1. Predicting the Onset of AIDS
Robert Arnold, Alex Cardenas, Zeb Russo
LMU Biology Department
10/5/2011

2. Outline
What causes a subject to develop AIDS from HIV and what separates AIDS from HIV? Focusing on dS/dN ratio
The definition of AIDS, the subjects affected, and their similarities, ALIVE information
New hypothesis involving the division of subjects into those with AIDS, trending towards AIDS, and AIDS free trending away
Research comparison, proving assumptions incorrect
Further comparisons between the subjects with AIDS and those without
Comparing our results with our paper

3. dS/dN ratio related to AIDS development
determined that low dS/dN ratios, subjects that select either for nonsynonymous mutation or not against it were the subjects to develop AIDS
The subjects picked were 4, 9, 11, and 14, all with 0.0 dS/dN ratios along with subject 10 with a 0.2 and subject 1 with a 0.3

4. Outline
What causes a subject to develop AIDS from HIV and what separates AIDS from HIV? Focusing on dS/dN ratio
The definition of AIDS, the subjects affected, and their similarities, ALIVE information
New hypothesis involving the division of subjects into those with AIDS, trending towards AIDS, and AIDS free trending away
Research comparison, proving assumptions incorrect
Further comparisons between the subjects with AIDS and those without
Comparing our results with our paper

5. AIDS and CD4 counts CDC definition of AIDS is a CD4 count below 200
Once diagnosed, cannot be reversed
Makes our first hypothesis irrelevant since all ‘rapid progressors’ drop below 200, AKA all 6 have AIDS
Subjects 1, 3, 4, 10, 11, 15

6. Outline
What causes a subject to develop AIDS from HIV and what separates AIDS from HIV? Focusing on dS/dN ratio
The definition of AIDS, the subjects affected, and their similarities, ALIVE information
New hypothesis involving the division of subjects into those with AIDS, trending towards AIDS, and AIDS free trending away
Research comparison, proving assumptions incorrect
Further comparisons between the subjects with AIDS and those without

7. Revised hypothesis separating those with AIDS from others
Separated into 3 categories
Those with AIDS: 1, 3, 4, 10, 11, 15
Those trending to AIDS: 7, 8, 9, 14
Those free of and trending away from AIDS: 2, 5, 6, 12, 13
New vision; which subjects developed AIDS?
Began to focus on ALIVE research to go beyond Markham’s 4 year period

8. Development of two new questions
Since we can tell who has AIDS, we would now like to determine whether there are any similar clones of the env gene across the AIDS subjects
Does a median ds/dn ratio below 1.0 or lower determine whether you will get AIDS or not?

9. Outline
What causes a subject to develop AIDS from HIV and what separates AIDS from HIV? Focusing on dS/dN ratio
The definition of AIDS, the subjects affected, and their similarities, ALIVE information
New hypothesis involving the division of subjects into those with AIDS, trending towards AIDS, and AIDS free trending away
Research comparison, proving assumptions incorrect
Further comparisons between the subjects with AIDS and those without
Comparing our results with our paper

10. Our division of the Patients

11. Random clonal comparison
To determine whether there were any similarities between clones of those who developed AIDS during the study and those at risk, we performed a ClustalW on a random selection of two clones from each subject

12. 2 Clones Rooted Tree

13. Comparison of dS/dN Subject No. of observations CD4
Median intravisit nucleotide differences among clones
Virus copy number (×103)
Annual rate of CD4 T cell decline
Slope of change in intravisit nucleotide differences per clone per year
Slope of divergence (% nucleotides mutated from baseline consensus sequence per year)
Median dS/dN
AIDS
Subject 4 4
1,028
0.9
6.8
−593
4.64
2.09
Subject 10 5
833
1.71
99.3
−363
3.16 1
0.2
Subject 11
753
2.27
62.2
1.11
0.32
Subject 15
707
15.16
171
−362
−2.94
0.68
0.7
Subject 3
819
1.82
302.5
−294
0.53
0.74
Subject 1 3
464
5.64
307.6
−117
5.1
1.55
0.3
At Risk
Subject 7
1,072
317.6
−392
−0.79
1.35
1.3
Subject 8 7
538
1.24
209
−92
1.68
1.16
0.5
Subject 9 8
489
9.49
265
−11
1.58
1.21
Subject 14 9
523
50.9
−51
1.69
0.6
Not at Risk
Subject 2
715
1.64
21.6 30
1.32
0.49
1.8
Subject 5
749
2.5
260.6
−41
0.06
1.4
Subject 6
405
2.82
321.4 52
1.92
0.82
0.4
Subject 12 6
772
2.8 44
0.62
0.13
Subject 13
671
0.87
1.7 53
0.28
3.5

