1
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Lee J, Stewart C, Schaefer A, Leaf EM, Park YJ, Asarnow D, Powers JM, Treichel C, Corti D, Baric R, King NP, Veesler D. A broadly generalizable stabilization strategy for sarbecovirus fusion machinery vaccines. bioRxiv 2023:2023.12.12.571160. [PMID: 38168207 PMCID: PMC10760017 DOI: 10.1101/2023.12.12.571160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Continuous evolution of SARS-CoV-2 alters the antigenicity of the immunodominant spike (S) receptor-binding domain and N-terminal domain, undermining the efficacy of vaccines and monoclonal antibody therapies. To overcome this challenge, we set out to develop a vaccine focusing antibody responses on the highly conserved but metastable S2 subunit, which folds as a spring-loaded fusion machinery. Here, we describe a protein design strategy enabling prefusion-stabilization of the SARS-CoV-2 S2 subunit and high yield recombinant expression of trimers with native structure and antigenicity. We demonstrate that our design strategy is broadly generalizable to all sarbecoviruses, as exemplified with the SARS-CoV-1 (clade 1a) and PRD-0038 (clade 3) S2 fusion machineries. Immunization of mice with a prefusion-stabilized SARS-CoV-2 S2 trimer vaccine elicits broadly reactive sarbecovirus antibody responses and neutralizing antibody titers of comparable magnitude against Wuhan-Hu-1 and the immune evasive XBB.1.5 variant. Vaccinated mice were protected from weight loss and disease upon challenge with SARS-CoV-2 XBB.1.5, providing proof-of-principle for fusion machinery sarbecovirus vaccines motivating future development.
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Affiliation(s)
- Jimin Lee
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Cameron Stewart
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Alexandra Schaefer
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Elizabeth M. Leaf
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Daniel Asarnow
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | | | - Catherine Treichel
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Ralph Baric
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Neil P. King
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
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2
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Kapingidza AB, Marston DJ, Harris C, Wrapp D, Winters K, Mielke D, Xiaozhi L, Yin Q, Foulger A, Parks R, Barr M, Newman A, Schäfer A, Eaton A, Flores JM, Harner A, Catanzaro NJ, Mallory ML, Mattocks MD, Beverly C, Rhodes B, Mansouri K, Van Itallie E, Vure P, Dunn B, Keyes T, Stanfield-Oakley S, Woods CW, Petzold EA, Walter EB, Wiehe K, Edwards RJ, Montefiori DC, Ferrari G, Baric R, Cain DW, Saunders KO, Haynes BF, Azoitei ML. Engineered immunogens to elicit antibodies against conserved coronavirus epitopes. Nat Commun 2023; 14:7897. [PMID: 38036525 PMCID: PMC10689493 DOI: 10.1038/s41467-023-43638-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 11/15/2023] [Indexed: 12/02/2023] Open
Abstract
Immune responses to SARS-CoV-2 primarily target the receptor binding domain of the spike protein, which continually mutates to escape acquired immunity. Other regions in the spike S2 subunit, such as the stem helix and the segment encompassing residues 815-823 adjacent to the fusion peptide, are highly conserved across sarbecoviruses and are recognized by broadly reactive antibodies, providing hope that vaccines targeting these epitopes could offer protection against both current and emergent viruses. Here we employ computational modeling to design scaffolded immunogens that display the spike 815-823 peptide and the stem helix epitopes without the distracting and immunodominant receptor binding domain. These engineered proteins bind with high affinity and specificity to the mature and germline versions of previously identified broadly protective human antibodies. Epitope scaffolds interact with both sera and isolated monoclonal antibodies with broadly reactivity from individuals with pre-existing SARS-CoV-2 immunity. When used as immunogens, epitope scaffolds elicit sera with broad betacoronavirus reactivity and protect as "boosts" against live virus challenge in mice, illustrating their potential as components of a future pancoronavirus vaccine.
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Affiliation(s)
- A Brenda Kapingidza
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | - Daniel J Marston
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | - Caitlin Harris
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | - Daniel Wrapp
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | - Kaitlyn Winters
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | - Dieter Mielke
- Department of Surgery, Duke University, Durham, NC, USA
- Center for Human Systems Immunology, Duke University, Durham, NC, USA
| | - Lu Xiaozhi
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | - Qi Yin
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | - Andrew Foulger
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | - Rob Parks
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | - Maggie Barr
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | - Amanda Newman
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Amanda Eaton
- Department of Surgery, Duke University, Durham, NC, USA
| | - Justine Mae Flores
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | - Austin Harner
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | - Nicholas J Catanzaro
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Michael L Mallory
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Melissa D Mattocks
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Christopher Beverly
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | - Brianna Rhodes
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | | | - Elizabeth Van Itallie
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | - Pranay Vure
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | - Brooke Dunn
- Department of Surgery, Duke University, Durham, NC, USA
| | - Taylor Keyes
- Department of Surgery, Duke University, Durham, NC, USA
| | | | - Christopher W Woods
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
- Center for Infectious Diseases and Diagnostic Innovation, Duke University Medical Center, Durham, NC, USA
| | - Elizabeth A Petzold
- Center for Infectious Diseases and Diagnostic Innovation, Duke University Medical Center, Durham, NC, USA
| | - Emmanuel B Walter
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Pediatrics, Duke University, Durham, NC, USA
| | - Kevin Wiehe
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | - Robert J Edwards
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | | | - Guido Ferrari
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Surgery, Duke University, Durham, NC, USA
- Center for Human Systems Immunology, Duke University, Durham, NC, USA
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
| | - Ralph Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Derek W Cain
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | - Kevin O Saunders
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Surgery, Duke University, Durham, NC, USA
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
- Department of Immunology, Duke University, Durham, NC, USA
| | - Barton F Haynes
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
- Department of Immunology, Duke University, Durham, NC, USA
| | - Mihai L Azoitei
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA.
- Department of Medicine, Duke University, Durham, NC, USA.
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3
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Heise M, Dillard J, Taft-Benz S, Knight A, Anderson E, Pressey K, Parotti B, Martinez S, Diaz J, Sarkar S, Madden E, De la Cruz G, Adams L, Dinnon K, Leist S, Martinez D, Schaefer A, Powers J, Yount B, Castillo I, Morales N, Burdick J, Evangelista MK, Ralph L, Pankow N, Linnertz C, Lakshmanane P, Montgomery S, Ferris M, Baric R, Baxter V. Adjuvant-dependent effects on the safety and efficacy of inactivated SARS-CoV-2 vaccines during heterologous infection by a SARS-related coronavirus. Res Sq 2023:rs.3.rs-3401539. [PMID: 37961507 PMCID: PMC10635311 DOI: 10.21203/rs.3.rs-3401539/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Inactivated whole virus SARS-CoV-2 vaccines adjuvanted with aluminum hydroxide (Alum) are among the most widely used COVID-19 vaccines globally and have been critical to the COVID-19 pandemic response. Although these vaccines are protective against homologous virus infection in healthy recipients, the emergence of novel SARS-CoV-2 variants and the presence of large zoonotic reservoirs provide significant opportunities for vaccine breakthrough, which raises the risk of adverse outcomes including vaccine-associated enhanced respiratory disease (VAERD). To evaluate this possibility, we tested the performance of an inactivated SARS-CoV-2 vaccine (iCoV2) in combination with Alum against either homologous or heterologous coronavirus challenge in a mouse model of coronavirus-induced pulmonary disease. Consistent with human results, iCoV2 + Alum protected against homologous challenge. However, challenge with a heterologous SARS-related coronavirus, Rs-SHC014-CoV (SHC014), up to at least 10 months post-vaccination, resulted in VAERD in iCoV2 + Alum-vaccinated animals, characterized by pulmonary eosinophilic infiltrates, enhanced pulmonary pathology, delayed viral clearance, and decreased pulmonary function. In contrast, vaccination with iCoV2 in combination with an alternative adjuvant (RIBI) did not induce VAERD and promoted enhanced SHC014 clearance. Further characterization of iCoV2 + Alum-induced immunity suggested that CD4+ T cells were a major driver of VAERD, and these responses were partially reversed by re-boosting with recombinant Spike protein + RIBI adjuvant. These results highlight potential risks associated with vaccine breakthrough in recipients of Alum-adjuvanted inactivated vaccines and provide important insights into factors affecting both the safety and efficacy of coronavirus vaccines in the face of heterologous virus infections.
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Affiliation(s)
- Mark Heise
- University of North Carolina at Chapel Hill
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Boyd Yount
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill
| | | | | | | | | | | | | | | | - Prem Lakshmanane
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC
| | | | | | | | - Victoria Baxter
- Texas Biomedical Research Institute, San Antonio, Texas, USA
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4
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Kapingidza B, Marston DJ, Harris C, Wrapp D, Winters K, Mielke D, Xiaozhi L, Yin Q, Foulger A, Parks R, Barr M, Newman A, Schäfer A, Eaton A, Flores JM, Harner A, Cantazaro NJ, Mallory ML, Mattocks MD, Beverly C, Rhodes B, Mansouri K, Itallie EV, Vure P, Manness B, Keyes T, Stanfield-Oakley S, Woods CW, Petzold EA, Walter EB, Wiehe K, Edwards RJ, Montefiori D, Ferrari G, Baric R, Cain DW, Saunders KO, Haynes BF, Azoitei ML. Engineered Immunogens to Elicit Antibodies Against Conserved Coronavirus Epitopes. bioRxiv 2023:2023.02.27.530277. [PMID: 36909627 PMCID: PMC10002628 DOI: 10.1101/2023.02.27.530277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
Immune responses to SARS-CoV-2 primarily target the receptor binding domain of the spike protein, which continually mutates to escape acquired immunity. Other regions in the spike S2 subunit, such as the stem helix and the segment encompassing residues 815-823 adjacent to the fusion peptide, are highly conserved across sarbecoviruses and are recognized by broadly reactive antibodies, providing hope that vaccines targeting these epitopes could offer protection against both current and emergent viruses. Here we employed computational modeling to design scaffolded immunogens that display the spike 815-823 peptide and the stem helix epitopes without the distracting and immunodominant RBD. These engineered proteins bound with high affinity and specificity to the mature and germline versions of previously identified broadly protective human antibodies. Epitope scaffolds interacted with both sera and isolated monoclonal antibodies with broadly reactivity from individuals with pre-existing SARS-CoV-2 immunity. When used as immunogens, epitope scaffolds elicited sera with broad betacoronavirus reactivity and protected as "boosts" against live virus challenge in mice, illustrating their potential as components of a future pancoronavirus vaccine.
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5
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Sessions Z, Bobrowski T, Martin HJ, Beasley JMT, Kothari A, Phares T, Li M, Alves VM, Scotti MT, Moorman NJ, Baric R, Tropsha A, Muratov EN. Praemonitus praemunitus: can we forecast and prepare for future viral disease outbreaks? FEMS Microbiol Rev 2023; 47:fuad048. [PMID: 37596064 PMCID: PMC10532129 DOI: 10.1093/femsre/fuad048] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 07/04/2023] [Accepted: 08/17/2023] [Indexed: 08/20/2023] Open
Abstract
Understanding the origins of past and present viral epidemics is critical in preparing for future outbreaks. Many viruses, including SARS-CoV-2, have led to significant consequences not only due to their virulence, but also because we were unprepared for their emergence. We need to learn from large amounts of data accumulated from well-studied, past pandemics and employ modern informatics and therapeutic development technologies to forecast future pandemics and help minimize their potential impacts. While acknowledging the complexity and difficulties associated with establishing reliable outbreak predictions, herein we provide a perspective on the regions of the world that are most likely to be impacted by future outbreaks. We specifically focus on viruses with epidemic potential, namely SARS-CoV-2, MERS-CoV, DENV, ZIKV, MAYV, LASV, noroviruses, influenza, Nipah virus, hantaviruses, Oropouche virus, MARV, and Ebola virus, which all require attention from both the public and scientific community to avoid societal catastrophes like COVID-19. Based on our literature review, data analysis, and outbreak simulations, we posit that these future viral epidemics are unavoidable, but that their societal impacts can be minimized by strategic investment into basic virology research, epidemiological studies of neglected viral diseases, and antiviral drug discovery.
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Affiliation(s)
- Zoe Sessions
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, 301 Pharmacy Ln, Chapel Hill, NC 27599, United States
| | - Tesia Bobrowski
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, 301 Pharmacy Ln, Chapel Hill, NC 27599, United States
| | - Holli-Joi Martin
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, 301 Pharmacy Ln, Chapel Hill, NC 27599, United States
| | - Jon-Michael T Beasley
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, 301 Pharmacy Ln, Chapel Hill, NC 27599, United States
| | - Aneri Kothari
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, 301 Pharmacy Ln, Chapel Hill, NC 27599, United States
| | - Trevor Phares
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, 301 Pharmacy Ln, Chapel Hill, NC 27599, United States
- School of Chemistry, University of Louisville, 2320 S Brook St, Louisville, KY 40208, United States
| | - Michael Li
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, 301 Pharmacy Ln, Chapel Hill, NC 27599, United States
| | - Vinicius M Alves
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, 301 Pharmacy Ln, Chapel Hill, NC 27599, United States
| | - Marcus T Scotti
- Department of Pharmaceutical Sciences, Federal University of Paraiba, Campus I Lot. Cidade Universitaria, PB, 58051-900, Brazil
| | - Nathaniel J Moorman
- Department of Microbiology and Immunology, University of North Carolina, 116 Manning Drive, Chapel Hill, NC 27599, United States
| | - Ralph Baric
- Department of Epidemiology, University of North Carolina, 401 Pittsboro St, Chapel Hill, NC 27599, United States
| | - Alexander Tropsha
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, 301 Pharmacy Ln, Chapel Hill, NC 27599, United States
| | - Eugene N Muratov
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, 301 Pharmacy Ln, Chapel Hill, NC 27599, United States
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6
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Milligan EC, Olstad K, Williams CA, Mallory M, Cano P, Cross KA, Munt JE, Garrido C, Lindesmith L, Watanabe J, Usachenko JL, Hopkins L, Immareddy R, Shaan Lakshmanappa Y, Elizaldi SR, Roh JW, Sammak RL, Pollard RE, Yee JL, Herbek S, Scobey T, Miehlke D, Fouda G, Ferrari G, Gao H, Shen X, Kozlowski PA, Montefiori D, Hudgens MG, Edwards DK, Carfi A, Corbett KS, Graham BS, Fox CB, Tomai M, Iyer SS, Baric R, Reader R, Dittmer DP, Van Rompay KKA, Permar SR, De Paris K. Infant rhesus macaques immunized against SARS-CoV-2 are protected against heterologous virus challenge 1 year later. Sci Transl Med 2023; 15:eadd6383. [PMID: 36454813 PMCID: PMC9765459 DOI: 10.1126/scitranslmed.add6383] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The U.S. Food and Drug Administration only gave emergency use authorization of the BNT162b2 and mRNA-1273 SARS-CoV-2 vaccines for infants 6 months and older in June 2022. Yet questions regarding the durability of vaccine efficacy, especially against emerging variants, in this age group remain. We demonstrated previously that a two-dose regimen of stabilized prefusion Washington SARS-CoV-2 S-2P spike (S) protein encoded by mRNA encapsulated in lipid nanoparticles (mRNA-LNP) or purified S-2P mixed with 3M-052, a synthetic Toll-like receptor (TLR) 7/8 agonist, in a squalene emulsion (Protein+3M-052-SE) was safe and immunogenic in infant rhesus macaques. Here, we demonstrate that broadly neutralizing and spike-binding antibodies against variants of concern (VOCs), as well as T cell responses, persisted for 12 months. At 1 year, corresponding to human toddler age, we challenged vaccinated rhesus macaques and age-matched nonvaccinated controls intranasally and intratracheally with a high dose of heterologous SARS-CoV-2 B.1.617.2 (Delta). Seven of eight control rhesus macaques exhibited severe interstitial pneumonia and high virus replication in the upper and lower respiratory tract. In contrast, vaccinated rhesus macaques had faster viral clearance with mild to no pneumonia. Neutralizing and binding antibody responses to the B.1.617.2 variant at the day of challenge correlated with lung pathology and reduced virus replication. Overall, the Protein+3M-052-SE vaccine provided superior protection to the mRNA-LNP vaccine, emphasizing opportunities for optimization of current vaccine platforms. The observed efficacy of both vaccines 1 year after vaccination supports the implementation of an early-life SARS-CoV-2 vaccine.
