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Publications

2023

Shuchen Feng, Amornrat O'Brien, Da-Yuan Chen, Mohsan Saeed, and Susan Baker. (2023)  SARS-CoV-2 nonstructural protein 6 from Alpha to Omicron: Evolution of a transmembrane protein.  mBio (accepted)

 

 

Da-Yuan Chen, Jacquelyn Turcinovic, Shuchen Feng, Devin J Kenney, Chue Vin Chin, Manish C Choudhary, Hasahn L Conway, Marc Semaan, Brianna J Close, Alexander H Tavares, Scott Seitz, Nazimuddin Khan, Sebastian Kapell, Nicholas A Crossland, Jonathan Z Li, Florian Douam, Susan C. Baker, John H Conno, and Mohsan Saeed. (2023) Cell culture systems for isolation of SARS-CoV-2 clinical isolates and generation of recombinant virus. IScience (accepted).

Anne H. Rowley, David Arrollo, Stanford T. Shulman, Abigail Torres, Amornrat O'Brien, Kristine Wylie, Kwang-Youn A. Kim,  Susan C. Baker. (2023) Analysis of Plasmablasts from Children with Kawasaki Disease Reveals Evidence of a Convergent Antibody Response to a Specific Protein Epitope. J Infect Dis  Feb 18. DOI: 10.1093/infdis/jiad048.

Da-Yuan Chen, Chue Vin Chin, Devin Kenney, Alexander H. Tavares, Nazimuddin Khan, Hasahn L. Conway, GuanQun Liu, Manish C. Choudhary, Hans P. Gertje, Aoife K. O’Connell, Scott Adams, Darrell N. Kotton, Alexandra Herrmann, Armin Ensser, John H. Connor, Markus Bosmann, Jonathan Z. Li, Michaela U. Gack, Susan C. Baker, Robert N. Kirchdoerfer,
Yachana Kataria, Nicholas A. Crossland, Florian Douam, Mohsan Saeed (2023)
 Spike and nsp6 are Key Determinants of SARS-CoV-2 Omicron BA.1 Attenuation.  Nature  Jan 11. DOI: 10.1038/s41586-023-05697-2.

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2022

Michaela U. Gack and Susan C. Baker. (2022) Editorial overview: 2022 "Virus-Host Interaction" section of Current Opinion in Virology. Current Opinion in Virology Jun;54:101229. DOI: 10.1016/j.coviro.2022.101229.

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Shuchen Feng, Mudassir S. Ali, Monika Evdokimova, Gail E. Reid, Nina M. Clark, Susan L. Uprichard, Susan C. Baker. (2022)  Sequencing during Times of Change: Evaluating SARS-CoV-2 Clinical Samples during the Transition from the Delta to Omicron Wave. Viruses. Jun 28;14 (7): 1408. DOI: 10.3390/v14071408.

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Chen, K.Y. T. Krischuns, L. Ortega-Varga, E. Harigua, S. Paisant, A. Zetor, J. Chiaravalli, D. Courtney, A. O’Brien, S.C. Baker, F. Agou, C. Isel, Y. Jacob, A. Blondel, and N. Naffakh. (2022). A Highly Sensitive Cell-Based Luciferase Assay for High-Throughput Automated Screening of SARS-CoV-2 nsp5/3CLpro Inhibitors. Antiviral Research. DOI: 10.1016/j.antiviral.2022.105272. 

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Susan L. Uprichard, Amornrat O’Brien, Monika Evdokimova, Cynthia L Rowe, Cara Joyce, Matthew Hackbart, Yazmin E. Cruz-Pulido,  Courtney Cohen, Michelle Rocks, John M. Dye, Paul Kuehnert, Keersten M. Ricks, Mary Beth Casper, Lori Linhart, Katrina Anderson, Laura Kirk, Jack A. Maggiore, Andrew S. Herbert, Nina M. Clark, Gail E. Reid, and Susan C. Baker(2022). Antibody Response to SARS-CoV-2 Infection and Vaccination in COVID-19-Naïve and Experienced IndividualsViruses. DOI: 10.3390/v14020370.

