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.

[AMPByrne]

Hi, the H5 Nextclade datasets have been really useful, thanks for making these available. There's been a recent publication detailing an updated classification for H9 avian influenza viruses (https://pubmed.ncbi.nlm.nih.gov/39043566/). Is anyone interested in developing a Nextclade build for this? I'd be happy to be involved.

[lmoncla]

Hey @AMPByrne! I'm so glad to hear that you are finding the H5 datasets useful. We are definitely planning to expand the same approach out for the H7s and H9s, though we would be happy to have help/collaboration on this. But yes, this is definitely in the plans!

[AMPByrne]

Hi @lmoncla thanks for getting back to me. I made a start with the H9 build just for my own learning and to get a hang of what is needed for the dataset itself. I'm just doing some testing on that but it would be great to collaborate on this if possible.

[ivan-aksamentov]

Hi @AMPByrne,

Nextclade dev here.

Happy that you are considering contributing a dataset!

Don't forget to check the dataset author's guide and feel free to open new GitHub issues if you have concrete questions or encounter problems.

You can share a link to your GitHub repo where you are preparing your datasets, so that people could review and perhaps join the efforts. You can also submit a draft pull request to our data repository, with a link to your source repository so that other people know where the work is being done.

You can also join Nextstrain forums where you can talk to the Nextstrain team and to other Nextstrain and Nextclade users:
https://discussion.nextstrain.org/

uBioinfo Slack is a great place to communicate with the broad international bioinformatics community. Here is an invitation link if you are not there yet:
https://join.slack.com/t/microbial-bioinfo/shared_invite/zt-2tnw3y3aa-18t14MD2N21XG5be~gltVQ

Good luck!

[ivan-aksamentov]

@jurresiegers have opened an issue for H9: #1552. Let's continue the discussion about H9 there.