title: Evolution of HIV-1 tropism at quasispecies level after 5 years of combination antiretroviral therapy in patients always suppressed or experiencing episodes of virological failure.
abstract: OBJECTIVE
  Tropism evolution of HIV-1 quasispecies was analysed by ultra-deep pyrosequencing (UDPS) in patients on first-line combination antiretroviral therapy (cART) always suppressed or experiencing virological failure episodes.
  
  
  METHODS
  Among ICONA patients, two groups of 20 patients on cART for ≥5 years, matched for baseline viraemia and therapy duration, were analysed [Group I, patients always suppressed; and Group II, patients experiencing episode(s) of virological failure]. Viral tropism was assessed by V3 UDPS on plasma RNA before therapy (T0) and on peripheral blood mononuclear cell proviral DNA before-after therapy (T0-T1), using geno2pheno false positive rate (FPR) (threshold for X4: 5.75). For each sample, quasispecies tropism was assigned according to X4 variant frequency: R5, <0.3% X4; minority X4, 0.3%-19.9% X4; and X4, ≥20% X4. An R5-X4 switch was defined as a change from R5/minority X4 in plasma/proviral genomes at T0 to X4 in provirus at T1.
  
  
  RESULTS
  At baseline, mean FPR and %X4 of viral RNA were positively correlated with those of proviral DNA. After therapy, proviral DNA load significantly decreased in Group I; mean FPR of proviral quasispecies significantly decreased and %X4 increased in Group II. An R5-X4 switch was observed in five patients (two in Group I and three in Group II), all harbouring minority X4 variants at T0.
  
  
  CONCLUSIONS
  UDPS analysis reveals that the tropism switch is not an 'on-off' phenomenon, but may result from a profound re-shaping of viral quasispecies, even under suppressive cART. However, episodes of virological failure seem to prevent reduction of proviral DNA and to accelerate viral evolution, as suggested by decreased FPR and increased %X4 at T1 in Group II patients.
authors.affiliation: National Institute for Infectious Diseases L. Spallanzani, Rome, Italy.
authors.forename: Gabriella
authors.initials: G
authors.lastname: Rozera
authors.affiliation: National Institute for Infectious Diseases L. Spallanzani, Rome, Italy isabella.abbate@inmi.it.
authors.forename: Isabella
authors.initials: I
authors.lastname: Abbate
authors.affiliation: National Institute for Infectious Diseases L. Spallanzani, Rome, Italy.
authors.forename: Emanuela
authors.initials: E
authors.lastname: Giombini
authors.affiliation: San Raffaele Scientific Institute, Milan, Italy.
authors.forename: Antonella
authors.initials: A
authors.lastname: Castagna
authors.affiliation: Siena University Hospital, Siena, Italy.
authors.forename: Andrea
authors.initials: A
authors.lastname: De Luca
authors.affiliation: University of Rome Tor Vergata, Rome, Italy.
authors.forename: Francesca
authors.initials: F
authors.lastname: Ceccherini-Silberstein
authors.affiliation: University College London, London, UK.
authors.forename: Alessandro
authors.initials: A
authors.lastname: Cozzi Lepri
authors.affiliation: Galliera Hospital, Genova, Italy.
authors.forename: Giovanni
authors.initials: G
authors.lastname: Cassola
authors.affiliation: University Department of Infectious Diseases, University of Brescia, Brescia, Italy Unit of Infectious Diseases, University 'Magna Græcia', Catanzaro, Italy.
authors.forename: Carlo
authors.initials: C
authors.lastname: Torti
authors.affiliation: Clinic of Infectious Diseases, San Paolo Hospital, University of Milan, Milan, Italy.
authors.forename: Antonella
authors.initials: A
authors.lastname: d'Arminio Monforte
authors.affiliation: National Institute for Infectious Diseases L. Spallanzani, Rome, Italy.
authors.forename: Giuseppe
authors.initials: G
authors.lastname: Ippolito
authors.affiliation: National Institute for Infectious Diseases L. Spallanzani, Rome, Italy.
authors.forename: Maria R
authors.initials: MR
authors.lastname: Capobianchi
mesh_terms: D000328:Adult; D044966:Anti-Retroviral Agents / Q000008:administration & dosage*; D015331:Cohort Studies; D004359:Drug Therapy, Combination; D019143:Evolution, Molecular; D005260:Female; D015658:HIV Infections / Q000188:drug therapy* / Q000235:genetics*; D015497:HIV-1 / Q000187:drug effects / Q000235:genetics*; D006801:Humans; D008297:Male; D008875:Middle Aged; D011446:Prospective Studies; D013997:Time Factors; D018523:Tropism / Q000187:drug effects / Q000235:genetics*; D019562:Viral Load / Q000187:drug effects / Q000235:genetics
chemical_list: D044966:Anti-Retroviral Agents
keywords: HIV quasispecies; cART; co-receptor usage; tropism switch; ultra-deep pyrosequencing