Defeating the Virus

Recent discoveries are spurring a renaissance in HIV vaccine research and development.

By | May 1, 2015


Measles is back. After declaring it eliminated in 2000, the United States is now dealing with an uptick in cases. The latest outbreak began in California’s Disneyland theme park last December and, by early April, had ballooned to 159 cases across 18 states, according to the US Centers for Disease Control and Prevention (CDC). This troubling situation serves as a stark reminder of the importance of immunization, which for many years had kept this once ubiquitous and sometimes deadly childhood disease in check. Developed in the late 1960s under the guidance of longtime Merck scientist Maurice Hilleman, the two-dose regimen of the combination vaccine against measles, mumps, and rubella (MMR) is estimated to be 97 percent effective at preventing measles in a vaccinated individual.

But developing vaccines against measles and other diseases was relatively straightforward when compared with the process scientists must use today to fight much more complex pathogens, such as HIV. Part of what makes HIV such a difficult virus to combat is its ability to furiously mutate the trimeric envelope protein on its outer surface. This high mutation rate gives rise to multiple HIV subtypes that circulate around the globe, allowing the virus to escape the responses that human immune systems mount against it. The approach that proved so successful for the MMR vaccine—using attenuated versions of the pathogens to immunize people—isn’t feasible for HIV because of concerns that the virus could mutate and regain its pathogenicity. And using a killed or inactivated virus—the other classic approach of vaccinology, used to develop vaccines against polio and influenza viruses, among others—doesn’t effectively address the unprecedented genetic variability of HIV.

Developing vaccines against measles and other diseases was relatively straightforward when compared with the process scientists must use today to develop vaccines against much more complex and diffi­cult pathogens, such as HIV.

There are other challenges unique to HIV. Quickly following transmission, the virus disseminates and establishes a persistent infection, including hidden reservoirs from which it can strike again at any time. (See “Hidden Menace.”) The opportunity for a vaccine-induced response to prevent infection or to control the initial, limited infection is thus short-lived. And while many people mount an effective immune response to and recover from most other viral infections, not a single person infected with HIV has cleared the virus on his or her own. The lone individual considered cured of HIV—Timothy Ray Brown, also known as the Berlin patient—only reached this milestone after receiving two bone marrow transplants to treat acute myeloid leukemia, which he’d developed after a decade of living with HIV and taking antiretroviral drugs. Doctors deliberately chose a stem cell donor with a genetic mutation that is known to confer resistance to HIV infection, in addition to a panoply of other chemotherapies and immune suppressive treatments to treat his acute myeloid leukemia. Attempts to repeat the success of this complex approach in other individuals with both cancer and HIV have so far been futile.

Scientists still don’t understand how to elicit specific, durable, and protective immune responses against HIV. Animal models, while informative, can only hint at what works. This means HIV vaccine researchers need to be as wily as the virus we are trying to combat. Progress during the past five years is spurring creative and promising new approaches. Armed with intriguing results from clinical trials and tremendous progress in isolating and understanding the evolution of broadly neutralizing antibodies against HIV, the field is now poised to elucidate the rules of immunogenicity and accelerate progress toward an effective vaccine.

Success cannot come too soon. Despite considerable advances in preventing new HIV infections and in delivering lifesaving treatment to those already infected, 2.1 million people worldwide contracted HIV in 2013, according to the Joint United Nations Programme on HIV/AIDS (UNAIDS). In the same year, some 1.6 million people died of HIV/AIDS or related complications. Altogether, since it was identified in 1983, HIV has infected 78 million people and killed half of them. An effective vaccine is a critical component to ending the morbidity and mortality caused by the disease.

