Bloom lab
@jbloomlab.bsky.social
Lab studying molecular evolution of proteins and viruses. Affiliated with Fred Hutch & HHMI.
Opinions are my own and do not reflect those of my employer.
https://jbloomlab.org/
Opinions are my own and do not reflect those of my employer.
https://jbloomlab.org/
The final published version of this study is now available in Journal of Virology at journals.asm.org/doi/10.1128/...
Spike mutations that affect the function and antigenicity of recent KP.3.1.1-like SARS-CoV-2 variants | Journal of Virology
This study measures how mutations to the spike of a SARS-CoV-2 variant that circulated
in early 2025 affect its function and recognition by both the polyclonal antibodies
produced by the human immune ...
journals.asm.org
October 14, 2025 at 4:22 PM
The final published version of this study is now available in Journal of Virology at journals.asm.org/doi/10.1128/...
Finally, we plan to repeat this effort in ~6 months prior to next vaccine strain selection. If you have sera cohorts that you think would be well suited for this type of study and are potentially interesting in collaborating, please feel free to reach out.
September 8, 2025 at 9:55 PM
Finally, we plan to repeat this effort in ~6 months prior to next vaccine strain selection. If you have sera cohorts that you think would be well suited for this type of study and are potentially interesting in collaborating, please feel free to reach out.
Thanks to @ckikawa.bsky.social & @huddlej.bsky.social for leading study, also: Andrea Loes, Sam Turner, Jover Lee, Ian Barr, Ben Cowling, Jan Englund, Alex Greninger, Ruth Harvey, H Hasegawa, Faith Ho, K Lacombe, Nancy Leung, Nicola Lewis, Heidi Peck, Shinji Watanabe, Derek Smith, Trevor Bedford
September 8, 2025 at 9:55 PM
Thanks to @ckikawa.bsky.social & @huddlej.bsky.social for leading study, also: Andrea Loes, Sam Turner, Jover Lee, Ian Barr, Ben Cowling, Jan Englund, Alex Greninger, Ruth Harvey, H Hasegawa, Faith Ho, K Lacombe, Nancy Leung, Nicola Lewis, Heidi Peck, Shinji Watanabe, Derek Smith, Trevor Bedford
Many more analyses are possible w these data. But we have made all data & code available now at github.com/jbloomlab/fl...
Reason is to provide near real-time titer data that can be leveraged by scientific community for real-time decisions like vaccine strain selection.
Reason is to provide near real-time titer data that can be leveraged by scientific community for real-time decisions like vaccine strain selection.
GitHub - jbloomlab/flu-seqneut-2025
Contribute to jbloomlab/flu-seqneut-2025 development by creating an account on GitHub.
github.com
September 8, 2025 at 9:53 PM
Many more analyses are possible w these data. But we have made all data & code available now at github.com/jbloomlab/fl...
Reason is to provide near real-time titer data that can be leveraged by scientific community for real-time decisions like vaccine strain selection.
Reason is to provide near real-time titer data that can be leveraged by scientific community for real-time decisions like vaccine strain selection.
Above visualizations just scratch surface of data: there is tremendous heterogeneity across sera from different individuals not easily summarized by median/mean.
Indeed, we previously found this heterogeneity may be important for influenza evolution: elifesciences.org/reviewed-pre...
Indeed, we previously found this heterogeneity may be important for influenza evolution: elifesciences.org/reviewed-pre...
September 8, 2025 at 9:53 PM
Above visualizations just scratch surface of data: there is tremendous heterogeneity across sera from different individuals not easily summarized by median/mean.
Indeed, we previously found this heterogeneity may be important for influenza evolution: elifesciences.org/reviewed-pre...
Indeed, we previously found this heterogeneity may be important for influenza evolution: elifesciences.org/reviewed-pre...
Working w @huddlej.bsky.social & Trevor Bedford, we mapped neutralization titers on interactive Nextstrain trees to visualize neutralization across subclades and natural mutations.
See:
nextstrain.org/groups/blab/...
nextstrain.org/groups/blab/...
