Differences among hosts, resulting from genetic variation in the immune system or
heterogeneity in drug treatment, can impact within-host pathogen evolution. Genetic …

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 …

Studies of host genetic determinants of pathogen sequence variations can identify sites of
genomic conflicts, by highlighting variants that are implicated in immune response on the …

Human leukocyte antigen (HLA) class I proteins play a crucial role in the presentation of viral
peptide antigens to cytotoxic T cells during viral infection, which is necessary for mounting …

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 …

Genetic linkage causes the fate of new mutations in a population to be contingent on the
genetic background on which they appear. This makes it challenging to identify how …

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 …

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 …

Abstract Currently, 1.1 million individuals in the United States are living with HIV-1 infection.
Although this is a relatively small proportion of the global pandemic, the remarkable mix of …

The outcome after infection with the human immunodeficiency virus type 1 (HIV-1) is a
complex phenotype determined by interactions among the pathogen, the human host and …