Just out📢 Our new paper published in @natmicrobiol.nature.com describes highly potent cross-neutralizing human monoclonal antibodies against H5Nx influenza viruses. Close collaboration with Sara Andrews lab and Tongqing Zhou lab at the VRC. Link to the article: rdcu.be/eKV9T 1/2

In new study led by @ckikawa.bsky.social, we provide near real-time data on human neutralizing antibody landscape to influenza by measuring ~26,000 titers to >100 recent viral strains Data can inform vaccine selection & evolutionary/epidemiological modeling www.biorxiv.org/content/10.1...

In new study led by Xiaohui Ju, we define how mutations to Chikungunya virus envelope proteins affect entry in human vs mosquito cells. Sheds light on functional constraints & enables us to make loss-of-tropism mutants, which could be of use for vaccines. www.biorxiv.org/content/10.1...

In new study led by @bdadonaite.bsky.social, we measure how spike mutations affect function & antigenicity of spike of KP.3.1.1 strain of SARS-CoV-2. Sheds light on how key neutralizing epitopes are changing & importance of RBD up/down motion. www.biorxiv.org/content/10.1...

Our lab has an opening for a research technician to contribute to our efforts to understand RSV evolution & its impact on antibody countermeasures (see journals.asm.org/doi/full/10....). The tech will also help w lab management. If interested, apply here: careers-fhcrc.icims.com/jobs/29940/job

Wanted to flag this interesting study led by our collaborators @kinglabipd.bsky.social suggesting that at least in some contexts, the immunogenicity of H5 influenza vaccines can be improved by mutations that stabilize the HA protein.

In new study led by @timyu.bsky.social, we measure how mutations to H3 flu HA affect cell entry, stability & antibody escape We find pleiotropic effects of mutations on these phenotypes shape evolution: epistasis alleviates cell-entry but not stability constraints www.biorxiv.org/content/10.1...

In study led by @ckikawa.bsky.social & Andrea Loes, we use new assay to measure ~10,000 neutralization titers to recent influenza strains & show titers correlate w evolutionary success of viral strains Similar data could help forecast evolution for vaccine selection www.biorxiv.org/content/10.1...

In study led by @csimonich.bsky.social & Teagan McMahon, we quantify antigenic evolution of RSV F Important because: 1️⃣ RSV top cause of infant hospitalization in USA 2️⃣ New antibodies & vax can prevent hospitalizations 3️⃣ Will virus evolution erode their efficacy? www.biorxiv.org/content/10.1...

In a new study led by Caelan Radford, we use deep mutational scanning to systematically compare the escape mutations from two broadly neutralizing antibodies in a clade A versus clade B HIV Envelope. www.biorxiv.org/content/10.1...

In new study, we find dramatic differences in specificities of serum neutralizing antibodies in infants w single infection by a recent SARS-CoV-2 strain versus adults/children imprinted by an early viral strain. www.biorxiv.org/content/10.1...

In new study, we measure how all mutations to rabies G affect cell entry & antibody neutralization Sheds light on constraints on type III fusion proteins, suggests ways to stabilize G vaccine antigens, and quantifies antibody robustness to rabies variation www.biorxiv.org/content/10.1...

I’ve updated SARSCoV2 RBD antibody-escape calculator w new deep mutational scanning data of Yunlong Cao & Fanchong Jian. My interpretation: antigenic evolution currently constrained by pleiotropic effects of mutations on RBD-ACE2 affinity, RBD up-down position & antibody neutralization

Hi friends new and old! I study how microbes interact and evolve in complex communities like the human gut microbiome.🦠🧬💩 I'm thrilled to share that I'm starting a lab at UC Irvine in April 2025 and am recruiting at all levels - please spread the word! kxuelab.com More about my work below...🧵1/n

If you are searching literature, these sites are E190 and Q226 in H3 numbering, E186 and Q222 in mature H5 numbering, and E202 and Q238 in sequential H5 numbering (see: dms-vep.org/Flu_H5_Ameri...)

Excellent summary thread here by @scottehensley.bsky.social. To add a few more important notes, the sequence (GISAID EPI_ISL_19548836) is ambiguous at *both* site Q226 (as Scott mentions above) and site E190 (H3 numbering) Both these sites play an important role in sialic acid binding specificity

The preliminary sequence from the H5N1 human case in British Columbia has been posted and it is not good news. The virus potentially has a quasispecies at HA residue 226 (H3 numbering). This is bad news because we know that mutations at residue 226 can increase binding to human receptors. 1/

The final version of our study using pseudovirus deep mutational scanning to measure the effects of mutations influenza H5 hemagglutinin to inform viral surveillance is now published in PLoS Biology: journals.plos.org/plosbiology/...

