Current sequencing technologies have created unprecedented opportunities for studying
microbial populations. For pathogens with comparatively low per-site mutation rates, such as …

The pace of pathogen discovery is rapidly accelerating. This reflects not only factors that
enable the appearance and globalization of new microbial infections, but also improvements …

It is unclear whether West Nile virus (WNV) circulates between Africa and Europe, despite
numerous studies supporting an African origin and high transmission in Europe. We …

Antiretroviral therapy (ART) suppresses viral replication in people living with HIV. Yet,
infected cells persist for decades on ART and viremia returns if ART is stopped. Persistence …

Ancestral reconstruction is the extrapolation back in time from measured characteristics of
individuals (or populations) to their common ancestors. It is an important application of …

Next-generation sequencing (NGS) technologies enable new insights into the diversity of
virus populations within their hosts. Diversity estimation is currently restricted to single …

There have been a variety of approaches taken to try to characterize and identify the genetic
basis of adaptation in nature, spanning theoretical models, experimental evolution studies …

The evolution of viral pathogens is shaped by strong selective forces that are exerted during
jumps to new hosts, confrontations with host immune responses and antiviral drugs, and …

Given that HIV evolution and latent reservoir establishment occur continually within-host,
and that latently infected cells can persist long-term, the HIV reservoir should comprise a …

Despite combined antiretroviral therapy (cART), HIV+ patients still develop neurological
disorders, which may be due to persistent HIV infection and selective evolution in brain …