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1. Pathogenicity and transmissibility of bovine H5N1 influenza virus

Author

Eisfeld, Amie J., Biswas, Asim, Guan, Lizheng, Gu, Chunyang, Maemura, Tadashi, Trifkovic, Sanja, Wang, Tong, Babujee, Lavanya, Dahn, Randall, Halfmann, Peter J., Barnhardt, Tera, Neumann, Gabriele, Suzuki, Yasuo, Thompson, Alexis, Swinford, Amy K., Dimitrov, Kiril M., Poulsen, Keith, and Kawaoka, Yoshihiro

Published
2024
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2. 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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5. 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

6. Characterization of SARS-CoV-2 Omicron BA.2.75 clinical isolates

Author

Uraki, Ryuta, Iida, Shun, Halfmann, Peter J., Yamayoshi, Seiya, Hirata, Yuichiro, Iwatsuki-Horimoto, Kiyoko, Kiso, Maki, Ito, Mutsumi, Furusawa, Yuri, Ueki, Hiroshi, Sakai-Tagawa, Yuko, Kuroda, Makoto, Maemura, Tadashi, Kim, Taksoo, Mine, Sohtaro, Iwamoto, Noriko, Li, Rong, Liu, Yanan, Larson, Deanna, Fukushi, Shuetsu, Watanabe, Shinji, Maeda, Ken, Wang, Zhongde, Ohmagari, Norio, Theiler, James, Fischer, Will, Korber, Bette, Imai, Masaki, Suzuki, Tadaki, and Kawaoka, Yoshihiro

Published
2023
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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

9. Characterization of SARS-CoV-2 Omicron BA.4 and BA.5 isolates in rodents

Author

Uraki, Ryuta, Halfmann, Peter J., Iida, Shun, Yamayoshi, Seiya, Furusawa, Yuri, Kiso, Maki, Ito, Mutsumi, Iwatsuki-Horimoto, Kiyoko, Mine, Sohtaro, Kuroda, Makoto, Maemura, Tadashi, Sakai-Tagawa, Yuko, Ueki, Hiroshi, Li, Rong, Liu, Yanan, Larson, Deanna, Fukushi, Shuetsu, Watanabe, Shinji, Maeda, Ken, Pekosz, Andrew, Kandeil, Ahmed, Webby, Richard J., Wang, Zhongde, Imai, Masaki, Suzuki, Tadaki, and Kawaoka, Yoshihiro

Published
2022
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10. Characterization and antiviral susceptibility of SARS-CoV-2 Omicron BA.2

Author

Uraki, Ryuta, Kiso, Maki, Iida, Shun, Imai, Masaki, Takashita, Emi, Kuroda, Makoto, Halfmann, Peter J., Loeber, Samantha, Maemura, Tadashi, Yamayoshi, Seiya, Fujisaki, Seiichiro, Wang, Zhongde, Ito, Mutsumi, Ujie, Michiko, Iwatsuki-Horimoto, Kiyoko, Furusawa, Yuri, Wright, Ryan, Chong, Zhenlu, Ozono, Seiya, Yasuhara, Atsuhiro, Ueki, Hiroshi, Sakai-Tagawa, Yuko, Li, Rong, Liu, Yanan, Larson, Deanna, Koga, Michiko, Tsutsumi, Takeya, Adachi, Eisuke, Saito, Makoto, Yamamoto, Shinya, Hagihara, Masao, Mitamura, Keiko, Sato, Tetsuro, Hojo, Masayuki, Hattori, Shin-ichiro, Maeda, Kenji, Valdez, Riccardo, Okuda, Moe, Murakami, Jurika, Duong, Calvin, Godbole, Sucheta, Douek, Daniel C., Maeda, Ken, Watanabe, Shinji, Gordon, Aubree, Ohmagari, Norio, Yotsuyanagi, Hiroshi, Diamond, Michael S., Hasegawa, Hideki, Mitsuya, Hiroaki, Suzuki, Tadaki, and Kawaoka, Yoshihiro

Published
2022
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11. Characterization of a new SARS-CoV-2 variant that emerged in Brazil

