Ryan N. Willhite Week 5

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  • Trying to come up with a question to research
  • We are interested in the subjects 6,7,10, 11 and 13.
  • We see a similarity in CD4 decline within these subjects separated by labels of what type of progressors they are.
  • Some are so similar we are wondering if their sequences give light as to why they are classified as a rapid, moderate, or nonprogressors.
  • Our focus is mainly on divergence because based on how similar/different the sequences are, it may give some insight as to why they were classified as the types of progressors they are classified as.


Reevaluating the standards of categorizing HIV progressors based on CD4 T cell decline rates by examining divergence and diversity in HIV-env sequences


We predict similarities in divergence and diversity based on sequence analysis in subject 7 and subject 10/11, as well as subject 6 and subject 13. We also predict differences in decline rate based off divergence and diversity in subject 7 and subject 6 because although they are moderate progressors they will be more divergent considering they are closer to the other types of progressors.


1. Upload approximately 30 sequences from each subject from Visit xx. 2.Conduct Clustdist multiple sequence alignment between the following pairs and generate phylogenetic trees:

    • 7:10
    • 6:13
    • 7:6

3.Calculate S, Theta, and the Minimum and Maximum

4.Interpret phylogenetic trees and statistical data

Journal, More Recent Other Previously Published Work:

  1. Hill MD and Hernández W. Nucleotide and amino acid mutations in human immunodeficiency virus corresponding to CD4+ decline. Arch Virol. 2006 Jun;151(6):1149-58. DOI:10.1007/s00705-005-0693-8 | PubMed ID:16385396 | HubMed [Paper1]