HIV Type 1 Viral Encephalitis After Development of Viral Resistance to Plasma Suppressive Antiretroviral Therapy

H uman immunodeficiency virus (HIV) disseminates to the central nervous system soon after primary infection and remains detectable in the cerebrospinal fluid (CSF) in a majority of untreated subjects during the entire infectious course. ¹ Combination antiretroviral therapy has had a major impact on morbidity and mortality in HIV-1-infected patients, restoring immune function and thereby preventing opportunistic infections and other disease complications. ^2,3 Thus, since the introduction of combination antiretroviral therapy the incidence of HIV-1-associated dementia (HAD) has markedly declined. ³ But even in the presence of appropriate highly active antiretroviral therapy (HAART) and a strong antiviral immune response, there are published cases of CSF viral escape with HIV-1 RNA above the levels of detection of standard assays in CSF despite having undetectable levels in blood. ^{1,4 –6} Indeed, HIV-1 infection in the CNS becomes increasingly compartmentalized during disease progression and this is reflected by the discordant HIV-1 evolution between CSF and plasma, with the possibility of developing isolated resistance- associated mutations. ^1,7

To date, most CNS-resistant viral strains have been linked to evolutionary HIV strains or after virological failure. Here, we describe two patients with HIV-1 viral encephalitis produced by resistant strains to antiretroviral drugs able to suppress viral replication in plasma, in probable relationship with suboptimal CNS viral suppression.

From January 2008 to December 2010 we identified two chronically HIV-1-infected patients presenting with acute or subacute neurological symptoms, an active viral replication in CSF contrasting with suppressed plasma viremia, and HAART that includes atazanavir/ritonavir. Individual patient's characteristics are detailed in Table 1. The two patients were men, with a previous AIDS diagnosis, a long duration of HIV infection, and more than 20 months of effective antiretroviral therapy including atazanavir boosted with ritonavir. Previously, they had received different antiretroviral regimens, including nelfinavir and lopinavir in the first case, and the latter drug in the second patient. At the time of the neurological episode, the patient's antiretroviral regimens had been unchanged for a median duration of 47 and 20 months, although the duration of HIV suppression in plasma lasted as long as 8 and 2 years, and no cases of previous virological failure or viral blips had been observed. The lowest CD4⁺ counts were 3 cells/μl and 90 cells/μl, although the two patients had CD4⁺ counts above 100 cells/μl at the time of diagnosis.

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Table 1.

Demographics, Clinical, Cerabrospinal Fluid Findings, and Therapy of Patients with HIV Viral Encephalitis

Variable	Patient #1	Patient #2
Age, years	57	47
Gender	Male	Male
Prior CDC stage	C-3	C-3
CD4+ count nadir	3	90
HIV RNA level at HIV diagnosis (log)	7.1	7.2
CD4+ count at time of viral encephalitis	222	144
HIV RNA level at diagnosis (copies/ml)	<50	<50
Antiretroviral therapy and time (months)	ABC + 3TC + r/ATV (47)	TDF + FTC + r/ATV (20)
CPE score	7	6
Time of HIV undetectable (months)	96	48
CSF analysis
WBC (cells/mm3)	300	15
Protein (gr/liter)	0.7	1.56
Glucose (mg/dl)	66	42
HIV RNA level (copies/ml)	24,000	6,850
First therapy	ABC + 3TC + r/lopinavir	ABC + 3TC + r/lopinavir
CPE score after first change	8	8
CSF analysis after first change
WBC (cells/mm3)	80	20
Protein (gr/liter)		1.71
Glucose (md/dl)	67	49
HIV RNA level (copies/ml)	6,850	2,530
Genotypic mutations:
RT	None	None
PRO	32I, 46I, 71V, 73S, 77I	13V, 16E, 18V, 46I, 53L
Final antiretroviral therapy	ABC + 3TC + r/DRV + RAL	ABC + 3TC + r/DRV + RAL
CPE score of final therapy	11	11

CPE, concentration penetration effectiveness; ABC, abacavir; 3TC, lamivudine; r/ATV, atazanavir boosted with ritonavir; TDF, tenofovir; FTC, emtricitabine; r/DRV, darunavir boosted with ritonavir; RAL, raltegravir; CSF, cerebrospinal fluid; RT, retrotranscriptase gene; PRO, protease gene.

Clinical manifestations were changes in recent memory, apathy, and emotional lability in one case and ataxia, tremor, and refusal of alimentation in patient 2. Clinical exploration was compatible with encephalitis (frontal liberation reflects, hyperreflexia, constructive apraxia, and recent memory difficulties), and magnetic resonance imaging (MRI) showed a diffuse, pointed, increase in the T2-weighted signal in the periventricular and subcortical white matter, with preferential affectation of the forebrain and the parietal lobe, and in one case affectation of the descendent white matter tract (internal and external capsule), suggestive of HIV direct damage. Neuropsychological examination showed a Minimental test altered, as well as an HIV dementia scale below 6 points. A lumbar puncture showed pleocytosis in the two cases, with bacterial, mycobacterial, and fungal cultures of CSF negative. Also, polymerase chain reaction (PCR) assays for herpes simplex virus (HSV), cytomegalovirus, JC virus, and varicella-zoster virus, and CSF VDRL assay and a cryptococcal antigen test were negative.

In the two cases, the plasma HIV viral load was undetectable (<50 copies/ml), but the CSF HIV viral load was 24000 and 6850 copies/ml, with final diagnosis of HIV-1 viral encephalitis. The patient's antiretroviral therapy was switched to lopinavir/r and abacavir plus lamivudine to improve CNS drug penetration. However, in both cases, and in spite of a mild improvement, there was the persistence of clinical and CSF abnormalities. Indeed, CNS viral load decreased, and a resistance test showed in both cases the existence of resistance to atazanavir and intermediate resistance to lopinavir. Finally, in the two cases, antiretroviral therapy with abacavir, lamivudine, darunavir boosted with ritonavir, and raltegravir produced slow but complete recovery of clinical conditions and normalization of MRI images.

