Louise H. Moncla

1/ 🚀 Exciting news: we’ve just released the first Nextclade dataset for Enterovirus D68 (EV-D68), developed in collaboration with the European Non-Polio Enterovirus Network (ENPEN).

👉🏻 Check out the dataset on Nextclade! clades.nextstrain.org?dataset-name...

#EVD68 #Enterovirus #OpenData

One note is that the NA sequence is currently not shown in the neuraminidase tree. It looks like we have an issue with purging out divergent NA subtypes, which we are working on fixing.

From a quick look at the sequences, neither 627K or 701N are present in PB2, and the HA does not appear to have any known adaptive mutations.

Thank you to the Washington State Department of Health for the rapid data generation and sharing. Hoping that this person recovers well.

could reflect unsampled infections/transmission chains in wild, North American birds prior to spillover. Enhanced surveillance/data would be useful for determining how widely and persistently these H5N5s are circulating, and for tracking their dissemination across the continent.

Across all gene segments, this human strain clusters with sequences sampled from gulls and ringed seals in Nova Scotia (Atlantic Flyway) and Nunavut (Atlantic, but very far North), which is a bit surprising. The HA sequence does have a few mutations from its closest relative, so this ..

Multiple transatlantic incursions of highly pathogenic avian influenza clade 2.3.4.4b A(H5N5) virus into North America and spillover to mammals Highly pathogenic avian influenza (HPAI) viruses have spread at an unprecedented scale, leading to mass mortalities in birds and mammals. In 2023, a t…

The incursions of these H5N5s have been described in a few papers, notably Erdelyan et al www.sciencedirect.com/science/arti... and Rahman et al academic.oup.com/ve/article/1..., though these prior introductions seemed mostly transient.

This human strain clusters with the A6 genotype viruses (Genoflu nomenclature), which include numerous H5N5 viruses that were introduced to North America from Europe. Though introduction patterns vary across the segment trees, these H5N5s always cluster together and descend from Europe.

Last week, a human in Washington was hospitalized for H5N5, the first human case of highly pathogenic H5N5 in the US. doh.wa.gov/newsroom/h5n.... Thanks to work from Anna Jaeger and Stephen Shank in our lab, we've added this strain to our North American phylogeny: nextstrain.org/groups/moncl...

H5N1 highly pathogenic avian influenza clade 2.3.4.4b in wild and domestic birds: Introductions into the United States and reassortments, December 2021–April 2022 Highly pathogenic avian influenza viruses (HPAIVs) of the A/goose/Guangdong/1/1996 lineage H5 clade 2.3.4.4b continue to have a devastating effect on …

And ONE final addendum: back in 2023, USDA authors wrote a lovely analysis of transmission in North America, and published many of the sequences they generated and used here. This is also the origin of Genoflu!: www.sciencedirect.com/science/arti...

Totally agree. Also a good reminder that I should have included their original paper describing the sequences in the thread. Hope you enjoy!

@thijskuiken.bsky.social we reached out to them, offered them authorship to anyone who was interested, and they opted for an acknowledgment instead. So we did try!

Nextstrain Real-time tracking of pathogen evolution

Finally, we maintain a North American focused build that includes continuous updates on circulating North American strains, genotypes (and their frequencies!), and metadata on host orders, flyways, etc... nextstrain.org/groups/moncl.... We plan to maintain this build in perpetuity.

colleagues at USDA ASPHIS for invaluable feedback on the work. If you'd like to see how we did any of this, all of our code is available on our lab github page (github.com/moncla-lab/N...). We also wrote a Nextstrain narrative to interact with the data (nextstrain.org/groups/moncl...).

Preventing new outbreaks in agriculture (and by extension, humans) may now require novel, layered approaches that seek to reduce wild:domestic interactions, while also targeting farm to farm spread. We thank all of the data generators for their incredible work sequencing, and our

which designates H5N1 as a foreign animal disease, should be re-evaluated. Finally, as these viruses establish in wild bird populations more globally, outbreaks and spillovers may increasingly be intertwined with evolution and transmission in wild birds.

