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Researchers use CRISPR extinction gene tech to render viruses harmless

WHY THIS MATTERS IN BRIEF

Imagine being able to wipe out deadly viruses by using themselves against themselves … that’s what this tech does at the genetic level.

 

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In our quest to fight disease and live longer researchers have been experimenting with all kinds of sci fi treatments, from cancer killing nanobots and hybrid human immune systems to in vivo gene therapies and contagious vaccines, and many many more. But, if your immune system or drugs can’t stop a viral infection then why not pit a virus against itself by using what’s increasingly being called an “Extinction Gene“?

 

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That’s the provocative idea several labs are pursuing. They are studying whether deliberately introducing engineered viruses into people infected with their natural relatives can “drive” a foreign gene into those viruses that ultimately wipes out an infection.

No lab has knocked down an infection in animals this way yet, but a group has now shown it’s theoretically possible. These so-called gene drives harness the genome editor CRISPR to perform genetic surgery that speeds the spread of a gene through progeny. So far, scientists have received the most attention for adding gene drives to animals such as rodents and mosquitoes to control their numbers. But in a preprint last week, the team reported a similar feat with herpesvirus-1 (HSV-1). When both engineered and unmodified herpesviruses were inoculated into mice, the gene drive converted up to 90% of the viruses – possibly enough to prevent an HSV-1 infection from causing symptoms such as painful cold sores. A second group has succeeded in putting gene drives into HSV-1 that is growing in infected cells in lab dishes.

The viral gene drive work is a long way from curing an infected person. No one knows, for example, what kind of genetic modification the drive should propagate to drive down an infection. But other scientists see its potential. The new studies are “compelling,” says Rebecca Shapiro, a molecular microbiologist at the University of Guelph who has experimented with gene drives in fungi. “This opens up a lot of exciting avenues to use these kinds of gene drive techniques to modify viral populations, and possibly use them as new therapeutics.”

 

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Researchers have developed gene drives mostly in animals that sexually reproduce. They’ve created genetically modified females or males whose odds of spreading a gene to their offspring are significantly higher than 50% – the typical Mendelian chance that a descendant will inherit a particular gene variant. Most experiments aim to spread modifications that kill the offspring or render them sterile, a possible strategy for pest control. Such work has only been done in labs so far, however, because of concerns that releasing animals with gene drives could have dire consequences, such as accidentally wiping out an entire species or harming animals that aren’t the target.

Unlike people, viruses don’t have gene-scrambling sex with each other when they replicate. They simply command infected cells to read their genes and produce new viruses. But if multiple virions infect a single cell – as happens with herpesviruses – they often do something akin to sex, randomly swapping genetic sequences inside the nucleus. This “recombination” leads to viral progeny that spread the new genomes, and a gene drive hijacks this natural process to introduce and boost genetic changes that might ultimately disable a whole population of viruses.

HSV-1, HSV-2, human cytomegalovirus (hCMV), Epstein-Barr virus, and other herpesviruses are particularly attractive candidates for tackling with a gene drive because they can cause lifelong, latent infections that periodically flare and cause symptomatic disease. Some drugs can tamp down viral reactivation, but in people who have compromised immune systems, those drugs often fail and herpesviruses run riot, damaging many parts of the body and even causing death. This is a particular problem with people who have untreated HIV infections or receive organ or bone marrow transplants.

 

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Three years ago, virologists Marius Walter and Eric Verdin at the Buck Institute for Research on Aging demonstrated that a gene drive might be feasible in a herpesvirus. They showed in cell culture experiments that hCMVs endowed with a gene drive built from CRISPR could spread the drive to other hCMVs in infected cells. The gene drive mainly consisted of genetic sequences coding for CRISPR’s two components: a DNA-cutting enzyme known as Cas and a guide RNA that directs the enzyme to a specific place in a viral genome, where it makes a break, enabling a copy of the CRISPR-Cas genetic cassette to insert itself. The researchers attached a gene for a fluorescent marker to the complex so they could track the drive as a chain reaction spread it to yet more herpesviruses.

The study also hinted that a gene drive could reduce, if not eliminate, a viral population. The guide RNA shuttled the drive to park inside of a specific viral gene. The target wasn’t actually chosen to hobble the virus but the gene encoded a protein that protects the pathogen from immune attack. When the insertion disabled the gene, it reduced levels of the protective protein and rendered the virus more vulnerable.

The paper, which appeared in Nature Communications in September 2020, received scant attention. “Publishing a paper during a pandemic that’s happening with another virus is not a great way of having people notice it,” says Walter, who was a postdoctoral researcher in Verdin’s lab and has since moved to Keith Jerome’s lab at the Fred Hutchinson Cancer Center.

 

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The few researchers who did read it were skeptical, questioning whether a viral gene drive would cripple enough viruses to meaningfully reduce the population, Verdin recalls.

“One of the arguments that we heard is, ‘Oh, you’re never going have enough of the two viruses together in this same cell to actually make it work.’” But the 8 December preprint by Walter, Verdin, Jerome, and colleagues now shows that a gene drive can spread genes through much of the viral population in a mouse in at least some infected tissues.

Walter and Verdin view their work as a proof-of-concept experiment, as does a team led by virologist Dai Hongsheng of China’s Southern Medical University and his colleagues, which describes its cell culture success with an HSV-1 gene drive in a 4 December posting in bioRxiv. In tissue cultures, HSV-1 gene drives worked better than the hCMV ones, Dai notes. “The gene drive in HSV-1 spread steadily and at a speed not achievable with hCMV,” he says.

 

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But the mouse experiment suggests the HSV-1 gene drive needs to move even faster. As shown by the fluorescent marker gene it carried, the drive spread at different rates across the mice’s body regions, with the variation being most pronounced in the brain: In the cortex, the marker propagated to 25% of the viruses, whereas it ended up in as much as 90% of the viruses in the brain stem. Still, Walter says the results suggest the technology might one day help people.

“You have enough coinfection occurring in vivo for a gene drive to be something that we can potentially use,” he says.

All of the involved researchers stress that gene drives for herpesviruses are far from ready for tests in humans. Walter plans future experiments in animal models, hoping to show whether a gene drive can suppress a chronic HSV-1 infection enough to prevent reactivation and disease.

 

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Britt Glaunsinger, a biochemist at the University of California, Berkeley who specializes in studying herpesviruses, sees the promise of the concept, but cautions that the modified viruses could cause disease themselves – especially in immunocompromised people – if the gene drive does not sufficiently weaken the viruses it targets. Still, she wrote in an email, “I look forward to seeing where the field takes this!”

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