Clues from trials

PUTTING VACCINES TO THE TEST: A recently launched clinical trial in South Africa investigates an HIV vaccine regimen based on the promising RV144 study, which showed a 31.2 percent reduction in HIV infection rates in volunteers receiving a prime/boost combination of two different vaccine candidates. The South African trial, called HVTN 100, has been adapted to the HIV subtype that predominates in the region.BROOKE AUCHINCLOSSThe HIV vaccine field has had its fair share of disappointing results from large, late-stage clinical trials. In 2007, vaccinations were stopped in the STEP and Phambili trials of a vaccine candidate that used replication-defective adenovirus serotype 5 (Ad5) to deliver HIV antigens designed to induce cellular immune responses against HIV. Then in 2013, vaccinations were terminated in the HVTN 505 trial, which tested a different Ad5 candidate in a prime/boost combination with a DNA-based vaccine. All three candidates failed to prevent HIV infection or blunt the disease’s course in those who became infected.

But in 2009, the field did get a first, albeit modest, clinical signal for feasibility of an HIV vaccine in humans, when scientists at the US Military HIV Research Program (MHRP) reported that a prime/boost combination of two different vaccines reduced the rate of HIV infection by 31.2 percent in more than 16,000 volunteers in Thailand.1,2 That trial, known as RV144, tested the canarypox virus–vectored vaccine candidate ALVAC-HIV, followed by a modified HIV gp120 protein subunit vaccine named AIDSVAX gp120 B/E, which had provided no protection in previous efficacy trials when administered on its own.

Researchers are working to determine the immune responses that led to this modest level of protection. Meanwhile, further insights may come from a new round of clinical efficacy trials for this prime/boost combination. Expected to begin in South Africa in late 2016, the new trials are designed to evaluate modifications to the vaccine candidates and regimen, including testing related HIV immunogens, different adjuvants, and new immunization schedules with additional booster shots intended to improve both strength and durability of immune responses.

Going broad

VACCINATING AGAINST HIV: The strategies that have been used to develop most of today’s successful vaccines—using attenuated, killed, or inactivated pathogens—don’t work for HIV, which boasts unprecedented genetic variability and a high mutation rate. Researchers are now testing a number of tactics in parallel to protect people against the wide range of HIV subtypes that continue to infect the human population.
See full infographic: JPG
Researchers widely agree that an ideal HIV vaccine would induce the production of so-called broadly neutralizing antibodies, which are capable of neutralizing a broad swath of HIV strains and are produced naturally by approximately 25 percent of chronically HIV-infected people. To accomplish this, researchers must first identify what immunogens can elicit such a response. Although this remains a challenge, some scientists are making significant progress by employing reverse-engineering or structure-assisted vaccine discovery. This new approach starts with isolating broadly neutralizing antibodies from chronically infected HIV patients whose immune systems produce them. Researchers can then identify an antibody’s target on the virus, use the molecular structure of this target site to design immunogens that mimic these sites, and immunize volunteers with these mimics to try to elicit the desired antibody response.

HIV vaccine researchers were buoyed recently by promising results from the use of this structure-based design strategy to produce a vaccine candidate against pediatric respiratory syncytial virus (RSV), which is the leading cause of hospitalization for children under five years of age worldwide. Peter Kwong and colleagues at the Vaccine Research Center (VRC) of the US National Institute of Allergy and Infectious Diseases first identified a site on an RSV envelope glycoprotein that extremely potent neutralizing antibodies target before the virus fuses with the host cell membrane. The researchers then identified and incorporated a series of mutations to stabilize the RSV protein in this conformation, engineered a version of the target site, and used it to immunize mice and rhesus macaques, eliciting high titers of neutralizing antibodies against RSV in both species.3 Similar results were also observed after vaccination with computationally derived RSV proteins.4

