1. The HIV Genome Is A Busy Place
Overlapping Genes and Underlying RNA Elements
Indicate Space Is At A Premium

2. What drives evolution beyond simple protein function?
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

8. 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.

9. For An Enzyme the Catalytic Site Is Invariant, Followed By Amino Acids Around
the Catalytic Residues, Then the Hydrophobic Core, Then Surface Residues

10. 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

11. 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. * * * * * * *
V82A is the primary resistance mutation to RTV.
It appears first followed by more active site
then compensatory mutations.
Resch et al. JV 2005

16. 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
CSF
CD4+ T cells
Macrophages
Perivascular Macrophages
Microglia
Periphery
CNS/Brain
Is there a relationship between HIV CNS/CSF
Compartmentalization and HIV-Associated Dementia?

17. Representative HTA Data (V4/V5): CSF Compartmentalization and HTA Reproducibility

18. ‘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