Thank you for this great resource!
Does anyone know where the nomenclature of the RSV genotypes based on FG is coming from? For RSV-A some clade names start with A.D. I have looked at Ramaekers et al. (2020) but was not able to find that nomenclature. rsv/config/clades_genome_a.tsv at master · nextstrain/rsv · GitHub, does seem to have the same nomenclature as Ramaekers (e.g. A1-A23 for RSV-A).
Thank you in advance!
Thomas
Welcome @Thomas and thanks for your great question!
Can you confirm that you were looking at this Nextstrain tree: auspice?
The default clades include A.D and you’re right that this doesn’t match the clades.tsv that is linked from the description at the bottom of the build: rsv/config/clades_genome_a.tsv at master · nextstrain/rsv · GitHub
The clade nomenclature shown is the new “consortium” clade system under active development. You can find the Github repo defining the clades here: GitHub - rsv-lineages/lineage-designation-A: RSV-A lineage definitions and proposals It’s a 3rd clade system, that uses lineage identifiers inspired by Pango lineages. As the clade system is still in beta stage there’s not yet an extensive specification out there.
I will open an issue on the RSV-A Github repo that the description needs to be updated. Thanks for noticing this and bringing it to our attention!
Should be fixed soon: fix: Update description to point to new clade nomenclature by corneliusroemer · Pull Request #48 · nextstrain/rsv · GitHub
Thanks for reporting @Thomas!
Hi Cornelius,
Yes, this is the tree I looked at. Thanks a lot for pointing me to the Github repo defining the clades!
Best,
Thomas
