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1. A compendium of multi-omics data illuminating host responses to lethal human virus infections

Author

Eisfeld, Amie J., Anderson, Lindsey N., Fan, Shufang, Walters, Kevin B., Halfmann, Peter J., Westhoff Smith, Danielle, Thackray, Larissa B., Tan, Qing, Sims, Amy C., Menachery, Vineet D., Schäfer, Alexandra, Sheahan, Timothy P., Cockrell, Adam S., Stratton, Kelly G., Webb-Robertson, Bobbie-Jo M., Kyle, Jennifer E., Burnum-Johnson, Kristin E., Kim, Young-Mo, Nicora, Carrie D., Peralta, Zuleyma, N’jai, Alhaji U., Sahr, Foday, van Bakel, Harm, Diamond, Michael S., Baric, Ralph S., Metz, Thomas O., Smith, Richard D., Kawaoka, Yoshihiro, and Waters, Katrina M.

Published
2024
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2. The NSP3 protein of SARS-CoV-2 binds fragile X mental retardation proteins to disrupt UBAP2L interactions

Author

Garvanska, Dimitriya H, Alvarado, R Elias, Mundt, Filip Oskar, Lindqvist, Richard, Duel, Josephine Kerzel, Coscia, Fabian, Nilsson, Emma, Lokugamage, Kumari, Johnson, Bryan A, Plante, Jessica A, Morris, Dorothea R, Vu, Michelle N, Estes, Leah K, McLeland, Alyssa M, Walker, Jordyn, Crocquet-Valdes, Patricia A, Mendez, Blanca Lopez, Plante, Kenneth S, Walker, David H, Weisser, Melanie Bianca, Överby, Anna K, Mann, Matthias, Menachery, Vineet D, and Nilsson, Jakob

Published
2024
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3. SARS-CoV-2 Uses Nonstructural Protein 16 To Evade Restriction by IFIT1 and IFIT3

Author

Schindewolf, Craig, Lokugamage, Kumari, Vu, Michelle N, Johnson, Bryan A, Scharton, Dionna, Plante, Jessica A, Kalveram, Birte, Crocquet-Valdes, Patricia A, Sotcheff, Stephanea, Jaworski, Elizabeth, Alvarado, Rojelio E, Debbink, Kari, Daugherty, Matthew D, Weaver, Scott C, Routh, Andrew L, Walker, David H, Plante, Kenneth S, and Menachery, Vineet D

Subjects
Pneumonia & Influenza, Emerging Infectious Diseases, Lung, Infectious Diseases, Vaccine Related, Biotechnology, Biodefense, Prevention, Pneumonia, Aetiology, 2.1 Biological and endogenous factors, Infection, Respiratory, Good Health and Well Being, Adaptor Proteins, Signal Transducing, COVID-19, Interferon Type I, Intracellular Signaling Peptides and Proteins, Methyltransferases, RNA-Binding Proteins, SARS-CoV-2, Viral Nonstructural Proteins, Animals, Cricetinae, 2'-O-methyltransferase, IFIT1, IFIT3, interferon-stimulated gene, NSP16, antiviral agents, coronavirus, Biological Sciences, Agricultural and Veterinary Sciences, Medical and Health Sciences, Virology
Abstract

Understanding the molecular basis of innate immune evasion by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an important consideration for designing the next wave of therapeutics. Here, we investigate the role of the nonstructural protein 16 (NSP16) of SARS-CoV-2 in infection and pathogenesis. NSP16, a ribonucleoside 2'-O-methyltransferase (MTase), catalyzes the transfer of a methyl group to mRNA as part of the capping process. Based on observations with other CoVs, we hypothesized that NSP16 2'-O-MTase function protects SARS-CoV-2 from cap-sensing host restriction. Therefore, we engineered SARS-CoV-2 with a mutation that disrupts a conserved residue in the active site of NSP16. We subsequently show that this mutant is attenuated both in vitro and in vivo, using a hamster model of SARS-CoV-2 infection. Mechanistically, we confirm that the NSP16 mutant is more sensitive than wild-type SARS-CoV-2 to type I interferon (IFN-I) in vitro. Furthermore, silencing IFIT1 or IFIT3, IFN-stimulated genes that sense a lack of 2'-O-methylation, partially restores fitness to the NSP16 mutant. Finally, we demonstrate that sinefungin, an MTase inhibitor that binds the catalytic site of NSP16, sensitizes wild-type SARS-CoV-2 to IFN-I treatment and attenuates viral replication. Overall, our findings highlight the importance of SARS-CoV-2 NSP16 in evading host innate immunity and suggest a target for future antiviral therapies. IMPORTANCE Similar to other coronaviruses, disruption of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) NSP16 function attenuates viral replication in a type I interferon-dependent manner. In vivo, our results show reduced disease and viral replication at late times in the hamster lung, but an earlier titer deficit for the NSP16 mutant (dNSP16) in the upper airway. In addition, our results confirm a role for IFIT1 but also demonstrate the necessity of IFIT3 in mediating dNSP16 attenuation. Finally, we show that targeting NSP16 activity with a 2'-O-methyltransferase inhibitor in combination with type I interferon offers a novel avenue for antiviral development.

