Evidence map›Paper›PMID 41494536›Full record

ArticleImmunity2026

Population-level genomic analysis of immunoglobulin loci variation in rhesus macaques reveals extensive germline diversity.

Ayelet Peres, Amit A Upadhyay, Vered Klein, Swati Saha, Oscar L Rodriguez, Zachary M Vanwinkle, Kirti Karunakaran, Amanda Metz, William Lauer, Mark C Lin and 24 more

Abstract read
In one paragraph

Article in Immunity, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.

0numbers the graph read from it
0cells of the map it votes in
6citing 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

6 citing papers in PubMed.

  1. Deletions in variable region 1 of the HIV envelope accelerate V3-glycan bNAb induction in SHIV-infected rhesus macaques.Proceedings of the National Academy of Sciences of the United States of America · 2026
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4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

34 authors.

Ayelet PeresDepartment of Pathology, Yale School of Medicine, New Haven, CT 06250, USA; Faculty of Engineering, Bar Ilan University, Ramat Gan, Israel; Bar Ilan institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan, Israel.
Amit A UpadhyayEmory National Primate Research Center, Atlanta, GA 30329, USA; Department of Pathology & Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA.
Vered KleinFaculty of Engineering, Bar Ilan University, Ramat Gan, Israel; Bar Ilan institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan, Israel.
Swati SahaDepartment of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY 40292, USA.
Oscar L RodriguezDepartment of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY 40292, USA.
Zachary M VanwinkleEmory National Primate Research Center, Atlanta, GA 30329, USA.
Kirti KarunakaranEmory National Primate Research Center, Atlanta, GA 30329, USA.
Amanda MetzEmory National Primate Research Center, Atlanta, GA 30329, USA.
William LauerDepartment of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY 40292, USA.
Mark C LinEmory National Primate Research Center, Atlanta, GA 30329, USA.
Timothy MeltonEmory National Primate Research Center, Atlanta, GA 30329, USA.
Lukas GranholmEmory National Primate Research Center, Atlanta, GA 30329, USA.
Pazit PolakFaculty of Engineering, Bar Ilan University, Ramat Gan, Israel.
Samuel M PetersonDivision of Genetics, Oregon National Primate Research Center, Beaverton, OR 97006, USA.
Eric J PetersonWisconsin National Primate Research Center, Madison, WI 53175, USA.
Nagarajan RajuEmory National Primate Research Center, Atlanta, GA 30329, USA.
Kaitlyn ShieldsDepartment of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY 40292, USA.
Steven SchultzeDepartment of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY 40292, USA.
Thang TonEmory National Primate Research Center, Atlanta, GA 30329, USA.
Adam J EricsenEmory National Primate Research Center, Atlanta, GA 30329, USA.
Stacey A LappEmory National Primate Research Center, Atlanta, GA 30329, USA.
Francois VillingerNew Iberia Research Center, University of Louisiana at Lafayette, Lafayette, LA 70562, USA.
Mats OhlinDepartment of Immunotechnology, Lund University, Lund, Sweden; SciLifeLab, Lund University, Lund, Sweden.
Christopher A CottrellDepartment of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA.
Rama R AmaraEmory National Primate Research Center, Atlanta, GA 30329, USA; Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA.
Cynthia A DerdeynDepartment of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA; Infectious Diseases and Translational Medicine Unit, Washington National Primate Research Center, University of Washington, Seattle, WA 98195, USA.
Shane CrottyConsortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA; Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA.
William R SchiefDepartment of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Moderna, Inc., Cambridge, MA 02142, USA.
Gunilla B Karlsson HedestamDepartment of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
Melissa L SmithDepartment of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY 40292, USA.
William LeesFaculty of Engineering, Bar Ilan University, Ramat Gan, Israel; Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY 40292, USA.
Corey T WatsonDepartment of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY 40292, USA. Electronic address: corey.watson@louisville.edu.
Gur YaariDepartment of Pathology, Yale School of Medicine, New Haven, CT 06250, USA; Faculty of Engineering, Bar Ilan University, Ramat Gan, Israel; Bar Ilan institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan, Israel. Electronic address: gur.yaari@yale.edu.
Steven E BosingerEmory National Primate Research Center, Atlanta, GA 30329, USA; Department of Pathology & Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA. Electronic address: steven.bosinger@emory.edu.

