FightAIDS@Home World Community Grid

To date, we have completed 33 FAAH tasks, with 2 more in progress. You can view our progress by going to the following website: www.worldcommunitygrid.org.

HIV Questions

1) Why is the elevated mutation rate in HIV a positive aspect for this phylogenetic study?
The elevated mutation rate in HIV creates multiple different strains. Because of these differences, certain infectious strains can be easily traced between patients. The ability to trace each strain by its mutations allows for this study to determine if the outbreak in Glenochil prison came from the same source.
2) What do env, pol and gag code for in HIV? Why do they differ in their mutation rates? Why, then, did this study choose to sequence gag and env?
Env codes for a protein, gp160. It is the protein that creates the markers on the outside of the HIV virus. Pol codes for four proteins, reverse transcriptase, protease, RNAse H, and integrase. Gag codes for the capsid protein, the matrix protein, nucleocapsid protein, and p6. They differ in mutation rates because the genes code for different proteins. Certain proteins, such as reverse transcriptase, cannot have significant mutations or they will not work; therefore, the gene pol cannot readily mutate and have the virus survive. This study choose to sequence gag and env because the mutation rates and high, which creates distinct similarities among related strains. (Dan Stowell http://www.mcld.co.uk/hiv/)
3) How can you tell, by lookin at the phylogenetic trees, that there is a single source of infection for the Glenochil cohort? Could you accurately describe the HIV genes in these prisoners as orthologous? Why or why not?
Each virus goes back to a common ancestor. The genes could technically be called orthologous because HIV started as SIV in monkeys, however, I would not call them orthologous because the mutations in the genes arose in one species, humans.
4) Why was it important to include unrelated HIV strains in this phylogentic analysis?
Showing the unrelated HIV strains allows for comparison of the strains that the study was focusing on. If there were no related strains, it would look as though the different strains in the patients all came from different sources.
5) Have there been other measures taken to reduce the spread of HIV in prisons since this paper was written (10 years ago)? At blood center like the one your interview described?
In countries other than the US, prisons have instituted condom distribution and needle exchange programs to combat behaviors such as unprotected sex and intervenous drug use. (Kelly, Christopher and Hiller, Matthew. "HIV, Public Health, and Corrections: Policies and Implications") Prisons in the US have started treating HIV + inmates with antiviral medications and also administrating counseling. (Center for AIDS Prevention Studies - University of California, San Fransisco)

6) On the next page you will find a figure from Science entitled "Application and Accuracy of Molecular Phylogenies" (Hillis et al. 1994: Vol. 264: 671-677). In the study referenced, the authors considered the allegations of 7 patients (A-G) that they had contracted HIV from their dentist. Were their allegations correct? Describe how the authors might have generated this tree.

It is a high possibility that these 7 patients were correct in saying they contracted HIV from their dentist. After extensive studies in which their viral gene samples were studied and compared/contrasted against the samples from the dentist and local population individuals, it was noted that a single evolutionary lineage exists between the dentist and the effected patients. Although there are potential confounding variables when considering the spread and evolution of this disease, the generated phylogenetic tree included all the patients without other identified risk factors and excluded all patients with other confirmed risk factors. It is consistent with the independent epidemiologic data and further studies have proven this phylogenetic tree to be an accurate representation of the spread of the disease between the dentist and patients.

Transmission of SIV to humans

Here are a couple of pictures that Dr. Nemechek provided us. They show how the apes are slaughtered at the Kinsasha meat market in Africa, which is how the SIV virus was transfered to humans. The conditions are not very sanitary and there is no regulation on testing of the animals before they are sold. Many people have misconceptions about how humans were infected with SIV, so this will, hopefully, help.