Troublesome Threesome for Vaccine Development

The need for new vaccines for HIV, Tuberculosis (TB) and malaria are all greater after the pandemic, but will vaccine advances for SARS-CoV-2 help?

SARS-CoV-2 has been relatively easy to vaccinate against. In June 2020, the US Food and Drug Administration (FDA) set out an initial target of 50% efficacy for vaccines to prevent COVID-19. This figure was blown out of the water by December 2020, when both the Moderna and Pfizer–BioNTech vaccines reported more than 90% effectiveness.

Not all pathogens are so straightforward. “SARS-CoV-2 was amazingly easy to control with a vaccine,” says Wolfgang Leitner, who heads up the innate immune section at the National Institutes of Health. He acknowledges that three tough diseases remain a challenge for vaccine development: HIV, TB and malaria. Unfortunately, the impact of COVID-19 on the fight against HIV, TB and malaria has been devastating, according to a recent global health report. Deaths from these diseases had dropped by almost half since 2004, but the pandemic has caused resources to be shifted away from these killers. It estimated, for example, that one million fewer people with TB were treated in 2020 compared with 2019.

Malaria                      

Vaccinologist Adrian Hill from the Jenner Institute in Oxford estimates that over 40 vaccine candidates have gone into human arms that targeted the malaria parasite as it travels from mosquito to liver (the sporozoite). “There’s been no lack of effort,” says Hill.

Usually, a few dozen Plasmodium parasites multiply in liver cells, generating thousands of parasites that break out, infect red blood cells and cause malaria symptoms. The liver-stage parasite has been a target of vaccines for 50 years, and there have been renewed efforts, described in Nature, this summer. There have been many other approaches too.

The first to show any efficacy against malaria is the RTS,S vaccine. After 30 years in development, children in Ghana, Kenya and Malawi began receiving this vaccine as part of a Phase IV rollout in 2019. Earlier this year, the World Health Organization said that this had already benefited 650,000 children. Made by GlaxoSmithKline (GSK), it relies on a fragment of protein from the surface of the sporozoite (the circumsporozoite protein) latched onto a hepatitis B protein, together with an adjuvant from GSK called ASO1. It has been termed a suboptimal vaccine, and has an efficacy of around 30%. As the world’s first malaria vaccine, it is a significant milestone, nonetheless.

Targeting the sporozoite is challenging, because huge titers of antibodies are necessary to prevent all mosquito-injected parasites from reaching the liver. The powerful ASO1 adjuvant, which seems especially good at inducing CD4 helper T cells, encourages a strong antibody response to RTS,S.  But if one parasite reaches the liver, blood stage infection can occur, causing illness and potentially death.

A new hope shines in the form of the R21 vaccine from Hill’s lab in Oxford. This contains the same surface protein as RTS,S, but in greater quantities relative to the Hep B antigen than RTS,S – which, says Hill, competed against a good immune response to the parasite protein. This summer, the R21 vaccine candidate achieved 77% efficacy over 12 months of follow-up in a Phase II trial of children in Burkina Faso. This was with a high dose of Matrix-M adjuvant, now owned by Novavax and used in its COVID-19 vaccine candidate. Adjuvants are added to vaccines to encourage a stronger immune response. For many decades, alum (aluminium salts) was the only adjuvant in approved vaccines, but this situation has shifted, dramatically. "Adjuvants have really taken off in the last 10 to 15 years," virologist John Tregoning at Imperial College London said.

Hill’s lab chose this Matrix-M on the back of a comparison back in 2009 of around a dozen different adjuvants in combination with R21. “Comparing our R21 with ASO1 from GSK and Matrix-M showed they were very, very similar,” he says. There are supply concerns with ASO1, since it comprises three main ingredients, one of which is a saponin (QS-21) from the bark of a South American tree. A single gram of QS-21 costs more than $100,000 and is also used in the Novavax vaccine candidate. ASO1 is used in the Shingrix vaccine, the only way to protect against shingles and a vaccine that generated almost £2 billion in 2020 for GSK. “That adjuvant is in limited supply globally,” says Hill. Matrix-M (used with Hill’s R21) also uses this ingredient, “but you need 20 times more saponin in ASO1 compared to Matrix-M,” according to Hill. The Serum Institute of India has agreed to fund a Phase III trial of this vaccine – already underway in Africa, with data expected in 2021 – that promises to manufacture 200 to 300 million doses, says Hill. That’s important, considering there were 229 million cases of malaria in 2019, with 409,000 deaths (274,000 of them children).

