Evidence map›Paper›PMID 35922441›Full record

ArticleNature communications2022

Identification of IOMA-class neutralizing antibodies targeting the CD4-binding site on the HIV-1 envelope glycoprotein.

Jelle van Schooten, Elinaz Farokhi, Anna Schorcht, Tom L G M van den Kerkhof, Hongmei Gao, Patricia van der Woude, Judith A Burger, Tim G Rijkhold Meesters, Tom Bijl, Riham Ghalaiyini and 15 more

Open access · goldAbstract read
In one paragraph

Article in Nature communications, 2022. 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
1.5field-weighted citation impact, top 15% of its field
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, 20 citations in OpenAlex.

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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

25 authors at 5 institutions in 2 countries.

Jelle van SchootenDepartment of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, 1105AZ, The Netherlands.ORCID http://orcid.org/0000-0002-5202-355X
Elinaz FarokhiDepartment of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.ORCID http://orcid.org/0000-0003-3822-5857
Anna SchorchtDepartment of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, 1105AZ, The Netherlands.
Tom L G M van den KerkhofDepartment of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, 1105AZ, The Netherlands.
Hongmei GaoDepartment of Surgery, Duke University Medical Center, Durham, NC, 27710, USA.
Patricia van der WoudeDepartment of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, 1105AZ, The Netherlands.
Judith A BurgerDepartment of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, 1105AZ, The Netherlands.
Tim G Rijkhold MeestersDepartment of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, 1105AZ, The Netherlands.ORCID http://orcid.org/0000-0002-4750-8552
Tom BijlDepartment of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, 1105AZ, The Netherlands.
Riham GhalaiyiniDepartment of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, 1105AZ, The Netherlands.
Hannah L TurnerDepartment of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
Jessica DorningCenter for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA.
Barbera D C van SchaikBioinformatics Laboratory, Department of Epidemiology and Data Science, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, 1105AZ, The Netherlands.
Antoine H C van KampenBioinformatics Laboratory, Department of Epidemiology and Data Science, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, 1105AZ, The Netherlands.
Celia C LabrancheDepartment of Surgery, Duke University Medical Center, Durham, NC, 27710, USA.ORCID http://orcid.org/0000-0002-6653-6655
Robyn L StanfieldDepartment of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
Devin SokDepartment of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
David C MontefioriDepartment of Surgery, Duke University Medical Center, Durham, NC, 27710, USA.ORCID http://orcid.org/0000-0003-0856-6319
Dennis R BurtonDepartment of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA.ORCID http://orcid.org/0000-0001-6711-9864
Michael S SeamanCenter for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA.
Gabriel OzorowskiDepartment of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.ORCID http://orcid.org/0000-0002-9695-8138
Ian A WilsonDepartment of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.ORCID http://orcid.org/0000-0002-6469-2419
Rogier W SandersDepartment of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, 1105AZ, The Netherlands.ORCID http://orcid.org/0000-0002-2324-8573
Andrew B WardDepartment of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.ORCID http://orcid.org/0000-0001-7153-3769
Marit J van GilsDepartment of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, 1105AZ, The Netherlands. M.J.vangils@amsterdamumc.nl.ORCID http://orcid.org/0000-0003-3422-8161
Amsterdam University Medical Centers · NLScripps Research Institute · USDuke Medical Center · USBeth Israel Deaconess Medical Center · USCornell University · US

Funding

Identification of neutralizing epitopes on SARS-CoV-2 spike for design of vaccines and small-molecule antiviralsUM1AI144462 · NIAID · SCRIPPS RESEARCH INSTITUTE, THE · PI BURTON, DENNIS R. · 2019 to 2025
$201.6M
Structural studies of native-like SOSIP trimersP01AI110657 · NIAID · WEILL MEDICAL COLL OF CORNELL UNIV · PI MOORE, JOHN P · 2015 to 2024
$35.4M
X-ray Absorption Spectroscopy (XAS) pp.711-759P41GM103393 · NIGMS · STANFORD UNIVERSITY · PI HODGSON, KEITH O · 2012 to 2019
$30.6M
User Training and OutreachP30GM124169 · NIGMS · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI PAUL David ADAMS, Gregory L Hura · 2017 to 2026
$28.6M
Gates Foundation INV-002022NIAID NIH HHS HHSN272201800004CNIAID NIH HHS P01 AI110657NIAID NIH HHS UM1 AI144462NIGMS NIH HHS P30 GM124169NIGMS NIH HHS P41 GM103393
6 · The paper itself

Abstract

A major goal of current HIV-1 vaccine design efforts is to induce broadly neutralizing antibodies (bNAbs). The VH1-2-derived bNAb IOMA directed to the CD4-binding site of the HIV-1 envelope glycoprotein is of interest because, unlike the better-known VH1-2-derived VRC01-class bNAbs, it does not require a rare short light chain complementarity-determining region 3 (CDRL3). Here, we describe three IOMA-class NAbs, ACS101-103, with up to 37% breadth, that share many characteristics with IOMA, including an average-length CDRL3. Cryo-electron microscopy revealed that ACS101 shares interactions with those observed with other VH1-2 and VH1-46-class bNAbs, but exhibits a unique binding mode to residues in loop D. Analysis of longitudinal sequences from the patient suggests that a transmitter/founder-virus lacking the N276 glycan might have initiated the development of these NAbs. Together these data strengthen the rationale for germline-targeting vaccination strategies to induce IOMA-class bNAbs and provide a wealth of sequence and structural information to support such strategies.

Indexed as

HIV-1HIV InfectionsAntibodies, NeutralizingAntigens, ViralBinding SitesBroadly Neutralizing AntibodiesCD4 AntigensComplementarity Determining RegionsCryoelectron MicroscopyGlycoproteinsHIV AntibodiesHumansAntibodies, NeutralizingAntigens, ViralBroadly Neutralizing AntibodiesCD4 AntigensComplementarity Determining RegionsGlycoproteinsHIV Antibodies

Identifiers

PMID35922441
PMCPMC9349188
OpenAlexW4289654196

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.