Samantha M. Hurndon Week 4

1. My collegue and I decided that we wanted to investigate the five subjects who didn’t fall into the category of showing no evidence of a predominant single viral strain throughout an extended period of time. Therefore our question is:
   • Which of the 15 subjects did show evidence of predominance of a single strain? Did these five subjects said to show this predominance fall under rapid, moderate or nonprogressors? Lastly, what characteristics do these five subjects share that could have possibly caused them to have similar viral train findings?
2. We predict that the subjects will fall under one category. We assume this due to their similar characteristics, which may cause them to have the same reaction to a viral strain.
3. We will use subjects 2, 3, 4, 6, 12 and 13. We will use the database for these that gives us the number of sequences and number of distinct sequences. Once we retrieve this information will take the ratios of the sequences to identify which fall under 0.5, indicating that they are significant to our study. Once we find this information we can build a phylogenetic tree based off their visits and clones and analyze those to hopefully discover some exciting information.
4. Out method of comparing ratios of unique sequences to number of sequences was used for the subjects whose phylogentic trees were not shown in the Markham paper. The subjects trees who were shown, 5. 6, 8, 9 and 14, provided us with the information necessary to cancel them out as one of the possible subjects who showed evidence for predominance of a single strain. Therefore it was not necessary to do calculations on their sequences. The subjects that contain the lowest ratio indicates that they hold the lowest amount of distinct sequences. Consequently, these particular subjects will then be further investigated as main candidates for those that may contain a single predominant strain.