How did California connect a million SARS-CoV-2 sequencing data with epidemiology data? And how did we use this to better public health? This huge effort is now published and we are excited about where it will go next.

@debwadford.bsky.social · last wk.

journals.plos.org/digitalhealt... Congratulations to @rahilryder.bsky.social @jelder099.bsky.social and Team!! Great work!!!

Here is a link to slides I will present today at Options XIII Conference for Control of Influenza meeting: slides.com/jbloom/optio... Slides describe using sequencing-based neutralization assays to characterize human neutralizing antibody landscape to seasonal influenza virus in near real time

…recurring mut pattern in chronic infections that involves S:D936H/Y, M:H155N, ORF3a:∆255-257, & ORF1a:R3164H/L3201P. (Note the other long bottom branch has S:D936Y). Why these mutations occur together is a mystery. My preprint on these mutation patterns: www.biorxiv.org/content/10.6... 5/14

Coevolving Mutations in Chronic SARS-CoV-2 Infections

The SARS-CoV-2 pandemic has been marked by two outstanding features that have had major impacts on global public health: the repeated emergence and growth of highly divergent saltation variants with n...

biorxiv.org

Throughout history, persecuting scientists for saving lives is a frightening marker for the collapse of a society.

Fourteen more PJ.2.1 wastewater detections. It is dominant in many sites. NYC (8), Maui (2). Maine, Virginia, Florida and DC. No obvious uptick in cases in any of these places that I could find though.

In new study led by @bdadonaite.bsky.social, we show many influenza HAs (H5, H7, H9, H1, H2, H3) can use avian or human MHC-II to enter cells. We then use novel combo of deep mutational scanning & cryoEM to define how H5 HA binds to avian MHC-II. Preprint: doi.org/10.64898/202...

🚨New Pre-Print!🚨 Want to search for variation in influenza A virus sequences, but find the amount of data overwhelming? Wondering if new avian flu strains have signs of mammalian adaptation? The #Flu-MutationExplorer, a new online tool, can help (1/n) www.biorxiv.org/content/10.6...

Led by Anna Jaeger and Elena Cruz-Adames, we have a new preprint out on within-sample diversity and local spread of H5N1 in Pennsylvania! www.biorxiv.org/content/10.6.... We developed a sequencing protocol and bioinformatic pipeline to sequence residual RNA from H5+ wild and domestic birds in PA.

Within- and between-host dynamics of highly pathogenic avian influenza in domestic birds from Pennsylvania farms and live bird markets

Since late 2021, highly pathogenic avian influenza viruses (HPAI) of the H5 subtype clade 2.3.4.4b have spread across the Americas, devastating wildlife, agricultural animals, and resulting in dozens ...

biorxiv.org

A JN.1.51 with 38 spike mutations (and likely ≥10 more at S:407-471, where there is no coverage) showed up in this Queensland upload as well. Wild one. Closest related sequence was collected over 2 years ago, in early April 2024.

Stefan Pöhlmann@snpoehlm.bsky.social · 2mo ago

1/n 169 new sequences from Queensland, Australia 🇦🇺, collected June - July 2026.

A new publication from my team! Beyond traditional outbreak investigation: Using genomic data for enhanced detection of COVID-19 disease clusters in Utah. journals.plos.org/plosone/arti...

Beyond traditional outbreak investigation: Using genomic data for enhanced detection of COVID-19 disease clusters in Utah

Background Traditional disease surveillance, such as manual case investigation, was the primary method for identifying disease clusters during the COVID-19 pandemic. However, the pandemic also provide...

journals.plos.org

Do you live in Philly? Has your cat been acting crazy? Well, it is likely this craziness is not due to H5N1 infection--but rather the fact that your cat is a cat. In this new preprint with @lhmoncla.bsky.social we find low H5N1 seroprevalence rates in Philly cats. www.biorxiv.org/content/10.6...

Clade 2.3.4.4b H5N1 influenza virus and SARS-CoV-2 seroprevalence among owned and feral cats in Philadelphia and surrounding communities

Clade 2.3.4.4b H5NX influenza viruses have spread widely in birds since 2020. In addition to causing disease in birds, these viruses have infected a variety of mammals, including humans. Clade 2.3.4.4...

biorxiv.org

The emergence and spread of highly mutated variants have shaped the COVID-19 pandemic. In our new work (tinyurl.com/ncov-saltati...), we find that such jumps aren’t rare anomalies but a recurring feature of SARS-CoV-2 evolution, occurring at low but detectable rates over time & across geographies.

SARS-CoV-2 saltational events are recurrent and trace to persistent human infections

SARS-CoV-2 evolution is characterized by gradual mutation accumulation but has been punctuated by rare yet impactful highly mutated variants. Whether such saltational jumps are a broad feature of SARS...

tinyurl.com

Want to know how to protect outdoor pets from New World screwworm? Pet owners who live in areas with New World screwworm cases should monitor their cats and dogs closely, inspecting them every day for behavior changes or signs of infestation. Read more: ow.ly/xxHm50Zc4xY

A new preprint was released this week that helps explain why there seems to be more BA.3.2 infections of children. 1/ www.biorxiv.org/content/10.6...

