Limits to detecting epistasis in the fitness landscape of HIV
The rapid evolution of HIV is constrained by interactions between mutations which affect
viral fitness. In this work, we explore the role of epistasis in determining the mutational …
viral fitness. In this work, we explore the role of epistasis in determining the mutational …
The role of epistasis in determining the fitness landscape of HIV proteins
The rapid evolution of HIV is constrained by interactions between mutations which affect
viral fitness. In this work, we explore the role of epistasis in determining the fitness …
viral fitness. In this work, we explore the role of epistasis in determining the fitness …
Clonal interference can cause wavelet-like oscillations of multilocus linkage disequilibrium
Within-host adaptation of pathogens such as human immunodeficiency virus (HIV) often
occurs at more than two loci. Multiple beneficial mutations may arise simultaneously on …
occurs at more than two loci. Multiple beneficial mutations may arise simultaneously on …
Immunogenetics of spontaneous control of HIV
M Carrington, BD Walker - Annual review of medicine, 2012 - annualreviews.org
Host genetic variation is presently estimated to account for about one-fourth of the observed
differences in control of HIV across infected individuals. Genome-wide association studies …
differences in control of HIV across infected individuals. Genome-wide association studies …
A practical guide to estimating the heritability of pathogen traits
Pathogen traits, such as the virulence of an infection, can vary significantly between patients.
A major challenge is to measure the extent to which genetic differences between infecting …
A major challenge is to measure the extent to which genetic differences between infecting …
[HTML][HTML] Author Correction: A high-resolution HLA reference panel capturing global population diversity enables multi-ancestry fine-mapping in HIV host response
In the version of this Article initially published, the author list and affiliations were incomplete.
Karl Heilbron and Adam Auton, both with 23andMe, Inc., have been added to the author list …
Karl Heilbron and Adam Auton, both with 23andMe, Inc., have been added to the author list …
Fitness costs and diversity of the cytotoxic T lymphocyte (CTL) response determine the rate of CTL escape during acute and chronic phases of HIV infection
ABSTRACT HIV-1 often evades cytotoxic T cell (CTL) responses by generating variants that
are not recognized by CTLs. We used single-genome amplification and sequencing of …
are not recognized by CTLs. We used single-genome amplification and sequencing of …
A non-parametric analytic framework for within-host viral phylogenies and a test for HIV-1 founder multiplicity
Phylogenetics is a powerful tool for understanding the diversification dynamics of viral
pathogens. Here we present an extension of the spectral density profile of the modified …
pathogens. Here we present an extension of the spectral density profile of the modified …
Structural topology defines protective CD8+ T cell epitopes in the HIV proteome
Mutationally constrained epitopes of variable pathogens represent promising targets for
vaccine design but are not reliably identified by sequence conservation. In this study, we …
vaccine design but are not reliably identified by sequence conservation. In this study, we …
Genotypic and functional impact of HIV-1 adaptation to its host population during the North American epidemic
LA Cotton, XT Kuang, AQ Le, JM Carlson, B Chan… - PLoS …, 2014 - journals.plos.org
HLA-restricted immune escape mutations that persist following HIV transmission could
gradually spread through the viral population, thereby compromising host antiviral immunity …
gradually spread through the viral population, thereby compromising host antiviral immunity …