The main takeaway is that wild birds drove the North America H5N1 epizootic. This matches global observations of increasing wild bird involvement in supporting H5 spread, and suggests that enhanced surveillance in wild birds is now necessary for viral tracking. We believe that current US policy,

Agricultural and geographic factors shaped the North American 2015 highly pathogenic avian influenza H5N2 outbreak Author summary The highly pathogenic avian influenza outbreak among poultry farms in the midwestern United States appears to be influenced by agricultural and geographic factors. After initial introdu...

from past US outbreaks. Wild birds were overwhelmingly the inferred sources of transmission, allowing for repeated spillovers into agriculture. This contrasts with the epizootic of 2015, during which farm-to-farm spread was the main driver (see: journals.plos.org/plospathogen...)

Dispersal occurred rapidly westward between adjacent flyways, with transmission most well supported in Anseriformes, suggesting that these species are good targets for surveillance. We also compare transmission in wild and domestic birds, and show that the 2022 panzootic was fundamentally different

In short: We analyzed publicly available HA sequences from 2021-mid-2023, and reconstructed transmission into and within North American using discrete trait models. We show that the epizootic was repeatedly introduced into North America, including at least 7 introductions into the Pacific flyway.

Ecology and spread of the North American H5N1 epizootic - Nature The panzootic of highly pathogenic H5N1 since 2021 was driven by around nine introductions into the Atlantic and Pacific flyways, followed by rapid dissemination through wild migratory birds, primaril...

Our lab's paper describing the North American H5N1 epizootic is out now in Nature! So thrilled to have this out, and congratulations to @lambod50.bsky.social for all the fantastic work on this: www.nature.com/articles/s41...

Congrats!

We hope these are useful, and plan to add more features and subtypes in the future! Get in touch if there are alternative features you'd love to see, or other subtypes you'd be excited about. Congrats Jordan, and thanks to CEIRR for the support!

Nextclade Genetic sequence alignment, clade assignment, mutation calling, phylogenetic placement, and quality checks for SARS-CoV-2, Influenza (Flu), Monkeypox, Respiratory Syncytial Virus (RSV) and other patho...

like annotations for cleavage site sequences, and updated quality metrics to reflect the high circulating diversity. Our paper has all these details, and you can use these at clades.nextstrain.org by selecting he H5Nx, 2.3.2.1, or 2.3.4.4 datasets.

Nextclade Genetic sequence alignment, clade assignment, mutation calling, phylogenetic placement, and quality checks for SARS-CoV-2, Influenza (Flu), Monkeypox, Respiratory Syncytial Virus (RSV) and other patho...

Supported by the CEIRR Comp Modeling Core, we developed and validated datasets for H5Nx (all clades), and the 2.3.2.1 and 2.3.4.4 clades (which currently circulate). We benchmarked against LABEL, and show that NextClade based assignments are both fast and accurate. We added some H5 specific features

Development of avian influenza A(H5) virus datasets for Nextclade enables rapid and accurate clade assignment Abstract. The 2022 panzootic of highly pathogenic avian influenza (HPAI) A(H5) viruses has led to unprecedented transmission to multiple mammalian species.

Our lab's first paper is out! Led by Jordan Ort, we developed NextClade datasets that enable rapid H5 clade assignment via NextClade. We deployed these during the start of the H5 cattle outbreak, and we finally published the paper in Virus Evolution academic.oup.com/ve/article/1...

Thanks Michelle! This preprint is now published in Virus Evolution academic.oup.com/ve/article/1...

I've always loved Ted Chiang and his writing

TreeSort is out at MBE! Fresh off the press so DOI below is not yet working, but you can find the article here: academic.oup.com/mbe/article/...

💡If you want to apply it to your data - please see the tutorial here github.com/flu-crew/Tre...

Emma is great, and leading the way on making better ways to share and aggreggate data. This is an awesome opportunity!!

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