Background:  HIV-1-associated encephalopathy in children leads to cognitive and developmental delays and has been associated with elevated cerebrospinal fluid (CSF) HIV-1 RNA levels. The precise mechanisms, however, leading to HIV-1-associated encephalopathy remain unclear; and may involve direct/indirect pathways leading to monocyte/macrophage trafficking into the brain with viral persistence even on effective ART. Monocyte/macrophages with HIV DNA may represent viral reservoirs where circulating monocyte/macrophages migrate into the CNS facilitated by monocyte chemoattractant protein-1 (MCP-1). The objective of the study was to assess the feasibility of measuring HIV DNA and associated single nucleotide polymorphism (SNP) of MCP-1 in pediatric CSF. Measuring both factors in CSF may help us understand the pathogenesis of HIV-1-associated encephalopathy.

Methods:  Repository specimens from 27 perinatally HIV-1-infected children with HIV-1-associated encephalopathy were assessed for HIV DNA copy by real-time polymerase chain reaction (RT-PCR). HIV DNA copies were compared to MCP-1 2578G SNP mutations, which were measured by digesting amplified 361-bp fragments with PvuII restriction enzyme. In a small subset, MCP-1 levels were measured by ELISA.

Results:  CSF DNA from 27 children were available where plasma and CSF HIV RNA were undetectable (<50 copies/mL) in 22 of 27 and 18 of 27 specimens, respectively. Specimens were obtained from children with some degree of HIV-1-associated encephalopathy, however the samples were archived with no other clinical parameters. HIV DNA were detected in all 27 CSF specimens with higher HIV DNA copies in specimens with MCP1 2578G SNP mutations in 10 CSF DNA (median 3.17x10^–6 copies; range 1.31x10^–6 to 6.67x10^–6) compared to 14 without SNP mutations (median 2.00x10^–8 copies; range 1.47x10^–8 to 1.40x10^–9) and 3 indeterminate mutations (median 6.53x10^–7 copies; range 5.19x10^–7 to 7.21x10^–7), p <0.01. Comparing HIV DNA levels only between those with and without MCP-1 2578G SNP, there continued to be a significant difference, p <0.01. No levels were detected in HIV-1-seronegative control specimens; 6 CSF specimens had sufficient supernatant to measure MCP-1 levels, which showed high levels in those with the MCP1 2578G mutation, p = 0.10.

Conclusions:  This study demonstrates, for the first time, that CSF HIV DNA and MCP-1 SNP can be measured and could be potential markers in future clinical studies to understand the pathogenesis of pediatric HIV-1-associated encephalopathy.