Bloom lab

In new study, we show that SARS-CoV-2 has evolved decreased inherent antigenicity in humans, as quantified by a ~3-fold decrease in the number of naïve human B cells that can bind the spike RBD. doi.org/10.64898/202...

More generally, reduced inherent antigenicity to naive B cells is one mechanism (alongside glycan masking & positioning of RBD in down conformation) by which evolution of human endemic CoV can affect antibody elicitation. Understanding these mechanisms can improve vaccine / antibody development.

However, newer viral variants remain immunogenic, albeit probably at modestly reduced levels--so this work does not support alarmism about immunity no longer recognizing SARSCoV2. Antibody response has amazing ability to recognize diverse antigens, although it recognizes some more easily than others

Given some follow-up posts re this study (especially on X), I am pasting as image below last paragraph of Discussion. Multiple studies (eg, pmc.ncbi.nlm.nih.gov/articles/PMC..., thelancet.com/journals/lan... show exposure to new variants still elicits antibodies, albeit w different specificities.

So while I'm unaware of head-to-head quantitative assessments of human post-primary exposure homologous titers to newer vs older variants, but primary exposure to new variants still elicits decent homologous neutralizing antibody titers.

However, decrease in inherent antigenicity is modest (~3-fold), and plenty of naïve human B cells still bind newer variant RBDs. We lack data to assess how much ~3-fold drop in inherent antigenicity affects human neutralizing antibody response. Interesting area for future work.

This study was led by Catherine Jacob-Dolan in collaboration with @jimboonya.bsky.social

Importantly, this decrease in inherent antigenicity is specific to the human antibody repertoire. Mice naïve B cells bind newer vs older viral variant RBDs similarly (see below).

Our interpretation: early viral variant RBDs strongly targeted by “public” human germline antibodies, putting pressure on virus to change those epitopes. As epitopes mutated, sometimes they became less recognized by human germline repertoire, decreasing inherent antigenicity.

It’s known SARS-CoV-2 evolves to erode antibodies from prior infection/vaccination. We asked: has it also become inherently less recognized by human germline antibodies? As shown below, answer is yes. ~3-fold fewer naïve human B cells bind newer vs old viral variant RBDs.

biorxiv.orgNear 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 mutantsHuman 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...

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...

The work was led by @ckikawa.bsky.social, Andrew Butler, and @huddlej.bsky.social. Thanks also to S Turner, H Peck, J Englund, K Lacombe, M Busch, M Lanteri, M Stone, B Spencer, A Greninger, D Smith, S Wallace, H Marshall, S Tosif, @scottehensley.bsky.social, & Ian Barr.

nature.comFlu season could kick off ‘incredibly’ early — what scientists are watchingCases in the Northern Hemisphere are cropping up weeks early, and they are dominated by a virus with a concerning mutation.

See also this recent Nature News article for a very early update on how the influenza season is going so far... bsky.app/profile/mari...

Mariana Lenharo@marilenharo.bsky.social

The flu season seems to be off to an early start in the Northern Hemisphere and scientists are worried about one particular mutation. That means it's a good idea to go get vaccinated as soon as possible! I wrote about what the early data tell us: www.nature.com/articles/d41...

For additional details, see: Preprint: www.biorxiv.org/content/10.6... Interactive plots that show above findings in more detail: jbloomlab.github.io/flu-seqneut-... Recent slides: slides.com/jbloom/optio...

This is third installment of our efforts to generate near real-time data on human neutralizing antibody landscape to influenza. Our hope is that these data can improve vaccine-strain selection and ability to forecast short-term evolution of human seasonal influenza.

But effect of G155E mutation in H1N1 is highly variable across people. For most sera, strains with G155E have only mildly reduced neutralization---but some sera neutralize G155E strains much more poorly. Individuals who are strongly affected by G155E tend to be younger.

For H3N2, some new subclade K strains, especially those with mutations in antigenic region D (eg, V223I) have mildly reduced neutralization by human sera. See this paper from @scottehensley.bsky.social for possible explanation: www.medrxiv.org/content/10.6...

We assembled set of 78 H3N2 and 62 H1N1 HAs from naturally occurring human seasonal strains that largely cover recent diversity of influenza circulating in human population. We measured neutralization of these viruses by 325 recent human sera.

For H1N1, many new natural strains have modestly reduced neutralization by human sera relative to strain in 2026-2027 Northern Hemisphere vaccine. Strains w lowest neutralization often have G155E, which has emerged repeatedly in natural strains, especially in D.3.1.1 subclade.

