Are We Finally Closing In On a Universal Influenza Vaccine?

THANKS TO A remarkable ability to keep a step ahead of human immunity, seasonal influenza (flu) returns every year with a vengeance to afflict more than 28 million U.S. residents, resulting in 460,000 hospitalizations and more than 40,000 deaths.¹ While vaccination is the primary intervention for influenza prevention, the effectiveness of flu vaccines is limited, as well as time-limited to a single flu season. Less than two-thirds of U.S. children and just 45 percent of adults bother to get the annual flu shot,² facilitating transmission of circulating viral strains and further boosting the flu caseload. “Among the two dozen vaccinepreventable diseases, including measles, mumps, polio, smallpox and hepatitis, seasonal influenza is the only one for which a new vaccine is recommended every year. A more efficient approach is long overdue,” noted Anthony Fauci, MD, director of the National Institute of Allergy and Infectious Diseases (NIAID).

Influenza A and B viruses owe their special ability to evade human immunity to the constant generation of minor RNA mutations that alter the antigenic appearance of the large mushroom-like head region of the hundreds of hemagglutinin proteins that coat the membrane surface and enable the virus to attach to our cells. Collectively, these mutations confound the ability of antibodies produced against earlier influenza strains to bind and inhibit viral entry into cells; our immune system fails to recognize the new “drifted” influenza virus strain. The result is the annual necessity of an elaborate and costly global effort to isolate strains projected to circulate in the upcoming season, and produce customized flu vaccines against those strains in time to try to provide protective immunity.

But the extraordinary pace of mutation of flu viruses creates a second problem. Once influenza hunters identify the strains believed likeliest to become epidemic, ongoing genetic drift can significantly alter their antigenic appearance over the six months or more that elapse between identification of the presumptive epidemic strain and shipment of egg- or cell culturebased vaccine to pharmacies and clinics.

As a result, influenza vaccine effectiveness varies from one season to the next. Over the 15 flu seasons between 2004-2005 and 2018-2019, vaccine effectiveness ranged from as high as 60 percent to as low as 10 percent, averaging just 35 percent over the five most recent flu seasons (Figure 1).³ This rather dismal record tends to erode public confidence in the value of flu vaccines and accounts in part for the low annual immunization rates.

As if antigenic drift doesn’t present enough of a challenge, sporadic influenza A pandemics can also occur — as has happened four times over the past century — when one particular viral subtype acquires the HA-encoding gene segment of a different subtype to create a reassortant virus for which we have no preexisting immunity. There is an ever-present worry about the potential for a future pandemic that could rival the catastrophic 1918 Spanish flu pandemic, which claimed more than 650,000 U.S. lives. And because production of a vaccine reasonably well-matched to a newly emergent pandemic influenza strain requires months, there is currently no way to prevent spread of a highly virulent pandemic influenza virus through the population.

For decades, scientists have discussed the concept of a “universal” flu vaccine that, with one or perhaps two doses, could provide broad protection against seasonal and pandemic influenza viruses. This universal vaccine would eliminate the need for annual vaccination, confer some degree of herd immunity to reduce risk of infection for those who fail to get immunized, and protect against the ever-looming threat of a lethal pandemic influenza strain. The NIAID recently defined four criteria for any universal influenza vaccine. It should:⁴

• Be at least 75 percent effective;
• Protect against both group I and II influenza A viruses;
• Have durable protection that lasts at least one year; and
• Be suitable for all age groups.

While the optimal universal vaccine would provide protection against all influenza A viruses and potentially influenza B viruses, it is fully acknowledged that a particular “universal” vaccine’s breadth of coverage may end up falling somewhere along a continuum — such as subtypespecific or multi-subtype — that is short of true universality (Figure 2).⁵

Recent advances in influenza virology, immunology and vaccinology have convinced many experts that development of an effective universal or near-universal influenza vaccine is attainable. Particularly encouraging has been the discovery of a number of antibodies with broadly neutralizing activity against different influenza strains.⁶ A number of promising universal influenza vaccine candidates have emerged from academic, private sector and government research laboratories, several of which are now in early or mid-stage clinical testing.

