Viruses are sneaky things. When they die, their DNA often sticks around. Some of them transform into freely roaming DNA that evades treatment. Others tunnel into their host’s genome and lie dormant, sometime for decades.

But dormant doesn’t mean gone. When the time is right, they strike. If a patient with hepatitis B virus (HBV) or HIV stops taking antiviral drugs, it can trigger a severe rebound of the disease. Stress, aging, and other factors that dampen the immune system can also reactivate the chickenpox virus, triggering the painful, blistering rash known as shingles.

Now, scientists have found a way to shut down one of these biological sleeper agents. Called epigenetic silencing, the technology hunts down lingering HBV genes in infected mice and adds a chemical tag that switches the genes off, without cutting the viral DNA. Unlike gene editing tools that shred genetic material, potentially causing collateral damage to the host’s genome, the epigenetic approach could be safer but still long-lasting.

After three monthly doses, roughly 90 percent of the mice showed no signs of the virus for at least six months after their final shot. A safety test in monkeys found no notable side effects, including any signs of a runaway immune response.

The team stopped short of calling it a cure. But if proven to be as helpful in humans, the injections could replace daily pills charged with keeping the virus in check and help millions of people laden with chronic hepatitis B. Earlier this year, the first patient was treated with the formulation in an ongoing Phase 1/2 clinical trial, which is testing for safety and early efficacy. If successful, the work could lead to treatments that silence the DNA of other viruses too.

“This differentiated mechanism has the potential to enable durable antiviral control,” wrote the team at nChroma Bio, a biotechnology company based in Boston, and collaborators.

Shape Shifter

Chronic HBV infection is a silent killer. A person can feel totally healthy. Meanwhile, the virus repeatedly cycles between dormant and active states, triggering the immune system to attack infected cells in the liver. Over time, the repeated assaults leave scar tissue that slowly replaces the organ’s healthy architecture and causes it to malfunction. Even with its considerable regenerative capability, the liver struggles to do its usual work, from making enzymes that break down food to producing proteins that help blood clot. Blood pressure in the digestive system skyrockets, increasing the risk of deadly stomach bleeding.

Even more insidious, the virus increases the risk of liver cancer, sometimes before notable tissue damage or symptoms. When HBV DNA integrates into the host’s genome, it can alter nearby gene activity, disrupt tumor-suppressing genes, or even rearrange chromosomes.  Meanwhile, constant inflammation can further fuel the development of cancer.

There are ways to fight back: Vaccines prevent infection, and antivirals suppress the virus. These drugs mimic the DNA letters HBV needs to replicate. Once incorporated into the viral genome, they block any further copying. But they’re a Band-Aid, not a cure. Stop taking them, and HBV rebounds in nearly everyone thanks to its two stubborn forms of DNA.

One of these is called cccDNA, a tiny, chromosome-like structure that sits inside infected cells and acts as a reservoir for the virus. It’s “the driver of HBV persistence,” wrote the team. The other is viral DNA that has integrated into the host genome. These fragments continuously churn out viral proteins, which train the host’s immune system to recognize them as friendly. Whole viruses can then escape surveillance and continue replicating.

“Thus, effective therapies for chronic hepatitis B must ultimately address both forms of viral DNA,” the team wrote.

Easy Silence

Previous methods have used various gene editors to hunt down and destroy viral DNA. In mice and monkeys, these tools have suppressed viral loads by up to 96 percent, with some effects lasting over a year.

The approach nChroma is developing, CRMA-1001, works differently. Rather than cutting viral DNA with the gene editor CRISPR-Cas9 or rewriting DNA with base editing, nChroma turned to epigenetics, the system of chemical tags that control whether genes are turned on or off.

The new treatment mimics an epigenetic process for silencing genes called methylation. It combines genetic instructions to build a DNA methylation enzyme with a version of Cas9, stripped of its cutting ability. Here, Cas9 acts like a molecular docking system, while a guide RNA directs the machinery to a specific site in the HBV genome. All components are packaged into lipid nanoparticles. After injection into the bloodstream, they predominantly travel to the liver and methylate the viral DNA reservoir and integrated HBV DNA.

In mice, a single dose slashed viral DNA activity and HBV surface protein levels more than a thousandfold. Among animals given three monthly doses, roughly 90 percent maintained undetectable viral load after six months. Adding standard antivirals to the mix lowered viral DNA levels even further.

The team then tested escalating doses in cynomolgus monkeys for safety. At the highest dose, liver enzymes rose in the blood, suggesting the liver’s cells were stressed or injured. But the levels returned to normal within four weeks of the last dose. The animals didn’t show clinical symptoms of liver damage, such as anatomical changes or blood-clotting issues.

The therapy has now entered the clinic. The team launched a trial in Hong Kong and received authorization to begin trials in New Zealand and the United Kingdom.

They have competition too. In May, Seattle-based Tune Therapeutics reported early results from an ongoing phase 1/2 trial of its own epigenetic silencer. After a single dose, several HBV-associated biomarkers plummeted for at least 17 months, and none of the participants experienced severe side effects.

In Shanghai, China, Epigenic Therapeutics is pursuing a similar strategy. Its formulation showed promise in preclinical models and is advancing toward a clinical trial, although details on how their silencer works are scant.

How long the effects will last is an open question. Can patients eventually stop taking antivirals and be functionally cured? And whether the therapies can silence the full range of HBV variants, whose genomes can differ by more than eight percent, is also unknown. Then there’s the risk these therapies go rogue and methylate other parts of the host genome with unintended consequences.

Costs could pose another challenge. Most people with chronic hepatitis B live in less economically developed regions in Southeast Asia and Sub-Saharan Africa, where access to expensive, specialized treatments may be limited.

Still, “epigenetic editing is an exciting, reversible solution that can long-term silence viral repertoires without the genotoxicity of gene editing,” wrote Marleen van der Laan at the University of Groningen and colleagues in an independent review. “Its success in functionally curing chronic hepatitis B is highly promising, but further steps are required to ensure its applicability.”