Author

Imai, Masaki, Halfmann, Peter J., Yamayoshi, Seiya, Iwatsuki-Horimoto, Kiyoko, Chiba, Shiho, Watanabe, Tokiko, Nakajima, Noriko, Ito, Mutsumi, Kuroda, Makoto, Kiso, Maki, Maemura, Tadashi, Takahashi, Kenta, Loeber, Samantha, Hatta, Masato, Koga, Michiko, Nagai, Hiroyuki, Yamamoto, Shinya, Saito, Makoto, Adachi, Eisuke, Akasaka, Osamu, Nakamura, Morio, Nakachi, Ichiro, Ogura, Takayuki, Baba, Rie, Fujita, Kensuke, Ochi, Junichi, Mitamura, Keiko, Kato, Hideaki, Nakajima, Hideaki, Yagi, Kazuma, Hattori, Shin-ichiro, Maeda, Kenji, Suzuki, Tetsuya, Miyazato, Yusuke, Valdez, Riccardo, Gherasim, Carmen, Furusawa, Yuri, Okuda, Moe, Ujie, Michiko, Lopes, Tiago J. S., Yasuhara, Atsuhiro, Ueki, Hiroshi, Sakai-Tagawa, Yuko, Eisfeld, Amie J., Baczenas, John J., Baker, David A., O’Connor, Shelby L., O’Connor, David H., Fukushi, Shuetsu, Fujimoto, Tsuguto, Kuroda, Yudai, Gordon, Aubree, Maeda, Ken, Ohmagari, Norio, Sugaya, Norio, Yotsuyanagi, Hiroshi, Mitsuya, Hiroaki, Suzuki, Tadaki, and Kawaoka, Yoshihiro

Published
2021

13. SARS-CoV-2 Omicron virus causes attenuated disease in mice and hamsters

Author

Halfmann, Peter J., Iida, Shun, Iwatsuki-Horimoto, Kiyoko, Maemura, Tadashi, Kiso, Maki, Scheaffer, Suzanne M., Darling, Tamarand L., Joshi, Astha, Loeber, Samantha, Singh, Gagandeep, Foster, Stephanie L., Ying, Baoling, Case, James Brett, Chong, Zhenlu, Whitener, Bradley, Moliva, Juan, Floyd, Katharine, Ujie, Michiko, Nakajima, Noriko, Ito, Mutsumi, Wright, Ryan, Uraki, Ryuta, Warang, Prajakta, Gagne, Matthew, Li, Rong, Sakai-Tagawa, Yuko, Liu, Yanan, Larson, Deanna, Osorio, Jorge E., Hernandez-Ortiz, Juan P., Henry, Amy R., Ciuoderis, Karl, Florek, Kelsey R., Patel, Mit, Odle, Abby, Wong, Lok-Yin Roy, Bateman, Allen C., Wang, Zhongde, Edara, Venkata-Viswanadh, Chong, Zhenlu, Franks, John, Jeevan, Trushar, Fabrizio, Thomas, DeBeauchamp, Jennifer, Kercher, Lisa, Seiler, Patrick, Gonzalez-Reiche, Ana Silvia, Sordillo, Emilia Mia, Chang, Lauren A., van Bakel, Harm, Simon, Viviana, Douek, Daniel C., Sullivan, Nancy J., Thackray, Larissa B., Ueki, Hiroshi, Yamayoshi, Seiya, Imai, Masaki, Perlman, Stanley, Webby, Richard J., Seder, Robert A., Suthar, Mehul S., García-Sastre, Adolfo, Schotsaert, Michael, Suzuki, Tadaki, Boon, Adrianus C. M., Diamond, Michael S., and Kawaoka, Yoshihiro

Published
2022
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15. Broadly neutralizing antibodies overcome SARS-CoV-2 Omicron antigenic shift