Universal Influenza Vaccine Strategies

To clear invading influenza viruses, the human immune system mostly targets epitopes on the exposed — but perpetually mutating — hemagglutinin globular head. Most universal vaccine candidates are designed to induce antibody or cellular immunity to viral proteinaceous structures conserved across different strains and subtypes. There are currently three leading vaccine strategies:⁷

• Recombinant stalk-specific hemagglutinin. The stalk domain anchors the globular head of HA to the viral membrane and is highly similar across viral strains and types. A concern is that investigational head-deleted hemagglutinin stalk vaccines can induce anti-stalk antibodies, but against epitopes that are inaccessible in a natural influenza virus infection.
• Chimeric recombinant hemagglutinin. This universal vaccine is a construct that fuses the stalk of a widely circulating influenza strain (e.g., the H1 subtype of influenza A) to the globular head of a nonhuman influenza A strain. Again, the objective is to generate widely cross-reactive antibodies against the conserved stalk domain. A potential downside of this strategy is a tendency for chimeric hemagglutinin vaccine candidates to enrich for hemagglutinin head antibodies but not the desired stalk-specific antibodies.
• Recombinant M2 ion channel protein. Until recently, the highly conserved M2 protein has not been a major focus of vaccine development on account of its poor accessibility by antibodies. But recent vaccine candidates have been specifically designed to generate broadly neutralizing antibodies against its exposed surface domain.

Several vaccines are also targeting neuraminidase, a second surface protein that, together with hemagglutinin, decorates the influenza virus membrane (Figure 3).

Targeting Conserved Regions of Hemagglutinin

Current seasonal flu vaccines induce production of antibodies that recognize and bind to the hemagglutinin head, inhibiting its ability to mediate viral entry into cells. By the following flu season, rapid mutation in the head region has created new influenza A and B strains that escape the antibodies generated by these vaccines. The hemagglutinin stalk is far more resistant to mutations, making it particularly appealing for universal flu vaccine development.

In a very productive collaboration, researchers at the University of Michigan tracked household flu transmission in a cohort of Nicaraguan families, focusing on the 2013 and 2015 flu seasons. Blood samples drawn from 300 household members who lived with 88 individuals with confirmed influenza were sent to the laboratory of Florian Krammer, PhD, at the Icahn School of Medicine at Mount Sinai in New York. Using a novel assay to specifically measure hemagglutinin stalk antibodies, tests run by Dr. Krammer’s team showed a rise of four times in the stalk antibody levels correlated with a 42 percent reduction in symptomatic influenza.

Chimeric hemagglutinin. Over the last several years, Dr. Krammer and colleagues have developed and tested intact hemagglutinin vaccines with the intention of inducing an immune response to conserved epitopes on the stalk domain. But antibodies generated in animals immunized with vaccines containing the entire hemagglutinin protein tended, as in humans, to target only the head domain. In an attempt to redirect the immune response, the Mount Sinai team designed hemagglutinin chimeras comprising the head domain from a nonhuman, typically exotic virus such as a bird flu, and the stalk domain from a human influenza A subtype, such as H1, H2 or H9.

When animals were vaccinated twice over a few weeks with chimeric hemagglutinin vaccines that included identical stalks but different heads, their immune systems generated many more antibodies against the stalk region common to both flu strains than to the head regions. Somehow these chimeric hemagglutinins “redirect the immune response to the stalk domain, which is more conserved, so at least in animal models, they work much better than the regular vaccines that we used,” Dr. Krammer noted.⁸

