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COVID-19 Viral Genome Analysis Pipeline
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Mutant Rainbow Tree

Last data update: Jul 31, 2021

See Rainbow trees to track interesting Spike sites

Position Site of Interest
Region   Site
Make a tree using correlated variant sequences help use only sequences with   do not use all sequences with
         Site   AA
use all sequences  
Ignore X or -

Lineage definitions

This tool lists CoV-2 lineages as defined by Pangolin ( The WHO Greek letter designations are in parentheses.

Correlated variants

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

As an example, one can use this tool to explore how often the E484K mutation is increasing or decreasing in the world at any geographic level based on all Spike backbones using just the top part of the tool, and with the default “Correlated variant” setting of “Do not consider”.

But one of the contexts in which the E484K mutation can be found in is in the B.1.1.7 variant Spike backbone; B.1.1.7 tends in increase in frequency once it has entered a population, and one can explore how this compares to E484K+B.1.1.7. This tool will identify all geographic locations in GISAID that have more than 10 examples of the E484K+B.1.1.7, and will determine if the fraction of E484+B.1.1.7 is increasing or decreasing relative to other forms of B.1.1.7 over time in those populations.

last modified: Tue Mar 9 09:14 2021

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