Intranasal vaccines aim to stop COVID-19 where it starts

“Most people don’t like to watch,” the pharmacist told me as I stared at the thin needle piercing my arm. After more than a year of lockdowns and disrupted economies and millions of lost lives, this shot felt like salvation—a moment that countless future moments all hinged upon—and I wanted to see it happen. It predictably stung, and my arm hurt for days: a small price to pay for the power of immunity.

That shot tricked my body into thinking that the virus had breached its defenses, and I felt completely wiped out the next day. Within weeks, my immune cells were pumping antibodies into my blood, where they would circulate and seep out into my airways and give me a strong chance of warding off any SARS-CoV-2 that I breathed in once I lowered my mask.

The vaccine was granting me systemic immunity, tapping into the branch of the immune system that is on constant patrol throughout the body. It’s the type of protection offered by nearly all our common vaccines—an approach so ingrained in modern medicine that the very word vaccine conjures an image of a hypodermic needle. But getting shots isn’t the only way to develop immunity. And considering how most pathogens, including coronaviruses, get into our bodies, shots might not even be the best way.

SARS-CoV-2 often enters through our noses, where it encounters a protein called ACE2, which is found in abundance in our nasal passages. ACE2 is the virus’s doorway into our cells. In fact, the mucosal membranes that line our airways, digestive systems, and reproductive tracts are often the first parts of our bodies to face an invading pathogen. A network of immune cells resides underneath our mucous membranes, or mucosae, and forms a front line of defense against invaders, and they prevent most infections from taking root. This is the mucosal immune system, and some immunologists think we have been seriously underestimating it.

“When you think about it, that’s where we acquire most of our infections: we inhale them, we consume them, or we get them through sex,” says Michael W. Russell, a mucosal immunologist and professor emeritus at the University at Buffalo.

Our mucosal immune cells make a special class of antibodies that are constantly secreted from the mucous membranes to protect the nose, gut, and other vulnerable sites from pathogens we’ve seen in the past. “But if you don’t stimulate the immune system in the mucosae, you don’t obtain mucosal immune responses,” says Pierre Charneau, head of the Molecular Virology and Vaccinology Unit at the Pasteur Institute.

Yet most research on SARS-CoV-2 and our immune systems has overlooked mucosal immunity in favor of the easier-to-study systemic immunity. “When the pandemic hit last year and I started to see papers coming out about immunity, it really quite staggered me to see an absence of attention to the mucosal immune response,” Russell says.

Charneau and a group of scientists in Paris have shown that natural SARS-CoV-2 infections trigger both systemic and mucosal immunity. But our current crop of COVID-19 vaccines offer only systemic protection. Developing vaccines that are sprayed up the nose, rather than injected into the arm, could change that, Charneau says. Mucosal immunity in our noses could be like a guard at the door, potentially helping stop even small infections of SARS-CoV-2 right where they start.

It’s a tantalizing notion, but whether it’s a viable one is up for debate.

Intranasal vaccines have historically garnered little interest and investment in the vaccine industry—a situation some hope that COVID-19 could change. Although the COVID-19 vaccines authorized in the US and Europe are incredibly effective, we don’t have enough of them to vaccinate the whole world. Intranasal vaccines, which might be easier to use and distribute than needle-based vaccines, could help close the gap. They could also make for useful booster shots against emerging variants of the virus. And if they work for COVID-19, some immunologists hope that they could kick off a new wave of investment in intranasal vaccines for other diseases.

After all, the pandemic provided a chance for messenger RNA (mRNA) vaccine technology to finally prove its worth, and mucosal immunologists are hoping that this will be a moment for intranasal vaccines to do the same. “This climate is a game changer,” says Hiroshi Kiyono, codirector of the University of California San Diego Center for Mucosal Immunology, Allergy, and Vaccines. “This is a great opportunity to advance nasal vaccines, not just for COVID-19 but for other respiratory diseases.”

Woes in the nose

The bias toward needle-based vaccines goes all the way back to Louis Pasteur’s 1880s-era experiments immunizing chickens and sheep with injections of weakened cholera and anthrax. The proclivity for the needle has continued ever since, although a few exceptions prove there are other ways to trigger immunity. Vaccines for cholera, polio, rotavirus disease, and typhoid are now available orally, as a pill or liquid, and they stimulate mucosal immunity in the gut, where these pathogens normally infect us.

