Stanford publishes Nature Medicine: The Critical Role of Viral Genome Packaging in Replication

Programmable antiviral drugs (blue and red) attach to the viral genetic material (white) and prevent the folding

Like savvy international travelers, viruses know exactly how to pack

Now, a stanford Medical School study of the flu and SARS-CoV-2 (the virus that causes COVID-19) suggests that antiviral drugs that disrupt this genomic Tetris game can stop infection

Because reliable packaging strategies are shared among members of the viral family, an antiviral drug can be effective against several closely related viruses, such as seasonal influenza A, swine flu, and avian influenza

Dr Jeffrey Glenn, professor of microbiology and immunology, said: "These antiviral drugs can be tailored

The study was conducted in lab-grown mice, hamsters and human cells, and the results were published Aug.

Tools for the next pandemic

The finding suggests that it is possible to rapidly contain the spread

The findings are the first of Stanford's newly formed SyneRx, one of nine centers for the discovery of antiviral drugs for pandemic pathogens funded by the National Institute of Allergy and Infectious Diseases, ViRx@Stanford the Biosecurity and Pandemic Preparedness Program

Vaccines against the virus typically prompt the body's immune system to recognize and respond to key viral proteins, such as the spike protein

Glenn and Hagey wondered if antiviral drugs could target more common but equally important steps in the virus's life cycle— such as genome packaging— to stop or slow infection

For example, the genome of the influenza A virus consists of 8 independent single-stranded RNA fragments

The researchers used an analytical method and computational model called SHAPE to identify a fragment of RNA called PSL2, which has a predicted three-dimensional structure that is nearly 100 percent identical

Hagey and her colleagues then designed several short fragments of single-stranded DNA that can recognize and bind to matching sequences on PSL2, locking in and interfering with PSL2's ability to twist it into the precise shape

Nowhere to go

The researchers found that treating lab-grown cells with specific LNAs before or after infection with the H1N1 flu strain or swine flu strain significantly reduced the virus's ability to
make new infectious particles.
In addition, even after several generations, they found no signs of the virus mutating to escape the effects
of LNA.
Instead, when they treated the cell with Tamiflu, the virus quickly changed its genome, eschewing anti-flu drugs that inhibited the activity of a viral protein that helps release new viral particles
from infected cells.

"We found that if we designed drugs to combat these highly conserved structures necessary for viral genome packaging, there were very few pathways for viruses to escape,"
Glenn said.
This structure is found in all known influenza A isolates, including avian and swine flu
.
So if we can translate these findings into humans, it's possible that we could see universal protection
that only requires one dose of vaccine.
”

The researchers then tested whether the most effective LNA protected lab mice from flu infection
.
They found that injecting a dose of an antiviral drug into an animal's nose a week before the animal was exposed to a lethal dose of the virus protected 100 percent of the animal from death
.
In contrast, the animals in the control group developed a serious illness and were humanely executed
on day six.
They then increased the dose of LNA and injected
it two weeks before exposure to the virus.
Similarly, no rats died, most were only mild diseases
.

Finally, the researchers explored whether the low levels of viral replication that mice experienced in the first series of experiments could protect them from infection
in the future.
After they were initially infected 65 days later, the researchers were again exposed to the same mice, but used 10 times
the normal lethal dose.

"They didn't even blink an eye," Glenn said
.
"They didn't lose weight and they didn't get sick
.
This suggests that their initial exposure resulted in enough residual virus replication to stimulate a broad immune response that remained protective months later
.
”

Tests for COVID-19

The researchers conducted a series of similar experiments
on the SARS-CoV-2 virus.
Like the flu, they found that LNAs targeting highly conserved structural regions in the viral genome inhibited the replication
of the virus in lab-grown human cells.
Even the highly mutated SARS-CoV-2 virus isolated from chronic cancer patients could not replicate
with antiviral drugs.

This protective effect extends to Syrian hamsters, an animal
commonly used to study SARS-CoV-2 infection.
Hamsters that sniffed LNA twice a day remained healthy before playing with infected companions, and after 4 days, they had significantly less virus in their lungs than in the control group
.

The researchers are now testing this approach in pigs, and they hope to one day use the same dosage and intranasal applicator
in humans.
They predict that during the next pandemic, strategically designed LNAs (which they call programmable antivirals) could be used to treat people who are already infected, protect people during the lag between vaccination and development of protective immunity, or provide preventive protection
in the absence of a vaccine available.

Glenn said: "COVID-19 caught us off guard
.
But what really keeps me up at night is the possibility of a highly pathogenic virus, like the 1918 flu pandemic or a new weaponized flu
.
Today we don't have anything to stop its spread, and a virus like this can kill hundreds of millions of people
.
But our approach can be developed in advance and provide protection
against a variety of viruses.
”