Breakthrough HKUST-led research on mapping of HIV weak spots paves way for vaccine

Data scientists have discovered a way to map weak spots in HIV, potentially paving the way for researchers to design a vaccine.

An international team of scientists led by the Hong Kong University of Science and Technology processed data from 1,918 HIV-infected patients globally to map the protein protrusions on the virus’ surface that predict how it mutates and its ability to replicate.

HIV, which attacks the immune system, is hard to tackle because it rapidly mutates and changes its appearance to evade antibodies that a person’s immune system produces to fight off the virus.

By using a computational framework they developed, the scientists were able for the first time to identify a fitness landscape – a map that shows how it mutates, and its ability to assemble and replicate itself in the body.

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“The fitness landscape of the HIV virus is currently not well understood … what we can do with our landscape is that we can predict for any mutation, whether it’s fit or not,” said Matthew McKay, associate professor in HKUST’s department of electronic and computer engineering.

Depending on what part of the protein an antibody targets, the protein can mutate into a stronger or weaker virus.

Their five-year study was recently published in international academic journal Proceedings of the National Academy of Sciences of the United States of America.

The scientific breakthrough comes with the world still struggling to develop a vaccine to tackle the global epidemic.

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According to the Department of Health, there were just under 9,000 people infected in the city as of September last year, while the government’s Advisory Council on Aids also predicted that the numbers would continue to surge in coming years.

Some 1,200 people in the city have developed Aids, a potentially life-threatening illness that occurs at the final stage of an HIV infection.

An estimated 36.7 million people worldwide were living with HIV in 2016, while around one million people died from Aids-related illnesses in that year alone, according to UNAids.

McKay said one of the potential uses of their computer model was to help researchers design and develop vaccines.

“It’s now been close to 40 years [since HIV was discovered] and we still have no effective functioning vaccines to prevent HIV. If we want to curb this growing trend with more and more people getting infected, the drugs are helping us, but they’re not fully solving the problem, there’s still really an urgent need for a vaccine against this virus,” he said.

With their data analysis from 20,000 sequences of a virus subtype, a map showing the protein’s weaker areas could be useful in narrowing down target areas for vaccine development and research.

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Such vaccines ideally would elicit an immune response to produce antibodies to specifically target the weak areas, and force mutations of the virus into forms that severely compromise its ability to reproduce and infect human cells, eventually leading to its death.

But researchers said the discovery, although significant, is still far from finding a cure for the virus.

“Ideally [a cure] is what everyone would love, it would be a huge benefit to humanity, but at the moment what we have is a computational model which we validated against experiments … this is an ingredient that could potentially help [narrow down that search for] the rational design of vaccines and vaccine protocols,” McKay said.

“To what extent that is actually effective in practice, we don’t know. We would hope that it may be effective, but there’s a big gap, and an enormous amount of work that needs to be done.”