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 …

HIV can evolve remarkably quickly in response to antiretroviral therapies and the immune
system. This evolution stymies treatment effectiveness and prevents the development of an …

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 …

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 …

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

During chronic infection, HIV-1 engages in a rapid coevolutionary arms race with the host's
adaptive immune system. While it is clear that HIV exerts strong selection on the adaptive …

Mutation rates and fitness costs of deleterious mutations are difficult to measure in vivo but
essential for a quantitative understanding of evolution. Using whole genome deep …

Analysis of HIV-1 gene sequences sampled longitudinally from infected individuals can
reveal the evolutionary dynamics that underlie associations between disease outcome and …

During chronic infection, HIV-1 engages in a rapid coevolutionary arms race with the host's
adaptive immune system. While it is clear that HIV exerts strong selection on the adaptive …

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 …