Janelle N. Ruiz Assignment 5

Question: Are their 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’ (defined as CD4 T cell counts which fall rapidly, or linearly, over time (slope ~ -1)?

Prediction: We predict that participants with high variability in T cell count between visits will show a lower HIV-1 diversity and divergence than participants with linear progression. This is predicted under two assumptions
 * (1) High diversity and divergence of HIV-1 variants indicates a more rapidly progressing virus (and thus a steadily falling CD4 T cell count)
 * (2) high variability in T-Cell count will indicate a participant’s immune system was able to manage this virus better than a participant with a steadily falling CD4 counts. If we do see high diversity in participants with high variability in T cell count between visits, we predict that these will be predominantly synonymous mutations as opposed to non-synonymous mutations (which we would expect to see with linear progressors).

Subjects Chosen:
 * Linear Progressors: (slope: -1) Subject: 4, 10
 * High Variability between visits: Subject 12, 8
 * Low Variability between visits: 5

Article: Early viral load and CD4+ T cell count, but not percentage of CCR5+ or CXCR4+ CD4+ T cells, are associated with R5-to-X4 HIV type 1 virus evolution.*
 * 1) Paper1 pmid=12803997