Phylogenetic results and resources are described in this blog post: 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've continued to track evolution and spread of H5N1 in cattle at as data has been shared by @USDA_APHIS. 1/3

We also include a new Nextclade dataset to call measles genotype at This work is described on the Nextstrain blog at

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 as well as the N450 segment at 1/2

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:

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: Or open a Github issue: 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.

We have a migration guide to help you transition from v2 to v3 here: Full release notes are available on Github: Nextclade docs have been updated for v3: 7/9.

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: 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.

To facilitate discovery of datasets and guide users to the most suitable dataset, Nextclade quickly compares kmers from the input sequence to an index and highlights good matches. The CLI has a sub-command `sort` that will split input sequences into suitable subsets. 4/9

Instead of just attaching sequences to the reference tree, Nextclade now resolves phylogenetic structure in the analyzed sequences. This makes the tree view much more informative. [Caveat: it’s a greedy tree builder that’s not a substitute for proper phylogenetics.]. 3/9

With the support for splicing and slippage, we can now provide a dataset that annotates all mature proteins of SARS-CoV-2. Going forward, this enables datasets for HIV or Hepatitis B virus. 2/9

After many months of work, we are releasing Nextclade v3 with major changes:.- Splicing, slippage, and circular genomes.- Local tree-building.- Auto-suggestion of suitable datasets.- Align more divergent sequences.- Community datasets. (desktop only) .1/9

23I (BA.2.86), the parent of 23G (XBB.1.5.70) - XBB.1.5 - and the ancestor of 23H (HK.3) - EG.5 - have all been designated as Variants of Interest (VOI) by @WHO. More information by WHO TAG-VE can be seen here:. 9/9.

Additionally, we've updated the Nextclade datasets to appropriately call clade 23G, 23H, and 23I viruses at If you use #Nextclade in the browser, make sure to reload the tab from time to time so that you get the most recent datasets. 8/9

The growth patterns of all these lineages mean they meet our designation criteria, & the mutation profiles also support a public health interest in designation. Further rationale for the decision to designate these clades can be found here: 7/9.

You can take a closer look at 23G, 23H, and 23I in the 2-month Nextstrain build below:. 6/9

23I (BA.2.86) sublineage JN.1 (sometimes referred to as 'Pirola') has extra RBD mutation L455S & shows a further increase in growth. It likely emerged in Europe, where it is most common, and makes up around half of all 23I sequences. 5/9