Bloom lab

RSV F evolution escapes some monoclonal antibodies but does not strongly erode neutralization by human polyclonal sera | Journal of Virology We describe an efficient approach to measure how antibodies inhibit infection by historical and recent human strains of respiratory syncytial virus (RSV). This approach is useful for understanding how...

Final version of this paper is published in Journal of Virology: journals.asm.org/doi/10.1128/...

If you are interested in implementing RSV pseudovirus neutralization assays, the plasmids are now available in AddGene (www.addgene.org/browse/artic...) and we are happy to share the 293T-TIM1 cells.

For anyone not familiar with early SARS-CoV-2 phylogenetics, here is an accompany interactive Nextstrain narrative that makes it possible to examine the underlying data and different possible roots: nextstrain.org/groups/jbloo...

The Data are Insufficient to Confidently Root the SARS-CoV-2 Phylogenetic Tree Abstract. Several years ago, I published a paper that described the discrepancy between outgroup and date-based methods for rooting the SARS-CoV-2 phylogen

I wrote a full response here that explains why there is a discrepancy between outgroup- and date-based rooting that makes it impossible to confidently root the tree: academic.oup.com/mbe/article/...

If you aren't familiar with early SARS-CoV-2 phylogenetic trees, I also made an interactive Nextstrain narrative you can use to look at different representations of the underlying data: nextstrain.org/groups/jbloo...

The Data are Insufficient to Confidently Root the SARS-CoV-2 Phylogenetic Tree Abstract. Several years ago, I published a paper that described the discrepancy between outgroup and date-based methods for rooting the SARS-CoV-2 phylogen

I wrote a full response to this here, which explains why there remains a discrepancy between outgroup- and date-based rooting that still makes it impossible to reliably root the tree: academic.oup.com/mbe/article/...

All the data are available for visualization and download at dms-vep.org/Flu_H3_Massa...

Thanks to @timyu.bsky.social for leading study, and also @ckikawa.bsky.social, @bdadonaite.bsky.social, Andrea Loes, & Jane Englund.

Overall, these results show how pleiotropic effects of mutations constrain HA evolution. Epistasis can alleviate these constraints w respect to cell entry in receptor binding pocket, but we find no evidence that mutations that strongly destabilize HA ever fix in H3N2 evolution.

To examine implications for antigenic evolution, we measured how all HA mutations affected serum antibody neutralization.

Mutations at key trimer interface sites that cause substantial antibody escape but destabilize HA have never fixed.

We found extensive entrenchment w respect to cell entry in receptor binding pocket (see below), consistent w prior work by @wchnicholas.bsky.social @rpdevrieslab.bsky.social
www.nature.com/articles/s41...
www.biorxiv.org/content/10.1...

But there was minimal entrenchment w respect to HA stability

We then looked for evidence of epistasis by examining whether mutations had become entrenched. A mutation is entrenched if reverting it to the ancestral amino acid is deleterious in recent HAs, as schematized below.

As can be seen below, constraint due to mutational impacts on cell entry are widely distributed across HA including receptor-binding pocket and fusion peptide. But mutational constraint due to HA stability is concentrated at trimer and HA1-HA2 interface.

We used pseudovirus deep mutational scanning to characterize all mutations to a recent H3N2 HA. This approach uses virions that can only undergo one round of cell entry & so are not pathogens capable of causing disease.

All measurements available here: dms-vep.org/Flu_H3_Massa...

Pleiotropic mutational effects on function and stability constrain the antigenic evolution of influenza hemagglutinin The evolution of human influenza virus hemagglutinin (HA) involves simultaneous selection to acquire antigenic mutations that escape population immunity while preserving protein function and stability...

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...

Deep mutational scanning of rabies glycoprotein defines mutational constraint and antibody-escape mutations Rabies virus causes nearly 60,000 human deaths annually. Antibodies that target the rabies glycoprotein (G) are being developed as post-exposure proph…

Final version of our pseudovirus deep mutational scanning of rabies glycoprotein now published in
@cp-cellhostmicrobe.bsky.social: sciencedirect.com/science/arti...

Main addition to preprint summarized above is additional validations of prefusion stabilization candidate mutations in Fig S4 and S5.