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Affiliation(s)
- Emma C Milligan
- Department of Microbiology and Immunology, Children's Research Institute, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Katherine Olstad
- California National Primate Research Center, University of California at Davis, Davis, CA 95616, USA
| | - Caitlin A Williams
- Department of Pediatrics, Weill Cornell Medical College, New York, NY 10065, USA
| | - Michael Mallory
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Patricio Cano
- Lineberger Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kaitlyn A Cross
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jennifer E Munt
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Carolina Garrido
- Center for Immunology and Infectious Diseases, University of California at Davis, Davis, CA 95616, USA
| | - Lisa Lindesmith
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jennifer Watanabe
- California National Primate Research Center, University of California at Davis, Davis, CA 95616, USA
| | - Jodie L Usachenko
- California National Primate Research Center, University of California at Davis, Davis, CA 95616, USA
| | - Lincoln Hopkins
- California National Primate Research Center, University of California at Davis, Davis, CA 95616, USA
| | - Ramya Immareddy
- California National Primate Research Center, University of California at Davis, Davis, CA 95616, USA
| | | | - Sonny R Elizaldi
- Center for Immunology and Infectious Diseases, University of California at Davis, Davis, CA 95616, USA.,Graduate Group in Immunology, University of California at Davis, Davis, CA 95616, USA
| | - Jamin W Roh
- Center for Immunology and Infectious Diseases, University of California at Davis, Davis, CA 95616, USA.,Graduate Group in Immunology, University of California at Davis, Davis, CA 95616, USA
| | - Rebecca L Sammak
- California National Primate Research Center, University of California at Davis, Davis, CA 95616, USA
| | - Rachel E Pollard
- School of Veterinary Medicine, University of California at Davis, Davis, CA 95616, USA
| | - JoAnn L Yee
- California National Primate Research Center, University of California at Davis, Davis, CA 95616, USA
| | - Savannah Herbek
- Department of Pediatrics, Weill Cornell Medical College, New York, NY 10065, USA
| | - Trevor Scobey
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Dieter Miehlke
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA.,Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Genevieve Fouda
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA.,Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Guido Ferrari
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA.,Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Hongmei Gao
- Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - Xiaoying Shen
- Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - Pamela A Kozlowski
- Department of Microbiology, Immunology and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - David Montefiori
- Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - Michael G Hudgens
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | | | - Kizzmekia S Corbett
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Barney S Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20852, USA
| | - Christopher B Fox
- Access to Advanced Health Institute, Seattle, WA 98102, USA.,Department of Global Health, University of Washington, Seattle, WA 98105, USA
| | - Mark Tomai
- 3M Corporate Research Materials Laboratory, Saint Paul, MN 55144, USA
| | - Smita S Iyer
- California National Primate Research Center, University of California at Davis, Davis, CA 95616, USA.,Center for Immunology and Infectious Diseases, University of California at Davis, Davis, CA 95616, USA
| | - Ralph Baric
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Rachel Reader
- California National Primate Research Center, University of California at Davis, Davis, CA 95616, USA
| | - Dirk P Dittmer
- Department of Microbiology and Immunology, Children's Research Institute, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Department of Pediatrics, Weill Cornell Medical College, New York, NY 10065, USA
| | - Koen K A Van Rompay
- California National Primate Research Center, University of California at Davis, Davis, CA 95616, USA.,Department of Pathology, Microbiology and Immunology, University of California at Davis, Davis, CA 95616, USA
| | - Sallie R Permar
- Department of Pediatrics, Weill Cornell Medical College, New York, NY 10065, USA
| | - Kristina De Paris
- Department of Microbiology and Immunology, Children's Research Institute, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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7
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Halfmann PJ, Frey SJ, Loeffler K, Kuroda M, Maemura T, Armbrust T, Yang JE, Hou YJ, Baric R, Wright ER, Kawaoka Y, Kane RS. Multivalent S2-based vaccines provide broad protection against SARS-CoV-2 variants of concern and pangolin coronaviruses. EBioMedicine 2022; 86:104341. [PMID: 36375316 PMCID: PMC9651965 DOI: 10.1016/j.ebiom.2022.104341] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 10/12/2022] [Accepted: 10/18/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The COVID-19 pandemic continues to cause morbidity and mortality worldwide. Most approved COVID-19 vaccines generate a neutralizing antibody response that primarily targets the highly variable receptor-binding domain (RBD) of the SARS-CoV-2 spike (S) protein. SARS-CoV-2 "variants of concern" have acquired mutations in this domain allowing them to evade vaccine-induced humoral immunity. Recent approaches to improve the breadth of protection beyond SARS-CoV-2 have required the use of mixtures of RBD antigens from different sarbecoviruses. It may therefore be beneficial to develop a vaccine in which the protective immune response targets a more conserved region of the S protein. METHODS Here we have developed a vaccine based on the conserved S2 subunit of the S protein and optimized the adjuvant and immunization regimen in Syrian hamsters and BALB/c mice. We have characterized the efficacy of the vaccine against SARS-CoV-2 variants and other coronaviruses. FINDINGS Immunization with S2-based constructs elicited a broadly cross-reactive IgG antibody response that recognized the spike proteins of not only SARS-CoV-2 variants, but also SARS-CoV-1, and the four endemic human coronaviruses. Importantly, immunization reduced virus titers in respiratory tissues in vaccinated animals challenged with SARS-CoV-2 variants B.1.351 (beta), B.1.617.2 (delta), and BA.1 (omicron) as well as a pangolin coronavirus. INTERPRETATION These results suggest that S2-based constructs can elicit a broadly cross-reactive antibody response resulting in limited virus replication, thus providing a framework for designing vaccines that elicit broad protection against coronaviruses. FUNDING NIH, Japan Agency for Medical Research and Development, Garry Betty/ V Foundation Chair Fund, and NSF.
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Affiliation(s)
- Peter J Halfmann
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, 53711, USA
| | - Steven J Frey
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Kathryn Loeffler
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Makoto Kuroda
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, 53711, USA
| | - Tadashi Maemura
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, 53711, USA
| | - Tammy Armbrust
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, 53711, USA
| | - Jie E Yang
- Department of Biochemistry, University of Wisconsin, Madison, WI, 53706, USA; Cryo-EM Research Center, Department of Biochemistry, University of Wisconsin, Madison, WI, 53706, USA; Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI, 53706, USA
| | - Yixuan J Hou
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Ralph Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Elizabeth R Wright
- Department of Biochemistry, University of Wisconsin, Madison, WI, 53706, USA; Cryo-EM Research Center, Department of Biochemistry, University of Wisconsin, Madison, WI, 53706, USA; Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI, 53706, USA
| | - Yoshihiro Kawaoka
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, 53711, USA; Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan.
| | - Ravi S Kane
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA; Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
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8
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Hutchinson G, Abiona O, Ziwawo C, Werner A, Ellis D, Tsybovsky Y, Leist S, Palandjian C, West A, Fritch E, Wang N, Wrapp D, Boyoglu-Barnum S, Ueda G, Baker D, Kanekiyo M, McLellan J, Baric R, King N, Graham B, Corbett K. Nanoparticle display of prefusion coronavirus spike elicits S1-focused cross-reactive protection across divergent subgroups. Res Sq 2022:rs.3.rs-2199814. [PMID: 36380759 PMCID: PMC9645427 DOI: 10.21203/rs.3.rs-2199814/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Multivalent antigen display is a fast-growing area of interest towards broadly protective vaccines. Current nanoparticle-based vaccine candidates demonstrate the ability to confer antibody-mediated immunity against divergent strains of notably mutable viruses. In coronaviruses, this work is predominantly aimed at targeting conserved epitopes of the receptor-binding domain. However, targeting other conserved non-RBD epitopes could further limit the potential for antigenic escape. To further explore new potential targets, we engineered protein nanoparticles displaying CoV_S-2P trimers derived from MERS-CoV, SARS-CoV-1, SARS-CoV-2, hCoV-HKU1, and hCoV-OC43 and assessed their immunogenicity in mice. Monotypic SARS-1_S-2P nanoparticles elicited cross-neutralizing antibodies against MERS_S and protected against MERS-CoV challenge. MERS and SARS-I53_dn5 nanoparticles elicited S1-focused antibodies, revealing a conserved site on the NTD. Moreover, mosaic nanoparticles co-displaying distinct CoV_S-2P trimers elicited antibody responses to distant cross-group antigens while protecting against MERS challenge despite diminished valency of MERS_S-2P. Our findings will inform further efforts towards the development of pan-coronavirus vaccines.
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9
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Brewer-Jensen PD, Reyes Y, Becker-Dreps S, González F, Mallory ML, Gutiérrez L, Zepeda O, Centeno E, Vielot N, Diez-Valcarce M, Vinjé J, Baric R, Lindesmith LC, Bucardo F. Norovirus Infection in Young Nicaraguan Children Induces Durable and Genotype-Specific Antibody Immunity. Viruses 2022; 14:v14092053. [PMID: 36146859 PMCID: PMC9501366 DOI: 10.3390/v14092053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/05/2022] [Accepted: 09/08/2022] [Indexed: 11/22/2022] Open
Abstract
There are significant challenges to the development of a pediatric norovirus vaccine, mainly due to the antigenic diversity among strains infecting young children. Characterizing human norovirus serotypes and understanding norovirus immunity in naïve children would provide key information for designing rational vaccine platforms. In this study, 26 Nicaraguan children experiencing their first norovirus acute gastroenteritis (AGE) episode during the first 18 months of life were investigated. We used a surrogate neutralization assay that measured antibodies blocking the binding of 13 different norovirus virus-like particles (VLPs) to histo-blood group antigens (HBGAs) in pre- and post-infection sera. To assess for asymptomatic norovirus infections, stools from asymptomatic children were collected monthly, screened for norovirus by RT-qPCR and genotyped by sequencing. Seroconversion of an HBGA-blocking antibody matched the infecting genotype in 25 (96%) of the 26 children. A subset of 13 (50%) and 4 (15%) of the 26 children experienced monotypic GII and GI seroconversion, respectively, strongly suggesting a type-specific response in naïve children, and 9 (35%) showed multitypic seroconversion. The most frequent pairing in multitypic seroconversion (8/12) were GII.4 Sydney and GII.12 noroviruses, both co-circulating at the time. Blocking antibody titers to these two genotypes did not correlate with each other, suggesting multiple exposure rather than cross-reactivity between genotypes. In addition, GII titers remained consistent for at least 19 months post-infection, demonstrating durable immunity. In conclusion, the first natural norovirus gastroenteritis episodes in these young children were dominated by a limited number of genotypes and induced responses of antibodies blocking binding of norovirus VLPs in a genotype-specific manner, suggesting that an effective pediatric norovirus vaccine likely needs to be multivalent and include globally dominant genotypes. The duration of protection from natural infections provides optimism for pediatric norovirus vaccines administered early in life.
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Affiliation(s)
- Paul D. Brewer-Jensen
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Yaoska Reyes
- Department of Microbiology, Faculty of Medical Sciences, National Autonomous University of Nicaragua, León 21000, Nicaragua
- Division of Molecular Medicine and Virology, Department of Clinical and Experimental Medicine, Linköping University, SE-581 83 Linköping, Sweden
| | - Sylvia Becker-Dreps
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Family Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Fredman González
- Department of Microbiology, Faculty of Medical Sciences, National Autonomous University of Nicaragua, León 21000, Nicaragua
| | - Michael L. Mallory
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Lester Gutiérrez
- Department of Microbiology, Faculty of Medical Sciences, National Autonomous University of Nicaragua, León 21000, Nicaragua
| | - Omar Zepeda
- Department of Microbiology, Faculty of Medical Sciences, National Autonomous University of Nicaragua, León 21000, Nicaragua
| | - Edwing Centeno
- Department of Microbiology, Faculty of Medical Sciences, National Autonomous University of Nicaragua, León 21000, Nicaragua
| | - Nadja Vielot
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Marta Diez-Valcarce
- Division of Viral Diseases, U.S. Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Jan Vinjé
- Division of Viral Diseases, U.S. Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Ralph Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Lisa C. Lindesmith
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Filemon Bucardo
- Department of Microbiology, Faculty of Medical Sciences, National Autonomous University of Nicaragua, León 21000, Nicaragua
- Correspondence: ; Tel.: +505-89040938
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10
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Gallichotte EN, Henein S, Nivarthi U, Delacruz M, Scobey T, Bonaparte M, Moser J, Munteanu A, Baric R, de Silva AM. Vaccine-induced antibodies to contemporary strains of dengue virus type 4 show a mechanistic correlate of protective immunity. Cell Rep 2022; 39:110930. [PMID: 35675766 DOI: 10.1016/j.celrep.2022.110930] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 02/18/2022] [Accepted: 05/18/2022] [Indexed: 11/25/2022] Open
Abstract
The four dengue virus serotypes (DENV1-4) are mosquito-borne flaviviruses of humans. Several live-attenuated tetravalent DENV vaccines are at different stages of clinical development and approval. In children with no baseline immunity to DENVs, a leading vaccine (Dengvaxia) is efficacious against vaccine-matched DENV4 genotype II (GII) strains but not vaccine-mismatched DENV4 GI viruses. We use a panel of recombinant DENV4 viruses displaying GI or GII envelope (E) proteins to map Dengvaxia-induced neutralizing antibodies (NAbs) linked to protection. The vaccine stimulated antibodies that neutralize the DENV4 GII virus better than the GI virus. The neutralization differences map to 5 variable amino acids on the E protein located within a region targeted by DENV4 NAbs, supporting a mechanistic role for these epitope-specific NAbs in protection. In children with no baseline immunity to DENVs, levels of DENV4 serotype- and genotype-specific NAbs induced by vaccination are predictive of vaccine efficacy.
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Affiliation(s)
- Emily N Gallichotte
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Sandra Henein
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Usha Nivarthi
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Matthew Delacruz
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Trevor Scobey
- Department of Epidemiology, University of North Carolina School of Public Health, Chapel Hill, NC, USA
| | | | | | | | - Ralph Baric
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC, USA; Department of Epidemiology, University of North Carolina School of Public Health, Chapel Hill, NC, USA.
| | - Aravinda M de Silva
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC, USA.
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11
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Milligan EC, Olstad K, Cano P, Munt J, Lindesmith L, Scobey T, Mallory M, Edwards D, Carfi A, Corbett K, Graham BS, Tomai MA, Iyer SS, Baric R, Reader R, Van Rompay K, Dittmer DP, Permar S, De Paris K. Efficacy of pediatric SARS-CoV-2 vaccines against high-dose B.1.617.2 challenge one year after vaccination of infant rhesus macaques. The Journal of Immunology 2022. [DOI: 10.4049/jimmunol.208.supp.65.21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Abstract
To advance SARS-CoV-2 vaccines in infants younger than 5 years, we tested the efficacy of two SARS-CoV-2 vaccine platforms against challenge with the delta variant one year after immunization of infant rhesus macaques (RM).
Infant RMs (n=8/ group; 2 month-old) were immunized intramuscularly at weeks 0 and 4 with 30 mg stabilized prefusion SARS-CoV-2 S-2P spike (S) protein (Washington strain) encoded by mRNA encapsulated in lipid nanoparticles (mRNA-LNP) or 15 mg S protein mixed with 3M-052 in stable emulsion (Protein). At 1 year, vaccinated and age-matched unvaccinated RM (n=8) were challenged intranasally (106 pfu) and intratracheally (2×106 pfu) with B.1.617.2. Lung pathology was blindly assessed on day 7. Viral RNA copies of the N gene (vRNA) were measured by qPCR in nasal and pharyngeal swabs.
Severe lung pathology was observed in 7 of 8 controls compared to 1 of 8 or 0 of 8 RM in the mRNA-LNP or protein group, respectively. On days 2 and 4, vRNA copies/ml were significantly higher in pharyngeal swabs of control RM (day 2: 4.2p>
Supported by grants from NIH PO1 AI117915
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Affiliation(s)
- Emma C Milligan
- 1Department of Microbiology and Immunology, Children’s Research Institute, School of Medicine, University of North Carolina at Chapel Hill
| | - Katherine Olstad
- 2California National Primate Research Center, University of California at Davis
| | - Patricio Cano
- 3Lineberger Cancer Center, University of North Carolina at Chapel Hill
| | - Jenny Munt
- 4Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill
| | - Lisa Lindesmith
- 4Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill
| | - Trevor Scobey
- 4Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill
| | - Michael Mallory
- 4Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill
| | | | | | | | | | | | - Smita S. Iyer
- 2California National Primate Research Center, University of California at Davis
- 8Center for Immunology and Infectious Diseases, University of California at Davis
| | - Ralph Baric
- 4Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill
| | - Rachel Reader
- 2California National Primate Research Center, University of California at Davis
| | - Koen Van Rompay
- 2California National Primate Research Center, University of California at Davis
| | - Dirk P. Dittmer
- 1Department of Microbiology and Immunology, Children’s Research Institute, School of Medicine, University of North Carolina at Chapel Hill
- 4Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill
| | - Sallie Permar
- 9Department of Pediatrics, Weill Cornell Medical College
| | - Kristina De Paris
- 1Department of Microbiology and Immunology, Children’s Research Institute, School of Medicine, University of North Carolina at Chapel Hill
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12
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Voss W, Huang Y, Marchioni J, Seeger A, Paresi C, Kain J, Townsend D, Munt J, Baric R, Georgiou G, Lavinder J, Ippolito G. Differential serological immune imprinting following SARS-CoV-2 infection, vaccination, and breakthrough infection. The Journal of Immunology 2022. [DOI: 10.4049/jimmunol.208.supp.112.09] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Abstract
Extensive efforts have been made to study the human immune response following SARS-CoV-2 infection. Recent work by our lab provided insights into the molecular-level composition of the circulating IgG antibody repertoire evoked by SARS-CoV-2 primary infection and revealed key properties of the spike-directed antibodies and the epitopes they target in convalescent plasma (Voss et al., Science 2021). We showed that the antibody response in mild SARS-CoV-2 infection is directed to epitopes outside the RBD and primarily to the S2 domain of the spike glycoprotein.
The continual emergence of globally circulating SARS-CoV-2 variants underscores the need for an ongoing study of the long-term evolution of our adaptive immune response to this virus. Collective knowledge about the molecular composition of human serological IgG memory to SARS-CoV-2 is limited. Our research uses single-cell sequencing and plasma IgG proteomics to better understand the evolving plasma antibody response to infection, vaccination, and breakthrough infection.
In volunteers with a primary infection prior to vaccination, we can identify the serological recall of somatically mutated, pre-existing IgG antibodies targeting the S2 domain of the SARS-CoV-2 spike that cross-react with conserved epitopes expressed by endemic β-coronaviruses, indicating the existence of serological immune imprinting by prior infections. In contrast, in volunteers who received a full vaccine regimen and then had a breakthrough infection, the serological recall is markedly different—as shall be discussed. Collectively, these data reveal that the molecular nature of serological IgG recall appears to depend on the sequence and mode of exposure to SARS-CoV-2 spike antigen.
Supported by NIH NCI COVID-19 SeroNet grant U54-CA260543 (R.S.B.)