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2021

Nir Drayman, Jennifer K. DeMarco, Krysten A. Jones, Saara-Anne Azizi, Heather M. Froggatt, Kemin Tan, Natalia Ivanovna Maltseva, Siquan Chen, Vlad Nicolaescu, Steve Dvorkin, Kevin Furlong, Rahul S. Kathayat, Mason R. Firpo, Vincent Mastrodomenico, Emily A. Bruce, Madaline M. Schmidt, Robert Jedrzejczak, Miguel Á. Muñoz-Alía, Brooke Schuster, Vishnu Nair, Kyu-yeon Han, Amornrat O’Brien, Anastasia Tomatsidou, Bjoern Meyer, Marco Vignuzzi, Dominique Missiakas, Jason W. Botten, Christopher B. Brooke, Hyun Lee, Susan C. Baker, Bryan C. Mounce, Nicholas S. Heaton, William Severson, Kenneth Palmer, Bryan C. Dickinson, Andrzej Jaochimiak, Glenn Randall, Savaş Tay. (2021). Masitinib as a Broad Coronavirus 3CLpro Inhibitor that Blocks Replication of SARS-CoV-2. Science 20 Jul 2021. DOI: 10.1126/Science.abg5827

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Deng, Xufang, Monika Evdokimova, Amornrat O’Brien, Cynthia L. Rowe, Nina M. Clark, Amanda Harrington, Gail E. Reid, Susan L. Uprichard, and Susan C. Baker. (2021). Breakthrough Infections with Multiple Lineages of SARS-CoV-2 Variants Reveal Continued Risk of Severe Disease in Immunosuppressed Patients. Viruses 2021, 13, 1743. DOI: 10.3390/v13091743.

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Mihelc, E.M., Baker, S.C., Lanman, J.K. (2021). Coronavirus Infection Induces Progressive Restructuring of the Endoplasmic Reticulum Involving the Formation and Degradation of Double Membrane Vesicles. Virology. DOI:10.1016/j.virol.2020.12.007

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Deng, Xufang, Alexandra C. Buckley, Angela Pillatzki, Kelly M. Lager, Susan C. Baker, Kay S. Faaberg. (2021). Development and Utilization of an Infectious Clone for Porcine Deltacoronavirus Strain USA/IL/2014/026. Virology 553:35-45.  DOI: 10.1016/j.virol.2020.11.002

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O’Brien, A., Da-Yuan Chen, Matthew Hackbart, Brianna Close, Timothy E. O’Brien, Mohsan Saeed, and Susan C. Baker. (2021). Detecting SARS-CoV-2 3CLpro Expression and Activity Using a Polyclonal Antiserum and a Luciferase-Based Biosensor. Virology 556: 73-78. DOI: 10.1016/j.virol.2021.01.010

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Chen, Da-Yuan, N. Khan, B. J. Close, R. K. Goel, B. Blum, A. H. Tavares, D. Kenney, H. L. Conway, J. K. Ewoldt, S. Kapell, V. C. Chitalia, N. A. Crossland, C. S. Chen, D. N. Kotton, S. C. Baker, S.Y. Fuchs, J. H. Connor, F. Douam, A Emili, Mohsan Saeed.  (2021). SARS-CoV-2 Disrupts Proximal Elements in the JAK-STAT Pathway. J. Virol. DOI:10.1128/JVI.00862-21.

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2020

Gorbalenya, A.E., Baker, S.C., Baric, R.S. et al. The Species Severe Acute Respiratory Syndrome-Related Coronavirus: Classifying 2019-nCoV and Naming it SARS-CoV-2. Nat Microbiol 5, 536–544 (2020). DOI:10.1038/s41564-020-0695-z

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Rowley, A. H., Susan C. Baker, D. Arrollo, L. J. Gruen, T. Bodnar, N. Innocentini, M. Hackbart, Y. Cruz-Pulido, K. M. Wylie, K. A. Kim, and S.T. Shulman. (2020). A Protein Epitope Targeted by the Antibody Response to Kawasaki Disease. Journal of Infectious Diseases. DOI: 10.1093/infdis/jiaa066

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Deng, Xufang, Y. Chen, A. M. Mielech, M. Hackbart, K. R. Kesely, R. C. Mettelman, A. O’Brien, M. E. Chapman, A. D. Mesecar, and Susan C. Baker. (2020). Structure-Guided Mutagenesis Alters Deubiquitinating Activity and Attenuates Pathogenesis of Murine Coronavirus. Journal of Virology. DOI: 10.1128/JVI.01734-19.

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Volk, A., Matthew Hackbart, Xufang Deng, Yazmin Cruz-Pulido, Amornrat O’Brien, and Susan C. Baker  (2020). Coronavirus Endoribonuclease and Deubiquitinating Interferon Antagonists Differentially Modulate the Host Response during Replication in Macrophages. Journal of Virology. DOI: 10.1128/JVI.00178-20.

