.3.20 clade 21L (Omicron) +20H clade 20C +20H nuc 23012 A +20H nuc 23063 T +20H nuc 23403 G +20H nuc 26456 T + +20I clade 20B +20I nuc 14676 T +20I nuc 15279 T +20I nuc 23063 T + +20J clade 20B +20J nuc 733 C +20J nuc 2749 T +20J nuc 3828 T +20J nuc 5648 C +20J nuc 12778 T +20J nuc 13860 T + +21A clade 20A +21A nuc 21618 G +21A nuc 26767 C +21A nuc 28461 G + +21B clade 20A +21B nuc 17523 T +21B nuc 22917 G +21B nuc 23012 C +21B nuc 27638 C +21B nuc 28881 T +21B nuc 29402 T + +21C clade 20C +21C nuc 17014 T +21C nuc 21600 T +21C nuc 22018 T +21C nuc 22917 G + +21D clade 20A +21D nuc 14407 T +21D nuc 20724 G +21D nuc 23593 C +21D nuc 24224 C +21D nuc 24748 T + +21E clade 20B +21E nuc 12049 T +21E nuc 23341 C +21E nuc 23604 A +21E nuc 24187 A +21E nuc 24836 A + +21F clade 20C +21F nuc 16500 C +21F nuc 20262 G +21F nuc 21575 T +21F nuc 22320 G + +21G clade 20D +21G nuc 21786 T +21G nuc 21789 T +21G nuc 22917 A +21G nuc 23031 C + +21H clade 20A +21H nuc 3428 G +21H nuc 4878 T +21H nuc 11451 G +21H nuc 13057 T +21H nuc 17491 T +21H nuc 27925 A + +21I clade 21A +21I nuc 5184 T +21I nuc 9891 T +21I nuc 22227 T + +21J clade 21A +21J nuc 11332 G +21J nuc 19220 T + +21K clade 21M +21K nuc 15240 T +21K nuc 23202 A +21K nuc 23525 T +21K nuc 27259 C + +21L clade 21M +21L nuc 21618 T +21L nuc 22775 A + +21M clade 20B +21M nuc 18163 G +21M nuc 23599 G + +22A clade 21L +22A nuc 12160 A +22A nuc 9866 C +22A nuc 28724 T + +22B clade 21L +22B nuc 12160 A +22B nuc 9866 C +22B nuc 27259 A + +22C clade 21L +22C nuc 22917 A +22C nuc 23673 T + +22D clade 21L +22D nuc 3796 T +22D nuc 26275 G + +22E clade 22B +22E nuc 14257 C +22E nuc 16935 A +22E nuc 28312 T +22E nuc 22942 A + +22F clade 21L +22F nuc 15461 A +22F nuc 17859 C +22F nuc 23019 C +22F nuc 26275 G + +23A clade 22F +23A nuc 22317 T +23A nuc 23018 C +23A nuc 27915 T + +23B clade 22F +23B nuc 12730 A +23B nuc 14856 G +23B nuc 18703 T +23B nuc 28447 G + +BA.2.3.20 clade 21L BA.2.3.20 nuc 6770 G BA.2.3.20 nuc 22332 A BA.2.3.20 nuc 17678 T BA.2.3.20 nuc 23013 G -BN.1 clade 22D (Omicron) +BN.1 clade 22D BN.1 nuc 22599 C BN.1 nuc 22629 C BN.1 nuc 23031 C @@ -201,7 +207,7 @@ XAY nuc 22899 A XAY nuc 23679 T XAY nuc 27575 G -CH.1.1 clade 22D (Omicron) +CH.1.1 clade 22D CH.1.1 nuc 3857 A CH.1.1 nuc 23019 C CH.1.1 nuc 22599 C @@ -209,17 +215,56 @@ CH.1.1 nuc 20741 G CH.1.1 nuc 22893 C CH.1.1 nuc 22917 G -FE.1 clade 22F (Omicron) +FE.1 clade 22F FE.1 nuc 3662 G FE.1 nuc 8001 G FE.1 nuc 26012 G -XBB.1.9 clade 22F (Omicron) +XBB.1.9 clade 22F XBB.1.9 nuc 5720 A XBB.1.9 nuc 12789 T XBB.1.9 nuc 28297 C -XBB.2.3 clade 22F (Omicron) +XBB.1.9.1 clade XBB.1.9 +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 \ No newline at end of file +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 +XBB.1.22.1 nuc 28297 C + +XBB.1.42 clade 22F +XBB.1.42 nuc 5720 A +XBB.1.42 nuc 12789 T +XBB.1.42 nuc 16878 T +XBB.1.42 nuc 23401 G +XBB.1.42 nuc 28297 C + +XBB.1.17.1 clade 22F +XBB.1.17.1 nuc 1670 T +XBB.1.17.1 nuc 22205 C +XBB.1.17.1 nuc 23018 C +XBB.1.17.1 nuc 27995 C + +XBB.1.19 clade 22F +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 \ No newline at end of file