iiinova — where your digital self keeps evolving

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670rv @670rv.bsky.social · 07/10/2026

www.medrxiv.org/content/10.6... Effects of XFG-adapted mRNA vaccination on SARS-CoV-2 variant neutralisation

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Louise H. Moncla @lhmoncla.bsky.social · 28/09/2026

Due to some really great work from the @nextstrain.org team, it is now easier to put together new builds! We've recently released H7Nx and H10Nx builds onto the main avian-flu page along with all the standard features. Check them out! nextstrain.org/avian-flu/h1...

nextstrain.org

auspice

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Federico Gueli @siamosolocani.bsky.social · 26/09/2026

This is a milestone paper. Read it and read the 3D that makes everyone able to access very difficult informations. Congrats to @turville.bsky.social for this giant 4-5years long work.

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Ryan Hisner @ryanhisner.bsky.social · 26/09/2026

Phenomenal 🧵 (& paper) about why Omicron is less efficient at infecting the lung than previous variants. Initial ideas on this were proven wrong, & it's been an utter mystery since. Stuart, doing work on one else is doing, has largely explained it & revealed vital aspects of the SARS-2 life cycle.

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Louise H. Moncla @lhmoncla.bsky.social · 23/09/2026

Our lab just put out a new preprint! Led by Maria Maltepes, we've been working with @tavisanderson.bsky.social and @alexey-markin.bsky.social to understand how host species impacts the fundamentals of how influenza viruses evolve. TLDR, reassortment and selection rates vary widely across species.

scholar.google.com

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Rahil Ryder @rahilryder.bsky.social · 22/09/2026

I was shocked when my supervisor told me she was getting threats and needed security at her house.

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Federico Gueli @siamosolocani.bsky.social · 21/09/2026

New update of the wonderful tool created by @solidevidence.bsky.social #lungfish team: lungfish-science.github.io/wastewater-d... Again PJ.2.1 is clearly the fastest growing. Behind it good performances for BA.3.2(!) RW.1.1 TA.1, XFZ and maybe TK.1 and SV.2.4, with SW.2.1 and RF.5 apparently slower

lungfish-science.github.io

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Ryan Hisner @ryanhisner.bsky.social · 18/09/2026

New paper from phylogenetics/evolution arch-guru Richard Neher (@neher.io) and Luca Sesta! Tantalizing title ("Epistasis and the changing fitness landscapes of SARS-CoV-2") and abstract. Paywalled, unfortunately. academic.oup.com/genetics/adv...

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Bloom lab @jbloomlab.bsky.social · 17/09/2026

We have measured 47,851 neutralization titers of current human sera vs current influenza strains to inform vaccine update & analyses of viral evolution. New H1N1 strains (eg, D.3.1.1 + G155E) have reduced neutralization, as do some H3N2 subclade K descendants. www.biorxiv.org/content/10.6...

biorxiv.org

Near real-time data on the human neutralizing antibody landscape to influenza virus in summer of 2026 shows antigenic advance of H3N2 subclade K region D mutants and H1N1 D.3.1.1 Sa mutants

Human seasonal influenza evolves rapidly, necessitating twice yearly decisions about whether to update the strains in the vaccine. To help inform this decision, we have been using high-throughput sequ...

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Ryan Hisner @ryanhisner.bsky.social · 11/09/2026

Great thread on the PJ.2.1 variant situation, what we do & do not know, & where it stands now. Worth emphasizing that a recent Yunlong Cao preprint found PJ.2.1 has very high ACE2 affinity, meaning that, like BA.2.75 or BA.2.86, it has plenty of space to acquire new Ab-evading spike mutations.

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Rahil Ryder @rahilryder.bsky.social · 03/09/2026

HUGE shoutout to @debwadford.bsky.social for recognizing the value of this work, helping bring it to light, and understanding the impact the IGED can have on public health. Another huge shoutout to my colleague, @jelder099.bsky.social. It was a privilege to work alongside you on this.

