ArticlePloS one2010
Amino-acid co-variation in HIV-1 Gag subtype C: HLA-mediated selection pressure and compensatory dynamics.
Article in PloS one, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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.
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.
Who cites it
25 citing papers in PubMed, 52 citations in OpenAlex.
- Role of transmitted Gag CTL polymorphisms in defining replicative capacity and early HIV-1 pathogenesis.PLoS pathogens · 2012Trial
- Clinical and evolutionary consequences of HIV adaptation to HLA: implications for vaccine and cure.Current opinion in HIV and AIDS · 2019Review
- Rapid HIV disease progression following superinfection in an HLA-B*27:05/B*57:01-positive transmission recipient.Retrovirology · 2018Article
- Pairwise growth competition assay for determining the replication fitness of human immunodeficiency viruses.Journal of visualized experiments : JoVE · 2015Article
- Deep sequencing of protease inhibitor resistant HIV patient isolates reveals patterns of correlated mutations in Gag and protease.PLoS computational biology · 2015Article
- Preexisting compensatory amino acids compromise fitness costs of a HIV-1 T cell escape mutation.Retrovirology · 2014Article
- Analysis of human rotaviruses from a single location over an 18-year time span suggests that protein coadaption influences gene constellations.Journal of virology · 2014Article
- Host genetics and viral load in primary HIV-1 infection: clear evidence for gene by sex interactions.Human genetics · 2014Article
- Review
- Host-specific adaptation of HIV-1 subtype B in the Japanese population.Journal of virology · 2014Article
- Increased sequence coverage through combined targeting of variant and conserved epitopes correlates with control of HIV replication.Journal of virology · 2014Article
- Genetic mutations in influenza H3N2 viruses from a 2012 epidemic in Southern China.Virology journal · 2013Article
- HLA-B*57 versus HLA-B*81 in HIV-1 infection: slow and steady wins the race?Journal of virology · 2013Article
- Evolutionary characterization of the pandemic H1N1/2009 influenza virus in humans based on non-structural genes.PloS one · 2013Article
- Correlates of protective cellular immunity revealed by analysis of population-level immune escape pathways in HIV-1.Journal of virology · 2012Article
- Intersubtype differences in the effect of a rare p24 gag mutation on HIV-1 replicative fitness.Journal of virology · 2012Article
- Temporal association of HLA-B*81:01- and HLA-B*39:10-mediated HIV-1 p24 sequence evolution with disease progression.Journal of virology · 2012Article
- Aminopeptidase substrate preference affects HIV epitope presentation and predicts immune escape patterns in HIV-infected individuals.Journal of immunology (Baltimore, Md. : 1950) · 2012Article
- Impact of HLA-B*81-associated mutations in HIV-1 Gag on viral replication capacity.Journal of virology · 2012Article
- Human leukocyte antigen variants B*44 and B*57 are consistently favorable during two distinct phases of primary HIV-1 infection in sub-Saharan Africans with several viral subtypes.Journal of virology · 2011Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
17 authors at 6 institutions in 3 countries.
Funding
Abstract
backgroundDespite high potential for HIV-1 genetic variation, the emergence of some mutations is constrained by fitness costs, and may be associated with compensatory amino acid (AA) co-variation. To characterize the interplay between Cytotoxic T Lymphocyte (CTL)-mediated pressure and HIV-1 evolutionary pathways, we investigated AA co-variation in Gag sequences obtained from 449 South African individuals chronically infected with HIV-1 subtype C. METHODOLOGY/PRINCIPAL
findingsIndividuals with CTL responses biased toward Gag presented lower viral loads than individuals with under-represented Gag-specific CTL responses. Using methods that account for founder effects and HLA linkage disequilibrium, we identified 35 AA sites under Human Leukocyte Antigen (HLA)-restricted CTL selection pressure and 534 AA-to-AA interactions. Analysis of two-dimensional distances between co-varying residues revealed local stabilization mechanisms since 40% of associations involved neighboring residues. Key features of our co-variation analysis included sites with a high number of co-varying partners, such as HLA-associated sites, which had on average 55% more connections than other co-varying sites. CONCLUSIONS/SIGNIFICANCE: Clusters of co-varying AA around HLA-associated sites (especially at typically conserved sites) suggested that cooperative interactions act to preserve the local structural stability and protein function when CTL escape mutations occur. These results expose HLA-imprinted HIV-1 polymorphisms and their interlinked mutational paths in Gag that are likely due to opposite selective pressures from host CTL-mediated responses and viral fitness constraints.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.