@pratikkatte.bsky.social and I just released Lorax π², a tool for interactive exploration of biobank-scale ancestral recombination graphs (ARGs).
If youβve ever wanted to scroll across the ancestries of thousands of genomesβ¦ 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 π 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
π¨New Pre-Printπ¨
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 yearβs vaccine if you havenβt 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:
β’ Community transmission of clade Ib mpox in LA area
β’ Flu virus characteristics and vax effectiveness data supporting WHO 2025β26 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/...
New preprint alert from the PHA4GE Wastewater Subgroup:
Community-led standards for global wastewater-based infectious disease surveillance. π§
Read the full work:
zenodo.org/records/1778...
Share feedback via GitHub:
github.com/pha4ge/waste...
#PHA4GE #WastewaterSurveillance
Three more BA.3.2 detections from US wastewater. Rhode Island (different sewershed, but near the previous one), Vermont, and Florida. All from CDC NWSS data.
Looks like it might be getting a foothold in New England.
@snpoehlm.bsky.social @ryanhisner.bsky.social @siamosolocani.bsky.social
As wastewater has become a core part of infectious disease surveillance worldwide, new guidance from WHO, GLOWACON, ASTHO, and others has laid key foundations for public health. But in practice, itβs not always obvious how to apply these recommendations or choose among available tools.
Thank you!!! Please inform other scientists on any call to action. Ive just been posting on my social medias. A unifying voice is stronger and we are all wanting to do something. π«‘ π§ π
Another US wastewater detection of BA.3.2.2 (from CDC-NWSS surveillance)
This time from Austin on 11/19
The score:
Wastewater 2
Patient surveillance 0
The West Coast Health Alliance, @capublichealth.bsky.social , and Leading National Medical Organizations Continue to Recommend Hepatitis B Vaccination for Newborns
www.cdph.ca.gov/Programs/OPA...
Fascinating π§΅. The grotesquely mutated spike of this NJ Cryptic binds ACE2 very tightly.
It raises a broader question: Can cryptic wastewater-like lineages transmit?
YES
We knew it happened once. Now we know it's happened at least twice. The results in both cases were not pretty. 1/15
Amazing working β€οΈβ€οΈβ€οΈ!!!
They are trying to get more support to stop mandated vaccines like how they already did in Idaho π‘
Nice thank you!!
Thank you!! NA gene seems to sit with the same gull as the other segments. If you put the HA gene muts in the deep mutation scan i see that 172T has high sera escape values. So far the only interesting thing ive seen so far. Im not sure what to compare the NA to to check for mutations though.
Where are you seeing this? Thank you!
I want to spell this out in case the implications aren't clear:
This means all public tools/webapps of GISAID data (all the ones you've been used to seeing thru the pandemic, as far as we can tell) are prohibited.
The file allowed this. Cut that - cut off all tools the public & others were using.
π looks like a lot of folks are\have switched to NCBI... Hopefully that database could be easily transitioned to?