As background, human seasonal influenza evolves rapidly. HA protein of H3N2 influenza has accumulated >45 amino-acid mutations over last 18 years. This evolution erodes immunity, so vaccine updates considered twice per year (Sept & Feb for Southern & Northern hemisphere vaccines).

We recently developed sequencing-based neutralization assays that measure how serum antibodies neutralize many viral strains. This enables us to measure in near real-time how new naturally emerging strains are neutralized by current human sera.

30 Aug

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.comslides.com

30 Aug

Measurements are informative for vaccine strain choice. Our latest data from last few weeks identifies emerging variants of seasonal H3N2 & H1N1 to which current human sera has reduced titers. These include H3N2 subclade K variants w V223I, and H1N1 subclade D.3.1.1 variants including w G155E.

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30 Aug

All raw data along with interactive visualizations are available at links in the slides. The section on our latest unpublished data starts on slide 19 (slides.com/jbloom/optio...)

slides.comslides.com

Bloom lab reposted

Harmit Singh Malik

@harmitmalik.bsky.social

6 Aug

Come be our colleague. I have been in this Division for 27 years (4 as a postdoc and 23 as a PI). It is an amazing place to work, collaborate, and be inspired. If you are applying to be an Assistant or Associate Professor this Fall, don't miss this deadline.

Fred Hutch Basic Sciences Division@basicsci.fredhutch.org

Join @FredHutch.org's Basic Sciences Division as an Assistant or Associate Professor and help shape the future of fundamental biology. We welcome applicants whose work will complement, extend, or bring new directions to the division.

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...

Note our study used pseudoviruses and conditionally replicative virions to ensure biosafety, and reports deep mutational scanning only for HA usage of tufted duck MHC-II to limit any information hazard concerns.

doi.orgDefining the molecular interaction between influenza hemagglutinin and MHC-IIThe hemagglutinin (HA) of some influenza viruses can interact with major histocompatibility complex class II (MHC-II), but how these proteins interact is unclear. Here we demonstrate that diverse H5 HAs can use MHC-II to enter cells, with avian MHC-II enabling more efficient entry than human MHC-II for most H5 HAs. To define the molecular interface, we use pseudovirus deep mutational scanning to measure how mutations to H5 HA affect its interaction with tufted duck MHC-II, and identify mutations that restrict HA to exclusively MHC-II or sialic acid receptors. We leverage identification of H5 HA mutations that increase binding to tufted duck MHC-II to determine a 4.8 Å cryo-EM model of the complex. To support the structural model, we measure how all mutations to tufted duck MHC-II affect its interaction with H5 HA, and find the alpha chain is the dominant determinant but beta chain sites near the peptide-binding groove also contribute. To generalize these findings, we use deep mutational scanning to show that a H7 HA interacts with MHC-II similarly to H5 HA. Finally, we show that H1, H2, H3, and H9 HAs interact with avian or human MHC-II, although interactions vary among strains that evolved in different hosts. ### Competing Interest Statement J.D.B. and B.D. are inventors on Fred Hutch licensed patents related to the pseudovirus deep mutational scanning and a provisional patent on MHC-II binding deficient HA vaccine antigens. J.D.B consults for Apriori Bio, GSK, Merck, and Pfizer. J.D.B. holds stock options in the Vaccine Company. N.P.K. is a paid consultant of AstraZeneca. National Institute of Allergy and Infectious Diseases, 75N93021C00015, U19AI181881 National Cancer Institute, P30CA015704 Washington Research Foundation, https://ror.org/00hasdx88, postdoctoral fellowship to Sara Sunshine Howard Hughes Medical Institute, https://ror.org/006w34k90

Please see the preprint for additional details: doi.org/10.64898/202... Thanks to @bdadonaite.bsky.social for leading study, and Annie Dosey, @jahn0.bsky.social, @timyu.bsky.social, Sara Sunshine, Ariana Farrell, and @kinglabipd.bsky.social for valuable contributions.

Although breadth of MHC-II usage among HAs suggests evolutionary selection in some strains/hosts, further work needed to understand biological relevance. Hypotheses include that it could impact cell entry or immunogenicity in actual infection of some hosts.

dms-vep.orgHow mutations to an H5 HA affect its interaction with tufted duck MHC-IIPseudovirus deep mutational scanning of how mutations to HA from A/American Wigeon/South Carolina/USDA-000345-001/2021 (H5N1) affects its interaction with tufted duck MHC-II

All our data is available along with rich set of interactive plots: dms-vep.org/Flu-H5N1-Ame...