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Affiliation(s)
| | | | | | | | | | | | | | - Jenny Munt
- 2University of North Carolina at Chapel Hill
| | - Ralph Baric
- 2University of North Carolina at Chapel Hill
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13
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Fischer WA, Eron JJ, Holman W, Cohen MS, Fang L, Szewczyk LJ, Sheahan TP, Baric R, Mollan KR, Wolfe CR, Duke ER, Azizad MM, Borroto-Esoda K, Wohl DA, Coombs RW, James Loftis A, Alabanza P, Lipansky F, Painter WP. A phase 2a clinical trial of molnupiravir in patients with COVID-19 shows accelerated SARS-CoV-2 RNA clearance and elimination of infectious virus. Sci Transl Med 2022; 14:eabl7430. [PMID: 34941423 PMCID: PMC10763622 DOI: 10.1126/scitranslmed.abl7430] [Citation(s) in RCA: 196] [Impact Index Per Article: 98.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 10/01/2021] [Accepted: 12/21/2021] [Indexed: 12/19/2022]
Abstract
There is an urgent need for an effective, oral, direct-acting therapeutic to block transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and prevent progression to severe coronavirus disease 2019 (COVID-19). In a phase 2a double-blind, placebo-controlled, randomized, multicenter clinical trial, we evaluated the safety, tolerability, and antiviral efficacy of the nucleoside analog molnupiravir in 202 unvaccinated participants with confirmed SARS-CoV-2 infection and symptom duration <7 days. Participants were randomized 1:1 to receive molnupiravir (200 mg) or placebo and then 3:1 to receive molnupiravir (400 or 800 mg) or placebo, orally twice daily for 5 days. Antiviral activity was assessed by reverse transcriptase polymerase chain reaction (RT-PCR) for SARS-CoV-2 RNA in nasopharyngeal swabs. Infectious virus was assessed by inoculation of cultured Vero cells with samples from nasopharyngeal swabs and was detected by RT-PCR. Time to viral RNA clearance (primary endpoint) was decreased in the 800-mg molnupiravir group (median 14 days) compared to the placebo group (median 15 days) (log rank P value = 0.013). Of participants receiving 800 mg of molnupiravir, 92.5% achieved viral RNA clearance compared with 80.3% of placebo recipients by study end (4 weeks). Infectious virus (secondary endpoint) was detected in swabs from 1.9% of the 800-mg molnupiravir group compared with 16.7% of the placebo group at day 3 of treatment (P = 0.016). At day 5 of treatment, infectious virus was not isolated from any participants receiving 400 or 800 mg of molnupiravir compared with 11.1% of placebo recipients (P = 0.034 and 0.027, respectively). Molnupiravir was well tolerated across all doses.
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Affiliation(s)
- William A. Fischer
- Institute for Global Health and Infectious Diseases, Division of Pulmonary Diseases and Critical Care Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Joseph J. Eron
- Department of Medicine, Division of Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Myron S. Cohen
- Department of Medicine, Division of Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | | | - Timothy P. Sheahan
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ralph Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Katie R. Mollan
- Gillings School of Global Public Health, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Cameron R. Wolfe
- Department of Medicine, Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA
| | - Elizabeth R. Duke
- Fred Hutchinson Cancer Research Center, University of Washington, Seattle, WA, USA
| | | | | | - David A. Wohl
- Department of Medicine, Division of Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Robert W. Coombs
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Amy James Loftis
- Institute for Global Health and Infectious Diseases, Division of Pulmonary Diseases and Critical Care Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Paul Alabanza
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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14
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Puhl AC, Gomes GF, Damasceno S, Fritch EJ, Levi JA, Johnson NJ, Scholle F, Premkumar L, Hurst BL, LeeMontiel F, Veras FP, Batah SS, Fabro AT, Moorman NJ, Yount BL, Dickmander R, Baric R, Pearce KH, Cunha FQ, Alves-Filho JC, Cunha TM, Ekins S. Vandetanib Reduces Inflammatory Cytokines and Ameliorates COVID-19 in Infected Mice. bioRxiv 2021:2021.12.16.472155. [PMID: 34981062 PMCID: PMC8722599 DOI: 10.1101/2021.12.16.472155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The portfolio of SARS-CoV-2 small molecule drugs is currently limited to a handful that are either approved (remdesivir), emergency approved (dexamethasone, baricitinib) or in advanced clinical trials. We have tested 45 FDA-approved kinase inhibitors in vitro against murine hepatitis virus (MHV) as a model of SARS-CoV-2 replication and identified 12 showing inhibition in the delayed brain tumor (DBT) cell line. Vandetanib, which targets the vascular endothelial growth factor receptor (VEGFR), the epidermal growth factor receptor (EGFR), and the RET-tyrosine kinase showed the most promising results on inhibition versus toxic effect on SARS-CoV-2-infected Caco-2 and A549-hACE2 cells (IC50 0.79 μM) while also showing a reduction of > 3 log TCID50/mL for HCoV-229E. The in vivo efficacy of vandetanib was assessed in a mouse model of SARS-CoV-2 infection and statistically significantly reduced the levels of IL-6, IL-10, TNF-α, and mitigated inflammatory cell infiltrates in the lungs of infected animals but did not reduce viral load. Vandetanib rescued the decreased IFN-1β caused by SARS-CoV-2 infection in mice to levels similar to that in uninfected animals. Our results indicate that the FDA-approved vandetanib is a potential therapeutic candidate for COVID-19 positioned for follow up in clinical trials either alone or in combination with other drugs to address the cytokine storm associated with this viral infection.
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Affiliation(s)
- Ana C. Puhl
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, NC 27606, USA
| | - Giovanni F. Gomes
- Center for Research in Inflammatory Diseases (CRID), Ribeirao Preto Medical School, University of Sao Paulo, Avenida Bandeirantes, 3900, Ribeirao Preto, 14049-900 ; Sao Paulo, Brazil
| | - Samara Damasceno
- Center for Research in Inflammatory Diseases (CRID), Ribeirao Preto Medical School, University of Sao Paulo, Avenida Bandeirantes, 3900, Ribeirao Preto, 14049-900 ; Sao Paulo, Brazil
| | - Ethan J. Fritch
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill NC 27599, USA
| | - James A. Levi
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Nicole J. Johnson
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Frank Scholle
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Lakshmanane Premkumar
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill NC 27599, USA
| | - Brett L. Hurst
- Institute for Antiviral Research, Utah State University, Logan, UT, USA
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT, USA
| | - Felipe LeeMontiel
- PhenoVista Biosciences, 6195 Cornerstone Ct E. #114 San Diego CA 92121
| | - Flavio P. Veras
- Center for Research in Inflammatory Diseases (CRID), Ribeirao Preto Medical School, University of Sao Paulo, Avenida Bandeirantes, 3900, Ribeirao Preto, 14049-900 ; Sao Paulo, Brazil
| | - Sabrina S. Batah
- Department of Pathology and Legal Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Alexandre T. Fabro
- Department of Pathology and Legal Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Nathaniel J. Moorman
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill NC 27599, USA
- Rapidly Emerging Antiviral Drug Discovery Initiative, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Boyd L. Yount
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Rebekah Dickmander
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill NC 27599, USA
- Rapidly Emerging Antiviral Drug Discovery Initiative, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Ralph Baric
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill NC 27599, USA
- Rapidly Emerging Antiviral Drug Discovery Initiative, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kenneth H. Pearce
- Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, USA
- UNC Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina 27599, USA
| | - Fernando Q. Cunha
- Center for Research in Inflammatory Diseases (CRID), Ribeirao Preto Medical School, University of Sao Paulo, Avenida Bandeirantes, 3900, Ribeirao Preto, 14049-900 ; Sao Paulo, Brazil
| | - José C. Alves-Filho
- Center for Research in Inflammatory Diseases (CRID), Ribeirao Preto Medical School, University of Sao Paulo, Avenida Bandeirantes, 3900, Ribeirao Preto, 14049-900 ; Sao Paulo, Brazil
| | - Thiago M. Cunha
- Center for Research in Inflammatory Diseases (CRID), Ribeirao Preto Medical School, University of Sao Paulo, Avenida Bandeirantes, 3900, Ribeirao Preto, 14049-900 ; Sao Paulo, Brazil
| | - Sean Ekins
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, NC 27606, USA
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15
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Henein S, Adams C, Bonaparte M, Moser JM, Munteanu A, Baric R, de Silva AM. Dengue vaccine breakthrough infections reveal properties of neutralizing antibodies linked to protection. J Clin Invest 2021; 131:147066. [PMID: 34003796 DOI: 10.1172/jci147066] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 05/13/2021] [Indexed: 01/01/2023] Open
Abstract
The 4 serotypes of dengue virus (DENV1-4) are mosquito-borne flaviviruses that infect humans. Live attenuated tetravalent DENV vaccines are at different phases of clinical testing. DENV vaccine developers have relied on neutralizing antibodies (NAbs) as a correlate of protection. A leading tetravalent vaccine (Dengvaxia) stimulated NAbs to the 4 DENV serotypes, yet overall vaccine efficacy was low in children who were DENV seronegative at baseline before vaccination. We compared the properties of (a) NAbs induced by WT DENV1 or DENV3 infections, which are strongly correlated with protection from repeat infections, and (b) NAbs induced by Dengvaxia in individuals who subsequently experienced DENV1 or DENV3 breakthrough infections. WT infections induced NAbs that recognized epitopes unique (type specific) to each serotype, whereas the vaccine stimulated qualitatively different NAbs that recognized epitopes conserved (crossreactive) between serotypes. Our results indicate that, among children who were DENV-seronegative at baseline, unbalanced replication of the DENV type 4 vaccine component in the tetravalent vaccine stimulates Abs capable of crossneutralizing DENV1 and DENV3 in vitro, but not protecting in vivo. In DENV-seronegative individuals who are vaccinated, we propose that type-specific NAbs are a better correlate of protection than total levels of NAbs.
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Affiliation(s)
- Sandra Henein
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Cameron Adams
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | | | | | | | - Ralph Baric
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA.,Department of Epidemiology, Gillings School of Public Health, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Aravinda M de Silva
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
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16
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Fischer W, Eron JJ, Holman W, Cohen MS, Fang L, Szewczyk LJ, Sheahan TP, Baric R, Mollan KR, Wolfe CR, Duke ER, Azizad MM, Borroto-Esoda K, Wohl DA, Loftis AJ, Alabanza P, Lipansky F, Painter WP. Molnupiravir, an Oral Antiviral Treatment for COVID-19. medRxiv 2021. [PMID: 34159342 DOI: 10.1101/2021.06.17.21258639] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Background Easily distributed oral antivirals are urgently needed to treat coronavirus disease-2019 (COVID-19), prevent progression to severe illness, and block transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We report the results of a Phase 2a trial evaluating the safety, tolerability, and antiviral efficacy of molnupiravir in the treatment of COVID-19 ( ClinicalTrials.gov NCT04405570 ). Methods Eligible participants included outpatients with confirmed SARS-CoV-2 infection and symptom onset within 7 days. Participants were randomized 1:1 to 200 mg molnupiravir or placebo, or 3:1 to molnupiravir (400 or 800 mg) or placebo, twice-daily for 5 days. Antiviral activity was assessed as time to undetectable levels of viral RNA by reverse transcriptase polymerase chain reaction and time to elimination of infectious virus isolation from nasopharyngeal swabs. Results Among 202 treated participants, virus isolation was significantly lower in participants receiving 800 mg molnupiravir (1.9%) versus placebo (16.7%) at Day 3 (p = 0.02). At Day 5, virus was not isolated from any participants receiving 400 or 800 mg molnupiravir, versus 11.1% of those receiving placebo (p = 0.03). Time to viral RNA clearance was decreased and a greater proportion overall achieved clearance in participants administered 800 mg molnupiravir versus placebo (p = 0.01). Molnupiravir was generally well tolerated, with similar numbers of adverse events across all groups. Conclusions Molnupiravir is the first oral, direct-acting antiviral shown to be highly effective at reducing nasopharyngeal SARS-CoV-2 infectious virus and viral RNA and has a favorable safety and tolerability profile.
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17
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Walls AC, Miranda MC, Pham MN, Schäfer A, Greaney A, Arunachalam PS, Navarro MJ, Tortorici MA, Rogers K, O'Connor MA, Shireff L, Ferrell DE, Brunette N, Kepl E, Bowen J, Zepeda SK, Starr T, Hsieh CL, Fiala B, Wrenn S, Pettie D, Sydeman C, Johnson M, Blackstone A, Ravichandran R, Ogohara C, Carter L, Tilles SW, Rappuoli R, O'Hagan DT, Van Der Most R, Van Voorhis WC, McLellan JS, Kleanthous H, Sheahan TP, Fuller DH, Villinger F, Bloom J, Pulendran B, Baric R, King N, Veesler D. Elicitation of broadly protective sarbecovirus immunity by receptor-binding domain nanoparticle vaccines. bioRxiv 2021:2021.03.15.435528. [PMID: 33758839 PMCID: PMC7986998 DOI: 10.1101/2021.03.15.435528] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Understanding the ability of SARS-CoV-2 vaccine-elicited antibodies to neutralize and protect against emerging variants of concern and other sarbecoviruses is key for guiding vaccine development decisions and public health policies. We show that a clinical stage multivalent SARS-CoV-2 receptor-binding domain nanoparticle vaccine (SARS-CoV-2 RBD-NP) protects mice from SARS-CoV-2-induced disease after a single shot, indicating that the vaccine could allow dose-sparing. SARS-CoV-2 RBD-NP elicits high antibody titers in two non-human primate (NHP) models against multiple distinct RBD antigenic sites known to be recognized by neutralizing antibodies. We benchmarked NHP serum neutralizing activity elicited by RBD-NP against a lead prefusion-stabilized SARS-CoV-2 spike immunogen using a panel of single-residue spike mutants detected in clinical isolates as well as the B.1.1.7 and B.1.351 variants of concern. Polyclonal antibodies elicited by both vaccines are resilient to most RBD mutations tested, but the E484K substitution has similar negative consequences for neutralization, and exhibit modest but comparable neutralization breadth against distantly related sarbecoviruses. We demonstrate that mosaic and cocktail sarbecovirus RBD-NPs elicit broad sarbecovirus neutralizing activity, including against the SARS-CoV-2 B.1.351 variant, and protect mice against severe SARS-CoV challenge even in the absence of the SARS-CoV RBD in the vaccine. This study provides proof of principle that sarbecovirus RBD-NPs induce heterotypic protection and enables advancement of broadly protective sarbecovirus vaccines to the clinic.
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Affiliation(s)
- Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Marcos C Miranda
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Minh N Pham
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Allison Greaney
- Basic Sciences and Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98109, USA
| | - Prabhu S Arunachalam
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Mary-Jane Navarro
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - M Alejandra Tortorici
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institut Pasteur and CNRS UMR 3569, Unité de Virologie Structurale, Paris, France
| | - Kenneth Rogers
- New Iberia Research Center and Department of Biology, University of Louisiana at Lafayette, New Iberia, LA, 70560 USA
| | - Megan A O'Connor
- Washington National Primate Research Center, Seattle, WA 98121, USA
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | - Lisa Shireff
- New Iberia Research Center and Department of Biology, University of Louisiana at Lafayette, New Iberia, LA, 70560 USA
| | - Douglas E Ferrell
- New Iberia Research Center and Department of Biology, University of Louisiana at Lafayette, New Iberia, LA, 70560 USA
| | - Natalie Brunette
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Elizabeth Kepl
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - John Bowen
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Samantha K Zepeda
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Tyler Starr
- Basic Sciences and Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Ching-Lin Hsieh
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Brooke Fiala
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Samuel Wrenn
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Deleah Pettie
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Claire Sydeman
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Max Johnson
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Alyssa Blackstone
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Rashmi Ravichandran
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Cassandra Ogohara
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Lauren Carter
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Sasha W Tilles
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | | | | | | | - Wesley C Van Voorhis
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | | | - Timothy P Sheahan
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Deborah H Fuller
- Washington National Primate Research Center, Seattle, WA 98121, USA
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | - Francois Villinger
- New Iberia Research Center and Department of Biology, University of Louisiana at Lafayette, New Iberia, LA, 70560 USA
| | - Jesse Bloom
- Basic Sciences and Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98109, USA
| | - Bali Pulendran
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Ralph Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Neil King
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
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18
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Li Z, Wu J, Yuan B, Dinnon K, Mo L, Zhou F, Dong Y, Gully K, Baric R, Graham R, Xu Y, Chen R. Abstract P35: Targeting vimentin impacts multiple cellular processes, blocks the spike protein-ACE2-mediated pseudoviral infection in vitro and reduces the symptom and lung injury in aged mice with mouse-adapted SARS-CoV-2 infection in vivo. Clin Cancer Res 2021. [DOI: 10.1158/1557-3265.covid-19-21-p35] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Vimentin intermediate filament is involved in multiple steps of viral infection such as viral entry, trafficking and egress, as well as in various mechanisms of hyperinflammation such as the restraint of Treg cell functions and the activation of NLRP3 inflammasome. We evaluated a vimentin-binding small molecule compound ALD-R491 for its effects on cellular processes related to viral infection and for its efficacy in treating SARS-CoV2 infection in vitro and in vivo. In cultured cells, the compound could reduce endocytosis by 10%, endosomal trafficking by 40% and exosomal release by over 30%. In an infection system consisting of a lentiviral pseudotype bearing the SARS-CoV-2 spike protein and HEK293 cells over-expressing the human ACE2 receptor with multiplicity of infection (MOI) of 1, 10 and 100, the compound inhibited the infection up to a maximum of over 90%, with IC50 < 50 nM, CC50 > 10 μM, and SI > 200. After oral administration of ALD-R491 in rats, the plasma concentration of the compound reached the peak (Tmax) at around 5 h with a half-life (T1/2) of about 5 h. The compound was widely distributed and enriched in tissues in vivo in rats with a volume of distribution (Vd) of over 2,000 ml/kg. The lung and the lymph nodes were among the tissues with high drug exposures. In rats receiving oral gavage of the compound at 30 mg/kg, the drug exposure in the lung and the lymph nodes maintained at levels over 1 μM from 1 h to 6 h after the oral dosing. In the syngeneic mouse tumor CT26 model, ALD-R491 was found to activate regulatory T cells (Tregs) in vivo and enhance de novo generation of Tregs in lymph nodes of the mice. In the Mouse-Adapted SARS-CoV2 model, aged mice (11-12 months) were used to provide a harder test of recovery from infection that reflects the severeness of COVID-19 in old patients. For therapeutic treatment, the mice were orally administered with the compound 24 h after the SARS-CoV2 infection once per day on Day 1, Day 2 and Day 4. At 10 mg/kg, ALD-R491 significantly reduced the body weight loss of the mice (p<0.01 on Day 5 post-infection). At both 3 mg/kg and 10 mg/kg, the compound significantly reduced the hemorrhagic score for the lungs (p<0.01 and p<0.05, respectively, on Day 5). These results indicate that vimentin intermediate filament is an effective host-directed antiviral target. Importantly, the vimentin-binding small molecule ALD-R491 impacts multiple aspects of SARS-CoV2 infection, has a favorable oral pharmacokinetics and a wide therapeutic window, and therefore may be a promising therapeutic candidate for treating COVID-19. Statement: Aluda Pharmaceuticals, Inc. has utilized the non-clinical and pre-clinical services program offered by the National Institute of Allergy and Infectious Diseases.
