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
Article first published online: 19 SEP 2012
Copyright © 2012 Wiley Periodicals, Inc.
Journal of Medical Virology
Volume 84, Issue 6, pages 839–844, June 2012
How to Cite
Rozera, G., Abbate, I., Ciccozzi, M., Presti, A. L., Bruselles, A., Vlassi, C., D'Offizi, G., Narciso, P., Giombini, E., Bartolini, B., Ippolito, G. and Capobianchi, M. R. (2012), 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. J. Med. Virol., 84: 839–844. doi: 10.1002/jmv.23292
- Issue published online: 12 APR 2012
- Article first published online: 19 SEP 2012
- Manuscript Accepted: 13 MAR 2012
- Istituto Superiore di Sanita' (National AIDS Project). Grant Numbers: n. 40H54, n. 40H59
- Italian Ministry of Health (Fondi Ricerca Corrente and Ricerca Finalizzata)
- HIV reservoirs;
- co-receptor usage
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. J. Med. Virol. 84:839–844, 2012. © 2012 Wiley Periodicals, Inc.