Researchers identify proteins that contribute to the pathogenicity of COVID-19 virus

Researchers at Texas Biomedical Research Institute (Texas Biomed) have narrowed down the proteins enabling SARS-CoV-2 to cause disease. Using advanced genetic engineering techniques developed at Texas Biomed, they systematically deleted the genetic code for five of the virus's accessory proteins, one at a time, to see how each one affected the virus's ability to spread and cause illness. The research was published online this month in the Journal of Virology.

They found two proteins that seem to contribute most to the virus's pathogenicity, or ability to cause COVID-19 disease. When individually lacking those proteins, the virus did not replicate as much as the natural virus in cells, suggesting they play a critical role in its spread. In contrast, spread was not significantly reduced when the other proteins were deleted.

Similar results were found in mouse models for COVID-19. While the virus lacking either of these two proteins still caused disease, infection severity and inflammation related to the immune response decreased compared to the natural virus.

Other studies have shown these two proteins interfere with the human body's immune response and help induce cell death. Given that, I was surprised that deleting one or the other was not enough to completely prevent disease. There is more going on that we don't yet understand."

Jesus Silvas, PhD, Study First Author and Virologist, Texas Biomedical Research Institute

The research relied on several advanced genetic tools, including the K18 hACE2 transgenic mouse model for studying COVID-19 first tested with SARS-CoV-2 at Texas Biomed, and the reverse genetic approaches to engineer recombinant SARS-CoV-2, also developed at Texas Biomed by virologists Chengjin Ye, Ph.D. and Luis Martinez-Sobrido, Ph.D., who led the research.

"Reverse genetics approaches are the most powerful tools in modern virology to study a virus," said Dr. Martinez-Sobrido, a Professor in the Disease Intervention & Prevention program. "It allows us to do things that we cannot do with the natural virus, such as editing, adding or deleting parts of the virus genome."

Usually, DNA is translated into RNA, which then goes on to make proteins. With reverse genetics, the researchers start with SARS-CoV-2, which is an RNA virus, they turn it into DNA, which they can edit. This is not currently possible with RNA. The edited virus complementary DNA copy can then be introduced into susceptible cells to generate recombinant viruses. This work is done in biocontainment labs for maximum safety and security.

For this study, collaborators at the Icahn School of Medicine at Mount Sinai in New York helped with deep sequencing to confirm the targeted sections of the virus genome were successfully deleted and did not result in additional, unwanted mutations.

The team is next looking into what happens when more than one protein is deleted at the same time. The ultimate goal is to find a combination that will lead to a live, "attenuated" virus that can be used as a live-attenuated vaccine. These weakened versions of the virus could then safely replicate in the body to illicit an immune response, but without causing illness.

"This could potentially lead to even more effective vaccines because it allows the body to develop an immune response to the entire virus, not just the envelope spike protein, which is the key feature of currently available vaccines," said Dr. Martinez-Sobrido.