Combating Respiratory RNA Viruses with Adaptable Tools and Innate Host Defenses

In the 21st century, the world has already experienced two pandemics caused by respiratory RNA viruses, the 2009 H1N1 “swine-flu” pandemic, and the ongoing COVID-19 pandemic. The 2009 pandemic was, thankfully, mild in terms of casualties; however, it revealed certain failings in existing systems. As a circulating virus, we had approved, in-use antiviral treatments for influenza, but the 2009 H1N1 viruses were resistant to an entire class, adamantanes. Also, the requirement for annually updated influenza vaccines meant there were systems in place for large-scale vaccine production, yet reliance on eggs dramatically limited the ability to scale-up a new vaccine quickly. Finally, global vaccine inequities meant many countries remained relatively unvaccinated against the H1N1 virus, even as the pandemic was declared over in August 2010. The COVID-19 pandemic has been a very different story on some fronts, most notably the death toll, which exceeds 6 million globally. Also, the decade of progress in vaccine research since 2009 has been evident in the rapid development of many highly effective COVID-19 vaccines using different platforms, while vaccine distribution issues remain. Finally, an entire lack of approved coronavirus antivirals required swift action to identify existing drugs and treatments to alleviate disease. The research and clinical response to the COVID-19 pandemic took advantage of existing technologies, pharmaceuticals, and systems and adapted them to solve the present crisis. The problem of this dissertation is to extend these efforts by investing in adaptable research tools, methods, and subjects to prepare for potential future respiratory RNA virus pandemics.In Chapters 2 and 3, we generated virus-specific research tools that are rapidly adaptable to new viral strains. Chapter 2 describes a fluorescent reporter of coronavirus protease activity that may be used to screen antiviral drugs and is compatible with diverse coronavirus protease proteins. Chapter 3 discusses a novel method for generating influenza reporter viruses with wide research applications, notably this manner of introducing exogenous proteins requires minimal genome rearrangements increasing transferability to newly identified strains. These projects demonstrate that even research tools requiring updates with the emergence of new strains can be designed to prioritize rapid adaptability. In Chapters 4 and 5, we interrogate the innate immune responses that determine the outcomes of viral infections. Chapter 4 identifies ETV7 as a negative regulator of the antiviral type I interferon response using CRISPR activation screening. ETV7 was previously known to be induced by interferon, but its role during the response to viral infection remained undetermined. We found ETV7 limits transcription of interferon stimulated gene expression, influencing the antiviral state of a responding cell. Chapter 5 reviews the impact of influenza viral disease outside the site of infection, the respiratory tract, and established methods of studying these effects using animal models. Many of the circulating cytokines implicated in non-respiratory influenza disease from these models, IL-6, IFNs, and TNF-alpha, are known to play a role in influenza and COVID-19 patient disease severity. These investigations show that our understanding of how innate immunity is regulated, and dysregulated, continues to require updating even as the main pathway members and downstream effectors have been identified.