See:
nextstrain.org/groups/blab/...
nextstrain.org/groups/blab/...
auspice
nextstrain.org
September 8, 2025 at 9:52 PM
Working w @huddlej.bsky.social & Trevor Bedford, we mapped neutralization titers on interactive Nextstrain trees to visualize neutralization across subclades and natural mutations.
See:
nextstrain.org/groups/blab/...
nextstrain.org/groups/blab/...
See:
nextstrain.org/groups/blab/...
nextstrain.org/groups/blab/...
We then measured how 188 human sera recently collected at four different sites neutralized all 140 influenza strains in library.
Titers are summarized below; can be examined interactively at jbloomlab.github.io/flu-seqneut-... & jbloomlab.github.io/flu-seqneut-...
Titers are summarized below; can be examined interactively at jbloomlab.github.io/flu-seqneut-... & jbloomlab.github.io/flu-seqneut-...
September 8, 2025 at 9:52 PM
We then measured how 188 human sera recently collected at four different sites neutralized all 140 influenza strains in library.
Titers are summarized below; can be examined interactively at jbloomlab.github.io/flu-seqneut-... & jbloomlab.github.io/flu-seqneut-...
Titers are summarized below; can be examined interactively at jbloomlab.github.io/flu-seqneut-... & jbloomlab.github.io/flu-seqneut-...
In spring of 2025, we designed library of naturally occurring human seasonal influenza strains that represented diversity of available sequences at that time; this library continues to cover most sequenced diversity of H3N2 and H1N1 hemagglutinin today.
September 8, 2025 at 9:51 PM
In spring of 2025, we designed library of naturally occurring human seasonal influenza strains that represented diversity of available sequences at that time; this library continues to cover most sequenced diversity of H3N2 and H1N1 hemagglutinin today.
To do this, we used sequencing-based neutralization assays that measure many neutralization curves simultaneously (journals.asm.org/doi/10.1128/... & elifesciences.org/reviewed-pre...)
Approach enabled one grad student (@ckikawa.bsky.social) to measure ~26,000 neutralization curves in ~5 months.
Approach enabled one grad student (@ckikawa.bsky.social) to measure ~26,000 neutralization curves in ~5 months.
September 8, 2025 at 9:51 PM
To do this, we used sequencing-based neutralization assays that measure many neutralization curves simultaneously (journals.asm.org/doi/10.1128/... & elifesciences.org/reviewed-pre...)
Approach enabled one grad student (@ckikawa.bsky.social) to measure ~26,000 neutralization curves in ~5 months.
Approach enabled one grad student (@ckikawa.bsky.social) to measure ~26,000 neutralization curves in ~5 months.
But because it takes time to perform experiments, measurement of how current strains are neutralized by human serum antibodies can lag timeline for vaccine strain selection.
Our goal was to use new approach to characterize human antibody landscape at scale in near real-time.
Our goal was to use new approach to characterize human antibody landscape at scale in near real-time.
September 8, 2025 at 9:49 PM
But because it takes time to perform experiments, measurement of how current strains are neutralized by human serum antibodies can lag timeline for vaccine strain selection.
Our goal was to use new approach to characterize human antibody landscape at scale in near real-time.
Our goal was to use new approach to characterize human antibody landscape at scale in near real-time.
As background, seasonal influenza evolves to erode antibody immunity.
Viruses w more antibody escape spread in human population & people more likely to be infected by strains their antibodies neutralize less well.
Vaccine updated bi-annually to keep pace w viral evolution.
Viruses w more antibody escape spread in human population & people more likely to be infected by strains their antibodies neutralize less well.
Vaccine updated bi-annually to keep pace w viral evolution.
September 8, 2025 at 9:49 PM
As background, seasonal influenza evolves to erode antibody immunity.
Viruses w more antibody escape spread in human population & people more likely to be infected by strains their antibodies neutralize less well.
Vaccine updated bi-annually to keep pace w viral evolution.
Viruses w more antibody escape spread in human population & people more likely to be infected by strains their antibodies neutralize less well.
Vaccine updated bi-annually to keep pace w viral evolution.
Data in interactive form at dms-vep.org/CHIKV-181-25...
