Accessory Proteins Found to Influence SARS-CoV-2 Severity

SARS-CoV-2 spike proteins have been a hot area of research for several years, but less is known about how the multiple other genes within the coronavirus’ genome impact disease severity and symptomology. Researchers at the University of Maryland School of Medicine decided to tackle these discrepancies head-on in their most recent study, published in The Proceedings of the National Academy of Sciences.

The most recent Omicron virus strain currently in circulation, BA.5, has surpassed the BA.4 version that was active earlier this year. Both strains appear to evade the immune system due to changes in their spike proteins. The research team claims earlier vaccines are less successful at preventing disease due to these spike mutations.

“What is interesting is that both BA.4 and BA.5 variants have the same genetic sequence for the spike protein,” says senior author Matthew Frieman, Ph.D., Alicia and Yaya Foundation Professor of Viral Pathogen Research in The Department of Microbiology & Immunology at UMSOM. “This means it’s the other genes, the non-spike protein genes, that seem to affect the way the virus copies itself and causes disease. So, mutations in these other accessory genes are what has allowed variants like BA.5 to outcompete the earlier versions of the virus.”

The SARS-CoV-2 virus has three distinct classes of genes: those that produce further copies of the virus, those that build the structure of the virus, and accessory genes with multiple different roles. This new study aimed to determine the impact of these accessory genes. The team first created artificial viruses devoid of all four auxiliary proteins, infected mice with either the new or original viruses, and observed the effects. Then, the scientists examined the impact of each virus on the mice.

The researchers discovered that the virus lacking the ORF3a/b gene led to much more mild infections than the original SARS-CoV-2 virus. Compared to mice infected with the original virus, mice with this strain lost less weight and had less virus within their lungs. These results suggested that the ORF3a/b gene likely contributes to viral replication or the immune response post-infection.

They also found that mice infected with viruses lacking the ORF8 gene were sicker than mice infected with the original strain of SARS-CoV-2. When compared to mice infected with the original SARS-CoV-2 virus, these mice displayed more significant lung inflammation. According to the researchers, the immunological response in the lungs appears to be regulated by ORF8.

“By inhibiting the immune response, ORF8 helps the virus to replicate more in the lungs which worsens infection. When removed, it allowed the immune system to fight back harder,” says Dr. Frieman.

Next, the team analyzed the spike protein’s role in disease severity for each SARS-CoV-2 variant. They started with the original virus and replaced the spike gene with either the alpha, beta, gamma or delta variant’s spike gene. After infecting the mice and cells, they observed each virus reproducing and infiltrating healthy cells. They found that the viruses use the spike protein to attach to ACE2 receptors to enter and infect lung cells.

Dr. Frieman’s team found that the spike protein determines the severity of some, but not all, of the variants. The gamma variant’s infection and replication capacities were less than that of other variations. According to the researchers, genetic alterations, particularly in the ORF8 gene, appear to have a role in making this version weaker than others. For example, although the gamma variety circulated in Brazil, it did not spread further because more robust variants supplanted it.

“While the spike mutations are important for enhancing receptor binding and entry into cells, the researchers also found that the mutations in the accessory proteins can alter clinical disease presentation,” says author Mark T. Gladwin, M.D., Vice President for Medical Affairs at the University of Maryland, Baltimore and the John Z. and Akiko K. Bowers Distinguished Professor and Dean, UMSOM. “We need to learn more about the role of accessory protein mutations in COVID-19 infection, especially as new variants and subvariants keep emerging where these other proteins may play more of a starring role.”