evolution is pretty fundamentally linked to the ecology and spread of LPAI viruses, which we should probably surveil and understand better.
Huge thank you to all the people at USDA who generated these sequence data, to @lambod50.bsky.social and Nicola for all their fantastic work on this!
Together, this study suggests that reassortment is frequent, seasonal, and mostly driven by viral prevalence and mixing with LPAIs. This suggests that aspects of reassortment (timing, host, locations) may be more predictable if we understood transmission better. Our data also suggest that HPAI
Using these time-varying rates, we show that the probability of reassortment in the 6 months leading up to the emergence of B3.13 and D1.1 was ~0.15, meaning that viruses evolving during particular times of year are likely to be reassortants, regardless of whether reassortment was beneficial.
We find that that reassortment is frequent, seasonal and mostly driven by mixing between high and low path viruses. Peaks in HPAI reassortment are best predicted by LPAI cases, indicating that LPAI ecology plays a major role in the timing of HPAI reassortment.
Next, Nicola developed a new version of CoalRE that allows reassortment to be modelled as a function of prevalence. We inferred the full reassortment network and measured reassortment rates over time, and used a GLM to assess whether cases of HPAI or LPAI correlated with reassortment.
generating less. Ducks contributed the most to transmission, and contributed about half of all reassortant segments! So ducks are really the source of new H5 genotypes in North America, making them a useful target for surveillance.
flyway, and time of genotype origins as a proxy for reassortment. We find that genotypes mostly arise in flyways and hosts proportional to what you would expect based on the transmission they support, with the Central flyway and geese generating more reassortment than you would expect, and cattle
In collaboration with Nicola Muller, and led by @lambod50.bsky.social, we have a new preprint out that's all about reassortment! www.biorxiv.org/content/10.6...
Using TargetedBeast, we built massive (9000 tips!) Bayesian phylogenies of North American H5Nx viruses, and inferred the host...
A 3x3 grid of coloured images of influenza virus particles in the style of an Andy Warhol screen print. Image credit Naina Nair / Ed Hutchinson (MRC-University of Glasgow Centre for Virus Research)
🚨New Influenza Tool🚨
Interested in IAV mutations?
Looking for markers of mammalian adaptation?
Frustrated by converting between IAV numbering systems?
The #Flu-MutationExplorer, a new tool from @cvrbioinfo.bsky.social and @royalvetcollege.bsky.social, is here to help:
flu-gdb.cvr.gla.ac.uk
(1/n)
Big news for those of us clicking around on trees all the time!
Nooooo I'm so sorry!
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 ..
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...
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!
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,
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
