The HIV genome encodes a small number of viral proteins (ie, 16), invariably establishing
cooperative associations among HIV proteins and between HIV and host proteins, to invade …

The unprecedented coverage offered by next-generation sequencing (NGS) technology has
facilitated the assessment of the population complexity of intra-host RNA viral populations at …

Potts Hamiltonian models of protein sequence co-variation are statistical models constructed
from the pair correlations observed in a multiple sequence alignment (MSA) of a protein …

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 …

Understanding the complex mutation patterns that give rise to drug resistant viral strains
provides a foundation for developing more effective treatment strategies for HIV/AIDS …

Virus evolution is strongly affected by antagonistic co-evolution of virus and host. Host
immunity positively selects for viruses that evade the immune response, which in turn may …

The development of drug resistance in HIV is the result of primary mutations whose effects
on viral fitness depend on the entire genetic background, a phenomenon called 'epistasis' …

Background Genetic recombination is a tremendous source of intrahost diversity in viruses
and is critical for their ability to rapidly adapt to new environments or fitness challenges …

Drug-resistant mutations often have deleterious impacts on replication fitness, posing a
fitness cost that can only be overcome by compensatory mutations. However, the role of …

The ability of HIV-1 to rapidly mutate leads to antiretroviral therapy (ART) failure among
infected patients. Drug-resistance mutations (DRMs), which cause a fitness penalty to …