Citation Format: Zhizhen Li, Jianping Wu, Baoshi Yuan, Kenneth Dinnon, III, Lian Mo, Fei Zhou, Yingying Dong, Kendra Gully, Ralph Baric, Rachel Graham, Ying Xu, Ruihuan Chen. Targeting vimentin impacts multiple cellular processes, blocks the spike protein-ACE2-mediated pseudoviral infection in vitro and reduces the symptom and lung injury in aged mice with mouse-adapted SARS-CoV-2 infection in vivo [abstract]. In: Proceedings of the AACR Virtual Meeting: COVID-19 and Cancer; 2021 Feb 3-5. Philadelphia (PA): AACR; Clin Cancer Res 2021;27(6_Suppl):Abstract nr P35.
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Affiliation(s)
- Zhizhen Li
- 1Cambridge-Su Genomic Resource Center, Medical College of Soochow University, Suzhou, China (Mainland),
| | - Jianping Wu
- 2School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing; Luoda Biosciences, Inc., Chuzhou, China (Mainland),
| | - Baoshi Yuan
- 1Cambridge-Su Genomic Resource Center, Medical College of Soochow University, Suzhou, China (Mainland),
| | - Kenneth Dinnon
- 3Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC,
| | - Lian Mo
- 4Aluda Pharmaceuticals, Inc., Menlo Park, CA
| | - Fei Zhou
- 1Cambridge-Su Genomic Resource Center, Medical College of Soochow University, Suzhou, China (Mainland),
| | - Yingying Dong
- 1Cambridge-Su Genomic Resource Center, Medical College of Soochow University, Suzhou, China (Mainland),
| | - Kendra Gully
- 3Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC,
| | - Ralph Baric
- 3Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC,
| | - Rachel Graham
- 3Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC,
| | - Ying Xu
- 1Cambridge-Su Genomic Resource Center, Medical College of Soochow University, Suzhou, China (Mainland),
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19
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Zhou S, Hill CS, Clark MU, Sheahan TP, Baric R, Swanstrom R. Primer ID Next-Generation Sequencing for the Analysis of a Broad Spectrum Antiviral Induced Transition Mutations and Errors Rates in a Coronavirus Genome. Bio Protoc 2021; 11:e3938. [PMID: 33796612 DOI: 10.21769/bioprotoc.3938] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 12/21/2020] [Accepted: 03/05/2021] [Indexed: 12/25/2022] Open
Abstract
Next generations sequencing (NGS) has become an important tool in biomedical research. The Primer ID approach combined with the MiSeq platform overcomes the limitation of PCR errors and reveals the true sampling depth of population sequencing, making it an ideal tool to study mutagenic effects of potential broad-spectrum antivirals on RNA viruses. In this report we describe a protocol using Primer ID sequencing to study the mutations induced by antivirals in a coronavirus genome from an in vitro cell culture model and an in vivo mouse model. Viral RNA or total lung tissue RNA is tagged with Primer ID-containing cDNA primers during the initial reverse transcription step, followed by two rounds of PCR to amplify viral sequences and incorporate sequencing adaptors. Purified and pooled libraries are sequenced using the MiSeq platform. Sequencing data are processed using the template consensus sequence (TCS) web-app. The Primer ID approach provides an accurate sequencing protocol to measure mutation error rates in viral RNA genomes and host mRNA. Sequencing results suggested that β-D-N4-hydroxycytidine (NHC) greatly increased the transition substitution rate but not the transversion substitution rate in the viral RNA genomes, and cytosine (C) to uridine (U) was found as the most frequently seen mutation.
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Affiliation(s)
- Shuntai Zhou
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, USA
| | - Collin S Hill
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, USA
| | - Michael U Clark
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, USA
| | - Timothy P Sheahan
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, USA
| | - Ralph Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, USA.,Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, USA
| | - Ronald Swanstrom
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, USA.,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, USA
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20
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Markmann AJ, Giallourou N, Bhowmik DR, Hou YJ, Lerner A, Martinez DR, Premkumar L, Root H, van Duin D, Napravnik S, Graham SD, Guerra Q, Raut R, Petropoulos CJ, Wrin T, Cornaby C, Schmitz J, Kuruc J, Weiss S, Park Y, Baric R, de Silva AM, Margolis DM, Bartelt LA. Sex disparities and neutralizing antibody durability to SARS-CoV-2 infection in convalescent individuals. medRxiv 2021:2021.02.01.21250493. [PMID: 33564775 PMCID: PMC7872367 DOI: 10.1101/2021.02.01.21250493] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome-related coronavirus-2 (SARS-CoV-2) has now caused over 2 million deaths worldwide and continues to expand. Currently, much is unknown about functionally neutralizing human antibody responses and durability to SARS-CoV-2. Using convalescent sera collected from 101 COVID-19 recovered individuals 21-212 days after symptom onset with forty-eight additional longitudinal samples, we measured functionality and durability of serum antibodies. We also evaluated associations between individual demographic and clinical parameters with functional neutralizing antibody responses to COVID-19. We found robust antibody durability out to six months, as well as significant positive associations with the magnitude of the neutralizing antibody response and male sex. We also show that SARS-CoV-2 convalescent neutralizing antibodies are higher in individuals with cardio-metabolic comorbidities.
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Affiliation(s)
- Alena J. Markmann
- Department of Medicine, Division of Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill NC 27599, USA
| | - Natasa Giallourou
- Centre of Excellence in Biobanking and Biomedical Research, Molecular Medicine Research Center, University of Cyprus, Nicosia, Cyprus
| | - D. Ryan Bhowmik
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill NC 27599, USA
| | - Yixuan J. Hou
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Aaron Lerner
- Department of Medicine, University of North Carolina School of Medicine, Chapel Hill NC 27599, USA
| | - David R. Martinez
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lakshmanane Premkumar
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill NC 27599, USA
| | - Heather Root
- Department of Medicine, Division of Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill NC 27599, USA
| | - David van Duin
- Department of Medicine, Division of Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill NC 27599, USA
| | - Sonia Napravnik
- Department of Medicine, Division of Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill NC 27599, USA
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Stephen D. Graham
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill NC 27599, USA
| | - Quique Guerra
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill NC 27599, USA
| | - Rajendra Raut
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill NC 27599, USA
| | | | - Terri Wrin
- LabCorp-Monogram Biosciences, South San Francisco, CA 94080
| | - Caleb Cornaby
- Department of Pathology & Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill NC 27599, USA
| | - John Schmitz
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill NC 27599, USA
- Department of Pathology & Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill NC 27599, USA
| | - JoAnn Kuruc
- Department of Medicine, Division of Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill NC 27599, USA
- UNC HIV Cure Center, University of North Carolina School of Medicine, Chapel Hill NC 27599, USA
| | - Susan Weiss
- Department of Pathology & Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill NC 27599, USA
| | - Yara Park
- Department of Pathology & Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill NC 27599, USA
| | - Ralph Baric
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill NC 27599, USA
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Aravinda M. de Silva
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill NC 27599, USA
| | - David M. Margolis
- Department of Medicine, Division of Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill NC 27599, USA
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill NC 27599, USA
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- UNC HIV Cure Center, University of North Carolina School of Medicine, Chapel Hill NC 27599, USA
| | - Luther A. Bartelt
- Department of Medicine, Division of Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill NC 27599, USA
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21
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Atyeo C, Slein MD, Fischinger S, Burke J, Schäfer A, Leist SR, Kuzmina NA, Mire C, Honko A, Johnson R, Storm N, Bernett M, Tong P, Zuo T, Lin J, Zuiani A, Linde C, Suscovich T, Wesemann DR, Griffiths A, Desjarlais JR, Juelg BD, Goudsmit J, Bukreyev A, Baric R, Alter G. Dissecting strategies to tune the therapeutic potential of SARS-CoV-2-specific monoclonal antibody CR3022. JCI Insight 2021; 6:143129. [PMID: 33427208 PMCID: PMC7821590 DOI: 10.1172/jci.insight.143129] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 11/25/2020] [Indexed: 02/06/2023] Open
Abstract
The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), coupled with a lack of therapeutics, has paralyzed the globe. Although significant effort has been invested in identifying antibodies that block infection, the ability of antibodies to target infected cells through Fc interactions may be vital to eliminate the virus. To explore the role of Fc activity in SARS-CoV-2 immunity, the functional potential of a cross–SARS-reactive antibody, CR3022, was assessed. CR3022 was able to broadly drive antibody effector functions, providing critical immune clearance at entry and upon egress. Using selectively engineered Fc variants, no protection was observed after administration of WT IgG1 in mice or hamsters. Conversely, the functionally enhanced Fc variant resulted in increased pathology in both the mouse and hamster models, causing weight loss in mice and enhanced viral replication and weight loss in the more susceptible hamster model, highlighting the pathological functions of Fc-enhancing mutations. These data point to the critical need for strategic Fc engineering for the treatment of SARS-CoV-2 infection.
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Affiliation(s)
- Caroline Atyeo
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA.,Program in Virology, Division of Medical Sciences, Harvard University, Boston, Massachusetts, USA
| | - Matthew D Slein
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA
| | - Stephanie Fischinger
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA.,Program in Immunology and Virology, University of Duisburg-Essen, Essen, Germany
| | - John Burke
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA
| | - Alexandra Schäfer
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Sarah R Leist
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Natalia A Kuzmina
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, USA.,Galveston National Laboratory, Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas, USA
| | - Chad Mire
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, USA.,Galveston National Laboratory, Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas, USA
| | - Anna Honko
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, USA.,National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
| | - Rebecca Johnson
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, USA.,National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
| | - Nadia Storm
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, USA.,National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
| | | | - Pei Tong
- Department of Medicine, Brigham and Women's Hospital; Division of Allergy and Clinical Immunology; and Division of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Teng Zuo
- Department of Medicine, Brigham and Women's Hospital; Division of Allergy and Clinical Immunology; and Division of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Junrui Lin
- Department of Medicine, Brigham and Women's Hospital; Division of Allergy and Clinical Immunology; and Division of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Adam Zuiani
- Department of Medicine, Brigham and Women's Hospital; Division of Allergy and Clinical Immunology; and Division of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | | | | | - Duane R Wesemann
- Department of Medicine, Brigham and Women's Hospital; Division of Allergy and Clinical Immunology; and Division of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Anthony Griffiths
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, USA.,National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
| | | | - Boris D Juelg
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA
| | - Jaap Goudsmit
- Departments of Epidemiology and Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Alexander Bukreyev
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, USA.,Galveston National Laboratory, Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas, USA.,Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Ralph Baric
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Departments of Microbiology and Immunology and Genetics, School of Medicine, and.,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA
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Anderson EJ, Rouphael NG, Widge AT, Jackson LA, Roberts PC, Makhene M, Chappell JD, Denison MR, Stevens LJ, Pruijssers AJ, McDermott AB, Flach B, Lin BC, Doria-Rose NA, O'Dell S, Schmidt SD, Corbett KS, Swanson PA, Padilla M, Neuzil KM, Bennett H, Leav B, Makowski M, Albert J, Cross K, Edara VV, Floyd K, Suthar MS, Martinez DR, Baric R, Buchanan W, Luke CJ, Phadke VK, Rostad CA, Ledgerwood JE, Graham BS, Beigel JH. Safety and Immunogenicity of SARS-CoV-2 mRNA-1273 Vaccine in Older Adults. N Engl J Med 2020; 383:2427-2438. [PMID: 32991794 PMCID: PMC7556339 DOI: 10.1056/nejmoa2028436] [Citation(s) in RCA: 1014] [Impact Index Per Article: 253.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND Testing of vaccine candidates to prevent infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in an older population is important, since increased incidences of illness and death from coronavirus disease 2019 (Covid-19) have been associated with an older age. METHODS We conducted a phase 1, dose-escalation, open-label trial of a messenger RNA vaccine, mRNA-1273, which encodes the stabilized prefusion SARS-CoV-2 spike protein (S-2P) in healthy adults. The trial was expanded to include 40 older adults, who were stratified according to age (56 to 70 years or ≥71 years). All the participants were assigned sequentially to receive two doses of either 25 μg or 100 μg of vaccine administered 28 days apart. RESULTS Solicited adverse events were predominantly mild or moderate in severity and most frequently included fatigue, chills, headache, myalgia, and pain at the injection site. Such adverse events were dose-dependent and were more common after the second immunization. Binding-antibody responses increased rapidly after the first immunization. By day 57, among the participants who received the 25-μg dose, the anti-S-2P geometric mean titer (GMT) was 323,945 among those between the ages of 56 and 70 years and 1,128,391 among those who were 71 years of age or older; among the participants who received the 100-μg dose, the GMT in the two age subgroups was 1,183,066 and 3,638,522, respectively. After the second immunization, serum neutralizing activity was detected in all the participants by multiple methods. Binding- and neutralizing-antibody responses appeared to be similar to those previously reported among vaccine recipients between the ages of 18 and 55 years and were above the median of a panel of controls who had donated convalescent serum. The vaccine elicited a strong CD4 cytokine response involving type 1 helper T cells. CONCLUSIONS In this small study involving older adults, adverse events associated with the mRNA-1273 vaccine were mainly mild or moderate. The 100-μg dose induced higher binding- and neutralizing-antibody titers than the 25-μg dose, which supports the use of the 100-μg dose in a phase 3 vaccine trial. (Funded by the National Institute of Allergy and Infectious Diseases and others; mRNA-1273 Study ClinicalTrials.gov number, NCT04283461.).
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Affiliation(s)
- Evan J Anderson
- From the Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta and the Department of Pediatrics, Emory University School of Medicine (E.J.A., V.V.E., K.F., M.S.S., C.A.R.), and Emory Vaccine Center, Yerkes National Primate Research Center, Emory University (M.S.S.), Atlanta, and Hope Clinic, Department of Medicine, Emory University School of Medicine, Decatur (E.J.A., N.G.R., V.K.P.) - both in Georgia; the Vaccine Research Center (A.T.W., A.B.M., B.F., B.C.L., N.A.D.-R., S.O., S.D.S., K.S.C., P.A.S., M.P., J.E.L., B.S.G.) and the Division of Microbiology and Infectious Diseases (P.C.R., M. Makhene, W.B., C.J.L., J.H.B.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, the University of Maryland School of Medicine, Baltimore (K.M.N.), and the Emmes Company, Rockville (M. Makowski, J.A., K.C.) - all in Maryland; Kaiser Permanente Washington Health Research Institute, Seattle (L.A.J.); the Department of Pediatrics (J.D.C., M.R.D., L.J.S., A.J.P.), the Vanderbilt Institute for Infection, Immunology, and Inflammation (J.D.C., M.R.D., A.J.P.), and the Departments of Pathology, Microbiology, and Immunology (M.R.D.), Vanderbilt University Medical Center, Nashville; Moderna, Cambridge, MA (H.B., B.L.); and the Departments of Epidemiology and Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill (D.R.M., R.B.)
| | - Nadine G Rouphael
- From the Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta and the Department of Pediatrics, Emory University School of Medicine (E.J.A., V.V.E., K.F., M.S.S., C.A.R.), and Emory Vaccine Center, Yerkes National Primate Research Center, Emory University (M.S.S.), Atlanta, and Hope Clinic, Department of Medicine, Emory University School of Medicine, Decatur (E.J.A., N.G.R., V.K.P.) - both in Georgia; the Vaccine Research Center (A.T.W., A.B.M., B.F., B.C.L., N.A.D.-R., S.O., S.D.S., K.S.C., P.A.S., M.P., J.E.L., B.S.G.) and the Division of Microbiology and Infectious Diseases (P.C.R., M. Makhene, W.B., C.J.L., J.H.B.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, the University of Maryland School of Medicine, Baltimore (K.M.N.), and the Emmes Company, Rockville (M. Makowski, J.A., K.C.) - all in Maryland; Kaiser Permanente Washington Health Research Institute, Seattle (L.A.J.); the Department of Pediatrics (J.D.C., M.R.D., L.J.S., A.J.P.), the Vanderbilt Institute for Infection, Immunology, and Inflammation (J.D.C., M.R.D., A.J.P.), and the Departments of Pathology, Microbiology, and Immunology (M.R.D.), Vanderbilt University Medical Center, Nashville; Moderna, Cambridge, MA (H.B., B.L.); and the Departments of Epidemiology and Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill (D.R.M., R.B.)
| | - Alicia T Widge
- From the Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta and the Department of Pediatrics, Emory University School of Medicine (E.J.A., V.V.E., K.F., M.S.S., C.A.R.), and Emory Vaccine Center, Yerkes National Primate Research Center, Emory University (M.S.S.), Atlanta, and Hope Clinic, Department of Medicine, Emory University School of Medicine, Decatur (E.J.A., N.G.R., V.K.P.) - both in Georgia; the Vaccine Research Center (A.T.W., A.B.M., B.F., B.C.L., N.A.D.-R., S.O., S.D.S., K.S.C., P.A.S., M.P., J.E.L., B.S.G.) and the Division of Microbiology and Infectious Diseases (P.C.R., M. Makhene, W.B., C.J.L., J.H.B.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, the University of Maryland School of Medicine, Baltimore (K.M.N.), and the Emmes Company, Rockville (M. Makowski, J.A., K.C.) - all in Maryland; Kaiser Permanente Washington Health Research Institute, Seattle (L.A.J.); the Department of Pediatrics (J.D.C., M.R.D., L.J.S., A.J.P.), the Vanderbilt Institute for Infection, Immunology, and Inflammation (J.D.C., M.R.D., A.J.P.), and the Departments of Pathology, Microbiology, and Immunology (M.R.D.), Vanderbilt University Medical Center, Nashville; Moderna, Cambridge, MA (H.B., B.L.); and the Departments of Epidemiology and Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill (D.R.M., R.B.)