With these proof-of-principle studies demonstrating the effectiveness of this approach, coupled with recent advances in identifying HIV-specific broadly neutralizing antibodies, HIV vaccine researchers are now working to apply these principles to design and screen new vaccine candidates. In 2009, a consortium of research institutions reported the isolation of two potent broadly neutralizing antibodies from an HIV-infected donor who was part of a large cohort study led by the International AIDS Vaccine Initiative (IAVI), where I serve as chief scientific officer. These new antibodies neutralized HIV at 10- to 100-fold lower concentrations than the previously identified antibodies and were effective against a broader swath of viruses.5 This finding kicked off a flurry of new antibody discoveries, leading to the isolation of hundreds of HIV-specific broadly neutralizing antibodies, many targeting a relatively small number of specific sites on the virus. Characterization of these target sites has led to identification of the molecular structures of at least four highly conserved regions on HIV’s envelope protein that can now be used to design vaccine immunogens. (See illustration.)

This boon in antibody isolation and characterization represents a major advance for structure-based HIV vaccine design efforts. Encouragingly, these antibodies can protect monkeys from infection with a hybrid simian/human immunodeficiency virus (SHIV), suggesting that a vaccine capable of inducing them in humans may afford protection against HIV.

Another major advance toward developing an effective HIV vaccine came in 2013 when a team of researchers led by John Moore at Weill Cornell Medical College in New York City and Ian Wilson at the Scripps Research Institute in La Jolla, California, obtained an atomic-level image of the HIV envelope trimer, the principal target for broadly neutralizing antibodies.6,7 To capture this detailed image, the researchers first had to engineer a more stable form of this notoriously unstable protein, then use cryo-electron microscopy and X-ray crystallography to reveal its structure. A high-resolution structural model of the pre-fusion, closed form of HIV envelope by Kwong and colleagues at the VRC soon followed.8 The vaccine field had been stymied for years by failed efforts to stabilize HIV’s floppy surface protein. But with these detailed structures now in hand, a stable HIV envelope trimer that itself may be useful as a starting point from which to design an immunogen, and a suite of newly identified, conserved viral epitopes, scientists are entering a new phase of vaccine design.

No ordinary antibodies

At the same time that researchers are identifying potential vaccine immunogens to elicit broadly neutralizing antibodies, there is also a renewed focus on understanding how these potent antibody responses develop naturally in chronically HIV-infected individuals. Researchers are trying to determine how the virus or a vaccine immunogen can direct the immune system to make antibodies that recognize the highly conserved HIV epitopes. By tracking the arms race that occurs between virus and immune system in the course of natural infection, researchers have found that neutralizing antibody responses don’t appear until several months after HIV infection occurs, by which time the virus has mutated enough that these responses are unable to adequately control viremia. Antibody responses that can neutralize HIV more broadly—the type researchers seek to elicit with a vaccine—appear only after two or more years of chronic HIV infection.

Careful examination of the antibodies themselves also indicates these are no ordinary antibodies. Many have variable regions with unusually high levels of somatic hypermutation, the process by which B cells accrue genetic mutations that lead to an improved affinity for the pathogen. This high hypermutation suggests that B cells giving rise to these broadly neutralizing antibodies go through several rounds of mutation and selection in response to chronic exposure to HIV proteins, which could also be why they take so long to appear and then only in a subset of HIV-infected people.

In this context, developing a vaccine to elicit broadly neutralizing antibodies is a formidable task indeed. The vaccine will have to guide the immune system to do something it only sometimes accomplishes in natural infection, and do so in a fraction of the time. This will likely require some coaxing. One method, championed by Bart Haynes of Duke University, involves administering a series of HIV envelope immunogens in a set sequence to elicit antibody maturation that mimics the natural process observed in chronically infected individuals. This sequential immunization strategy is currently being tested in monkeys, and may soon advance to human trials.

Bill Schief and colleagues at IAVI’s Neutralizing Antibody Center at Scripps in La Jolla are testing another approach that involves starting with a computationally derived HIV immunogen that can bind multiple broadly neutralizing antibodies and their precursors.9 This immunogen is presented on nanoparticles that can be used as a priming vaccination to kick off the process of somatic hypermutation. Eliciting fully matured, neutralizing antibodies, however, will likely require additional boosting with different immunogens along the way that are more representative of native HIV epitopes.

