Nextstrain

Nextstrain is happy to announce a major update to our tuberculosis analysis, making it our first real-time (continually updated) analysis for a bacterial pathogen. Please see our new blog post for details: nextstrain.org/blog/2025-11-1…

Full blog post explaining situation and background is available here: nextstrain.org/blog/2025-11-0…

Closing these public analyses puts the world more in the dark and concretely harms surveillance as it becomes more difficult for variant spotters to contribute to global situational awareness. 4/5

On Oct 1, 2025, @GISAID informed us that they had ended updates to the flat file of SARS-CoV-2 genomic sequences and associated metadata that we had used to update Nextstrain analyses since Feb 2020. GISAID's stated rationale was that their "resources are limited". 1/5

@0bFuSc8 @USDA_APHIS @LouiseHMoncla @RajlabN Thanks to quick work by Karthik G and Praneeth G to update SRA assemblies at github.com/andersen-lab/a…, we now have house mouse sequences up at the live site at nextstrain.org/avian-flu/h5n1…

@nextstrain @USDA_APHIS @LouiseHMoncla @RajlabN You're very welcome! Yes, seems like USDA created a new/ separate BioProject for sequences from peridomestic animals. LMK if you figure out what animal that "HOSP" sequence is from 😅😅😅

We've continued to track evolution and spread of H5N1 in cattle at nextstrain.org/avian-flu/h5n1… as data has been shared by @USDA_APHIS. 1/3

@0bFuSc8 @USDA_APHIS @LouiseHMoncla @RajlabN Thanks for the pointer! It looks like these 4 sequences are in a separate USDA BioProject (ncbi.nlm.nih.gov/bioproject/PRJ…) from the primary USDA BioProject for the cattle sequences (ncbi.nlm.nih.gov/bioproject/PRJ…). BioProject PRJNA1122849 wasn't included in ingest. We'll look into including.

@nextstrain @USDA_APHIS @LouiseHMoncla 2/2 Based on @RajlabN's tweets: x.com/RajlabN/status…

@0bFuSc8 @USDA_APHIS @LouiseHMoncla Looking now, I don't see "mouse" represented in NCBI GenBank sequences, NCBI SRA sequences or GISAID sequences. If you have an accession that would be helpful.

@nextstrain @USDA_APHIS Have the house mouse #H5N1 sequences (I think there were 2) made it to the @nextstrain builds yet? I didn't see any but easily could've missed them. @LouiseHMoncla

Phylogenetic results and resources are described in this blog post: nextstrain.org/blog/2024-06-1… 3/3

We've set up automated ingest routines to combine data from NCBI GenBank with data from the SRA. Including SRA data allows for a more up-to-date view of evolution. 2/3

We also include a new Nextclade dataset to call measles genotype at clades.nextstrain.org/?dataset-name=…. This work is described on the Nextstrain blog at nextstrain.org/blog/2024-06-1….

Thanks to work by Kim Andrews, we've recently updated our analyses and resources for measles virus. We now include automatically updated views of evolution of both the full genome at nextstrain.org/measles/genome as well as the N450 segment at nextstrain.org/measles/N450. 1/2

@eyalherlin We've been generally mirroring content between here and Mastodon (quiet there as well since Jan). We'd plan to continue this pattern of posting to both for the time being.

@nextstrain Are you back to being active here or is mastodon the place to get updates?

We've been less active on Twitter / X for the last few months. A decent summary of recent Nextstrain activities and future directions can be seen in our annual update posted to the blog in March: nextstrain.org/blog/2024-03-2…

We hope that this will enable many exciting applications in the future. Let us know if anything doesn’t work, what you like or don’t like, and what can be improved! Ask a question on: discussion.nextstrain.org Or open a Github issue: github.com/nextstrain/nex… 9/9

This was an enormous amount of work. Congratulations to @ivan_aksamentov, @corneliusroemer and the @nextstrain team for pushing it across the finish line! 8/9

Nextclade might be useful for many more viruses that our team can support. We therefore added the possibility of community datasets and hope that some of you will contribute datasets! We have a new tutorial to help get started: github.com/nextstrain/nex… 6/9

The seed matching step of the pairwise alignment now copes with sequences up to 15% divergence such that diverse viruses like HIV-1 can be aligned. 5/9