Published
2023

4. Defining the risk of SARS-CoV-2 variants on immune protection

Author

DeGrace, Marciela M, Ghedin, Elodie, Frieman, Matthew B, Krammer, Florian, Grifoni, Alba, Alisoltani, Arghavan, Alter, Galit, Amara, Rama R, Baric, Ralph S, Barouch, Dan H, Bloom, Jesse D, Bloyet, Louis-Marie, Bonenfant, Gaston, Boon, Adrianus CM, Boritz, Eli A, Bratt, Debbie L, Bricker, Traci L, Brown, Liliana, Buchser, William J, Carreño, Juan Manuel, Cohen-Lavi, Liel, Darling, Tamarand L, Davis-Gardner, Meredith E, Dearlove, Bethany L, Di, Han, Dittmann, Meike, Doria-Rose, Nicole A, Douek, Daniel C, Drosten, Christian, Edara, Venkata-Viswanadh, Ellebedy, Ali, Fabrizio, Thomas P, Ferrari, Guido, Fischer, Will M, Florence, William C, Fouchier, Ron AM, Franks, John, García-Sastre, Adolfo, Godzik, Adam, Gonzalez-Reiche, Ana Silvia, Gordon, Aubree, Haagmans, Bart L, Halfmann, Peter J, Ho, David D, Holbrook, Michael R, Huang, Yaoxing, James, Sarah L, Jaroszewski, Lukasz, Jeevan, Trushar, Johnson, Robert M, Jones, Terry C, Joshi, Astha, Kawaoka, Yoshihiro, Kercher, Lisa, Koopmans, Marion PG, Korber, Bette, Koren, Eilay, Koup, Richard A, LeGresley, Eric B, Lemieux, Jacob E, Liebeskind, Mariel J, Liu, Zhuoming, Livingston, Brandi, Logue, James P, Luo, Yang, McDermott, Adrian B, McElrath, Margaret J, Meliopoulos, Victoria A, Menachery, Vineet D, Montefiori, David C, Mühlemann, Barbara, Munster, Vincent J, Munt, Jenny E, Nair, Manoj S, Netzl, Antonia, Niewiadomska, Anna M, O’Dell, Sijy, Pekosz, Andrew, Perlman, Stanley, Pontelli, Marjorie C, Rockx, Barry, Rolland, Morgane, Rothlauf, Paul W, Sacharen, Sinai, Scheuermann, Richard H, Schmidt, Stephen D, Schotsaert, Michael, Schultz-Cherry, Stacey, Seder, Robert A, Sedova, Mayya, Sette, Alessandro, Shabman, Reed S, Shen, Xiaoying, Shi, Pei-Yong, Shukla, Maulik, Simon, Viviana, Stumpf, Spencer, Sullivan, Nancy J, Thackray, Larissa B, and Theiler, James

Subjects
Medical Microbiology, Biomedical and Clinical Sciences, Biological Sciences, Emerging Infectious Diseases, Pneumonia, Vaccine Related, Pneumonia & Influenza, Infectious Diseases, Biodefense, Immunization, Biotechnology, Prevention, Lung, Prevention of disease and conditions, and promotion of well-being, 2.1 Biological and endogenous factors, 3.4 Vaccines, Aetiology, Infection, Good Health and Well Being, Animals, Biological Evolution, COVID-19, COVID-19 Vaccines, Humans, National Institute of Allergy and Infectious Diseases (U.S.), Pandemics, Pharmacogenomic Variants, SARS-CoV-2, United States, Virulence, General Science & Technology
Abstract

The global emergence of many severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants jeopardizes the protective antiviral immunity induced after infection or vaccination. To address the public health threat caused by the increasing SARS-CoV-2 genomic diversity, the National Institute of Allergy and Infectious Diseases within the National Institutes of Health established the SARS-CoV-2 Assessment of Viral Evolution (SAVE) programme. This effort was designed to provide a real-time risk assessment of SARS-CoV-2 variants that could potentially affect the transmission, virulence, and resistance to infection- and vaccine-induced immunity. The SAVE programme is a critical data-generating component of the US Government SARS-CoV-2 Interagency Group to assess implications of SARS-CoV-2 variants on diagnostics, vaccines and therapeutics, and for communicating public health risk. Here we describe the coordinated approach used to identify and curate data about emerging variants, their impact on immunity and effects on vaccine protection using animal models. We report the development of reagents, methodologies, models and notable findings facilitated by this collaborative approach and identify future challenges. This programme is a template for the response to rapidly evolving pathogens with pandemic potential by monitoring viral evolution in the human population to identify variants that could reduce the effectiveness of countermeasures.

