Evidence map›Paper›PMID 31097697›Full record

ArticleNature communications2019

Kappa chain maturation helps drive rapid development of an infant HIV-1 broadly neutralizing antibody lineage.

Cassandra A Simonich, Laura Doepker, Duncan Ralph, James A Williams, Amrit Dhar, Zak Yaffe, Lauren Gentles, Christopher T Small, Brian Oliver, Vladimir Vigdorovich and 6 more

Open access · goldAbstract read
In one paragraph

Article in Nature communications, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
27citing papers in PubMed, 1 pooled it
3.3field-weighted citation impact, top 7% 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

27 citing papers in PubMed, 1 synthesis or guideline pooled it, 41 citations in OpenAlex.

  1. Pooled it
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  6. An updated AL-base reveals ranked enrichment of immunoglobulin light chain variable genes in AL amyloidosis.Amyloid : the international journal of experimental and clinical investigation : the official journal of the International Society of Amyloidosis · 2025
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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

16 authors at 5 institutions in 3 countries.

Cassandra A SimonichDivision of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA.
Laura DoepkerDivision of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA.ORCID http://orcid.org/0000-0003-4514-5003
Duncan RalphPublic Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA.
James A WilliamsDepartment of Medicinal Chemistry, University of Washington, Seattle, WA, 98195, USA.
Amrit DharPublic Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA.
Zak YaffeMedical Scientist Training Program, University of Washington School of Medicine, Seattle, WA, 98195, USA.
Lauren GentlesDepartment of Microbiology, University of Washington, Seattle, WA, 98195, USA.
Christopher T SmallPublic Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA.
Brian OliverCenter for Infectious Disease Research, Seattle, WA, 98109, USA.
Vladimir VigdorovichCenter for Infectious Disease Research, Seattle, WA, 98109, USA.ORCID http://orcid.org/0000-0003-4195-4858
Vidya Mangala PrasadDepartment of Medicinal Chemistry, University of Washington, Seattle, WA, 98195, USA.
Ruth NduatiDepartment of Pediatrics and Child Health, University of Nairobi, Nairobi, Kenya.
D Noah SatherCenter for Infectious Disease Research, Seattle, WA, 98109, USA.
Kelly K LeeDepartment of Medicinal Chemistry, University of Washington, Seattle, WA, 98195, USA.
Frederick A Matsen IvPublic Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA.ORCID http://orcid.org/0000-0003-0607-6025
Julie OverbaughDivision of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA. joverbau@fredhutch.org.
University of Washington · USFred Hutch Cancer Center · USCenter for Infectious Disease Research · USCape Town HVTN Immunology Laboratory / Hutchinson Centre Research Institute of South Africa · ZAUniversity of Nairobi · KE

Funding

University of Washington/Fred Hutch Center for AIDS ResearchP30AI027757 · NIAID · UNIVERSITY OF WASHINGTON · PI Judith Tsui · 1988 to 2026
$104.9M
University of Washington Medical Scientist Training Program: MD/PhDT32GM007266 · NIGMS · UNIVERSITY OF WASHINGTON · PI HORWITZ, MARSHALL S. · 1985 to 2023
$30.4M
VENEREAL DISEASET32AI007140 · NIAID · UNIVERSITY OF WASHINGTON · PI Julia Cook Dombrowski · 1985 to 2026
$19.4M
Modeling the dynamics and evolution of immune responses to influenza virusesU19AI117891 · NIAID · EMORY UNIVERSITY · PI AHMED, RAFI, ANTIA, RUSTOM NOSHIR · 2015 to 2019
$8.4M
Leveraing deep sequencing data to understand antibody maturationR01GM113246 · NIGMS · FRED HUTCHINSON CANCER RESEARCH CENTER · PI MATSEN, FREDERICK ALBERT · 2014 to 2018
$1.9M
Characterizing broadly neutralizing antibody responses of HIV-1-infected infantsF30AI122866 · NIAID · UNIVERSITY OF WASHINGTON · PI SIMONICH, CASSANDRA ARIEN LYNN · 2016 to 2018
$125k
NIAID NIH HHS F30 AI122866NIAID NIH HHS P30 AI027757NIAID NIH HHS T32 AI007140NIAID NIH HHS U19 AI117891NIGMS NIH HHS R01 GM113246NIGMS NIH HHS T32 GM007266
6 · The paper itself

Abstract

HIV-infected infants develop broadly neutralizing plasma responses with more rapid kinetics than adults, suggesting the ontogeny of infant responses could better inform a path to achievable vaccine targets. Here we reconstruct the developmental lineage of BF520.1, an infant-derived HIV-specific broadly neutralizing antibody (bnAb), using computational methods developed specifically for this purpose. We find that the BF520.1 inferred naive precursor binds HIV Env. We also show that heterologous cross-clade neutralizing activity evolved in the infant within six months of infection and that, ultimately, only 2% SHM is needed to achieve the full breadth of the mature antibody. Mutagenesis and structural analyses reveal that, for this infant bnAb, substitutions in the kappa chain were critical for activity, particularly in CDRL1. Overall, the developmental pathway of this infant antibody includes features distinct from adult antibodies, including several that may be amenable to better vaccine responses.

Indexed as

Age FactorsAIDS VaccinesAntibodies, NeutralizingComputational BiologyCross ReactionsDrug Designenv Gene Products, Human Immunodeficiency VirusHIV-1HIV AntibodiesHIV InfectionsHumansImmunoglobulin kappa-ChainsInfantLeukocytes, MononuclearMutagenesisSequence Analysis, DNAAIDS VaccinesAntibodies, Neutralizingenv Gene Products, Human Immunodeficiency VirusHIV AntibodiesImmunoglobulin kappa-Chains

Identifiers

PMID31097697
PMCPMC6522554
OpenAlexW2945941055

What OpenQuestion holds

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LicenceCC BY
Read underepoch 390

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.