BIOL368/F14:Isabel Gonzaga Week 5

HIV Evolution Research Project - Introduction

• Question: Is there a relationship between the genetic identities in the viral strains present in Subjects with or progressing towards AIDS diagnosis, compared to subjects who are not?
• Hypothesis: I predict that in comparing and analyzing subjects of these three categories (diagnosed with AIDS, trending towards AIDS and no trend), higher diversity will be found in the AIDS diagnosed and in those trending towards AIDS. I also hypothesize that the 'no trend' group will maintain some genetic similarity across viruses.

Methods and Results

• The following sequences was taken from the BEDROCK HIV Problem Space Database, from the Markham et al. (1998) study. The sequence were compiled into a single text document in FASTA format:

Table 1: Sequences analyzed

Group	Subject	Visit	Sequences
AIDS Diagnosed	3 10 15	1 6 1 6 1 4	1, 2, 3 3, 5, 6 3 , 5, 7 4, 6, 8 6, 9 , 12 2, 6, 8
AIDS Progressing	8 9 14	1 7 1 8 1 9	1, 2, 4 3, 5, 7 2, 3, 4 2, 4, 8 2, 5 , 6 3, 6, 9
No Trend	5 6 13	1 5 1 8 1 5	2, 4, 6 1, 3, 4 1, 2, 3 4, 6, 8 2, 3, 4 1, 2, 4

Biology WorkBench was used to compare and analyze the dataset. The sequence file was uploaded onto a new session for analysis. A ClustalW was performed for all sequences from the first visit, and all sequences from the final visit. The following rootless trees were generated and color coded:

Figure 1. Unrooted phylogenetic tree generated for all sequences from Visit 1 after sequence alignment with a ClustalW matrix. Red indicates subjects diagnosed with AIDS, yellow represents subjects progressing towards AIDS and blue represents subjects with no trend of progression

Figure 2. Unrooted phylogenetic tree generated for all sequences from Visit 1 after sequence alignment with a ClustalW matrix. Red indicates subjects diagnosed with AIDS, yellow represents subjects progressing towards AIDS and blue represents subjects with no trend of progression

In both trees, Red represents subjects diagnosed with AIDs, Yellow represents subjects trending towards AIDS and Blue represents subjects with no trend of progression towards the disease. ClustalW was performed for each group from Visit 1. Sequences were aligned and further analyzed using the ClustalDist analysis, where minimum and maximum base pair differences were calculated within each AIDs status group. Groupings were further analyzed in comparison to each other. ClustalW was performed for AIDS diagnosed and AIDS progressing subjects. The sequences were aligned and a Clustaldist was performed to calculate minimum and maximum differences between strains within the two groups. This was repeated for AIDS diagnosed and No Trend, as well as AIDS progressing and no trend. These processes were repeated for the Final Visit sequences. The findings and calculations are as follows:

Figure 3. ClustalW alignment for all AIDS-diagnosed sequences at the time of the first visit. Black, non-asterisked segments denote individual base pair differences between the 9 strands. These differences were counted and used to calculated the S and θ values to determine differences between the AIDS Diagnosed groups.

Figure 4. ClustalW alignment for all AIDS-progressing sequences at the time of the first visit. Black, non-asterisked segments denote individual base pair differences between the 9 strands. These differences were counted and used to calculated the S and θ values to determine differences between the AIDS Progressing groups.

Figure 5. ClustalW alignment for all No-Trend sequences at the time of the first visit. Black, non-asterisked segments denote individual base pair differences between the 9 strands. These differences were counted and used to calculated the S and θ values to determine differences between the Non-Trending groups.

Figure 6. Clustadist analysis for all AIDS-diagnosed sequences at the time of their initial visits. Minimum and Maximum base pair values were calculated using this matrix

Figure 7. Clustadist analysis for all AIDS-progressing sequences at the time of their initial visits. Minimum and Maximum base pair values were calculated using this matrix

Figure 8. Clustadist analysis for all Non-trending sequences at the time of their initial visits. Minimum and Maximum base pair values were calculated using this matrix

Figure 9. Clustadist analysis comparing AIDS diagnosed and AIDS-Progressing sequences at the time of their initial visits. Minimum and Maximum base pair values were calculated using this matrix

Figure 10. Clustadist analysis comparing AIDS diagnosed and Non-Trending sequences at the time of their initial visits. Minimum and Maximum base pair differences were calculated using this matrix

Figure 11. Clustadist analysis comparing AIDS-Progressing and Non-Trending sequences at the time of their initial visits. Minimum and Maximum base pair differences were calculated using this matrix

Figure 12. ClustalW alignment for all AIDS-diagnosed sequences at the time of their final visits. Black, non-asterisked segments denote individual base pair differences between the 9 strands. These differences were counted and used to calculated the S and θ values to determine differences between the AIDS Diagnosed groups.

Figure 13. ClustalW alignment for all AIDS-progressing sequences at the time of their final visits. Black, non-asterisked segments denote individual base pair differences between the 9 strands. These differences were counted and used to calculated the S and θ values to determine differences between the AIDS Progressing groups.

Figure 14. ClustalW alignment for all Non-Trending sequences at the time of their final visits. Black, non-asterisked segments denote individual base pair differences between the 9 strands. These differences were counted and used to calculated the S and θ values to determine differences between the Non-Trending groups.

Figure 15. Clustadist analysis for all AIDS-diagnosed sequences at the time of their final visits. Minimum and Maximum base pair values were calculated using this matrix

Figure 16. Clustadist analysis for all AIDS-progressing sequences at the time of their final visits. Minimum and Maximum base pair values were calculated using this matrix

Figure 17. Clustadist analysis for all Non-Trending sequences at the time of their final visits. Minimum and Maximum base pair values were calculated using this matrix

Figure 18. Clustadist analysis comparing AIDS diagnosed and AIDS-Progressing sequences at the time of their final visits. Minimum and Maximum base pair values were calculated using this matrix

Figure 19. Clustadist analysis comparing AIDS diagnosed and Non-Trending sequences at the time of their final visits. Minimum and Maximum base pair values were calculated using this matrix

Figure 20. Clustadist analysis comparing AIDS Progressing and Non-Trending sequences at the time of their final visits. Minimum and Maximum base pair values were calculated using this matrix

Initial Visit

Group	S	θ	Minimum Base Pair Difference	Maximum Base Pair Difference
AIDS Diagnosed	70	26	1	46
AIDS Progressing	50	18	2	31
No Trend	64	24	1	47

Initial Visit Comparisons

Groups Compared	Minimum Base Pair Difference	Maximum Base Pair Difference
AIDS Diagnosed vs. AIDS Progressing	13	42
AIDS Diagnosed vs. No Trend	29	53
AIDS Progressing vs. No Trend	13	43

Final Visit

Group	S	θ	Minimum Base Pair Difference	Maximum Base Pair Difference
AIDS Diagnosed	76	28	2	51
AIDS Progressing	71	26	1	48
No Trend	61	22	1	43

Final Visit Comparisons

Groups Compared	Minimum Base Pair Difference	Maximum Base Pair Difference
AIDS Diagnosed vs. AIDS Progressing	17	51
AIDS Diagnosed vs. No Trend	30	51
AIDS Progressing vs. No Trend	25	49