ORCID

https://orcid.org/0009-0006-4737-8627

Date of Award

5-7-2025

Author's School

Graduate School of Arts and Sciences

Author's Department

Biology & Biomedical Sciences (Plant & Microbial Biosciences)

Degree Name

Doctor of Philosophy (PhD)

Degree Type

Dissertation

Abstract

Human immunodeficiency virus type I (HIV-1) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are the causative agents of two unique pandemics. For a successful replication cycle to occur, viruses need to strategically outmaneuver host cell defenses. The innate immune system is the first line of defense against viruses and other pathogens. Host pattern recognition receptors detect viral nucleic acids and initiate signaling cascades that culminate in the expression of interferon (IFN) and transcriptional upregulation of antiviral interferon-stimulated genes (ISGs). This dissertation examines the involvement of the innate immune response during early, post-entry steps of HIV-1 and SARS-CoV-2 infection. During HIV-1 maturation, the viral core is formed when the capsid (CA) protein arranges into a conical lattice around the viral RNA genome and associated proteins and replicative enzymes. Mutations in CA have been linked to innate immune sensing of HIV-1, suggesting that the CA lattice may shield viral nucleic acids from host sensor proteins that initiate antiviral responses. We utilized orthogonal genetic and chemical approaches to manipulate the stability of the CA lattice and determine the effects on innate immune recognition of HIV-1. We examined expression levels of ISGs after infection of cells with wild-type and mutant viruses containing cores of altered stability. We show that decreasing the stability of HIV-1 cores diminishes or enhances innate immune sensing in a reverse transcription-dependent manner. Surprisingly, due to the combined effects of enhanced reverse transcription and defects in nuclear entry, mutants that form hyperstable cores induce innate immune sensing more potently than destabilizing CA mutations. At low concentrations, CA-targeting compounds lenacapavir and GS-CA1 impact capsid lattice stability in cells and modestly enhance innate immune sensing of HIV-1. Innate immune activation observed with CA mutants depends on reverse transcription and the DNA-sensing cGAS-STING pathway. Overall, our findings demonstrate that CA lattice stability and reverse transcription are balanced to minimize sensing of viral DNA. Other than the cognate ACE2 receptor, host factors that determine the cellular tropism of SARS-CoV-2 are poorly defined. We sought to determine the mechanism(s) responsible for post-entry restriction of viral replication in a subset of ACE2-postive airway-derived cell lines. We show that high baseline levels of IFN pathway genes are responsible for inhibiting SARS-CoV-2 replication in infected cells. We determined that mitochondrial DNA leakage and naturally occurring cGAS and STING variants trigger constitutive activation of the cGAS-STING pathway that results in the IFN-mediated response. Notably, SARS-CoV-2 antagonizes the IFN pathway, as ISG expression is demonstrated mainly by uninfected bystander cells. Our findings suggest that constitutive activation of the cGAS-STING and IFN pathways impacts cellular tropism of SARS-CoV-2 in ACE2-expressing cell lines. Collectively, this dissertation provides insight into the involvement of the innate DNA-sensing cGAS-STING pathway during early steps of HIV-1 and SARS-CoV-2 infection. Our work contributes to the growing collection of evidence that HIV-1 CA lattice stability is critical for evasion of the host’s innate immune response. Furthermore, we provide evidence for the involvement of the host innate immune response in determining cellular tropism of SARS-CoV-2.

Language

English (en)

Chair and Committee

Sebla Kutluay

Committee Members

Barbara Kunkel; Carolina Lopez; Hani Zaher; Rebecca Bart

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Virology Commons

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