What is a lineage?
As described in Rambaut et al. (2020), a Pango lineage is as a cluster of sequences that are associated with an epidemiological event, for instance an introduction of the virus into a distinct geographic area with evidence of onward spread. Lineages are designed to capture the emerging edge of the pandemic and are at a fine-grain resolution suitable to genomic epidemiological surveillance and outbreak investigation.
*Note that C.1 is equivalent to B.188.8.131.52, with C being an alias for B.1.1.1 to shorten the name so it does not become infinitely long while still preserving the link to the parent lineages
Is this cluster of sequences a new lineage?
- Monophyly and cluster together on the global tree
- Convincing support values on the base node of the lineage (e.g. transfer bootstrap or ultrafast bootstrap)
- Epidemiological support (e.g. location, travel history)
- Introduction into a novel geographic region
- Evidence of circulation in that region (i.e. internal nodes within the lineage)
- A defining SNP