The Importance of Grid Computing and Understanding the Evolution of HIV

Our group used the not for profit program rosetta@home to fold proteins that could one day help find cures for many different diseases, such as HIV.  From this project, we have learned that HIV is a disease that is tricky to understand due to it's ability to mutate rapidly. Grid computing is an important process that may one day help us to better understand the mutations in the HIV strands. It is also important to research the evolution of HIV in order to understand how it has previously mutated, and how it is becoming resistant to treatments. It became clear to us how important it is to study the evolution of HIV when we visited the blood bank. How fast and often certain strands mutate is information that is necessary in order to keep blood transfusions safe.

Total units: 6,487
Average units: 74.88
Manager: BOINC

Response to HIV Questions

1. HIV evolves rapidly, and the transcriptase enzyme that is necessary for replication is very prone to mutation. Mutation is a positive aspect in this study when it comes to being able to trace when the disease was spread. If two strands in separate individuals are similar (and from the same source), this would indicate that the transmission of HIV was recent because the strand has not yet had time to mutate. HIV's fast mutation rate is problematic when we are looking at developing interventions and effective treatments; however, when tracking it epidemically, it is useful to know which sequences of HIV are likely to mutate rapidly and which are likely to be conserved. That way, we can compare these sequences between individuals and determine whether or not there exists an epidemiological connection.

2. The env segment codes for the protein gp160, which eventually in the life cycle of HIV is transformed into the two proteins gp120 and gp41. Gp120 serves as the main binding site for CD4 receptors on target cells of the HIV virus. The main function of the pol gene is that it codes for the reverse transcriptase protein of HIV; the protein that enables its backwards RNA to DNA copying. Pol also codes for the proteins protease, RNAse H, and integrase. The gag gene in HIV codes for four separate proteins which make up the viral core: p24, p17, p9, and p6.
        The gene env mutates very rapidly, while the gene pol is highly conserved. These genes differ in their mutation rates because they have different tolerances for mutation based on their unique sequences of amino acids. Since some amino acids have multiple codons, mutations in these specific amino acids can be tolerated more frequently because it doesn't alter the overall effectiveness of the gene. So apparently env is highly redundant in its amino acids in that a lot of them have multiple codons, whereas the amino acids that make up pol are not as flexible and thus do not tolerate mutation as much. When mutations do occur, the gene is most likely lost. Therefore, the pol genes that are functional in the HIV viral strain are the ones that have remained highly conserved.
        The researchers of this study chose to sequence gag and env because although env evolves very rapidly, similarities can still be detected if the period between transmission and testing is very short. The gag gene is most effective for determining epidemiological relationships when studied alongside the env gene. They chose not to sequence the pol gene because although it is a gene that undergoes relatively few mutations in the HIV strand, gene sequences for pol can appear to be very similar even between unrelated strands of HIV.

3.  Looking at the phylogenetic trees for the gag and env sequences of the Glenochil cohort, we think that the data gives sufficient proof that the source of infection was the same for all individuals because they all share the most recent node, the most recent ancestor of the viral strain. We think that the HIV genes in these prisoners could be accurately described as orthologous because orthologous simply means that the gene sequences are homologous—they share a common ancestor. The phylogenies show this to be very likely on multiple levels (both from the gag sequence and the env sequence).

4. The unrelated HIV strains in this phylogenetic analysis serve as the control group. HIV mutates extremely rapidly, but the researchers wanted to show that even though the individual strains had mutated, the strains in the Glenochil cohort were still more closely related to each other than they were to a “control” strain—or just some other random strain from the HIV population. They utilized a variety of unrelated “control” strains to show that the Glenochil strains were still likely to have come from the same source, even when compared to a variety of other HIV strains.

5. In the past decade, there have been four main measures taken to decrease the spread of HIV in prisons. The first is making bleach available for all inmates. This prevents the use of needles and syringes that are not properly sterilized. The second method is providing clean syringes and needles to the inmates. The provision of clean needles and syringes will prevent inmates from sharing dirty needles. The third mechanism is substitution treatment programs. These programs have proven to lower the amount of drugs being used and the amount of drugs traded. The last mechanism to reduce the spread of HIV is making condoms readily available.   These are usually distributed by machines in the facility. Although these four mechanisms do not stop drug use, they make it slightly safer and decrease the spread of HIV.
        Some prisons have also introduced voluntary HIV testing and counseling. Like we learned from our interview with Dr. Menitove, our methods for detecting the HIV virus are now a lot more advanced than in the early 90s, so it is much faster and more reliable now to test people for HIV. However, it's been proven that separating the housing of HIV-positive inmates in prisons has not had a significant effect on decreasing the spread of HIV, mainly because inmates are still gathering and potentially infecting each other through shared needles or unprotected sex. The measures listed above have given inmates opportunities to be safer, but unfortunately not all prisons make these preventions readily available. Many countries' governments have unfortunately turned a blind eye to the prevalence of injecting drug use and unprotected sex in prisons, so funding for HIV/AIDS education and testing/counseling (along with the other sterilization measures) has been hard to come by. Where these programs have been implemented, only positive changes have occurred in the prisons. It is obvious that the prison communities should be granted all of the same HIV/AIDS prevention and treatment programs that are available to the general population; only then can we hope to see a decrease in the HIV rate among prisoners.

