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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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4. Host range, transmissibility and antigenicity of a pangolin coronavirus

Author

Hou, Yixuan J., Chiba, Shiho, Leist, Sarah R., Meganck, Rita M., Martinez, David R., Schäfer, Alexandra, Catanzaro, Nicholas J., Sontake, Vishwaraj, West, Ande, Edwards, Catlin E., Yount, Boyd, Lee, Rhianna E., Gallant, Samuel C., Zost, Seth J., Powers, John, Adams, Lily, Kong, Edgar F., Mattocks, Melissa, Tata, Aleksandra, Randell, Scott H., Tata, Purushothama R., Halfmann, Peter, Crowe, Jr, James E., Kawaoka, Yoshihiro, and Baric, Ralph S.

Published
2023
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6. 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

8. Tracing the origin of SARS-CoV-2 omicron-like spike sequences detected in an urban sewershed: a targeted, longitudinal surveillance study of a cryptic wastewater lineage

Author

Shafer, Martin M, Bobholz, Max J, Vuyk, William C, Gregory, Devon A, Roguet, Adelaide, Haddock Soto, Luis A, Rushford, Clayton, Janssen, Kayley H, Emmen, Isla E, Ries, Hunter J, Pilch, Hannah E, Mullen, Paige A, Fahney, Rebecca B, Wei, Wanting, Lambert, Matthew, Wenzel, Jeff, Halfmann, Peter, Kawaoka, Yoshihiro, Wilson, Nancy A, Friedrich, Thomas C, Pray, Ian W, Westergaard, Ryan, O’Connor, David H, and Johnson, Marc C

Published
2024
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9. 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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10. 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

12. 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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14. 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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15. 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

16. Cow’s Milk Containing Avian Influenza A(H5N1) Virus — Heat Inactivation and Infectivity in Mice

Author

Guan, Lizheng, primary, Eisfeld, Amie J., additional, Pattinson, David, additional, Gu, Chunyang, additional, Biswas, Asim, additional, Maemura, Tadashi, additional, Trifkovic, Sanja, additional, Babujee, Lavanya, additional, Presler, Robert, additional, Dahn, Randall, additional, Halfmann, Peter J., additional, Barnhardt, Tera, additional, Neumann, Gabriele, additional, Thompson, Alexis, additional, Swinford, Amy K., additional, Dimitrov, Kiril M., additional, Poulsen, Keith, additional, and Kawaoka, Yoshihiro, additional

Published
2024
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17. Comparative analysis of SARS-CoV-2 neutralization titers reveals consistency between human and animal model serum and across assays

Author

Mühlemann, Barbara, primary, Wilks, Samuel H., additional, Baracco, Lauren, additional, Bekliz, Meriem, additional, Carreño, Juan Manuel, additional, Corman, Victor M., additional, Davis-Gardner, Meredith E., additional, Dejnirattisai, Wanwisa, additional, Diamond, Michael S., additional, Douek, Daniel C., additional, Drosten, Christian, additional, Eckerle, Isabella, additional, Edara, Venkata-Viswanadh, additional, Ellis, Madison, additional, Fouchier, Ron A. M., additional, Frieman, Matthew, additional, Godbole, Sucheta, additional, Haagmans, Bart, additional, Halfmann, Peter J., additional, Henry, Amy R., additional, Jones, Terry C., additional, Katzelnick, Leah C., additional, Kawaoka, Yoshihiro, additional, Kimpel, Janine, additional, Krammer, Florian, additional, Lai, Lilin, additional, Liu, Chang, additional, Lusvarghi, Sabrina, additional, Meyer, Benjamin, additional, Mongkolsapaya, Juthathip, additional, Montefiori, David C., additional, Mykytyn, Anna, additional, Netzl, Antonia, additional, Pollett, Simon, additional, Rössler, Annika, additional, Screaton, Gavin R., additional, Shen, Xiaoying, additional, Sigal, Alex, additional, Simon, Viviana, additional, Subramanian, Rahul, additional, Supasa, Piyada, additional, Suthar, Mehul S., additional, Türeli, Sina, additional, Wang, Wei, additional, Weiss, Carol D., additional, and Smith, Derek J., additional