Progress has been slower with intranasal vaccines, with only one approved in the US: AstraZeneca’s seasonal influenza vaccine, FluMist.

FluMist was first approved for people aged 5 to 49 in the US in 2003. Despite a large marketing campaign, the vaccine was a commercial flop, partly because it was more expensive than traditional flu shots and partly because it wasn’t approved for people 50 and older. Although sales eventually increased over the next decade, it is no longer widely used in the US. People who believe that intranasal vaccines are undervalued point to FluMist as an example that mucosal immunity in the nose is protective. Yet those who are skeptical about the benefits of intranasal vaccines point to FluMist’s commercial struggles as evidence that nasal sprays are simply not as potent as a good old-fashioned shot. The reality is more complicated.

While traditional flu vaccines tend to use inactivated or killed flu viruses, FluMist uses four strains of live attenuated flu virus—ones that have been weakened by being grown in cold temperatures. “The live part is key,” says Ravi Jhaveri, a professor of pediatrics at Northwestern University Feinberg School of Medicine and a physician specializing in infectious disease. “It needs to replicate in your nose to generate the kind of immunity that will protect you.” The tiny infection caused by FluMist can induce both a mucosal and systemic antibody response. But as with all flu vaccines, FluMist’s effectiveness waxes and wanes from year to year.

Troubles for FluMist began in the 2013–14 flu season, when researchers noticed that kids who got the nasal spray were left unprotected against the predominant H1N1 flu strain in circulation that year. Two years later, FluMist again stood out for its poor protection against H1N1 infections. Researchers discovered that one of the virus strains included in the vaccine didn’t replicate well in the lab—and presumably also didn’t replicate well in the nose. AstraZeneca eventually fixed the problem, but the US Centers for Disease Control and Prevention (CDC) stopped recommending the vaccine in the 2016–17 flu season, and FluMist’s reputation was damaged among doctors in the US. The CDC eventually reversed course, but FluMist never regained steam.

Despite all this, intranasal vaccine developers say FluMist set an important precedent. “It really demonstrated that mucosal immunity could protect people,” says Scot Roberts, chief scientific officer of the intranasal vaccine company Altimmune. In fact, FluMist often worked better than traditional shots in young kids, although the reverse was often true in adults. There’s also evidence that FluMist provided better protection than the injected flu vaccines in years when none of the flu vaccines were well matched to the circulating strains, a trait that some immunologists attribute to mucosal antibodies’ ability to more easily cross-react with multiple strains of a virus.

But it’s been hard to tease apart which of the advantages and disadvantages of FluMist are due to its being a nasal spray and which are due to its use of live viruses rather than dead ones. People that previously had the flu might have antibodies that block the viruses in FluMist—and if the viruses never replicate in the nose, they can’t boost immunity. “That is a difficulty with live attenuated virus vaccines delivered intranasally. If the host neutralizes them, they don’t work well,” says Herman Ford Staats, who studies adjuvants for intranasal vaccines at Duke University School of Medicine.

FluMist’s clinical woes and struggling sales have likely made it hard for other intranasal vaccine programs to gain traction. Staats notes that there is another episode that’s made pharma companies wary about spraying vaccines up the nose. An intranasal flu vaccine made by Berna Biotech and approved in Switzerland in 1997 was linked to rare cases of Bell’s palsy—a usually temporary facial paralysis—after it was commercialized.

The vaccine contained a small amount of bacterial enterotoxin as an adjuvant for boosting the mucosal immune response. Although it initially appeared safe in the studies that led to the vaccine’s approval, a closer examination of mice that got the vaccine revealed a potential problem. The toxin and the virus particles from the vaccine were accumulating in the olfactory bulb, which connects the smell receptors of the nose to the brain. “People began to become very concerned that nasal immunization with adjuvants might lead to some type of an inflammatory response in the central nervous system,” Staats says. He thinks this episode lingers in the memory of vaccine developers, making them hesitant to invest in intranasal vaccines.

Many mucosal immunologists view the troubles with FluMist and safety concerns related to the nose’s close proximity to the brain as flukes of specific vaccine programs that unjustly cast a pall over intranasal vaccine development. “I think a lot of this basically boils down to doing what works. There is a lot of conservatism in the field,” Russell says.