| | - Lisa A Jackson
- From the Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta and the Department of Pediatrics, Emory University School of Medicine (E.J.A., V.V.E., K.F., M.S.S., C.A.R.), and Emory Vaccine Center, Yerkes National Primate Research Center, Emory University (M.S.S.), Atlanta, and Hope Clinic, Department of Medicine, Emory University School of Medicine, Decatur (E.J.A., N.G.R., V.K.P.) - both in Georgia; the Vaccine Research Center (A.T.W., A.B.M., B.F., B.C.L., N.A.D.-R., S.O., S.D.S., K.S.C., P.A.S., M.P., J.E.L., B.S.G.) and the Division of Microbiology and Infectious Diseases (P.C.R., M. Makhene, W.B., C.J.L., J.H.B.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, the University of Maryland School of Medicine, Baltimore (K.M.N.), and the Emmes Company, Rockville (M. Makowski, J.A., K.C.) - all in Maryland; Kaiser Permanente Washington Health Research Institute, Seattle (L.A.J.); the Department of Pediatrics (J.D.C., M.R.D., L.J.S., A.J.P.), the Vanderbilt Institute for Infection, Immunology, and Inflammation (J.D.C., M.R.D., A.J.P.), and the Departments of Pathology, Microbiology, and Immunology (M.R.D.), Vanderbilt University Medical Center, Nashville; Moderna, Cambridge, MA (H.B., B.L.); and the Departments of Epidemiology and Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill (D.R.M., R.B.)
| | - Paul C Roberts
- From the Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta and the Department of Pediatrics, Emory University School of Medicine (E.J.A., V.V.E., K.F., M.S.S., C.A.R.), and Emory Vaccine Center, Yerkes National Primate Research Center, Emory University (M.S.S.), Atlanta, and Hope Clinic, Department of Medicine, Emory University School of Medicine, Decatur (E.J.A., N.G.R., V.K.P.) - both in Georgia; the Vaccine Research Center (A.T.W., A.B.M., B.F., B.C.L., N.A.D.-R., S.O., S.D.S., K.S.C., P.A.S., M.P., J.E.L., B.S.G.) and the Division of Microbiology and Infectious Diseases (P.C.R., M. Makhene, W.B., C.J.L., J.H.B.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, the University of Maryland School of Medicine, Baltimore (K.M.N.), and the Emmes Company, Rockville (M. Makowski, J.A., K.C.) - all in Maryland; Kaiser Permanente Washington Health Research Institute, Seattle (L.A.J.); the Department of Pediatrics (J.D.C., M.R.D., L.J.S., A.J.P.), the Vanderbilt Institute for Infection, Immunology, and Inflammation (J.D.C., M.R.D., A.J.P.), and the Departments of Pathology, Microbiology, and Immunology (M.R.D.), Vanderbilt University Medical Center, Nashville; Moderna, Cambridge, MA (H.B., B.L.); and the Departments of Epidemiology and Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill (D.R.M., R.B.)
| | - Mamodikoe Makhene
- From the Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta and the Department of Pediatrics, Emory University School of Medicine (E.J.A., V.V.E., K.F., M.S.S., C.A.R.), and Emory Vaccine Center, Yerkes National Primate Research Center, Emory University (M.S.S.), Atlanta, and Hope Clinic, Department of Medicine, Emory University School of Medicine, Decatur (E.J.A., N.G.R., V.K.P.) - both in Georgia; the Vaccine Research Center (A.T.W., A.B.M., B.F., B.C.L., N.A.D.-R., S.O., S.D.S., K.S.C., P.A.S., M.P., J.E.L., B.S.G.) and the Division of Microbiology and Infectious Diseases (P.C.R., M. Makhene, W.B., C.J.L., J.H.B.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, the University of Maryland School of Medicine, Baltimore (K.M.N.), and the Emmes Company, Rockville (M. Makowski, J.A., K.C.) - all in Maryland; Kaiser Permanente Washington Health Research Institute, Seattle (L.A.J.); the Department of Pediatrics (J.D.C., M.R.D., L.J.S., A.J.P.), the Vanderbilt Institute for Infection, Immunology, and Inflammation (J.D.C., M.R.D., A.J.P.), and the Departments of Pathology, Microbiology, and Immunology (M.R.D.), Vanderbilt University Medical Center, Nashville; Moderna, Cambridge, MA (H.B., B.L.); and the Departments of Epidemiology and Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill (D.R.M., R.B.)
| | - James D Chappell
- From the Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta and the Department of Pediatrics, Emory University School of Medicine (E.J.A., V.V.E., K.F., M.S.S., C.A.R.), and Emory Vaccine Center, Yerkes National Primate Research Center, Emory University (M.S.S.), Atlanta, and Hope Clinic, Department of Medicine, Emory University School of Medicine, Decatur (E.J.A., N.G.R., V.K.P.) - both in Georgia; the Vaccine Research Center (A.T.W., A.B.M., B.F., B.C.L., N.A.D.-R., S.O., S.D.S., K.S.C., P.A.S., M.P., J.E.L., B.S.G.) and the Division of Microbiology and Infectious Diseases (P.C.R., M. Makhene, W.B., C.J.L., J.H.B.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, the University of Maryland School of Medicine, Baltimore (K.M.N.), and the Emmes Company, Rockville (M. Makowski, J.A., K.C.) - all in Maryland; Kaiser Permanente Washington Health Research Institute, Seattle (L.A.J.); the Department of Pediatrics (J.D.C., M.R.D., L.J.S., A.J.P.), the Vanderbilt Institute for Infection, Immunology, and Inflammation (J.D.C., M.R.D., A.J.P.), and the Departments of Pathology, Microbiology, and Immunology (M.R.D.), Vanderbilt University Medical Center, Nashville; Moderna, Cambridge, MA (H.B., B.L.); and the Departments of Epidemiology and Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill (D.R.M., R.B.)
| | - Mark R Denison
- From the Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta and the Department of Pediatrics, Emory University School of Medicine (E.J.A., V.V.E., K.F., M.S.S., C.A.R.), and Emory Vaccine Center, Yerkes National Primate Research Center, Emory University (M.S.S.), Atlanta, and Hope Clinic, Department of Medicine, Emory University School of Medicine, Decatur (E.J.A., N.G.R., V.K.P.) - both in Georgia; the Vaccine Research Center (A.T.W., A.B.M., B.F., B.C.L., N.A.D.-R., S.O., S.D.S., K.S.C., P.A.S., M.P., J.E.L., B.S.G.) and the Division of Microbiology and Infectious Diseases (P.C.R., M. Makhene, W.B., C.J.L., J.H.B.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, the University of Maryland School of Medicine, Baltimore (K.M.N.), and the Emmes Company, Rockville (M. Makowski, J.A., K.C.) - all in Maryland; Kaiser Permanente Washington Health Research Institute, Seattle (L.A.J.); the Department of Pediatrics (J.D.C., M.R.D., L.J.S., A.J.P.), the Vanderbilt Institute for Infection, Immunology, and Inflammation (J.D.C., M.R.D., A.J.P.), and the Departments of Pathology, Microbiology, and Immunology (M.R.D.), Vanderbilt University Medical Center, Nashville; Moderna, Cambridge, MA (H.B., B.L.); and the Departments of Epidemiology and Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill (D.R.M., R.B.)
| | - Laura J Stevens
- From the Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta and the Department of Pediatrics, Emory University School of Medicine (E.J.A., V.V.E., K.F., M.S.S., C.A.R.), and Emory Vaccine Center, Yerkes National Primate Research Center, Emory University (M.S.S.), Atlanta, and Hope Clinic, Department of Medicine, Emory University School of Medicine, Decatur (E.J.A., N.G.R., V.K.P.) - both in Georgia; the Vaccine Research Center (A.T.W., A.B.M., B.F., B.C.L., N.A.D.-R., S.O., S.D.S., K.S.C., P.A.S., M.P., J.E.L., B.S.G.) and the Division of Microbiology and Infectious Diseases (P.C.R., M. Makhene, W.B., C.J.L., J.H.B.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, the University of Maryland School of Medicine, Baltimore (K.M.N.), and the Emmes Company, Rockville (M. Makowski, J.A., K.C.) - all in Maryland; Kaiser Permanente Washington Health Research Institute, Seattle (L.A.J.); the Department of Pediatrics (J.D.C., M.R.D., L.J.S., A.J.P.), the Vanderbilt Institute for Infection, Immunology, and Inflammation (J.D.C., M.R.D., A.J.P.), and the Departments of Pathology, Microbiology, and Immunology (M.R.D.), Vanderbilt University Medical Center, Nashville; Moderna, Cambridge, MA (H.B., B.L.); and the Departments of Epidemiology and Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill (D.R.M., R.B.)
| | - Andrea J Pruijssers
- From the Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta and the Department of Pediatrics, Emory University School of Medicine (E.J.A., V.V.E., K.F., M.S.S., C.A.R.), and Emory Vaccine Center, Yerkes National Primate Research Center, Emory University (M.S.S.), Atlanta, and Hope Clinic, Department of Medicine, Emory University School of Medicine, Decatur (E.J.A., N.G.R., V.K.P.) - both in Georgia; the Vaccine Research Center (A.T.W., A.B.M., B.F., B.C.L., N.A.D.-R., S.O., S.D.S., K.S.C., P.A.S., M.P., J.E.L., B.S.G.) and the Division of Microbiology and Infectious Diseases (P.C.R., M. Makhene, W.B., C.J.L., J.H.B.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, the University of Maryland School of Medicine, Baltimore (K.M.N.), and the Emmes Company, Rockville (M. Makowski, J.A., K.C.) - all in Maryland; Kaiser Permanente Washington Health Research Institute, Seattle (L.A.J.); the Department of Pediatrics (J.D.C., M.R.D., L.J.S., A.J.P.), the Vanderbilt Institute for Infection, Immunology, and Inflammation (J.D.C., M.R.D., A.J.P.), and the Departments of Pathology, Microbiology, and Immunology (M.R.D.), Vanderbilt University Medical Center, Nashville; Moderna, Cambridge, MA (H.B., B.L.); and the Departments of Epidemiology and Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill (D.R.M., R.B.)
| | - Adrian B McDermott
- From the Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta and the Department of Pediatrics, Emory University School of Medicine (E.J.A., V.V.E., K.F., M.S.S., C.A.R.), and Emory Vaccine Center, Yerkes National Primate Research Center, Emory University (M.S.S.), Atlanta, and Hope Clinic, Department of Medicine, Emory University School of Medicine, Decatur (E.J.A., N.G.R., V.K.P.) - both in Georgia; the Vaccine Research Center (A.T.W., A.B.M., B.F., B.C.L., N.A.D.-R., S.O., S.D.S., K.S.C., P.A.S., M.P., J.E.L., B.S.G.) and the Division of Microbiology and Infectious Diseases (P.C.R., M. Makhene, W.B., C.J.L., J.H.B.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, the University of Maryland School of Medicine, Baltimore (K.M.N.), and the Emmes Company, Rockville (M. Makowski, J.A., K.C.) - all in Maryland; Kaiser Permanente Washington Health Research Institute, Seattle (L.A.J.); the Department of Pediatrics (J.D.C., M.R.D., L.J.S., A.J.P.), the Vanderbilt Institute for Infection, Immunology, and Inflammation (J.D.C., M.R.D., A.J.P.), and the Departments of Pathology, Microbiology, and Immunology (M.R.D.), Vanderbilt University Medical Center, Nashville; Moderna, Cambridge, MA (H.B., B.L.); and the Departments of Epidemiology and Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill (D.R.M., R.B.)
| | - Britta Flach
- From the Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta and the Department of Pediatrics, Emory University School of Medicine (E.J.A., V.V.E., K.F., M.S.S., C.A.R.), and Emory Vaccine Center, Yerkes National Primate Research Center, Emory University (M.S.S.), Atlanta, and Hope Clinic, Department of Medicine, Emory University School of Medicine, Decatur (E.J.A., N.G.R., V.K.P.) - both in Georgia; the Vaccine Research Center (A.T.W., A.B.M., B.F., B.C.L., N.A.D.-R., S.O., S.D.S., K.S.C., P.A.S., M.P., J.E.L., B.S.G.) and the Division of Microbiology and Infectious Diseases (P.C.R., M. Makhene, W.B., C.J.L., J.H.B.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, the University of Maryland School of Medicine, Baltimore (K.M.N.), and the Emmes Company, Rockville (M. Makowski, J.A., K.C.) - all in Maryland; Kaiser Permanente Washington Health Research Institute, Seattle (L.A.J.); the Department of Pediatrics (J.D.C., M.R.D., L.J.S., A.J.P.), the Vanderbilt Institute for Infection, Immunology, and Inflammation (J.D.C., M.R.D., A.J.P.), and the Departments of Pathology, Microbiology, and Immunology (M.R.D.), Vanderbilt University Medical Center, Nashville; Moderna, Cambridge, MA (H.B., B.L.); and the Departments of Epidemiology and Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill (D.R.M., R.B.)
| | - Bob C Lin
- From the Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta and the Department of Pediatrics, Emory University School of Medicine (E.J.A., V.V.E., K.F., M.S.S., C.A.R.), and Emory Vaccine Center, Yerkes National Primate Research Center, Emory University (M.S.S.), Atlanta, and Hope Clinic, Department of Medicine, Emory University School of Medicine, Decatur (E.J.A., N.G.R., V.K.P.) - both in Georgia; the Vaccine Research Center (A.T.W., A.B.M., B.F., B.C.L., N.A.D.-R., S.O., S.D.S., K.S.C., P.A.S., M.P., J.E.L., B.S.G.) and the Division of Microbiology and Infectious Diseases (P.C.R., M. Makhene, W.B., C.J.L., J.H.B.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, the University of Maryland School of Medicine, Baltimore (K.M.N.), and the Emmes Company, Rockville (M. Makowski, J.A., K.C.) - all in Maryland; Kaiser Permanente Washington Health Research Institute, Seattle (L.A.J.); the Department of Pediatrics (J.D.C., M.R.D., L.J.S., A.J.P.), the Vanderbilt Institute for Infection, Immunology, and Inflammation (J.D.C., M.R.D., A.J.P.), and the Departments of Pathology, Microbiology, and Immunology (M.R.D.), Vanderbilt University Medical Center, Nashville; Moderna, Cambridge, MA (H.B., B.L.); and the Departments of Epidemiology and Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill (D.R.M., R.B.)
| | - Nicole A Doria-Rose
- From the Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta and the Department of Pediatrics, Emory University School of Medicine (E.J.A., V.V.E., K.F., M.S.S., C.A.R.), and Emory Vaccine Center, Yerkes National Primate Research Center, Emory University (M.S.S.), Atlanta, and Hope Clinic, Department of Medicine, Emory University School of Medicine, Decatur (E.J.A., N.G.R., V.K.P.) - both in Georgia; the Vaccine Research Center (A.T.W., A.B.M., B.F., B.C.L., N.A.D.-R., S.O., S.D.S., K.S.C., P.A.S., M.P., J.E.L., B.S.G.) and the Division of Microbiology and Infectious Diseases (P.C.R., M. Makhene, W.B., C.J.L., J.H.B.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, the University of Maryland School of Medicine, Baltimore (K.M.N.), and the Emmes Company, Rockville (M. Makowski, J.A., K.C.) - all in Maryland; Kaiser Permanente Washington Health Research Institute, Seattle (L.A.J.); the Department of Pediatrics (J.D.C., M.R.D., L.J.S., A.J.P.), the Vanderbilt Institute for Infection, Immunology, and Inflammation (J.D.C., M.R.D., A.J.P.), and the Departments of Pathology, Microbiology, and Immunology (M.R.D.), Vanderbilt University Medical Center, Nashville; Moderna, Cambridge, MA (H.B., B.L.); and the Departments of Epidemiology and Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill (D.R.M., R.B.)
| | - Sijy O'Dell
- From the Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta and the Department of Pediatrics, Emory University School of Medicine (E.J.A., V.V.E., K.F., M.S.S., C.A.R.), and Emory Vaccine Center, Yerkes National Primate Research Center, Emory University (M.S.S.), Atlanta, and Hope Clinic, Department of Medicine, Emory University School of Medicine, Decatur (E.J.A., N.G.R., V.K.P.) - both in Georgia; the Vaccine Research Center (A.T.W., A.B.M., B.F., B.C.L., N.A.D.-R., S.O., S.D.S., K.S.C., P.A.S., M.P., J.E.L., B.S.G.) and the Division of Microbiology and Infectious Diseases (P.C.R., M. Makhene, W.B., C.J.L., J.H.B.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, the University of Maryland School of Medicine, Baltimore (K.M.N.), and the Emmes Company, Rockville (M. Makowski, J.A., K.C.) - all in Maryland; Kaiser Permanente Washington Health Research Institute, Seattle (L.A.J.); the Department of Pediatrics (J.D.C., M.R.D., L.J.S., A.J.P.), the Vanderbilt Institute for Infection, Immunology, and Inflammation (J.D.C., M.R.D., A.J.P.), and the Departments of Pathology, Microbiology, and Immunology (M.R.D.), Vanderbilt University Medical Center, Nashville; Moderna, Cambridge, MA (H.B., B.L.); and the Departments of Epidemiology and Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill (D.R.M., R.B.)
| | - Stephen D Schmidt
- From the Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta and the Department of Pediatrics, Emory University School of Medicine (E.J.A., V.V.E., K.F., M.S.S., C.A.R.), and Emory Vaccine Center, Yerkes National Primate Research Center, Emory University (M.S.S.), Atlanta, and Hope Clinic, Department of Medicine, Emory University School of Medicine, Decatur (E.J.A., N.G.R., V.K.P.) - both in Georgia; the Vaccine Research Center (A.T.W., A.B.M., B.F., B.C.L., N.A.D.-R., S.O., S.D.S., K.S.C., P.A.S., M.P., J.E.L., B.S.G.) and the Division of Microbiology and Infectious Diseases (P.C.R., M. Makhene, W.B., C.J.L., J.H.B.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, the University of Maryland School of Medicine, Baltimore (K.M.N.), and the Emmes Company, Rockville (M. Makowski, J.A., K.C.) - all in Maryland; Kaiser Permanente Washington Health Research Institute, Seattle (L.A.J.); the Department of Pediatrics (J.D.C., M.R.D., L.J.S., A.J.P.), the Vanderbilt Institute for Infection, Immunology, and Inflammation (J.D.C., M.R.D., A.J.P.), and the Departments of Pathology, Microbiology, and Immunology (M.R.D.), Vanderbilt University Medical Center, Nashville; Moderna, Cambridge, MA (H.B., B.L.); and the Departments of Epidemiology and Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill (D.R.M., R.B.)