Author

Cameroni, Elisabetta, Bowen, John E., Rosen, Laura E., Saliba, Christian, Zepeda, Samantha K., Culap, Katja, Pinto, Dora, VanBlargan, Laura A., De Marco, Anna, di Iulio, Julia, Zatta, Fabrizia, Kaiser, Hannah, Noack, Julia, Farhat, Nisar, Czudnochowski, Nadine, Havenar-Daughton, Colin, Sprouse, Kaitlin R., Dillen, Josh R., Powell, Abigail E., Chen, Alex, Maher, Cyrus, Yin, Li, Sun, David, Soriaga, Leah, Bassi, Jessica, Silacci-Fregni, Chiara, Gustafsson, Claes, Franko, Nicholas M., Logue, Jenni, Iqbal, Najeeha Talat, Mazzitelli, Ignacio, Geffner, Jorge, Grifantini, Renata, Chu, Helen, Gori, Andrea, Riva, Agostino, Giannini, Olivier, Ceschi, Alessandro, Ferrari, Paolo, Cippà, Pietro E., Franzetti-Pellanda, Alessandra, Garzoni, Christian, Halfmann, Peter J., Kawaoka, Yoshihiro, Hebner, Christy, Purcell, Lisa A., Piccoli, Luca, Pizzuto, Matteo Samuele, Walls, Alexandra C., Diamond, Michael S., Telenti, Amalio, Virgin, Herbert W., Lanzavecchia, Antonio, Snell, Gyorgy, Veesler, David, and Corti, Davide

Published
2022
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16. Resilience of S309 and AZD7442 monoclonal antibody treatments against infection by SARS-CoV-2 Omicron lineage strains

Author

Case, James Brett, Mackin, Samantha, Errico, John M., Chong, Zhenlu, Madden, Emily A., Whitener, Bradley, Guarino, Barbara, Schmid, Michael A., Rosenthal, Kim, Ren, Kuishu, Dang, Ha V., Snell, Gyorgy, Jung, Ana, Droit, Lindsay, Handley, Scott A., Halfmann, Peter J., Kawaoka, Yoshihiro, Crowe, Jr., James E., Fremont, Daved H., Virgin, Herbert W., Loo, Yueh-Ming, Esser, Mark T., Purcell, Lisa A., Corti, Davide, and Diamond, Michael S.

Published
2022
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17. Site of vulnerability on SARS-CoV-2 spike induces broadly protective antibody against antigenically distinct Omicron subvariants

Author

Changrob, Siriruk, Halfmann, Peter J., Liu, Hejun, Torres, Jonathan L., McGrath, Joshua J.C., Ozorowski, Gabriel, Li, Lei, Wilbanks, G. Dewey, Kuroda, Makoto, Maemura, Tadashi, Huang, Min, Zheng, Nai-Ying, Turner, Hannah L., Erickson, Steven A., Fu, Yanbin, Yasuhara, Atsuhiro, Singh, Gagandeep, Monahan, Brian, Mauldin, Jacob, Srivastava, Komal, Simon, Viviana, Krammer, Florian, Sather, D. Noah, Ward, Andrew B., Wilson, Ian A., Kawaoka, Yoshihiro, and Wilson, Patrick C.

Subjects
Viral antibodies -- Health aspects, Antibodies -- Health aspects, Health care industry
Abstract

The rapid evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variants has emphasized the need to identify antibodies with broad neutralizing capabilities to inform future monoclonal therapies and vaccination strategies. Herein, we identified S728-1157, a broadly neutralizing antibody (bnAb) targeting the receptor-binding site (RBS) that was derived from an individual previously infected with WT SARS-CoV-2 prior to the spread of variants of concern (VOCs). S728-1157 demonstrated broad cross-neutralization of all dominant variants, including D614G, Beta, Delta, Kappa, Mu, and Omicron (BA.1/BA.2/BA.2.75/BA.4/BA.5/BL.1/XBB). Furthermore, S728-1157 protected hamsters against in vivo challenges with WT, Delta, and BA.1 viruses. Structural analysis showed that this antibody targets a class 1/RBS-A epitope in the receptor binding domain via multiple hydrophobic and polar interactions with its heavy chain complementarity determining region 3 (CDR-H3), in addition to common motifs in CDR-H1/CDR-H2 of class 1/RBS-A antibodies. Importantly, this epitope was more readily accessible in the open and prefusion state, or in the hexaproline (6P)-stabilized spike constructs, as compared with diproline (2P) constructs. Overall, S728-1157 demonstrates broad therapeutic potential and may inform target-driven vaccine designs against future SARS-CoV-2 variants., Introduction Since the start of the pandemic in December 2019, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus has led to over 660 million cases of coronavirus disease 2019 [...]

