Variability in rapid progressors in comparison to non-rapid progressors


Student 1 and Student 2

Introduction
This particular study was conducted using bioinformatics to analyze several subjects that had contracted HIV. The study was conducted within our Immunology laboratory and was used to determine if variability exists between subjects with rapid progressing HIV strains in comparison to subjects with non-rapidily progressing strains of HIV. We chose 6 subjects to compare, three with rapid progressing strains and three with non-rapid
progressing strains. Using Case It! Software developed for bioinformatics, we constructed several phylogenetic trees to analyze the variability in each of the subject’s respective strains from their first visit and from their last visit.

Question
Do rapid progressing subjects contain more variability in their viral strains when compared to non-rapid progressing subjects, when examining early strains and later strains?

Hypothesis
We hypothesize that rapidly progressing subjects will show more variability in viral strains collected from later visits than in strains collected from earlier visits. Furthermore, we hypothesize that subjects with non-rapidly progressing strains will show less variability in comparison to subjects with rapidly progressing strains.

Data Analysis
Analysis of a phylogenetic tree is a very useful method in determining variability. This can be analyzed by the length of each line; a longer line resulting in more variability. The scale of the tree needs to be noted when looking at line length. Another good way to analyze a tree is to look at the roots of each line; one common root shows a common ancestral point or sequence.

Rapid Progressing Subjects:
~Subject 3:
Through analyzing the phylogenetic tree for this subject's viral strains, we can see that the strains from visit 1(V1), and also one strain from visit 3 (V3), contain much more variability when compared to the strains of the subject's later visit(V6). The V1,V3 strains all stem from a single common ancestral point, whereas V6 strains stem from three ancestral points. Also, V1,V3 strains have much longer lines, thus showing more variability
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~Subject 10:
Through analysis of this subject's phylogenetic tree, we see slightly more variability of the viral strains in the subject's last visit (V6) as opposed to the subject's first visit (V1). Viral strains from V6 all have one ancestral point, however, V1 strains have 5 ancestral points showing that V1 has slightly more variability there. As for the length of line, strains from V6 have much longer length than V1 strains concluding that, even though V6 strains have one common ancestral point, there has been much more variability within the V6 strains from that point. Thus we conclude that V6 strains have more variability overall.
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~Subject 15:
This subject's phylogenetic tree shows slightly more variability of viral strains in the first visit (V1) and less variability in the viral strains of the last visit (V4). This tree shows that V1 strains all have a common ancestral point that is also common with a point of two V4 strains. V4 strain have 3 total common ancestral points. However, V1 strains have much longer lines showing more overall variability within the viral strains.
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Non-Rapid Progressing Subjects:
~Subject 6:
For this subjects early visits, we have viral strains from visit 1 (V1) and visit 2 (V2). For the last visit, we used viral strains from visit 9 (V9). V1 and V2 strains have 2 common ancetral points whereas V9 strains only have one common ancestral point. However, V9 strains have much more variability from that ancestral point as opposed to V1 and V2 strains from there ancestral points. This shows that V9 strains have more variability within them than do V1 and V2 strains.
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~Subject 13:
This tree shows a vast amount of variability within both early strains (V1,V2), and later strains (V5). V1 and V2 strain have three common ancestral points and fairly long variability lines within three of the four V1 strains. On the other hand, V5 strains have 4 common ancestral points and long variability lines in all five V5 strains. This concludes that V5 strains have slightly more variability over V1 and V2 strains.

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~Subject 14:
This subject's early visit viral strains (V1) have short variability lines showing little variability, but do have five common ancetral points. This subject's last visit strains (V9) only have one common ancestral point, however, V9 strains have much longer variability lines showing much more variability in V9 strains over V1 strains.
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Results and Conclusions:
In analyzing the data and results for rapid progressing strains contracted by subjects 3, 10 and 15 and for the non-rapid progressing strains contracted by subjects 6, 13 and 14, we can conclude that our data provides non-compelling support for our original hypothesis.

In analyzing the phylogenetic trees for the rapidly progressing strains in subject 3, there exists little variation during earlier visits and still very little in later visits. Additionally, in subject 15, there exists a relative amount of variation when looking at earlier visits and a considerable amount less in later visits, which is opposite of what was hypothesized. Subject 10 is the only subject having a rapidly progressing strain who demonstrates
increased variability in later visits when compared to earlier visits. When examining the phylogenetic trees of the non-rapidly progressing strains in subjects 6, 13, and 14, we determined that it further invalidates our hypothesis. In subjects 6 and 14, there exists increased variability in strains collected in later visits than do the strains form earlier visits. Subject 13 demonstrates very little change from strains obtained during both early and late visits and proves difficult to draw any substantial conclusions through phylogenetic tree analysis.

In conclusion, we have determined that our hypothesis is unsupported by the results obtained through the phylogenetic analysis. Our results have proven to show increased variability in subjects that had contracted non-rapidly progressing strains and was opposite of our expectations. Two of the non-rapid progressing strains show increased variability at later visits whereas only a single rapidly-progressing strain shows increased variability at later visits. Having obtained inconclusive results for our hypothesis, we may need to investigate more subjects or possibly consider all visits made by each subject to obtain definitive support for the evidence provided. In future directions, we may consider the use of different types of phylogenetic trees or examining the specific amino acid sequence for each respective viral strain to gain conclusive evidence.