| | - Kizzmekia S Corbett
- From the Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta and the Department of Pediatrics, Emory University School of Medicine (E.J.A., V.V.E., K.F., M.S.S., C.A.R.), and Emory Vaccine Center, Yerkes National Primate Research Center, Emory University (M.S.S.), Atlanta, and Hope Clinic, Department of Medicine, Emory University School of Medicine, Decatur (E.J.A., N.G.R., V.K.P.) - both in Georgia; the Vaccine Research Center (A.T.W., A.B.M., B.F., B.C.L., N.A.D.-R., S.O., S.D.S., K.S.C., P.A.S., M.P., J.E.L., B.S.G.) and the Division of Microbiology and Infectious Diseases (P.C.R., M. Makhene, W.B., C.J.L., J.H.B.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, the University of Maryland School of Medicine, Baltimore (K.M.N.), and the Emmes Company, Rockville (M. Makowski, J.A., K.C.) - all in Maryland; Kaiser Permanente Washington Health Research Institute, Seattle (L.A.J.); the Department of Pediatrics (J.D.C., M.R.D., L.J.S., A.J.P.), the Vanderbilt Institute for Infection, Immunology, and Inflammation (J.D.C., M.R.D., A.J.P.), and the Departments of Pathology, Microbiology, and Immunology (M.R.D.), Vanderbilt University Medical Center, Nashville; Moderna, Cambridge, MA (H.B., B.L.); and the Departments of Epidemiology and Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill (D.R.M., R.B.)
| | - Phillip A Swanson
- From the Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta and the Department of Pediatrics, Emory University School of Medicine (E.J.A., V.V.E., K.F., M.S.S., C.A.R.), and Emory Vaccine Center, Yerkes National Primate Research Center, Emory University (M.S.S.), Atlanta, and Hope Clinic, Department of Medicine, Emory University School of Medicine, Decatur (E.J.A., N.G.R., V.K.P.) - both in Georgia; the Vaccine Research Center (A.T.W., A.B.M., B.F., B.C.L., N.A.D.-R., S.O., S.D.S., K.S.C., P.A.S., M.P., J.E.L., B.S.G.) and the Division of Microbiology and Infectious Diseases (P.C.R., M. Makhene, W.B., C.J.L., J.H.B.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, the University of Maryland School of Medicine, Baltimore (K.M.N.), and the Emmes Company, Rockville (M. Makowski, J.A., K.C.) - all in Maryland; Kaiser Permanente Washington Health Research Institute, Seattle (L.A.J.); the Department of Pediatrics (J.D.C., M.R.D., L.J.S., A.J.P.), the Vanderbilt Institute for Infection, Immunology, and Inflammation (J.D.C., M.R.D., A.J.P.), and the Departments of Pathology, Microbiology, and Immunology (M.R.D.), Vanderbilt University Medical Center, Nashville; Moderna, Cambridge, MA (H.B., B.L.); and the Departments of Epidemiology and Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill (D.R.M., R.B.)
| | - Marcelino Padilla
- From the Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta and the Department of Pediatrics, Emory University School of Medicine (E.J.A., V.V.E., K.F., M.S.S., C.A.R.), and Emory Vaccine Center, Yerkes National Primate Research Center, Emory University (M.S.S.), Atlanta, and Hope Clinic, Department of Medicine, Emory University School of Medicine, Decatur (E.J.A., N.G.R., V.K.P.) - both in Georgia; the Vaccine Research Center (A.T.W., A.B.M., B.F., B.C.L., N.A.D.-R., S.O., S.D.S., K.S.C., P.A.S., M.P., J.E.L., B.S.G.) and the Division of Microbiology and Infectious Diseases (P.C.R., M. Makhene, W.B., C.J.L., J.H.B.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, the University of Maryland School of Medicine, Baltimore (K.M.N.), and the Emmes Company, Rockville (M. Makowski, J.A., K.C.) - all in Maryland; Kaiser Permanente Washington Health Research Institute, Seattle (L.A.J.); the Department of Pediatrics (J.D.C., M.R.D., L.J.S., A.J.P.), the Vanderbilt Institute for Infection, Immunology, and Inflammation (J.D.C., M.R.D., A.J.P.), and the Departments of Pathology, Microbiology, and Immunology (M.R.D.), Vanderbilt University Medical Center, Nashville; Moderna, Cambridge, MA (H.B., B.L.); and the Departments of Epidemiology and Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill (D.R.M., R.B.)
| | - Kathy M Neuzil
- From the Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta and the Department of Pediatrics, Emory University School of Medicine (E.J.A., V.V.E., K.F., M.S.S., C.A.R.), and Emory Vaccine Center, Yerkes National Primate Research Center, Emory University (M.S.S.), Atlanta, and Hope Clinic, Department of Medicine, Emory University School of Medicine, Decatur (E.J.A., N.G.R., V.K.P.) - both in Georgia; the Vaccine Research Center (A.T.W., A.B.M., B.F., B.C.L., N.A.D.-R., S.O., S.D.S., K.S.C., P.A.S., M.P., J.E.L., B.S.G.) and the Division of Microbiology and Infectious Diseases (P.C.R., M. Makhene, W.B., C.J.L., J.H.B.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, the University of Maryland School of Medicine, Baltimore (K.M.N.), and the Emmes Company, Rockville (M. Makowski, J.A., K.C.) - all in Maryland; Kaiser Permanente Washington Health Research Institute, Seattle (L.A.J.); the Department of Pediatrics (J.D.C., M.R.D., L.J.S., A.J.P.), the Vanderbilt Institute for Infection, Immunology, and Inflammation (J.D.C., M.R.D., A.J.P.), and the Departments of Pathology, Microbiology, and Immunology (M.R.D.), Vanderbilt University Medical Center, Nashville; Moderna, Cambridge, MA (H.B., B.L.); and the Departments of Epidemiology and Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill (D.R.M., R.B.)
| | - Hamilton Bennett
- From the Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta and the Department of Pediatrics, Emory University School of Medicine (E.J.A., V.V.E., K.F., M.S.S., C.A.R.), and Emory Vaccine Center, Yerkes National Primate Research Center, Emory University (M.S.S.), Atlanta, and Hope Clinic, Department of Medicine, Emory University School of Medicine, Decatur (E.J.A., N.G.R., V.K.P.) - both in Georgia; the Vaccine Research Center (A.T.W., A.B.M., B.F., B.C.L., N.A.D.-R., S.O., S.D.S., K.S.C., P.A.S., M.P., J.E.L., B.S.G.) and the Division of Microbiology and Infectious Diseases (P.C.R., M. Makhene, W.B., C.J.L., J.H.B.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, the University of Maryland School of Medicine, Baltimore (K.M.N.), and the Emmes Company, Rockville (M. Makowski, J.A., K.C.) - all in Maryland; Kaiser Permanente Washington Health Research Institute, Seattle (L.A.J.); the Department of Pediatrics (J.D.C., M.R.D., L.J.S., A.J.P.), the Vanderbilt Institute for Infection, Immunology, and Inflammation (J.D.C., M.R.D., A.J.P.), and the Departments of Pathology, Microbiology, and Immunology (M.R.D.), Vanderbilt University Medical Center, Nashville; Moderna, Cambridge, MA (H.B., B.L.); and the Departments of Epidemiology and Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill (D.R.M., R.B.)
| | - Brett Leav
- From the Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta and the Department of Pediatrics, Emory University School of Medicine (E.J.A., V.V.E., K.F., M.S.S., C.A.R.), and Emory Vaccine Center, Yerkes National Primate Research Center, Emory University (M.S.S.), Atlanta, and Hope Clinic, Department of Medicine, Emory University School of Medicine, Decatur (E.J.A., N.G.R., V.K.P.) - both in Georgia; the Vaccine Research Center (A.T.W., A.B.M., B.F., B.C.L., N.A.D.-R., S.O., S.D.S., K.S.C., P.A.S., M.P., J.E.L., B.S.G.) and the Division of Microbiology and Infectious Diseases (P.C.R., M. Makhene, W.B., C.J.L., J.H.B.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, the University of Maryland School of Medicine, Baltimore (K.M.N.), and the Emmes Company, Rockville (M. Makowski, J.A., K.C.) - all in Maryland; Kaiser Permanente Washington Health Research Institute, Seattle (L.A.J.); the Department of Pediatrics (J.D.C., M.R.D., L.J.S., A.J.P.), the Vanderbilt Institute for Infection, Immunology, and Inflammation (J.D.C., M.R.D., A.J.P.), and the Departments of Pathology, Microbiology, and Immunology (M.R.D.), Vanderbilt University Medical Center, Nashville; Moderna, Cambridge, MA (H.B., B.L.); and the Departments of Epidemiology and Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill (D.R.M., R.B.)
| | - Mat Makowski
- From the Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta and the Department of Pediatrics, Emory University School of Medicine (E.J.A., V.V.E., K.F., M.S.S., C.A.R.), and Emory Vaccine Center, Yerkes National Primate Research Center, Emory University (M.S.S.), Atlanta, and Hope Clinic, Department of Medicine, Emory University School of Medicine, Decatur (E.J.A., N.G.R., V.K.P.) - both in Georgia; the Vaccine Research Center (A.T.W., A.B.M., B.F., B.C.L., N.A.D.-R., S.O., S.D.S., K.S.C., P.A.S., M.P., J.E.L., B.S.G.) and the Division of Microbiology and Infectious Diseases (P.C.R., M. Makhene, W.B., C.J.L., J.H.B.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, the University of Maryland School of Medicine, Baltimore (K.M.N.), and the Emmes Company, Rockville (M. Makowski, J.A., K.C.) - all in Maryland; Kaiser Permanente Washington Health Research Institute, Seattle (L.A.J.); the Department of Pediatrics (J.D.C., M.R.D., L.J.S., A.J.P.), the Vanderbilt Institute for Infection, Immunology, and Inflammation (J.D.C., M.R.D., A.J.P.), and the Departments of Pathology, Microbiology, and Immunology (M.R.D.), Vanderbilt University Medical Center, Nashville; Moderna, Cambridge, MA (H.B., B.L.); and the Departments of Epidemiology and Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill (D.R.M., R.B.)
| | - Jim Albert
- From the Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta and the Department of Pediatrics, Emory University School of Medicine (E.J.A., V.V.E., K.F., M.S.S., C.A.R.), and Emory Vaccine Center, Yerkes National Primate Research Center, Emory University (M.S.S.), Atlanta, and Hope Clinic, Department of Medicine, Emory University School of Medicine, Decatur (E.J.A., N.G.R., V.K.P.) - both in Georgia; the Vaccine Research Center (A.T.W., A.B.M., B.F., B.C.L., N.A.D.-R., S.O., S.D.S., K.S.C., P.A.S., M.P., J.E.L., B.S.G.) and the Division of Microbiology and Infectious Diseases (P.C.R., M. Makhene, W.B., C.J.L., J.H.B.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, the University of Maryland School of Medicine, Baltimore (K.M.N.), and the Emmes Company, Rockville (M. Makowski, J.A., K.C.) - all in Maryland; Kaiser Permanente Washington Health Research Institute, Seattle (L.A.J.); the Department of Pediatrics (J.D.C., M.R.D., L.J.S., A.J.P.), the Vanderbilt Institute for Infection, Immunology, and Inflammation (J.D.C., M.R.D., A.J.P.), and the Departments of Pathology, Microbiology, and Immunology (M.R.D.), Vanderbilt University Medical Center, Nashville; Moderna, Cambridge, MA (H.B., B.L.); and the Departments of Epidemiology and Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill (D.R.M., R.B.)
| | - Kaitlyn Cross
- From the Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta and the Department of Pediatrics, Emory University School of Medicine (E.J.A., V.V.E., K.F., M.S.S., C.A.R.), and Emory Vaccine Center, Yerkes National Primate Research Center, Emory University (M.S.S.), Atlanta, and Hope Clinic, Department of Medicine, Emory University School of Medicine, Decatur (E.J.A., N.G.R., V.K.P.) - both in Georgia; the Vaccine Research Center (A.T.W., A.B.M., B.F., B.C.L., N.A.D.-R., S.O., S.D.S., K.S.C., P.A.S., M.P., J.E.L., B.S.G.) and the Division of Microbiology and Infectious Diseases (P.C.R., M. Makhene, W.B., C.J.L., J.H.B.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, the University of Maryland School of Medicine, Baltimore (K.M.N.), and the Emmes Company, Rockville (M. Makowski, J.A., K.C.) - all in Maryland; Kaiser Permanente Washington Health Research Institute, Seattle (L.A.J.); the Department of Pediatrics (J.D.C., M.R.D., L.J.S., A.J.P.), the Vanderbilt Institute for Infection, Immunology, and Inflammation (J.D.C., M.R.D., A.J.P.), and the Departments of Pathology, Microbiology, and Immunology (M.R.D.), Vanderbilt University Medical Center, Nashville; Moderna, Cambridge, MA (H.B., B.L.); and the Departments of Epidemiology and Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill (D.R.M., R.B.)
| | - Venkata Viswanadh Edara
- From the Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta and the Department of Pediatrics, Emory University School of Medicine (E.J.A., V.V.E., K.F., M.S.S., C.A.R.), and Emory Vaccine Center, Yerkes National Primate Research Center, Emory University (M.S.S.), Atlanta, and Hope Clinic, Department of Medicine, Emory University School of Medicine, Decatur (E.J.A., N.G.R., V.K.P.) - both in Georgia; the Vaccine Research Center (A.T.W., A.B.M., B.F., B.C.L., N.A.D.-R., S.O., S.D.S., K.S.C., P.A.S., M.P., J.E.L., B.S.G.) and the Division of Microbiology and Infectious Diseases (P.C.R., M. Makhene, W.B., C.J.L., J.H.B.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, the University of Maryland School of Medicine, Baltimore (K.M.N.), and the Emmes Company, Rockville (M. Makowski, J.A., K.C.) - all in Maryland; Kaiser Permanente Washington Health Research Institute, Seattle (L.A.J.); the Department of Pediatrics (J.D.C., M.R.D., L.J.S., A.J.P.), the Vanderbilt Institute for Infection, Immunology, and Inflammation (J.D.C., M.R.D., A.J.P.), and the Departments of Pathology, Microbiology, and Immunology (M.R.D.), Vanderbilt University Medical Center, Nashville; Moderna, Cambridge, MA (H.B., B.L.); and the Departments of Epidemiology and Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill (D.R.M., R.B.)
| | - Katharine Floyd
- From the Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta and the Department of Pediatrics, Emory University School of Medicine (E.J.A., V.V.E., K.F., M.S.S., C.A.R.), and Emory Vaccine Center, Yerkes National Primate Research Center, Emory University (M.S.S.), Atlanta, and Hope Clinic, Department of Medicine, Emory University School of Medicine, Decatur (E.J.A., N.G.R., V.K.P.) - both in Georgia; the Vaccine Research Center (A.T.W., A.B.M., B.F., B.C.L., N.A.D.-R., S.O., S.D.S., K.S.C., P.A.S., M.P., J.E.L., B.S.G.) and the Division of Microbiology and Infectious Diseases (P.C.R., M. Makhene, W.B., C.J.L., J.H.B.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, the University of Maryland School of Medicine, Baltimore (K.M.N.), and the Emmes Company, Rockville (M. Makowski, J.A., K.C.) - all in Maryland; Kaiser Permanente Washington Health Research Institute, Seattle (L.A.J.); the Department of Pediatrics (J.D.C., M.R.D., L.J.S., A.J.P.), the Vanderbilt Institute for Infection, Immunology, and Inflammation (J.D.C., M.R.D., A.J.P.), and the Departments of Pathology, Microbiology, and Immunology (M.R.D.), Vanderbilt University Medical Center, Nashville; Moderna, Cambridge, MA (H.B., B.L.); and the Departments of Epidemiology and Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill (D.R.M., R.B.)
| | - Mehul S Suthar
- From the Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta and the Department of Pediatrics, Emory University School of Medicine (E.J.A., V.V.E., K.F., M.S.S., C.A.R.), and Emory Vaccine Center, Yerkes National Primate Research Center, Emory University (M.S.S.), Atlanta, and Hope Clinic, Department of Medicine, Emory University School of Medicine, Decatur (E.J.A., N.G.R., V.K.P.) - both in Georgia; the Vaccine Research Center (A.T.W., A.B.M., B.F., B.C.L., N.A.D.-R., S.O., S.D.S., K.S.C., P.A.S., M.P., J.E.L., B.S.G.) and the Division of Microbiology and Infectious Diseases (P.C.R., M. Makhene, W.B., C.J.L., J.H.B.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, the University of Maryland School of Medicine, Baltimore (K.M.N.), and the Emmes Company, Rockville (M. Makowski, J.A., K.C.) - all in Maryland; Kaiser Permanente Washington Health Research Institute, Seattle (L.A.J.); the Department of Pediatrics (J.D.C., M.R.D., L.J.S., A.J.P.), the Vanderbilt Institute for Infection, Immunology, and Inflammation (J.D.C., M.R.D., A.J.P.), and the Departments of Pathology, Microbiology, and Immunology (M.R.D.), Vanderbilt University Medical Center, Nashville; Moderna, Cambridge, MA (H.B., B.L.); and the Departments of Epidemiology and Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill (D.R.M., R.B.)
| | - David R Martinez
- From the Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta and the Department of Pediatrics, Emory University School of Medicine (E.J.A., V.V.E., K.F., M.S.S., C.A.R.), and Emory Vaccine Center, Yerkes National Primate Research Center, Emory University (M.S.S.), Atlanta, and Hope Clinic, Department of Medicine, Emory University School of Medicine, Decatur (E.J.A., N.G.R., V.K.P.) - both in Georgia; the Vaccine Research Center (A.T.W., A.B.M., B.F., B.C.L., N.A.D.-R., S.O., S.D.S., K.S.C., P.A.S., M.P., J.E.L., B.S.G.) and the Division of Microbiology and Infectious Diseases (P.C.R., M. Makhene, W.B., C.J.L., J.H.B.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, the University of Maryland School of Medicine, Baltimore (K.M.N.), and the Emmes Company, Rockville (M. Makowski, J.A., K.C.) - all in Maryland; Kaiser Permanente Washington Health Research Institute, Seattle (L.A.J.); the Department of Pediatrics (J.D.C., M.R.D., L.J.S., A.J.P.), the Vanderbilt Institute for Infection, Immunology, and Inflammation (J.D.C., M.R.D., A.J.P.), and the Departments of Pathology, Microbiology, and Immunology (M.R.D.), Vanderbilt University Medical Center, Nashville; Moderna, Cambridge, MA (H.B., B.L.); and the Departments of Epidemiology and Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill (D.R.M., R.B.)