Thanks to Xiaohui Ju for leading study
Special thanks to @msdiamondlab.bsky.social for help
Also Will Hannon, Caelan Radford, Brendan Larsen, Daved Fremont, Ofer Zimmerman, Tomasz Kaszuba, Chris Nelson, Israel Baltazar-Perez, Samantha Nelson
Thanks to Xiaohui Ju for leading study
Special thanks to @msdiamondlab.bsky.social for help
Also Will Hannon, Caelan Radford, Brendan Larsen, Daved Fremont, Ofer Zimmerman, Tomasz Kaszuba, Chris Nelson, Israel Baltazar-Perez, Samantha Nelson
September 4, 2025 at 11:20 PM
Data in interactive form at dms-vep.org/CHIKV-181-25...
Thanks to Xiaohui Ju for leading study
Special thanks to @msdiamondlab.bsky.social for help
Also Will Hannon, Caelan Radford, Brendan Larsen, Daved Fremont, Ofer Zimmerman, Tomasz Kaszuba, Chris Nelson, Israel Baltazar-Perez, Samantha Nelson
Thanks to Xiaohui Ju for leading study
Special thanks to @msdiamondlab.bsky.social for help
Also Will Hannon, Caelan Radford, Brendan Larsen, Daved Fremont, Ofer Zimmerman, Tomasz Kaszuba, Chris Nelson, Israel Baltazar-Perez, Samantha Nelson
Overall, these results shed light on how Chikungunya virus naturally infects cells from highly diverse species.
Sequence-function information can aid in immunogen engineering, and loss-of-tropism mutants could be useful in vaccines as well.
Sequence-function information can aid in immunogen engineering, and loss-of-tropism mutants could be useful in vaccines as well.
September 4, 2025 at 11:17 PM
Overall, these results shed light on how Chikungunya virus naturally infects cells from highly diverse species.
Sequence-function information can aid in immunogen engineering, and loss-of-tropism mutants could be useful in vaccines as well.
Sequence-function information can aid in immunogen engineering, and loss-of-tropism mutants could be useful in vaccines as well.
After using pseudoviruses & reporter particles to show mutations *loss* of function, we engineered into Chikungunya virus: mutants lost ability to infect human or mosquito cells.
So we reduced natural tropism for both human & mosquito cells to just one type of cell.
So we reduced natural tropism for both human & mosquito cells to just one type of cell.
September 4, 2025 at 11:17 PM
After using pseudoviruses & reporter particles to show mutations *loss* of function, we engineered into Chikungunya virus: mutants lost ability to infect human or mosquito cells.
So we reduced natural tropism for both human & mosquito cells to just one type of cell.
So we reduced natural tropism for both human & mosquito cells to just one type of cell.
We next used non-replicative single-cycle alphavirus reporter particles (which provide another safe way to study mutations) to validate that mutations identified in deep mutational scanning indeed specifically impaired entry in human or mosquito cells only.
September 4, 2025 at 11:16 PM
We next used non-replicative single-cycle alphavirus reporter particles (which provide another safe way to study mutations) to validate that mutations identified in deep mutational scanning indeed specifically impaired entry in human or mosquito cells only.
Sites where mutations specifically impair entry in 293T-MXRA8 cells mostly at MXRA8 binding interface.
We also find sites where mutations specifically impair entry in C6/36 cells. Although mosquito receptor unknown, we hypothesize these sites at its binding interface.
We also find sites where mutations specifically impair entry in C6/36 cells. Although mosquito receptor unknown, we hypothesize these sites at its binding interface.
September 4, 2025 at 11:15 PM
Sites where mutations specifically impair entry in 293T-MXRA8 cells mostly at MXRA8 binding interface.
We also find sites where mutations specifically impair entry in C6/36 cells. Although mosquito receptor unknown, we hypothesize these sites at its binding interface.
We also find sites where mutations specifically impair entry in C6/36 cells. Although mosquito receptor unknown, we hypothesize these sites at its binding interface.
Most mutations similarly affect entry in all three cells, but some have cell-specific effects.
