Nicolette S. Harmon Week 4
HIV Evolution Project
- The question I have developed from the Markham paper is if there is a pattern in immune responses among the non-progressors, moderate progressors, and rapid progressors that were part of this study. Using both the rooted and unrooted phylogenetic trees, I will be looking at the genetic diversity in various subjects and the points of divergence in these trees in order to explain why the virus progressed more rapidly in some subjects but not in others.
- I predict there is a more equal spread of diversity among the non-progressor types. I believe the virus is selected against in non-progressors based on the quantity of a strain, when one strain starts to grow rapidly the immune system attacks it leaving the different strains in roughly equal numbers. I also predict there is dominance by a single or a few strands in rapid progressors, I think certain viral sequences are not selected against so they are in larger numbers causing the disease to progress more rapidly.
- The subjects that will be examined are 3,7,11,12,13,14. Subjects 3 and 11 are the rapid progressors, subjects 7 and 14 are the moderate progressors, subjects 12 and 13 are the non-progressors that will be examined. The subjects chosen were done so because they had approximately 50 sequences, making them more compatible with the Workbench program. In most subjects all of the clones and visits will be used, except for subjects 7 and 14 (both moderates) due to the number of clones subject 14 had. Four visits, from approximately the same time periods, were selected from these two subjects.