14. Neither Assumption is Definitive
Using the original data from the Bedrock website, we determined who actually developed AIDS over the full study
1, 3, 4, 6, 7, 8, 9, 10, 11, 14, 15
Only 2, 5, 12 and 13 avoided the progression to AIDS over the course of the study

15. Outline
What causes a subject to develop AIDS from HIV and what separates AIDS from HIV? Focusing on dS/dN ratio
The definition of AIDS, the subjects affected, and their similarities, ALIVE information
New hypothesis involving the division of subjects into those with AIDS, trending towards AIDS, and AIDS free trending away
Research comparison, proving assumptions incorrect
Further comparisons between the subjects with AIDS and those without
Comparing our results with our paper

16. 2 Clones Rooted Tree Redux

17. Comparison of dS/dN Subject No. of observations CD4
Median intravisit nucleotide differences among clones
Virus copy number (×103)
Annual rate of CD4 T cell decline
Slope of change in intravisit nucleotide differences per clone per year
Slope of divergence (% nucleotides mutated from baseline consensus sequence per year)
Median dS/dN
AIDS
Subject 4 4
1,028
0.9
6.8
−593
4.64
2.09
Subject 10 5
833
1.71
99.3
−363
3.16 1
0.2
Subject 11
753
2.27
62.2
1.11
0.32
Subject 15
707
15.16
171
−362
−2.94
0.68
0.7
Subject 3
819
1.82
302.5
−294
0.53
0.74
Subject 1 3
464
5.64
307.6
−117
5.1
1.55
0.3
At Risk
Subject 7
1,072
317.6
−392
−0.79
1.35
1.3
Subject 8 7
538
1.24
209
−92
1.68
1.16
0.5
Subject 9 8
489
9.49
265
−11
1.58
1.21
Subject 14 9
523
50.9
−51
1.69
0.6
Not at Risk
Subject 2
715
1.64
21.6 30
1.32
0.49
1.8
Subject 5
749
2.5
260.6
−41
0.06
1.4
Subject 6
405
2.82
321.4 52
1.92
0.82
0.4
Subject 12 6
772
2.8 44
0.62
0.13
Subject 13
671
0.87
1.7 53
0.28
3.5

18. Immune Relaxation Hypothesis
Evolutionary rates slow due to disrupting immune function
In relation to our claims, the virus infects specific CD4+ T cell count.
The immune system is the positive selecting agent in C2-V5 region of env.
With progression to AIDS, the immune effectors and the virus can alter the course of evolution.
Lower dS/dN ratios were observed in a single patient
CD4+ T Cells disrupted by infection respond to epitopes coded by env and in driving env sequence evolution.

19. Divergence Non-synonymous divergence stabilizes
Seems to coincide with disease progression
Synonymous divergence does not seem to stabilize
Phylogenetic methods can’t be used per say in this paper
No recombination is generally assumed
And studies show that recombination rate in HIV populations in vivo is high

20. For our studies, < 1 indicated AIDs and > 1 indicated no AIDs
Ratios
dN/dS ratios
> 1 indicates widespread adaptive evolution
Most common among data sets, indicative of positive selection
< 1 some sites are selectively constrained
For our studies, < 1 indicated AIDs and > 1 indicated no AIDs

21. CD4+ T Cells In direct correlation with distinguishing AIDs
Subjects < 300 AIDs
Related it back to < 200 from previous graphs and tables.
“Feedback loop” in play. Virus impairs HIV specific responses

22. Findings
11/15  AIDs
CD4 T Cell Count
dN/dS ratio
New ?’s

23. Citations
Markham RB, et al Patterns of HIV-1 evolution in individuals with differing rates of CD4 T cell decline.
Proc. Natl. Acad. Sci. USA 95:
Williamson S, et al A Statistical Characterization of Consistent Patterns of Human Immunodeficiency Virus Evolution Within Infected Patients. Molecular Biology of Evolution, 22(3): Retrieved off of Web of Science September 28th, 2011.