In the absence of effective antiviral therapy, HIV-1 evolves in response to the within-host
environment, of which the immune system is an important aspect. During the earliest stages …

Natural selection often acts on multiple traits simultaneously. For example, the virus HIV-1
faces pressure to evade host immunity while also preserving replicative fitness. While past …

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 …

Identifying the genetic drivers of adaptation is a necessary step in understanding the
dynamics of rapidly evolving pathogens and cancer. However, signals of selection are …

Human immunodeficiency virus (HIV) evolves within infected persons to escape being
destroyed by the host immune system, thereby preventing effective immune control of …

Using likelihood-based evolutionary methods, we demonstrate that the broad genetic
diversity of human immunodeficiency virus type 1 (HIV-1) in an infected individual is a …

Modern HIV research depends crucially on both viral sequencing and population
measurements. To directly link mechanistic biological processes and evolutionary dynamics …

Convergent evolution describes the process of di erent populations acquiring similar
phenotypes or genotypes. Complex organisms with large genomes only rarely and only …

Blood plasma viral loads and the time to progress to AIDS differ widely among untreated HIV-
infected humans. Although people with certain HLA (HLA-I) alleles are more likely to control …

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 …