6. According to the phylogenetic tree generated by the researchers for the dental clade of patients infected by HIV, we think the allegations were correct that the dentist was indeed the source of the virus. The authors probably generated this tree in a manner similar to the case of the Glenochil cohort, by comparing certain genes (probably the env and gag) between all the patients/individuals and looking for distinct similarities in the viral strains. The article said that the researchers were able to successfully track down the patients and obtain samples of their HIV strains to compare to the dentist and to each other within 2 or 3 years of the supposed infection date; that had been a short enough period of time for them to notice strong similarities and construct the phylogeny. However, if they had waited longer, their evidence that the dentist was the source may not have been as compelling.

Response to Interview Questions

1. Describe your feelings about or response to the interview.
    - As a group, we were all very impressed regarding the outcome of the interview. Dr. Menitove was very educated on the subject of HIV and the possible transmission of HIV through blood transfusions. He was able to answer all of our questions with insightful comments. He had his own views and opinions on certain aspects of HIV. We learned a lot about the evolution of HIV, but even more about the evolution of treatments for HIV. This interview made me personally feel like there are many aspects of HIV research that don't get as much attention or are not as well known. I felt like I walked away from the interview knowing a lot more about HIV research and testing than I had known before. 

2. What changes occurred for you as a result of your interview?
    -Before the interview, I thought that it would be common sense to want to know the evolution of a disease, especially if you are diagnosed with the disease. When talking with Dr. Menitove, he asked us if we would want to know how rapidly a disease evolves if we had it. It made me realize that knowing the rapid evolution of HIV would fill me with the fear of never finding a cure, rather than filling me with courage. I do believe it is important for people to know how serious this disease is and to educate them on the consequences of certain actions, but this interview made me realize that maybe it isn't always the best idea to educate people with certain diseases about the evolution of that disease. I think it would be more encouraging to educate them on what is being done in research labs to treat the disease. 

3. Did anything about the interview disturb you?
    What I found surprising was the test used to detect HIV when donating blood is not 100% effective. There is a 11 day period that starts at the very beginning of infection that can not be detected by the HIV test. This is due to the lack of virus built up in the blood. Dr. Menitove went on to explain that theoretically, more people could be getting HIV from blood transfusions than actually do. There was 1 case in the past 4 years. He explained that this number is so low, because people who know they have HIV don't come in to donate blood. People who want to donate blood are doing it for the right reasons. If people know they are sick, they are not going to come in to donate and potentially make someone else sick. Even though there is only a slight risk for contracting HIV via blood transfusions, it was still a little disturbing to me that someone receiving a blood transfusion is still at a risk. 
 4. Describe the connections you found between the interview and your research & classwork
    -Grid-computing is a recent technology that can help to find cures for diseases that have been studied for many years. After this interview, we realized how important grid-computing really is. HIV is a very complex disease that continues to evolve, making it hard for a cure to be discovered. Understanding how HIV works and evolves could open up new opportunities for researchers. Even though HIV is constantly evolving, the tests do not need to change. This has allowed researchers to look at new options for treatment.He explained that there is new technology in Europe that could possible eliminate many diseases from blood transfusions without having to spend money on the same tests every year. This test is called the pathogen-reduction test. This is a novel idea, but it doesn't sit well with many people for the mer fact that it hasn't been proven to be 100% effective. The pathogen-reduction test uses UV light to destroy pathogens in the blood before they are even used in transfusions. It would not only destroy HIV, but other pathogens and diseases as well. Dr. Menitove did seem confident, however, that these tests will become almost foolproof and will eventually be the future of eradicating HIV from the blood banks. 

Interview with Dr. Jay Menitove, M.D.

