New inhaled COVID-19 therapy blocks viral replication in the lungs

An image shows a scientist using a pipette to transfer liquid to a laboratory plate.

UC Berkeley postdoctoral fellow Chi Zhu is part of a team of researchers developing a new COVID-19 therapeutic that can be administered as a nasal spray. The experimental treatment is effective against all SARS-CoV-2 “variants of concern” and can be easily modified to target other RNA viruses. (UC Berkeley photo by Brittany Hosea-Small)

Researchers at the University of California, Berkeley, have created a new COVID-19 therapeutic agent that could one day make treating SARS-CoV-2 infections as easy as using a nasal spray for allergies.

The therapeutic uses short pieces of synthetic DNA to chew up the genetic machinery that allows SARS-CoV-2 to replicate in the body.

In a new study published online in the journal Nature communication, the team shows that these short fragments, called antisense oligonucleotides (ASOs), are highly effective in preventing the virus from replicating in human cells. When administered intranasally, these ASOs are also effective in preventing and treating COVID-19 infection in mice and hamsters.

An illustration of the SARS-CoV-2 virus

The therapeutic works by disrupting a key region of the SARS-CoV-2 genome. (Illustration by CDC)

“Vaccines make a huge difference, but vaccines are not universal, and there is still a huge need for other approaches,” said Anders Näär, professor of metabolic biology in the Department of Nutritional Sciences and Toxicology (NST) at UC Berkeley and senior author of the paper. “A nasal spray that is cheaply available everywhere and can prevent someone from getting infected or prevent serious illness can be enormously helpful.”

Because the ASO treatment targets a part of the viral genome that is highly conserved among different variants, it is effective against all SARS-CoV-2 “variants of concern” in human cells and in animal models. It is also chemically stable and relatively inexpensive to produce on a large scale, making it ideal for treating COVID-19 infections in areas of the world that lack access to electricity or refrigeration.

If the treatment proves safe and effective in humans, the ASO technology can be easily modified to target other RNA viruses. The research team is already looking for a way to use this to disrupt the flu virus, which also has pandemic potential.

“If we can design ASOs that target entire virus families, then when a new pandemic emerges, as long as we know which family the virus belongs to, we can use the nasally delivered ASOs to suppress the pandemic in its early stages, ” said study first author Chi Zhu, a postdoctoral fellow in NST at UC Berkeley. “That’s the beauty of this new therapy.”

An image shows five individuals standing in a biological laboratory.  Each person wears lab coats and a face mask.

Näär lab members (left to right) Justin Lee, Chi Zhu, Lei Xu, Federico Gonzalez and Caslin Gilroy, pictured in summer 2021. (UC Berkeley photo by Brittany Hosea-Small)

Hack the viral copier

Like DNA, RNA carries genetic information encoded in a sequence of bases – but unlike DNA, RNA usually comes in a single strand, without a second, complementary strand to form a double helix. However, RNA still readily binds to complementary base pair sequences. ASOs are short strands of lab-made, DNA-like molecules that, like molecular Velcro, are programmed to stick to specific RNA sequences in viruses and cells.

For more than a decade, Näär and his team have been studying how these molecules can be used to modify the activity of messenger RNA and microRNA in the human body, potentially reversing conditions such as obesity, type 2 diabetes, fatty liver disease and Duchenne muscular dystrophy. When the COVID-19 pandemic hit, his team quickly mobilized to study whether ASOs could also be used to disrupt SARS-CoV-2.

“The SARS-CoV-2 genome is single-stranded RNA, similar to messenger RNA or microRNA,” Näär said. “We thought that maybe we could use these ASOs to attach to the viral RNA and prevent it from working.”

An image shows a person holding up a gloved hand.  Numbers are written on the glove with a red pen.

Chi Zhu checks the calculations on the gloves before preparing a new batch of antisense oligonucleotides (ASOs) in the lab. (UC Berkeley photo by Brittany Hosea-Small)

Working with Associate Professor Sarah Stanley’s lab at UC Berkeley and researchers at the Innovative Genomics Institute, the team began pitting the SARS-CoV-2 virus against hundreds of different ASOs. Each of these ASOs was designed to interfere with a different region of the viral RNA, including the region that codes for the infamous “spike” protein that helps the SARS-CoV-2 virus hijack host cells.

Of all these targets, they identified one that was far and above the most effective at disrupting the virus. This target was a non-coding sequence of viral RNA that forms a hairpin loop structure and appears to play a key role in helping SARS-CoV-2 replicate.

“We showed that if you bind an ASO to this hairpin, it dissolves the hairpin, and the RNA forms a straight line instead of a bubble structure,” Näär said. “We think that this prevents the virus from effectively translating and replicating, and we found that it was incredibly effective at preventing virus replication in human cells.”

When they administered ASOs into the noses of infected hamsters and mice, the team found that they were also highly effective in both preventing and treating COVID-19 infections. Importantly, these experiments also showed that the ASOs did not appear to stimulate any significant immune response, indicating that ASOs are unlikely to produce toxic side effects in humans.

Because the hairpin loop structure is found in all known variants of SARS-CoV-2, ASOs should be effective against all of them. To prove this is the case, the team repeated their experiments against all the major variants of concern, including Delta and the highly contagious Omicron.

An image shows a glove pipette liquid into an orange well plate.

The team tested hundreds of different ASOs, each designed to disrupt a different region of the SARS-CoV-2 genome, before identifying one that was highly effective at blocking the activity of the virus. (UC Berkeley photo by Brittany Hosea-Small)

“[SARS-CoV-2] enters the body and hijacks our own machinery to become a copy machine to produce tons of virus copies for more infection and spread,” study author and UC Berkeley NST student Justin Lee said in a winning UC Grad Slam talk. “We were able to find the key code in the viral RNA that allows the replicator to run, and all the variants, including Delta and Omicron, share the same key code.”

According to Näär, the team has already identified an additional ASO target found in the genetic code of all SARS family viruses, including the SARS-CoV-1 virus that caused the SARS outbreak in 2002. A “cocktail” of these two ASOs may be even more effective at suppressing the virus – and would be nearly impossible for a new variant to avoid.

The team has further experiments to conduct before the ASO treatment will be approved for clinical trials in humans. However, Näär is optimistic that the therapy could one day be used as part of a spectrum of treatments for COVID-19 and other viral diseases.

“It’s very clear that this virus is not going away,” Näär said. “We need many different pathways to tackle it, and therapeutics like ours that are agnostic to the variants can play a big role.”

Additional study co-authors include Jia Z. Woo and Silvi Rouskin of the Whitehead Institute for Biomedical Research; Lei Xu, Xammy Nguyenla, Livia H. Yamashiro, Scott B. Biering, Erik Van Dis, Federico Gonzalez, Douglas Fox, Eddie Wehri, Julia Schaletzky, Eva Harris, and Sarah Stanley of UC Berkeley; Fei Ji and Ruslan I. Sadreyev of Massachusetts General Hospital; Arjun Rustagi, Benjamin A. Pinsky, and Catherine A. Blish of Stanford University; Charles Chiu at the University of California, San Francisco; and Sakari Kauppinen from Aalborg University, Denmark.

This research was supported in part by Fast Grants and by the Innovative Genomics Institute.

In his winning talk at the 2022 UC Grad Slam, Justin Lee describes how the new treatment works by “jamming the COVID-19 copier.” (Video from University of California)

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