Below is brief analysis of HA mutations in two recent cases of H5N1 influenza in humans w contact w dairy cattle in California. Summary is that while virus continues to evolve, nothing about HA mutations in these human cases is obviously alarming.

Our paper describing a new sequencing-based neutralization assay for influenza virus is now published in Journal of Virology: journals.asm.org/doi/10.1128/... This new approach makes it possible to measure 100s (or even ~1000) neutralization titers in a single 96-well plate.

Here is analysis of HA mutations in H5 influenza case in Missouri resident without known contact w animals or raw milk. TLDR: there is one HA mutation that strongly affects antigenicity, and another that merits some further study.

We’ve updated our pre-print on deep mutational scanning of influenza clade 2.3.4.4b H5 HA to identify recent viruses w mutations that alter relevant phenotypes. This identifies viruses w >10x reduced neutralization by sera from candidate vaccine viruses: www.biorxiv.org/content/10.1...

In new study led by Bernadeta Dadonaite, we measure how all mutations to H5 influenza HA affect four molecular phenotypes relevant to pandemic risk: www.biorxiv.org/content/10.1...   Results can inform surveillance of ongoing evolution of H5N1.

In new study led by Brendan Larsen in collab w Veesler & Crowe labs, we map functional & antigenic landscape of Nipah virus receptor binding protein (RBP) www.biorxiv.org/content/10.1...   Results elucidate constraints on RBP function & provide insight into protein’s evolutionary potential

In new study led by Andrea Loes, we develop sequencing-based neutralization assay that measures replicate curves for hundreds of virus-serum pairs per 96-well plate (see image below) www.biorxiv.org/content/10.1...   We apply assay to characterize response to repeat influenza vaccination

Niche post for anyone like me who frequently finds themselves trying to determine which spike mutations are in some new SARS-CoV-2 clade not yet in outbreak.info, covariants.org, etc I made simple notebook to make plots like below for any set of Pango clades: github.com/jbloom/SARS2...

In new study led by Caleb Carr & Kate Crawford, we measure how all mutation to Lassa virus glycoprotein complex (GPC) affect cell entry & antibody escape   Results show how prospective assessment of effects of mutations can inform design of countermeasures www.biorxiv.org/content/10.1...

In new study led by Frances Welsh, we map how mutations to influenza affect neutralization by antibodies from humans of various ages   We find differences in mutation effects among age groups   Virus seems to evolve especially to escape antibodies of teenagers   www.biorxiv.org/content/10.1...

I wanted to highlight this pre-print by David Ho’s group on the neutralizing antibody response to new (XBB.1.5-based) COVID vaccine booster, as it illustrates some points related to paradigm of updating SARS-CoV-2 vaccines to keep pace w viral evolution. www.biorxiv.org/content/10.1...

In study led by Bernadeta Dadoniate, we measure how mutations to XBB.1.5 spike affect cell entry, ACE2 binding & serum escape www.biorxiv.org/content/10.1...   Two key findings:   1️⃣ Mutations outside RBD meaningfully affect ACE2 binding   2️⃣ Measurements help predict viral clade growth in real world

In new work led by Will Hannon, we have created interactive tool for visualizing deep mutational scanning data on protein structures, such as to aid in understanding effects of viral mutations.   Tool is at dms-viz.github.io   Pre-print describing tool: www.biorxiv.org/content/10.1...

Niche post for those using my & Richard Neher's SARS-CoV-2 mutation fitness estimates I have updated jbloomlab.github.io/SARS2-mut-fi... to include latest sequences Changes mostly small as marginal increase in sequence # small in last 3 months But newer estimates should be slightly more accurate

Here are data from new XBB.1.5 spike deep mutational scanning by Bernadeta in our group   Go to dms-vep.github.io/SARS-CoV-2_X... to see how mutations affect:   1️⃣ Neutralization by human XBB breakthrough sera 2️⃣ Spike-mediated pseudovirus entry in 293T-ACE2 cells 3️⃣ Spike affinity for ACE2

I have updated my BA.2.86 slides: slides.com/jbloom/new_2... Slides still up-to-date re spike mutations. But enough seqs now identified slides no longer effective way to track those Instead see nextstrain.org/groups/neher... Also wastewater twitter.com/TanjaStadler... twitter.com/dr_leshan/st...

I have updated my slides to reflect identification of 7th sequence of highly mutated BA.2.86 SARS-CoV-2 lineage: slides.com/jbloom/new_2... For latest on details of BA.2.86 sequences, see this Nextstrain tree from Cornelius Roemer and Richard Neher: twitter.com/CorneliusRoe...

Slides summarizing new highly mutated BA.2.86 SARS-CoV-2 variant https://slides.com/jbloom/new_2nd_gen_ba2_variant Analysis is for those (like me) scientifically interested in SARS2 evolution Anyone else is completely within reason to ignore right now, but it does merit scientific monitoring