From 2e7bd3d6c0ab1f6405b203c8ed0710ff84779b1f Mon Sep 17 00:00:00 2001 From: Trevor Bedford Date: Tue, 12 Apr 2022 20:04:03 -0700 Subject: [PATCH 1/3] Update emerging lineages Current emerging lineages are quite outdated. This isn't as comprehensive as we might like things, but it's a good start. --- defaults/emerging_lineages.tsv | 224 ++++----------------------------- 1 file changed, 25 insertions(+), 199 deletions(-) diff --git a/defaults/emerging_lineages.tsv b/defaults/emerging_lineages.tsv index b14072138..a091e484c 100644 --- a/defaults/emerging_lineages.tsv +++ b/defaults/emerging_lineages.tsv @@ -1,201 +1,27 @@ clade gene site alt -AY.4.2 (Delta) nuc 22917 G -AY.4.2 (Delta) nuc 22995 A -AY.4.2 (Delta) nuc 24410 A -AY.4.2 (Delta) nuc 27638 C -AY.4.2 (Delta) nuc 28881 T -AY.4.2 (Delta) nuc 29402 T -AY.4.2 (Delta) S 222 V -AY.4.2 (Delta) S 145 H - -AY.34 (Delta) nuc 22917 G -AY.34 (Delta) nuc 22995 A -AY.34 (Delta) nuc 24410 A -AY.34 (Delta) nuc 27638 C -AY.34 (Delta) nuc 28881 T -AY.34 (Delta) nuc 29402 T -AY.34 (Delta) nuc 9441 T -AY.34 (Delta) S 677 H - -AY.36 (Delta) nuc 22917 G -AY.36 (Delta) nuc 22995 A -AY.36 (Delta) nuc 24410 A -AY.36 (Delta) nuc 27638 C -AY.36 (Delta) nuc 28881 T -AY.36 (Delta) nuc 15628 C -AY.36 (Delta) nuc 21846 T -AY.36 (Delta) nuc 28461 G - -AY.39 + S:1073N (Delta) nuc 22917 G -AY.39 + S:1073N (Delta) nuc 22995 A -AY.39 + S:1073N (Delta) nuc 24410 A -AY.39 + S:1073N (Delta) nuc 27638 C -AY.39 + S:1073N (Delta) nuc 28881 T -AY.39 + S:1073N (Delta) nuc 27604 A -AY.39 + S:1073N (Delta) S 1073 N - -B.1.1.529 (Omicron) nuc 8782 C -B.1.1.529 (Omicron) nuc 14408 T -B.1.1.529 (Omicron) nuc 23403 G -B.1.1.529 (Omicron) nuc 28881 A -B.1.1.529 (Omicron) nuc 28882 A -B.1.1.529 (Omicron) nuc 23525 T -B.1.1.529 (Omicron) nuc 23599 G -B.1.1.529 (Omicron) nuc 27259 C - -BA.2 (Omicron) nuc 8782 C -BA.2 (Omicron) nuc 14408 T -BA.2 (Omicron) nuc 23403 G -BA.2 (Omicron) nuc 28881 A -BA.2 (Omicron) nuc 28882 A -BA.2 (Omicron) nuc 21618 T -BA.2 (Omicron) nuc 22775 A -BA.2 (Omicron) nuc 23525 T -BA.2 (Omicron) nuc 23599 G -BA.2 (Omicron) nuc 24424 T -BA.2 (Omicron) nuc 27259 C - -BA.1 (Omicron) nuc 8782 C -BA.1 (Omicron) nuc 14408 T -BA.1 (Omicron) nuc 23403 G -BA.1 (Omicron) nuc 28881 A -BA.1 (Omicron) nuc 28882 A -BA.1 (Omicron) nuc 15240 T -BA.1 (Omicron) nuc 23202 A -BA.1 (Omicron) nuc 23525 T -BA.1 (Omicron) nuc 23599 G -BA.1 (Omicron) nuc 24424 T -BA.1 (Omicron) nuc 27259 C - -19A nuc 8782 C -19A nuc 14408 C - -19B nuc 8782 T -19B nuc 28144 C - -20A nuc 8782 C -20A nuc 14408 T -20A nuc 23403 G - -20B nuc 