Tracking Proteins That Help the COVID-19 Virus Replicate

Scientists have identified dozens of human proteins that SARS-CoV-2, the virus that causes COVID-19, depends on to replicate and spread, according to a recent study published in the journal PLOS Biology.

The results of the study could pave the way for new antiviral treatments that target the host rather than the virus itself, said Judd Hultquist, PhD, assistant professor of Medicine in the Division of Infectious Diseases and of Microbiology-Immunology, who was a co-author of the study.

“SARS-CoV-2, like any virus, needs to enter the cell, start replicating its genome, and then start making all of the building blocks needed to make new progeny viruses,” Hultquist said. “For a lot of these processes, the virus uses our own cellular architecture, but we had an incomplete understanding of exactly which human proteins the virus was using for which stages of its replication cycle.”

Unlike earlier studies that screened for genes causing the largest change in viral replication in a single large pool of cells, this research employed a more sensitive, but resource-intensive method, where the impact of each gene was measured individually in large arrays. This approach enabled scientists to measure the impact of silencing each gene in the human genome on SARS-CoV-2 replication and then map the exact stage of the viral lifecycle for which it was important.

Using this technology, the team identified 69 proteins required by the virus to replicate, including 10 required for viral entry into the host cell, 32 required for replication of the viral genome, and 27 required to assemble new viral particles. Many of these proteins were also found to be important for the lifecycle of related coronaviruses, including other pandemic coronaviruses (like SARS-CoV-1 and MERS-CoV) and even some seasonal coronaviruses (like OC43-CoV) that cause the common cold. This suggests that these proteins might be universal targets for broad-spectrum antiviral drugs that could treat many different infections.

“Our strategy of individually targeting each gene in the genome allowed us to uncover a lot of new biology and host factors that uniquely impacted the late stages of viral replication,” Hultquist said. “These include many genes and proteins that are important for the viral lifecycle, but that we would never have been able to identify using standard methods.”

By combining their results with data from previous genetic and protein studies, the investigators uncovered three major cellular pathways involved in viral replication. The first was involved in cell communication and development; the second was tied to cellular energy production, and the third was linked to inflammation and cell stress responses.

Finally, the investigators looked to see if any drugs targeting these proteins and pathways were capable of inhibiting SARS-CoV-2 replication in mice with COVID-19. They found some drugs that were able to significantly decrease the viral load in the mice, according to the findings.

“These drugs are actually in clinical trial for the treatment of cancer and are being actively explored as part of a strategy to cure HIV, so it was quite exciting to see that they might also act as antiviral drugs against SARS-CoV-2,” Hultquist said.

Taken together, these new insights not only deepen scientific understanding of how SARS-CoV-2 interacts with host cells but also highlight potential targets for drugs that could stop the virus by disabling the host factors it relies on.

Moving forward, Hultquist said he and his collaborators will work to identify drugs that are effective against multiple strains of coronaviruses.

“We’re trying to use the protein networks described in this study to identify conserved drug targets for drug screening in the search for broad antiviral medications,” Hultquist said. “In addition, we’re focused on understanding mechanistically how several of these proteins influence the viral lifecycle of SARS-CoV-2 and other related coronaviruses.”

The study was a collaboration among scientists worldwide, including investigators at Imperial College London, the Scripps Research Institute in California, and the Harbin Veterinary Research Institute in China.

“Over half of the authors on this paper are graduate students, medical students, and postdocs who had the opportunity through this work to participate in fundamental research and be trained in scientific thinking. This type of education is critical for training the next-generation of scientists and doctors, and it was only made possible by the support we had from federal grants and agencies,” Hultquist said.

The study was supported by National Institutes of Health grants U19 AI118610 and U19 AI135972. This work was also supported by philanthropic donations from Dinah Ruch and Susan and James Blair, from the JPB Foundation, the Open Philanthropy Project and a grant from the James B. Pendleton Charitable Trust.