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Viruses mutated faster to avoid genetic edits in bird flu resistant CRISPR super chickens

WHY THIS MATTERS IN BRIEF

At first the genetically engineered chickens were resistant to bird flu, but then the researchers found that the virus mutated faster to avoid the genetic edits … this is interesting but dangerous territory.

 

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The powerful, world changing, gene editing tool CRISPR may be crucial in fighting off one of the deadliest viruses circulating the globe, like Bovine TB as we saw a while ago with CRISPR super cows, and now it has yet another virus that has killed hundreds of millions since 2020 in its sights. It’s not Covid-19, of course – the virus is a type of especially aggressive bird flu that’s decimated chicken populations worldwide. Heartbreakingly, numerous flocks have been culled to contain the disease. Those skyrocketing price tags for a dozen eggs? This flu strain is partly to blame.

 

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Grocery bills aside, the virus’ wildfire spread among poultry also raises the alarming prospect it could hop into other species – including humans. According to the World Health Organization, 10 countries across three continents have reported signs of the bird flu virus in mammals since 2022, sparking worries of another pandemic.

Several countries have launched vaccination campaigns to battle the virus. But it’s a formidable enemy. Like human flu strains, the virus rapidly mutates and makes vaccines less effective over time. But what if we could nip infections in the bud?

This week, a team from the UK engineered “super chickens” resilient to a common bird flu. In chicken primordial germ cells – those that develop into sperm and egg – they used CRISPR-Cas9 to tweak a single gene that’s critical for virus reproduction.

The edited chickens grew and behaved like their non-edited “control” peers. They were healthy, laid eggs in the usual numbers, and clucked happily in their pens. But their genetic enhancement shined through when challenged with a real-life dose of flu similar to what might circulate in an infected coop. The edited chickens fought off the virus. All control birds caught the flu.

 

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The results are “a long-awaited achievement,” Dr. Jiří Hejnar at the Czech Academy of Sciences’s Institute of Molecular Genetics, who was not involved in the study, told Science. Back in 2020, Hejnar used CRISPR to engineer chickens resistant to a cancer-causing virus, paving the road for efficient gene editing in birds.

The technology still has a ways to go though before its commercialised. Despite the genetic boost, half of the edited birds got sick when challenged with a large dose of virus. This part of the experiment also raised a red flag: the virus rapidly adapted to the gene edits with mutations that made it a better spreader – not just among birds, but also gaining transgenic mutations that could hop into humans.

“This showed us a proof of concept that we can move towards making chickens resistant to the virus,” study author Dr. Wendy Barclay at Imperial College London said in a press conference. “But we’re not there yet.”

In 2016, Barclay discovered a chicken gene that bird flu viruses use to infect and grow inside chicken cells. Called ANP32A, it’s part of a gene family that translates DNA information into other biochemical messengers to build proteins. Once inside a bird cell, the flu virus can co-opt the gene’s products to make more copies of itself and spread to nearby cells.

 

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ANP32A isn’t the only genetic link between cells and virus. A later study found a second “protective” gene that blocks flu viruses from growing in cells. The gene is similar to ANP32A, but with two major changes severing the virus’ connection to the cell like closing a door. Because viruses require a host to reproduce, the roadblock essentially cuts off their lifeline.

“If you could disrupt that [gene-virus] interaction in some way…perhaps by this gene editing, then the virus would not be able to replicate,” said Barclay.

The new study followed this line of thought. Using CRISPR, they altered ANP32A in chicken primordial germ cells by splicing in the two genetic changes observed in the protective gene. The cells, when injected into chicken embryos, grew into edited sperm and eggs in healthy mature chickens, who went on to have chicks with the edited ANP32A gene.

The process sounds technical, but it’s basically a 21st-century speed-up of an ancient farming technique: breed animals to preserve wanted traits – in this case, resistance against viruses. The team then tested the edited chickens with several virus challenges.

In one, they squirted a dose of bird flu virus into the noses of 20 two-week-old chicks – half of which were genetically-modified, the others normally bred. The procedure sounds intense, but the amount of virus was carefully tailored to that normally present in an infected coop.

 

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All 10 control birds got sick. In contrast, only one of the edited chickens was infected. And even so, it didn’t transmit the virus to the other edited birds.

In a second test, the team amped up the dosage to about 1,000 times more than the original nose spritz. Every single bird, regardless of their genetic makeup, caught the virus. However, the edited birds took longer to develop flu symptoms. They also harboured lower levels of the virus and were less likely to transmit it to others in their coop – regardless of genetic makeup.

At first glance, the results sound promising. But they also raised a red flag. The reason the viruses infected the edited chickens despite their protective “super genes” was that the buggers rapidly adapted to the genetic edits. In other words, a gene swap meant to protect livestock could, ironically, push the virus to evolve more rapidly.

Why would this happen? Several tests found mutations in the viral genome likely allowed the viruses to grab onto other members of the ANP32A family. These proteins normally sit on the bench during viral invasions of flu and silently resist viral replication. But over time, the virus learned to work with each gene to boost its reproduction.

 

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The team is well aware that similar changes could allow the virus to infect other species, including humans.

“We were not alarmed by the mutations that we saw, but the fact we got breakthrough [infection] means we need more rigorous edits going forward,” said Barclay.

Dr. Sander Herfst at Erasmus University Medical Center, who studies bird flu’s incursion into mammals, agrees. “A water-tight system where no more [viral] replication takes place in chickens is necessary,” he told Science.

One potential solution is more gene editing. ANP32A is only one of three gene members that help viruses thrive. In a preliminary test, the team disabled all three genes in cells in a petri dish. The edited cells resisted a highly dangerous strain of flu virus.

But it’s still not a perfect solution. These genes are multitaskers that regulate health and fertility. Editing all three could damage a chicken’s health and ability to reproduce. The challenge now is to find gene edits that ward off viruses but still maintain normal function.

Biotechnology aside, regulations and public opinion are also struggling to catch up to the gene-editing world. CRISPRed animals are currently considered Genetically Modified Organisms (GMOs) under European Union laws, a designation that comes with a load of regulatory baggage and public perception troubles. However, because gene edits like the ones in the study mimic those that might naturally occur in nature – rather than splicing genes from one organism into another – some CRISPRed animals may be more acceptable to consumers.

 

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“I think the world is changing,” said study author Dr. Helen Sang, an expert who’s worked on flu-resistant birds for three decades. Regulations on gene-edited animals for food will likely shift as the technology matures – but in the end, what’s acceptable will depend on multicultural views.

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