The HIV Genome Is A Busy Place

1
The HIV Genome Is A Busy Place
Overlapping Genes and Underlying RNA
Elements Indicate Space Is At A Premium
2
Viral Proteins Can Carry Out Identical
Functions (e.g. HIV and MLV RT) With Very
Different Sequences
MLV E L I L L Q Y V D D L L L A A T S E L D C
Q HIV D I V I Y Q Y M D D L Y V G S D L E I G
Q H
What drives evolution beyond simple protein
function?
3

• Viral Coding Sequences Change Because Of
• Selection due to a change in the interaction
  between a
• viral and a host protein, e.g. with a change in
  host species

4

• Viral Coding Sequences Change Because Of
• Selection due to a change in the interaction
  between a
• viral and a host protein, e.g. with a change in
  host species
• 2. Selection by the host innate and adaptive
  immune system

5

• Viral Coding Sequences Change Because Of
• Selection due to a change in the interaction
  between a
• viral and a host protein, e.g. with a change in
  host species
• 2. Selection by the host innate and adaptive
  immune system
• 3. Fixation of deleterious mutations due to
  genetic bottlenecks,
• e.g. during a transmission event or
  compartmentalization

6

• Viral Coding Sequences Change Because Of
• Selection due to a change in the interaction
  between a
• viral and a host protein, e.g. with a change in
  host species
• 2. Selection by the host innate and adaptive
  immune system
• 3. Fixation of deleterious mutations due to
  genetic bottlenecks,
• e.g. during a transmission event or
  compartmentalization
• 4. Compensatory mutations to restore protein
  function

7

• Viral Coding Sequences Change Because Of
• Selection due to a change in the interaction
  between a
• viral and a host protein, e.g. with a change in
  host species
• 2. Selection by the host innate and adaptive
  immune system
• 3. Fixation of deleterious mutations due to
  genetic bottlenecks,
• e.g. during a transmission event or
  compartmentalization
• 4. Compensatory mutations to restore protein
  function
• Viral Coding Sequences Are On A Treadmill Of
• Genetic Change That Is The Price Of Replication

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How Do HIV Protein Coding Sequences Evolve?

• Mutations are (mostly) random
• About 1 in 3 new HIV genomes has a point
  mutation
• 2. APOBEC3G/F apply continuous G to A mutation
  pressure
• Most mutations are deleterious and are filtered
  out
• by selection
• Is There A Pattern In The Mutations
• That Become Fixed?
• Yes, but one pattern for maintaining function
• and a different pattern for changing function.

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For An Enzyme the Catalytic Site Is Invariant,
Followed By Amino Acids Around the Catalytic
Residues, Then the Hydrophobic Core, Then Surface
Residues
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HIV-1 Evolution With A Change In Function

• 1. Protease Inhibitor Resistance
• Complete With Compensatory Mutations
• 2. The Coreceptor Switch in Env
• From CCR5 to CXCR4
• CNS Compartmentalization in HIV-Associated
  Dementia
• Functional Correlates TBD

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Changing Under Selection - PI Resistance

• 1. Some positions have
• the same variability
• (SURFACE)
• 2. Some invariant positions
• gain variability
• (ACTIVE SITE)
• 3. Some positions increase
• in variability
• (COMPENSATORY
• MUTATIONS -
• Flanking Active Site)

Hoffman et al. Virology 2003
12







V82A is the primary resistance mutation to
RTV. It appears first followed by more active
site then compensatory mutations.
Resch et al. JV 2005
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HIV-1 Infection of Cerebrospinal Fluid (CSF)

• Often high concentration of HIV-1 in CSF
• Brain and blood HIV-1 variants are
  compartmentalized (Korber et. al., 1994
  DiStefano, et. al., 1996 Wong et. al., 1997)
• Compartmentalization in CSF
• CSF viral load is often, but not always
  associated with neurological status

Is there a relationship between HIV
CNS/CSF Compartmentalization and HIV-Associated
Dementia?
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Representative HTA Data (V4/V5) CSF
Compartmentalization and HTA Reproducibility
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Absolute Compartmentalized CSF Viral Load Is
Associated with Neurological Status
Compartmentalization implies independent viral
evolution in the CSF/CNS associated with disease.
19
Acknowledgement
UNC Pat Harrington Noah Hoffman Li-Hua
Ping Wolfgang Resch Kim Ritola Joe Eron Susan
Fiscus Clyde Hutchison Colin Hall Kevin Robertson
Friends Dale Kempf Scott Letendre Dick
Price Celia Schiffer
Funded by NIH