Early this year, Dr. Krammer’s team reported that a single vaccination with an adjuvanted inactivated chimeric influenza vaccine construct induced high antihemagglutinin stalk antibody titers. Further, these anti-stalk antibodies against the H1 subtype were cross-reactive with the H2, H9 and H18 hemagglutinin subtypes. A single dose of this chimeric, hemagglutinin-based adjuvanted vaccine thus “might induce protective titers against all group 1 hemagglutinin-expressing viruses, making it an excellent candidate for development as a group 1 pandemic vaccine,” the investigators concluded.⁹

Hemagglutinin stalk nanoparticles. A team of NIAID scientists has developed an entirely different experimental universal flu vaccine candidate that genetically fuses the conserved HA stalk portion from an H1N1 influenza virus to the surface of a microscopic nanoparticle made of nonhuman ferritin. This construct, called “H1ssF_3298,” protected animals from infection with an entirely different influenza subtype (H5N1), indicating the antibodies induced by the vaccine can protect against other influenza subtypes within the same group.¹⁰

One or two intramuscular doses of H1ssF_3298 are currently being evaluated in a Phase 1 safety, tolerability and immunogenicity study in 70 healthy adults, whose health status and antibody response to the vaccine will be monitored over 12 months to 15 months.¹¹

Conserved hemagglutinin head region epitopes. Perhaps furthest along in the clinical pipeline is a peptide-based vaccine developed by the Israeli biotechnology firm BiondVax Pharmaceuticals, dubbed M-001, which contains nine highly conserved HA head domain epitopes that are common to some 40,000 influenza viruses isolated over the years and listed in a National Institutes of Health database. BiondVax early trials found M-001 and a standard killed virus flu vaccine appear to have a synergistic effect: While M-001 by itself does not stimulate antibodies against HA, it does when followed by an inactivated flu vaccine.

In mid-2018 NIAID launched a Phase 2 randomized, double-blind, placebocontrolled clinical trial to assess the reactogenicity, immunogenicity and safety of two priming doses of M-001, followed by a seasonal quadrivalent inactivated influenza vaccine in healthy adults aged 18 years to 49 years.

Just ahead of the 2018-2019 Northern Hemisphere flu season, BiondVax initiated a Phase 3 clinical trial of M-001 — the first-ever pivotal trial of any universal influenza vaccine candidate. The study will enroll and randomize 12,460 eastern European participants aged 50 years and older to be immunized twice with M-001 or saline placebo and followed for up to two seasons.¹² Clinical endpoints include the frequency of confirmed influenza cases and severity of illness in each group. Initial results are expected late this year.

FLU-v: Peptides That Induce Cellular Immunity

Most universal influenza vaccine candidates are designed to induce a protective antibody response to infecting virus. But small animal challenge studies dating back to the early 1990s have shown it is also possible, in the absence of neutralizing antibodies, to induce cytotoxic CD8+ T lymphocytes that target conserved viral antigens to provide broadly cross-reactive cellular immune protection.^13,14

More than a decade ago, UK-based SEEK Group and its collaborators showed FLU-v, a mixture of four polypeptides encoding conserved T cell-immunoreactive regions common to all influenza A and B viruses, protected mice against a lethal challenge with influenza virus; this protection occurred entirely in the absence of neutralizing antibodies.¹⁵

Earlier this year, results from a randomized, placebo-controlled Phase 2 study in 175 healthy adult volunteers found adjuvanted FLU-v mediated a protective vaccine-specific cellular response compared to adjuvanted placebo.¹⁶ Participants who received a single dose of FLU-v were significantly less likely than control subjects to develop mild-tomoderate influenza disease following intranasal challenge with a single H1N1 influenza A strain (32.5 percent versus 54.8 percent).¹⁷ “Larger studies are now needed to evaluate how the vaccine interacts with influenza strains in different cohorts in a real-world setting,” said lead study investigator Olga Pleguezuelos, PhD.

Targeting Matrix Proteins and Nucleoprotein

As opposed to the high degree of variability in surface proteins across influenza virus strains and subtypes, there is far greater similarity between the essential proteins — nucleoprotein and matrix proteins 1 and 2 — found internally within these viruses. These proteins are beyond the reach of antibodies that deliver the first line of immune defense, but memory T cells that have seen these deeper-placed proteins during prior flu infections can recall their unique antigenic “signature” and be reawakened to contain the infection once it is underway.

