This repository contains descriptions of constellations of mutations for the SARS-CoV-2 virus.
A constellation is a collection of mutations which are functionally meaningful, but which may arise independently a number of times.
Here we include files that define:
- lineages of concern - for these lineages, the defining mutations have been extracted so that individual sequences can be classified deterministically
- genomically interesting regions e.g. RBD sites which interact with ACE2
In addition we include a JSON file describing the reference sequence and the coordinates of genes/proteins. Mutations can therefore be described with respect to the amino acid position within these features.
At a minimum, JSON files must contain the following:
label
: a unique string to represent the constellationsites
: a list of defining mutationsrules
: the rules used by scorpio to classify whether a sequence belongs to a constellation
The general format of a mutation code is: gene
:[ref
]coordinates
[alt
] where gene
is a gene code (or nuc
for the genomic nucleotide sequence), ref
is the nucleotide or amino acids in the reference, alt
is the specific nucleotide or amino acid for the mutatant. Either of ref
or alt
can be missing if no specific state is required. See https://github.com/cov-lineages/scorpio for more definitions.
Rules can either specify [min|max]_[ref|alt|ambig|oth] OR the call required at a mutation e.g. "N:S235F": (not )[ref|alt|ambig|oth]
description
: human readable string of informationsources
: reference material for the definition where appropriatetype
: at present all definitions are of typevariant
although we conceived of having constellations investigating e.g. furin cleavage sitesvariant
: for all constellations of type variant, information which exists because it is a variant. e.g.mrca_lineage
: the pangolin-lineage of the MRCA of the constellationPHE_label
: PHE label where appropriateWHO_label
: WHO label where appropriatelineage_name
andparent_lineage
are used together to allow scorpio to handle parent/child constellations. Without them, a parent would be favoured over a child lineage as having all the defining sites instead of possibly missing a few. Theparent_lineage
says that the constellation should only be called if the parent has also been called and should be favoured over the parent if it has enough support. Thelineage_name
should be in the same format. Note there are constellations which include multiple lineages, for which this would not work.incompatible_lineage_calls
: used bypangolin
usually in the context of a parent/child relationship. This tells pangolin that ifscorpio
called the given (parent) lineage andpangolin
called the incompatible (child) lineage, thescorpio
lineage should override. The default behaviour inpangolin
is to allow children of a constellation called byscorpio
as we want to allow a VOC/VUI to continue to evolve and have descendant lineages. However in these cases where we have a constellation for a child lineage, we care about lineage calls meeting a very specific definition so we want thescorpio
call to override.tags
: any other names given to this constellationPango_lineages
: unused, human-readable list of relevant tango-lineagesrepresentative_genome
: may be used in future, a genome representing the mutations
ancestral_sites
: definitions created withscorpio define
may use an outgroup to partition sites into those that are defining and those that belonged to the outgroup and predate this new variant. These sites are included when classifying (includingpangolin
) but not when runningscorpio haplotype
intermediate_sites
: definitions created withscorpio define
use a default threshold of 98% when defining mutation sites. e.g. a mutation has to be present in 98% of defining sequences to be included. If it appears below this threshold in more than 25% of defining sequences, we list it as an intermediate site. These are for reference for a manual curation step