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.

Gabriella Rozera, Isabella Abbate, Massimo Ciccozzi, Alessandra Lo Presti, Alessandro Bruselles, Chrysoula Vlassi, Gianpiero D'Offizi, Pasquale Narciso, Emanuela Giombini, Barbara Bartolini, Giuseppe Ippolito, Maria R. Capobianchi

Research output: Contribution to journalArticle


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.

Original languageEnglish
Pages (from-to)839-844
Number of pages6
JournalJournal of Medical Virology
Issue number6
Publication statusPublished - Jun 2012


ASJC Scopus subject areas

  • Virology
  • Infectious Diseases

Cite this