1. Patterns of HIV-1 evolution in individuals with differing rates of CD4 T cell decline
Markham RB, Wang WC, Weisstein AE, Wang Z, Munoz A, Templeton A, Margolick J, Vlahov D, Quinn T, Farzadegan H, Yu XF
(1998) Proc Natl Acad Sci USA 95:
Michael Pina, Salomon Garcia
Journal Club Presentation
BIOL398-01/S10: Bioinformatics Laboratory
March 2, 2010

2. Outline Introduction to the Markham et al. paper
Our question about the article
Methods
Results
Conclusion

3. CD4 T-cell count associated with diversity and divergence
The evolution of the HIV-1 gene was studied in 15 seroconverting participants (intravenous drug users)
They were selected for differences in the rate of their CD4 T-cell decline
Rates of diversity and divergence both showed a pattern of increase among the progressor groups

4. Evolution of the HIV-1 virus in the participants
Viral evolution among the progressor groups showed a selection for nonsynonymous mutants
Nonprogressors with low viral loads selected against nonsynonymous mutations
For the progressor groups, this may have resulted in higher reproduction rates of the virus

5. HIV-1 variants over the course of the study
No single variant was dominant across all participants
Evolution away from a variant was followed by evolution towards a variant
This may show selection against a predominant strain or the product of independent evolutions within different host environments

6. The importance of CD4 T-cells
Differences of CD4 T-cell count reflect not only the quantity of mutations, but differences in the mutations that may be best suited to the host environment

7. CD4 T cell trajectory, diversity, and divergence over time since first seropositive visit (t = 0) in each of the 15 subjects

8. Taking a closer look at the paper
We wanted to know how the amino acid changes are affecting the interaction between the virus and host environment
“The overall pattern is one in which viral strains from nonprogressors showed possible selection against amino acid change, while those from progressors showed selection for such change (or against the absence of change).”

9. Our question regarding the paper
What can the dS-dN value tell us about the selection for/against amino acid change?
Our hypothesis is that subject 10 will show more nonsynonymous changes and subject 13 will show more synonymous changes.

10. Methods to find an answer
Subjects 10 and 13 were chosen because of their quintessential qualities as “rapid progressor” and “nonprogressor”, respectively
They have nearly the same amount of data points collected over a similar time span
All of their DNA sequences were obtained from the Bedrock website, in addition to other data from the study
The online Biology Workbench tools were used for a variety of tasks

11. Statistical calculations
Subject
# clones S
Theta
Min Diff
Max Diff 10 49 74
16.3
1.14
20.0 13 26 24
6.43
9.12

12. Using the Biology Workbench
CLUSTALW was used for multiple sequences alignments for all available sequences of subjects 10 and 13
Phylogenetic trees were also generated
CLUSALDIST was used to generate a distance matrix

13. Phylogenetic trees for subject 10 and 13

14. dS-dN values Converted to log scale for consistency among data values10 13 .5 -
n/a 1
-0.118
-0.861 2
0.530 3
-0.333 4
-0.133
1.724 5
-0.447
0.479 6
0.785 7 8 9 11 12
Converted to log scale for consistency among data values
Negative value indicates synonymous mutations
Positive value indicates nonsynonymous mutations

15. An answer to our question
It was determined that subjects 10 and 13 do indeed differ in their diversity and divergence as represented visually in their phylogenetic trees and also in our statistical calculations
The dS-dN values are so similar and limited that it is difficult to say whether or not progressors show a selection for amino acid change

16. A more recent article
Functional diversity of HIV-1 envelope proteins expressed by contemporaneous plasma viruses.
“…clones carrying unique mutations in V3 often displayed low infectivity”
No correlation was observed between viral infectivity and sensitivity to entry inhibitors