This is uncharted territory, and ideally the best of these designer immunogens will be tested in a series of human trials to better define the rules of immunogenicity and to develop a vaccine that most effectively exploits those rules.

Bypassing the immune system

In the absence of immunogens capable of eliciting neutralizing antibodies against HIV, researchers are also exploring whether direct injection of HIV-neutralizing antibodies may be an efficient means of preventing HIV infection. This so-called passive immunization approach is now in Phase 1 clinical trials involving both HIV-positive patients and uninfected volunteers to determine the safety and pharmacokinetics of these vaccines. Early data from monkey studies suggest that such direct injection of broadly neutralizing antibodies may also have therapeutic benefits or even be part of a multifaceted HIV cure strategy.10

Antibody responses that can neutralize HIV more broadly—the type researchers seek to elicit with a vaccine—appear only after two or more years of chronic HIV infection.

Meanwhile, work is underway to optimize the antibodies used for such passive immunization by introducing mutations that increase their potency and/or half-life and by improving the function of the antibody’s Fc portion, which can interact with monocytes and natural killer cells to lyse virus-infected cells. There are also plans to study a cocktail of antibodies in passive immunization studies to increase the breadth of activity against HIV.

Yet another approach to circumvent the immune system’s role in making broadly neutralizing antibodies is to use an adeno-associated-virus (AAV) vector to deliver the genes encoding such antibodies into cells, which could then express the antibodies. Philip Johnson of the Children’s Hospital of Philadelphia pioneered this approach and now, in collaboration with IAVI, is testing an AAV1 vector carrying the genes for the broadly neutralizing HIV antibody PG9 in an ongoing Phase 1 trial. If it is successful, a cocktail of vectors carrying two or more broadly neutralizing antibodies will be tested. Similarly, David Baltimore of Caltech is using another AAV vector (AAV8) to deliver a broadly neutralizing HIV antibody targeting the virus’s CD4 binding site, an approach that was effective in protecting humanized mice from mucosal HIV transmission.11

In addition to expressing the genes for broadly neutralizing antibodies, AAV vectors may also be engineered to express synthetic proteins that prevent the virus’s entry into host cells. Michael Farzan of Scripps in Florida and colleagues recently demonstrated the success of this approach in preventing SHIV infection in rhesus macaques.12 Collectively, these efforts are paving the way for a nontraditional immunoprophylaxis that can protect against HIV infection without depending on the lengthy and complex antibody maturation process required to generate broadly neutralizing antibodies through immunization.

Cellular immunity

In parallel with studies focused on eliciting broadly neutralizing antibodies, scientists continue to pursue strategies to elicit cell-mediated immune responses against HIV. Induction of CD4+ T cells can boost the potency and durability of broadly neutralizing antibodies and also help activate robust cytotoxic CD8+ T cells aimed at controlling HIV infection. But, as with effective antibodies, such cellular immune strategies face the challenge of high levels of genetic diversity among circulating HIV subtypes.

Bette Korber and colleagues at Los Alamos National Laboratory are designing so-called mosaic antigens to overcome HIV diversity. These are computationally derived proteins created by stitching together genetic sequences from across the entire HIV genome. (See illustration.) These mosaic antigens, when delivered via viral vectors either alone or in combination with each other or a protein booster component, can provide greater breadth of cellular immune responses against HIV variants and protect against SHIV infection in monkeys.13 Researchers recently initiated Phase 1 trials of this approach.

An alternative tactic for tackling the variability of HIV is to focus on eliciting cellular immune responses to the most conserved regions of the HIV proteome, an approach championed by Andrew McMichael and Tomas Hanke of Oxford University. Most recently, mosaic antigens that are focused solely on these conserved regions of HIV were designed to optimize coverage of such immunogens across HIV’s global diversity. These conserved mosaic antigens are undergoing preclinical testing.

