Whole Genome Deep Sequencing of HIV-1 Reveals the Impact of Early Minor Variants Upon Immune Recognition During Acute Infection

Genetic impact of vaccination on breakthrough HIV-1 sequences from the STEP trial

(2011) Morgane Rolland et al.   NATURE MEDICINE

Dynamics of Viral Evolution and CTL Responses in HIV-1 Infection

(2011) Yi Liu et al.   PLoS One

Coordinate linkage of HIV evolution reveals regions of immunological vulnerability

(2011) V. Dahirel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Relationship between Functional Profile of HIV-1 Specific CD8 T Cells and Epitope Variability with the Selection of Escape Mutants in Acute HIV-1 Infection

(2011) Guido Ferrari et al.   PLoS Pathogens

Reducing chimera formation during PCR amplification to ensure accurate genotyping

(2010) R.P. Smyth et al.   GENE

Comparison of standard PCR/cloning to single genome sequencing for analysis of HIV-1 populations

(2010) Michael R. Jordan et al.   JOURNAL OF VIROLOGICAL METHODS

Whole-Genome Characterization of Human and Simian Immunodeficiency Virus Intrahost Diversity by Ultradeep Pyrosequencing

(2010) B. N. Bimber et al.   JOURNAL OF VIROLOGY

Mathematical Modeling of Ultradeep Sequencing Data Reveals that Acute CD8+ T-Lymphocyte Responses Exert Strong Selective Pressure in Simian Immunodeficiency Virus-Infected Macaques but Still Fail To Clear Founder Epitope Sequences

(2010) T. M. T. Love et al.   JOURNAL OF VIROLOGY

Mosaic vaccines elicit CD8+ T lymphocyte responses that confer enhanced immune coverage of diverse HIV strains in monkeys

(2010) Sampa Santra et al.   NATURE MEDICINE

Dynamics of HIV-1 Quasispecies during Antiviral Treatment Dissected Using Ultra-Deep Pyrosequencing

(2010) Charlotte Hedskog et al.   PLoS One

Transmission of Single HIV-1 Genomes and Dynamics of Early Immune Escape Revealed by Ultra-Deep Sequencing

(2010) Will Fischer et al.   PLoS One

Phylogenetic Approach Reveals That Virus Genotype Largely Determines HIV Set-Point Viral Load

(2010) Samuel Alizon et al.   PLoS Pathogens

The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection

(2009) Nilu Goonetilleke et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Low-Abundance Drug-Resistant Viral Variants in Chronically HIV-Infected, Antiretroviral Treatment–Naive Patients Significantly Impact Treatment Outcomes

(2009) Birgitte B. Simen et al.   JOURNAL OF INFECTIOUS DISEASES

Human Immunodeficiency Virus Type 1-Specific CD8+ T-Cell Responses during Primary Infection Are Major Determinants of the Viral Set Point and Loss of CD4+ T Cells

(2009) H. Streeck et al.   JOURNAL OF VIROLOGY

Ultradeep Pyrosequencing Detects Complex Patterns of CD8+ T-Lymphocyte Escape in Simian Immunodeficiency Virus-Infected Macaques

(2009) B. N. Bimber et al.   JOURNAL OF VIROLOGY

Quantitating the Multiplicity of Infection with Human Immunodeficiency Virus Type 1 Subtype C Reveals a Non-Poisson Distribution of Transmitted Variants

(2009) M.-R. Abrahams et al.   JOURNAL OF VIROLOGY

Phylogenetic Analysis of Population-Based and Deep Sequencing Data to Identify Coevolving Sites in the nef Gene of HIV-1

(2009) A. F.Y. Poon et al.   MOLECULAR BIOLOGY AND EVOLUTION

Adaptation of HIV-1 to human leukocyte antigen class I

(2009) Yuka Kawashima et al.   NATURE

Quantitative Deep Sequencing Reveals Dynamic HIV-1 Escape and Large Population Shifts during CCR5 Antagonist Therapy In Vivo

(2009) Athe M. N. Tsibris et al.   PLoS One

HLA-Associated Immune Escape Pathways in HIV-1 Subtype B Gag, Pol and Nef Proteins

(2009) Zabrina L. Brumme et al.   PLoS One

Variable Fitness Impact of HIV-1 Escape Mutations to Cytotoxic T Lymphocyte (CTL) Response

(2009) Ryan M. Troyer et al.   PLoS Pathogens

Inflammatory Genital Infections Mitigate a Severe Genetic Bottleneck in Heterosexual Transmission of Subtype A and C HIV-1

(2009) Richard E. Haaland et al.   PLoS Pathogens

Transmission of HIV-1 Gag immune escape mutations is associated with reduced viral load in linked recipients

(2008) Paul A. Goepfert et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Immune-driven recombination and loss of control after HIV superinfection

(2008) Hendrik Streeck et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Cross‐Clade Detection of HIV‐1–Specific Cytotoxic T Lymphocytes Does Not Reflect Cross‐Clade Antiviral Activity

(2008) Michael S. Bennett et al.   JOURNAL OF INFECTIOUS DISEASES

HIV‐1 Variation before Seroconversion in Men Who Have Sex with Men: Analysis of Acute/Early HIV Infection in the Multicenter AIDS Cohort Study

(2008) Geoffrey S. Gottlieb et al.   JOURNAL OF INFECTIOUS DISEASES

Minority Human Immunodeficiency Virus Type 1 Variants in Antiretroviral-Naive Persons with Reverse Transcriptase Codon 215 Revertant Mutations

(2008) Y. Mitsuya et al.   JOURNAL OF VIROLOGY

Structural and Functional Constraints Limit Options for Cytotoxic T-Lymphocyte Escape in the Immunodominant HLA-B27-Restricted Epitope in Human Immunodeficiency Virus Type 1 Capsid

(2008) A. Schneidewind et al.   JOURNAL OF VIROLOGY

HLA-B57/B*5801 Human Immunodeficiency Virus Type 1 Elite Controllers Select for Rare Gag Variants Associated with Reduced Viral Replication Capacity and Strong Cytotoxic T-Lymphotye Recognition

(2008) T. Miura et al.   JOURNAL OF VIROLOGY

Deciphering Human Immunodeficiency Virus Type 1 Transmission and Early Envelope Diversification by Single-Genome Amplification and Sequencing

(2008) J. F. Salazar-Gonzalez et al.   JOURNAL OF VIROLOGY

Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection

(2008) B. F. Keele et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenetic Dependency Networks: Inferring Patterns of CTL Escape and Codon Covariation in HIV-1 Gag

(2008) Jonathan M. Carlson et al.   PLoS Computational Biology

Transmission of HIV-1 CTL Escape Variants Provides HLA-Mismatched Recipients with a Survival Advantage

(2008) Denis R. Chopera et al.   PLoS Pathogens