Within-host genetic sequencing from samples collected over time provides a dynamic view
of how viruses evade host immunity. Immune-driven mutations might stimulate neutralization …

Single genome sequencing of early HIV-1 genomes provides a sensitive, dynamic
assessment of virus evolution and insight into the earliest anti-viral immune responses in …

We used ultra-deep sequencing to obtain tens of thousands of HIV-1 sequences from
regions targeted by CD8+ T lymphocytes from longitudinal samples from three acutely …

Deep sequencing technologies have the potential to transform the study of highly variable
viral pathogens by providing a rapid and cost-effective approach to sensitively characterize …

Eliciting maximal immune responses to highly divergent viruses is a challenge and a focus
in AIDS vaccine development. Another challenge is to identify the immune correlates of …

To understand the interplay between host cytotoxic T-lymphocyte (CTL) responses and the
mechanisms by which HIV-1 evades them, we studied viral evolutionary patterns associated …

Cellular immune control of HIV is mediated, in part, by induction of single amino acid
mutations that reduce viral fitness, but compensatory mutations limit this effect. Here, we …

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 …

Cytotoxic T-lymphocytes (CTLs) recognize viral protein fragments displayed by major
histocompatibility complex molecules on the surface of virally infected cells and generate an …

Background Following transmission, HIV-1 evolves into a diverse population, and next
generation sequencing enables us to detect variants occurring at low frequencies. Studying …