Lastly, researchers are harnessing the unique qualities of cytomegalovirus (CMV) that evoke robust and broad cellular immune responses by using this virus as a vector for HIV vaccine development. In monkey studies spearheaded by Louis Picker of Oregon Health & Science University, administration of the rhesus form of cytomegalovirus (RhCMV) expressing proteins from simian immunodeficiency virus (SIV), the monkey equivalent of HIV, led to durable control of SIV infection following challenge, including evidence of complete clearance of pathogenic SIV infection in some animals.14 The precise mechanism for this protection remains unknown, but effector memory T-cell responses appear to play a role. Picker and colleagues are now developing a prototype CMV vector to assess safety and immunogenicity in humans. This approach should advance to clinical testing by 2016.

Beyond HIV

© MISHAL/SHUTTERSTOCKAlthough many challenges remain, the development and deployment of a safe and effective HIV vaccine is an urgent global health priority. Recent progress is reinvigorating vaccine discovery efforts, and research to better understand HIV and the immune response against it will help to inform broader vaccine efforts. Already, researchers have identified broad and potent neutralizing antibodies against influenza, dengue, hepatitis C, and other complex pathogens. And investigators are applying structure-based vaccine discovery to a wide spectrum of infectious diseases for which vaccines are still needed.

Similarly, new technologies of genetic and immune monitoring and of systems biology, coupled with novel strategies for induction of cellular immune responses, are being applied for development of prophylactic and therapeutic vaccines against infectious diseases and cancers. The prospect of decoding the immune system and unravelling the rules of immunogenicity in humans now offers the potential to usher in a golden age of vaccinology that will relegate HIV and other modern global killers to the same fate as the childhood diseases of the 1950s that are now easily prevented through vaccination. 

Wayne C. Koff is the chief scientific officer at the International AIDS Vaccine Initiative (IAVI).


  1. S. Rerks-Ngarm et al., “Vaccination with ALVAC and AIDSVAX to prevent HIV-1 infection in Thailand,” N Engl J Med, 361:2209-20, 2009.
  2. M.L. Robb et al., “Risk behaviour and time as covariates for efficacy of the HIV vaccine regimen ALVAC-HIV (vCP1521) and AIDSVAX B/E: a post-hoc analysis of the Thai phase 3 efficacy trial RV 144,” Lancet Infect Dis, 12:531-37, 2012.
  3. J.S. McLellan et al., “Structure-based design of a fusion glycoprotein vaccine for respiratory syncytial virus,” Science, 342:592-98, 2013.
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  5. L.M. Walker et al., “Broad and potent neutralizing antibodies from an African donor reveal a new HIV-1 vaccine target,” Science, 326:285-89, 2009.
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  8. M. Pancera et al., “Structure and immune recognition of trimeric pre-fusion HIV-1 Env,” Nature, 514:455-61, 2014.
  9. J. Jardine et al., “Rational HIV immunogen design to target specific germline B cell receptors,” Science, 340:711-16, 2013.
  10. D.H. Barouch et al., “Therapeutic efficacy of potent neutralizing HIV-1-specific monoclonal antibodies in SHIV-infected rhesus monkeys,” Nature, 503:224-28, 2013.
  11. A.B. Balazs et al., “Vectored immunoprophylaxis protects humanized mice from mucosal HIV transmission,” Nat Med, 20:296-300, 2014.
  12. M.R. Gardner et al., “AAV-expressed eCD4-Ig provides durable protection from multiple SHIV challenges,” Nature, 519:87-91, 2015.
  13. D.H. Barouch et al., “Protective efficacy of a global HIV-1 mosaic vaccine against heterologous SHIV challenges in rhesus monkeys,” Cell, 155:531-39, 2013.
  14. S.G. Hansen et al., “Immune clearance of highly pathogenic SIV infection,” Nature, 502:100-04, 2013.

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