diversity and divergence in hiv-1 viral variants between patients with high cd4+ t cell variability...
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Diversity and Divergence in HIV-1 Viral Variants between
patients with high CD4+ T Cell Variability and Patients with Rapid CD4+ T Cell Decline
Kevin Paiz-RamirezJanelle N. Ruiz
Biology 398.01Professor Kam D. Dahlquist, Ph.D.
Department of BiologyLoyola Marymount University
March 2nd, 2009
OutlineI. HIV-1 Background
II. Markham et al. Previous Studies
III. Research Questions
IV. Results
A. Diversity Between Groups
B. Divergence Between Groups
V. Interpretations between synonymous & non-synonymous Groups
VI. Limitations To Results
VII. Interpretations In Light of Recent Studies
VIII. References
Background HIV-1
• Human Immunodeficiency Virus, is categorized into 3 stages
• Seroconversion ~7-8 weeks
• Latency ~variable period of years
• Acquired Immune Deficency Syndrome
Center for Disease Control’s Public Health Image Library #10000
Markham, et al.
• Markham et al. explored analyses of synonymous and non-synonymous differences and rates of divergence to reveal selective heterogeneity as a function of disease progression category
• We chose to examine if there are differences in HIV-1 diversity or divergence between participants with high CD4 T-Cell variability within the study, between visits as compared to participants with linear progression
Research Question
• Are their differences in HIV-1 diversity or divergence between participants with high CD4 T cell variability between visits as compared to participants with rapid CD4+ T Cell decline (slope ~ -1)?
Linear Progressors High Variability
How Were Subjects Chosen?
• Linear Progressors: Patients with rapid CD4+ T Cell Decline
• High Variability: Patients with high CD4 T cell variability between visits
How Were Subjects Chosen?
• High Variability: Patients with high CD4 T cell variability between visits
How Were Subjects Chosen?
• Low Variability: Patients with low CD4 T cell variability between visits
How Were Subjects Chosen?
Diversity and Divergence Between Groups
Subject ClassificationNumber of visits
# of Clones (all visits) S Theta Min Difference
Max Difference
Median dS/dN
4 Linear Progressor 4 47 59 12.86 0.007 0.074 0
10 Linear Progressor 5 47 67 14.61 0.004 0.032 0.2
12 High Variability 5 29 36 9.17 0.007 0.056 0.9
8 High Variability 5 29 36 9.17 0.004 0.025 0.5
6 High Variability 5 29 50 12.73 0.007 0.049 0.4
5 Low Variability 5 29 54 13.75 0.007 0.056 1.4
Diversity and Divergence Between Groups
Subject ClassificationNumber of visits
# of Clones (all visits) S Theta Min Difference
Max Difference
Median dS/dN
4 Linear Progressor 4 47 59 12.86 0.007 0.074 0
10 Linear Progressor 5 47 67 14.61 0.004 0.032 0.2
12 High Variability 5 29 36 9.17 0.007 0.056 0.9
8 High Variability 5 29 36 9.17 0.004 0.025 0.5
6 High Variability 5 29 50 12.73 0.007 0.049 0.4
5 Low Variability 5 29 54 13.75 0.007 0.056 1.4
LowVariability
DIVERSITY:Comparing Number of Clones
for all Visits Across Groups
Diversity and Divergence Between Groups
Subject ClassificationNumber of visits
# of Clones (all visits) S Theta Min Difference
Max Difference
Median dS/dN
4 Linear Progressor 4 47 59 12.86 0.007 0.074 0
10 Linear Progressor 5 47 67 14.61 0.004 0.032 0.2
12 High Variability 5 29 36 9.17 0.007 0.056 0.9
8 High Variability 5 29 36 9.17 0.004 0.025 0.5
6 High Variability 5 29 50 12.73 0.007 0.049 0.4