For our interview with an expert, our group chose to interview Dr. Jay Menitove, M.D.—President/CEO and Medical Director of the Community Blood Center here on Main Street in Kansas City, MO. Dr. Menitove completed his training in internal medicine and hematology; he eventually decided that going into blood banking would be a good complement to his training in hematology without getting involved in the oncology side. He worked on his blood banking training at the blood center in Milwaukee around the time that the AIDS pandemic was beginning in the early 1980s. Dr. Menitove and his colleagues worked closely with a lot of hemophilic patients. Around 1982 they started noticing that hemophilic children receiving commercially produced clotting factor 8 concentrates that came from donors all around the country had about a 50% chance of experiencing some immunodeficiency problems, whereas the children receiving individual blood units from the Milwaukee area were virtually not exposed to this risk. They were starting to realize there was a problem with the blood in some of these blood banks; however, since the AIDS pandemic had not really reached the Midwest yet, it wasn’t a problem in the Milwaukee blood banks at this time. Dr. Menitove became knowledgeable on the study of HIV and AIDS through his experience of working in blood banks over these years, but he also came to know a lot about the HIV blood-testing process once the blood test was created in 1985. He now works as the head of the Community Blood Center in Kansas City, which works hard to ensure that all blood donations are free of infectious agents (especially HIV) and that patients are receiving the safest blood transfusions possible.

                After learning more about his experiences with HIV in the 1980s, we asked Dr. Menitove if he interacts a lot with HIV patients here in Kansas City, and he explained to us part of the blood-testing process that happens when people come in to donate blood. He explained that prior to the blood test for HIV came out in 1985, blood banks only had lists of either behaviors or groups of people who were risk factors for HIV (drug users, men who have had sex with other men). People who fell into these groups or engaged in these behaviors were asked not to donate blood, and for the most part they complied. However, when the test came out it really helped blood banks determine who had the virus and who did not; since then, the tests have gotten progressively better. The original testing for HIV was antibody testing. This is still used today, but in 1999 they added nucleic acid testing (a form of PCR testing) which tests for the RNA of the virus. Now both tests are always performed on every donor to assure that blood banks are receiving the safest blood possible. When the antibody test first came out in 1985, the window period between exposure to the virus and the ability to detect the virus in the blood was a couple of months. Since then this window period for detecting antibodies has shrunken down to 21 days after exposure; for RNA testing the window period is only 11 days after exposure. With these great improvements in our blood tests, today the risk of contracting HIV through a blood transfusion is estimated at only one out of every two million—theoretically no more than ten cases a year. In reality though, there has only been one reported case of HIV transmission through blood transfusion in the last four years, and it actually just happened in the last three or four months in the state of Missouri. This person was most likely tested during those first 11 days after exposure when the concentration of the virus is not high enough to be detected via RNA testing. He denied that he was indeed a risk factor for spreading the virus because he was a married man who had had a lot of extramarital affairs—unfortunately when they followed up on the recipients of this donor’s blood, one of them tested positive for HIV.

                The next question we asked Dr. Menitove pertained to the evolution of testing for HIV.  We asked, “How have the tests for HIV evolved as the virus continued to mutate?” To our surprise, Dr. Menitove explained that the tests haven’t evolved a significant amount in the past couple of years. He went on to explain that a particular section of the genome of the HIV virus is the same for every strand. Even though some strands are more resistant to treatment than others, they all still share an identical section of their genome. This allows blood banks to use the same tests without making expensive, dramatic changes to the tests that are already in place. We found it interesting that there could be several different strands of HIV, but the same testing kit could detect all. Dr Menitove is very confident in the current testing mechanisms. He explained that the current tests are very accurate for all strands of HIV today, but when we asked if these same tests would still be able to detect HIV after many mutations he said, “If it mutates significantly, that’s a risk. We could miss it.” So far though, this has not occurred—not even in response to the shift after the drug AZT started selecting for resistant strands of HIV. He said, “if drugs still [relatively] work, you have a sense of knowing that the virus has not mutated too much. If they stop working, you could have a different virus.”

                Because the testing has become so accurate, Dr. Menitove said that they do not often have donors come in who test positive for HIV—only about one person per year tests positive for HIV out of the 130,000 donors at Community Blood Center. He said if people are donating blood in a more public setting (at work, university) and are embarrassed to disclose that they are a risk factor, they can call back and say not to use their blood. They try to avoid “test-seekers,” as he described them—people who abuse the altruistic system of blood donating just to get a free and confidential testing for HIV. “We do not want to be the place where people come to experiment if they’re positive,” said Dr. Menitove. This really just puts others at risk by trying to donate potentially contaminated blood to innocent people who need transfusions.

                When we asked Dr. Menitove if he thought it was important for people living with HIV to know about its evolutionary history, he said, “I don’t know if knowing the history is going to get you protected from getting HIV as much as knowing how it’s transmitted is going to protect you.” This sparked some thought-provoking conversation though, as we continued to talk hypothetically about if we were diagnosed with HIV and knew about how rapidly it could change, we would be a lot more nervous knowing that treatments could become out-dated and a cure could be a long way away. We talked about how people can sometimes fall into complacency about a vaccine being developed in the near future, but really it’s a bit more unknown than other epidemics because the virus can keep mutating and evolving in response to different drug treatments.

