Evidence map›Paper›PMID 38724518›Full record

ArticleNature communications2024

Contemporary HIV-1 consensus Env with AI-assisted redesigned hypervariable loops promote antibody binding.

Hongjun Bai, Eric Lewitus, Yifan Li, Paul V Thomas, Michelle Zemil, Mélanie Merbah, Caroline E Peterson, Thujitha Thuraisamy, Phyllis A Rees, Agnes Hajduczki and 18 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.

0numbers the graph read from it
0cells of the map it votes in
9citing 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

9 citing papers in PubMed.

  1. Trial
  2. Article
  3. Review
  4. Article
  5. Article
  6. Designs for Vaccine Studies.Annual review of statistics and its application · 2025
    Article
  7. Article
  8. Review
  9. 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

28 authors.

Hongjun BaiU.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA.ORCID http://orcid.org/0000-0002-3501-3974
Eric LewitusU.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA.ORCID http://orcid.org/0000-0001-6459-2437
Yifan LiU.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA.ORCID http://orcid.org/0000-0001-7038-2671
Paul V ThomasHenry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA.ORCID http://orcid.org/0000-0002-6772-3997
Michelle ZemilU.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA.ORCID http://orcid.org/0000-0002-1700-6658
Mélanie MerbahU.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA.
Caroline E PetersonHenry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA.
Thujitha ThuraisamyU.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA.
Phyllis A ReesHenry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA.
Agnes HajduczkiHenry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA.
Vincent DussuptU.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA.ORCID http://orcid.org/0000-0002-8579-6356
Bonnie SlikeU.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA.ORCID http://orcid.org/0000-0003-4132-4637
Letzibeth Mendez-RiveraU.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA.
Annika SchmidU.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA.
Erin KavusakU.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA.
Mekhala RaoU.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA.
Gabriel SmithU.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA.
Jessica FreyU.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA.ORCID http://orcid.org/0009-0007-1456-8720
Alicea SimsU.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA.ORCID http://orcid.org/0009-0001-9249-5228
Lindsay WieczorekU.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA.
Victoria PolonisU.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA.
Shelly J KrebsU.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA.ORCID http://orcid.org/0000-0003-1136-1760
Julie A AkeU.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA.
Sandhya VasanU.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA.ORCID http://orcid.org/0000-0002-6378-6288
Diane L BoltonU.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA.ORCID http://orcid.org/0000-0003-1897-499X
M Gordon JoyceHenry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA.
Samantha TownsleyU.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA.
Morgane RollandU.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA. mrolland@hivresearch.org.ORCID http://orcid.org/0000-0003-3650-8490

Funding

Designing HIV-1 envelope immunogens to maximize neutralization breadth through use of multiple founder envelope antigensR01AI176520 · NIAID · HENRY M. JACKSON FDN FOR THE ADV MIL/MED · PI BOLTON, DIANE L. · 2023 to 2025
$3.3M
NIAID NIH HHS R01 AI176520
6 · The paper itself

Abstract

An effective HIV-1 vaccine must elicit broadly neutralizing antibodies (bnAbs) against highly diverse Envelope glycoproteins (Env). Since Env with the longest hypervariable (HV) loops is more resistant to the cognate bnAbs than Env with shorter HV loops, we redesigned hypervariable loops for updated Env consensus sequences of subtypes B and C and CRF01_AE. Using modeling with AlphaFold2, we reduced the length of V1, V2, and V5 HV loops while maintaining the integrity of the Env structure and glycan shield, and modified the V4 HV loop. Spacers are designed to limit strain-specific targeting. All updated Env are infectious as pseudoviruses. Preliminary structural characterization suggests that the modified HV loops have a limited impact on Env's conformation. Binding assays show improved binding to modified subtype B and CRF01_AE Env but not to subtype C Env. Neutralization assays show increases in sensitivity to bnAbs, although not always consistently across clades. Strikingly, the HV loop modification renders the resistant CRF01_AE Env sensitive to 10-1074 despite the absence of a glycan at N332.

Indexed as

Antibodies, Neutralizingenv Gene Products, Human Immunodeficiency VirusHIV-1HIV AntibodiesAIDS VaccinesConsensus SequenceEpitopesHEK293 CellsHIV InfectionsHumansNeutralization TestsProtein BindingAIDS VaccinesAntibodies, Neutralizingenv Gene Products, Human Immunodeficiency VirusEpitopesHIV Antibodies

Identifiers

PMID38724518
PMCPMC11082178

What OpenQuestion holds

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Registered trials

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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.