Emma Winkler


Date of Award

Spring 5-15-2023

Author's School

Graduate School of Arts and Sciences

Author's Department

Biology & Biomedical Sciences (Immunology)

Degree Name

Doctor of Philosophy (PhD)

Degree Type



In the past decade, newly emerged and re-emerged pathogenic RNA viruses such as Ebola, H1N1, and Zika virus have become substantial threats to global health. Two notable examples include the explosive re-appearance of chikungunya virus in the 2000s in Asia and the Western Hemisphere and, more recently, the global COVID-19 pandemic. Therefore, an improved understanding of immunity to emerging RNA viruses is critical for defining host susceptibility and restriction factors to viral infection as well as appropriate vaccine and antiviral therapeutic design. Chikungunya virus (CHIKV) is a mosquito-transmitted alphavirus that is maintained in an urban epidemic transmission cycle. While most CHIKV infections cause an acute febrile illness lasting weeks, a subset of individuals progresses to debilitating, persistent musculoskeletal pain and inflammation lasting months to years. The magnitude and duration of viremia in humans correlate with mosquito infection and transmission. Although alphavirus viremia is a key determinant of disease severity and vector transmission, little is known about the acquired and genetic factors that impact the levels of virus in the human host circulation.

Herein, I describe one of these factors, the impact of the mammalian intestinal microbiome on alphavirus infection and dissemination. CHIKV infection of oral antibiotic-treated or germ-free mice resulted in increased viral burden in the blood and in tissues distant from the site of inoculation. Perturbation of the microbiome altered TLR7-MyD88 signaling in plasmacytoid dendritic cells (pDCs) and blunted systemic production of type I interferon (IFN). Consequently, circulating monocytes expressed fewer IFN-stimulated genes and become permissive for CHIKV infection. Reconstitution with a single bacterial species, Clostridium scindens, or its derived metabolite, the secondary bile acid deoxycholic acid, could restore pDC- and MyD88-dependent type I IFN responses to restrict systemic CHIKV infection and transmission back to vector mosquitoes. Thus, symbiotic intestinal bacteria modulate antiviral immunity and levels of circulating alphaviruses within hours of infection through a bile acid-pDC-IFN signaling axis, which affects viremia, dissemination, and potentially transmission. Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is the recently emerged RNA virus responsible for the Coronavirus Disease 2019 (COVID-19) pandemic that has led to over 163 million infections and over 3 million deaths. The development of countermeasures that reduce COVID-19 morbidity and mortality has been a global priority, and animal models are essential for this effort. Although animal models have been evaluated for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, none have fully recapitulated the lung disease phenotypes seen in humans who have been hospitalized. Herein, I evaluated transgenic mice expressing the human angiotensin I-converting enzyme 2 (ACE2) receptor driven by the cytokeratin-18 (K18) gene promoter (K18-hACE2) as a model of SARS-CoV-2 infection and pathogenesis. Intranasal inoculation of SARS-CoV-2 in K18-hACE2 mice resulted in high levels of viral infection in lungs, with spread to other organs. A decline in pulmonary function occurred 4 days after peak viral titer and correlated with infiltration of monocytes, neutrophils and activated T cells. SARS-CoV-2-infected lung tissues showed a massively upregulated innate immune response with signatures of nuclear factor-κB-dependent, type I and II interferon signaling, and leukocyte activation pathways. Thus, the K18-hACE2 model of SARS-CoV-2 infection shares many features of severe COVID-19 infection and can be used to define the basis of lung disease and test immune and antiviral-based countermeasures. One approach for both prevention and treatment of COVID-19 has been the development of SARS-CoV-2-neutralizing monoclonal antibodies (mAbs) directed against the spike (S) glycoprotein of SARS-CoV-2. Although passively delivered neutralizing antibodies against SARS-CoV-2 show promise in clinical trials, mechanisms of protection in vivo can be due to multiple factors including direct virus neutralization and engagement of complement or Fc gamma receptors (FcRs) on leukocytes. Fc effector functions of antibodies can promote immune-mediated cellular clearance, enhance antigen presentation and CD8+ T cell responses, and reshape inflammation through engagement of FcRs on specific cells. In contrast, under certain circumstances, Fc-FcR interactions can promote antibody-dependent enhancement of virus infection (ADE) or cause pathological immune skewing, which is at least a theoretical concern of antibody-based therapies and vaccines against SARS-CoV-2. Thus, a more complete understanding of the contribution of Fc effector functions in the context of antibody-based therapies is needed.

Herein, I define correlates of protection of neutralizing human monoclonal antibodies (mAbs) in SARS-CoV-2-infected animals. Whereas Fc effector functions are dispensable when representative neutralizing mAbs are administered as prophylaxis, they are required for optimal protection as therapy. When given after infection, intact mAbs reduce SARS-CoV-2 burden and lung disease in mice and hamsters better than loss-of-function Fc variant mAbs. Fc engagement of neutralizing antibodies mitigates inflammation and improves respiratory mechanics, and transcriptional profiling suggests these phenotypes are associated with diminished innate immune signaling and preserved tissue repair. Immune cell depletion experiments establish that neutralizing mAbs require monocytes and CD8+ T cells for optimal clinical and virological benefit. Thus, potently neutralizing mAbs utilize Fc effector functions during therapy to mitigate lung infection and disease.


English (en)

Chair and Committee

Michael S. Diamond

Committee Members

Deborah Lenschow, Megan Baldridge, Jacco Boon, Gwen Randolph,