Published
2023
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18. Syrian hamsters as a small animal model for SARS-CoV-2 infection and countermeasure development

Author

Imai, Masaki, Iwatsuki-Horimoto, Kiyoko, Hatta, Masato, Loeber, Samantha, Halfmann, Peter J., Nakajima, Noriko, Watanabe, Tokiko, Ujie, Michiko, Takahashi, Kenta, Ito, Mutsumi, Yamada, Shinya, Fan, Shufang, Chiba, Shiho, Kuroda, Makoto, Guan, Lizheng, Takada, Kosuke, Armbrust, Tammy, Balogh, Aaron, Furusawa, Yuri, Okuda, Moe, Ueki, Hiroshi, Yasuhara, Atsuhiro, Sakai-Tagawa, Yuko, Lopes, Tiago J. S., Kiso, Maki, Yamayoshi, Seiya, Kinoshita, Noriko, Ohmagari, Norio, Hattori, Shin-ichiro, Takeda, Makoto, Mitsuya, Hiroaki, Krammer, Florian, Suzuki, Tadaki, and Kawaoka, Yoshihiro

Published
2020

19. Protective Immunity and Persistent Lung Sequelae in Domestic Cats after SARS-CoV-2 Infection

Author

Chiba, Shiho, Halfmann, Peter J., Hatta, Masato, Maemura, Tadashi, Fan, Shufang, Armbrust, Tammy, Swartley, Olivia M., Crawford, LaTasha K., and Kawaoka, Yoshihiro

Subjects
Respiratory tract diseases -- Development and progression -- Care and treatment, Immune response -- Physiological aspects, Health
Abstract

Previous studies have demonstrated the transmissibility of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) by direct or indirect contact between domestic cats (1,2). Given the close relationship between cats and humans, [...]

Published
2021
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20. Airway surveillance and lung viral control by memory T cells induced by COVID-19 mRNA vaccine

Author

Kingstad-Bakke, Brock, primary, Cleven, Thomas, additional, Bussan, Hailey, additional, Yount, Boyd L., additional, Uraki, Ryuta, additional, Iwatsuki-Horimoto, Kiyoko, additional, Koga, Michiko, additional, Yamamoto, Shinya, additional, Yotsuyanagi, Hiroshi, additional, Park, Hongtae, additional, Mishra, Jay S., additional, Kumar, Sathish, additional, Baric, Ralph S., additional, Halfmann, Peter J., additional, Kawaoka, Yoshihiro, additional, and Suresh, M., additional

Published
2023
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22. 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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24. Revealing fine-scale spatiotemporal differences in SARS-CoV-2 introduction and spread

Author

Moreno, Gage K., Braun, Katarina M., Riemersma, Kasen K., Martin, Michael A., Halfmann, Peter J., Crooks, Chelsea M., Prall, Trent, Baker, David, Baczenas, John J., Heffron, Anna S., Ramuta, Mitchell, Khubbar, Manjeet, Weiler, Andrea M., Accola, Molly A., Rehrauer, William M., O’Connor, Shelby L., Safdar, Nasia, Pepperell, Caitlin S., Dasu, Trivikram, Bhattacharyya, Sanjib, Kawaoka, Yoshihiro, Koelle, Katia, O’Connor, David H., and Friedrich, Thomas C.

