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Detection of HIV-1 Matrix Protein p17 Quasispecies Variants in Plasma of Chronic HIV-1–Infected Patients by Ultra-Deep Pyrosequencing

Giombini, Emanuela PhD*; Dolcetti, Riccardo MD; Caccuri, Francesca PhD; Selleri, Marina PhD*; Rozera, Gabriella PhD*; Abbate, Isabella PhD*; Bartolini, Barbara PhD*; Martorelli, Debora PhD; Faè, Damiana Antonia PhD; Fiorentini, Simona PhD; Giagulli, Cinzia PhD; Capobianchi, Maria R. PhD*; Caruso, Arnaldo MD

JAIDS Journal of Acquired Immune Deficiency Syndromes: 1 July 2014 - Volume 66 - Issue 3 - p 332–339
doi: 10.1097/QAI.0000000000000164
Epidemiology and Prevention

Background: The HIV-1 matrix protein p17 (p17MA) is a pleiotropic protein that plays a key role in the HIV-1 life cycle. It has been long believed to have a highly conserved primary amino acid sequence and a well-preserved structural integrity to avoid severe fitness consequences. However, recent data revealed that the carboxy (COOH)-terminus of p17MA possesses high levels of predicted intrinsic disorder, which would subtend to at least partially unfolded status of this region. This finding pointed to the need of investigating p17MA heterogeneity.

Methods: The degree of intrapatient variations in the p17MA primary sequence was assessed on plasma viral RNA by using ultra-deep pyrosequencing.

Results: Data obtained support a complex nature of p17MA quasispecies, with variants present at variable frequency virtually in all patients. Clusters of mutations were scattered along the entire sequence of the viral protein, but they were more frequently detected within the COOH-terminal region of p17MA. Moreover, deletions and insertions also occurred in a restricted area of the COOH-terminal region.

Conclusions: On the whole, our data show that the intrapatient level of sequence diversity in the p17MA is much higher than predicted before. Our results pave the way for further studies aimed at unraveling possible correlations between the presence of distinct p17MA variants and peculiar clinical evolutions of HIV-1 disease. The presence of p17MA quasispecies diversity may offer new tools to improve our understanding of the viral adaptation during the natural history of HIV-1 infection.

*National Institute for Infectious Diseases “L. Spallanzani,” Rome, Italy;

Cancer Bio-Immunotherapy Unit, Centro di Riferimento Oncologico, IRCCS—National Cancer Institute, Aviano (PN), Italy; and

Section of Microbiology, Department of Molecular and Translational Medicine, University of Brescia Medical School, Brescia, Italy.

Correspondence to: Arnaldo Caruso, MD, Section of Microbiology, Department of Molecular and Translational Medicine, University of Brescia Medical School, Piazzale Spedali Civili, 1, 25123 Brescia, Italy (e-mail: arnaldo.caruso@unibs.it).

Supported by the Associazione Italiana per la Ricerca sul Cancro (contract 14287 to R.D.); the Italian Ministry of Health, Programma di Ricerca Corrente e Finalizzata (to M.R.C.); and the Italian Ministry of Health, Programma di Ricerca di Rilevante Interesse Nazionale, AIDS Grant (contract 40G.16 to A.C.).

The authors have no conflicts of interest to disclose.

Principal contributions of authors are study conception (E.G., R.D., F.C., M.R.C., A.C.); study design (E.G., R.D., F.C., D.M., D.A.F., S.F., C.G., M.R.C., A.C.); clinical data collection (M.S., G.R., D.M., D.A.F.); data acquisition and analysis (E.G., M.S., G.R., I.A., B.B.); statistical analysis (E.G., M.S., G.R., I.A., B.B.); drafting the article (A.C., R.D., M.R.C., E.G., F.C.); and supervision of the study (A.C.). All the authors contributed to the interpretation of the results, gave relevant input to the intellectual content of the manuscript, revised it, and approved its final version.

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Received November 29, 2013

Accepted March 11, 2014

© 2014 by Lippincott Williams & Wilkins