Published
2022

5. Genetic loci regulate Sarbecovirus pathogenesis: A comparison across mice and humans

Author

Schäfer, Alexandra, Gralinski, Lisa E., Leist, Sarah R., Hampton, Brea K., Mooney, Michael A., Jensen, Kara L., Graham, Rachel L., Agnihothram, Sudhakar, Jeng, Sophia, Chamberlin, Steven, Bell, Timothy A., Scobey, D. Trevor, Linnertz, Colton L., VanBlargan, Laura A., Thackray, Larissa B., Hock, Pablo, Miller, Darla R., Shaw, Ginger D., Diamond, Michael S., de Villena, Fernando Pardo Manuel, McWeeney, Shannon K., Heise, Mark T., Menachery, Vineet D., Ferris, Martin T., and Baric, Ralph S.

Published
2024
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6. Interaction between host G3BP and viral nucleocapsid protein regulates SARS-CoV-2 replication and pathogenicity

Author

Yang, Zemin, Johnson, Bryan A., Meliopoulos, Victoria A., Ju, Xiaohui, Zhang, Peipei, Hughes, Michael P., Wu, Jinjun, Koreski, Kaitlin P., Clary, Jemma E., Chang, Ti-Cheng, Wu, Gang, Hixon, Jeff, Duffner, Jay, Wong, Kathy, Lemieux, Rene, Lokugamage, Kumari G., Alvarado, R. Elias, Crocquet-Valdes, Patricia A., Walker, David H., Plante, Kenneth S., Plante, Jessica A., Weaver, Scott C., Kim, Hong Joo, Meyers, Rachel, Schultz-Cherry, Stacey, Ding, Qiang, Menachery, Vineet D., and Taylor, J. Paul

Published
2024
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7. Hypergraph Models of Biological Networks to Identify Genes Critical to Pathogenic Viral Response

Author

Feng, Song, Heath, Emily, Jefferson, Brett, Joslyn, Cliff, Kvinge, Henry, Mitchell, Hugh D., Praggastis, Brenda, Eisfeld, Amie J., Sims, Amy C., Thackray, Larissa B., Fan, Shufang, Walters, Kevin B., Halfmann, Peter J., Westhoff-Smith, Danielle, Tan, Qing, Menachery, Vineet D., Sheahan, Timothy P., Cockrell, Adam S., Kocher, Jacob F., Stratton, Kelly G., Heller, Natalie C., Bramer, Lisa M., Diamond, Michael S., Baric, Ralph S., Waters, Katrina M., Kawaoka, Yoshihiro, McDermott, Jason E., and Purvine, Emilie

Subjects
Quantitative Biology - Quantitative Methods, Mathematics - Combinatorics, 92C42, 92-08, 05C65
Abstract

Background: Representing biological networks as graphs is a powerful approach to reveal underlying patterns, signatures, and critical components from high-throughput biomolecular data. However, graphs do not natively capture the multi-way relationships present among genes and proteins in biological systems. Hypergraphs are generalizations of graphs that naturally model multi-way relationships and have shown promise in modeling systems such as protein complexes and metabolic reactions. In this paper we seek to understand how hypergraphs can more faithfully identify, and potentially predict, important genes based on complex relationships inferred from genomic expression data sets. Results: We compiled a novel data set of transcriptional host response to pathogenic viral infections and formulated relationships between genes as a hypergraph where hyperedges represent significantly perturbed genes, and vertices represent individual biological samples with specific experimental conditions. We find that hypergraph betweenness centrality is a superior method for identification of genes important to viral response when compared with graph centrality. Conclusions: Our results demonstrate the utility of using hypergraphs to represent complex biological systems and highlight central important responses in common to a variety of highly pathogenic viruses.