8782 C -20B nuc 14408 T -20B nuc 23403 G -20B nuc 28881 A -20B nuc 28882 A - -20C nuc 1059 T -20C nuc 8782 C -20C nuc 14408 T -20C nuc 23403 G -20C nuc 25563 T - -20D nuc 4002 T -20D nuc 10097 A -20D nuc 13536 T -20D nuc 23731 T - -20E (EU1) nuc 8782 C -20E (EU1) nuc 14408 T -20E (EU1) nuc 23403 G -20E (EU1) nuc 22227 T -20E (EU1) nuc 28932 T -20E (EU1) nuc 29645 T - -20F nuc 1163 T -20F nuc 7540 C -20F nuc 16647 T -20F nuc 18555 T -20F nuc 22992 A -20F nuc 23401 A - -20G nuc 10319 T -20G nuc 18424 G -20G nuc 21304 T -20G nuc 25907 T -20G nuc 27964 T -20G nuc 28472 T -20G nuc 28869 T - -20H (Beta, V2) nuc 1059 T -20H (Beta, V2) nuc 8782 C -20H (Beta, V2) nuc 14408 T -20H (Beta, V2) nuc 23403 G -20H (Beta, V2) nuc 25563 T -20H (Beta, V2) nuc 23063 T -20H (Beta, V2) nuc 23012 A -20H (Beta, V2) nuc 26456 T - -20I (Alpha, V1) nuc 8782 C -20I (Alpha, V1) nuc 14408 T -20I (Alpha, V1) nuc 23403 G -20I (Alpha, V1) nuc 28881 A -20I (Alpha, V1) nuc 28882 A -20I (Alpha, V1) nuc 23063 T -20I (Alpha, V1) nuc 14676 T -20I (Alpha, V1) nuc 15279 T - -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) nuc 22917 G -21A (Delta) nuc 22995 A -21A (Delta) nuc 27638 C -21A (Delta) nuc 28881 T -21A (Delta) nuc 29402 T - -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) nuc 17014 T -21C (Epsilon) nuc 21600 T -21C (Epsilon) nuc 22018 T -21C (Epsilon) nuc 22917 G - -21D (Eta) nuc 14407 T -21D (Eta) nuc 21717 G -21D (Eta) nuc 24224 C -21D (Eta) nuc 24748 T - -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) nuc 16500 C -21F (Iota) nuc 20262 G -21F (Iota) nuc 21575 T -21F (Iota) nuc 22320 G - -21G (Lambda) nuc 21786 T -21G (Lambda) nuc 21789 T -21G (Lambda) nuc 22917 A -21G (Lambda) nuc 23031 C - -21H (Mu) nuc 11451 G -21H (Mu) nuc 13057 T -21H (Mu) nuc 17491 T -21H (Mu) nuc 21995 A -21H (Mu) nuc 21993 C -21H (Mu) nuc 22599 A - -21I (Delta) nuc 5184 T -21I (Delta) nuc 9891 T -21I (Delta) nuc 11418 C -21I (Delta) nuc 11514 T -21I (Delta) nuc 22227 T - -21J (Delta) nuc 4181 T -21J (Delta) nuc 11201 G -21J (Delta) nuc 11332 G -21J (Delta) nuc 19220 T -21J (Delta) nuc 27874 T +BA.1.1 nuc 8782 C +BA.1.1 nuc 14408 T +BA.1.1 nuc 18163 G +BA.1.1 nuc 23403 G +BA.1.1 nuc 28881 A +BA.1.1 nuc 28882 A +BA.1.1 nuc 15240 T +BA.1.1 nuc 23202 A +BA.1.1 nuc 23525 T +BA.1.1 nuc 23599 G +BA.1.1 nuc 27259 C +BA.1.1 nuc 2470 T +BA.1.1 nuc 22599 A + +BA.2.3 nuc 8782 C +BA.2.3 nuc 14408 T +BA.2.3 nuc 18163 G +BA.2.3 nuc 23403 G +BA.2.3 nuc 28881 A +BA.2.3 nuc 28882 A +BA.2.3 nuc 21618 T +BA.2.3 nuc 22775 A +BA.2.3 nuc 23599 G +BA.2.3 nuc 8991 T +BA.2.3 nuc 25810 