The messy mucosa

Despite the roadblocks, academic scientists and small biotech companies have continued efforts to make intranasal vaccines for a variety of respiratory pathogens, including flu viruses, respiratory syncytial virus, and even anthrax. When the COVID-19 pandemic began, many of these groups pivoted to develop nasal sprays to protect against SARS-CoV-2 infection.

Of the approximately 300 experimental COVID-19 vaccines being developed around the globe, only a small number are intranasal vaccines—more than a dozen by C&EN’s count. Only a few of these programs are backed by firms with the capacity to fill large orders for the vaccines if they pass muster in clinical trials. For instance, AstraZeneca is testing the safety of an intranasal version of its COVID-19 vaccine that’s already authorized for use in Europe and India as an injection. And two of the largest vaccine manufacturers in India—the Serum Institute of India and Bharat Biotech—have signed deals to make intranasal vaccines designed in the US.

Over the past year, preclinical studies of intranasal vaccines have reinforced the notion that mucosal immunity matters. Several research groups developing intranasal COVID-19 vaccines have dripped the vaccines into the noses of mice and hamsters or sprayed the vaccines into the noses of monkeys. Later, when scientists infected those animals with SARS-CoV-2, they found almost no virus replicating in the animals’ nasal cavities. Animals that got injected versions of the same vaccines, in contrast, still had easily detectable virus replicating in their noses.

A particular kind of antibody made by mucosal immune cells is likely responsible for that strong protection. Companies developing injected vaccines study the immune responses of their shots largely by measuring a class of antibodies in the blood called immunoglobulin G, or in the parlance of immunologists, IgG. The authorized COVID-19 vaccines induce high levels of IgG that seep from their high concentration in the blood out into the lower depths of the lungs, where junctions between cells are leaky. That’s how IgG protects us from severe infections and keeps us out of hospitals, Altimmune’s Roberts says. “As you go up the respiratory tract, the junctions get tighter, and it is more difficult for the antibody to get across,” he says. “But it does happen. It is just inefficient.”

Mucosal immune cells constantly make an antibody called secretory immunoglobulin A (IgA), which gets released into the mucous membranes of the nose, mouth, airways, and gut. Pound for pound, we produce more IgA than any other antibody, Russell says, although most of it is broken down and sneezed, coughed, or pooped out within a few days.

And critically, while injected vaccines induce only systemic immunity, vaccines delivered to mucosal sites can induce both systemic and mucosal immunity, he says.

That fact is evident in animal studies of a vaccine being developed by David T. Curiel and Michael Diamond at Washington University in St. Louis. Both the injected and intranasal forms of their vaccine triggered the production of IgG antibodies, but only the intranasal route triggered mucosal immune cells to secrete IgA that blocked the virus from replicating in the nose. A day after they published preprint data demonstrating as much in July 2020, the Indian vaccine company Bharat Biotech contacted the university’s technology-transfer office to license the intranasal vaccine in India, where it is being tested in a clinical trial. “How that will play out clinically remains to be seen,” Curiel says. “But this animal model finding suggests, qualitatively, that we have some additional benefit.”

Qualitatively, rather than quantitatively, because secreted IgA is tricky to measure. “It is a lot easier to measure things from the blood than it is to measure from mucosa,” says Michael Barry, who has developed an experimental intranasal vaccine for COVID-19 at the Mayo Clinic. To determine how much IgA a mouse or hamster has produced after vaccination typically requires killing the animal to wash IgA off its lungs, he says. Russell, who has worked with IgA for decades, says that the antibodies “are much messier things to handle, in some cases quite obnoxious, and also extremely variable.” In humans, IgA can be measured by collecting nasal fluid or saliva, but the IgA levels will vary depending on how the sample is collected.

Getting the dose right with intranasal delivery is tricky too. “If you use a nasal spray, it often doesn’t take long before you can taste it. And if you can taste it, it has left your nose,” Staats says.

The vaccine can come back out the same way it went in too. Like us, mice sneeze, and sometimes rodents that sneeze after scientists pipette an intranasal vaccine in their noses don’t develop any immunity. Hildegund Ertl, a vaccine scientist at the Wistar Institute, sees this problem when her dog gets an intranasal vaccine for kennel cough. “He just takes a deep breath and sneezes it right out. And that is the risk with intranasal vaccines,” she says.

