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Mutant Rainbow Tree


Last data update: Sep 18, 2020

See Rainbow trees to track interesting Spike sites

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Position Site of Interest
Region   Site
Clade
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Correlated variant

The "correlated variant" feature can be used to enable tracking mutations that are part of a subclade.

For example, the GR and GH clades are sub-lineages of the G clade (G clade carries 4 mutations and includes the D614G mutation), To track changes in GR or GH frequencies, using the subset of sequences that carries D614G will enable and exploration of how the GR and GH clades are changing within the context of the G614 clade.

The G clade is the dominant form of the SARS COV-2 pandemic as of summer of 2020. It carries with it 4 nucleotide changes reactive to the Wuhan form: C241T, C3037T, C14408T, A23403G
Note: GISAID formally refers to an ancestral state of the G clade with just 3 base changes, as their definition of the G clade: C241T, C3037T, A23403G.
The change mutation at C14408 was part of the set of 4 mutations that were expanded together and now the now dominant G clade. A23403G encodes the D614G mutation.

The GR clade carries the G clade four base changes, plus a 3 contiguous base changes G28881A, G28882A and G28883C. The GR clade includes the S D614G mutation and the N G204R mutation.

The GH clade carries the G clade four base changes, plus the G25563T mutation. The GH clade includes the S D614G mutation and the NS3 (ORF3a) Q57H mutation.

last modified: Tue Sep 1 15:57 2020



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