SARS-CoV-2 BA.3.2.2 is more evasive of neutralization by sera from young children

Dominant SARS-CoV-2 variants have most prominently displayed greater evasion of serum neutralizing antibodies than predecessor strains. BA.3.2, a descendant of Omicron BA.3, carrying 43 additional spi...

biorxiv.org

These 2 new #H5N1 #birdflu infected herds in Texas & Utah have made it to #USDA 's official count. total now 1,109 herds in 19 states. www.aphis.usda.gov/livestock-po...

Helen Branswell 🇨🇦@helenbranswell.bsky.social · 3mo ago

There are media reports of 2 new #H5N1 #birdflu outbreaks in dairy cows, in Texas and Utah. They haven't yet been added to #USDA 's dashboard. If confirmed by USDA, there will have been 1,109 herds infected in 19 states. www.telemundoutah.com/noticias/loc... and www.kbtx.com/2026/06/04/h...

ARTIC network has published Bundibugyo (BDBV) sequencing resources as the 2026 outbreak continues in DRC & Uganda. We have compiled guidance for labs wishing to sequence, assemble and analyse BDBV genomes: artic.network/viruses/bdbv/bdbv-sequencing-guide.html

FDA’s Vaccines and Related Biological Products Advisory Committee (VRBPAC) recommends XFG variant as target for fall’s updated COVID vaccines. XFG is a hybrid of two Omicron subvariants and has mutations linked to immune escape. ow.ly/MV5c50Z5MSL 📷: NIAID / Flickr cc

Excited to share a preprint on how CA linked almost 1 million SARS-CoV-2 sequencing data to the patient data. This was a huge effort by multiple groups and we hope this can be used as a model for other emerging pathogens to enhance genomic epidemiology. www.medrxiv.org/content/10.6...

Looking to find out more about genomic epidemiology and Hantavirus/ANDV? I'll be chairing a excellent panel of experts tomorrow (alongside some great opening speakers) - stop by and hear what they have to say!

@pha4ge.bsky.social · 4mo ago

🚨 Hantavirus and genomic epidemiology: Has it been smooth sailing? Join a special PHA4GE & IPSN webinar exploring how genomics supported the response to the Hantavirus outbreak. 📅 20 May 2026 🕒 14:00 CEST 📍 Zoom Register: bit.ly/4ulwHKm #PHA4GE #Hantavirus

virological.org/t/initial-ge...

Initial genomes from May 2026 Bundibugyo Virus Disease Outbreak in the Democratic Republic of the Congo and Uganda

Initial genomes from May 2026 Bundibugyo Virus Disease Outbreak in the Democratic Republic of the Congo and Uganda, reveal a new spillover event Context On 15 May 2026, the Ministry of Public Health, ...

virological.org

Wtf is Bundibugyo virus & why should you care? 1. It’s a type of ebolavirus 2. This outbreak is very bad already & we don’t have any idea how big it is. It’s been going on for weeks or even months. 3. We’re about to enter the find out stage of #MAHA #FAFO. And the US has a lot to account for.

Quick takes: -Fatal H5N6 avian flu case -Cruise ship norovirus outbreak -Dermatophilosis in MSM Read more: ow.ly/BVWe50YXRUf.

Quick takes: Fatal H5N6 avian flu case, cruise ship norovirus outbreak, dermatophilosis in MSM

The dermatophilosis rash has caused only mild cases in men who have sex with men in Europe.

ow.ly

I've built some initial Nextstrain phylogenies of the Andes Hantavirus variant, which include the sequence generated by HUG & UniZurich, Switzerland. Please interpret with caution. By segment: S: nextstrain.org/groups/hodcr... M: nextstrain.org/groups/hodcr... L: nextstrain.org/groups/hodcr...

First genome sequence from Andes hantavirus strain from ongoing ship outbreak posted on Virological: virological.org/t/complete-s... courtesy Swiss National Reference Centre for Emerging Viral Infections, Geneva University Hospitals, University of Zurich

Complete sequence of Orthohantavirus andesense virus: Swiss resident 2026

Posted on behalf of the Swiss National Reference Center for Emerging Viral Infections, Geneva University Hospitals and the Institute of Medical Virology, University of Zurich (Partner Laboratory Natio...

virological.org

We did a thing: Scientists find a new way coronaviruses can get into human cells www.cam.ac.uk/research/new...

Scientists find a new way coronaviruses can get into human cells

An international team of researchers has identified an East African bat coronavirus capable of entering human cells.

cam.ac.uk

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...

🚨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...

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...

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

Ryan Hisner@ryanhisner.bsky.social · 6mo ago

So it's clear that BA.3.2 preferentially infects children, something we have never seen before in a SARS-CoV-2 variant. Why? The question's baffled me, but after a suggestion from @darrenmartin.bsky.social, I think I have an explanation that makes sense. 1/16