| | - Ralph Baric
- From the Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta and the Department of Pediatrics, Emory University School of Medicine (E.J.A., V.V.E., K.F., M.S.S., C.A.R.), and Emory Vaccine Center, Yerkes National Primate Research Center, Emory University (M.S.S.), Atlanta, and Hope Clinic, Department of Medicine, Emory University School of Medicine, Decatur (E.J.A., N.G.R., V.K.P.) - both in Georgia; the Vaccine Research Center (A.T.W., A.B.M., B.F., B.C.L., N.A.D.-R., S.O., S.D.S., K.S.C., P.A.S., M.P., J.E.L., B.S.G.) and the Division of Microbiology and Infectious Diseases (P.C.R., M. Makhene, W.B., C.J.L., J.H.B.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, the University of Maryland School of Medicine, Baltimore (K.M.N.), and the Emmes Company, Rockville (M. Makowski, J.A., K.C.) - all in Maryland; Kaiser Permanente Washington Health Research Institute, Seattle (L.A.J.); the Department of Pediatrics (J.D.C., M.R.D., L.J.S., A.J.P.), the Vanderbilt Institute for Infection, Immunology, and Inflammation (J.D.C., M.R.D., A.J.P.), and the Departments of Pathology, Microbiology, and Immunology (M.R.D.), Vanderbilt University Medical Center, Nashville; Moderna, Cambridge, MA (H.B., B.L.); and the Departments of Epidemiology and Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill (D.R.M., R.B.)
| | - Wendy Buchanan
- From the Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta and the Department of Pediatrics, Emory University School of Medicine (E.J.A., V.V.E., K.F., M.S.S., C.A.R.), and Emory Vaccine Center, Yerkes National Primate Research Center, Emory University (M.S.S.), Atlanta, and Hope Clinic, Department of Medicine, Emory University School of Medicine, Decatur (E.J.A., N.G.R., V.K.P.) - both in Georgia; the Vaccine Research Center (A.T.W., A.B.M., B.F., B.C.L., N.A.D.-R., S.O., S.D.S., K.S.C., P.A.S., M.P., J.E.L., B.S.G.) and the Division of Microbiology and Infectious Diseases (P.C.R., M. Makhene, W.B., C.J.L., J.H.B.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, the University of Maryland School of Medicine, Baltimore (K.M.N.), and the Emmes Company, Rockville (M. Makowski, J.A., K.C.) - all in Maryland; Kaiser Permanente Washington Health Research Institute, Seattle (L.A.J.); the Department of Pediatrics (J.D.C., M.R.D., L.J.S., A.J.P.), the Vanderbilt Institute for Infection, Immunology, and Inflammation (J.D.C., M.R.D., A.J.P.), and the Departments of Pathology, Microbiology, and Immunology (M.R.D.), Vanderbilt University Medical Center, Nashville; Moderna, Cambridge, MA (H.B., B.L.); and the Departments of Epidemiology and Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill (D.R.M., R.B.)
| | - Catherine J Luke
- From the Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta and the Department of Pediatrics, Emory University School of Medicine (E.J.A., V.V.E., K.F., M.S.S., C.A.R.), and Emory Vaccine Center, Yerkes National Primate Research Center, Emory University (M.S.S.), Atlanta, and Hope Clinic, Department of Medicine, Emory University School of Medicine, Decatur (E.J.A., N.G.R., V.K.P.) - both in Georgia; the Vaccine Research Center (A.T.W., A.B.M., B.F., B.C.L., N.A.D.-R., S.O., S.D.S., K.S.C., P.A.S., M.P., J.E.L., B.S.G.) and the Division of Microbiology and Infectious Diseases (P.C.R., M. Makhene, W.B., C.J.L., J.H.B.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, the University of Maryland School of Medicine, Baltimore (K.M.N.), and the Emmes Company, Rockville (M. Makowski, J.A., K.C.) - all in Maryland; Kaiser Permanente Washington Health Research Institute, Seattle (L.A.J.); the Department of Pediatrics (J.D.C., M.R.D., L.J.S., A.J.P.), the Vanderbilt Institute for Infection, Immunology, and Inflammation (J.D.C., M.R.D., A.J.P.), and the Departments of Pathology, Microbiology, and Immunology (M.R.D.), Vanderbilt University Medical Center, Nashville; Moderna, Cambridge, MA (H.B., B.L.); and the Departments of Epidemiology and Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill (D.R.M., R.B.)
| | - Varun K Phadke
- From the Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta and the Department of Pediatrics, Emory University School of Medicine (E.J.A., V.V.E., K.F., M.S.S., C.A.R.), and Emory Vaccine Center, Yerkes National Primate Research Center, Emory University (M.S.S.), Atlanta, and Hope Clinic, Department of Medicine, Emory University School of Medicine, Decatur (E.J.A., N.G.R., V.K.P.) - both in Georgia; the Vaccine Research Center (A.T.W., A.B.M., B.F., B.C.L., N.A.D.-R., S.O., S.D.S., K.S.C., P.A.S., M.P., J.E.L., B.S.G.) and the Division of Microbiology and Infectious Diseases (P.C.R., M. Makhene, W.B., C.J.L., J.H.B.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, the University of Maryland School of Medicine, Baltimore (K.M.N.), and the Emmes Company, Rockville (M. Makowski, J.A., K.C.) - all in Maryland; Kaiser Permanente Washington Health Research Institute, Seattle (L.A.J.); the Department of Pediatrics (J.D.C., M.R.D., L.J.S., A.J.P.), the Vanderbilt Institute for Infection, Immunology, and Inflammation (J.D.C., M.R.D., A.J.P.), and the Departments of Pathology, Microbiology, and Immunology (M.R.D.), Vanderbilt University Medical Center, Nashville; Moderna, Cambridge, MA (H.B., B.L.); and the Departments of Epidemiology and Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill (D.R.M., R.B.)
| | - Christina A Rostad
- From the Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta and the Department of Pediatrics, Emory University School of Medicine (E.J.A., V.V.E., K.F., M.S.S., C.A.R.), and Emory Vaccine Center, Yerkes National Primate Research Center, Emory University (M.S.S.), Atlanta, and Hope Clinic, Department of Medicine, Emory University School of Medicine, Decatur (E.J.A., N.G.R., V.K.P.) - both in Georgia; the Vaccine Research Center (A.T.W., A.B.M., B.F., B.C.L., N.A.D.-R., S.O., S.D.S., K.S.C., P.A.S., M.P., J.E.L., B.S.G.) and the Division of Microbiology and Infectious Diseases (P.C.R., M. Makhene, W.B., C.J.L., J.H.B.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, the University of Maryland School of Medicine, Baltimore (K.M.N.), and the Emmes Company, Rockville (M. Makowski, J.A., K.C.) - all in Maryland; Kaiser Permanente Washington Health Research Institute, Seattle (L.A.J.); the Department of Pediatrics (J.D.C., M.R.D., L.J.S., A.J.P.), the Vanderbilt Institute for Infection, Immunology, and Inflammation (J.D.C., M.R.D., A.J.P.), and the Departments of Pathology, Microbiology, and Immunology (M.R.D.), Vanderbilt University Medical Center, Nashville; Moderna, Cambridge, MA (H.B., B.L.); and the Departments of Epidemiology and Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill (D.R.M., R.B.)
| | - Julie E Ledgerwood
- From the Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta and the Department of Pediatrics, Emory University School of Medicine (E.J.A., V.V.E., K.F., M.S.S., C.A.R.), and Emory Vaccine Center, Yerkes National Primate Research Center, Emory University (M.S.S.), Atlanta, and Hope Clinic, Department of Medicine, Emory University School of Medicine, Decatur (E.J.A., N.G.R., V.K.P.) - both in Georgia; the Vaccine Research Center (A.T.W., A.B.M., B.F., B.C.L., N.A.D.-R., S.O., S.D.S., K.S.C., P.A.S., M.P., J.E.L., B.S.G.) and the Division of Microbiology and Infectious Diseases (P.C.R., M. Makhene, W.B., C.J.L., J.H.B.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, the University of Maryland School of Medicine, Baltimore (K.M.N.), and the Emmes Company, Rockville (M. Makowski, J.A., K.C.) - all in Maryland; Kaiser Permanente Washington Health Research Institute, Seattle (L.A.J.); the Department of Pediatrics (J.D.C., M.R.D., L.J.S., A.J.P.), the Vanderbilt Institute for Infection, Immunology, and Inflammation (J.D.C., M.R.D., A.J.P.), and the Departments of Pathology, Microbiology, and Immunology (M.R.D.), Vanderbilt University Medical Center, Nashville; Moderna, Cambridge, MA (H.B., B.L.); and the Departments of Epidemiology and Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill (D.R.M., R.B.)
| | - Barney S Graham
- From the Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta and the Department of Pediatrics, Emory University School of Medicine (E.J.A., V.V.E., K.F., M.S.S., C.A.R.), and Emory Vaccine Center, Yerkes National Primate Research Center, Emory University (M.S.S.), Atlanta, and Hope Clinic, Department of Medicine, Emory University School of Medicine, Decatur (E.J.A., N.G.R., V.K.P.) - both in Georgia; the Vaccine Research Center (A.T.W., A.B.M., B.F., B.C.L., N.A.D.-R., S.O., S.D.S., K.S.C., P.A.S., M.P., J.E.L., B.S.G.) and the Division of Microbiology and Infectious Diseases (P.C.R., M. Makhene, W.B., C.J.L., J.H.B.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, the University of Maryland School of Medicine, Baltimore (K.M.N.), and the Emmes Company, Rockville (M. Makowski, J.A., K.C.) - all in Maryland; Kaiser Permanente Washington Health Research Institute, Seattle (L.A.J.); the Department of Pediatrics (J.D.C., M.R.D., L.J.S., A.J.P.), the Vanderbilt Institute for Infection, Immunology, and Inflammation (J.D.C., M.R.D., A.J.P.), and the Departments of Pathology, Microbiology, and Immunology (M.R.D.), Vanderbilt University Medical Center, Nashville; Moderna, Cambridge, MA (H.B., B.L.); and the Departments of Epidemiology and Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill (D.R.M., R.B.)
| | - John H Beigel
- From the Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta and the Department of Pediatrics, Emory University School of Medicine (E.J.A., V.V.E., K.F., M.S.S., C.A.R.), and Emory Vaccine Center, Yerkes National Primate Research Center, Emory University (M.S.S.), Atlanta, and Hope Clinic, Department of Medicine, Emory University School of Medicine, Decatur (E.J.A., N.G.R., V.K.P.) - both in Georgia; the Vaccine Research Center (A.T.W., A.B.M., B.F., B.C.L., N.A.D.-R., S.O., S.D.S., K.S.C., P.A.S., M.P., J.E.L., B.S.G.) and the Division of Microbiology and Infectious Diseases (P.C.R., M. Makhene, W.B., C.J.L., J.H.B.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, the University of Maryland School of Medicine, Baltimore (K.M.N.), and the Emmes Company, Rockville (M. Makowski, J.A., K.C.) - all in Maryland; Kaiser Permanente Washington Health Research Institute, Seattle (L.A.J.); the Department of Pediatrics (J.D.C., M.R.D., L.J.S., A.J.P.), the Vanderbilt Institute for Infection, Immunology, and Inflammation (J.D.C., M.R.D., A.J.P.), and the Departments of Pathology, Microbiology, and Immunology (M.R.D.), Vanderbilt University Medical Center, Nashville; Moderna, Cambridge, MA (H.B., B.L.); and the Departments of Epidemiology and Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill (D.R.M., R.B.)
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Sherwood J, Sonderegger I, Braun R, Brinkman A, Baric R, Lindesmith L. Norovirus vaccine induces a cross-genotype protective immune response. Int J Infect Dis 2020. [DOI: 10.1016/j.ijid.2020.09.1241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Rydyznski Moderbacher C, Ramirez SI, Dan JM, Grifoni A, Hastie KM, Weiskopf D, Belanger S, Abbott RK, Kim C, Choi J, Kato Y, Crotty EG, Kim C, Rawlings SA, Mateus J, Tse LPV, Frazier A, Baric R, Peters B, Greenbaum J, Ollmann Saphire E, Smith DM, Sette A, Crotty S. Antigen-Specific Adaptive Immunity to SARS-CoV-2 in Acute COVID-19 and Associations with Age and Disease Severity. Cell 2020; 183:996-1012.e19. [PMID: 33010815 PMCID: PMC7494270 DOI: 10.1016/j.cell.2020.09.038] [Citation(s) in RCA: 1243] [Impact Index Per Article: 310.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 08/21/2020] [Accepted: 09/11/2020] [Indexed: 12/29/2022]
Abstract
Limited knowledge is available on the relationship between antigen-specific immune responses and COVID-19 disease severity. We completed a combined examination of all three branches of adaptive immunity at the level of SARS-CoV-2-specific CD4+ and CD8+ T cell and neutralizing antibody responses in acute and convalescent subjects. SARS-CoV-2-specific CD4+ and CD8+ T cells were each associated with milder disease. Coordinated SARS-CoV-2-specific adaptive immune responses were associated with milder disease, suggesting roles for both CD4+ and CD8+ T cells in protective immunity in COVID-19. Notably, coordination of SARS-CoV-2 antigen-specific responses was disrupted in individuals ≥ 65 years old. Scarcity of naive T cells was also associated with aging and poor disease outcomes. A parsimonious explanation is that coordinated CD4+ T cell, CD8+ T cell, and antibody responses are protective, but uncoordinated responses frequently fail to control disease, with a connection between aging and impaired adaptive immune responses to SARS-CoV-2.
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Affiliation(s)
- Carolyn Rydyznski Moderbacher
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Sydney I Ramirez
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Jennifer M Dan
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Kathryn M Hastie
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Simon Belanger
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Robert K Abbott
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Christina Kim
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Jinyong Choi
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Yu Kato
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Eleanor G Crotty
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Cheryl Kim
- Flow Cytometry Core Facility, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Stephen A Rawlings
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Jose Mateus
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Long Ping Victor Tse
- Department of Epidemiology, UNC Chapel Hill School of Public Health, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - April Frazier
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Ralph Baric
- Department of Epidemiology, UNC Chapel Hill School of Public Health, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Bjoern Peters
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Jason Greenbaum
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Erica Ollmann Saphire
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Davey M Smith
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA.
| | - Shane Crotty
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA.
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Wahl A, Gralinski L, Johnson C, Yao W, Kovarova M, Dinnon K, Liu H, Madden V, Krzystek H, De C, White K, Schäfer A, Zaman T, Leist S, Grant P, Gully K, Askin F, Browne E, Jones C, Pickles R, Baric R, Garcia JV. Acute SARS-CoV-2 Infection is Highly Cytopathic, Elicits a Robust Innate Immune Response and is Efficiently Prevented by EIDD-2801. Res Sq 2020. [PMID: 32995766 PMCID: PMC7523135 DOI: 10.21203/rs.3.rs-80404/v1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
All known recently emerged human coronaviruses likely originated in bats. Here, we used a single experimental platform based on human lung-only mice (LoM) to demonstrate efficient in vivo replication of all recently emerged human coronaviruses (SARS-CoV, MERS-CoV, SARS-CoV-2) and two highly relevant endogenous pre-pandemic SARS-like bat coronaviruses. Virus replication in this model occurs in bona fide human lung tissue and does not require any type of adaptation of the virus or the host. Our results indicate that bats harbor endogenous coronaviruses capable of direct transmission into humans. Further detailed analysis of pandemic SARS-CoV-2 in vivo infection of LoM human lung tissue showed predominant infection of human lung epithelial cells, including type II pneumocytes present in alveoli and ciliated airway cells. Acute SARS-CoV-2 infection was highly cytopathic and induced a robust and sustained Type I interferon and inflammatory cytokine/chemokine response. Finally, we evaluated a pre-exposure prophylaxis strategy for coronavirus infection. Our results show that prophylactic administration of EIDD-2801, an oral broad spectrum antiviral currently in phase II clinical trials for the treatment of COVID-19, dramatically prevented SARS-CoV-2 infection in vivo and thus has significant potential for the prevention and treatment of COVID-19.
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Linsky TW, Vergara R, Codina N, Nelson JW, Walker MJ, Su W, Hsiang TY, Esser-Nobis K, Yu K, Hou YJ, Priya T, Mitsumoto M, Pong A, Lau UY, Mason ML, Chen J, Chen A, Berrocal T, Peng H, Clairmont NS, Castellanos J, Lin YR, Josephson-Day A, Baric R, Walkey CD, Swanson R, Gale M, Blancas-Mejia LM, Yen HL, Silva DA. De novo design of ACE2 protein decoys to neutralize SARS-CoV-2. bioRxiv 2020. [PMID: 32793910 DOI: 10.1101/2020.08.03.231340] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
There is an urgent need for the ability to rapidly develop effective countermeasures for emerging biological threats, such as the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that causes the ongoing coronavirus disease 2019 (COVID-19) pandemic. We have developed a generalized computational design strategy to rapidly engineer de novo proteins that precisely recapitulate the protein surface targeted by biological agents, like viruses, to gain entry into cells. The designed proteins act as decoys that block cellular entry and aim to be resilient to viral mutational escape. Using our novel platform, in less than ten weeks, we engineered, validated, and optimized de novo protein decoys of human angiotensin-converting enzyme 2 (hACE2), the membrane-associated protein that SARS-CoV-2 exploits to infect cells. Our optimized designs are hyperstable de novo proteins (∼18-37 kDa), have high affinity for the SARS-CoV-2 receptor binding domain (RBD) and can potently inhibit the virus infection and replication in vitro. Future refinements to our strategy can enable the rapid development of other therapeutic de novo protein decoys, not limited to neutralizing viruses, but to combat any agent that explicitly interacts with cell surface proteins to cause disease.
