Evolution of RNA viruses occurs through disequilibria of collections of closely related mutant
spectra or mutant clouds termed viral quasispecies. Here we review the origin of the …

Abstract The development of High-Throughput Sequencing (HTS) technologies is having a
major impact on the genomic analysis of viral populations. Current HTS platforms can …

Abstract HIV-1 envelope glycoproteins (Envs) of most primary HIV-1 strains exist in closed
conformation and infrequently sample open states, limiting access to internal epitopes. Thus …

Elite controllers (EC) represent a small subset of HIV-1-infected people that spontaneously
control viral replication. However, natural virological suppression and absence of immune …

The emergence and worldwide spread of SARS-CoV-2 during the COVID-19 pandemic
necessitated the adaptation and rapid deployment of viral WGS and analysis techniques that …

HIV-1 is a chimpanzee virus which was transmitted to humans by several zoonotic events
resulting in infection with HIV-1 groups M–P, and in parallel transmission events from sooty …

Mutation and recombination drive the evolution of most pathogens by generating the genetic
variants upon which selection operates. Those variants can, for example, confer resistance …

One of the most intriguing puzzles in biology is the degree to which evolution is repeatable.
The repeatability of evolution, or parallel evolution, has been studied in a variety of model …

ABSTRACT RNA viruses replicate as complex mutant spectra termed viral quasispecies.
The frequency of each individual genome in a mutant spectrum depends on its rate of …

The understanding of the evolutionary processes underlying HIV-1 fitness recovery is
fundamental for HIV-1 pathogenesis, antiretroviral treatment and vaccine design. It is known …