Published
2020
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26. Characterization and antiviral susceptibility of SARS-CoV-2 Omicron BA.2

Author

Uraki, Ryuta, Kiso, Maki, Iida, Shun, Imai, Masaki, Takashita, Emi, Kuroda, Makoto, Halfmann, Peter J., Loeber, Samantha, Maemura, Tadashi, Yamayoshi, Seiya, Fujisaki, Seiichiro, Wang, Zhongde, Ito, Mutsumi, Ujie, Michiko, Iwatsuki-Horimoto, Kiyoko, Furusawa, Yuri, Wright, Ryan, Chong, Zhenlu, Ozono, Seiya, Yasuhara, Atsuhiro, Ueki, Hiroshi, Sakai-Tagawa, Yuko, Li, Rong, Liu, Yanan, Larson, Deanna, Koga, Michiko, Tsutsumi, Takeya, Adachi, Eisuke, Saito, Makoto, Yamamoto, Shinya, Hagihara, Masao, Mitamura, Keiko, Sato, Tetsuro, Hojo, Masayuki, Hattori, Shin-ichiro, Maeda, Kenji, Valdez, Riccardo, Okuda, Moe, Murakami, Jurika, Duong, Calvin, Godbole, Sucheta, Douek, Daniel C., Maeda, Ken, Watanabe, Shinji, Gordon, Aubree, Ohmagari, Norio, Yotsuyanagi, Hiroshi, Diamond, Michael S., Hasegawa, Hideki, Mitsuya, Hiroaki, Suzuki, Tadaki, and Kawaoka, Yoshihiro

Abstract

The recent emergence of SARS-CoV-2 Omicron (B.1.1.529 lineage) variants possessing numerous mutations has raised concerns of decreased effectiveness of current vaccines, therapeutic monoclonal antibodies and antiviral drugs for COVID-19 against these variants1,2. The original Omicron lineage, BA.1, prevailed in many countries, but more recently, BA.2 has become dominant in at least 68 countries3. Here we evaluated the replicative ability and pathogenicity of authentic infectious BA.2 isolates in immunocompetent and human ACE2-expressing mice and hamsters. In contrast to recent data with chimeric, recombinant SARS-CoV-2 strains expressing the spike proteins of BA.1 and BA.2 on an ancestral WK-521 backbone4, we observed similar infectivity and pathogenicity in mice and hamsters for BA.2 and BA.1, and less pathogenicity compared with early SARS-CoV-2 strains. We also observed a marked and significant reduction in the neutralizing activity of plasma from individuals who had recovered from COVID-19 and vaccine recipients against BA.2 compared to ancestral and Delta variant strains. In addition, we found that some therapeutic monoclonal antibodies (REGN10987 plus REGN10933, COV2-2196 plus COV2-2130, and S309) and antiviral drugs (molnupiravir, nirmatrelvir and S-217622) can restrict viral infection in the respiratory organs of BA.2-infected hamsters. These findings suggest that the replication and pathogenicity of BA.2 is similar to that of BA.1 in rodents and that several therapeutic monoclonal antibodies and antiviral compounds are effective against Omicron BA.2 variants.

Published
2024
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28. Coronavirus Immunotherapeutic Consortium Database

Author

Mahita, Jarjapu, primary, Ha, Brendan, additional, Gambiez, Anais, additional, Schendel, Sharon L, additional, Li, Haoyang, additional, Hastie, Kathryn M, additional, Dennison, S Moses, additional, Li, Kan, additional, Kuzmina, Natalia, additional, Periasamy, Sivakumar, additional, Bukreyev, Alexander, additional, Munt, Jennifer E, additional, Osei-Twum, Mary, additional, Atyeo, Caroline, additional, Overton, James A, additional, Vita, Randi, additional, Guzman-Orozco, Hector, additional, Mendes, Marcus, additional, Kojima, Mari, additional, Halfmann, Peter J, additional, Kawaoka, Yoshihiro, additional, Alter, Galit, additional, Gagnon, Luc, additional, Baric, Ralph S, additional, Tomaras, Georgia D, additional, Germann, Tim, additional, Bedinger, Daniel, additional, Greenbaum, Jason A, additional, Saphire, Erica Ollmann, additional, and Peters, Bjoern, additional

Published
2023
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29. Evolution of a globally unique SARS-CoV-2 Spike E484T monoclonal antibody escape mutation in a persistently infected, immunocompromised individual.

