title: Single genome analysis reveals genetic characteristics of Neuroadaptation across HIV-1 envelope.
abstract: BACKGROUND
  The widespread use of highly effective, combination antiretroviral therapy (cART) has led to a significant reduction in the incidence of HIV-associated dementia (HAD). Despite these advances, the prevalence of HIV-1 associated neurocognitive disorders (HANDs) has been estimated at approximately 40%-50%. In the cART era, the majority of this disease burden is represented by asymptomatic neurocognitive impairment and mild neurocognitive disorder (ANI and MND respectively). Although less severe than HAD, these diagnoses carry with them substantial morbidity.
  
  
  RESULTS
  In this cross-sectional study, single genome amplification (SGA) was used to sequence 717 full-length HIV-1 envelope (env) clade B variants from the paired cerebrospinal fluid (CSF) and blood plasma samples of fifteen chronically infected HIV-positive individuals with normal neurocognitive performance (NCN), ANI and MND. Various degrees of compartmentalization were found across disease states and history of cART utilization. In individuals with compartmentalized virus, mean HIV-1 env population diversity was lower in the CSF than plasma-derived variants. Overall, mean V1V2 loop length was shorter in CSF-derived quasispecies when compared to contemporaneous plasma populations, and this was found to correlate with a lower mean number of N-linked glycosylation sites in this region. A number of discrete amino acid positions that correlate strongly with compartmentalization in the CSF were identified in both variable and constant regions of gp120 as well as in gp41. Correlated mutation analyses further identified that a subset of amino acid residues in these compartmentalization "hot spot" positions were strongly correlated with one another, suggesting they may play an important, definable role in the adaptation of viral variants to the CSF. Analysis of these hot spots in the context of a well-supported crystal structure of HIV-1 gp120 suggests mechanisms through which amino acid differences at the identified residues might contribute to viral compartmentalization in the CSF.
  
  
  CONCLUSIONS
  The detailed analyses of SGA-derived full length HIV-1 env from subjects with both normal neurocognitive performance and the most common HAND diagnoses in the cART era allow us to identify novel and confirm previously described HIV-1 env genetic determinants of neuroadaptation and relate potential motifs to HIV-1 env structure and function.
authors.affiliation: Aaron Diamond AIDS Research Center, an affiliate of the Rockefeller University, New York, USA. tevering@adarc.org.
authors.forename: Teresa H
authors.initials: TH
authors.lastname: Evering
authors.forename: Edwin
authors.initials: E
authors.lastname: Kamau
authors.forename: Leslie
authors.initials: L
authors.lastname: St Bernard
authors.forename: Charles B
authors.initials: CB
authors.lastname: Farmer
authors.forename: Xiang-Peng
authors.initials: XP
authors.lastname: Kong
authors.forename: Martin
authors.initials: M
authors.lastname: Markowitz
mesh_terms: D000328:Adult; D003072:Cognition Disorders / Q000134:cerebrospinal fluid / Q000821:virology*; D003430:Cross-Sectional Studies; D005260:Female; D006031:Glycosylation; D015699:HIV Envelope Protein gp120 / Q000235:genetics*; D015658:HIV Infections / Q000134:cerebrospinal fluid / Q000821:virology*; D015497:HIV-1 / Q000235:genetics*; D006801:Humans; D008297:Male; D008875:Middle Aged
chemical_list: D015699:HIV Envelope Protein gp120