High-resolution structure of HIV-1 protease quasispecies.
Int Conf AIDS 2002 Jul 7-12; 14:(abstract no. A10035)
Fernandez G, Clotet B, Martinez MA Fundacio irsiCaixa. Hospital Universitari Germans Trias i Pujol, 08916 Badalona, Spain
We analyzed at high-resolution (1%) the genetic structure of two HIV-1 protease quasispecies obtained from two HIV-1 infected individuals. As it is well known, HIV-1 encoded protease is essential for the replication of the virus and has been extensively used as the target of HIV-1 therapeutics. Two antiretroviral naïve patients (A and B) with an HIV-1 plasma load of 17094 and 15662 copies/ml and CD4+ cell counts of 471 and 607 cells/ é l, respectively, were chosen for this study. Proviral fragments of the protease-coding region were PCR amplified from PBMCs. Forty separate PCR amplifications were done for each sample. Product DNAs were pooled, digested with Xho I and EcoRI and ligated to Xho I-EcoRI-digested bacteriophage lambda. One hundred clones from each sample were sequenced. The mean intrasample DNA genetic distances were similar in the two samples analyzed (1.2% and 1.5% for patient A and B, respectively). Furthermore, a similar diversity was observed in both samples, that is, 76% (Shannon entropy of 0.8, patient A) and 70% (Shannon entropy of 0.8, patient B) of the nucleotide sequences were different. However, when the amino acids substitutions were computed, a significant difference between both samples was detected: 1.2% (Shannon entropy of 0.4) and 2.9% (Shannon entropy of 0.8) for patient A and B, respectively. In both samples, two major amino acid forms with frequencies of 38 and 28% (patient A) and 28 and 14% (patient B) were identified. Interestingly, within the patient B variant spectrum was possible to identify 43 different amino acid sequences, while patient A only showed 10 different amino acid protease variants. Finally, different catalytic efficiencies were also detected among proteases present in the patient B quasispecies. Our findings suggest that different selective forces are acting in different infected individuals, which affect the HIV-1 protease amino acid diversification.
Keywords: AEGIS, HIV Protease, HIV-1, HIV Protease Inhibitors, Variation (Genetics), Base Sequence, Amino Acid Sequence, HIV-1 Reverse Transcriptase, Phylogeny, Human, genetics, classification
