Shea Lowery

Shea LoweryMicrobiolgy Graduate Program

Mentor: Stanley Perlman, MD, PhD

Year Entered Into Program: 2018



Understanding the role of the internal N gene in betacoronavirus pathogenicity. Coronaviruses (CoV) encode a variety of lineage-specific accessory genes that are involved in innate immune modulation and are dispensable for replication, including the internal N gene encoded in the +1 ORF of the nucleocapsid gene. This gene is known as ORF9b, ORF8b, and I for Severe Acute Respiratory Syndrome (SARS-CoV-2), Middle East Respiratory Syndrome (MERS-CoV), and Mouse Hepatitis virus (MHV), respectively. The internal N genes are poorly conserved among betacoronaviruses with diverse amino acid composition and gene size; for example, MHV-JHM I gene encodes a premature stop codon, reducing gene length by 200bp compared with MHV-A59 strain. Since the internal N gene was shown to antagonize Type I Interferon (IFN-I) pathway for SARS- and MERS-CoV, we generated SARS-CoV-2 9b, MERS-CoV 8b, and MHV-JHM I gene knockout (KO) viruses to understand their role in in-vivo pathogenicity. MERS 8b KO virus showed increased virulence in mice, with significant increases in virus titer and expression levels of inflammatory cytokines, including IFN-a, IFN-b, and ISG15 in the lungs. Lung pathology indicated progressive alveolar damage such as edema. In contrast, SARS-CoV-2 9b and JHM I KO viruses were modestly attenuated in-vivo, with animals displaying less weight loss and decreased mortality. In-vitro infection of bone marrow-derived macrophages with JHM I KO was attenuated at the replication level, but less so at the genomic level, indicating a potential unclear structural or assembly role of the I gene. Interestingly, a MHV-A59 I KO virus did not show attenuation in vivo and was seen present in the virion in a previous study. The current and past research indicates the internal N gene function varies across betacoronaviruses and likely plays a role in immune antagonism and possibly virion assembly, which requires further characterization.

Role of monocytes in SARS-CoV-2 infection.

 Severe COVID-19 is characterized by substantial immunopathology in the lungs and other organs that is thought to be mediated by a pathogenic innate immune response that is characterized in part by extensive infiltration of neutrophils and inflammatory monocytes in the lungs. Ms4a3 is a gene specifically expressed by granulocyte-macrophage progenitors (GMPs), which differentiate into both granulocytes, including neutrophils, and monocytes. Using Ms4a3-Cre mice crossed to a TdTomato reporter line, neutrophils and monocytes are labeled while lung-resident macrophages, along with lymphocytes and dendritic cells, are not. Using these mice, we assessed the extent to which GMP-derived inflammatory monocytes and neutrophils contribute to lung infiltration during infection with mouse-adapted SARS-CoV-2. Further, using Ms4a3-Cre mice crossed to Cre-inducible DTR knock-in mice, we depleted these cells by diphtheria toxin administration to determine their role in lung pathogenesis and mortality. 

Determining the Role of Nsp9 in virus replication.

Nsp9 is a part of the CoV replication complex; however, its exact function in this model is unclear. Current data indicates Nsp9 is an RNA binding protein that may loosely hold RNA during the replication process; furthermore, it is NMPylated by Nsp12’s NiRaN domain (Nidovirus RdRp-associated nucleotidyltransferase) which may begin the replication and transcription process. We utilize live virus and replicon assays to determine the role of key Nsp9 residues in virus replication and we collaborate with researchers that also determine the RNA binding affinities of these residues.



B.S., Biology, Georgia College and State University (2015-2018)
Research: Environmental studies Mycobacteriophages and role as antibacterial; HCMV placental cell tropism 



T32 AI007533 Training Grant in Molecular Virology, Viral Pathogenesis, and Viral Vectors through the NIH. 2021-2024


Select Presentations

Annual Center for Immunology and Immune- based Disease Retreat. “Characterization of Betacoronavirus Internal N Gene Reveals Diverse Pathological Functions.” Poster Presentation. August 2021.

Nidovirus 2021 “Characterization of Betacoronavirus Internal N Gene in Pathogenesis.” Poster presentation. June 2021.

American Society of Virology Annual meeting “Characterization of Betacoronavirus Internal N Gene in Pathogenesis.” Oral presentation. July 2021.

Jakobsen Memorial Conference poster presentation “Antiviral Effects of CDK8 Inhibitor Senexin A in BSL2 Model EBOV GP/rVSV Infection” March-2019

All Iowa Virology Symposium poster presentation “Antiviral Effects of CDK8 Inhibitor Senexin A in BSL2 Model EBOV GP/rVSV Infection” March-2019


Select Publications

Dene R. Littler, Biswaranjan Mohanty, Shea A. Lowery, Rhys N. Colson, Benjamin S. Gully, Stanley Perlman, Martin Scanlon and Jamie Rossjohn. Pyrimidine RNA base-mimicking compounds bind near Phe-40 in the SARS-CoV-2 Nsp9 replicase. Submitted to Journal of Biological Chemistry June 2021.

Littler D. R., Liu M., McAuley J.L., Lowery S. A., Illing P.T. Gully B. S., Purcell A. W., Thal D.M., Chandrashekaran I.R., Perlman S, Purcell D.F.J., Quinn R.J & Rossjohn J. “Plant-derived ent-kaurane-based natural products inhibit coronaviral replication by  binding to the conserved Nsp9 SARS-COV-2 protein.” Submitted to Science Advances June 2021. Pending.

Shea A. Lowery, Alan Sariol, and Stanley Perlman. “Innate immune and inflammatory responses to SARS-CoV-2: implications for COVID-19.” Cell Host Microbe. June, 2021

Lok-Yin Roy, Wong, Jian Zheng, Alan Sariol, Shea Lowery, David K. Meyerholz, Tom Gallagher, & Stanley Perlman. “Middle-East Respiratory syndrome coronavirus spike protein exhibits geographic region differences in virulence.” PNAS. May, 2021.

Morris, S. A., et. al. “Mycobacterium phage Adonis, complete genome” GenBank: MH001453.1. Published. February- 2018

Morris, S. "Genetic Diversity of Mycobacteriophages and the Unique Abilities of Cluster K." The Corinthian Journal. Published. April- 2017