Critical step in COVID viral infection identified

Researchers at Texas Biomedical Research Institute and University of Chicago have uncovered a mechanism that SARS-CoV-2, the virus that causes COVID-19, uses to protect itself inside the body as it works to replicate and infect more cells. Without this protective mechanism, viral infection is dramatically reduced.

The finding, published in Nature Communications, not only provides a potential target for new COVID-19 therapies but also offers insights that could inform future vaccine and antiviral development. The study builds on earlier work from Texas Biomed that identified the viral proteins that are most important for the virus’s pathogenicity, or ability to cause disease.

“In 2021, we found that the accessory protein ORF3a is one of the most important proteins for the virus and when we knock it out, the virus becomes much less harmful – but we didn’t know why,” said Texas Biomed Staff Scientist Chengjin Ye, Ph.D. “Now, working together with our collaborators at University of Chicago, we understand the mechanism.”

A dense security detail

Specifically, SARS-CoV-2 ORF3a appears to play a vital role in protecting structural proteins, most notably the spike protein that facilitates spread into other cells, as they are assembled on the surface of viral particles. It does this by driving the formation of a dense group of proteins that surround the spike protein and provide protection while in transit, much like security detail protecting a person or an armored vehicle carrying cash to the bank.

The team in Chicago, led by Assistant Professor Jueqi Chen, Ph.D., termed these protective complexes “3a dense bodies” or 3DBs for short.

It appears that 3DBs help prevent the spike protein from being cut into smaller components. When ORF3a is missing, these 3DBs fail to form, and the spike protein often arrives damaged, severely impairing the nascent virus’s ability to infect new cells.

“ORF3a could therefore be a good target for drugs to block the virus,” said Texas Biomed Professor Luis Martinez-Sobrido, Ph.D. “This discovery could also be instrumental for vaccine development, as we illustrated previously.”

A surprise evolution

Since the ORF3a gene is present in other coronaviruses, the team was curious if those viruses also sparked the formation of 3DBs. They found that 3DBs are formed by related coronaviruses carried by bats and pangolins. However, it was surprising to find that SARS-

CoV and coronaviruses found in civets do not, which could help explain the lower transmission and infection rates during the 2003 SARS outbreak compared to the COVID-19 pandemic. About 8,000 people were infected with SARS, while there are more than 770 million reported COVID-19 cases, according to the World Health Organization.

The research is a good example of multidisciplinary collaboration: Dr. Chen’s expertise in cellular biology and high-resolution microscopy complemented the virology and virus engineering experience of Drs. Ye and Martinez-Sobrido.

“After identifying the 3DB structures and pinpointing the ORF3a parts residues critical for 3DB assembly, we collaborated with Drs. Ye and Martinez-Sobrido to engineer an attenuated virus lacking the ability to form 3DB,” said Dr. Chen. “Coronaviruses have the largest genomes among RNA viruses and therefore the reverse genetics expertise of Drs. Ye and Martinez-Sobrido was critical for the functional studies of 3DB during infection.”

Next steps

Now that they have identified why ORF3a is so important, the two labs would like to dig deeper and figure out what is breaking apart the spike protein when left unprotected, which could reveal another avenue for therapeutic development. They would also like to study other SARS-CoV-2 variants to see if mutations in the ORF3a gene affect 3DB formation and infection rates.

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Paper:

Hartmann, S., Radochonski, L., Ye, C. et al. SARS-CoV-2 ORF3a drives dynamic dense body formation for optimal viral infectivity. Nat Commun 16, 4393 (2025). https://doi.org/10.1038/s41467-025-59475-x

About Texas Biomed

Texas Biomed is a nonprofit research institute dedicated to protecting the global community from infectious diseases. Through basic research, preclinical testing and innovative partnerships, we accelerate diagnostics, therapies and vaccines for the world’s deadliest pathogens. Our San Antonio campus hosts high containment laboratories and the Southwest National Primate Research Center. Our scientists collaborate with industry and researchers globally, and have helped deliver the first COVID-19 vaccine, the first Ebola treatment and first Hepatitis C therapy.