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 …

The new field of viral dynamics, based on within-host modeling of viral infections, began with
models of human immunodeficiency virus (HIV), but now includes many viral infections …

Genome sequences of transmitted/founder (T/F) HIV-1 have been inferred by analyzing
single genome amplicons of acute infection plasma viral RNA in the context of a …

Once the first SARS-CoV-2 vaccine became available, mass vaccination was the main pillar
of the public health response to the COVID-19 pandemic. It was very effective in reducing …

Sexual transmission of HIV-1 is an inefficient process, with only one or few variants of the
donor quasispecies establishing the new infection. A critical, and as yet unresolved …

HIV-1 accumulates mutations in and around reactive epitopes to escape recognition and
killing by CD8+ T cells. Measurements of HIV-1 time to escape should therefore provide …

Single genome sequencing of early HIV-1 genomes provides a sensitive, dynamic
assessment of virus evolution and insight into the earliest anti-viral immune responses in …

Determining sharp conditions for the global stability of equilibria remains one of the most
challenging problems in the analysis of models for the management and control of biological …

The odds of living a long and healthy life with HIV infection have dramatically improved with
the advent of combination antiretroviral therapy. Along with the early development and …

Major histocompatibility complex class I (MHC-I) molecules play a crucial role in immunity by
capturing peptides for presentation to T cells and natural killer (NK) cells. The peptide …