BioWorld International Correspondent

LONDON - Researchers in Australia have developed a computer program to help scientists work out which parts of the human immunodeficiency virus should be included in a vaccine against HIV. Their studies, which were carried out on a population level, show that HIV is able to mutate to evade surveillance by the immune system, and that the immune response of some patients is easier to escape than that of others.

The Australian group, led by Simon Mallal, executive director of the Centre for Clinical Immunology and Biomedical Statistics at the Royal Perth Hospital in Perth, Western Australia, set up a company, called Epipop, to distribute the computer program, which also is called Epipop.

Mallal, together with colleagues at the Royal Perth Hospital and at the University of Western Australia, also in Perth, reports his findings in a paper in the May 24, 2002, issue of Science titled "Evidence of HIV-1 Adaptation to HLA-Restricted Immune Responses at a Population Level."

Mallal told BioWorld International: "What is very exciting about this piece of work is that it provides a completely novel way of identifying the interaction between patients' immune responses and the infection. It also has broad applicability, and will be useful for studying many infections other than HIV, including, for example, hepatitis."

He is setting up an international collaboration to allow participants to pool their data and run the Epipop program on them.

The information gained, he said, will facilitate the design of vaccines to protect against HIV because it indicates which HIV peptides (epitopes) stimulate the strongest cell-mediated protective immune response against the virus after infection. Those same epitopes should afford the strongest protection if given in a vaccine before exposure to the virus.

Cytotoxic T lymphocytes (CTLs) are capable of seeking out and destroying HIV-infected cells. The CTLs can, however, only kill an infected cell if they encounter an appropriate epitope while it is held in the groove of a Class I HLA molecule on the surface of the infected cell.

"If the virus mutates its genetic material so that this peptide no longer binds to the Class I HLA molecule, then the virus can go on replicating in that cell, and HIV-specific CTLs will fail to recognize the cell as infected with HIV," Mallal said. "A virus that can do this has selective advantages, and the mutant virus soon takes over as the dominant strain in the patient."

Mallal and his colleagues knew that scientists had observed such a phenomenon occurring in individual patients infected with HIV. They decided to investigate whether the correlation held true on the population level. They already had a cohort of patients with HIV who had been studied in detail.

"We had sequencing information on the gene encoding the reverse transcriptase enzyme of HIV, HLA typing information, and 2,200 patient-years of follow-up of viral drug resistance testing," Mallal said.

The team found that the sequence of the gene for reverse transcriptase was different in each of 473 patients. Nevertheless, the mutations did not occur at random. Using the Epipop program, Mallal and his colleagues examined which factor best predicted whether the reverse transcriptase in a patient had a "conventional" amino acid at a particular location, or whether the gene encoding it had mutated.

"We found that there was a strong association between particular HLA types and mutations in a particular position," Mallal said. So, for example, a patient with HLA-B51 typically had a mutation, leading to a change of amino acid, at position 135 of the reverse transcriptase gene.

"This is very reminiscent of the way the virus mutates to become resistant to the effects of an antiviral drug. All the drugs are known to induce characteristic resistance mutations," Mallal said. "Once we had done our analysis, we could tell from the patient's HLA type where to look for the mutations, and we found that if the virus had more mutations at these sites, the viral load of the person was likely to be higher."

That observation makes it possible to explain, at least in part, Mallal said, why patients vary in their viral loads even before they start treatment. "It is largely dependent on the degree to which their virus has managed to escape from their own HLA-restricted immune response," he said.

Commenting on the paper in a "News and Views" article in the same issue of Science, Andrew McMichael of the Weatherall Institute of Molecular Medicine in Oxford, UK, and Paul Klenerman of the Medawar Centre for Pathogen Research, also in Oxford, said that it confirms that HIV is an "astounding escape artist." In their article, titled "HLA leaves its footprints on HIV," they wrote that the finding is "worrying news" for vaccine development.

Mallal explained: "The traditional approach is to try to include conserved epitopes - stretches of viral proteins that are eight to 12 amino acids long, that are invariably present in all HIV variants. However, our studies indicate that the virus and its ancestors have evolved under intense selective pressure from HLA-restricted immune responses and therefore tend not to have conserved epitopes recognized by common HLA types."

McMichael and Klenerman conclude: "HIV vaccines will have to match the relevant circulating virus, but must also elicit very broad responses to multiple epitopes in order to stay one step ahead of HIV variation."

Mallal pointed out that a paper published in November in Immunology Letters reported a similar finding following work with simian immunodeficiency virus (SIV). That group, led by David O'Connor of Wisconsin Regional Primate Research Center at the University of Wisconsin at Madison, speculated that the detection of SIV variants that had mutations in epitopes important to recognition by CTLs implied that cells infected with wild-type virus could be successfully cleared by the immune system.

They concluded: "Rather than engendering responses to regions of the virus that do not escape, we reason that vaccination needs to accelerate the development of the initial immune responses that effectively select for amino acid variants during acute infection."

Mallal told BioWorld International: "Our population-based approach efficiently defines these epitopes."