HIV-1 phylogenetic analysis shows HIV-1 transits through the meninges to brain and peripheral tissues

Abstract

Brain infection by the human immunodeficiency virus type 1 (HIV-1) has been investigated in many reports with a variety of conclusions concerning the time of entry and degree of viral compartmentalization. To address these diverse findings, we sequenced HIV-1 gp120 clones from a wide range of brain, peripheral and meningeal tissues from five patients who died from several HIV-1 associated disease pathologies. High-resolution phylogenetic analysis confirmed previous studies that showed a significant degree of compartmentalization in brain and peripheral tissue subpopulations. Some intermixing between the HIV-1 subpopulations was evident, especially in patients that died from pathologies other than HIV-associated dementia. Interestingly, the major tissue harboring virus from both the brain and peripheral tissues was the meninges. These results show that (1) HIV-1 is clearly capable of migrating out of the brain, (2) the meninges are the most likely primary transport tissues, and (3) infected brain macrophages comprise an important HIV reservoir during highly active antiretroviral therapy.

Figure 1. HIV p24 stain of meninges: localization to perivascular and parenchyma macrophages in patient CX

Three different magnifications of tissue are shown (A and B = 100X, C = 400X). In Panel A, SA indicates the subarachnoid space. HIV positive cells stain brown. Intermittent HIV-infected cells are found throughout the tissues (Panels A and B); however a large number of HIV positive cells are found lining up against the blood vessel (arrows in Panels A and C).

Figure 2. Bayesian genealogies of HIV-1

Bayesian maximum clade credibility trees assuming a relaxed molecular clock and constant population size coalescent prior generated from the posterior distribution of trees less a 50% burn-in. Branch lengths are shown according to the scale bar at the bottom of each panel, in relative units of time. Posterior probabilities greater than 85% are indicated with an asterisk. Internal branches are colored according to the maximum parsimony reconstruction of the ancestral tissue origin. Brain to periphery migrations are indicated with black arrows. Periphery to brain migrations are indicated with orange arrows. Branches are colored according to tissue from which virus was isolated: red branches indicate brain tissue, green branches indicate peripheral tissue, blue branches indicate meninges, gray branches indicate multiple equally parsimonious (i.e. uncertain) reconstructions. Phylogenies are shown for patient CX (A), GA (B), AZ (C), DY (D) and BW (E).

Figure 2. Bayesian genealogies of HIV-1

Bayesian maximum clade credibility trees assuming a relaxed molecular clock and constant population size coalescent prior generated from the posterior distribution of trees less a 50% burn-in. Branch lengths are shown according to the scale bar at the bottom of each panel, in relative units of time. Posterior probabilities greater than 85% are indicated with an asterisk. Internal branches are colored according to the maximum parsimony reconstruction of the ancestral tissue origin. Brain to periphery migrations are indicated with black arrows. Periphery to brain migrations are indicated with orange arrows. Branches are colored according to tissue from which virus was isolated: red branches indicate brain tissue, green branches indicate peripheral tissue, blue branches indicate meninges, gray branches indicate multiple equally parsimonious (i.e. uncertain) reconstructions. Phylogenies are shown for patient CX (A), GA (B), AZ (C), DY (D) and BW (E).

Figure 3. The layers of the meninges and proposed models for movement of virus to and from brain

The three major layers of the meninges are shown along with the subarachnoid space. Blood vessels in the CSF and Pia Mater are indicated. In early infection, viruses may enter the brain due to the elevated number of HIV infected macrophages in the CSF due to early encephalitis. Certain viral variants may be more suited to the brain environment and set up a slower long-term dementia process in which viruses evolve within brain tissue resident macrophages. In other cases, patients may develop a late-stage HAD when the patient is again at risk for encephalitis. This, in combination with complete immune breakdown and other disease processes such as lymphoma, atherosclerosis or lipid disorders, may damage both the vessels of the Pia Mater and subarachnoid space, as well as cause breaches across the BBB and allow more rapid movement of virus in and out of the brain.