SARS-CoV-2 neutralizing antibody specificities differ dramatically between recently infected infants and immune-imprinted individuals | Journal of Virology We show that a person’s exposure history to different SARS-CoV-2 strains strongly affects which regions on the viral spike that their neutralizing antibodies target. In particular, infants who have ju...

The final published version of our study (described in thread above) on the differences in SARS2 antibody specificities in imprinted adults versus recently infected infants is now out: journals.asm.org/doi/10.1128/...

Functional and antigenic landscape of the Nipah virus receptor-binding protein Nipah virus recurrently spills over to humans, causing fatal infections. The viral receptor-binding protein (RBP or G) attaches to host receptors and …

The final version of our pseudovirus deep mutational scanning of the Nipah virus receptor-binding protein is now published.
www.sciencedirect.com/science/arti...

GitHub - jbloomlab/flu_seqneut_H3N2_2023-2024: sequencing-based neutralization assay on H3N2 HA variants from 2023-2024 sequencing-based neutralization assay on H3N2 HA variants from 2023-2024 - jbloomlab/flu_seqneut_H3N2_2023-2024

All data described above are at github.com/jbloomlab/fl...

Thanks to @ckikawa.bsky.social & Andrea Loes for leading study, w important contributions from @huddlej.bsky.social , M Figgins, P Steinberg, T Griffiths, E Troisi, Heidi Peck, Ian Barr, Jan Englund, @scottehensley.bsky.social, T Bedford

We hope that high-throughput measurements of neutralization of many recent influenza strains by many human sera, which are feasible to make w these new methods, can help w efforts to forecast influenza evolution for vaccine strain selection.

The actual growth rates of viral strains were highly correlated w fraction of sera w low titers to strains, as shown below.

But there was no correlation if we just pooled all the sera and measured titers: per-serum measurements are needed to capture population heterogeneity.

Can these measurements of antibody immunity across human population help us understand influenza evolution?

To address that question, we worked w T Bedford, @huddlej.bsky.social, M Figgins, P Steinberg to estimate growth rates of different H3N2 strains in 2023 using multinomial logistic regression.

Below are titers of a large set of sera against all the strains.

The plot shows the extensive heterogeneity of population antibody immunity: titers against different strains vary widely across individuals.

Different sera were better or worse at neutralizing different viral strains.

Below plot shows a 14-year old child neutralized most strains but had lower titers to strains mutated at site 145; a 24-year old neutralized those strains well but had lower titers to other strains.

We used this assay to measure neutralizing titers of a large set of >100 children and adult sera against a panel of viruses representing the H3N2 influenza diversity circulating in humans in 2023.

We recently developed high-throughput sequencing-based assay to measure how serum antibodies neutralize different influenza strains.

With assay, we can measure 1,872 neutralization curves per 96-well plate, compared to traditional assays that yield 8 or 12 curves per plate.

As background, human seasonal influenza evolves to erode immunity. Vaccine updated regularly to keep pace w evolution, but forecasting which viral strains will dominate next season is hard.

One limitation is we don’t fully understand human immune landscape that drives evolution.

High-throughput neutralization measurements correlate strongly with evolutionary success of human influenza strains Human influenza viruses rapidly acquire mutations in their hemagglutinin (HA) protein that erode neutralization by antibodies from prior exposures. Here, we use a sequencing-based assay to measure neu...

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...

New assays described here use single-cycle pseudoviruses, so enable study of F mutations w/o generating actual mutant viruses.

Thanks to @csimonich.bsky.social & Teagan McMahon, Xiaohui Ju, Tim Yu, Natalie Brunette, Terry Stevens-Ayers, Michael Boeckh, @kinglabipd.bsky.social, Alex Greninger

Overall, RSV F antigenic evolution slower than for influenza hemagglutinin or SARS2 spike.

However, natural mutations can escape antibodies & modestly affect sera.

As antibodies become widely used, important to monitor for antigenic changes.

Assay we describe here will help enable that monitoring

Interestingly, we found that the rare sporadic RSV strains with nirsevimab escape mutations also have reduced neutralization by human sera. Therefore, escape mutations selected by antibodies could have a moderate impact on polyclonal antibody immunity, and so merit monitoring.

However, RSV F evolution has escaped some monoclonal antibodies, and we validated that rare sporadic strains have mutations that escape the currently recommended nirsevimab antibody.