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Identify "prototype virus" for each putative clade #66

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huddlej opened this issue Aug 31, 2021 · 0 comments
Open

Identify "prototype virus" for each putative clade #66

huddlej opened this issue Aug 31, 2021 · 0 comments
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enhancement New feature or request

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@huddlej
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huddlej commented Aug 31, 2021

Context
Phylogenetic trees of HA/NA help us identify emerging clades that should be tracked by routine surveillance. For each of these emerging clades, we need a way to identify candidate strains for testing by experiment assays like HI, FRA, HINT, etc.

Description
Identify one or more prototype virus strains named for each putative clade (identified as in #65). The prototypes must be real strains. These could represent strains identified computationally or experimentally as the best representatives.

Possible solution
Produce reference alignments with currently circulating diversity and identify the closest strain(s) to each auto-assigned clade. Most likely, these strains will need to be manually curated after the clades are automatically identified.

Consider labeling the auto-assigned clades (from #65) with the names of the prototype strains we curate here.

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