“The reason why RTS,S and our R21 work better than any of the other 40 vaccines that have been in the clinic is because of much higher antibody levels,” Hill explains. One key ingredient here is the adjuvants. Multiple jabs will likely be needed, because the high antibody titers to the parasite decline rapidly over the first three years. Higher antibody levels means better protection.

Tuberculosis

The number one infectious disease, outside a pandemic, is TB. Yet the only licensed vaccine for this bacterial disease is BCG, which celebrated its 100^th anniversary this summer. This vaccine originated from Mycobacterium bovis, a bacterium from cows and a cousin of Mycobacterium tuberculosis. BCG protects young children against TB, but it is far less effective at protecting adults from the lung infection. An estimated two billion people are infected latently with this bacterium, which can awaken and cause disease, often when someone becomes immune suppressed.

“There hasn’t been a breakthrough in the TB field, but not for a lack of trying,” says Leitner. One notable failure was a IIb viral vector vaccine in infants that had showed promise in animal studies. Presently, the Tuberculosis Vaccine Initiative website shows a pipeline of vaccine candidates: three in Phase I, four in Phase IIa, four in IIb and two in Phase III trials. That's 13 in total. This includes a range of vaccine strategies, from inactivated vaccines to protein subunit to viral vectors to weakened live mycobacterium. M. tuberculosis hides away in lung tissue and is well adapted in manipulating our immune response. Also, it is not clear which protein should be chosen as an antigen for a TB vaccine. There are lots to choose from; SARS-CoV-2 has just over two dozen proteins that are potential options, notes Leitner, whereas malaria has 5,000 and M. tuberculosis 10,000.

Immunologists are uncertain, even now, what a successful vaccine-induced immune response to TB should look like. This partly explains the diversity of vaccine candidates for TB. “The dogma in the field was that it is all about CD4 T cells that make interferon gamma, and that if you could induce those cells, you were in good shape [for a TB vaccine],” says Leitner. But the tuberculosis bacterium is a complicated organism, well adapted to humans, "and it is not going to let one parameter decide its faith,” says Leitner. “We need to look at this in a more holistic way.” Increasingly, many TB researchers believe that antibodies may be important, as well as tissue-resident (lung) CD8 T cells, which can kill infected cells. The National Institute of Allergy and Infectious Diseases (NIAID) at the NIH launched a program in 2019 to better understand the immune response needed to protect against infection with M. tuberculosis.

There have been some more hopeful surprises with TB. A protein subunit vaccine achieved an efficacy in adults of almost 50% after three years in a study involving over 3500 participants. The vaccine consisted of a recombinant fusion protein made up of two antigens (M72), along with the ASO1 adjuvant. The results surprised many. “This was a level of protection that had not been seen with a subunit vaccine before [for TB],” says Leitner. “It challenged the dogma that it had to be something extremely complex.” The adjuvant – ASO1 – is seen as playing a role here too. Adjuvanted protein subunit vaccines hold the highest benefit of safety, notes Rasmus Mortenson, vaccine researcher at the Statens Serum Institut in Copenhagen, “Which is of particular importance given the high occurrence of TB in HIV-prevalent settings.” He notes that adjuvants that induce novel immune signatures, such as for CD8 T cells are "missing and therefore a priority", but this might change due to “knowledge gained from the development of SARS-CoV-2 vaccines”.

HIV

HIV is consistently viewed as one of the hardest human pathogens to develop a vaccine against. There are many reasons why HIV vaccines have remained out of reach. “The virus is highly evolved to avoid immune responses, and it is extremely variable, so that means you’ve got hundreds of thousands of strains of HIV,” says Dennis Burton, immunologist and HIV researcher at the Scripps Research Institute in La Jolla, California.