Published
2024
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19. 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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21. 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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22. 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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23. 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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24. 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

25. 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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27. Anti-Ebola virus mAb 3A6 with unprecedented potency protects highly viremic animals from fatal outcome and physically lifts its glycoprotein target from the virion membrane

Author

Saphire, Erica, primary, Salie, Zhe Li, additional, Ke, Zunlong, additional, Halfmann, Peter, additional, DeWald, Lisa Evans, additional, McArdle, Sara, additional, Grinyo, Ariadna, additional, Davidson, Edgar, additional, Schendel, Sharon, additional, Hariharan, Chitra, additional, Norris, Michael, additional, Yu, Xiaoying, additional, Chennareddy, Chakravarthy, additional, Xiong, Xiaoli, additional, Heinrich, Megan, additional, Holbrook, Michael, additional, Doranz, Benjamin, additional, Crozier, Ian, additional, Hastie, Kathryn, additional, Kawaoka, Yoshihiro, additional, Branco, Luis, additional, Kuhn, Jens, additional, Briggs, John, additional, Worwa, Gabriella, additional, Davis, Carl, additional, and Ahmed, Rafi, additional

Published
2023
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29. 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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31. Mapping SARS-CoV-2 antigenic relationships and serological responses

Author

Wilks, Samuel H., primary, Mühlemann, Barbara, additional, Shen, Xiaoying, additional, Türeli, Sina, additional, LeGresley, Eric B., additional, Netzl, Antonia, additional, Caniza, Miguela A., additional, Chacaltana-Huarcaya, Jesus N., additional, Corman, Victor M., additional, Daniell, Xiaoju, additional, Datto, Michael B., additional, Dawood, Fatimah S., additional, Denny, Thomas N., additional, Drosten, Christian, additional, Fouchier, Ron A. M., additional, Garcia, Patricia J., additional, Halfmann, Peter J., additional, Jassem, Agatha, additional, Jeworowski, Lara M., additional, Jones, Terry C., additional, Kawaoka, Yoshihiro, additional, Krammer, Florian, additional, McDanal, Charlene, additional, Pajon, Rolando, additional, Simon, Viviana, additional, Stockwell, Melissa S., additional, Tang, Haili, additional, van Bakel, Harm, additional, Veguilla, Vic, additional, Webby, Richard, additional, Montefiori, David C., additional, and Smith, Derek J., additional

Published
2023
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34. 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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37. Neutralizing Immunity Against Antigenically Advanced Omicron BA.5 in Children After SARS-CoV-2 Infection.

Author

Belongia, Edward A, Petrie, Joshua G, Feldstein, Leora R, Guan, Lizheng, Halfmann, Peter J, King, Jennifer P, Neumann, Gabriele, Pattinson, David, Rolfes, Melissa A, McLean, Huong Q, and Kawaoka, Yoshihiro

Subjects
COVID-19, IMMUNOGLOBULINS, COVID-19 vaccines, RESEARCH funding, CHILDREN
Abstract

We assessed serum neutralization of Omicron BA.5 in children following SARS-CoV-2 infection during the Delta or Omicron BA.1/BA.2 variant period. Convalescent BA.5 titers were higher following infections during the Omicron BA.1/BA.2 vs Delta variant period, and in vaccinated vs unvaccinated children. Titers against BA.5 did not differ by age group. [ABSTRACT FROM AUTHOR]

Published
2024
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38. Comparative Analysis of SARS-CoV-2 Antigenicity across Assays and in Human and Animal Model Sera

