Founder effects in the assessment of HIV polymorphisms and HLA allele associations

T Bhattacharya, M Daniels, D Heckerman, B Foley… - science, 2007 - science.org
Escape from T cell–mediated immune responses affects the ongoing evolution of rapidly
evolving viruses such as HIV. By applying statistical approaches that account for …

Evidence of HIV-1 adaptation to HLA-restricted immune responses at a population level

CB Moore, M John, IR James, FT Christiansen, CS Witt… - Science, 2002 - science.org
Antigen-specific T cell immunity is HLA-restricted. Human immunodeficiency virus–type 1
(HIV-1) mutations that allow escape from host immune responses may therefore be HLA …

Phylogenetic dependency networks: inferring patterns of CTL escape and codon covariation in HIV-1 Gag

JM Carlson, ZL Brumme, CM Rousseau… - PLoS computational …, 2008 - journals.plos.org
HIV avoids elimination by cytotoxic T-lymphocytes (CTLs) through the evolution of escape
mutations. Although there is mounting evidence that these escape pathways are broadly …

Correlates of protective cellular immunity revealed by analysis of population-level immune escape pathways in HIV-1

JM Carlson, CJ Brumme, E Martin, J Listgarten… - Journal of …, 2012 - Am Soc Microbiol
ABSTRACT HLA class I-associated polymorphisms identified at the population level mark
viral sites under immune pressure by individual HLA alleles. As such, analysis of their …

Central role of reverting mutations in HLA associations with human immunodeficiency virus set point

PC Matthews, A Prendergast, A Leslie… - Journal of …, 2008 - Am Soc Microbiol
Much uncertainty still exists over what T-cell responses need to be induced by an effective
human immunodeficiency virus (HIV) vaccine. Previous studies have hypothesized that the …

Transmission and accumulation of CTL escape variants drive negative associations between HIV polymorphisms and HLA

A Leslie, D Kavanagh, I Honeyborne… - The Journal of …, 2005 - rupress.org
Human immunodeficiency virus (HIV)-1 amino acid sequence polymorphisms associated
with expression of specific human histocompatibility leukocyte antigen (HLA) class I alleles …

HLA class I-driven evolution of human immunodeficiency virus type 1 subtype c proteome: immune escape and viral load

CM Rousseau, MG Daniels, JM Carlson… - Journal of …, 2008 - Am Soc Microbiol
Human immunodeficiency virus type 1 (HIV-1) mutations that confer escape from cytotoxic T-
lymphocyte (CTL) recognition can sometimes result in lower viral fitness. These mutations …

Selective Escape from CD8+ T-Cell Responses Represents a Major Driving Force of Human Immunodeficiency Virus Type 1 (HIV-1) Sequence Diversity and Reveals …

TM Allen, M Altfeld, SC Geer, ET Kalife… - Journal of …, 2005 - Am Soc Microbiol
The sequence diversity of human immunodeficiency virus type 1 (HIV-1) represents a major
obstacle to the development of an effective vaccine, yet the forces impacting the evolution of …

Evidence of differential HLA class I-mediated viral evolution in functional and accessory/regulatory genes of HIV-1

ZL Brumme, CJ Brumme, D Heckerman… - PLoS …, 2007 - journals.plos.org
Despite the formidable mutational capacity and sequence diversity of HIV-1, evidence
suggests that viral evolution in response to specific selective pressures follows generally …

Rapid reversion of sequence polymorphisms dominates early human immunodeficiency virus type 1 evolution

B Li, AD Gladden, M Altfeld, JM Kaldor… - Journal of …, 2007 - Am Soc Microbiol
The error-prone replication of human immunodeficiency virus type 1 (HIV-1) enables it to
continuously evade host CD8+ T-cell responses. The observed transmission, and potential …