Evidence map›Paper›PMID 22448013›Full record

ArticleThe Journal of infectious diseases2012

Associations between phylogenetic clustering and HLA profile among HIV-infected individuals in San Diego, California.

Sanjay R Mehta, Sergei L Kosakovsky Pond, Jason A Young, Douglas Richman, Susan Little, Davey M Smith

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in The Journal of infectious diseases, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.

0numbers the graph read from it
0cells of the map it votes in
8citing 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

8 citing papers in PubMed.

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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

6 authors.

Sanjay R MehtaDepartment of Medicine, University of California, San Diego, CA 92093-0711, USA. srmehta@ucsd.edu
Sergei L Kosakovsky Pond
Jason A Young
Douglas Richman
Susan Little
Davey M Smith

Funding

WOMEN'S HEALTH AGENDAU01AI038858 · NIAID · SOCIAL AND SCIENTIFIC SYSTEMS, INC. · PI BENSON, CONSTANCE ANN · 1996 to 2008
$157.5M
VirologyP30AI036214 · NIAID · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI SONIA JAIN · 1994 to 2026
$78.4M
UCSD Department of Medicine HIV/AIDS Clinical Trials UnitUM1AI069432 · NIAID · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI TIMOTHY J. WILKIN · 2012 to 2026
$50.4M
STRUCTURAL NEUROIMAGING COREP30MH062512 · NIMH · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Jessica Lynette Montoya · 2001 to 2026
$50.4M
Primary Infection Resource Consortium (PIRC)R24AI106039 · NIAID · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI LITTLE, SUSAN JANET · 2013 to 2021
$23.1M
Southern California Primary Infection ProgramU01AI043638 · NIAID · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI RICHMAN, DOUGLAS D · 1998 to 2010
$21.3M
UCSD Department of Medicine HIV/AIDS Clinical Trials UnitU01AI069432 · NIAID · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI BENSON, CONSTANCE ANN · 2007 to 2011
$19.3M
WOMEN'S HEALTH AGENDAU01AI027670 · NIAID · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI BENSON, CONSTANCE ANN · 1988 to 2006
$13.7M
A Multi-Site Investigation into the Effect of HIV Clade on Neurocognitive ImpairmR01MH083552 · NIMH · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI SMITH, DAVID MITCHELL · 2008 to 2012
$3.3M
Biomathematical analysis of viral dynamics/evolutionR01AI047745 · NIAID · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI RICHMAN, DOUGLAS D · 2001 to 2011
$3.2M
ANTIVIRAL RESISTANCE IN AIDSR37AI029164 · NIAID · UNIVERSITY OF CALIFORNIA SAN DIEGO · PI RICHMAN, DOUGLAS D · 1994 to 2004
$2.0M
HIV-1 Adaptation in the Central Nervous SystemR01NS051132 · NINDS · NORTHERN CALIFORNIA INSTITUTE RES &EDUC · PI WONG, JOSEPH K · 2005 to 2009
$1.8M
NIAID NIH HHS AI047745NIAID NIH HHS AI064086NIAID NIH HHS AI077304NIAID NIH HHS AI080353NIAID NIH HHS AI087164NIAID NIH HHS AI093163NIAID NIH HHS AI27670NIAID NIH HHS AI29164NIAID NIH HHS AI36214NIAID NIH HHS AI38858NIAID NIH HHS AI43638NIAID NIH HHS AI43752NIAID NIH HHS AI57167NIAID NIH HHS AI69432NIAID NIH HHS K23 AI093163NIAID NIH HHS K24 AI064086NIAID NIH HHS P30 AI036214NIAID NIH HHS R01 AI043752NIAID NIH HHS R01 AI047745NIAID NIH HHS R01 AI057167NIAID NIH HHS R01 AI087164NIAID NIH HHS R21 AI047745NIAID NIH HHS R21 AI077304NIAID NIH HHS R21 AI080353NIAID NIH HHS R24 AI106039NIAID NIH HHS R37 AI029164NIAID NIH HHS R56 AI047745NIAID NIH HHS U01 AI027670NIAID NIH HHS U01 AI038858NIAID NIH HHS U01 AI043638NIAID NIH HHS U01 AI069432NIAID NIH HHS UM1 AI069432NIMH NIH HHS MH083552NIMH NIH HHS MH62512NIMH NIH HHS P30 MH062512NIMH NIH HHS R01 MH083552NINDS NIH HHS NS51132NINDS NIH HHS R01 NS051132
6 · The paper itself

Abstract

backgroundSpecific sequence changes of human immunodeficiency virus type 1 (HIV-1) in the presence of specific HLA molecules may alter the composition and processing of viral peptides, leading to immune escape. Persistence of these mutations after transmission may leave the genetic fingerprint of the transmitter's HLA profile. Here, we evaluated the associations between HLA profiles and the phylogenetic relationships of HIV sequences sampled from a cohort of recently infected individuals in San Diego, California.

methodsWe identified transmission clusters within the study cohort, using phylogenetic analysis of sampled HIV pol genotypes at a genetic distance of <1.5%. We then evaluated the association of specific HLA alleles, HLA homozygosity, HLA concordance, race and ethnicity, and mutational patterns within the clustering and nonclustering groups.

resultsFrom 350 cohort participants, we identified 162 clustering individuals and 188 nonclustering individuals. We identified trends for enrichment of particular alleles within individual clusters and evidence of viral escape within those clusters. We also found that discordance of HLA alleles was significantly associated with clustering individuals.

conclusionsSome transmission clusters demonstrate HLA enrichment, and viruses in these HLA-associated clusters often show evidence of escape to enriched alleles. Interestingly, HLA discordance was associated with clustering in our predominantly MSM population.

Indexed as

PhylogenyAllelesCaliforniaCluster AnalysisCohort StudiesDemographyFemaleGenes, polHIV-1HIV InfectionsHLA-A AntigensHLA-B AntigensHomosexuality, MaleHomozygoteHumansImmune EvasionHLA-A AntigensHLA-B Antigens

Identifiers

PMID22448013
PMCPMC3415817

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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.