Effect of a Protease Inhibitor-Induced Genetic Bottleneck on Human Immunodeficiency Virus Type 1 env Gene Populations

Abstract

The initiation of drug therapy or the addition of a new drug to preexisting therapy can have a significant impact on human immunodeficiency virus type 1 (HIV-1) populations within a person. Drug therapy directed at reverse transcriptase and protease can result in dramatic decreases in virus load, causing a contraction in the virus population that represents a potential genetic bottleneck as a subset of virus with genomes carrying resistance mutations repopulate the host. While this bottleneck exerts an effect directly on the region that is being targeted by the drugs, it also affects other regions of the viral genome. We have applied heteroduplex tracking assays (HTA) specific to variable regions 1 and 2 (V1/V2) and variable region 3 (V3) of the HIV-1 env gene to analyze the effect of a genetic bottleneck created by the selection of resistance to ritonavir, a protease inhibitor. Subjects were classified into groups on the basis of the extent of the initial drop in virus load and the duration of virus load reduction. Subjects with a strong initial drop in virus load exhibited a loss of heterogeneity in the env region at virus load rebound; in contrast, subjects with a weak initial drop in virus load exhibited little to no loss of heterogeneity at virus load rebound in either region of env examined. The duration of virus load reduction also affected env populations. Subjects that had prolonged reductions exhibited slower population diversification and the appearance of new V1/V2 species after rebound. The longer reduction of virus load in these subjects may have allowed for improved immune system function, which in turn could have selected for new escape mutants. Subjects with rapid rebound quickly reequilibrated the entry env variants back into the resistant population. When the pro gene developed further resistance mutations subsequent to virus load rebound, no changes were observed in V1/V2 or V3 populations, suggesting that the high virus loads allowed the env populations to reequilibrate rapidly. The rapid equilibration of env variants during pro gene sequence transitions at high virus load suggests that recombination is active in defining the HIV-1 sequence population. Conversely, part of the success of suppressive antiviral therapy may be to limit the potential for evolution through recombination, which requires dually infected cells.

Extensive Recombination among Human Immunodeficiency Virus Type 1 Quasispecies Makes an Important Contribution to Viral Diversity in Individual Patients

“…Consistent with the idea that recombination had occurred frequently, Rmin was elevated for all patients, with values of 49,24,33,28,47, and 33, respectively, for patients 1 to 6. The positions of these putative recombination events were scattered throughout the portions of the HIV genome sequenced.…”

“…The presence of such bottlenecks is consistent with the idea that during the evolution of drug resistance, the occurrence of specific combinations of resistance mutations that give a decisive fitness advantage is followed by strong selection of viruses carrying this genotype. Previous studies evaluating the impact of treatment-induced bottlenecks occurring in the protease or RT on diversity in other genomic regions have given varying results, with evidence of reduced diversity, transient reductions in diversity, or no effects having been observed (4,7,10,13,19,24,37,53). Our results suggest that because of the extensive recombination between viral quasispecies, bottlenecks in one region did not preclude the preservation of considerable diversity in other genomic regions.…”

The Remarkable Frequency of Human Immunodeficiency Virus Type 1 Genetic Recombination

“…Consistent with this, the more VOL. 73,2009 HIV-1 GENETIC RECOMBINATION 469 dramatic a drop in virus load observed upon drug treatment, the less recombination contributed to rebounding populations (171). Thus, undoubtedly less recombination occurs for patients whose virus replication is effectively contained than for patients where replication proceeds unchecked.…”

“…Reasons for this may include limited cell coinfection and differences in RNA packaging (161,217,265). Additionally, the compartmentalization of virus strains to particular organs or other isolated sites can limit effective population sizes and thus the potential for recombination (7,171,223).…”

HIV Pathogenesis: Dynamics and Genetics of Viral Populations and Infected Cells

“…Unlike the immune response, antiviral therapy can impose a significant physical and genetic bottleneck on the HIV-1 population, with drug-resistant virus that rebounds after monotherapy often showing substantially less diversity than the starting population (Kitrinos et al 2005).…”