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Hackbart, Matthew, Xufang Deng and Susan C. Baker. (2020). Coronavirus Endoribonuclease Targets Viral Poly-Uridine Sequences to Evade Activating Host Sensors. Proc. Natl. Acad. Sci. DOI: 10.1073/pnas.1921485117

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Deng, Xufang, A.C. Buckley, A. Pillatzki, K.M. Lager, K.S. Faaberg, and Susan C. Baker. (2020). Inactivating Three Interferon Antagonists Attenuates Pathogenesis of an Enteric Coronavirus. Journal of Virology. DOI: 10.1128/JVI.00565-20.

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2019

Deng, Xufang, Robert C. Mettelman, Amornrat O’Brien, and Susan C. Baker(2019). Analysis of Coronavirus Temperature-Sensitive Mutants Reveals an Interplay Between the Macrodomain and Papain-Like Protease Impacting Replication and Pathogenesis. Journal of Virology. DOI: 10.1128/JVI.02140-18

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Deng, Xufang, A. vanGeelen, A.C. Buckley, K.M. Lager, K.S. Faaberg, and Susan C. Baker. (2019). Coronavirus Endoribonuclease Activity in Porcine Epidemic Diarrhea Virus Suppresses Type I and Type III Interferon Responses. Journal of Virology. DOI: 10.1128/JVI.02000-18

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Mettelman, Robert C., Amornrat O’Brien, Gary R. Whittaker, and Susan C. Baker. (2019). Generating and Evaluating Type 1 Interferon Receptor-Deficient and Feline TMPRSS2-Expressing Cells for Propagating Serotype I Feline Infectious Peritonitis Virus. Virology. DOI: 10.1016/j.virol.2019.08.030

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2018

Deng, Xufang and Susan C. Baker. (2018). An “Old” Protein with a New Story: Coronavirus Endoribonuclease is Important for Evading Host Antiviral Defenses.  Virology 517: 157-163. DOI: 10.1016/j.virol.2017.12.024

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O’Brien, A., R.C. Mettelman, A. Volk, N.M. Andre, G.R. Whittaker, Susan C. Baker. (2018). Characterizing Replication Kinetics and Plaque Production of Type I Feline Infectious Peritonitis Virus in Three Feline Cell Lines. Virology 525: 1-9. DOI: 10.1016/j.virol.2018.08.022

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Niemeyer Daniela, Kirstin Mösbauer, Eva M. Klein, Andrea Sieberg, Robert C. Mettelman, Anna M. Mielech, Ronald Dijkman, Susan C. Baker, Christian Drosten, Marcel A. Müller. (2018). The Papain-Like Protease Determines a Virulence Trait that Varies Among Members of the SARS-Coronavirus Species. PLoS Pathog 14(9): e1007296. DOI: 10.1371/journal.ppat.1007296

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2017

Clasman, J.R., Baez-Santos, Y.M., Mettelman, R.C., O’Brien, A., Baker, S.C. and A.D. Mesecar. (2017). X-Ray Structure and Enzymatic Activity Profile of a Core Papain-Like Protease of MERS Coronavirus with Utility for Structure-Based Drug Design. Nature Scientific Reports 7, 40292; DOI: 10.1038/srep40292.

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Rowley, A.H., Baker, S.C., Kim, K.A., Shulman, S.T., Yang, A., Arrollo, D., DeBerge, M., Han, S., Sibinga, N.E.S., Pink, A.J., and E.B. Thorp. (2017). Allograft Inflammatory Factor-1 links T cell Activation, Interferon Response, and Macrophage Activation in Chronic Kawasaki Disease Arteritis. Journal of the Pediatric Infectious Disease Society. 15 May 2017. DOI:10.1093/jpids/pix025

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Deng, X.,  A. Mielech, M. Hackbart, R. C.Mettelman, A. O’Brien, G. Yi, C. C. Kao and Susan C. Baker. (2017). Coronavirus Nonstructural Protein 15 Mediates Evasion of dsRNA Sensors and Limits Apoptosis in Macrophages Proc. Natl. Acad. Sci. DOI: 10.1073/pnas.1618310114.