In the 1990s, it was recognized that some HIV patients do develop broadly neutralizing antibodies that target the envelope protein of the virus. These antibodies can be effective against different strains. “But [broadly neutralizing antibodies] often have unusual properties and they are not easy to induce or elicit through vaccination,” says Burton. There were some positive results earlier this year from a Phase I clinical trial for this approach.

Another challenge is that the virus can go latent, and so evade notice. Any vaccine relying on a strong antibody response must stop almost every single virus particle from hiding away in cells. “There is no margin of error. If they virus gets through, it can sit there and wait, and then explode out,” says Burton. “In order to provide this immunity to stop every virus particle, you need lots of antibodies and you need to keep levels up.”

The challenge was underlined recently, when the NIH revealed that a Phase IIb study, which enrolled 2,637 women in five countries starting in November 20017, failed to show sufficient protection against HIV infection. “The development of a safe and effective vaccine to prevent HIV infection has proven to be a formidable scientific challenge,” said NIAID Director Anthony S. Fauci in an institute statement. The vaccine relied on the adenovirus vector used in the Johnson & Johnson COVID-19 vaccine to carry four “mosaic antigens” to provoke an immune response. Burton was not surprised by the disappointing results. He says that developing a vaccine for HIV is an order of magnitude more difficult than anything else, including TB and malaria.

Newer vaccines

RNA vaccines work differently to protein subunit vaccines, which show the body a recombinant protein from the target pathogen. The RNA comes packaged in virus-like nanoparticles and is internalized inside immune cells. In the case of COVID-19 vaccines, the RNA contains the recipe for the spike protein of SARS-CoV-2. This gets translated inside the human cell – similar to what happens during natural infection – and then displayed outside the cell to tutor the immune system. Similarly, viral-vector vaccines for COVID-19 such as Johnson & Johnson’s (based on adenovirus subtype 26) and Oxford – AstraZeneca’s (based on a chimp adenovirus) carry instructions to make spike inside of cells. None of these COVID-19 vaccines require an adjuvant – they stimulate the immune system enough (often described as self-adjuvanted) – which is somewhat ironic, considering new adjuvants are finally becoming available.

Nonetheless, both new vaccine platforms can assist in vaccine development for the malarial parasite and TB. BioNTech announced plans to develop an mRNA vaccine candidate against malaria, with a clinical trial to begin by the end of 2022. The company said its collaboration with the Bill and Melinda Gates Foundation on a TB vaccine should deliver a vaccine candidate ready for clinical trials in the same year. It is also working on a HIV vaccine, in  collaboration with the Gates Foundation that preceded the pandemic. In August, BioNTech announced that it was looking to Rwanda and Senegal for malaria and TB vaccine production facilities. Meanwhile, Moderna plans to start a vaccine safety trial with its mRNA HIV candidate this year, which will mark the first trial to test an mRNA-based vaccine for HIV in humans.

It is not a given that the mRNA vaccines will work for these difficult pathogens. “People are now rushing into RNA vaccines for TB,” says Leitner. “I would be shocked if you got anywhere close to the efficacy that we are seeing with SARS-CoV-2.” His view is that there will be room for improvement, and novel adjuvants might be worth trying. Not everyone will agree.

The mRNA vaccine companies likely prefer their self-adjuvanted approach.

There is a pressing need for effective vaccines for TB, malaria and most especially HIV. Leitner has been promoting systematic side-by-side comparisons of adjuvants from smaller companies – which develop novel adjuvants only – with vaccines to see which pairings work best. Applications for a TB vaccine/adjuvant comparison initiative at the NIAID just closed. A second program that seeks to “fingerprint” the immune response to adjuvants remains open for applications until October 1, 2021.

Leitner, who leads these programs, remains optimistic that adjuvants can play a role in newer vaccine platforms, for difficult diseases. “The big discussion now is about adjuvants for RNA vaccines,” he adds. “The vast majority of adjuvants out there have never been tested with nucleic acids. It is a huge blank spot on the map.”