TY - JOUR
T1 - Detection of HIV-1 matrix protein P17 quasispecies variants in plasma of chronic HIV-1-infected patients by ultra-deep pyrosequencing
AU - Giombini, Emanuela
AU - Dolcetti, Riccardo
AU - Caccuri, Francesca
AU - Selleri, Marina
AU - Rozera, Gabriella
AU - Abbate, Isabella
AU - Bartolini, Barbara
AU - Martorelli, Debora
AU - Faè, Damiana Antonia
AU - Fiorentini, Simona
AU - Giagulli, Cinzia
AU - Capobianchi, Maria R.
AU - Caruso, Arnaldo
PY - 2014/4/11
Y1 - 2014/4/11
N2 - 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: We evaluated the degree of intra-patient 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 intra-patient 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 p17MAvariants 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.
AB - 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: We evaluated the degree of intra-patient 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 intra-patient 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 p17MAvariants 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.
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U2 - 10.1097/QAI.0000000000000164
DO - 10.1097/QAI.0000000000000164
M3 - Article
JO - Journal of Acquired Immune Deficiency Syndromes
JF - Journal of Acquired Immune Deficiency Syndromes
SN - 1525-4135
ER -