title: Performance of commonly used genotypic assays and comparison with phenotypic assays of HIV-1 coreceptor tropism in acutely HIV-1-infected patients.
abstract: OBJECTIVE
  Although founder viruses in primary HIV-1 infections (PHIs) typically use the CCR5 coreceptor (R5-tropic), 3%-19% of subjects also harbour CXCR4-using viruses (X4-tropic), making tropism determination before CCR5 antagonist usage mandatory. Genotypic methods can be used to accurately determine HIV-1 tropism in chronically infected patients.
  
  
  METHODS
  We compared the results of genotypic methods [geno2pheno, PSSMx4r5 including a novel nucleotide-input version (ntPSSM) and distant segments (ds)Kernel] to predict coreceptor usage in a cohort of 67 PHIs. Specimens with discrepant results were phenotypically tested after cloning the V3 gene region into proviral backbones. Recombinant viruses were used to infect U87 indicator cell lines bearing CD4 and either CCR5 or CXCR4.
  
  
  RESULTS
  Geno2pheno10%, PSSMx4r5 and (ds)Kernel gave identical predictions in 85% of cases. Geno2pheno10% predicted the presence of CXCR4 viruses in 18% of patients. Two patients were predicted to carry X4-tropic viruses by all algorithms and X4-tropic viruses were detected in at least one of the recombinant AD8 or NL4-3 backbone-based assays. Ten samples resulted in discordant predictions with at least one algorithm. Full concordance between tropism prediction by using population sequencing and phenotypic assays was observed only with ntPSSM. Geno2pheno prediction and the phenotypic assay gave the same results in a minority of 'discordant' patients.
  
  
  CONCLUSIONS
  Compared with both PSSMx4r5 versions, (ds)Kernel and our phenotypic assay, geno2pheno10% overestimated the frequency of X4-tropic viruses (18% versus 3%). ntPSSM was able to detect one additional X4 virus compared with (ds)Kernel that was confirmed with the phenotypic assay.
authors.affiliation: University Vita-Salute San Raffaele, Milan, Italy Laboratory of Microbiology, Ospedale San Raffaele, IRCCS, Milan, Italy.
authors.forename: Elisa Rita
authors.initials: ER
authors.lastname: Ceresola
authors.affiliation: Department of Infectious and Tropical Diseases, Ospedale San Raffaele, IRCCS, Milan, Italy.
authors.forename: Silvia
authors.initials: S
authors.lastname: Nozza
authors.affiliation: Laboratory of Microbiology, Ospedale San Raffaele, IRCCS, Milan, Italy.
authors.forename: Michela
authors.initials: M
authors.lastname: Sampaolo
authors.affiliation: Laboratory of Microbiology, Ospedale San Raffaele, IRCCS, Milan, Italy.
authors.forename: Angela Rosa
authors.initials: AR
authors.lastname: Pignataro
authors.affiliation: Laboratory of Microbiology, Ospedale San Raffaele, IRCCS, Milan, Italy.
authors.forename: Diego
authors.initials: D
authors.lastname: Saita
authors.affiliation: Laboratory of Microbiology, Ospedale San Raffaele, IRCCS, Milan, Italy.
authors.forename: Roberto
authors.initials: R
authors.lastname: Ferrarese
authors.affiliation: Department of Infectious and Tropical Diseases, Ospedale San Raffaele, IRCCS, Milan, Italy.
authors.forename: Marco
authors.initials: M
authors.lastname: Ripa
authors.affiliation: Department of Microbiology, University of Washington, Seattle, WA, USA.
authors.forename: Wenjie
authors.initials: W
authors.lastname: Deng
authors.affiliation: Department of Microbiology, University of Washington, Seattle, WA, USA.
authors.forename: James I
authors.initials: JI
authors.lastname: Mullins
authors.affiliation: Laboratory of Microbiology, Ospedale San Raffaele, IRCCS, Milan, Italy.
authors.forename: Enzo
authors.initials: E
authors.lastname: Boeri
authors.affiliation: Department of Infectious and Tropical Diseases, Ospedale San Raffaele, IRCCS, Milan, Italy.
authors.forename: Giuseppe
authors.initials: G
authors.lastname: Tambussi
authors.affiliation: University of Insubria Medical School, Department of Biotechnology and Life Sciences, Varese, Italy.
authors.forename: Antonio
authors.initials: A
authors.lastname: Toniolo
authors.affiliation: University Vita-Salute San Raffaele, Milan, Italy Department of Infectious and Tropical Diseases, Ospedale San Raffaele, IRCCS, Milan, Italy.
authors.forename: Adriano
authors.initials: A
authors.lastname: Lazzarin
authors.affiliation: University Vita-Salute San Raffaele, Milan, Italy Laboratory of Microbiology, Ospedale San Raffaele, IRCCS, Milan, Italy.
authors.forename: Massimo
authors.initials: M
authors.lastname: Clementi
authors.affiliation: Laboratory of Microbiology, Ospedale San Raffaele, IRCCS, Milan, Italy University of Insubria Medical School, Department of Biotechnology and Life Sciences, Varese, Italy canducci.filippo@gmail.com.
authors.forename: Filippo
authors.initials: F
authors.lastname: Canducci
mesh_terms: D005838:Genotype; D060005:Genotyping Techniques / Q000379:methods*; D015658:HIV Infections / Q000821:virology*; D015497:HIV-1 / Q000235:genetics / Q000302:isolation & purification / Q000502:physiology*; D006801:Humans; D010641:Phenotype; D015728:Receptors, HIV / Q000032:analysis*; D056189:Viral Tropism; D014776:Virus Cultivation / Q000379:methods*
chemical_list: D015728:Receptors, HIV
keywords: CCR5-tropic; HIV tropism; X4-tropic; maraviroc; primary HIV-1 infection