Evidence map›Paper›PMID 40345199›Full record

ArticleImmunity2025

Computationally designed proteins mimic antibody immune evasion in viral evolution.

Noor Youssef, Sarah Gurev, Fadi Ghantous, Kelly P Brock, Javier A Jaimes, Nicole N Thadani, Ann Dauphin, Amy C Sherman, Leonid Yurkovetskiy, Daria Soto and 13 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Immunity, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.

0numbers the graph read from it
0cells of the map it votes in
12citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

12 citing papers in PubMed.

  1. Review
  2. Review
  3. Review
  4. Article
  5. Article
  6. Review
  7. Machine learning reveals hidden dimensions of functional similarity in proteins.Proceedings of the National Academy of Sciences of the United States of America · 2026
    Article
  8. Review
  9. Constrained Evolutionary Funnels Shape Viral Immune Escape.bioRxiv : the preprint server for biology · 2025
    Article
  10. Article
  11. Review
  12. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

23 authors.

Noor YoussefDepartment of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02139, USA.
Sarah GurevDepartment of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02139, USA; Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA 02139, USA.
Fadi GhantousCenter for Virology and Vaccine Research Beth Israel Deaconess Medical Center, Boston, MA 02215, USA.
Kelly P BrockDepartment of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02139, USA.
Javier A JaimesProgram in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA.
Nicole N ThadaniDepartment of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02139, USA.
Ann DauphinProgram in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA.
Amy C ShermanDivision of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA.
Leonid YurkovetskiyProgram in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA.
Daria SotoProgram in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA.
Ralph EstanbouliehDepartment of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
Ben KotzenBroad Institute of Harvard and MIT, Cambridge, MA 02139, USA; Massachusetts General Hospital, Boston, MA 02114, USA.
Pascal NotinDepartment of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02139, USA.
Aaron W KollaschDepartment of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02139, USA.
Alexander A CohenDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
Sandra E DrossDepartment of Microbiology, University of Washington, Seattle, WA 98195, USA; National Primate Research Center, Seattle, WA 98109, USA.
Jesse ErasmusHDT Bio, Seattle, WA 98109, USA.
Deborah H FullerDepartment of Microbiology, University of Washington, Seattle, WA 98195, USA; National Primate Research Center, Seattle, WA 98109, USA.
Pamela J BjorkmanDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
Jacob E LemieuxBroad Institute of Harvard and MIT, Cambridge, MA 02139, USA; Massachusetts General Hospital, Boston, MA 02114, USA; Massachusetts Consortium on Pathogen Readiness, Boston, MA 02115, USA. Electronic address: lemieux@broadinstitute.org.
Jeremy LubanBroad Institute of Harvard and MIT, Cambridge, MA 02139, USA; Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA; Massachusetts Consortium on Pathogen Readiness, Boston, MA 02115, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA. Electronic address: jeremy.luban@umassmed.edu.
Michael S SeamanCenter for Virology and Vaccine Research Beth Israel Deaconess Medical Center, Boston, MA 02215, USA. Electronic address: mseaman@bidmc.harvard.edu.
Debora S MarksDepartment of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02139, USA. Electronic address: debbie@hms.harvard.edu.

Funding

The HUSH complex in HIV-1 latencyR37AI147868 · NIAID · UNIV OF MASSACHUSETTS MED SCH WORCESTER · PI JEREMY LUBAN · 2019 to 2026
$6.4M
NIAID NIH HHS R37 AI147868
6 · The paper itself

Abstract

Recurrent waves of viral infection necessitate vaccines and therapeutics that remain effective against emerging viruses. Our ability to evaluate interventions is currently limited to assessments against past or circulating variants, which likely differ in their immune escape potential compared with future variants. To address this, we developed EVE-Vax, a computational method for designing antigens that foreshadow immune escape observed in future viral variants. We designed 83 SARS-CoV-2 spike proteins that transduced ACE2-positive cells and displayed neutralization resistance comparable to variants that emerged up to 12 months later in the COVID-19 pandemic. Designed spikes foretold antibody escape from B.1-BA.4/5 bivalent booster sera seen in later variants. The designed constructs also highlighted the increased neutralization breadth elicited by nanoparticle-based, compared with mRNA-based, boosters in non-human primates. Our approach offers targeted panels of synthetic proteins that map the immune landscape for early vaccine and therapeutic evaluation against future viral strains.

Indexed as

Antibodies, ViralCOVID-19COVID-19 VaccinesImmune EvasionSARS-CoV-2Spike Glycoprotein, CoronavirusAngiotensin-Converting Enzyme 2AnimalsAntibodies, NeutralizingEvolution, MolecularHumansAngiotensin-Converting Enzyme 2Antibodies, NeutralizingAntibodies, ViralCOVID-19 VaccinesSpike Glycoprotein, Coronavirusspike protein, SARS-CoV-2antibody escapegenerative protein modelsimmune landscapemachine learningprotein designvaccine evaluationviral evolution

Identifiers

PMID40345199
PMCPMC13110123

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.