T From 358589cbbe0c0f3bb72e7bddcfd1339e3f6b5d14 Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Wed, 13 Apr 2022 22:53:36 +0200 Subject: [PATCH 2/3] feat: add BA.4 and BA.5 to emerging lineages --- defaults/emerging_lineages.tsv | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/defaults/emerging_lineages.tsv b/defaults/emerging_lineages.tsv index a091e484c..130910941 100644 --- a/defaults/emerging_lineages.tsv +++ b/defaults/emerging_lineages.tsv @@ -25,3 +25,29 @@ BA.2.3 nuc 22775 A BA.2.3 nuc 23599 G BA.2.3 nuc 8991 T BA.2.3 nuc 25810 T + +BA.4 nuc 8782 C +BA.4 nuc 14408 T +BA.4 nuc 18163 G +BA.4 nuc 23403 G +BA.4 nuc 28881 A +BA.4 nuc 28882 A +BA.4 nuc 21618 T +BA.4 nuc 22775 A +BA.4 nuc 23599 G +BA.4 nuc 12160 A +BA.4 nuc 9866 C +BA.4 nuc 27788 T + +BA.5 nuc 8782 C +BA.5 nuc 14408 T +BA.5 nuc 18163 G +BA.5 nuc 23403 G +BA.5 nuc 28881 A +BA.5 nuc 28882 A +BA.5 nuc 21618 T +BA.5 nuc 22775 A +BA.5 nuc 23599 G +BA.5 nuc 12160 A +BA.5 nuc 9866 C +BA.5 nuc 27259 A From 9001e9d598978535264daaee356dc326514c58b0 Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Wed, 13 Apr 2022 23:03:26 +0200 Subject: [PATCH 3/3] feat: adding S:L452 BA.2s to emerging lineages --- defaults/emerging_lineages.tsv | 50 ++++++++++++++++++++++++++++++++++ 1 file changed, 50 insertions(+) diff --git a/defaults/emerging_lineages.tsv b/defaults/emerging_lineages.tsv index 130910941..181612dfb 100644 --- a/defaults/emerging_lineages.tsv +++ b/defaults/emerging_lineages.tsv @@ -51,3 +51,53 @@ BA.5 nuc 23599 G BA.5 nuc 12160 A BA.5 nuc 9866 C BA.5 nuc 27259 A + +BA.2.9.1 nuc 8782 C +BA.2.9.1 nuc 14408 T +BA.2.9.1 nuc 18163 G +BA.2.9.1 nuc 23403 G +BA.2.9.1 nuc 28881 A +BA.2.9.1 nuc 28882 A +BA.2.9.1 nuc 21618 T +BA.2.9.1 nuc 22775 A +BA.2.9.1 nuc 23599 G +BA.2.9.1 nuc 22916 A +BA.2.9.1 nuc 24433 G +BA.2.9.1 nuc 3610 C + +BA.2.12.1 nuc 8782 C +BA.2.12.1 nuc 14408 T +BA.2.12.1 nuc 18163 G +BA.2.12.1 nuc 23403 G +BA.2.12.1 nuc 28881 A +BA.2.12.1 nuc 28882 A +BA.2.12.1 nuc 21618 T +BA.2.12.1 nuc 22775 A +BA.2.12.1 nuc 23599 G +BA.2.12.1 nuc 22917 A +BA.2.12.1 nuc 11674 T +BA.2.12.1 nuc 21721 T + +BA.2.13 nuc 8782 C +BA.2.13 nuc 14408 T +BA.2.13 nuc 18163 G +BA.2.13 nuc 23403 G +BA.2.13 nuc 28881 A +BA.2.13 nuc 28882 A +BA.2.13 nuc 21618 T +BA.2.13 nuc 22775 A +BA.2.13 nuc 23599 G +BA.2.13 nuc 22916 A +BA.2.13 nuc 23767 G + +BA.2.13 nuc 8782 C +BA.2.13 nuc 14408 T +BA.2.13 nuc 18163 G +BA.2.13 nuc 23403 G +BA.2.13 nuc 28881 A +BA.2.13 nuc 28882 A +BA.2.13 nuc 21618 T +BA.2.13 nuc 22775 A +BA.2.13 nuc 23599 G +BA.2.13 nuc 22917 A +BA.2.13 nuc 7820 C