 

High Impact Papers

Immunohistochemical stain for IgA plasma cells (PCs) in normal patients and those with Kawasaki disease (KD). A, Normal tracheal submucosal glands. B, Section of trachea from patient with KD showing a mild (grade 1) infiltrate of IgA PCs. C, Severe (grade 3) IgA PC infiltrate surrounds glands in the trachea of a patient with KD. D, Section of normal pancreatic duct from a control demonstrates no inflammation. E, Mild infiltrate of IgA PCs in a patient with KD is in close proximity to a pancreatic duct. F, Marked number of periductular IgA PCs are present in another patient with KD; cells spill over into surrounding interstitial tissue. G, Section of normal kidney. H, Few clusters of IgA PCs are noted in the renal parenchyma of a patient with KD. I, High-grade infiltrate is located adjacent to glomeruli and proximal tubules in a patient with KD. A–I, 340 objective.
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IgA Plasma Cell Infiltration of Proximal Respiratory Tract, Pancreas, Kidney, and Coronary Artery in Acute Kawasaki Disease

Rowley, A. H., S. T. Shulman, C. A. Mask, L. Finn, M. Terai, S. C. Baker, C. A. Galliani, K. Takahashi, S. Naoe, M. Kalelkar and S. E. Crawford.

The Journal of Infectious Diseases, Volume 182, Issue 4, October 2000

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RNA Replication of Mouse Hepatitis Virus Takes Place at Double-Membrane Vesicles

Gosert, R., A. Kanjanahaluethai, D. Egger, K. Bienz, and S. C. Baker.

J. Virol,  Vol. 76, No. 8, April 2002

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Cytoplasmic Inclusion Bodies Are Detected by Synthetic Antibody in Ciliated Bronchial Epithelium during Acute Kawasaki Disease

Rowley, A. H., S. C. Baker, S. T. Shulman, L. Fox, K. Takahasi, F. L. Garcia, S.E. Crawford, P. Chou, and J. M. Orenstein. 

The Journal of Infectious Diseases, Volume 192, Issue 10, November 2005

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The Papain-Like Protease of Severe Acute Respiratory Syndrome Coronavirus Has Deubiquitinating Activity

Barretto, N., D. Jukneliene, K. Ratia, Z. Chen, A. D. Mesecar and S. C. Baker. 

Journal of Virology, Vol. 79, No. 24, December 2005

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Severe Acute Respiratory Syndrome Coronavirus Papain-Like Protease: Structure of a Viral Deubiquitinating Enzyme

Ratia, K., K.S. Saikatendu, B.D. Santarsiero, N. Barretto, S. C. Baker, R.C. Stevens, and A.D. Mesecar.

PNAS, April 2006, 103 (15) 5717-5722

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A Noncovalent Class of Papain-Like Protease/Deubiquitinase Inhibitors Blocks SARS Virus Replication

Ratia, K., S. Pegan, J. Takayama, K. Sleeman, M. Coughlin, S. Baliji, R. Chaudhuri, W. Fu, B.S. Prabhakar, M.E. Johnson, S.C. Baker, A.K. Ghosh and A.D. Mesecar.

PNAS, October 2008, 105 (42) 16119-16124

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Middle East Respiratory Syndrome Coronavirus (MERS-CoV): Announcement of the Coronavirus Study Group

de Groot, Raoul, J., Susan C. Baker, Ralph S. Baric, Caroline S. Brown, Christian Drosten, Luis Enjuanes, Ron A.M. Fouchier, Monica Galiano, Alexander E. Gorbalenya, Ziad Memish, Stanley Perlman, Leo L.M. Poon, Eric J. Snijder, Gwen M. Stephens, Patrick C.Y. Woo, Ali M. Zaki, Maria Zambon, John Ziebuhr.

Journal of Virology, Volume 87, No. 14, June 2013

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Assessing Activity and Inhibition of Middle East Respiratory Syndrome Coronavirus Papain-Like and 3C-Like Proteases Using Luciferase-Based Biosensors

Kilianski, Andy, Anna Mielech, Xufang Deng and Susan C. Baker.

Journal of Virology, Volume 87, No. 21, October 2013

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Coronaviruses Resistant to a 3C-Like Protease Inhibitor Are Attenuated for Replication and Pathogenesis, Revealing a Low Genetic Barrier but High Fitness Cost of Resistance

Deng, Xufang, Sarah E. St. John, Heather L. Osswald, Amornrat O’Brien, Bridget S. Banach, Katrina Sleeman, Arun K. Ghosh, Andrew D. Mesecar, and Susan C. Baker.

Journal of Virology, Volume 88, No. 20, September 2014

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