The Gene Therapy Center occupies two floors of a modern red-brick building on the western rim of the University of North Carolina campus at Chapel Hill, which is lush with greenery on the May morning that I visit. Exams have just ended and the campus, normally full of students, is empty. Jude Samulski, the former director, is walking with a slight limp due to a back injury from a few months before. “I fought the Christmas tree, and I lost,” he says.

During his time there, the Gene Therapy Center has created myriad AAV vectors, which are being tested for a host of diseases, including ones that affect the muscles, brain and blood.

Samulski himself has continued to perfect gene delivery both in his lab and through start-ups. One of these – Bamboo Therapeutics – was recently bought by Pfizer, along with an AAV vector that it equipped with a version of a muscle gene called DMD. Pfizer is now testing this vector in people with Duchenne muscular dystrophy, a devastating condition where the muscles degenerate, caused by a lack of dystrophin, the protein DMD codes for.

Another large pharmaceutical company, Novartis, announced in April 2018 that it had acquired AveXis, a start-up behind a promising gene therapy for spinal muscular atrophy, a similarly devastating disease that, in its most severe form, is often fatal in early childhood.

That pharmaceutical giants are getting into the field signals that gene therapy, long plagued by the 1999 tragedy, is finally being taken seriously, Samulski says.

But this isn’t helping people like Matt. “The clinical research hasn’t tipped the scales for patients who have been excluded: if you are fortunate, you can get treated; if you are not fortunate, you can’t,” Samulski explains. “The field is now moving towards finding ways to overcome the remaining challenges, including pre-existing immunity.”

And the clues to this lie in the virus itself.

A viral particle is composed of a protein shell, or capsid, with its genetic material tucked inside. What exactly these viral proteins do is a mystery, and one of the many virologists trying to unlock it is Lauriel Freya Earley, a postdoctoral researcher at Samulski’s lab.

Earley has an encyclopedic knowledge of AAV. The capsid, she tells me, consists of three proteins – vp1, vp2 and vp3 – which somehow self-organise into an icosahedral, or 20-faced, structure that is 3,000 times smaller than the width of a human hair.

She hands me a piece of plastic that looks like a starfish, its surface rugged with tiny spikes. It’s a piece of a 3D-printed model of a blown-up AAV capsid. Besides shielding the viral DNA, the capsid also acts like a key to help the virus get inside different organs in the body. Bits of protein material stick out to form a bumpy surface, which – somehow – helps the virus enter cells.

In the 37 years since Samulski cloned the first AAV, which came to be known as AAV2, a number of other types have emerged. There’s estimated to be around a dozen that can infect human cells, and a number of these are being tested as gene therapy vectors for different diseases. The types are distinguished by their different capsids, which allow them to do different things. AAV5 and AAV8, for example, breeze into the liver. AAV9 can access the liver as well, and it can also cross the blood–brain barrier, an obstacle for many molecules, and so could deliver genes to the brain. As well as sending genes to different tissues, the diverse AAVs could also provide a way around the immune system.

The capsids also make viruses draw the fire of the immune system. When someone who has been exposed to a virus develops antibodies to it, it’s these distinctive structures that they target for destruction.

While the majority of people may have already been infected with AAV2 – studies with higher estimates suggest around 70 per cent of people have antibodies – it’s thought that exposure is lower for other AAV types. For people like Matt, who are immune to one, there’s hope they could be treated with another.

Researchers are also creating new variants in the lab. One way to do this is to engineer capsids so that they are no longer recognised by antibodies. This would be straightforward if researchers knew which bits of the capsid antibodies recognise, but that’s another part of AAV biology shrouded in mystery.

An alternative approach is to create many, many mutant capsid variants, and then select those that slide past the immune system unnoticed.

“There’s no reason that we should be at the mercy of whatever viruses nature has thrown over the fence at us,” says David Schaffer of the University of California, Berkeley, who is also a founder of 4D Molecular Therapeutics, a start-up for AAV design. He believes we should engineer AAVs, both to optimise them as gene delivery vehicles and to bypass the immune response. “If we make enough changes in the surface coat of proteins, we can evolve the virus so it’s no longer recognised by the pre-existing antibodies.”

A few years ago, Samulski applied this approach to a real-life situation. Six boys with Duchenne muscular dystrophy had taken part in an early-stage trial using a modified form of AAV2 as a vector for gene therapy. The aim had been not to treat them but to test whether this AAV2 was safe and effective at delivering the relevant gene – and it was. But, as a result, the boys had all developed high levels of AAV2 antibodies, which would preclude them from receiving another dose as treatment in the future.

So Samulski’s team collected blood from three of them, exposed a vast collection of mutated AAV2 capsids to the antibodies it contained, and selected any that evaded detection. AAV2 coated with these capsids could, in principle, be used to deliver therapies to these three boys. However, Samulski’s experiment was only an academic exercise to show that the approach worked.

Under current regulations, personalised gene therapy remains unrealistic. Regulatory agencies do not distinguish between naturally arising and artificially created AAV capsids, so each new variant has to go through onerous and costly clinical trials, says Samulski. “But given that thousands of patients are being excluded overall, there has to be some common-sense conversation between regulatory agencies and clinical need.”

However, even if the approval process were to become more streamlined for artificial AAVs, not everyone is on board. James Wilson, who has shifted the focus of his research from adenoviruses to AAVs, is concerned that engineering AAVs too much could turn a harmless virus into something more pernicious. Instead, he’s focused on isolating new natural AAVs from primates.

“These exotic AAVs are sufficiently different not to be recognised by the immune system,” Wilson says. “But are they good vectors? That’s what we’re working on now.”

Samulski, though, is undeterred by criticism of artificially creating viruses.

“You can look for natural viruses, but if you know how to evolve them, then that’s the same. Natural does not mean better. There is no evidence that engineered viruses could be dangerous.”