ENH: Avian flu datasets, e.g. H5

[corneliusroemer]

I've received a request for Avian flu datasets e.g. H5, via Twitter DM.

If you'd like this feature, feel free to leave a thumbs up here to signal support.

[ivan-aksamentov]

I wanted to add that if you are reading this and is an expert in Avian flu, consider contributing some of your expertise. Check out:

• data repo: that's where the raw dataset files are stored, processed and deployed to the internet: https://github.com/nextstrain/nextclade_data
• tree preparation repo: that's where reference trees (the tree.json part of the dataset) are prepared (including Augur config): https://github.com/neherlab/nextclade_data_workflows
• dataset docs: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html

[mcroxen]

Agree this would be great. Also swineH1, H7 and H9 schemes if there are acceptable ones would be fantastic.

[mcroxen]

Perhaps relevant, good starting point

swine H1 https://pubmed.ncbi.nlm.nih.gov/27981236/

H5 https://onlinelibrary.wiley.com/doi/10.1111/irv.12230 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4548997/ https://www.who.int/publications/m/item/evolution-of-the-influenza-a(h5)-haemagglutinin-who-oie-fao-h5-working-group-reports-a-new-clade-designated-2.3.4.4 https://cdn.who.int/media/docs/default-source/influenza/who-influenza-recommendations/vcm-northern-hemisphere-recommendation-2022-2023/202203_zoonotic_vaccinevirusupdate.pdf

H7 https://pubmed.ncbi.nlm.nih.gov/30226157/

H9 https://pubmed.ncbi.nlm.nih.gov/31871234/

[ammaraziz]

I also agree that this would be extremely helpful to avian influenza research and surveillance.

@corneliusroemer please let me know what I can do to assist. I can start collating data for H5 for the initial tree.

[Wen1953]

Great idea. It will be very useful for avian influenza research :)

[ivan-aksamentov]

We now have H5 community datasets by @lmoncla and @jordan-ort. Currently there's 3:

community/moncla-lab/iav-h5/ha/all-clades
community/moncla-lab/iav-h5/ha/2.3.2.1
community/moncla-lab/iav-h5/ha/2.3.4.4

• Nextclade Web (all-clades): https://clades.nextstrain.org/?dataset-name=community/moncla-lab/iav-h5/ha/all-clades

• Nextclade CLI: run with --dataset-name= and one of the names from above

• Nextclade data repo: https://github.com/nextstrain/nextclade_data/tree/master/data/community/moncla-lab/iav-h5/ha

• Sources: https://github.com/moncla-lab/h5nx-Clades

Please comment or create a new issue if there's still outstanding questions.