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
Yerkes National Primate Research Center Role of type-I IFN in regulating COVID-19 induced inflammation and pathogenesisP51OD011132 · OD · EMORY UNIVERSITY · PI Joon Sup Lee · 2012 to 2026
$167.0M
WNPRC Supplemental Request for Nonhuman Primate Enclosures to Equip HIV/AIDS-Related Research FacilitiesP51OD011106 · OD · UNIVERSITY OF WISCONSIN-MADISON · PI Dorota A. Grejner-Brzezinska · 2012 to 2026
$150.7M
Virology and Molecular Biomarkers CoreP30AI050409 · NIAID · EMORY UNIVERSITY · PI Ann M Chahroudi, Colleen F Kelley · 2002 to 2026
$74.0M
B and T Cell Biology of Protection from and Eradication of SIV/SHIV Infection - Administrative SupplementUM1AI124436 · NIAID · EMORY UNIVERSITY · PI AMARA, RAMA RAO, HUNTER, ERIC · 2016 to 2021
$42.3M
Using DNA/MVA/protein immunization of rhesus macaques to investigate how the background of the HIV-1 envelope and nature of the protein boost shape the genetic and functional antibody landscape.R01AI128837 · NIAID · EMORY UNIVERSITY · PI BOSINGER, STEVEN EDWARD, DERDEYN, CYNTHIA ANN · 2017 to 2021
$5.9M
Population genotyping of the germline immunoglobulin repertoire in AIDS-designated rhesus macaque breeding coloniesR24AI162317 · NIAID · EMORY UNIVERSITY · PI Steven Edward Bosinger, Corey Taylor Watson · 2021 to 2026
$5.5M
i-AKC: Integrated AIRR Knowledge CommonsU24AI177622 · NIAID · UT SOUTHWESTERN MEDICAL CENTER · PI LINDSAY G. COWELL · 2023 to 2026
$4.0M
Illumina NovaSeq 6000 High Throughput DNA Sequencer for Emory UniversityS10OD026799 · OD · EMORY UNIVERSITY · PI BOSINGER, STEVEN EDWARD · 2019 to 2019
$985k
Expanding regional capacity for single molecule sequencing through the purchase of the Sequel IIe sequencing systemS10OD034432 · OD · UNIVERSITY OF LOUISVILLE · PI SMITH, MELISSA LAIRD · 2023 to 2023
$484k
NIAID NIH HHS P30 AI050409NIAID NIH HHS R01 AI128837NIAID NIH HHS R24 AI162317NIAID NIH HHS U24 AI177622NIAID NIH HHS UM1 AI124436NIAID NIH HHS UM1 AI144462NIH HHS P51 OD011106NIH HHS P51 OD011132NIH HHS S10 OD026799NIH HHS S10 OD034432
6 · The paper itself

Abstract

Rhesus macaques (RMs) are a vital model for studying human disease and are invaluable to preclinical vaccine research, particularly for the study of broadly neutralizing antibody responses. Such studies require robust genetic resources for antibody-encoding genes within the immunoglobulin (IG) loci. The complexity of the IG loci has historically made them challenging to characterize accurately. To address this, we developed experimental and computational methodologies to generate a collection of integrated antibody repertoire and long-read genomic sequencing data in 106 Indian-origin RMs. We created a resource of IG heavy- and light-chain variable (V), diversity (D), and joining (J) alleles, as well as leader, intronic, and recombination signal sequences (RSSs). This includes the curation of 1,095 previously unidentified alleles, unveiling tremendous diversity and expanding existing IG allele sets by 40%. This publicly available, continually updated resource (https://vdjbase.org/reference_book/Rhesus_Macaque) provides the foundation for advancing RM immunogenomics, vaccine discovery, and translational research.

Indexed as

Genetic VariationMacaca mulattaAllelesAnimalsGenomicsHumansImmunoglobulin Variable RegionImmunoglobulin Variable RegionantibodiesB cell receptorbroadly neutralizing antibodiesdatabasegenomicsgermline inferenceHIVimmunoglobulinsrepertoirerhesus macaque

Identifiers

PMID41494536
PMCPMC13502367

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.