Published
2020

10. Engineering SARS-CoV-2 specific cocktail antibodies into a bispecific format improves neutralizing potency and breadth

Author

Ku, Zhiqiang, Xie, Xuping, Lin, Jianqing, Gao, Peng, Wu, Bin, El Sahili, Abbas, Su, Hang, Liu, Yang, Ye, Xiaohua, Tan, Eddie Yongjun, Li, Xin, Fan, Xuejun, Goh, Boon Chong, Xiong, Wei, Boyd, Hannah, Muruato, Antonio E., Deng, Hui, Xia, Hongjie, Zou, Jing, Kalveram, Birte K., Menachery, Vineet D., Zhang, Ningyan, Lescar, Julien, Shi, Pei-Yong, and An, Zhiqiang

Published
2022
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14. Variant mutation in SARS-CoV-2 nucleocapsid enhances viral infection via altered genomic encapsidation

Author

Kubinski, Hannah C., primary, Despres, Hannah W., additional, Johnson, Bryan A., additional, Schmidt, Madaline M., additional, Jaffrani, Sara A., additional, Mills, Margaret G., additional, Lokugamage, Kumari, additional, Dumas, Caroline M., additional, Shirley, David J., additional, Estes, Leah K., additional, Pekosz, Andrew, additional, Crothers, Jessica W., additional, Roychoudhury, Pavitra, additional, Greninger, Alexander L., additional, Jerome, Keith R., additional, Di Genova, Bruno Martorelli, additional, Walker, David H., additional, Ballif, Bryan A., additional, Ladinsky, Mark S., additional, Bjorkman, Pamela J., additional, Menachery, Vineet D., additional, and Bruce, Emily A., additional

Published
2024
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16. Nasal delivery of an IgM offers broad protection from SARS-CoV-2 variants

Author

Ku, Zhiqiang, Xie, Xuping, Hinton, Paul R., Liu, Xinli, Ye, Xiaohua, Muruato, Antonio E., Ng, Dean C., Biswas, Sujit, Zou, Jing, Liu, Yang, Pandya, Deepal, Menachery, Vineet D., Rahman, Sachi, Cao, Yu-An, Deng, Hui, Xiong, Wei, Carlin, Kevin B., Liu, Junquan, Su, Hang, Haanes, Elizabeth J., Keyt, Bruce A., Zhang, Ningyan, Carroll, Stephen F., Shi, Pei-Yong, and An, Zhiqiang

Published
2021
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17. The NSP3 protein of SARS-CoV-2 binds fragile X mental retardation proteins to disrupt UBAP2L interactions

Author

Garvanska, Dimitriya H., Alvarado, R. Elias, Mundt, Filip Oskar, Lindquist, Richard, Duel, Josephine Kerzel, Coscia, Fabian, Nilsson, Emma, Lokugamage, Kumari, Johnson, Bryan A., Plante, Jessica A., Morris, Dorothea R., Vu, Michelle N., Estes, Leah K., McLeland, Alyssa M., Walker, Jordyn, Crocquet-Valdes, Patricia A., Mendez, Blanca Lopez, Plante, Kenneth S., Walker, David H., Weisser, Melanie Bianca, Överby, Anna K., Mann, Matthias, Menachery, Vineet D., Nilsson, Jakob, Garvanska, Dimitriya H., Alvarado, R. Elias, Mundt, Filip Oskar, Lindquist, Richard, Duel, Josephine Kerzel, Coscia, Fabian, Nilsson, Emma, Lokugamage, Kumari, Johnson, Bryan A., Plante, Jessica A., Morris, Dorothea R., Vu, Michelle N., Estes, Leah K., McLeland, Alyssa M., Walker, Jordyn, Crocquet-Valdes, Patricia A., Mendez, Blanca Lopez, Plante, Kenneth S., Walker, David H., Weisser, Melanie Bianca, Överby, Anna K., Mann, Matthias, Menachery, Vineet D., and Nilsson, Jakob

Abstract

Viruses interact with numerous host factors to facilitate viral replication and to dampen antiviral defense mechanisms. We currently have a limited mechanistic understanding of how SARS-CoV-2 binds host factors and the functional role of these interactions. Here, we uncover a novel interaction between the viral NSP3 protein and the fragile X mental retardation proteins (FMRPs: FMR1, FXR1-2). SARS-CoV-2 NSP3 mutant viruses preventing FMRP binding have attenuated replication in vitro and reduced levels of viral antigen in lungs during the early stages of infection. We show that a unique peptide motif in NSP3 binds directly to the two central KH domains of FMRPs and that this interaction is disrupted by the I304N mutation found in a patient with fragile X syndrome. NSP3 binding to FMRPs disrupts their interaction with the stress granule component UBAP2L through direct competition with a peptide motif in UBAP2L to prevent FMRP incorporation into stress granules. Collectively, our results provide novel insight into how SARS-CoV-2 hijacks host cell proteins and provides molecular insight into the possible underlying molecular defects in fragile X syndrome.