“It is actually quite difficult to get the nasal spray to stay in the nasal tract,” says Victoria Kett, a drug delivery scientist at Queen’s University Belfast who has worked on intranasal vaccines. Her group, and others, have looked for formulations that improve the viscosity of nasal sprays and help them stick to the mucous membrane. Much like a sticky note, “you want it to have a small tack but not stick so hard that it damages the surfaces,” she says.

All this means that researchers aren’t sure of the exact dose a person receives. By contrast, injecting something into someone’s arm is a surefire way to get a systemic antibody response, says J. Robert Coleman, CEO and cofounder of Codagenix, which is developing an intranasal COVID-19 vaccine that’s being manufactured by the Serum Institute of India. Compared with the clear-cut IgG levels measured in injected vaccines, the immune response from an intranasal vaccine “is maybe a little more murky water,” he says. “We most likely won’t achieve the max antibody titer of mRNA vaccines. But that doesn’t mean we won’t be as efficacious.” After all, IgG isn’t the only thing that is important.

Altimmune is aiming for a broad immune response that generates neutralizing IgG antibodies, mucosal IgA antibodies, and T cells that hang out underneath the mucosae of the respiratory tract, Altimmune’s Roberts says. “In a natural infection, you get all three arms activated,” he says. IgA antibodies are like the guards at the door that try to prevent most viruses from making it past the nose, he explains. If some virus squeaks by, neutralizing antibodies can help prevent further infection. Any virus that does manage to infect a cell can be mopped up by T cells. “So a vaccine that is able to activate all three arms would seem to have an advantage,” he says.

Although the goal of triggering multiple kinds of immunity makes sense, Duke’s Staats cautions that we need more data to confirm that intranasal vaccines will consistently trigger both mucosal and systemic immunity. “We just haven’t done enough of those mucosal immunization studies in humans to know.”

Pandemic potential

Vaccine developers hoping to get answers to some of these questions saw the pandemic as one of their best opportunities yet to run clinical trials. But with several COVID-19 vaccines already authorized in many countries, it is becoming harder for some groups to recruit people for their trials—or to even get money to run the studies in the first place. Trials run by Altimmune, Bharat Biotech, and Codagenix could have preliminary data on the safety and immunogenicity of their intranasal vaccines as soon as this month, with AstraZeneca not far behind.

It’s possible that none of the intranasal COVID-19 vaccines in development will play a role in ending the pandemic. Many are still in preclinical studies run by academic investigators who don’t have the experience or funding to launch clinical trials. And with the notable exceptions of AstraZeneca and Bharat Biotech, most biotech companies developing intranasal vaccines have never brought a product to market.

Early in the pandemic, Altimmune said it would have Phase 1 safety data before the end of 2020, but it didn’t start the trial until this year, and preliminary data are now expected in June. “Altimmune was never going to be in the first wave of vaccines. We were not able to move that quickly and didn’t receive funding to move that quickly,” Roberts says. “We were always going to be a second-generation vaccine, and in that situation, you have to represent something that is improved.”

Altimmune is developing new versions of its intranasal COVID-19 vaccine based on the major viral variants that have emerged as the virus mutates around the world, Roberts says. The firm will pick one to test in a Phase 2 study. Most other intranasal vaccine groups are also working on vaccines for the variants as a way to stay relevant. TheraVectys, a spin-off from the Pasteur Institute, plans on testing an intranasal vaccine developed in Charneau’s lab as a booster for people already vaccinated with existing COVID-19 vaccines. Codagenix says that the Serum Institute of India has pledged to manufacture 100 million doses of its intranasal vaccine by the end of the year. And if AstraZeneca’s intranasal version of its COVID-19 vaccine proves to be safe and effective, it could be a sea change for the field.

Intranasal vaccine developers aren’t ready to be written off. “We shouldn’t be too hasty and assume that the game is over,” Roberts says. “When people have to get revaccinated because of waning immunity or because of a variant, that represents an opportunity for choice. And that is why we think we are still in this game.”

Even if intranasal vaccines don’t play a big role in ending this pandemic, this moment represents one of the best chances yet for developers to prove that you can induce immunity without a needle. And researchers might finally understand whether intranasal vaccines can tackle tough respiratory pathogens, such as the respiratory syncytial virus.

“The whole medical community has been so fixated on injected vaccines that a lot of people just don’t seem to be able to think beyond that. And clearly they work in the majority of cases, there is no arguing with that,” Russell says. “But the immune system doesn’t depend on having stuff injected. There are other ways of going about it.”