title: HIV-1 tropism determination using a phenotypic Env recombinant viral assay highlights overestimation of CXCR4-usage by genotypic prediction algorithms for CRF01_AE and CRF02_AG [corrected].
abstract: BACKGROUND
  Human Immunodeficiency virus type-1 (HIV) entry into target cells involves binding of the viral envelope (Env) to CD4 and a coreceptor, mainly CCR5 or CXCR4. The only currently licensed HIV entry inhibitor, maraviroc, targets CCR5, and the presence of CXCX4-using strains must be excluded prior to treatment. Co-receptor usage can be assessed by phenotypic assays or through genotypic prediction. Here we compared the performance of a phenotypic Env-Recombinant Viral Assay (RVA) to the two most widely used genotypic prediction algorithms, Geno2Pheno[coreceptor] and webPSSM.
  
  
  METHODS
  Co-receptor tropism of samples from 73 subtype B and 219 non-B infections was measured phenotypically using a luciferase-tagged, NL4-3-based, RVA targeting Env. In parallel, tropism was inferred genotypically from the corresponding V3-loop sequences using Geno2Pheno[coreceptor] (5-20% FPR) and webPSSM-R5X4. For discordant samples, phenotypic outcome was retested using co-receptor antagonists or the validated Trofile® Enhanced-Sensitivity-Tropism-Assay.
  
  
  RESULTS
  The lower detection limit of the RVA was 2.5% and 5% for X4 and R5 minority variants respectively. A phenotype/genotype result was obtained for 210 samples. Overall, concordance of phenotypic results with Geno2Pheno[coreceptor] was 85.2% and concordance with webPSSM was 79.5%. For subtype B, concordance with Geno2pheno[coreceptor] was 94.4% and concordance with webPSSM was 79.6%. High concordance of genotypic tools with phenotypic outcome was seen for subtype C (90% for both tools). Main discordances involved CRF01_AE and CRF02_AG for both algorithms (CRF01_AE: 35.9% discordances with Geno2Pheno[coreceptor] and 28.2% with webPSSM; CRF02_AG: 20.7% for both algorithms). Genotypic prediction overestimated CXCR4-usage for both CRFs. For webPSSM, 40% discordance was observed for subtype A.
  
  
  CONCLUSIONS
  Phenotypic assays remain the most accurate for most non-B subtypes and new subtype-specific rules should be developed for non-B subtypes, as research studies more and more draw conclusions from genotypically-inferred tropism, and to avoid unnecessarily precluding patients with limited treatment options from receiving maraviroc or other entry inhibitors.
authors.affiliation: Laboratory of Retrovirology, Centre Recherche Public de la Santé, Luxembourg, Luxembourg.
authors.forename: Martin
authors.initials: M
authors.lastname: Mulinge
authors.forename: Morgane
authors.initials: M
authors.lastname: Lemaire
authors.forename: Jean-Yves
authors.initials: JY
authors.lastname: Servais
authors.forename: Arkadiusz
authors.initials: A
authors.lastname: Rybicki
authors.forename: Daniel
authors.initials: D
authors.lastname: Struck
authors.forename: Eveline Santos
authors.initials: ES
authors.lastname: da Silva
authors.forename: Chris
authors.initials: C
authors.lastname: Verhofstede
authors.forename: Yolanda
authors.initials: Y
authors.lastname: Lie
authors.forename: Carole
authors.initials: C
authors.lastname: Seguin-Devaux
authors.forename: Jean-Claude
authors.initials: JC
authors.lastname: Schmit
authors.forename: Danielle Perez
authors.initials: DP
authors.lastname: Bercoff
mesh_terms: D000465:Algorithms; D003510:Cyclohexanes / Q000494:pharmacology; D005838:Genotype; D015699:HIV Envelope Protein gp120 / Q000378:metabolism*; D015497:HIV-1 / Q000502:physiology*; D006801:Humans; D008156:Luciferases; D000077592:Maraviroc; D010641:Phenotype; D019718:Receptors, CXCR4 / Q000378:metabolism*; D014230:Triazoles / Q000494:pharmacology; D056189:Viral Tropism / Q000502:physiology*; D053586:Virus Internalization / Q000187:drug effects*
chemical_list: C527276:CXCR4 protein, human; D003510:Cyclohexanes; D015699:HIV Envelope Protein gp120; D019718:Receptors, CXCR4; D014230:Triazoles; D008156:Luciferases; D000077592:Maraviroc