Published
2024
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18. Spike mutation D614G alters SARS-CoV-2 fitness

Author

Plante, Jessica A., Liu, Yang, Liu, Jianying, Xia, Hongjie, Johnson, Bryan A., Lokugamage, Kumari G., Zhang, Xianwen, Muruato, Antonio E., Zou, Jing, Fontes-Garfias, Camila R., Mirchandani, Divya, Scharton, Dionna, Bilello, John P., Ku, Zhiqiang, An, Zhiqiang, Kalveram, Birte, Freiberg, Alexander N., Menachery, Vineet D., Xie, Xuping, Plante, Kenneth S., Weaver, Scott C., and Shi, Pei-Yong

Published
2021
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19. Loss of furin cleavage site attenuates SARS-CoV-2 pathogenesis

Author

Johnson, Bryan A., Xie, Xuping, Bailey, Adam L., Kalveram, Birte, Lokugamage, Kumari G., Muruato, Antonio, Zou, Jing, Zhang, Xianwen, Juelich, Terry, Smith, Jennifer K., Zhang, Lihong, Bopp, Nathen, Schindewolf, Craig, Vu, Michelle, Vanderheiden, Abigail, Winkler, Emma S., Swetnam, Daniele, Plante, Jessica A., Aguilar, Patricia, Plante, Kenneth S., Popov, Vsevolod, Lee, Benhur, Weaver, Scott C., Suthar, Mehul S., Routh, Andrew L., Ren, Ping, Ku, Zhiqiang, An, Zhiqiang, Debbink, Kari, Diamond, Michael S., Shi, Pei-Yong, Freiberg, Alexander N., and Menachery, Vineet D.

Published
2021
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21. Rapid Generation of Neutralizing Antibody Responses in COVID-19 Patients

Author

Suthar, Mehul S., Zimmerman, Matthew G., Kauffman, Robert C., Mantus, Grace, Linderman, Susanne L., Hudson, William H., Vanderheiden, Abigail, Nyhoff, Lindsay, Davis, Carl W., Adekunle, Oluwaseyi, Affer, Maurizio, Sherman, Melanie, Reynolds, Stacian, Verkerke, Hans P., Alter, David N., Guarner, Jeannette, Bryksin, Janetta, Horwath, Michael C., Arthur, Connie M., Saakadze, Natia, Smith, Geoffrey H., Edupuganti, Srilatha, Scherer, Erin M., Hellmeister, Kieffer, Cheng, Andrew, Morales, Juliet A., Neish, Andrew S., Stowell, Sean R., Frank, Filipp, Ortlund, Eric, Anderson, Evan J., Menachery, Vineet D., Rouphael, Nadine, Mehta, Aneesh K., Stephens, David S., Ahmed, Rafi, Roback, John D., and Wrammert, Jens

Published
2020
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22. An Infectious cDNA Clone of SARS-CoV-2

Author

Xie, Xuping, Muruato, Antonio, Lokugamage, Kumari G., Narayanan, Krishna, Zhang, Xianwen, Zou, Jing, Liu, Jianying, Schindewolf, Craig, Bopp, Nathen E., Aguilar, Patricia V., Plante, Kenneth S., Weaver, Scott C., Makino, Shinji, LeDuc, James W., Menachery, Vineet D., and Shi, Pei-Yong

Published
2020
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25. Hypergraph models of biological networks to identify genes critical to pathogenic viral response

Author

Feng, Song, Heath, Emily, Jefferson, Brett, Joslyn, Cliff, Kvinge, Henry, Mitchell, Hugh D., Praggastis, Brenda, Eisfeld, Amie J., Sims, Amy C., Thackray, Larissa B., Fan, Shufang, Walters, Kevin B., Halfmann, Peter J., Westhoff-Smith, Danielle, Tan, Qing, Menachery, Vineet D., Sheahan, Timothy P., Cockrell, Adam S., Kocher, Jacob F., Stratton, Kelly G., Heller, Natalie C., Bramer, Lisa M., Diamond, Michael S., Baric, Ralph S., Waters, Katrina M., Kawaoka, Yoshihiro, McDermott, Jason E., and Purvine, Emilie

Published
2021
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26. SARS-CoV-2 RBD trimer protein adjuvanted with Alum-3M-052 protects from SARS-CoV-2 infection and immune pathology in the lung