We describe two patients with HIV viral encephalitis demonstrated by active viral replication, neuroradiological examinations suggestive of meningeal inflammation, and exclusion of other etiology, a clinical picture previously described. Previous studies have shown that CSF HIV-1 RNA generally responds well to antiretroviral therapy, ⁸ although antiretroviral treatment may fail in the CNS, because an important component of many regimens, protease inhibitors, can extensively bind to plasma proteins, ⁹ leaving little unbound drug to penetrate into the brain and CSF. Therefore, HIV-1 infection in the CNS can persist within macrophages and macrophage-related microglial cells despite prolonged and apparently effective HAART. ¹⁰ In these long-lived cells an autonomous viral replication may be sustained, producing an inflammatory state that then progresses to neurological disease. ¹¹ In our patients, the cause of the CNS HIV replication was the progressive development of resistance to an effective antiretroviral therapy that the patient was receiving for years, without previous failure nor viral “blips” that could favor CNS viral escape. Mutations caused by the antiretroviral drugs with the lowest intracerebral penetration would be expected in higher percentages in the CNS than in the periphery of the human body. ¹² Smit and co-workers showed that the evolution of resistance mutations can even differ between different brain subcompartments (e.g., the frontal, temporal, parietal, and occipital lobes, caudate body and nucleus, choroid plexus, putamen, cerebellum, periventricular white matter, anterior hippocampus, and corpus callosum). ¹³

Indeed, the emergence of resistance to the drugs that our patients were receiving supports the role of an incomplete, suboptimal CNS penetration of the drugs. Our patients were receiving atazanavir boosted with ritonavir, an antiretroviral with low CNS penetration, even with ritonavir boosting. ¹⁴ In a recent study, Best et al. describe CSF levels of atazanavir of less than 1% of plasma concentrations, and even 24% of samples had less than 5 ng/ml, an important fact taking into account that atazanavir wild-type IC₅₀ is around 10 ng/ml. ¹⁵ Recently, the concentration penetration effectiveness (CPE) ranking system has been proposed as a simple method for estimating the combined CNS effectiveness of antiretroviral treatment regimens and has been shown to correlate with CSF viral load in a cohort study. ¹⁶ In our subjects, the CPE ranking published version ¹⁷ and revised CPE rank was low initially, but there was only a moderate amelioration of the clinical situation in two patients after improving the CPE score, due to the existence of resistance. Moreover, the two patients had a slow but complete response to an adequate change in the HAART regimen, able to suppress resistant strains and with sufficient CNS penetration, consisting of darunavir boosted with ritonavir plus raltegravir.

Recently, Canestri et al. described 11 similar cases with clinical data from 2004 to 2009. ¹ In contrast to our patients, resistance was demonstrated in eight cases; only five of them had a plasma HIV RNA level that was undetectable, and only in five cases was there resistance to antiretroviral drugs that the patients were receiving (only one with atazanavir), and, indeed, in two of three cases it was possible to find the same mutations in plasma. Thus, some of the cases could be due to evolutionary changes in unsuppressed CSF HIV replication, more than to the selection of CSF-resistant strains due to the presence of antiretroviral drugs. Also, Lafeuillade et al. recently described three cases of encephalitis, two with CSF resistance, but the three patients had a detectable plasma HIV RNA level. ¹⁸ By contrast, our results suggest that an independent evolution of drug resistance mutations in the CNS may emerge as the consequence of incomplete suppression of HIV, probably related to suboptimal drug levels in the CNS and drug selection pressure. ¹³

We have observed only two symptomatic patients in 3 years. This number of patients represents only 0.4% of patients who had received atazanavir at our unit, and moreover they are only 2% of the 128 patients receiving atazanavir in recent years with CD4⁺ below 200 cells/μl. Thus, suboptimal levels were necessary but not sufficient to explain the development of encephalitis. HIV in CSF is thought to be a mixture from blood-derived and CNS-derived sources (i.e., HIV is trafficking into the CNS from the blood), and this mixture varies based on different factors, mainly CD4⁺ count. ¹⁹ Thus, individuals with the lowest CD4⁺ cell counts are more likely to have HIV in CSF that derives from the CNS itself. ¹⁹ The effectiveness of an antiretroviral drug in the CNS would be more clearly established when HIV in the CSF is derived from a CNS source, where only a drug that sufficiently penetrates the blood–brain barrier is able to reduce HIV replication in the CNS, ²⁰ and, inversely, it could explain the continued replication if drug levels are suboptimal. Therefore, the combination of a high initial HIV RNA level and a low CD4⁺ count, with subsequent CNS independent replication, could be the basis for the development of encephalitis, in the presence of suboptimal antiretroviral drug levels.

In conclusion, the development of CNS viral resistance in our patients may be the final effect of the combination of a high HIV RNA level and a low nadir CD4⁺ count, which produces a wide CNS dissemination and, perhaps, continuous viral replication, and of the low CNS drug levels of atazanavir. This combination, in time, conditions the selection of resistant strains able to produce clinical disease. The use of HAART has posed new challenges for the neurologist. It is not rare to encounter a patient who has good control of HIV load in plasma but is developing cognitive impairment. Once non-HIV-related causes have been excluded, physicians should be aware of the possibility of HIV-associated CNS disorders that should prompt a CSF evaluation with the determination of viral replication and genotypic resistance.