Characterizing the Diverse Mutational Pathways Associated with R5-Tropic Maraviroc Resistance: HIV-1 That Uses the Drug-Bound CCR5 Coreceptor.
Entry inhibitors represent a potent class of antiretroviral drugs that target a host cell protein, CCR5, an HIV-1 entry coreceptor, and not viral protein. Lack of sensitivity can occur due to preexisting virus that uses the CXCR4 coreceptor, while true resistance occurs through viral adaptation to use a drug-bound CCR5 coreceptor. To understand this R5 resistance pathway, we analyzed >500 envelope protein sequences and phenotypes from viruses of 20 patients from the clinical trials MOTIVATE 1 and 2, in which treatment-experienced patients received maraviroc plus optimized background therapy. The resistant viral population was phylogenetically distinct and associated with a genetic bottleneck in each patient, consistent with de novo emergence of resistance. Recombination analysis showed that the C2-V3-C3 region tends to genotypically correspond to the recombinant's phenotype, indicating its primary importance in conferring resistance. Between patients, there was a notable lack of commonality in the specific sites conferring resistance, confirming the unusual nature of R5-tropic resistance. We used coevolutionary and positive-selection analyses to characterize the genotypic determinants of resistance and found that (i) there are complicated covariation networks, indicating frequent coevolutionary/compensatory changes in the context of protein structure; (ii) covarying sites under positive selection are enriched in resistant viruses; (iii) CD4 binding sites form part of a unique covariation network independent of the V3 loop; and (iv) the covariation network formed between the V3 loop and other regions of gp120 and gp41 intersects sites involved in glycosylation and protein secretion. These results demonstrate that while envelope sequence mutations are the key to conferring maraviroc resistance, the specific changes involved are context dependent and thus inherently unpredictable.


OBJECTIVE
The entry inhibitor drug maraviroc makes the cell coreceptor CCR5 unavailable for use by HIV-1 and is now used in combination antiretroviral therapy. Treatment failure with drug-resistant virus is particularly interesting because it tends to be rare, with lack of sensitivity usually associated with the presence of CXCR4-using virus (CXCR4 is the main alternative coreceptor HIV-1 uses, in addition to CD4). We analyzed envelope sequences from HIV-1, obtained from 20 patients who enrolled in maraviroc clinical trials and experienced treatment failure, without detection of CXCR4-using virus. Evolutionary analysis was employed to identify molecular changes that confer maraviroc resistance. We found that in these individuals, resistant viruses form a distinct population that evolved once and was successful as a result of drug pressure. Further evolutionary analysis placed the complex network of interdependent mutational changes into functional groups that help explain the impediments to the emergence of maraviroc-associated R5 drug resistance.
Computational and Evolutionary Biology, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.
Xiaowei
X
Jiang
Computational and Evolutionary Biology, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom Department of Biology, University of Nevada, Reno, Nevada, USA.
Felix
F
Feyertag
School of Natural Sciences, National University of Ireland Galway, Galway, Ireland Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.
Conor J
CJ
Meehan
School of Natural Sciences, National University of Ireland Galway, Galway, Ireland.
Grace P
GP
McCormack
School of Natural Sciences, National University of Ireland Galway, Galway, Ireland South African National Bioinformatics Institute, South African MRC Bioinformatics Unit, University of the Western Cape, Bellville, South Africa.
Simon A
SA
Travers
The Research Network, Sandwich, United Kingdom Pfizer R&D, Sandwich, United Kingdom.
Charles
C
Craig
Pfizer R&D, Sandwich, United Kingdom.
Mike
M
Westby
The Research Network, Sandwich, United Kingdom Pfizer R&D, Sandwich, United Kingdom.
Marilyn
M
Lewis
Computational and Evolutionary Biology, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom david.robertson@manchester.ac.uk.
David L
DL
Robertson
D000595:Amino Acid Sequence; D001483:Base Sequence; D065100:CCR5 Receptor Antagonists / Q000627:therapeutic use*; D002986:Clinical Trials as Topic; D003510:Cyclohexanes / Q000627:therapeutic use*; D024882:Drug Resistance, Viral / Q000235:genetics*; D006031:Glycosylation; D015699:HIV Envelope Protein gp120 / Q000235:genetics; D015700:HIV Envelope Protein gp41 / Q000235:genetics; D023581:HIV Fusion Inhibitors / Q000627:therapeutic use*; D015658:HIV Infections / Q000188:drug therapy* / Q000821:virology; D015497:HIV-1 / Q000187:drug effects* / Q000378:metabolism; D006801:Humans; D000077592:Maraviroc; D008969:Molecular Sequence Data; D017434:Protein Structure, Tertiary; D019713:Receptors, CCR5 / Q000378:metabolism*; D019718:Receptors, CXCR4 / Q000378:metabolism; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA; D015398:Signal Transduction / Q000235:genetics; D017211:Treatment Failure; D014230:Triazoles / Q000627:therapeutic use*; D053586:Virus Internalization / Q000187:drug effects; D014779:Virus Replication / Q000235:genetics
D065100:CCR5 Receptor Antagonists; C584933:CCR5 protein, human; C527276:CXCR4 protein, human; D003510:Cyclohexanes; D015699:HIV Envelope Protein gp120; D015700:HIV Envelope Protein gp41; D023581:HIV Fusion Inhibitors; D019713:Receptors, CCR5; D019718:Receptors, CXCR4; D014230:Triazoles; C514793:gp120 protein, Human immunodeficiency virus 1; C514787:gp41 protein, Human immunodeficiency virus 1; D000077592:Maraviroc