                When we asked about the evolution of treatment and testing for HIV, Dr. Menitove explained that obviously the testing has changed a lot since it came out in 1985—the window period for detection is now a lot shorter, and even more recently the test has been modified to be able to detect strains of HIV-2, a rarer relative of the rampant HIV-1. He said that they are constantly looking at the tests to see if they are still accurately picking up the antibodies; they are always aware of this evolution as they continue studying their tests and how they are working. The improvements that have been made in the last 25 years of blood testing have all been funneled toward the ideal of a zero-risk blood supply; however, Dr. Menitove explained to us how this quest is really not achievable. Modifying these tests so that there are zero risks involved would raise the cost significantly of each test—a cost that our economy could not support. “In terms of evolution, I believe it is going to evolve from a zero-risk concept to a risk-based decision making.” He said that we should be asking ourselves, what are the risks? What are the benefits? Instead of putting all these dollars toward improving our tests, can we put them toward developing a vaccine? Would doubling the cost of testing really make a difference in the one or two cases that slip through the system each year? He foresees an evolution in blood banking from putting all our money towards testing to putting money into procedures that would avoid needing transfusions in the first place.

                One way that this idea has started to evolve is through pathogen-reduction technology. According to Dr. Menitove, there are developing procedures in which chemicals or UV light can be added to the blood to inactivate (or at least reduce the amount of) bacteria and viruses—even HIV—in the blood supply. This is licensed currently in European countries, but not yet in the United States. As we saw with the AIDS virus, it took a significant amount of time for a test to be developed after the virus became a problem. For all the new infectious agents that are entering our blood supply, we cannot develop tests fast enough to prevent them from becoming widespread problems. With pathogen-reduction technology, however, these agents could be killed from the start before they even have a chance to evolve and spread. Dr. Menitove thinks that this would be a great way to prevent innocent third-parties from receiving new and emerging diseases via donated blood. These procedures are not considered foolproof yet, thus the FDA cannot endorse them in the US without knowing that they are completely safe. Some are hopeful that within the next 10 years, we will see new technologies like pathogen-reduction being used in the United States.

                All in all, we learned so much from our interview with Dr. Jay Menitove—not only about the history of HIV evolution and blood testing, but also about where it could be going as the virus continues to evolve. Dr. Menitove was extremely friendly and informative, and we are very thankful that he could give so freely of his time to help in our grid-computing project.

The Basics on HIV and How Grid Computing is Beneficial

H - Human - Can only infect human beings
I - Immunodeficiency - Weakens the immune system by destroying the cells that fight infection and disease
V - Virus - A virus is only able to reproduce itself by taking over a cell in the body of its host

HIV lives and reproduces in blood and other body fluids such as pre-seminal fluid, semen, breast milk, vaginal fluid and rectal mucous. It can be transmitted from human to human through sexual contact, during pregnancy, childbirth and breastfeeding, as a result of injection drug use, occupational exposure and as a result of a blood transfusion. The virus takes a long time to show its effects on the body--so much that if it is not caught in time, it could have already done a large amount of damage to the body.

For most viruses that the body encounters, the immune system is able to clear it out on its own. However, with HIV, the immune system is not able to clear out the virus and begins to attack the T-cells and the CD4 cells in the immune system. The human body needs these cells in order to fight infections, but instead HIV invades them and uses them to make copies of itself before destroying them. Over time, this can lead to the prevention of fighting infections and disease which in turn can lead to AIDS (Acquired Immune Deficiency Syndrome).

Here is a short video to better understand the life cycle of HIV and how it enters the cell.

Normal people with healthy immune systems can be exposed to certain bacteria, viruses and parasites without experiencing serious sickness. For those living with HIV, however, these common maladies (known as "opportunistic infections") can cause serious illnesses when they come into contact with the host's weakened immune system. One example of an opportunistic infection is pneumonia--when people with healthy immune systems get pneumonia they are sick for a short while, but most fully recover. For someone living with HIV/AIDS, the body's defense would be so weak that this infection could lead to death.

Although at this time there is no cure for HIV/AIDS, scientists are continuously searching for a cure and developing treatments in the process. One thing that is helping find a cure for HIV is grid-computing: the process of our global community working together through the usage of personal computers to gather and calculate raw data pertinent to current biological and medical issues. By having individual computers on the grid, these grid-computing programs run in the background while the computer is on just crunching numbers and data, and periodically they send information back to the institution conducting research. For this service-learning project we are using Rosetta@home (http://boinc.bakerlab.org/rosetta/) to actively participate in finding the cure for HIV.

 

Here is a short video on how some of the medicines help treat HIV.

 

To learn more about how HIV's rapidly mutating composition has made it difficult to defeat and about HIV's immunity to drugs being produced today, check out this video as well.