HIV Mutation Activity – Feedback

From my post to the AP Biology Community. Feel free to comment here or reply on Twitter.

Happy New Year Community!

A few days ago Brad Williamson replied to another post about an activity for EK3, LO 30 on the evolution of HIV. This was originally published way back in 2005 and now is made a bit easier by the nice online phylogent/alignment tools out there.

I was experimenting with the more open inquiry activity. This activity is based on real data (unfortunately) from multiple HIV patients who were IV drug users. The data set contains sequences from HIV clonal data and also gives their CD4 counts as well.

The activity can be found HERE and the data set HERE.

So I put my student hat on and decided to run some experiments. I decided I wanted to see if there was any relationship in HIV gene diversity and CD4 decline over time. I picked Subject 9 who has 8 visits to the clinic from 1989 to 1993 and never missed a visit.

I used http://www.phylogeny.fr to run the amino acid sequences in the data set for all visits. Attached is the plylogenetic tree derived from this data. The subject and number is first and then their visit number, followed by the clone number. S9V4-2 (Subject 9, Visit 4, clone 2)

In this same time period, the CD4 values declined from 489 to 270.

So, wise community, help a brother out with this tree. In looking at it, it looks like the root of the tree shows 1 substitution and as diversity increases (more substitutions), the tree trends out to the right with the clade at the top (visit 8 mostly) showing the greatest amount of genetic diversity. Meaning, that during visit 8 the subject’s HIV had a greater diverstiy of genes becaue of high mutation rates then back in 1989 in visit 1 (base of the tree).

Please let me know if I am way off base here, on the right track, or if there are other things I am missing. 

The original paper published on this data set can be found HERE but it is pretty technical (at least for this paleontologist).

I appreciate your time and feedback!

Bob

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