Structure & deep mutational scanning suggest identity of peptide bound to MHC-II could influence interaction of HA & MHC-II. Also, HA binding would likely block ability of MHC-II to interact with T-cell (perhaps analogous to how EBV gp42 can bind to MHC-II to block T cell activation).

We also showed H7 HA binds tufted duck MHC-II similarly to H5 HA, & some H1, H2, H3, & H9 HAs also can use avian or human MHC-II. But patterns vary among strains. For instance, an avian influenza HA and the 1918 HA can use tufted duck MHC-II, but later human strains cannot.

To validate structure, we used inverted pseudotyping deep mutational scanning to measure how mutations to tufted duck MHC-II affect binding to H5 HA. Most mutations with big impact in alpha chain, but beta-chain mutations near peptide-binding groove also have effect.

So although structure only 4.8 A, it is corroborated by deep mutational scanning of both HA and MHC-II showing that sites in both proteins that affect binding are at structural interface. (Sites where mutations decrease binding are red in structure below)

The mutations that reduced MHC-II entry clustered in a region on HA head defining the MHC-II binding surface. We also directly measured how HA mutations affect binding to tufted duck MHC-II, and identified same binding surface.

To determine structure, we produced H5 HA protein w mutations that increased binding to tufted duck MHC-II. This HA increased fraction of particles bound to MHC-II in ns-EM, and we were able to use it solve cryo-EM structure of H5 HA bound to tufted duck MHC-II.

We tested 80 H5 HAs: most but not all could enter cells via tufted duck & to lesser extent human MHC-II. Note MHC-II highly variable within and between species. See dms-vep.org/Flu-H5N1-Ame... for interactive version of below plot.

To understand how HA interacts w MHC-II, we measured how all H5 HA mutations affect pseudovirus entry via sialic acid or tufted duck MHC-II. Identified loss-of-function mutants that could only use MHC-II or sialic acid.

nature.comMHC class II proteins mediate cross-species entry of bat influenza viruses - NatureThe DR isotype of the human leukocyte antigen of the MHC class II—or its homologues in bats, pigs, mice and chickens—is an essential cell entry determinant for bat influenza A viruses.

As background, influenza long known to use sialic acid as entry receptor. ~7 yrs ago was shown bat flu can enter cells via MHC-II (www.nature.com/articles/s41...); later shown for some H2 & H3 strains. We set out to assess how common MHC-II usage is & define how HA interacts w MHC-II.

We first measured ability of two H5 HAs to enter cells via sialic acid or MHC-II. As shown below, both HAs could use tufted duck & to lesser extent human MHC-II. [Note: experiments used pseudoviruses, which can only undergo single round of cell entry, providing safe way to study HA]

slides.comflu-seqneut-2025to2026Near real-time data on the human neutralizing antibody landscape to influenza virus to inform vaccine-strain selection in September 2025

6 Mar

Here are the slides I am presenting at this morning's @ceirrnetwork.bsky.social seminar related to characterizing the human neutralizing antibody landscape to human seasonal influenza for purposes such as vaccine strain selection: slides.com/jbloom/flu-s...

pnas.orgFunctional and antigenic constraints on the Nipah virus fusion protein | PNASNipah virus is a highly pathogenic virus in the family Paramyxoviridae that utilizes two distinct surface glycoproteins to infect cells. The recept...

In new study led by Brendan Larsen, we map functional constraint across the Nipah virus F protein to define constrained epitopes for antibody targeting and identify mutations that stabilize the prefusion conformation for vaccine immunogens. www.pnas.org/doi/10.1073/...

We also defined how F mutations affect neutralization by a panel of monoclonal antibodies. This allowed us to quantify the resilience of different antibodies to escape, and predict which antibodies also neutralize the related Hendra virus.

pnas.orgPNASProceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...

See the full paper for additional details and analyses: www.pnas.org/doi/10.1073/... Thanks to Brendan Larsen for leading study & our collaborators in @veeslerlab.bsky.social lab.

For this study, we used pseudoviruses that can only undergo a single round of cell entry (& so are not human pathogens) to measure how mutations to F affect its fusion function. We found F is more functionally constrained than the other Nipah surface protein, RBP.

A strategy for vaccines is to stabilize F in pre-fusion conformation. We identified sites where mutations to proline (which blocks helix formation) are disfavored. This identifies new candidate mutations for stabilizing F vaccine immunogens.