The innate immune antagonism of SARS-CoV-2 ORF3a, ORF6 and ORF7a

• Applicant: Dr. Konstantin Sparrer
• Subject Area: Immunology ; Virology
• Term: from 2021 to 2022
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 458681942

The human innate immune system is a powerful barrier against invading pathogens. For example, induction of the type-I interferon system leads to the expression of anti-viral interferon-stimulated genes (ISGs) and autophagy targets viral components for destruction. To establish an infection, pathogens such as the novel pandemic severe-acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) need to manipulate the human innate immune defense systems. Indeed, many clinical symptoms observed during the Coronavirus disease (COVID19) are related to perturbed immune activation. However, the pathogenicity of SARS-CoV-2 is lower than previous pandemic human CoVs, resulting in an efficient spread of the virus. In addition, the ability to antagonize human immune defense mechanisms was most likely a prerequisite for zoonotic transmission of SARS-CoV-2 to humans. Our data show that the proteins Nsp1, ORF3a, ORF6 and ORF7a of SARS-CoV-2 are potent antagonists of the interferon system or autophagy. However, most of the underlying molecular mechanisms remain to be determined. We could recently show that Nsp1 inhibits cellular translation by blocking the ribosome mRNA entry tunnel thus shutting down type-I interferon responses. To elucidate the molecular mechanism(s) of ORF3a, ORF6 and ORF7a, we conducted comparative proteome analysis of SARS-CoV-2 infected cells and cells expressing only the individual proteins. Our preliminary data identified GNG5, LYRM4, Rab5a or RILPL1 as highly likely targets of the molecular mechanism. Thus, we aim to explore how these factors are targeted and exploited by ORF3a, ORF6 or ORF7a to manipulate innate immunity. Next, to determine whether interferon and autophagy antagonism may have played a role in the rapid spread of SARS-CoV-2, we will compare the activities of ORF3a, ORF6 or ORF7a of all seven human CoVs. Finally, we intend to assess whether they facilitated zoonotic transmission of SARS-CoV-2 by assessing the activity of the accessory proteins of related non-human CoVs against the human innate immune system. This project will be the basis of future in-depth exploration of of the interplay between SARS-CoV-2 and the human innate immune system. This may help explain symptoms of COVID19 and thus give hints for new therapeutic targets. Conservation analysis will yield insights on the rapid spread and zoonotic transmission of SARS-CoV-2. Finally, identification of immune antagonists encoded by SARS-CoV-2 may help deliberately constructing an attenuated strain, that effectively activate our immune system. These strains may induce long-term immunity, aiding rational vaccine design.

• DFG Programme: Research Grants