title: Detection of quasispecies variants predicted to use CXCR4 by ultra-deep pyrosequencing during early HIV infection.
abstract: OBJECTIVE
  HIV-1 V3 quasispecies was analyzed by ultra-deep pyrosequencing, in early HIV-infected patients, to assess possible correlations between quasispecies diversity, frequency of variants predicted to use CXCR4 and need for early antiretroviral treatment.
  
  
  METHODS
  Twenty patients were retrospectively enrolled: 10 patients (group A) required HAART within 6 months from seroconversion and 10 (group B) remained free of therapy during this period. V3 quasispecies was assessed on plasma viral RNA and in peripheral blood mononuclear cell-associated proviral DNA. Prediction of coreceptor usage was performed by position-specific score matrix analysis.
  
  
  RESULTS
  Variants predicted to use CXCR4 were detected (frequency ≥0.3%) in the plasma of 50% of early infected patients (60% from group A and 40% from group B). Intrapatient frequency of these variants was highly variable (0.3-56.3%). A positive correlation was observed between the proportion of X4 variants and intrapatient quasispecies diversity. Quasispecies diversity and absolute numbers of X4 variants were significantly higher in patients from group A. The analysis of proviral DNA quasispecies, performed in a subgroup of five patients, showed that X4 variants were not detected in patients with RNA frequency below 0.3%, and detected at 3.6% in the patient with 56.3% of X4 plasma variants.
  
  
  CONCLUSIONS
  Our findings show that X4 variants may be frequently found, at variable intrapatient frequency, in early infected patients, and that quasispecies diversity and absolute numbers of X4 variants are significantly higher in patients undergoing early antiretroviral treatment. Further studies are mandatory to explore the clinical relevance of X4 variants present during early infection with respect to clinical progression and possible therapeutic implications.
authors.affiliation: Laboratory of Virology, Clinical Department, National Institute of Infectious Diseases INMI, Lazzaro Spallanzani, Italy. isabella.abbate@inmi.it
authors.forename: Isabella
authors.initials: I
authors.lastname: Abbate
authors.forename: Chrysoula
authors.initials: C
authors.lastname: Vlassi
authors.forename: Gabriella
authors.initials: G
authors.lastname: Rozera
authors.forename: Alessandro
authors.initials: A
authors.lastname: Bruselles
authors.forename: Barbara
authors.initials: B
authors.lastname: Bartolini
authors.forename: Emanuela
authors.initials: E
authors.lastname: Giombini
authors.forename: Angela
authors.initials: A
authors.lastname: Corpolongo
authors.forename: Gianpiero
authors.initials: G
authors.lastname: D'Offizi
authors.forename: Pasquale
authors.initials: P
authors.lastname: Narciso
authors.forename: Alessandro
authors.initials: A
authors.lastname: Desideri
authors.forename: Giuseppe
authors.initials: G
authors.lastname: Ippolito
authors.forename: Maria R
authors.initials: MR
authors.lastname: Capobianchi
mesh_terms: D000328:Adult; D023241:Antiretroviral Therapy, Highly Active; D005260:Female; D014644:Genetic Variation; D015658:HIV Infections / Q000188:drug therapy / Q000235:genetics* / Q000821:virology; D006679:HIV Seropositivity / Q000235:genetics; D015497:HIV-1 / Q000235:genetics*; D006801:Humans; D008297:Male; D008875:Middle Aged; D011533:Proviruses / Q000235:genetics; D012367:RNA, Viral / Q000235:genetics*; D019718:Receptors, CXCR4 / Q000235:genetics*; D012189:Retrospective Studies; D017422:Sequence Analysis, DNA; D055815:Young Adult
chemical_list: D012367:RNA, Viral; D019718:Receptors, CXCR4