5 Low Variability 5 29 54 13.75 0.007 0.056 1.4
Diversity and Divergence Between Groups
Subject ClassificationNumber of visits
# of Clones (all visits) S Theta Min Difference
Max Difference
Median dS/dN
4 Linear Progressor 4 47 59 12.86 0.007 0.074 0
10 Linear Progressor 5 47 67 14.61 0.004 0.032 0.2
12 High Variability 5 29 36 9.17 0.007 0.056 0.9
8 High Variability 5 29 36 9.17 0.004 0.025 0.5
6 High Variability 5 29 50 12.73 0.007 0.049 0.4
5 Low Variability 5 29 54 13.75 0.007 0.056 1.4
DIVERSITY:Comparing the S Value Across
Groups
Subject 4
Subject 10
Subject 12
Subject 8 Subject 6
Subject 5
Linear Progressors High Variability Low Variability
Group #
S V
alue
DIVERSITY:Comparing the S Value Across
Groups
Subject 4
Subject 10
Subject 12
Subject 8
Subject 5
Linear Progressors High Variability Low Variability
Group #
S V
alue
P Value: 0.021250765
Subject 6
DIVERSITY:Comparing the S Value Across
Groups
Subject 4
Subject 10
Subject 12
Subject 8 Subject 6
Subject 5
Linear Progressors High Variability Low Variability
Group #
S V
alue
P Value: 0.131255514
Diversity and Divergence Between Groups
Subject ClassificationNumber of visits
# of Clones (all visits) S Theta Min Difference
Max Difference
Median dS/dN
4 Linear Progressor 4 47 59 12.86 0.007 0.074 0
10 Linear Progressor 5 47 67 14.61 0.004 0.032 0.2
12 High Variability 5 29 36 9.17 0.007 0.056 0.9
8 High Variability 5 29 36 9.17 0.004 0.025 0.5
6 High Variability 5 29 50 12.73 0.007 0.049 0.4
5 Low Variability 5 29 54 13.75 0.007 0.056 1.4
DIVERGENCE:Comparing Theta Across
Groups
Subject 4
Subject 10
Subject 12
Subject 8 Subject 6
Subject 5
Group #
The
ta
Linear Progressors High Variability Low Variability
DIVERGENCE:Comparing Theta Across
Groups
Subject 4
Subject 10
Subject 12
Subject 8 Subject 6
Subject 5
Group #
The
ta
Linear Progressors High Variability Low Variability
P Value: 0.034831412
DIVERGENCE:Comparing Theta Across
Groups
Subject 4
Subject 10
Subject 12
Subject 8 Subject 6
Subject 5
Group #
The
ta
Linear Progressors High Variability Low Variability
P Value: 0.295428191
Diversity and Divergence Between Groups
Subject ClassificationNumber of visits
# of Clones (all visits) S Theta Min Difference
Max Difference
Median dS/dN
4 Linear Progressor 4 47 59 12.86 0.007 0.074 0
10 Linear Progressor 5 47 67 14.61 0.004 0.032 0.2
12 High Variability 5 29 36 9.17 0.007 0.056 0.9
8 High Variability 5 29 36 9.17 0.004 0.025 0.5
6 High Variability 5 29 50 12.73 0.007 0.049 0.4
5 Low Variability 5 29 54 13.75 0.007 0.056 1.4
DIVERGENCE:Comparing Min and Max
Differences Across Groups
Subject Classification# of Clones (all visits) Min Difference Max Difference
4 Linear Progressor 47 0.007 0.074
10 Linear Progressor 47 0.004 0.032
12 High Variability 29 0.007 0.056
8 High Variability 29 0.004 0.025
6 High Variability 29 0.007 0.049
5 Low Variability 29 0.007 0.056
P Value: >.05
DIVERGENCE:Comparing Min and Max
Differences Across Groups
Subject Classification# of Clones (all visits) Min Difference Max Difference
4 Linear Progressor 47 0.007 0.074
10 Linear Progressor 47 0.004 0.032
12 High Variability 29 0.007 0.056
8 High Variability 29 0.004 0.025
6 High Variability 29 0.007 0.049
5 Low Variability 29 0.007 0.056
P Value: >.05
Research Question
• Are their differences in HIV-1 diversity or divergence between participants with high CD4 T cell variability between visits as compared to participants with rapid CD4+ T Cell decline (slope ~ -1)?
