Dynamics of HIV-1 recombination in its natural target cells

Abstract

Genetic recombination is believed to assist HIV-1 diversification and escape from host immunity and antiviral therapies, yet this process remains largely unexamined within the natural target-cell populations. We developed a method for measuring HIV-1 recombination directly that employs reporter viruses bearing functional enhanced yellow fluorescent protein (YFP) and enhanced cyan fluorescent protein (CFP) genes in which recombination produces a modified GFP gene and GFP fluorescence in the infected cells. These reporter viruses allow simultaneous quantification of the dynamics of HIV-1 infection, coinfection, and recombination in cell culture and in animal models by flow-cytometric analysis. Multiround infection assays revealed that productive cellular coinfection was subject to little functional inhibition. As a result, generation of recombinants proceeded according to the square of the infection rate during HIV-1 replication in T lymphocytes and within human thymic grafts in severe combined immunodeficient (SCID)-hu (Thy/Liv) mice. These results suggest that increases in viral load may confer a compounding risk of virus escape by means of recombinational diversification. A single round of replication in T lymphocytes in culture generated an average of nine recombination events per virus, and infection of macrophages led to ≈30 crossover events, making HIV-1 up to an order of magnitude more recombinogenic than recognized previously and demonstrating that the infected cell exerts a profound influence on the frequency of recombination

HIV dynamics with multiple infections of target cells

“…2d does not vanish but eventually rises again following predator-prey dynamics (9), so T* also has a late rise.] This overall two-phase dynamics is similar to the infected cell dynamics observed in in vitro experiments (2). With the overall dynamics thus qualitatively mimicking experiments, we employ this description to investigate the dynamics of multiple infections.…”

“…3 as parametric plots of T* i (t) vs. T* 1 (t). Recall that Levy et al (2) found that coinfected cells, presumably mostly T* 2 , are proportional to (T* 1 ) 2 . (Note that T* 2 Ͻ Ͻ T* 1 in their experiments except near peak infection so that T* 1 Ϸ T*.)…”

“…multiple infection ͉ recombination ͉ scaling ͉ CD4 down-modulation ͉ mathematical model I n a significant shift from the prevalent paradigm of HIV infection that individual target cells are generally infected with single HIV virions, recent studies have demonstrated that multiple infections of cells occur far more frequently than single infections both in vivo (1,2) and in vitro (2)(3)(4). For instance, CD4 ϩ cells from the spleens of two HIV-infected individuals were found to harbor up to eight proviruses with three or four proviruses per cell on average (1).…”

Evolvability is a selectable trait

“…Additionally, a recent study of the dynamics of HIV-1 recombination suggests that HIV-1 may have evolved high recombination rates to foster rapid diversification and further its survival (66).…”

The Structure of HIV-1 Genomic RNA in the gp120 Gene Determines a Recombination Hot Spot in Vivo

“…Indeed, ex vivo experiments in HeLa CD4 ϩ -infected cells estimated that three events of template switching occur, on average, per replication cycle (16). Furthermore, it has recently been shown that the recombination rates are influenced by the type of cell infected, with the highest rates observed in macrophages (17). A crucial issue to address now is whether this high rate results from the presence of recombination hot spots interspersed among sequences yielding low recombination rates, or if it reflects a nearly constant frequency of strand transfer along the whole genome.…”