title: V3 net charge: additional tool in HIV-1 tropism prediction.
abstract: Genotype-based algorithms are valuable tools for the identification of patients eligible for CCR5 inhibitors administration in clinical practice. Among the available methods, geno2pheno[coreceptor] (G2P) is the most used online tool for tropism prediction. This study was conceived to assess if the combination of G2P prediction with V3 peptide net charge (NC) value could improve the accuracy of tropism prediction. A total of 172 V3 bulk sequences from 143 patients were analyzed by G2P and NC values. A phenotypic assay was performed by cloning the complete env gene and tropism determination was assessed on U87_CCR5(+)/CXCR4(+) cells. Sequences were stratified according to the agreement between NC values and G2P results. Of sequences predicted as X4 by G2P, 61% showed NC values higher than 5; similarly, 76% of sequences predicted as R5 by G2P had NC values below 4. Sequences with NC values between 4 and 5 were associated with different G2P predictions: 65% of samples were predicted as R5-tropic and 35% of sequences as X4-tropic. Sequences identified as X4 by NC value had at least one positive residue at positions known to be involved in tropism prediction and positive residues in position 32. These data supported the hypothesis that NC values between 4 and 5 could be associated with the presence of dual/mixed-tropic (DM) variants. The phenotypic assay performed on a subset of sequences confirmed the tropism prediction for concordant sequences and showed that NC values between 4 and 5 are associated with DM tropism. These results suggest that the combination of G2P and NC could increase the accuracy of tropism prediction. A more reliable identification of X4 variants would be useful for better selecting candidates for Maraviroc (MVC) administration, but also as a predictive marker in coreceptor switching, strongly associated with the phase of infection.
authors.affiliation: 1 Virology Section, Department of Molecular Medicine, Sapienza University , Rome, Italy .
authors.forename: Claudia
authors.initials: C
authors.lastname: Montagna
authors.forename: Elisa
authors.initials: E
authors.lastname: De Crignis
authors.forename: Isabella
authors.initials: I
authors.lastname: Bon
authors.forename: Maria Carla
authors.initials: MC
authors.lastname: Re
authors.forename: Ivano
authors.initials: I
authors.lastname: Mezzaroma
authors.forename: Ombretta
authors.initials: O
authors.lastname: Turriziani
authors.forename: Cecilia
authors.initials: C
authors.lastname: Graziosi
authors.forename: Guido
authors.initials: G
authors.lastname: Antonelli
mesh_terms: D065100:CCR5 Receptor Antagonists / Q000627:therapeutic use; D005838:Genotype; D015699:HIV Envelope Protein gp120 / Q000235:genetics / Q000502:physiology*; D023581:HIV Fusion Inhibitors / Q000627:therapeutic use; D015658:HIV Infections / Q000188:drug therapy / Q000821:virology; D015497:HIV-1 / Q000235:genetics / Q000502:physiology*; D006801:Humans; D021141:Nucleic Acid Amplification Techniques; D010446:Peptide Fragments / Q000235:genetics / Q000502:physiology*; D011237:Predictive Value of Tests; D015728:Receptors, HIV / Q000235:genetics / Q000502:physiology; D016415:Sequence Alignment; D016896:Treatment Outcome; D056189:Viral Tropism / Q000502:physiology
chemical_list: D065100:CCR5 Receptor Antagonists; D015699:HIV Envelope Protein gp120; D023581:HIV Fusion Inhibitors; C059762:HIV envelope protein gp120 (305-321); D010446:Peptide Fragments; D015728:Receptors, HIV