Introduction to the HIV Problem Space

This problem space contains data from a published study by Markham et al on HIV evolution within individual patients. The study involved 15 injection drug users in Baltimore, Maryland (USA) who became infected with HIV between 1989 and 1992. Patients came in at approximately six-month intervals ("visits") to have blood samples taken. From these samples, the researchers extracted and sequenced multiple copies of proviral DNA. Patients' CD4 counts were also measured at each visit to assess their level of immune function.
In this problem space, you will have access to the following materials:
background information on HIV/AIDS,
the original Markham et al. reference and other primary literature,
viral sequences from each visit of each patient,
patients' CD4 counts at each visit,
phylogenetic trees of the virus sequences from each patient,
a phylogenetic tree of each patient's starting consensus viral sequence,
a published activity using this data from the book Microbes Count!,
and additional materials prepared by other users of the problem space.
You can use this data to explore a number of different questions. Here are a few general questions to get you started:
Does the virus evolve the same way in different patients?
Are there any specific mutations that cause rapid immune decline?
What types of natural selection might be influencing HIV evolution?
Is HIV being transmitted between patients after initial infection?