From b9e8c11904ae602757dbffb834495ed28933fa4f Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Wed, 29 Nov 2023 17:27:08 +0100 Subject: [PATCH] Add ACE2 binding to BA.2.86, fix XBB ACE2 json --- .../sars-cov-2/BA.2.86/pathogen.json | 4451 ++++++++- data/nextstrain/sars-cov-2/XBB/pathogen.json | 8854 +++++++++-------- 2 files changed, 8877 insertions(+), 4428 deletions(-) diff --git a/data/nextstrain/sars-cov-2/BA.2.86/pathogen.json b/data/nextstrain/sars-cov-2/BA.2.86/pathogen.json index 3212ac85..5249dbab 100644 --- a/data/nextstrain/sars-cov-2/BA.2.86/pathogen.json +++ b/data/nextstrain/sars-cov-2/BA.2.86/pathogen.json @@ -6333,5 +6333,4452 @@ "authors": [ "Nextstrain team " ] - } -} + }, + "phenotypeData": [ + { + "aaRange": { + "begin": 330, + "end": 531 + }, + "data": [ + { + "name": "binding", + "weight": 1.0, + "locations": { + "330": { + "A": -0.08339, + "C": -0.61624, + "D": -0.1467, + "E": -0.14146, + "F": -0.53604, + "G": -0.14484, + "H": -0.19436, + "I": -0.46421, + 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"V": 0.02916, + "W": -0.02102, + "Y": 0.02543 + }, + "530": { + "A": -0.00165, + "C": -0.07587, + "D": 0.01072, + "E": -0.03799, + "F": -0.0569, + "G": 0.01716, + "H": -0.00595, + "I": 0.03046, + "K": 0.04674, + "L": 0.00106, + "M": -0.03732, + "N": 0.03836, + "P": -0.02462, + "Q": 0.0426, + "R": -0.02103, + "S": 0.04801, + "T": 0.0, + "V": 0.04638, + "W": -0.01288, + "Y": 0.05943 + } + } + } + ], + "description": "This column displays the predicted impact of RBD mutations on ACE2 binding, relative to a BA.2 baseline.\nA score is in log10 space. Hence a score of +1 should be interpreted as 10x higher affinity.\nThe score assumes that mutations do not interact. The underlying data looked at the impact of each mutation independently.\nThe score is calculated using the same data and logic as Bloom lab's ACE2 binding calculator (see https://doi.org/10.1101/2022.09.20.508745).", + "gene": "S", + "ignore": { + "clades": [ + "outgroup" + ] + }, + "name": "ace2_binding", + "nameFriendly": "ACE2 binding" + } + ] +} \ No newline at end of file diff --git a/data/nextstrain/sars-cov-2/XBB/pathogen.json b/data/nextstrain/sars-cov-2/XBB/pathogen.json index 4ee6129c..f0d33a6c 100644 --- a/data/nextstrain/sars-cov-2/XBB/pathogen.json +++ b/data/nextstrain/sars-cov-2/XBB/pathogen.json @@ -42736,4434 +42736,4436 @@ "begin": 330, "end": 531 }, - "data": { - "name": "binding", - "weight": 1.0, - "locations": { - "330": { - "A": -0.08339, - "C": -0.61624, - "D": -0.1467, - "E": -0.14146, - "F": -0.53604, - "G": -0.14484, - "H": -0.19436, - "I": -0.46421, - "K": -0.09607, - "L": -0.55369, - "M": -0.25741, - "N": 0.0, - "P": -0.06521, - "Q": -0.13873, - "R": 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displays the predicted impact of RBD mutations on ACE2 binding, relative to a BA.2 baseline.\nA score is in log10 space. Hence a score of +1 should be interpreted as 10x higher affinity.\nThe score assumes that mutations do not interact. The underlying data looked at the impact of each mutation independently.\nThe score is calculated using the same data and logic as Bloom lab's ACE2 binding calculator (see https://doi.org/10.1101/2022.09.20.508745).", "gene": "S", "ignore": {