Evidence map›Paper›PMID 29300007›Full record

ArticleNature2018

Sooty mangabey genome sequence provides insight into AIDS resistance in a natural SIV host.

David Palesch, Steven E Bosinger, Gregory K Tharp, Thomas H Vanderford, Mirko Paiardini, Ann Chahroudi, Zachary P Johnson, Frank Kirchhoff, Beatrice H Hahn, Robert B Norgren and 20 more

Open access · hybridAbstract readComparative Study
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.

0numbers the graph read from it
0cells of the map it votes in
49citing papers in PubMed
14.0field-weighted citation impact, top 1% 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

49 citing papers in PubMed, 140 citations in OpenAlex.

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  19. Heterogeneity of circulating CD4Scientific reports · 2022
    Article
  20. Genomic resources for rhesus macaques (Macaca mulatta).Mammalian genome : official journal of the International Mammalian Genome Society · 2022
    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

30 authors at 10 institutions in 2 countries.

David PaleschEmory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, Georgia 30329, USA.
Steven E BosingerEmory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, Georgia 30329, USA.
Gregory K TharpEmory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, Georgia 30329, USA.
Thomas H VanderfordEmory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, Georgia 30329, USA.
Mirko PaiardiniEmory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, Georgia 30329, USA.
Ann ChahroudiEmory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, Georgia 30329, USA.
Zachary P JohnsonEmory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, Georgia 30329, USA.
Frank KirchhoffInstitute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany.
Beatrice H HahnDepartments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
Robert B NorgrenDepartment of Genetics, Cell Biology and Anatomy, University of Nebraska, Medical Center, Omaha, Nebraska 68198, USA.
Nirav B PatelEmory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, Georgia 30329, USA.
Donald L SodoraCenter for Infectious Disease Research, formerly Seattle Biomedical Research Institute, Seattle, Washington 98109, USA.
Reem A DawoudEmory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, Georgia 30329, USA.
Caro-Beth StewartDepartment of Biological Sciences, University at Albany-State University of New York, Albany, New York 12222, USA.
Sara M SeepoDepartment of Biological Sciences, University at Albany-State University of New York, Albany, New York 12222, USA.
R Alan HarrisHuman Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.
Yue LiuHuman Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.
Muthuswamy RaveendranHuman Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.
Yi HanHuman Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.
Adam EnglishHuman Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.
Gregg W C ThomasDepartment of Biology and School of Informatics and Computing, Indiana University, Bloomington, Indiana 47405, USA.
Matthew W HahnDepartment of Biology and School of Informatics and Computing, Indiana University, Bloomington, Indiana 47405, USA.
Lenore PipesDepartment of Physiology and Biophysics, Weill Cornell Medical College, New York, New York 10065, USA.
Christopher E MasonDepartment of Physiology and Biophysics, Weill Cornell Medical College, New York, New York 10065, USA.
Donna M MuznyHuman Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.
Richard A GibbsHuman Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.
Daniel SauterInstitute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany.
Kim WorleyHuman Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.
Jeffrey RogersHuman Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.
Guido SilvestriEmory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, Georgia 30329, USA.
Emory University · USBaylor College of Medicine · USCornell University · USIndiana University Bloomington · USUniversität Ulm · DEAlbany State University · USCenter for Infectious Disease Research · USUniversity at Albany, State University of New York · USUniversity of Nebraska Medical Center · USUniversity of Pennsylvania · US

Funding

The Human Genome Sequencing CenterU54HG003273 · NHGRI · BAYLOR COLLEGE OF MEDICINE · PI GIBBS, RICHARD A · 2004 to 2015
$341.3M
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
Virology and Molecular Biomarkers CoreP30AI050409 · NIAID · EMORY UNIVERSITY · PI Carlos del Rio · 2002 to 2026
$74.0M
STUDIES OF NATURAL SIV INFECTION OF SOOTY MANGABEYSR37AI066998 · NIAID · EMORY UNIVERSITY · PI SILVESTRI, GUIDO · 2011 to 2020
$7.7M
Natural SIV Reservoirs and Human Zoonotic RiskR37AI050529 · NIAID · UNIVERSITY OF PENNSYLVANIA · PI HAHN, BEATRICE H · 2008 to 2017
$5.7M
Large Scale Sequencing Variation in Rhesue Macaques - HIV Vaccine SupplementR24OD011173 · OD · BAYLOR COLLEGE OF MEDICINE · PI ROGERS, JEFFREY A. · 2012 to 2017
$3.7M
Studies of Natural SIV Infection of Sooty MangabeysR01AI066998 · NIAID · UNIVERSITY OF PENNSYLVANIA · PI SILVESTRI, GUIDO · 2006 to 2010
$3.5M
Transcriptome resources for comparative primate models of lentivirus infectionR24OD010445 · OD · EMORY UNIVERSITY · PI SILVESTRI, GUIDO · 2013 to 2016
$3.2M
Large-Scale Discovery of Functional Genetic Variation in Rhesus MacaquesR24RR032329 · NCRR · BAYLOR COLLEGE OF MEDICINE · PI ROGERS, JEFFREY A. · 2011 to 2011
$549k
NCRR NIH HHS R24 RR032329NHGRI NIH HHS U54 HG003273NIAID NIH HHS P30 AI050409NIAID NIH HHS R01 AI066998NIAID NIH HHS R37 AI050529NIAID NIH HHS R37 AI066998NIH HHS P51 OD011132NIH HHS R24 OD010445NIH HHS R24 OD011173NIH HHS U54-HG006484-01
6 · The paper itself

Abstract

In contrast to infections with human immunodeficiency virus (HIV) in humans and simian immunodeficiency virus (SIV) in macaques, SIV infection of a natural host, sooty mangabeys (Cercocebus atys), is non-pathogenic despite high viraemia. Here we sequenced and assembled the genome of a captive sooty mangabey. We conducted genome-wide comparative analyses of transcript assemblies from C. atys and AIDS-susceptible species, such as humans and macaques, to identify candidates for host genetic factors that influence susceptibility. We identified several immune-related genes in the genome of C. atys that show substantial sequence divergence from macaques or humans. One of these sequence divergences, a C-terminal frameshift in the toll-like receptor-4 (TLR4) gene of C. atys, is associated with a blunted in vitro response to TLR-4 ligands. In addition, we found a major structural change in exons 3-4 of the immune-regulatory protein intercellular adhesion molecule 2 (ICAM-2); expression of this variant leads to reduced cell surface expression of ICAM-2. These data provide a resource for comparative genomic studies of HIV and/or SIV pathogenesis and may help to elucidate the mechanisms by which SIV-infected sooty mangabeys avoid AIDS.

Indexed as

Genetic Predisposition to DiseaseSimian Immunodeficiency VirusAcquired Immunodeficiency SyndromeAmino Acid SequenceAnimalsCell Adhesion MoleculesCercocebus atysExonsFemaleFrameshift MutationGenetic VariationGenomeGenomicsHIVHost SpecificityHumansCell Adhesion MoleculesToll-Like Receptor 4

Identifiers

PMID29300007
PMCPMC5843367
OpenAlexW2781976912

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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.