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...
Great work bringing this up to everyones attention 👏
The epi and statistical data would be great to confirm. Next we need a gwas by age about that orf deletion.
Is @ukhsa.bsky.social working on this? They should have the data?
A panel of immunohistochemistry images showing infection of a panel of IAV viruses (as 6:2 reassortants on a PR8 backbone) in epithelia from the teat and gland cisterns of Aberdeen Angus, Limousin and Holstein Friesian cattle
🚨New pre-print!🚨
Using a panel of different H5N1 clade 2.3.4.4b viruses and human seasonal influenza, and mammary explants from common beef and dairy cattle breeds, we add to the growing data showing that H5N1 spillovers into cattle should be seen as an ongoing risk
www.biorxiv.org/content/10.6...
Graph of receptor binding curves showing an ancestral and recent H5N1. The ancestral virus does not bind NeuGc receptor well, whereas the recent virus birds NeuGc and NeuAc containing receptors equally.
Really excited to be able to share our latest preprint, describing how during its evolution in cattle, H5N1 has got better at using a type of alternative receptor that's abundant in cows, but not found in humans and birds.
www.biorxiv.org/content/10.6...
Image of racoons on a fence. 📷: Andy Langager/Flickr cc
State public health labs are stepping up as the CDC pauses testing for various pathogens, including rabies and mpox.
The pause, which could affect disease surveillance, is due to the CDC’s ongoing review of its testing efficacy.
Read more: ow.ly/PR1Q50YCVkY
📷: Andy Langager/Flickr cc
Quick elaboration on this. The disproportionate rate at which BA.3.2 infects children is not driven by infants. The 0-1 age group is less overrepresented (by a large margin) than the 2-5 and 6-17 age groups in the countries we have data for.
1/4
Thank you!
Close up image of a chicken.
Italy has confirmed the first European human H9N2 avian flu case.
About 90% of human H9N2 avian flu cases have been reported in China, with detections in Cambodia, Vietnam, and India, as well.
Read more: ow.ly/zOBz50YyTjt
Someone suggested BA.3.2 might preferentially infect kids. I think they're right.
Ages of SARS-2 sequences since Dec 1 in Ireland:
non-BA.3.2
6/66 (9.1%) age 0-19, (0/1 hospital tests)
BA.3.2
43/91 (47.3%) age 0-19 (1/3 hospital tests)
1/4
Cool to see our MMWR paper published so quickly.
This paper really illustrates the power of wastewater surveillance.
1/
www.cdc.gov/mmwr/volumes...
Hi @rajlabn.bsky.social love this dashboard, is there a reason it hasnt been updating?
A figure showing a 'Simplot' which plots the similarity of a genome to other genomes across a graph, with similarity on the Y-axis and the genome position on the x-axis. Many coloured lines show the sequences being compared - those closest to the top (similarity of 1) are the closest matches in different parts of the genome.
1/5
Introducing SimPlot-CL! 🧬
Recombination plays an important role in viral evolution. Similarity plots are a great way to visualize recombination patterns, but generating them across many genomes can be cumbersome
(Work with my student, Keno Strotjohann!)
📂 github.com/hodcroftlab/simplot-cl
@pratikkatte.bsky.social and I just released Lorax 🌲, a tool for interactive exploration of biobank-scale ancestral recombination graphs (ARGs).
If you’ve ever wanted to scroll across the ancestries of thousands of genomes… this is for you.
BA.3.2 update. We're now up to 192 wastewater detections across 31 states.
1/
We have posted data providing real-time measurement of human neutralizing antibody landscape to seasonal influenza.
Data explain spread of subclades K (H3N2) & D.3.1.1 (H1N1), identify subclade K subvariants w reduced neutralization, & can inform choice of strains for next vaccine.
The North Carolina variant appeared again in December, so I decided to add it to the dashboard. NC-2
1/
dholab.github.io/public_viz/0...
Federal testing improves detection of H5N1 avian flu in US dairy herds
Early in the outbreak, the virus was more widespread than reported.
www.cidrap.umn.edu/a...
I googled this and the one in Texas popped up 😔 i had to manually enter "Arizona" to find the arizona one. Who would have guessed this would happen except for everyone
A data figure showing a phylogenetic tree of H3N2 with 2025-K highlighted, the structure of the HA trimer with mutations characteristic of K highlighted, and box and whisker plots showing % neutralisation of the 2022 H3N2 vaccine strain, and of 2025 clade K, by various human antisera
🚨New Pre-Print🚨
Although H3N2 subclade K has multiple mutations in HA, neutralisation assays with pre-epidemic human sera show only moderate antigenic drift, and vaccines used in the 2024/2025 flu season induced cross-neutralising immunity
www.medrxiv.org/content/10.6...
Really excited our paper about how H5N1 rapidly adapted to cattle (and how these adaptations also increased its ability to infect cells from the human respiratory tract) is now published! www.nature.com/articles/s41...
Any chance this could also be a virtual event?
Just because the US is pretending that viruses only come from labs & we shouldn't bother with prevention otherwise, H5N1 is still here & is still a huge pandemic threat.
Join me & my expert colleagues Mar 3-4 in DC as we figure out what to do about it.
www.eventbrite.com/e/johns-hopk...
David Ho et al on BA.3.2 and other variants neutralization by LP.8.1. vaccine serum: www.biorxiv.org/content/10.6...
h/t Euan Arnott
We find that subclade K viruses are antigenically advanced; however, this year's flu vaccine surprisingly elicited antibodies in many individuals that efficiently recognized these viruses. The implications are clear: go get this year’s vaccine if you haven’t already!
www.medrxiv.org/content/10.6...
1/ In the first half of 2025, I wondered whether BA.3.2 would return at all. A few weeks ago, I considered that it might present a gradual shift toward endemicity rather than achieving global dominance.
New! Public Health Alerts, a joint CIDRAP/NEJM Evidence effort to strengthen early detection and response to emerging health threats.
First 2 reports:
• Community transmission of clade Ib mpox in LA area
• Flu virus characteristics and vax effectiveness data supporting WHO 2025–26 strain selections
We've been doing wastewater metagenomics for 2 years.
In the first 20 months we never detected measles once.
However, in the last 4 months we've detected it 10 times across numerous states.
It's going endemic again; good reason to get vaccinated.
health.hawaii.gov/news/newsroo...
Tracking SARSCoV2 Lineage BA.3.2* ( #Cicada) over time | 12/15/25
Total BA.3.2* seqs: 184 (+4)
Countries reporting BA.3.2*: #Australia, #SouthAfrica, #Netherlands, #USA, #Germany, #Mozambique, #Slovenia, #UK, #Denmark, #Ireland, #Singapore
Tracker: public.tableau.com/app/profile/...
