This paper investigates the effect of drug treatment on the standard within-host virus model, assuming that therapy occurs periodically. It is shown that eradication is possible under these periodic regimens, and we quantitatively characterize successful drugs or drug combinations, both theoretically and numerically. We also consider certain optimization problems, motivated for instance, by the...

I ntegration of the retrovirus DNA genome into host chromosomes is essential for viral replication. After virus infection of the cell, synthesis of viral cDNA occurs by reverse transcription of the viral RNA genome. Integration of the viral DNA genome into cellular DNA is catalyzed by the viral integrase (IN) encapsulated within the infecting virus particle. Viral DNA integration has different ...

Pathogens are among the suspected causes of declining amphibian populations, but studying infectious diseases in small, threatened populations is ethically and experimentally questionable. Progress on understanding amphibian diseases requires model host-pathogen systems with populations large enough for robust experimental designs that do not threaten the amphibian host with extinction. We repo...

Viral fitness is determined by replication within hosts and transmission between them. We examine how pleiotropic mutations that have antagonistic effects (i.e., antibody evasion vs. receptor binding) on viral replication within hosts can impact viral immune escape in the host population. When the host population is vaccinated, the virus escapes from passive immunity by mutations in the antibod...

Human immunodeficiency virus-1 (HIV-1) dynamics reflect an intricate balance within the viruses’ host. The virus relies on host replication factors, but must escape or counter its host’s antiviral restriction factors. The interaction between the HIV-1 protein Vif and many cellular restriction factors from the APOBEC3 protein family is a prominent example of this evolutionary arms ra...

A virus infecting a host faces a heterogeneous and a spatially structured environment. Using a mathematical model that incorporates two types of target cells and spatial structuring, we investigate conditions for viral within-host diversification. We show that branching occurs for a wide range of parameters but that it always requires some spatial structure. Applying our model to the case of HI...

The non-structural protein 1 (NS1) of influenza A virus (IAV), coded by its third most diverse gene, interacts with multiple molecules within infected cells. NS1 is involved in host immune response regulation and is a potential contributor to the virus host range. Early phylogenetic analyses using 50 sequences led to the classification of NS1 gene variants into groups (alleles) A and B. We rean...

Most emerging infectious diseases in humans originate from animal reservoirs; to contain and eradicate these diseases we need to understand how and why some pathogens become capable of crossing host species barriers. Influenza virus illustrates the interaction of factors that limit the transmission and subsequent establishment of an infection in a novel host species. Influenza species barriers ...