Author

Routhu, Nanda Kishore, Cheedarla, Narayanaiah, Bollimpelli, Venkata Satish, Gangadhara, Sailaja, Edara, Venkata Viswanadh, Lai, Lilin, Sahoo, Anusmita, Shiferaw, Ayalnesh, Styles, Tiffany M., Floyd, Katharine, Fischinger, Stephanie, Atyeo, Caroline, Shin, Sally A., Gumber, Sanjeev, Kirejczyk, Shannon, Dinnon, III, Kenneth H., Shi, Pei-Yong, Menachery, Vineet D., Tomai, Mark, Fox, Christopher B., Alter, Galit, Vanderford, Thomas H., Gralinski, Lisa, Suthar, Mehul S., and Amara, Rama Rao

Published
2021
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28. Severe Acute Respiratory Syndrome Coronavirus 2 from Patient with Coronavirus Disease, United States

Author

Harcourt, Jennifer, Tamin, Azaibi, Lu, Xiaoyan, Kamili, Shifaq, Sakthivel, Senthil K., Murray, Janna, Queen, Krista, Tao, Ying, Paden, Clinton R., Zhang, Jing, Li, Yan, Uehara, Anna, Wang, Haibin, Goldsmith, Cynthia, Bullock, Hannah A., Wang, Lijuan, Whitaker, Brett, Lynch, Brian, Gautam, Rashi, Schindewolf, Craig, Lokugamage, Kumari G., Scharton, Dionna, Plante, Jessica A., Mirchandani, Divya, Widen, Steven G., Narayanan, Krishna, Makino, Shinji, Ksiazek, Thomas G., Plante, Kenneth S., Weaver, Scott C., Lindstrom, Stephen, Tong, Suxiang, Menachery, Vineet D., and Thornburg, Natalie J.

Subjects
United States. Centers for Disease Control and Prevention, Severe acute respiratory syndrome, Coronaviruses, Health
Abstract

A novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been identified as the source of a pneumonia outbreak in Wuhan, China, in late 2019 (2,2). The virus was [...]

Published
2020
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29. SARS-CoV-2 hijacks fragile X mental retardation proteins for efficient infection

Author

Garvanska, Dimitriya, primary, Alvarado, Rojelio E, additional, Mundt, Filip, additional, Nilsson, Emma, additional, Duel, Josephine, additional, Coscia, Fabian, additional, Lindqvist, Richard, additional, Lokugamage, Kumari, additional, Johnson, Bryan, additional, Plante, Jessica A, additional, Morris, Dorothea R., additional, Vu, Michelle N, additional, Estes, Leah, additional, McLeland, Alyssa, additional, Walker, Jordyn, additional, Crocquet-Valdes, Patricia, additional, Lopez-Mendez, Blanca, additional, Plante, Kenneth, additional, Walker, David H., additional, Weisser, Melanie B, additional, Overby, Anna K, additional, Mann, Matthias, additional, Menachery, Vineet D, additional, and Nilsson, Jakob, additional

Published
2023
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30. MERS-CoV and H5N1 influenza virus antagonize antigen presentation by altering the epigenetic landscape

Author

Menachery, Vineet D., Schäfer, Alexandra, Burnum-Johnson, Kristin E., Mitchell, Hugh D., Eisfeld, Amie J., Walters, Kevin B., Nicora, Carrie D., Purvine, Samuel O., Casey, Cameron P., Monroe, Matthew E., Weitz, Karl K., Stratton, Kelly G., Webb-Robertson, Bobbie-Jo M., Gralinski, Lisa E., Metz, Thomas O., Smith, Richard D., Waters, Katrina M., Sims, Amy C., Kawaoka, Yoshihiro, and Baric, Ralph S.

Published
2018

34. Interaction between host G3BP and viral nucleocapsid protein regulates SARS-CoV-2 replication

Author

Yang, Zemin, primary, Johnson, Bryan A., additional, Meliopoulos, Victoria A., additional, Ju, Xiaohui, additional, Zhang, Peipei, additional, Hughes, Michael P., additional, Wu, Jinjun, additional, Koreski, Kaitlin P., additional, Chang, Ti-Cheng, additional, Wu, Gang, additional, Hixon, Jeff, additional, Duffner, Jay, additional, Wong, Kathy, additional, Lemieux, Rene, additional, Lokugamage, Kumari G., additional, Alvardo, Rojelio E., additional, Crocquet-Valdes, Patricia A., additional, Walker, David H., additional, Plante, Kenneth S., additional, Plante, Jessica A., additional, Weaver, Scott C., additional, Kim, Hong Joo, additional, Meyers, Rachel, additional, Schultz-Cherry, Stacey, additional, Ding, Qiang, additional, Menachery, Vineet D., additional, and Taylor, J. Paul, additional

Published
2023
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36. Immunoregulatory Roles of TGF-β and IL-4 during Mouse-adapted SARS-CoV-2 Infection

