Michael R. Pina Week 5

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Week 5

Forming our question

We would like to observe the effects of amino acid change among the different progessor groups. The Markham et al. article states that viral strains from the nonprogressors showed a possible selection against amino acid change. We want to look more in to the validity of this statement. Our question is:

Is the Ds/Dn ratio more of a determinant on the progressor categories than the rate of CD4 T cell decline?

To determine this, the entire collected sequences from subject 10 (rapid progressor) and subject 13 (nonprogressor) will be examined. These subjects were chosen because they seem to display the qualities of a progressor/nonprogressor. Also, their visits were over roughly the same amount of time to ensure a fair comparison between the two. Subject 13 should have low diversity/divergence along with a dS/dN ratio near 1.

Finding another article

  1. Nora T, Bouchonnet F, Labrosse B, Charpentier C, Mammano F, Clavel F, and Hance AJ. Functional diversity of HIV-1 envelope proteins expressed by contemporaneous plasma viruses. Retrovirology. 2008 Feb 29;5:23. DOI:10.1186/1742-4690-5-23 | PubMed ID:18312646 | HubMed [Paper1]

In light of this article, it seems that variants of the HIV-1 virus that have mutations in the V3 region of the 'env' gene actually display low infectivity. This would support the hypothesis that the Ds/Dn ratio and the subsequent changes in the amino acid sequence may have more of an effect on diversity and divergence than the rate of CD4 T cell decline.

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