23.11.21 | Lineage summaries

AY lineage constellations

We’ve posted constellation files containing the associated mutations for each AY lineage here. These constellation files contain the mutations that have occurred along the phylogenetic path in the UShER global SARS-CoV-2 phylogenetic tree between the root of the tree and the common ancestor of the respective lineage (see figure below) and remain conserved within the lineage (defined as being found in at least 70% of sequences designated to the lineage). These are an extension of the lineage-defining mutations here which are the mutations that separate the lineage from closely related sequences (see figure below). Some constellations also contain an “intermediate” category. These are mutations that drop in and out in the Delta clade so may be associated with the lineage but may also be prone to artefacts.

We’ve posted these constellations for reference. They are not currently used by pangolin or scorpio but should be compatible with scorpio if researchers are interested in exploring them. By contrast, the constellation files used by scorpio (and pangolin) available here are only provided for VOC/VUI or lineages which are being watched. These typically do not include all mutations associated with each lineage, and are often calibrated in line with the PHE definitions of a variant.

Constellation and defining mutations. An example lineage and the branches contributing to its constellation and defining-mutation(s) is shown. The constellation consists of mutations that occur along the red and blue branches from the root of the phylogenetic tree to the common ancestor of the lineage. The mutations on red branches are shared by the lineage and other sequences. The blue branch is immediately ancestral to the lineage ancestor; the mutations on this branch separate the lineage from nearby sequences and are therefore the defining mutations for the lineage.

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