Michael R. Pina Week 3

Introduction

• Because the rate at which HIV replicates is so high, variants that are best suited to the environment arise and spread very quickly.
  • This is essentially extremely fast evolution.
• Unstable host environments can have variable effects.
  • It could lead to a dynamic immune response that would lead to little diversity.
  • Or the immune response could target only the most numerous variants, leading to a broader diversity.
• Previous studies did not examine sequence patterns, and did not analyze enough "time points" in each subject.
  • This study examines higher levels of diversity correlating with rapid CD4 T cell decline.

Methods

• 15 participants were selected from those who participated in ALIVE (injection drug users.)
  • Blood was collected every 6 months for testing over 4 years.
    • Rapid progressors = fewer than 200 CD4 T cells
    • Moderate progressors = 200-650
    • Nonprogressors = above 650
• 285 bp region of env was amplified from PBMC.
• env primers were used for cloning purposes, to find certain sequences.
• Plasma viral load was determined by reverse transcription–PCR
• Phylogenetic trees were made using a computer package.
  • Taxon labels were used to show the time where each train was isolated and number of identical replicates.
• Units of analysis were defined by pairs of visits from each individual.
  • 26 time points were collected from the 15 participants
  • Sequence data and CD4 T cell count were known 1 year later.
• dS/dN ratios used the Jukes-Cantor correction method.
  • Summary of this data was used for all subsequent analysis.

Results

• CD4 decline varied across participants
  • Nonprogressor groups generally had lower viral load.
• Sequence analysis focused on env region because it is important in host-virus interaction and tolerates mutation
  • 873 clones were analyzed
• Changes in HIV-1 sequences were defined by diversity at each visit and divergence.
• Viruses from 13 of the participants were originally homogeneous; 2 were heterogenous.
• Diversity and divergence increased over time in all progressor categories.
• Diversity and divergence were negatively correlated with CD4 T cell count 1 year later.
• Rapid and moderate progressors showed a dS/dN ratio of 0.4, which nonprogressors showed a ratio of 1.6.
  • A ratio of 1 indicates randomly occurring mutation
• Phylogenetic trees did not show predominance of a single strain.

Discussion

• Higher diversity and divergence are associated with a decline in CD4 T cells.
• Strains found in nonprogressors showed a possible selection against amino acid change; those in progressors showed selection for change.
• The relationship between CD4 T cell decline and increased diversity and divergence agrees with the hypothesis of Nowak.
  • For those subjects who contracted AIDS, diversity and divergence continued to increase
• Optimum environment for the virus could be continually changing because of different immune responses.
• A more effective immune response may be seen in the nonprogressors.