Author

Halfmann, Peter J, Minor, Nicholas R, III, Luis A Haddock, Maddox, Robert, Moreno, Gage K, Braun, Katarina M, Baker, David A, Riemersa, Kasen K, Prasad, Ankur, Alman, Kirsten J, Lambert, Matthew C, Florek, Kelsey, Bateman, Allen, Westergaard, Ryan, Safdar, Nasia, Andes, David R, Kawaoka, Yoshihiro, Fida, Madiha, Yao, Joseph D, and Friedrich, Thomas C

Subjects
SARS-CoV-2, IMMUNOCOMPROMISED patients, MONOCLONAL antibodies, SARS-CoV-2 Omicron variant
Abstract

Prolonged infections in immunocompromised individuals may be a source for novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants, particularly when both the immune system and antiviral therapy fail to clear the infection and enable within-host evolution. Here we describe a 486-day case of SARS-CoV-2 infection in an immunocompromised individual. Following monotherapy with the monoclonal antibody Bamlanivimab, the individual's virus acquired resistance, likely via the earliest known occurrence of Spike amino acid variant E484T. Recently, E484T has arisen again as a derivative of E484A in the Omicron Variant of Concern, supporting the hypothesis that prolonged infections can give rise to novel variants long before they become prevalent in the human population. [ABSTRACT FROM AUTHOR]

Published
2023
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31. Multivalent S2-based vaccines provide broad protection against SARS-CoV-2 variants of concern and pangolin coronaviruses

Author

Halfmann, Peter J., primary, Frey, Steven J., additional, Loeffler, Kathryn, additional, Kuroda, Makoto, additional, Maemura, Tadashi, additional, Armbrust, Tammy, additional, Yang, Jie E., additional, Hou, Yixuan J., additional, Baric, Ralph, additional, Wright, Elizabeth R., additional, Kawaoka, Yoshihiro, additional, and Kane, Ravi S., additional

Published
2022
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32. Evolution of a globally unique SARS-CoV-2 Spike E484T monoclonal antibody escape mutation in a persistently infected, immunocompromised individual

Author

Halfmann, Peter J, primary, Minor, Nicholas R, additional, Haddock III, Luis A, additional, Maddox, Robert, additional, Moreno, Gage K, additional, Braun, Katarina M, additional, Baker, David A, additional, Riemersa, Kasen K, additional, Prasad, Ankur, additional, Alman, Kirsten J, additional, Lambert, Matthew C, additional, Florek, Kelsey, additional, Bateman, Allen, additional, Westergaard, Ryan, additional, Safdar, Nasia, additional, Andes, David R, additional, Kawaoka, Yoshihiro, additional, Fida, Madiha, additional, Yao, Joseph D, additional, Friedrich, Thomas C, additional, and O’Connor, David H, additional

Published
2022
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33. Shedding of infectious SARS-CoV-2 despite vaccination

Author

Riemersma, Kasen K., primary, Haddock, Luis A., additional, Wilson, Nancy A., additional, Minor, Nicholas, additional, Eickhoff, Jens, additional, Grogan, Brittany E., additional, Kita-Yarbro, Amanda, additional, Halfmann, Peter J., additional, Segaloff, Hannah E., additional, Kocharian, Anna, additional, Florek, Kelsey R., additional, Westergaard, Ryan, additional, Bateman, Allen, additional, Jeppson, Gunnar E., additional, Kawaoka, Yoshihiro, additional, O’Connor, David H., additional, Friedrich, Thomas C., additional, and Grande, Katarina M., additional

Published
2022
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34. Parsing the role of NSP1 in SARS-CoV-2 infection

Author

Fisher, Tal, primary, Gluck, Avi, additional, Narayanan, Krishna, additional, Kuroda, Makoto, additional, Nachshon, Aharon, additional, Hsu, Jason C., additional, Halfmann, Peter J., additional, Yahalom-Ronen, Yfat, additional, Tamir, Hadas, additional, Finkel, Yaara, additional, Schwartz, Michal, additional, Weiss, Shay, additional, Tseng, Chien-Te K., additional, Israely, Tomer, additional, Paran, Nir, additional, Kawaoka, Yoshihiro, additional, Makino, Shinji, additional, and Stern-Ginossar, Noam, additional

