Lifesaving new vaccine protects against swine, human and bird flu

Pigs could play a key role in ending the flu as we know it. That’s the message behind new research testing a computer-designed vaccine that protects swine from flu—and may one day do the same for people.

The vaccine, created using software called Epigraph, was developed by virologist Eric Weaver and his team at the University of Nebraska–Lincoln. Their goal is ambitious: end the yearly flu shot by creating one vaccine that works against many strains of the virus. In tests, their Epigraph-based vaccine protected pigs from H1N1 flu and triggered immunity that could last for years.

Influenza A virus regularly infects 5–15% of humans each year and causes thousands of deaths. Although vaccines help reduce risk, they often fail to provide long-term protection. That’s because flu viruses constantly mutate, changing key proteins like hemagglutinin—the molecule that helps the virus enter cells. These mutations allow the virus to evade the immune system, even if a person has been vaccinated.

The flu virus also has a wide host range. It infects not only humans but also birds, pigs, horses, and dogs. Swine, in particular, are vulnerable to multiple flu strains because of the unique makeup of their respiratory tracts. This allows them to host both avian and human flu viruses at the same time, leading to the birth of new, hybrid viruses.

When a pig is co-infected with different flu strains, the virus can reshuffle its genetic code in a process called reassortment. This can lead to the creation of a new variant that’s dangerous to humans.

That’s what happened in 2009, when a novel swine-origin flu strain spread to people around the world. The outbreak infected about one in four people and caused hundreds of thousands of deaths in its first year alone.

To stop such events from happening again, scientists have turned their attention to pigs. Since 2010, there have been roughly 500 known cases of flu spreading from swine to humans in the United States. At the same time, flu causes about $700 million in losses each year for the pork industry. Both problems point to the need for better vaccines for swine.

Flu viruses in pigs are especially tough to control. The main subtypes found in swine are H1N1, H1N2, and H3N2. Among these, H1 viruses are the most common and the most genetically diverse. They also cause more severe illness. These viruses fall into several lineages and clades that don’t always cross-react, making it hard for a single vaccine to protect against them all.

Commercial swine vaccines often use a whole inactivated virus (WIV). These are given to pregnant sows to help protect their piglets through maternal antibodies. But these vaccines don’t always work well against strains they weren’t made for. In some cases, they’ve even made things worse by triggering enhanced respiratory disease. This happens when the vaccine stimulates a weak antibody response that can’t fully fight the virus but still causes inflammation.

Some farms have started using custom-made WIV vaccines that match the strains on their own premises. But these take time to produce and can be expensive. Others have tested newer methods, like replicon particle (RP) vaccines. These use a harmless virus as a delivery system and have shown promise in producing strong immune responses. Still, they can be blocked by the maternal antibodies passed from vaccinated sows to piglets.

The Epigraph vaccine offers a new way forward. Rather than using a virus grown in a lab or modified by hand, Epigraph uses powerful computer algorithms. It analyzes thousands of flu virus genomes to identify key regions—called epitopes—that appear across many different strains.

Epitopes are the parts of the virus that the immune system recognizes. A good vaccine needs to contain epitopes that spark a strong response in both B-cells, which produce antibodies, and T-cells, which destroy infected cells. The problem is that as flu viruses mutate, some of these regions disappear. Epigraph’s software picks the ones that are most likely to stick around.

In this case, the software analyzed over 6,000 flu strains from 1930 to 2021. It selected the most common epitopes from the hemagglutinin proteins of H1 viruses. These were used to design a new vaccine that, when tested, performed better than both the wild type and the commercial FluSure XP® vaccine.

In trials, pigs vaccinated with the Epigraph formulation developed strong antibody responses against flu strains from birds, humans, and swine—including the 2009 pandemic virus. The animals showed protection against 12 strains tested, while those vaccinated with the wild type version only responded to eight. Commercially vaccinated pigs had three to five times weaker responses and only reached protective levels for six strains.

Epigraph-vaccinated pigs also showed stronger T-cell responses. These are important for long-term immunity and for clearing infected cells. Unlike other vaccines, Epigraph avoided triggering vaccine-associated enhanced respiratory disease. Pigs didn’t show signs of illness, had lower virus shedding, and suffered fewer lung lesions after exposure to the flu.

A six-month follow-up showed that the immunity remained strong. Regression analysis even suggested that the immune protection could last up to 10 years.

“We want to be absolutely certain—and I have no doubt that this vaccine is better than the current vaccines,” said Weaver. “This research sets the stage for developing universal influenza vaccines so people won’t have to go to the doctor and get a flu shot every year.”

Weaver's lab had already shown the vaccine could work against H3 flu strains. But H1 is a much bigger challenge because it changes more often and has caused more global outbreaks. His success with H1 gives new hope for a universal flu vaccine.

“This H1 subtype is the largest and most genetically diverse subtype in pigs,” he explained. “It’s also among the viruses that jumped from swine to humans to cause the 2009 swine flu pandemic.”

The next step is combining the H1 and H3 versions into a single vaccine. Weaver hopes to work with a biotech company to test a human version in clinical trials.

“If we can prevent influenza in swine, we can also prevent zoonotic jumps from avians to swine to humans, or from swine directly to humans,” he said. “We could basically cut off this evolutionary arsenal or advantage that the virus has. The ultimate goal is to eliminate or eradicate influenza.”

Weaver believes that vaccine science is nearing a turning point. With better data, faster gene sequencing, and powerful tools like Epigraph, scientists are closer than ever to building a flu vaccine that works across strains, species, and decades.

“Our ability to understand how viruses evolve has increased exponentially in the past 20 years,” he said. “What I see on the horizon is a third wave, where we go from good vaccines to universal lifelong vaccines.”

Note: The article above provided above by The Brighter Side of News.

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