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Uncovering New Ways the Human Immune System Fights HIV

Publication date: December 1, 2011

More than 1.8 million people die of HIV-related causes each year—approximately 5,000 deaths per day. HIV is a particularly significant threat in the sub-Saharan region of Africa. In some areas, the occurrence of HIV is eight times higher for women than men; an estimated one in three women seeking care during pregnancy is HIV positive. By age 35, the infection rate for men rivals that of women in the region

Seeking Solutions in Africa

Today, the primary resource for combatting the HIV epidemic is prevention in the form of educational outreach. In many places, free antiretroviral (AVR) therapy is now available for HIV-positive persons, but the need for lifelong therapy, together with new cases, will be a growing challenge for even the most robust economies. Barring the discovery of a cure, the best way to slow—and potentially reverse—the progress of the epidemic is to vastly reduce the volume of new cases through vaccination.

“We spent the last decade building up an infrastructure here that allows us to do studies of the body’s defense mechanisms in the laboratory from blood specimens from these patients that will give us insights we otherwise would never get if we had to freeze down samples and ship them back to the U.S.”

— Bruce Walker, director, Ragon Institute; and professor of medicine, University of KwaZulu-Natal

A number of HIV vaccines are in various stages of development. A notable multi-organizational effort is laying the groundwork for testing future HIV vaccine candidates in Durban, South Africa—the location was selected due to the high rate of HIV infection in this area. The effort is led by Bruce Walker, director of the Ragon Institute at Massachusetts General Hospital, MIT and Harvard, and a professor of medicine at the University of KwaZulu-Natal.

Joining Walker and the Ragon Institute in this research are the Centre for the AIDS Programme of Research in South Africa (CAPRISA) and the KwaZulu-Natal Research Institute for Tuberculosis and HIV (K-RITH). Microsoft Research Connections is working with the Ragon Institute to quantify how the immune system attacks various fragments of HIV—data that we hope will, one day, lead to a vaccine.

Fighting HIV… with Data

Seeking solutions in South AfricaThe team has amassed vast amounts of data since the beginning of the research project, but Walker and his team were challenged with how to analyze and parse such a large quantity of data so that they could apply it to their research. Microsoft Research had been seeking a high-impact project in the biosciences that would help a lot of people if it proved successful and Walker’s HIV research project needed the kind of help we could provide.

“When we first met Bruce, he had a very tricky problem to analyze,” remembers David Heckerman, Distinguished Scientist and manager of the eScience group at Microsoft Research. “He had this great data set but he didn’t know how to analyze it. We happened to have just the right algorithm for it and this large bank of computers at Microsoft that could do this massive amount of computation. He gave us the problem on Friday. On Monday, we had a completed analysis for him.”

Microsoft Research is working with the Ragon Institute to quantify how the immune system attacks various fragments of HIV, by analyzing data sent from the Ragon team in Africa. The collaboration between the Ragon teams in Boston and South Africa, CAPRISA, and K-RITH is very fluid, Heckerman says. The teams in South Africa are constantly sending new data sets to Microsoft Research for analysis. Walker and his team have gathered data, including samples of HIV when it is infecting a particular individual. Microsoft Research analyzes the data and identifies interesting relationships within the data. 

The Human Face of HIV

Beyond the science and computations lies the reason a vaccine is so desperately needed: preventing further loss of life. Individuals who don’t die as a result of the virus are likely to suffer the loss of a “normal” life, asserts Zinhle Thabethe, deputy director for iTEACH in South Africa. She speaks from experience: Thabethe was diagnosed as HIV positive in 2001 at the age of 24. She began antiretroviral (AVR) therapy through a privately funded clinic a year later. Since beginning AVR therapy, her life has been dominated by the medications: remembering to take them, watching out for side effects, and dealing with the emotional stress of being infected with HIV.

“Taking pills for ARVs is really a challenge. With antiretrovirals, it has to be precisely on time. You just cannot miss any tablets, irrespective of what you’re doing. Your life is actually revolving around remembering that you have to take those pills, because they are the reason why you live.”

— Zinhle Thabethe, deputy director for iTEACH in South Africa

The precision required by AVR therapy is a dominant factor in the life of any HIV-positive individual. For Purity, a 30-year-old resident of KwaZulu Natal, it is a constant struggle. “Early in the morning at 8:00, I take I take Tenofovir and Lamivudine. After I eat my breakfast, I take Bactrim and vitamins. In the evening, at 8:00, I take Stocrin and Lamivudine.”

Purity does not know exactly when she contracted HIV. She knew she was ill, and sought treatment at the hospital. She was diagnosed with tuberculosis and then, soon after, HIV. “I thought my life was over,” she remembers. “People told us that if you are HIV positive, you’re dead—you’re not going to live. But there is always hope. There is always a way. And I’m here today. I’m fine.”

Applied Science

The HIV research being conducted as part of this vaccine project has the potential to help millions through the prevention of HIV and, perhaps one day, a cure. But it goes beyond just HIV, Walker notes. “Everything we learn studying HIV tells us how the immune system works and how it fails. I want people to understand that the immune system, on a daily basis, is not just protecting us against infections; it’s also protecting us against cancers. Everything we learn here is going to be applicable not just to HIV but to breast cancer and prostate cancer—and will ultimately change the way medicine is practiced. Because our ultimate goal is that we will learn how to harness the immune system to do a better job at what it was initially designed to do.”