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Rahil Ryder @rahilryder.bsky.social · 03/09/2026

This work was not always fully recognized for the value it could bring, and amid the chaos of this administration and significant funding cuts, the IGED came close to being set aside and underutilized.

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Rahil Ryder @rahilryder.bsky.social · 03/09/2026

*Performed GWAS to identify if there are mutations associated with disease severity (in progress) *Identified reinfections to get better insights into viral evolution (in progress)

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Rahil Ryder @rahilryder.bsky.social · 03/09/2026

We used the IGED to: *Overlay epi data on phylogenetic trees using a tool by UCSC (Big Tree Investigator) *Identified persistent infections and gain insights into viral evolution (published) *Notified local health jurisdictions when a concerning variant appeared (faster than w\o the IGED)

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Rahil Ryder @rahilryder.bsky.social · 03/09/2026

Having the right data infrastructure can make genomic epidemiology analyses faster, more streamlined, and more actionable. That’s where the Integrated Genomic Epidemiology Database (IGED) comes in.

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Rahil Ryder @rahilryder.bsky.social · 03/09/2026

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.

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Bloom lab @jbloomlab.bsky.social · 30/08/2026

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

slides.com

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Ryan Hisner @ryanhisner.bsky.social · 04/07/2026

…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

biorxiv.org

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...

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Rahil Ryder @rahilryder.bsky.social · 22/08/2026

Thank you for the detailed explanation 🙏

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Rahil Ryder @rahilryder.bsky.social · 21/08/2026

Hi Ryan, thanks for the clear info on this. Why do you think its a persistent infection? Could also be a lineage that's been going undetected?

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Dr. Lucky Tran @luckytran.com · 06/08/2026

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

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Solid Evidence @solidevidence.bsky.social · 29/07/2026

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.

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Rahil Ryder @rahilryder.bsky.social · 23/07/2026

Are these on a dashboard somewhere? Ive been following the Wastewater Scan but dont see it there

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Bloom lab @jbloomlab.bsky.social · 23/07/2026

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...

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Ed Hutchinson @socialinfluenza.bsky.social · 23/07/2026

🚨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...

An image in the style of an Andy Warhol screen print showing influenza virions in a variety of colours. (Image credit Ed Hutchinson and Naina Nair, MRC-University of Glasgow Centre for Virus Research)

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Louise H. Moncla @lhmoncla.bsky.social · 23/07/2026

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.

biorxiv.org

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 ...

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Ryan Hisner @ryanhisner.bsky.social · 22/07/2026

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.

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Hensley Lab @scottehensley.bsky.social · 05/07/2026

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...

biorxiv.org

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...

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Cécile Tran Kiem @ceciletk.bsky.social · 01/07/2026

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.

tinyurl.com

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...

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Rahil Ryder @rahilryder.bsky.social · 01/07/2026

Congrats!! Very well deserved 🎉🎉🎉

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CIDRAP @cidrap.bsky.social · 15/06/2026

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 brown and black shepherd dog sits at attention in a green field, with cattle in the background.

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Helen Branswell 🇨🇦 @helenbranswell.bsky.social · 08/06/2026

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...

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ARTIC network @artic.network · 01/06/2026

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

artic.network

Bundibugyo virus genomic sequencing resources | ARTIC network - pathogen genomics from sample to response

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CIDRAP @cidrap.bsky.social · 29/05/2026

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

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Rahil Ryder @rahilryder.bsky.social · 21/05/2026

At CA state University Monterey Bay, one time I started an experiment at 6pm and it ended up being a 12 hr+ thing. I got home at 8am. We have card key access to the building.

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Rahil Ryder @rahilryder.bsky.social · 20/05/2026

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...

medrxiv.org

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Dr Emma Hodcroft @firefoxx66.bsky.social · 19/05/2026

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!

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Angie Rasmussen @angierasmussen.bsky.social · 18/05/2026

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.

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Dr Emma Hodcroft @firefoxx66.bsky.social · 08/05/2026

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...

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