Understanding How Researchers are Tackling HIV's Genetic Variability

What new startegies are scientists developing to design broadly effective vaccines against HIV?

By Regina McEnery and Unmesh Kher

HIV’s remarkable genetic diversity has long hampered vaccine development. It stems from HIV’s virtually unrivaled mutability and the explosive replication of the virus after it invades its target cells. In a single HIV-infected individual, between one billion and 10 billion HIV particles are produced every day. Since the virus is remarkably sloppy in reproducing its genetic material, almost every one of those particles bears some kind of genetic mutation (see VAXAug. 2008 Primer on Understanding the Genetic Variation of HIV). Only the tiniest fraction of these mutants can be transmitted, yet enough get through to generate quite a menagerie of circulating viruses.

Though just a single group of the human immunodeficiency virus, known as HIV-1, accounts for most infections worldwide, that group is divided into nine different subtypes, or clades. Some of those clades have swapped genes to form major hybrid subtypes, and several genetic variants exist within each subtype as well (see VAX July 2006 Primeron Understanding HIV Clades). 

Not all of HIV’s nine genes mutate at the same pace. The genetic sequence of the envelope gene (env), which encodes the toadstool-shaped Envelope glycoprotein that the virus uses to latch onto its target cells, varies by as much as 35% between globally circulating clades of HIV. Others, such as the gag gene that encodes proteins that build the internal core of the virus, are relatively more conserved, varying by less than 10% from one clade to another.

That diversity poses a serious challenge to the immune system, which depends on the consistent recognition of telltale protein sequences and structures to detect invading pathogens. Since vaccines work by essentially “showing” the immune system these molecular markers—or antigens—HIV’s variability has proved to be quite a headache for vaccine designers as well. This partly explains why, despite nearly three decades of effort, researchers have only made one vaccine candidate capable of blocking HIV infection. And that candidate—tested in the RV144 Phase IIb trial in Thailand—provided only modest protection (31%). 

But AIDS researchers have also sought for many years to develop strategies to cut through HIV’s variability. One such approach harnesses computer software to design “mosaic antigens” that might provoke broadly effective responses against HIV. Such antigens are made from genetic sequences encoding pieces of a chosen protein—or peptides—just long enough to be recognized by T cells of the immune system. The partial gene sequences encoding those peptides are selected through the application of two criteria. First, a computer compares the peptide sequences between multiple HIV variants and generates a composite DNA sequence that best represents the fragment across the sampled sequences. The sequences are further optimized to reflect those peptides that have been shown to elicit vigorous cellular immune responses against HIV. Then they are stitched together to build a gene encoding a full-length protein that is used as an antigen in an HIV vaccine candidate.  

Another approach simply samples the entire HIV genome for sequences that are conserved across variants and clades, and stitches them together—making not a gene encoding a whole protein, but one that encodes a string of antigenic peptides from various HIV proteins. Both of these types of antigens primarily engage the cell-mediated response of the immune system, activating killer T cells, which destroy cells already infected with HIV. But scientists are also trying to design antigens that might stimulate neutralizing antibody responses, which can prevent HIV from invading those cells in the first place. 

No AIDS vaccine candidate has yet succeeded in inducing broadly neutralizing antibodies (bNAbs), which can cripple the majority of circulating HIV strains. But researchers have in recent years isolated a large number of bNAbs from the blood of HIV-infected individuals, and are now studying them closely for clues to the design of vaccines. All efforts to that end focus on the Env protein, simply because it is the only molecule on the surface of HIV that is available to antibodies (see VAX Mar. 2011 Primer on Understanding HIV’s Envelope Protein).

The Env protein is built from three sets of two proteins. The smaller of the two, gp41, traverses the membrane that encloses the virus. The other, gp120, juts out of the virus and binds to the CD4 molecule on T cells to begin the process of invasion. The protein has five highly variable loops that work like decoys, eliciting a largely ineffectual antibody response, but certain sequences in these regions are in fact prime targets for bNAbs. Further, some parts of the envelope are resistant to mutation because drastic changes in those areas would cripple the virus. Among these is the CD4 binding site. Researchers have also found a set of bNAbs that bind to this vulnerable site, and others that bind other functionally vital parts of the spike. 

Researchers are using various strategies to harness these and other bNAbs to devise antigens for AIDS vaccines—from modifying Env proteins to expose sites that might be bound by neutralizing antibodies and testing such engineered molecules as potential antigens to manipulating yeast cells to make molecules that mimic known bNAb targets. One particularly exhaustive approach involves determining what precise atomic arrangements on the envelope are contacted by a binding bNAb, and then using computational and gene engineering methods to stably reproduce those molecular structures for use as antigens (see VAX Sep. 2012 Spotlight article, Brave New World). 

It is currently unclear which, if any, of the above strategies will yield broadly effective vaccines against HIV. But it is likely that future vaccines will have to rely on eliciting some combination of the cell-mediated and antibody responses to effectively cut through HIV’s extraordinary diversity.