For instance, mutations at E2 site 119 are generally tolerated in C6/36 and 293T-TIM1 cells, but deleterious in 293T-MXRA8 cells.
(See dms-vep.org/CHIKV-181-25... for interactive plot.)
For instance, mutations at E2 site 119 are generally tolerated in C6/36 and 293T-TIM1 cells, but deleterious in 293T-MXRA8 cells.
(See dms-vep.org/CHIKV-181-25... for interactive plot.)
September 4, 2025 at 11:15 PM
Most mutations similarly affect entry in all three cells, but some have cell-specific effects.
For instance, mutations at E2 site 119 are generally tolerated in C6/36 and 293T-TIM1 cells, but deleterious in 293T-MXRA8 cells.
(See dms-vep.org/CHIKV-181-25... for interactive plot.)
For instance, mutations at E2 site 119 are generally tolerated in C6/36 and 293T-TIM1 cells, but deleterious in 293T-MXRA8 cells.
(See dms-vep.org/CHIKV-181-25... for interactive plot.)
We then measured how mutations affect entry in two other cells: the mosquito cell-line C6/36, and 293T cells expressing TIM1 which enables envelope protein independent cell binding by virion associated phosphatidylserine.
September 4, 2025 at 11:14 PM
We then measured how mutations affect entry in two other cells: the mosquito cell-line C6/36, and 293T cells expressing TIM1 which enables envelope protein independent cell binding by virion associated phosphatidylserine.
We first measured how mutations affect entry in 293T cells expressing human receptor MXRA8.
Below is constraint mapped on structure; see dms-vep.org/CHIKV-181-25... for interactive heatmap of these data.
Below is constraint mapped on structure; see dms-vep.org/CHIKV-181-25... for interactive heatmap of these data.
September 4, 2025 at 11:14 PM
We first measured how mutations affect entry in 293T cells expressing human receptor MXRA8.
Below is constraint mapped on structure; see dms-vep.org/CHIKV-181-25... for interactive heatmap of these data.
Below is constraint mapped on structure; see dms-vep.org/CHIKV-181-25... for interactive heatmap of these data.
We used pseudovirus deep mutational scanning to measure effects of all mutations to envelope proteins in context of single-cycle pseudotyped particles that provide a safe way to study viral protein mutations outside context of fully infectious virus.
September 4, 2025 at 11:13 PM
We used pseudovirus deep mutational scanning to measure effects of all mutations to envelope proteins in context of single-cycle pseudotyped particles that provide a safe way to study viral protein mutations outside context of fully infectious virus.
Chikungunya virus enters cell using its envelope proteins, which are also target of neutralizing antibodies and vaccine design.
A receptor for these viral proteins in mammalian cells is the protein MXRA8, but receptor in mosquito cells is unknown.
A receptor for these viral proteins in mammalian cells is the protein MXRA8, but receptor in mosquito cells is unknown.
September 4, 2025 at 11:13 PM
Chikungunya virus enters cell using its envelope proteins, which are also target of neutralizing antibodies and vaccine design.
A receptor for these viral proteins in mammalian cells is the protein MXRA8, but receptor in mosquito cells is unknown.
A receptor for these viral proteins in mammalian cells is the protein MXRA8, but receptor in mosquito cells is unknown.
As background, Chikungunya virus has transmission cycle that involves infecting both mosquitoes & humans or other primates.
Infection can cause fever and severe joint pain in humans.
Outbreaks are growing due to expanding mosquito range: www.nytimes.com/2025/08/19/h...
Infection can cause fever and severe joint pain in humans.
Outbreaks are growing due to expanding mosquito range: www.nytimes.com/2025/08/19/h...
September 4, 2025 at 11:12 PM
As background, Chikungunya virus has transmission cycle that involves infecting both mosquitoes & humans or other primates.
Infection can cause fever and severe joint pain in humans.
Outbreaks are growing due to expanding mosquito range: www.nytimes.com/2025/08/19/h...
Infection can cause fever and severe joint pain in humans.
Outbreaks are growing due to expanding mosquito range: www.nytimes.com/2025/08/19/h...