Author

Mühlemann, Barbara, primary, Wilks, Samuel Hedley, additional, Baracco, Lauren, additional, Bekliz, Meriem, additional, Carreno, Juan Manuel, additional, Corman, Victor M, additional, Davis-Gardner, Meredith E, additional, Dejnirattisai, Wanwisa, additional, Diamond, Michael, additional, Doueck, Danny, additional, Drosten, Christian, additional, Eckerle, Isabella, additional, Edara, Venkata Vishwanadh, additional, Ellis, Madison, additional, Fouchier, Ron AM, additional, Frieman, Matthew, additional, Godbole, Sucheta, additional, Haagmans, Bart, additional, Halfmann, Peter, additional, Henry, Amy R, additional, Jones, Terry C, additional, Katzelnick, Leah, additional, Kawaoka, Yoshihiro, additional, Kimpel, Janine, additional, Krammer, Florian, additional, Lai, Lilin, additional, Liu, Chang, additional, Lusvarghi, Sabrina, additional, Meyer, Benjamin, additional, Mongkolsapaya, Juthathip, additional, Montefiori, David, additional, Mykytyn, Anna Z, additional, Netzl, Antonia, additional, Pollett, Simon, additional, Rössler, Annika, additional, Screaton, Gavin, additional, Shen, Xiaoying, additional, Sigal, Alex, additional, Simon, Viviana, additional, Subramanian, Rahul, additional, Supasa, Piyada, additional, Suthar, Mehul, additional, Tureli, Sina, additional, Wang, Wei, additional, Weiss, Carol D., additional, and Smith, Derek J, additional

Published
2023
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41. 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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44. Sensitivity of rapid antigen tests for Omicron subvariants of SARS‐CoV‐2

Author

Sakai‐Tagawa, Yuko, primary, Yamayoshi, Seiya, additional, Halfmann, Peter J., additional, Wilson, Nancy, additional, Bobholz, Max, additional, Vuyk, William C., additional, Wei, Wanting, additional, Ries, Hunter, additional, O'Connor, David H., additional, Friedrich, Thomas C., additional, Sordillo, Emilia M., additional, van Bakel, Harm, additional, Simon, Viviana, additional, and Kawaoka, Yoshihiro, additional

Published
2023
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45. Antiviral and bivalent vaccine efficacy against an omicron XBB.1.5 isolate

Author

Uraki, Ryuta, primary, Ito, Mutsumi, additional, Kiso, Maki, additional, Yamayoshi, Seiya, additional, Iwatsuki-Horimoto, Kiyoko, additional, Furusawa, Yuri, additional, Sakai-Tagawa, Yuko, additional, Imai, Masaki, additional, Koga, Michiko, additional, Yamamoto, Shinya, additional, Adachi, Eisuke, additional, Saito, Makoto, additional, Tsutsumi, Takeya, additional, Otani, Amato, additional, Kikuchi, Tetsuhiro, additional, Yotsuyanagi, Hiroshi, additional, Halfmann, Peter J, additional, Pekosz, Andrew, additional, and Kawaoka, Yoshihiro, additional

Published
2023
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48. 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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49. 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

Abstract

Highly pathogenic H5N1 avian influenza (HPAI H5N1) viruses occasionally infect, but typically do not transmit, in mammals. In the spring of 2024, an unprecedented outbreak of HPAI H5N1 in bovine herds occurred in the USA, with virus spread within and between herds, infections in poultry and cats, and spillover into humans, collectively indicating an increased public health risk1–4. Here we characterize an HPAI H5N1 virus isolated from infected cow milk in mice and ferrets. Like other HPAI H5N1 viruses, the bovine H5N1 virus spread systemically, including to the mammary glands of both species, however, this tropism was also observed for an older HPAI H5N1 virus isolate. Bovine HPAI H5N1 virus bound to sialic acids expressed in human upper airways and inefficiently transmitted to exposed ferrets (one of four exposed ferrets seroconverted without virus detection). Bovine HPAI H5N1 virus thus possesses features that may facilitate infection and transmission in mammals.

Published
2024
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