Author

Sima, Solomon Taye, primary, Puebla-Clark, Lucinda, additional, Gonzalez-Orozco, Maria, additional, Shelite, Thomas R, additional, Federman, Hannah G, additional, Huante, Matthew B, additional, Martinez-Martinez, Yazmin Berenice, additional, Dann, Sara M, additional, Endsley, Mark A, additional, Siracusa, Mark C, additional, Menachery, Vineet D, additional, Endsley, Janice J, additional, Rajsbaum, Ricardo, additional, and Stephens, Robin, additional

Published
2023
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38. Loss-of-function mutation in Omicron variants reduces spike protein expression and attenuates SARS-CoV-2 infection

Author

Vu, Michelle N., primary, Morris, Dorothea R., additional, Alvarado, R. Elias, additional, Lokugamage, Kumari G., additional, Zhou, Yiyang, additional, Estes, Leah K., additional, McLeland, Alyssa M., additional, Schindewolf, Craig, additional, Plante, Jessica A., additional, Ahearn, Yani P., additional, Morgan, Angelica L., additional, Meyers, William M., additional, Murray, Jordan T., additional, Weaver, Scott C., additional, Walker, David H., additional, Russell, William K., additional, Routh, Andrew L., additional, Plante, Kenneth S., additional, and Menachery, Vineet, additional

Published
2023
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40. Author Correction: Spike mutation D614G alters SARS-CoV-2 fitness

Author

Plante, Jessica A., Liu, Yang, Liu, Jianying, Xia, Hongjie, Johnson, Bryan A., Lokugamage, Kumari G., Zhang, Xianwen, Muruato, Antonio E., Zou, Jing, Fontes-Garfias, Camila R., Mirchandani, Divya, Scharton, Dionna, Bilello, John P., Ku, Zhiqiang, An, Zhiqiang, Kalveram, Birte, Freiberg, Alexander N., Menachery, Vineet D., Xie, Xuping, Plante, Kenneth S., Weaver, Scott C., and Shi, Pei-Yong

Published
2021
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41. SARS-like WIV1-CoV poised for human emergence

Author

Menachery, Vineet D., Yount, Boyd L., Sims, Amy C., Debbink, Kari, Agnihothram, Sudhakar S., Gralinski, Lisa E., Graham, Rachel L., Scobey, Trevor, Plante, Jessica A., Royal, Scott R., Swanstrom, Jesica, Sheahan, Timothy P., Pickles, Raymond J., Corti, Davide, Randell, Scott H., Lanzavecchia, Antonio, Marasco, Wayne A., and Baric, Ralph S.

Published
2016

42. Development of Highly Potent Noncovalent Inhibitors of SARS-CoV-2 3CLpro

Author

Hou, Ningke, primary, Shuai, Lei, additional, Zhang, Lijing, additional, Xie, Xuping, additional, Tang, Kaiming, additional, Zhu, Yunkai, additional, Yu, Yin, additional, Zhang, Wenyi, additional, Tan, Qiaozhu, additional, Zhong, Gongxun, additional, Wen, Zhiyuan, additional, Wang, Chong, additional, He, Xijun, additional, Huo, Hong, additional, Gao, Haishan, additional, Xu, You, additional, Xue, Jing, additional, Peng, Chen, additional, Zou, Jing, additional, Schindewolf, Craig, additional, Menachery, Vineet, additional, Su, Wenji, additional, Yuan, Youlang, additional, Shen, Zuyuan, additional, Zhang, Rong, additional, Yuan, Shuofeng, additional, Yu, Hongtao, additional, Shi, Pei-Yong, additional, Bu, Zhigao, additional, Huang, Jing, additional, and Hu, Qi, additional

Published
2023
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45. SARS-CoV-2 Uses Nonstructural Protein 16 to Evade Restriction by IFIT1 and IFIT3

Author

Schindewolf, Craig, primary, Lokugamage, Kumari, additional, Vu, Michelle N., additional, Johnson, Bryan A., additional, Scharton, Dionna, additional, Plante, Jessica A., additional, Kalveram, Birte, additional, Crocquet-Valdes, Patricia A., additional, Sotcheff, Stephanea, additional, Jaworski, Elizabeth, additional, Alvarado, R. Elias, additional, Debbink, Kari, additional, Daugherty, Matthew D., additional, Weaver, Scott C., additional, Routh, Andrew L., additional, Walker, David H., additional, Plante, Kenneth S., additional, and Menachery, Vineet D., additional

Published
2022
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46. Vaccination Decreases the Infectious Viral Load of Delta Variant SARS-CoV-2 in Asymptomatic Patients