Published
2022
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37. Asymmetric and non-stoichiometric glycoprotein recognition by two distinct antibodies results in broad protection against ebolaviruses

Author

Milligan, Jacob C., primary, Davis, Carl W., additional, Yu, Xiaoying, additional, Ilinykh, Philipp A., additional, Huang, Kai, additional, Halfmann, Peter J., additional, Cross, Robert W., additional, Borisevich, Viktoriya, additional, Agans, Krystle N., additional, Geisbert, Joan B., additional, Chennareddy, Chakravarthy, additional, Goff, Arthur J., additional, Piper, Ashley E., additional, Hui, Sean, additional, Shaffer, Kelly C.L., additional, Buck, Tierra, additional, Heinrich, Megan L., additional, Branco, Luis M., additional, Crozier, Ian, additional, Holbrook, Michael R., additional, Kuhn, Jens H., additional, Kawaoka, Yoshihiro, additional, Glass, Pamela J., additional, Bukreyev, Alexander, additional, Geisbert, Thomas W., additional, Worwa, Gabriella, additional, Ahmed, Rafi, additional, and Saphire, Erica Ollmann, additional

Published
2022
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38. Co-administration of Favipiravir and the Remdesivir Metabolite GS-441524 Effectively Reduces SARS-CoV-2 Replication in the Lungs of the Syrian Hamster Model

Author

Chiba, Shiho, primary, Kiso, Maki, additional, Nakajima, Noriko, additional, Iida, Shun, additional, Maemura, Tadashi, additional, Kuroda, Makoto, additional, Sato, Yuko, additional, Ito, Mutsumi, additional, Okuda, Moe, additional, Yamada, Shinya, additional, Iwatsuki-Horimoto, Kiyoko, additional, Watanabe, Tokiko, additional, Imai, Masaki, additional, Armbrust, Tammy, additional, Baric, Ralph S., additional, Halfmann, Peter J., additional, Suzuki, Tadaki, additional, and Kawaoka, Yoshihiro, additional

Published
2022
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41. Broadly neutralizing antibodies overcome SARS-CoV-2 Omicron antigenic shift

Author

Cameroni, Elisabetta, primary, Bowen, John E., additional, Rosen, Laura E., additional, Saliba, Christian, additional, Zepeda, Samantha K., additional, Culap, Katja, additional, Pinto, Dora, additional, VanBlargan, Laura A., additional, De Marco, Anna, additional, di Iulio, Julia, additional, Zatta, Fabrizia, additional, Kaiser, Hannah, additional, Noack, Julia, additional, Farhat, Nisar, additional, Czudnochowski, Nadine, additional, Havenar-Daughton, Colin, additional, Sprouse, Kaitlin R., additional, Dillen, Josh R., additional, Powell, Abigail E., additional, Chen, Alex, additional, Maher, Cyrus, additional, Yin, Li, additional, Sun, David, additional, Soriaga, Leah, additional, Bassi, Jessica, additional, Silacci-Fregni, Chiara, additional, Gustafsson, Claes, additional, Franko, Nicholas M., additional, Logue, Jenni, additional, Iqbal, Najeeha Talat, additional, Mazzitelli, Ignacio, additional, Geffner, Jorge, additional, Grifantini, Renata, additional, Chu, Helen, additional, Gori, Andrea, additional, Riva, Agostino, additional, Giannini, Olivier, additional, Ceschi, Alessandro, additional, Ferrari, Paolo, additional, Cippà, Pietro E., additional, Franzetti-Pellanda, Alessandra, additional, Garzoni, Christian, additional, Halfmann, Peter J., additional, Kawaoka, Yoshihiro, additional, Hebner, Christy, additional, Purcell, Lisa A., additional, Piccoli, Luca, additional, Pizzuto, Matteo Samuele, additional, Walls, Alexandra C., additional, Diamond, Michael S., additional, Telenti, Amalio, additional, Virgin, Herbert W., additional, Lanzavecchia, Antonio, additional, Snell, Gyorgy, additional, Veesler, David, additional, and Corti, Davide, additional