M1-nucleoprotein vaccinia virus vector. In late 2017, United Kingdom-based Vaccitech successfully completed a small Phase 1 study of VTP-100, an investigational universal flu vaccine that exploits a nonreplicating vaccinia virus to infect human cells and direct production of nucleoprotein and matrix protein 1 (M1). “With a single dose, we saw a boost in preexisting T-cell responses of between eightand ten-fold in humans,” said Vaccitech co-founder and lead investigator Sarah Gilbert, PhD.⁶

But in January of this year, the company reported disappointing topline findings from a pair of clinical studies. A randomized field-based Phase 2b trial for seasonal influenza with 2,149 participants, VTP100 failed to achieve the targeted reduction in the incidence of laboratory-confirmed influenza when used as an add-on to a licensed quadrivalent influenza vaccine (QIV), compared to QIV alone. A placebocontrolled influenza challenge Phase 2 trial in 118 healthy adults similarly did not reach its primary endpoint of a 30 percent reduction in overall viral shedding. Like many candidate universal flu vaccines that have preceded it, the VTP-100 program has been discontinued.

M2-deleted influenza virus. A very different kind of replication-defective flu vaccine is being developed by Madison, Wis.-based FluGen: an M2-deleted, single replication (M2SR) influenza virus. The deletion of the M2 gene restricts the virus to a single replication cycle in the host. The body recognizes M2SR as an influenza infection and activates a robust immune response, but because the virus can only replicate once, it cannot spread to other cells and cause symptoms of a real-world infection. The hope is that by convincing the host’s immune system that it has been infected with influenza, M2SR will activate a broad and durable wild-type immune response. FluGen’s vaccine development effort has backing from both NIAID and the U.S. Department of Defense.

Topline results of a Phase 2 clinical trial in 99 healthy adults were announced by the company early last year.18 Subjects were intranasally vaccinated with placebo or FluGen’s M2SR vaccine matching a flu virus from 2007, then challenged with a mismatched live H3N2 influenza virus from the 2014-2015 flu season. Despite the significant mismatch, more than half of the participants receiving M2SR showed a serum antibody response to the vaccine and a 34 percent reduction of viral load during the challenge phase of the study, compared to placebo. Subjects who developed antibody to both M2SR and the challenge virus showed a 62 percent reduction in viral load, compared to placebo. These same groups showed 51 percent and 56 percent reductions, respectively, in symptom scores, indicating M2SR reduced both viral load and symptoms when the subject was challenged with a high dose of a highly mismatched H3N2 flu virus. “The remarkable results from this trial of FluGen’s M2SR vaccine mark an important step forward in the development of a more universal flu vaccine,” said FluGen clinical advisory board chair Robert Belshe, MD. Further clinical studies are planned.

Looking Forward to Real-World Studies

Epidemiologists estimate that, at current vaccination rates, a universal vaccine that can meet NIAID’s 75 percent efficacy goal could potentially avert 17 million influenza cases, 251,000 hospitalizations and 19,500 deaths each year; $3.5 billion could be saved annually in direct medical costs,¹ and even more in lost productivity costs.¹⁹ And as the ongoing COVID-19 pandemic reminds us, the value of a universal influenza vaccine capable of protecting against a future pandemic influenza strain is incalculable.

By far the most challenging hurdle for any universal influenza vaccine candidate still lies ahead: real-world testing in thousands of participants spanning multiple flu seasons to demonstrate efficacy against multiple strains or subtypes. A number of reported successful live virus challenge studies to date in healthy adult volunteers have been encouraging, but will the putative vaccine protect elderly individuals and very young children at high risk for hospitalization or death due to serious complications? We are still years away from an answer, but for the first time, we now have a number of promising vaccine candidates with a realistic chance to fulfill the dream.