Shivum Desai Journal Week 6

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HIV Evolution Notebook


The purpose of this investigation is to determine is there is a significant difference between pre-determined groups of HIV progressors and nonprogressors based upon dN/dS values.


It is hypothesized that a comparison between dN/dS values will reveal a correlation between non-synonymous mutations and subjects that are rapid progressors. It is also hypothesized that a larger theta value will be more common with those subjects considered rapid progressors because of their higher level of genetic diversity.


  1. The first step taken was to lay out a plan of action for todays work on the project.
  2. Next the Markham paper was located as well as all the subjects that participated in the study and their respective sequences.
    • For the purpose of simplicity, the average dN/dS values will be used to compare and differentiate groups of subjects but only the clones of the last visit of each subject will be used in the sequencing and alignment process.
  3. These sequences were then uploaded to the Biology Workbench and then using the multiple sequences alignment tool a tree will be formed which will show the disparity between the subjects.
  4. The s values were also taken for each subject and the theta values were calculated for each subject. This information will then be averaged together for the two distinctive groups, based on dN/dS values.
  5. The two resulting theta values will then be put through a T-test to figure out the statistical significance between the two numbers, thus giving us evidence of the disparity between the two groups.
  6. This information will allow us to conclude that there is a statistical significance between the dN/dS values of the nonprogressor and rapid progressor groups.

Data and Images

Pre-determined Groups and Respective dN/dS Ratios

  • Nonprogressor Group
Subject 4; 0
Subject 9; 0
Subject 11; 0
Subject 14; 0
  • Progressor Group
Subject 7; 1.3
Subject 5; 1.4
Subject 2; 1.8
Subject13; 3.5

Subject 2

  • S value: 36
  • θ value:9.6

Subject 4

  • S value:70
  • θ value:15.8

Subject 5

  • S value:58
  • θ value: 13.6

Subject 7

  • S value:55
  • θ value:12.7

Subject 9

  • S value:69
  • θ value:14.6

Subject 11

  • S value:41
  • θ value:10.2

Subject 13

  • S value:25
  • θ value: 6.6

Subject 14

  • S value:77
  • θ value:15.7

T-Test results

P value=0.146; No statistical significance

Unrooted Tree

Rooted Tree


The results of the t-test showed that there was no statistical significance between the averaged theta values form the previously picked progressor and nonprogressor groups. The value was 0.146 which is much higher than the required value of <0.05. Besides the quantitative results, the qualitative results provided by the rooted and unrooted trees showed that there was no evident separation between the progressor and non progressor groups because of the presence of subjects in the nonprogressor group in between progressor subjects, and vis versa.Thus, it can be seen that our experiment hypothesis was proven wrong and therefore we must accept our null hypothesis which claims that there is no statistical significance between the pre-determined progressor and nonprogressor based upon their dN/dS values.

Powerpoint Presentation

HIV-1 Presentation


Markham, R. B., Wang, W., Weisstein, A. E., Wang, Z., Munoz, A., Templeton, A., . . . Yu, X. (1998). Patterns of HIV-1 evolution in individuals with differing rates of CD4 T cell decline. Proceedings of the :National Academy of Sciences, 95(21), 12568-12573. doi:10.1073/pnas.95.21.12568

Spielman, S. J., & Wilke, C. O. (2015). The Relationship between dN/dS and Scaled Selection Coefficients. Molecular Biology and Evolution, 32(4), 1097-1108. doi:10.1093/ molbev/msv003

Subramaniam, S. (1998) The Biology Workbench--a seamless database and analysis environment for the biologist. Nucleic Acid Tools

Useful Links


I would like to thank Dr. Dahlquist and my partner, Zachary Goldstein, for their help on this investigation. I would also like to thank the Los Alamos National Lab HIV database for supplying HIV sequences, the paper "Patterns of HIV-1 evolution in individuals with differing rates of CD4 T cell decline" by Markham for its subjects and dN/dS values, and Biology Workbench for its sequence alignment and tree generating tools. Lastly, While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source. Shivum A Desai 19:42, 4 October 2016 (EDT):

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