title: Deep sequencing of HIV-1 variants from paired plasma and cerebrospinal fluid during primary HIV infection.
abstract: BACKGROUND
  Limited data exist comparing viral quasispecies between cerebrospinal fluid (CSF) and plasma compartments during primary HIV infection. Deep sequencing is a new method to examine the HIV plasma and CSF quasispecies.
  
  
  METHODS
  In this pilot study, deep sequencing of protease (PR) and reverse transcriptase (RT) was performed in plasma and CSF from participants during primary HIV infection. Estimated mutational load was calculated by mutant variant frequency multiplied by HIV-RNA level.
  
  
  RESULTS
  Paired plasma and CSF samples were studied from five antiretroviral therapy-naïve male participants with median 109 days post estimated transmission, age 32 years, CD4 cell count 580 cells/μL, HIV-RNA 5.18 log10copies/mL in plasma and 3.67 log10copies/mL in CSF. Plasma samples averaged 7,124 reads of PR and 2,448 reads of RT, whereas CSF samples averaged 7,082 and 2,792 reads, respectively. A distinct drug-resistance pattern with linked mutations present at significant levels (5-10%) was detected in one participant in CSF. Other low abundance variants (>0.2%) were detected in plasma and CSF of four out of five participants.
  
  
  CONCLUSIONS
  Deep sequencing of CSF HIV is technically possible with sufficient HIV-RNA levels. Differences between the quasispecies in the two compartments detected in one participant, which were present with a high mutational load in CSF at an estimated 3.6 months after HIV infection, suggest that early CNS compartmentalisation may be revealed by sensitive deep-sequencing methods. The presence of distinct low abundance (<1%) resistance variants in plasma and CSF of three other subjects may be significant, but further investigation is needed.
authors: Department of Medicine, School of Medicine, Yale University, New Haven, CT, USA.
authors: Arjet
authors: A
authors: Gega
authors: Department of Medicine, School of Medicine, Yale University, New Haven, CT, USA.
authors: Michael J
authors: MJ
authors: Kozal
authors: Department of Medicine, School of Medicine, Yale University, New Haven, CT, USA.
authors: Jennifer
authors: J
authors: Chiarella
authors: Department of Neurology, University of California San Francisco, CA, USA.
authors: Evelyn
authors: E
authors: Lee
authors: Department of Neurology, University of California San Francisco, CA, USA.
authors: Julia
authors: J
authors: Peterson
authors: Department of Medicine, University of California San Francisco, CA, USA.
authors: Frederick M
authors: FM
authors: Hecht
authors: Department of Medicine, University of California San Francisco, CA, USA.
authors: Teri
authors: T
authors: Liegler
authors: 454 Life Sciences (a Roche Company), Branford, CT, USA.
authors: Elizabeth P
authors: EP
authors: St John
authors: 454 Life Sciences (a Roche Company), Branford, CT, USA.
authors: Birgitte B
authors: BB
authors: Simen
authors: Department of Neurology, University of California San Francisco, CA, USA.
authors: Richard W
authors: RW
authors: Price
authors: Department of Neurology, School of Medicine, Yale University, New Haven, CT, USA.
authors: Serena S
authors: SS
authors: Spudich
keywords: HIV-1; HIV-associated neurocognitive disorder; cerebrospinal fluid; compartmentalisation; primary HIV infection; resistance mutations