Emergence of CXCR4-using human immunodeficiency virus type 1 (HIV-1) variants in a minority of HIV-1-infected patients following treatment with the CCR5 antagonist maraviroc is from a pretreatment CXCR4-using virus reservoir

Abstract

Antagonists of the human immunodeficiency virus type 1 (HIV-1) coreceptor, CCR5, are being developed as the first anti-HIV agents acting on a host cell target. We monitored the coreceptor tropism of circulating virus, screened at baseline for coreceptor tropism, in 64 HIV-1-infected patients who received maraviroc (MVC, UK-427,857) as monotherapy for 10 days. Sixty-two patients harbored CCR5-tropic virus at baseline and had a posttreatment phenotype result. Circulating virus remained CCR5 tropic in 60/62 patients, 51 of whom experienced an HIV RNA reduction from baseline of >1 log(10) copies/ml, indicating that CXCR4-using variants were not rapidly selected despite CCR5-specific drug pressure. In two patients, viral load declined during treatment and CXCR4-using virus was detected at day 11. No pretreatment factor predicted the emergence of CXCR4-tropic virus during maraviroc therapy in these two patients. Phylogenetic analysis of envelope (Env) clones from pre- and posttreatment time points indicated that the CXCR4-using variants probably emerged by outgrowth of a pretreatment CXCR4-using reservoir, rather than via coreceptor switch of a CCR5-tropic clone under selection pressure from maraviroc. Phylogenetic analysis was also performed on Env clones from a third patient harboring CXCR4-using virus prior to treatment. This patient was enrolled due to a sample labeling error. Although this patient experienced no overall reduction in viral load in response to treatment, the CCR5-tropic components of the circulating virus did appear to be suppressed while receiving maraviroc as monotherapy. Importantly, in all three patients, circulating virus reverted to predominantly CCR5 tropic following cessation of maraviroc.

FIG. 1.

Emergence of CXCR4-using virus following maraviroc treatment in 63 patients whose circulating virus was phenotypically characterized as CCR5 tropic at baseline was not related to baseline CD4 or virological response to therapy. Each symbol represents one patient. Patients A, B, and C are labeled.

FIG.2.

CXCR4-using variants are genetically distinct from CCR5-tropic clones in each patient. Shown are the results of phylogenetic analysis of pre- and posttreatment gp160 sequences from patients A, B, and C (panels A, B, and C, respectively). Neighbor-joining trees were generated using the Clustal W program from an alignment edited to remove V4 and V5. The “disregard gapped” columns and “correct for multiple hits” options were selected, and a consensus sequence was generated from the earliest set of clones and used as an outgroup to root the tree. The numbers at the nodes are values determined from 1,000 bootstrap trials Sequence diversity is represented by horizontal distance. The phenotypic tropism assignment of the clones is indicated on each panel.

FIG.2.

CXCR4-using variants are genetically distinct from CCR5-tropic clones in each patient. Shown are the results of phylogenetic analysis of pre- and posttreatment gp160 sequences from patients A, B, and C (panels A, B, and C, respectively). Neighbor-joining trees were generated using the Clustal W program from an alignment edited to remove V4 and V5. The “disregard gapped” columns and “correct for multiple hits” options were selected, and a consensus sequence was generated from the earliest set of clones and used as an outgroup to root the tree. The numbers at the nodes are values determined from 1,000 bootstrap trials Sequence diversity is represented by horizontal distance. The phenotypic tropism assignment of the clones is indicated on each panel.

FIG.2.

CXCR4-using variants are genetically distinct from CCR5-tropic clones in each patient. Shown are the results of phylogenetic analysis of pre- and posttreatment gp160 sequences from patients A, B, and C (panels A, B, and C, respectively). Neighbor-joining trees were generated using the Clustal W program from an alignment edited to remove V4 and V5. The “disregard gapped” columns and “correct for multiple hits” options were selected, and a consensus sequence was generated from the earliest set of clones and used as an outgroup to root the tree. The numbers at the nodes are values determined from 1,000 bootstrap trials Sequence diversity is represented by horizontal distance. The phenotypic tropism assignment of the clones is indicated on each panel.

FIG. 3.

Evidence that a CXCR4-using Env clone in patient B arose as a result of recombination between CCR5-tropic and CXCR4-using variants. An outlying CXCR4-using Env clone from day 433 was compared to CCR5-tropic (red) and CXCR4-using (blue) variants from the same patient using the RIP tool (Los Alamos HIV Sequence Database: http://www.hiv.lanl.gov/content/hiv-db/mainpage.html). The graph indicates the similarity between the outlying Env clone and the CCR5- and CXCR4-using variants (y axis) at each position along the entire gp160 sequence (x axis), using a window length of 200 bp. The thickness of each line indicates the confidence in the best match, with a thick line representing >95% confidence. The green arrow shows the point of likely recombination at approximately 1,050 bp.