title: Ultra-deep sequencing reveals hidden HIV-1 minority lineages and shifts of viral population between the main cellular reservoirs of the infection after therapy interruption.
abstract: Viral quasispecies population dynamics between monocytes and T-lymphocytes were analyzed in patients after highly active antiretroviral therapy (HAART) interruption, during a follow-up of 3-6 months. V3 env region underwent ultra-deep pyrosequencing. Co-receptor usage prediction was performed by Position Specific Score Matrix Analysis. Phylogenetic trees were constructed to evaluate the relationships between the variants. Gene flow was also investigated. Even though at the moment of therapy interruption monocyte-derived HIV-1 genomes presented higher genetic heterogeneity than that of T-lymphocytes, at subsequent times, this difference in genetic heterogeneity disappeared, due to different waves of expansion and reduction of quasispecies variability associated with monocytes and T-lymphocytes. Phylogenetic analysis and gene flow evaluation supported the hypothesis of extensive interchange of variants between cellular compartments of the infection. A spread of proviral X4 lineages hidden in monocytes to T cells was observed, but this was not associated with an overall shift towards CXCR4 using variants during the observation period.
authors.affiliation: National Institute for Infectious Diseases L.Spallanzani, Rome, Italy.
authors.forename: Gabriella
authors.initials: G
authors.lastname: Rozera
authors.forename: Isabella
authors.initials: I
authors.lastname: Abbate
authors.forename: Massimo
authors.initials: M
authors.lastname: Ciccozzi
authors.forename: Alessandra
authors.initials: A
authors.lastname: Lo Presti
authors.forename: Alessandro
authors.initials: A
authors.lastname: Bruselles
authors.forename: Chrysoula
authors.initials: C
authors.lastname: Vlassi
authors.forename: Gianpiero
authors.initials: G
authors.lastname: D'Offizi
authors.forename: Pasquale
authors.initials: P
authors.lastname: Narciso
authors.forename: Emanuela
authors.initials: E
authors.lastname: Giombini
authors.forename: Barbara
authors.initials: B
authors.lastname: Bartolini
authors.forename: Giuseppe
authors.initials: G
authors.lastname: Ippolito
authors.forename: Maria R
authors.initials: MR
authors.lastname: Capobianchi
mesh_terms: D023241:Antiretroviral Therapy, Highly Active; D004334:Drug Administration Schedule; D014644:Genetic Variation; D015699:HIV Envelope Protein gp120 / Q000235:genetics; D015658:HIV Infections / Q000188:drug therapy* / Q000821:virology; D015497:HIV-1 / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D009000:Monocytes / Q000821:virology*; D010446:Peptide Fragments / Q000235:genetics; D010802:Phylogeny; D019713:Receptors, CCR5 / Q000378:metabolism; D019718:Receptors, CXCR4 / Q000378:metabolism; D017422:Sequence Analysis, DNA; D013601:T-Lymphocytes / Q000821:virology*
chemical_list: D015699:HIV Envelope Protein gp120; C059762:HIV envelope protein gp120 (305-321); D010446:Peptide Fragments; D019713:Receptors, CCR5; D019718:Receptors, CXCR4