Linear Progressors High Variability
Differences exist in diversity and divergence of HIV-1 variants b/w
Groups• Linear Progressors show higher diversity HIV-1 variants
as shown by higher number of clones and higher S value compared to subjects with High Variability in CD4 count.
• Linear Progressors show higher divergence in HIV-1 variants as shown by higher value of theta compared to subjects with High Variability in CD4 count.
• Hypothesis supported?
Limitations to Results• Only looked at first 5 visits to maintain consistency
and due to limitations of analytical software
• Issues with Subject 8 versus Subject 6 in high variability group
• Missing data for subject 4 (visits 5-7)
• Only one subjects in low variability group; therefore could not run T Tests with this group
Synonymous versus Non-Synonymous mutations
Between Groups
Subject ClassificationNumber of visits
# of Clones (all visits) S Theta Min Difference
Max Difference
Median dS/dN
4 Linear Progressor 4 47 59 12.86 0.007 0.074 0
10 Linear Progressor 5 47 67 14.61 0.004 0.032 0.2
12 High Variability 5 29 36 9.17 0.007 0.056 0.9
8 High Variability 5 29 36 9.17 0.004 0.025 0.5
6 High Variability 5 29 50 12.73 0.007 0.049 0.4
5 Low Variability 5 29 54 13.75 0.007 0.056 1.4
P Value: >.05
Synonymous versus Non-Synonymous mutations
Between Groups
Subject ClassificationNumber of visits
# of Clones (all visits) S Theta Min Difference
Max Difference
Median dS/dN
4 Linear Progressor 4 47 59 12.86 0.007 0.074 0
10 Linear Progressor 5 47 67 14.61 0.004 0.032 0.2
12 High Variability 5 29 36 9.17 0.007 0.056 0.9
8 High Variability 5 29 36 9.17 0.004 0.025 0.5
6 High Variability 5 29 50 12.73 0.007 0.049 0.4
5 Low Variability 5 29 54 13.75 0.007 0.056 1.4
P Value: >.05
Synonymous versus Non-Synonymous mutations
Between Groups• Appears to be no significant differences in
synonymous versus non-synonymous mutations in HIV-1 variants between linear progressors and high variability group
• Participants with low variability in CD4 count appear to show selection against Non-synonymous mutations in HIV-1 variants
Templeton, et al.• Templeton’s article examined selection of 15 subjects similar to the Markham study, but further investigated a broader range of potential selective contexts.
•Overall disease progression categories: CD4 and CD8 T-Cell counts
•Mutations leading to amino acid substitutions were subject to positive selection over a broad range of clinical conditions in nonsyncytium inducing form (NSI)
•It was determined that the study must be focused in the V3 region
Templeton, et al.
•The results indicated that the V3 region is subject to selection, but cannot be summarized in a marginal fashion to a single variable such as CD4 counts.
•Diverse patterns of V3 region evolution depending on rapid and non-progressors. The V3 region is context dependent. Further studies of this region could be explored in the HIV-1 Genome.
References
• Markham RB, Wang WC, Weisstein AE, Wang Z, Munoz A, Templeton A, Margolick J, Vlahov D, Quinn T, Farzadegan H, and Yu XF. Patterns of HIV-1 evolution in individuals with differing rates of CD4 T cell decline. Proc Natl Acad Sci U S A 1998 Oct 13; 95(21) 12568-73
• Templeton Alan R, Reichert R, Weisstein A, Xia-Fang Y, Markham RB. Selection in Context: Patterns of Natural Selection in the Glycoprotein 120 Region of Human Immunodeficiency Virus 1 Within Infected Individuals. Genetics Society of America USA 2004, Dec 20: 103.02945