title: Performance of genotypic algorithms for predicting tropism of HIV-1CRF02_AG subtype.
abstract: BACKGROUND
  Several genotypic rules for predicting HIV-1 non-B subtypes tropism are commonly used, but there is no consensus about their performances.
  
  
  OBJECTIVE
  Three genotypic methods were compared for CRF02_AG HIV-1 tropism determination.
  
  
  METHODS
  V3 env region of 178HIV-1 CRF02_AG from Pitié-Salpêtrière and Saint-Antoine Hospitals was sequenced from plasma HIV-1 RNA. HIV-1 tropism was determined by Geno2Pheno algorithm, false positive rate (FPR) 5% or 10%, the 11/25 rule or the combined criteria of the 11/25 and net charge rule.
  
  
  RESULTS
  A concordance of 91.6% was observed between Geno2pheno 5% and the combined criteria. The results were nearly similar for the comparison between Geno2pheno 5% and the 11/25 rule. More mismatches were observed when Geno2pheno was used with the FPR 10%. A lower nadir CD4 cell count was associated with a discordance of tropism prediction between Geno2pheno 5% and the combined criteria or the 11/25 rule (p=0.02 and p=0.03, respectively). A lower HIV-1 viral load was associated with some discordance for the comparison of Geno2pheno 10% and the combined rule (p=0.02).
  
  
  CONCLUSIONS
  Geno2pheno FPR 5% or 10% predicted more X4-tropic viruses for this set of CRF02_AG sequences than the combined criteria or the 11/25 rule alone. Furthermore, Geno2pheno FPR 5% was more concordant with the 11/25 rule and the combined rule than Geno2pheno 10% to predict HIV-1 tropism. Overall, Geno2pheno 5% could be used to predict CRF02_AG tropism as well as other genotypic rules.
authors.affiliation: Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), F75013 Paris, France; AP-HP, Groupe hospitalier Pitié Salpêtrière, Laboratoire de Virologie, Paris F-75013, France. Electronic address: cathia.soulie@psl.aphp.fr.
authors.forename: C
authors.initials: C
authors.lastname: Soulié
authors.affiliation: Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), F75013 Paris, France; AP-HP, Hôpital Saint-Antoine, Service de Virologie, Paris F-75013, France.
authors.forename: D B
authors.initials: DB
authors.lastname: Fofana
authors.affiliation: AP-HP, Hôpital Saint-Antoine, Service de Virologie, Paris F-75013, France.
authors.forename: N
authors.initials: N
authors.lastname: Boukli
authors.affiliation: Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), F75013 Paris, France; AP-HP, Groupe hospitalier Pitié Salpêtrière, Laboratoire de Virologie, Paris F-75013, France.
authors.forename: S
authors.initials: S
authors.lastname: Sayon
authors.affiliation: Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), F75013 Paris, France; AP-HP, Groupe hospitalier Pitié Salpêtrière, Laboratoire de Virologie, Paris F-75013, France.
authors.forename: S
authors.initials: S
authors.lastname: Lambert-Niclot
authors.affiliation: Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), F75013 Paris, France; AP-HP, Groupe hospitalier Pitié Salpêtrière, Laboratoire de Virologie, Paris F-75013, France.
authors.forename: Marc
authors.initials: M
authors.lastname: Wirden
authors.affiliation: AP-HP, Hôpital Pitié-Salpêtrière, Service de Médecine Interne, Paris F-75013, France.
authors.forename: A
authors.initials: A
authors.lastname: Simon
authors.affiliation: AP-HP, Hôpital Pitié-Salpêtrière, Service de Maladies Infectieuses, Paris F-75013, France.
authors.forename: C
authors.initials: C
authors.lastname: Katlama
authors.affiliation: Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), F75013 Paris, France; AP-HP, Groupe hospitalier Pitié Salpêtrière, Laboratoire de Virologie, Paris F-75013, France.
authors.forename: V
authors.initials: V
authors.lastname: Calvez
authors.affiliation: AP-HP, Hôpital Saint Antoine, Service de Maladies Infectieuses, Paris F-75013, France.
authors.forename: P M
authors.initials: PM
authors.lastname: Girard
authors.affiliation: Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), F75013 Paris, France; AP-HP, Groupe hospitalier Pitié Salpêtrière, Laboratoire de Virologie, Paris F-75013, France.
authors.forename: A G
authors.initials: AG
authors.lastname: Marcelin
authors.affiliation: Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), F75013 Paris, France; AP-HP, Hôpital Saint-Antoine, Service de Virologie, Paris F-75013, France.
authors.forename: L
authors.initials: L
authors.lastname: Morand-Joubert
mesh_terms: D000465:Algorithms; D018791:CD4 Lymphocyte Count; D019295:Computational Biology; D005838:Genotype; D015699:HIV Envelope Protein gp120 / Q000235:genetics*; D015658:HIV Infections / Q000821:virology*; D015497:HIV-1 / Q000145:classification / Q000235:genetics / Q000502:physiology*; D006801:Humans; D010446:Peptide Fragments / Q000235:genetics*; D010641:Phenotype; D012367:RNA, Viral / Q000097:blood; D015728:Receptors, HIV; D019562:Viral Load; D056189:Viral Tropism
chemical_list: D015699:HIV Envelope Protein gp120; C059762:HIV envelope protein gp120 (305-321); D010446:Peptide Fragments; D012367:RNA, Viral; D015728:Receptors, HIV
keywords: Genotypic prediction; HIV tropism; Non B subtype