nextclade

Yellow Fever Virus Nextclade Dataset Tree

This workflow creates a phylogenetic tree that can be used as part of a Nextclade dataset to assign clades to yellow fever virus samples based on Mutebi et al. (J Virol. 2001 Aug;75(15):6999-7008) and Bryant et al. (PLoS Pathog. 2007 May 18;3(5):e75).

• Build a tree using samples from the ingest output, with the following sampling criteria:
  • Force-include the following samples:
    • genotype reference strains from the 2 papers cited above
• Assign genotypes to each sample and internal nodes of the tree with augur clades, using clade-defining mutations in defaults/clades.tsv
• Provide the following coloring options on the tree:
  • Genotype assignment from augur clades

The clades we annotate (Clade I-VII) are roughly equivalent with the following genotypes as described in the aforementioned two papers:

Clade	Genotype
Clade I	Angola
Clade II	East Africa
Clade III	East Central/Africa
Clade IV	West Africa I
Clade V	West Africa II
Clade VI	South America I
Clade VII	South America II

(N.b., this table is available as a TSV in this repo, at nextclade/defaults/clade-to-genotype.tsv.)

How to create a new tree

• Run the workflow: nextstrain build .
• Inspect the output tree by comparing genotype assignments from the following sources:
  • augur clades output
• If unwanted samples are present in the tree, add them to defaults/dropped_strains.tsv and re-run the workflow
• If any changes are needed to the clade-defining mutations, add changes to defaults/clades.tsv and re-run the workflow
• Repeat as needed