Table 1.
Subject population clinical and virological characteristics.
Table 2.
HIV-1 population characteristics in the CSF compartment.
Figure 1.
HIV-1 variants in the CSF of neurologically asymptomatic subjects can be R5 T cell-tropic.
(A) Maximum-likelihood phylogenetic trees. env sequences from the CSF are labeled with solid blue circles, and plasma sequences are labeled with solid red triangles. Bootstrap numbers ≥70 are indicated with an asterisk at the appropriate nodes, and bootstrap values are listed at critical nodes in the trees. The genetic distance scale bar indicates the number of nucleotide substitutions per site between env sequences. HIV-1 env sequences selected for phenotypic analyses are indicated with a black square, and X4-tropic envelopes are indicated with an underlined, superscript “X” following the envelope name; all other envelopes were R5-tropic. (B) Single-cycle infection of HIV-1 Env-pseudotyped reporter viruses on CD4lowCCR5high 293-Affinofile cells. Receptor expression was measured as follows: CD4low = 1,214 receptors/cell, CD4high = 97,003 receptors/cell, CCR5high = 34,431 receptors/cell. Data are expressed as means of quadruplicate wells ± s.d., and results are representative of two independent experiments. (C) Single-cycle infection of HIV-1 Env-pseudotyped reporter viruses on primary human MDM. Data shown are means of duplicate wells ± s.d. for one donor, and were normalized to infection of the control macrophage-tropic HIV-1 Ba-L envelope.
Figure 2.
Compartmentalized R5 T cell-tropic HIV-1 populations are found in the CSF of subjects diagnosed with HAD.
(A) Maximum-likelihood phylogenetic trees with compartmentalization and clonal amplification in the CSF. env sequences from the CSF are labeled with solid blue circles, and plasma sequences are labeled with solid red triangles. The phylogenetic tree characteristics are the same as those stated in Figure 1A. (B) Single-cycle infection of HIV-1 Env-pseudotyped reporter viruses on CD4lowCCR5high 293-Affinofile cells. Receptor expression was measured as follows: CD4low = 1,214 receptors/cell, CD4high = 97,003 receptors/cell, CCR5high = 34,431 receptors/cell. Data are expressed as means of quadruplicate wells ± s.d., and results are representative of two independent experiments. (C) Single-cycle infection of HIV-1 Env-pseudotyped reporter viruses on primary human MDM. Data shown are means of duplicate wells ± s.d. for one donor, and were normalized to infection of the control macrophage-tropic HIV-1 Ba-L envelope.
Figure 3.
Compartmentalized HIV-1 populations in the CSF are associated with HAD.
Maximum-likelihood phylogenetic trees are displayed for five HAD subjects with compartmentalization in the CSF. env sequences from the CSF are labeled with solid blue circles, and plasma sequences are labeled with solid red triangles. The phylogenetic tree characteristics are the same as those stated in Figure 1A.
Figure 4.
Compartmentalized HIV-1 populations in the CSF of some HAD subjects are macrophage-tropic.
Phenotype data is displayed for HIV-1 env sequences from Figure 3. (A) Single-cycle infection of HIV-1 Env-pseudotyped reporter viruses on CD4lowCCR5high 293-Affinofile cells. Receptor expression was measured as follows: CD4low = 1,214 receptors/cell, CD4high = 97,003 receptors/cell, CCR5high = 34,431 receptors/cell. Data are expressed as means of quadruplicate wells ± s.d., and results are representative of two independent experiments. (B) Single-cycle infection of HIV-1 Env-pseudotyped reporter viruses on primary human MDM. Data shown are means of duplicate wells ± s.d. for one donor, and were normalized to infection of the control macrophage-tropic HIV-1 Ba-L envelope.
Figure 5.
Macrophage-tropic HIV-1 variants in the CSF/CNS can be detected prior to the development of severe dementia.
(A) Longitudinal phylogenetic analysis of env sequences from one subject with dementia. The genetic distance scale bar indicates the number of nucleotide substitutions per site between env sequences. HIV-1 env sequences selected for phenotypic analyses are indicated with a black square, and the node of divergence for the CSF M-tropic population is indicated with a blue open circle. Bootstrap numbers ≥70 are indicated with an asterisk at the appropriate nodes, and bootstrap values are listed at critical nodes in the tree. Months from HAD diagnosis correspond to the following sample dates: 7/8/2002 (−21), 12/3/2002 (−16), 4/8/2004 (0), 5/11/2004 (1), and 6/3/2004 (2). (B) Single-cycle infection of HIV-1 Env-pseudotyped reporter viruses on CD4lowCCR5high 293-Affinofile cells. Receptor expression was measured as follows: CD4low = 1,214 receptors/cell, CD4high = 97,003 receptors/cell, CCR5high = 34,431 receptors/cell. Data are expressed as means of quadruplicate wells ± s.d., and results are representative of two independent experiments. (C) Single-cycle infection of HIV-1 Env-pseudotyped reporter viruses on primary human MDM. Data shown are means of duplicate wells ± s.d. for one donor, and were normalized to infection of the control macrophage-tropic HIV-1 Ba-L envelope.