Author

Plante, Jessica A., primary, Machado, Rafael R. G., additional, Mitchell, Brooke M., additional, Shinde, Divya P., additional, Walker, Jordyn, additional, Scharton, Dionna, additional, McConnell, Allan, additional, Saada, Nehad, additional, Liu, Jianying, additional, Khan, Bilal, additional, Campos, Rafael K., additional, Johnson, Bryan A., additional, Menachery, Vineet D., additional, Levine, Corri B., additional, Ren, Ping, additional, McLellan, Susan L. F., additional, Plante, Kenneth S., additional, and Weaver, Scott C., additional

Published
2022
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47. Development of highly potent non-covalent inhibitors of SARS-CoV-2 3CLpro

Author

Hou, Ningke, primary, Shuai, Lei, additional, Zhang, Lijing, additional, Xie, Xuping, additional, Tang, Kaiming, additional, Zhu, Yunkai, additional, Yu, Yin, additional, Zhang, Wenyi, additional, Tan, Qiaozhu, additional, Zhong, Gongxun, additional, Wen, Zhiyuan, additional, Wang, Chong, additional, He, Xijun, additional, Huo, Hong, additional, Gao, Haishan, additional, Xu, You, additional, Xue, Jing, additional, Peng, Chen, additional, Zou, Jing, additional, Schindewolf, Craig, additional, Menachery, Vineet, additional, Su, Wenji, additional, Yuan, Youlang, additional, Shen, Zuyuan, additional, Zhang, Rong, additional, Yuan, Shuofeng, additional, Yu, Hongtao, additional, Shi, Pei-Yong, additional, Bu, Zhigao, additional, Huang, Jing, additional, and Hu, Qi, additional

Published
2022
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49. A SARS-like cluster of circulating bat coronaviruses shows potential for human emergence

Author

Menachery, Vineet D., Yount, Jr., Boyd L., Debbink, Kari, Agnihothram, Sudhakar, Gralinski, Lisa E., Plante, Jessica A., Graham, Rachel L., Scobey, Trevor, Ge, Xing-Yi, Donaldson, Eric F., Randell, Scott H., Lanzavecchia, Antonio, Marasco, Wayne A., Shi, Zhengli-Li, and Baric, Ralph S.

Subjects
Monoclonal antibodies -- Health aspects -- Research, Biological sciences, Health
Abstract

The emergence of severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome (MERS)-CoV underscores the threat of cross-species transmission events leading to outbreaks in humans. Here we examine the disease potential of a SARS-like virus, SHC014-CoV, which is currently circulating in Chinese horseshoe bat populations (1). Using the SARS-CoV reverse genetics system (2), we generated and characterized a chimeric virus expressing the spike of bat coronavirus SHC014 in a mouse-adapted SARS-CoV backbone. The results indicate that group 2b viruses encoding the SHC014 spike in a wild-type backbone can efficiently use multiple orthologs of the SARS receptor human angiotensin converting enzyme II (ACE2), replicate efficiently in primary human airway cells and achieve in vitro titers equivalent to epidemic strains of SARS-CoV. Additionally, in vivo experiments demonstrate replication of the chimeric virus in mouse lung with notable pathogenesis. Evaluation of available SARS-based immune-therapeutic and prophylactic modalities revealed poor efficacy; both monoclonal antibody and vaccine approaches failed to neutralize and protect from infection with CoVs using the novel spike protein. On the basis of these findings, we synthetically re-derived an infectious full-length SHC014 recombinant virus and demonstrate robust viral replication both in vitro and in vivo. Our work suggests a potential risk of SARS-CoV re-emergence from viruses currently circulating in bat populations., The emergence of SARS-CoV heralded a new era in the cross-species transmission of severe respiratory illness with globalization leading to rapid spread around the world and massive economic impact (3,4). [...]

Published
2015

50. QTQTN motif upstream of the furin-cleavage site plays a key role in SARS-CoV-2 infection and pathogenesis

Author

Vu, Michelle N., primary, Lokugamage, Kumari G., additional, Plante, Jessica A., additional, Scharton, Dionna, additional, Bailey, Aaron O., additional, Sotcheff, Stephanea, additional, Swetnam, Daniele M., additional, Johnson, Bryan A., additional, Schindewolf, Craig, additional, Alvarado, R. Elias, additional, Crocquet-Valdes, Patricia A., additional, Debbink, Kari, additional, Weaver, Scott C., additional, Walker, David H., additional, Russell, William K., additional, Routh, Andrew L., additional, Plante, Kenneth S., additional, and Menachery, Vineet D., additional

Published
2022
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