Published
2021
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42. Cross-Neutralization of Emerging SARS-CoV-2 Variants of Concern by Antibodies Targeting Distinct Epitopes on Spike

Author

Changrob, Siriruk, primary, Fu, Yanbin, additional, Guthmiller, Jenna J., additional, Halfmann, Peter J., additional, Li, Lei, additional, Stamper, Christopher T., additional, Dugan, Haley L., additional, Accola, Molly, additional, Rehrauer, William, additional, Zheng, Nai-Ying, additional, Huang, Min, additional, Wang, Jiaolong, additional, Erickson, Steven A., additional, Utset, Henry A., additional, Graves, Hortencia M., additional, Amanat, Fatima, additional, Sather, D. Noah, additional, Krammer, Florian, additional, Kawaoka, Yoshihiro, additional, and Wilson, Patrick C., additional

Published
2021
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43. Highly Efficient SARS-CoV-2 Infection of Human Cardiomyocytes: Spike Protein-Mediated Cell Fusion and Its Inhibition

Author

Navaratnarajah, Chanakha K., primary, Pease, David R., additional, Halfmann, Peter J., additional, Taye, Biruhalem, additional, Barkhymer, Alison, additional, Howell, Kyle G., additional, Charlesworth, Jon E., additional, Christensen, Trace A., additional, Kawaoka, Yoshihiro, additional, Cattaneo, Roberto, additional, and Schneider, Jay W., additional

Published
2021
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47. Additional file 2 of 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

Abstract

Additional file 2. These figure is analogous to Figure 4 for additional z-score threshold z.

Published
2021
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48. Additional file 4 of 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

Abstract

Additional file 4. This figure is analogous to Figure 4 for additional z-score threshold z.

Published
2021
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49. Additional file 3 of 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

Abstract

Additional file 3. These figure is analogous to Figure 4 for additional z-score threshold z.

Published
2021
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50. Pulmonary lesions induced by SARS-CoV-2 infection in domestic cats.

Author

Patania, Olivia M., Chiba, Shiho, Halfmann, Peter J., Hatta, Masato, Maemura, Tadashi, Bernard, Kristen A., Kawaoka, Yoshihiro, and Crawford, LaTasha K.

Subjects
LUNGS, SARS-CoV-2, CATS, VASCULAR endothelium, COVID-19, FIBRIN
Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of coronavirus disease 2019, which ranges from fatal disease in some to mild or subclinical in most affected individuals. Many recovered human patients report persistent respiratory signs; however, lung disease in post-acute infection is poorly understood. Our objective was to describe histologic lung lesions and viral loads following experimental SARS-CoV-2 infection in 11 cats. Microscopic evaluation at 3, 6, 10, or 28 days postinoculation (DPI) identified mild to moderate patchy interstitial pneumonia, bronchiolar epithelial damage, and occlusive histiocytic bronchiolitis. Based on immunohistochemistry, alveolar septal thickening was due to CD204-positive macrophages, fewer B and T lymphocytes, type II pneumocytes, and capillary proliferation with a relative dearth of fibrosis. In blood vessel endothelium, there was reactive hypertrophy or vacuolar degeneration and increased MHC II expression at all time points. Unexpectedly, one cat from the 28 DPI group had severe subacute regionally extensive lymphohistiocytic pneumonia with multifocal consolidation, vasculitis, and alveolar fibrin. Reverse transcriptase-quantitative polymerase chain reaction identified SARS-CoV-2 RNA within the lung at 3 and 6 DPI, and viral RNA was below the limit of detection at 10 and 28 DPI, suggesting that pulmonary lesions persist beyond detection of viral RNA. These findings clarify our comparative understanding of disease induced by SARS-CoV-2 and suggest that cats can serve as an informative model to study post-acute pulmonary sequelae. [ABSTRACT FROM AUTHOR]

Published
2022
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