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Shang J, Wan Y, Liu C, Yount B, Gully K, Yang Y, Auerbach A, Peng G, Baric R, Li F. Structure of mouse coronavirus spike protein complexed with receptor reveals mechanism for viral entry. PLoS Pathog 2020; 16:e1008392. [PMID: 32150576 PMCID: PMC7082060 DOI: 10.1371/journal.ppat.1008392] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 03/19/2020] [Accepted: 02/08/2020] [Indexed: 12/03/2022] Open
Abstract
Coronaviruses recognize a variety of receptors using different domains of their envelope-anchored spike protein. How these diverse receptor recognition patterns affect viral entry is unknown. Mouse hepatitis coronavirus (MHV) is the only known coronavirus that uses the N-terminal domain (NTD) of its spike to recognize a protein receptor, CEACAM1a. Here we determined the cryo-EM structure of MHV spike complexed with mouse CEACAM1a. The trimeric spike contains three receptor-binding S1 heads sitting on top of a trimeric membrane-fusion S2 stalk. Three receptor molecules bind to the sides of the spike trimer, where three NTDs are located. Receptor binding induces structural changes in the spike, weakening the interactions between S1 and S2. Using protease sensitivity and negative-stain EM analyses, we further showed that after protease treatment of the spike, receptor binding facilitated the dissociation of S1 from S2, allowing S2 to transition from pre-fusion to post-fusion conformation. Together these results reveal a new role of receptor binding in MHV entry: in addition to its well-characterized role in viral attachment to host cells, receptor binding also induces the conformational change of the spike and hence the fusion of viral and host membranes. Our study provides new mechanistic insight into coronavirus entry and highlights the diverse entry mechanisms used by different viruses. Coronaviruses recognize many receptors using their envelope-anchored spike protein. The role of receptor binding in coronavirus entry into host cells is a fundamental question in virology. Mouse hepatitis coronavirus (MHV) is unique among all coronaviruses in that it uses the N-terminal domain (NTD) of its spike protein to bind a protein receptor CEACAM1a. While extensive research has been performed on the cell entry mechanisms of coronaviruses that use a different domain of their spike protein for receptor binding, the cell entry mechanism for MHV is still elusive. Here we determined the cryo-EM structure of MHV spike protein complexed with CEACAM1a. The structure reveals unique features of receptor binding by MHV spike that facilitate the structural changes of MHV spike and promote cell entry of MHV. We further confirmed the structural results with biochemical and negative-stain EM analyses. These results suggest that receptor binding plays dual roles in MHV entry: it promotes both viral attachment to host cells and the fusion of host and viral membranes. Our study provides insight into the molecular mechanism of MHV entry, demonstrating how cell entry of MHV has been adapted to its unique way of receptor binding.
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Affiliation(s)
- Jian Shang
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Yushun Wan
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Chang Liu
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Boyd Yount
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Kendra Gully
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Yang Yang
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Ashley Auerbach
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Guiqing Peng
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ralph Baric
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Fang Li
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota, United States of America
- * E-mail:
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28
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McClure RS, Wendler JP, Adkins JN, Swanstrom J, Baric R, Kaiser BLD, Oxford KL, Waters KM, McDermott JE. Unified feature association networks through integration of transcriptomic and proteomic data. PLoS Comput Biol 2019; 15:e1007241. [PMID: 31527878 PMCID: PMC6748406 DOI: 10.1371/journal.pcbi.1007241] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 07/02/2019] [Indexed: 11/18/2022] Open
Abstract
High-throughput multi-omics studies and corresponding network analyses of multi-omic data have rapidly expanded their impact over the last 10 years. As biological features of different types (e.g. transcripts, proteins, metabolites) interact within cellular systems, the greatest amount of knowledge can be gained from networks that incorporate multiple types of -omic data. However, biological and technical sources of variation diminish the ability to detect cross-type associations, yielding networks dominated by communities comprised of nodes of the same type. We describe here network building methods that can maximize edges between nodes of different data types leading to integrated networks, networks that have a large number of edges that link nodes of different-omic types (transcripts, proteins, lipids etc). We systematically rank several network inference methods and demonstrate that, in many cases, using a random forest method, GENIE3, produces the most integrated networks. This increase in integration does not come at the cost of accuracy as GENIE3 produces networks of approximately the same quality as the other network inference methods tested here. Using GENIE3, we also infer networks representing antibody-mediated Dengue virus cell invasion and receptor-mediated Dengue virus invasion. A number of functional pathways showed centrality differences between the two networks including genes responding to both GM-CSF and IL-4, which had a higher centrality value in an antibody-mediated vs. receptor-mediated Dengue network. Because a biological system involves the interplay of many different types of molecules, incorporating multiple data types into networks will improve their use as models of biological systems. The methods explored here are some of the first to specifically highlight and address the challenges associated with how such multi-omic networks can be assembled and how the greatest number of interactions can be inferred from different data types. The resulting networks can lead to the discovery of new host response patterns and interactions during viral infection, generate new hypotheses of pathogenic mechanisms and confirm mechanisms of disease.
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Affiliation(s)
- Ryan S. McClure
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA, United States of America
| | - Jason P. Wendler
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA, United States of America
| | - Joshua N. Adkins
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA, United States of America
| | - Jesica Swanstrom
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina, Chapel Hill, Chapel Hill, NC, United States of America
| | - Ralph Baric
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina, Chapel Hill, Chapel Hill, NC, United States of America
| | - Brooke L. Deatherage Kaiser
- Signatures Science and Technology Division, Pacific Northwest National Laboratory, Richland WA, United States of America
| | - Kristie L. Oxford
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA, United States of America
| | - Katrina M. Waters
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA, United States of America
| | - Jason E. McDermott
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA, United States of America
- Department of Molecular Microbiology and Immunology, Oregon Health & Sciences University, Portland, OR, United States of America
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29
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Cockrell AS, Beall A, Yount B, Baric R. Efficient Reverse Genetic Systems for Rapid Genetic Manipulation of Emergent and Preemergent Infectious Coronaviruses. Methods Mol Biol 2018; 1602:59-81. [PMID: 28508214 PMCID: PMC7120940 DOI: 10.1007/978-1-4939-6964-7_5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Emergent and preemergent coronaviruses (CoVs) pose a global threat that requires immediate intervention. Rapid intervention necessitates the capacity to generate, grow, and genetically manipulate infectious CoVs in order to rapidly evaluate pathogenic mechanisms, host and tissue permissibility, and candidate antiviral therapeutic efficacy. CoVs encode the largest viral RNA genomes at about 28-32,000 nucleotides in length, and thereby complicate efficient engineering of the genome. Deconstructing the genome into manageable fragments affords the plasticity necessary to rapidly introduce targeted genetic changes in parallel and assort mutated fragments while maximizing genome stability over time. In this protocol we describe a well-developed reverse genetic platform strategy for CoVs that is comprised of partitioning the viral genome into 5-7 independent DNA fragments (depending on the CoV genome), each subcloned into a plasmid for increased stability and ease of genetic manipulation and amplification. Coronavirus genomes are conveniently partitioned by introducing type IIS or IIG restriction enzyme recognition sites that confer directional cloning. Since each restriction site leaves a unique overhang between adjoining fragments, reconstruction of the full-length genome can be achieved through a standard DNA ligation comprised of equal molar ratios of each fragment. Using this method, recombinant CoVs can be rapidly generated and used to investigate host range, gene function, pathogenesis, and candidate therapeutics for emerging and preemergent CoVs both in vitro and in vivo.
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Affiliation(s)
- Adam S Cockrell
- Department of Epidemiology, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
| | - Anne Beall
- Departments of Microbiology and Immunology, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
| | - Boyd Yount
- Department of Epidemiology, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
| | - Ralph Baric
- Department of Epidemiology, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA. .,Departments of Microbiology and Immunology, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA.
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30
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Jordan R, Hogg A, Warren T, De Wit E, Sheahan T, Lo M, Soloveva V, Weidner J, Gomba L, Feldmann F, Cronin J, Sims A, Cockrell A, Feng J, Trantcheva I, Babusis D, Porter-Poulin D, Bannister R, Mackman R, Siegel D, Ray A, Denison M, Spiropoulou C, Nichol S, Cihlar T, Baric R, Feldmann H, Bavari S. Broad-spectrum Investigational Agent GS-5734 for the Treatment of Ebola, MERS Coronavirus and Other Pathogenic Viral Infections with High Outbreak Potential. Open Forum Infect Dis 2017. [PMCID: PMC5630887 DOI: 10.1093/ofid/ofx180.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Background Recent viral outbreaks with significant mortality such as Ebola virus (EBOV), SARS-coronavirus (CoV), and MERS-CoV reinforced the need for effective antiviral therapeutics to control future epidemics. GS-5734 is a novel nucleotide analog prodrug in the development for treatment of EBOV. Method Antiviral activity of GS-5734 has been established in vitro against a wide range of pathogenic RNA virus families, including filoviruses, coronaviruses, and paramyxoviruses (EC50 = 37 to 200 nM) (Warren et al., Nature 2016; Sheahan et al., Sci Transl Med 2017; Lo et al., Sci Rep 2017). Herein, we describe the in vivo translation of the broad-spectrum activity of GS-5734 in relevant animal disease models for Ebola, Marburg, MERS-CoV, and Nipah. Result Therapeutic efficacy against multiple filoviruses with 80–100% survival was observed in rhesus monkeys infected with lethal doses of EBOV (Kikwit/1995 or Makona/2014) or Marburg virus and treated with once daily intravenous (IV) administration of 5 to 10 mg/kg GS-5734 beginning 3 to 5 days post-infection (p.i.). In all rhesus monkey filovirus infection models, GS-5734 significantly reduced systemic viremia and ameliorated severe clinical disease signs and anatomic pathology. In mice infected with MERS-CoV, twice daily subcutaneous administration of 25 mg/kg GS-5734 beginning 1 day p.i. significantly reduced lung viral load and improved respiratory function. In rhesus monkeys, once-daily IV administration of 5 mg/kg GS-5734 initiated 1 day prior to MERS-CoV infection reduced lung viral load, improved clinical disease signs, and ameliorated severe lung pathology. Finally, in African green monkeys infected with a lethal dose of Nipah virus therapeutic once-daily IV administration of 10 mg/kg GS-5734, starting 1 day p.i. resulted in 100% survival to at least day 35 without any major respiratory or CNS symptoms. Conclusion GS-5734 is currently being tested in a phase 2 study in male Ebola survivors with persistent viral RNA in semen. Lyophilized drug formulation has been developed that can be administered to humans via a 30-minutes IV infusion and does not require cold chain storage. Together, these results support further development of GS-5734 as a broad-spectrum antiviral to treat viral infections with high mortality and significant outbreak potential. Disclosures R. Jordan, Gilead: Employee, Salary. J. Feng, Gilead: Employee, Salary I. Trantcheva, Gilead: Employee, Salary. D. Babusis, Gilead: Employee, Salary. D. Porter-Poulin, Gilead: Employee, Salary. R. Bannister, Gilead: Employee, Salary R. Mackman, Gilead: Employee, Salary. D. Siegel, Gilead: Employee, Salary A. Ray, Gilead: Employee, Salary, T. Cihlar, Gilead: Employee, Salary.
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Affiliation(s)
| | - Alison Hogg
- Gilead Sciences, Inc., Foster City, California
| | - Travis Warren
- United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland
| | - Emmie De Wit
- Laboratory of Virology, Division of Intramural Research, National Institute for Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana
| | - Timothy Sheahan
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Michael Lo
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Veronica Soloveva
- United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland
| | - Jessica Weidner
- United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland
| | - Laura Gomba
- United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland
| | - Friederike Feldmann
- Laboratory of Virology, Division of Intramural Research, National Institute for Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana
| | - Jacqueline Cronin
- Laboratory of Virology, Division of Intramural Research, National Institute for Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana
| | - Amy Sims
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Adam Cockrell
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Joy Feng
- Gilead Sciences, Inc., Foster City, California
| | | | | | | | | | | | | | - Adrian Ray
- Gilead Sciences, Inc., Foster City, California
| | - Mark Denison
- Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee
| | | | - Stuart Nichol
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | - Ralph Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Heinrich Feldmann
- Laboratory of Virology, Division of Intramural Research, National Institute for Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana
| | - Sina Bavari
- United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland
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31
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Henein S, Swanstrom J, Byers AM, Moser JM, Shaik SF, Bonaparte M, Jackson N, Guy B, Baric R, de Silva AM. Dissecting Antibodies Induced by a Chimeric Yellow Fever-Dengue, Live-Attenuated, Tetravalent Dengue Vaccine (CYD-TDV) in Naive and Dengue-Exposed Individuals. J Infect Dis 2017; 215:351-358. [PMID: 27932620 DOI: 10.1093/infdis/jiw576] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 11/21/2016] [Indexed: 11/13/2022] Open
Abstract
Sanofi Pasteur has developed a chimeric yellow fever-dengue, live-attenuated, tetravalent dengue vaccine (CYD-TDV) that is currently approved for use in several countries. In clinical trials, CYD-TDV was efficacious at reducing laboratory-confirmed cases of dengue disease. Efficacy varied by dengue virus (DENV) serotype and prevaccination dengue immune status. We compared the properties of antibodies in naive and DENV-exposed individuals who received CYD-TDV. We depleted specific populations of DENV-reactive antibodies from immune serum samples to estimate the contribution of serotype-cross-reactive and type-specific antibodies to neutralization. Subjects with no preexisting immunity to DENV developed neutralizing antibodies to all 4 serotypes of DENV. Further analysis demonstrated that DENV4 was mainly neutralized by type-specific antibodies whereas DENV1, DENV2, and DENV3 were mainly neutralized by serotype cross-reactive antibodies. When subjects with preexisting immunity to DENV were vaccinated, they developed higher levels of neutralizing antibodies than naive subjects who were vaccinated. In preimmune subjects, CYD-TDV boosted cross-reactive neutralizing antibodies while maintaining type-specific neutralizing antibodies acquired before vaccination. Our results demonstrate that the quality of neutralizing antibodies induced by CYD-TDV varies depending on DENV serotype and previous immune status. We discuss the implications of these results for understanding vaccine efficacy.
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Affiliation(s)
| | - Jesica Swanstrom
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina, Chapel Hill
| | | | | | | | | | | | | | - Ralph Baric
- Department of Microbiology and Immunology and.,Department of Epidemiology, Gillings School of Public Health, University of North Carolina, Chapel Hill
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32
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Wang M, Carver JJ, Phelan VV, Sanchez LM, Garg N, Peng Y, Nguyen DD, Watrous J, Kapono CA, Luzzatto-Knaan T, Porto C, Bouslimani A, Melnik AV, Meehan MJ, Liu WT, Crüsemann M, Boudreau PD, Esquenazi E, Sandoval-Calderón M, Kersten RD, Pace LA, Quinn RA, Duncan KR, Hsu CC, Floros DJ, Gavilan RG, Kleigrewe K, Northen T, Dutton RJ, Parrot D, Carlson EE, Aigle B, Michelsen CF, Jelsbak L, Sohlenkamp C, Pevzner P, Edlund A, McLean J, Piel J, Murphy BT, Gerwick L, Liaw CC, Yang YL, Humpf HU, Maansson M, Keyzers RA, Sims AC, Johnson AR, Sidebottom AM, Sedio BE, Klitgaard A, Larson CB, P CAB, Torres-Mendoza D, Gonzalez DJ, Silva DB, Marques LM, Demarque DP, Pociute E, O'Neill EC, Briand E, Helfrich EJN, Granatosky EA, Glukhov E, Ryffel F, Houson H, Mohimani H, Kharbush JJ, Zeng Y, Vorholt JA, Kurita KL, Charusanti P, McPhail KL, Nielsen KF, Vuong L, Elfeki M, Traxler MF, Engene N, Koyama N, Vining OB, Baric R, Silva RR, Mascuch SJ, Tomasi S, Jenkins S, Macherla V, Hoffman T, Agarwal V, Williams PG, Dai J, Neupane R, Gurr J, Rodríguez AMC, Lamsa A, Zhang C, Dorrestein K, Duggan BM, Almaliti J, Allard PM, Phapale P, Nothias LF, Alexandrov T, Litaudon M, Wolfender JL, Kyle JE, Metz TO, Peryea T, Nguyen DT, VanLeer D, Shinn P, Jadhav A, Müller R, Waters KM, Shi W, Liu X, Zhang L, Knight R, Jensen PR, Palsson BO, Pogliano K, Linington RG, Gutiérrez M, Lopes NP, Gerwick WH, Moore BS, Dorrestein PC, Bandeira N. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nat Biotechnol 2017; 34:828-837. [PMID: 27504778 DOI: 10.1038/nbt.3597] [Citation(s) in RCA: 2254] [Impact Index Per Article: 322.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 05/10/2016] [Indexed: 12/14/2022]
Abstract
The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry (MS) techniques are well-suited to high-throughput characterization of NP, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social Molecular Networking (GNPS; http://gnps.ucsd.edu), an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of 'living data' through continuous reanalysis of deposited data.
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Affiliation(s)
- Mingxun Wang
- Computer Science and Engineering, UC San Diego, La Jolla, United States.,Center for Computational Mass Spectrometry, UC San Diego, La Jolla, United States
| | - Jeremy J Carver
- Computer Science and Engineering, UC San Diego, La Jolla, United States.,Center for Computational Mass Spectrometry, UC San Diego, La Jolla, United States
| | - Vanessa V Phelan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Laura M Sanchez
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Neha Garg
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Yao Peng
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, United States
| | - Don Duy Nguyen
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, United States
| | - Jeramie Watrous
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Clifford A Kapono
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, United States
| | - Tal Luzzatto-Knaan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Carla Porto
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Amina Bouslimani
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Alexey V Melnik
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Michael J Meehan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Wei-Ting Liu
- Department of Microbiology and Immunology, Stanford University, Palo Alto, United States
| | - Max Crüsemann
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Paul D Boudreau
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | | | | | | | - Laura A Pace
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Robert A Quinn
- Biology Department, San Diego State University, San Diego, United States
| | - Katherine R Duncan
- Scottish Association for Marine Science, Scottish Marine Institute, Oban, United Kingdom.,Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Cheng-Chih Hsu
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, United States
| | - Dimitrios J Floros
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, United States
| | - Ronnie G Gavilan
- Center for Drug Discovery and Biodiversity, INDICASAT, City of Knowledge, Panama
| | - Karin Kleigrewe
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Trent Northen
- Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Rachel J Dutton
- FAS Center for Systems Biology, Harvard, Cambridge, United States
| | - Delphine Parrot
- Produits naturels - Synthèses - Chimie Médicinale, University of Rennes 1, Rennes Cedex, France
| | - Erin E Carlson
- Chemistry, University of Minnesota, Minneapolis, United States
| | - