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Detection of quasispecies variants predicted to use CXCR4 by ultra-deep pyrosequencing during early HIV infection.
AIDS. 2010 Dec 14;
Authors: Abbate I, Vlassi C, Rozera G, Bruselles A, Bartolini B, Giombini E, Corpolongo A, D'offizi G, Narciso P, Desideri A, Ippolito G, Capobianchi MR
OBJECTIVES:: HIV-1 V3 quasispecies was analyzed, by ultra-deep pyrosequencing, in early HIV-infected patients, to assess possible correlations between quasispecies diversity, frequency of variants predicted to use CXCR4 and need for early antiretroviral treatment. METHODS:: Twenty patients were retrospectively enrolled: 10 patients (group A) required HAART within 6 months from seroconversion, 10 (group B) remained free of therapy during this period. V3 quasispecies was assessed on plasma viral RNA and in PBMC-associated proviral DNA. Prediction of co-receptor usage was performed by PSSM. RESULTS:: Variants predicted to use CXCR4 were detected (frequency >=0.3%) in the plasma of 50% of early infected patients (60% from group A, 40% from group B). Intra-patient frequency of these variants was highly variable (0.3-56.3%). A positive correlation was observed between proportion of X4 variants and intra-patient quasispecies diversity. Quasispecies diversity and absolute numbers of X4 variants were significantly higher in patients from group A. The analysis of proviral DNA quasispecies, performed in a subgroup of 5 patients, showed that X4 variants were not detected in patients with RNA frequency
Detection of quasispecies variants predicted to use CXCR4 by ultra-deep pyrosequencing during early HIV infection.
AIDS. 2010 Dec 14;
Authors: Abbate I, Vlassi C, Rozera G, Bruselles A, Bartolini B, Giombini E, Corpolongo A, D'offizi G, Narciso P, Desideri A, Ippolito G, Capobianchi MR
OBJECTIVES:: HIV-1 V3 quasispecies was analyzed, by ultra-deep pyrosequencing, in early HIV-infected patients, to assess possible correlations between quasispecies diversity, frequency of variants predicted to use CXCR4 and need for early antiretroviral treatment. METHODS:: Twenty patients were retrospectively enrolled: 10 patients (group A) required HAART within 6 months from seroconversion, 10 (group B) remained free of therapy during this period. V3 quasispecies was assessed on plasma viral RNA and in PBMC-associated proviral DNA. Prediction of co-receptor usage was performed by PSSM. RESULTS:: Variants predicted to use CXCR4 were detected (frequency >=0.3%) in the plasma of 50% of early infected patients (60% from group A, 40% from group B). Intra-patient frequency of these variants was highly variable (0.3-56.3%). A positive correlation was observed between proportion of X4 variants and intra-patient quasispecies diversity. Quasispecies diversity and absolute numbers of X4 variants were significantly higher in patients from group A. The analysis of proviral DNA quasispecies, performed in a subgroup of 5 patients, showed that X4 variants were not detected in patients with RNA frequency