Longitudinal Analysis of Cerebrospinal Fluid and Plasma HIV-1 Envelope Sequences Isolated From a Single Donor with HIV Asymptomatic Neurocognitive Impairment

Abstract

Objective Combined antiretroviral treatment (cART) has changed the clinical presentation of HIV-associated neurocognitive disorders (HAND) to that of the milder forms of the disease. Asymptomatic neurocognitive impairment (ANI) is now more prevalent and is associated with increased morbidity and mortality risk in HIV-1–infected people. HIV-1 envelope (env) genetic heterogeneity has been detected within the central nervous system (CNS) of individuals with ANI. Changes within env determine co-receptor use, cellular tropism, and neuropathogenesis. We hypothesize that compartmental changes are associated with HIV-1 env C2V4 during ANI and sought to analyze paired HIV-1 env sequences from plasma and cerebrospinal fluid (CSF) of a female subject undergoing long-term cART. Methods Paired plasma and CSF samples were collected at 12-month intervals and HIV-1 env C2V4 was cloned and sequenced. Results Phylogenetic analysis of paired samples consistently showed genetic variants unique to the CSF. Phenotypic prediction showed CCR5 (R5) variants for all CSF-derived sequences and showed minor X4 variants (or dual-tropic) in the plasma at later time points. Viral compartmentalization was evident throughout the study, suggesting that the occurrence of distinctive env strains may contribute to the neuropathogenesis of HAND. Conclusions Our study provides new insights about the genetic characteristics within the C2V4 of HIV-1 env that persist after long-term cART and during the course of persistent ANI.

HIV Gp120 Sequence Variability Associated with HAND in Hispanic Women

“…In a longitudinal study using autologous sequences from an ANI patient, we found a significant difference in the V4 net charge when comparing clones from plasma and CSF [25]. As in our previous study using plasma derived-clones, clones derived from the PBMCs of a subject with ANI also had an overall charge of −2.…”

“…We sought to determine the genetic relationship among C2V4 sequences of isolates from subjects with or without HAND. We performed phylogenetic analysis of the C2V4 region of isolates, using MEGA 6.0 with default penalties [25]. Figure 1 shows the resulting neighbor-joining phylogenetic tree of the 73 C2V4 env sequences from clinical isolates and 5 reference env sequences used as outgroup controls.…”

“…We used validated tools for the prediction of co-receptor use and cellular tropism based on the V3 genotype [33] as previously described [25]. Briefly, the methods are based on the principle of the net V3 loop charge in combination with the presence of basic amino acid residues (i.e., lysine and aspartate) at position 11/25 in clade B subtypes.…”

“…We previously reported the longitudinal genetic occurrences within the C2V4 of HIV env sequences in plasma and cerebrospinal fluid of a HIV + subject with persistent ANI diagnosis [25]. Thus in the present study, we sought to characterize HIV env sequences obtained from PBMC co-cultures to determine the association between genetic occurrences within the C2V4 region and the severity of HAND diagnosis in 8 HIV + Hispanic female patients from the SNRP cohort as previously described [24].…”

Envelope Gene Evolution and HIV-1 Neuropathogenesis

“…A classic clinical study found that HIV-1 sequences from CSF were more genetically diverse within the C2V3 region of HIV + subjects with severe neurocognitive impairment than they were in those same regions of HIV + subjects without cognitive impairment (45). However, other studies show that the autologous genetic diversity within V3 in CSF env s is usually lower than plasma env genetic diversity (46, 47). …”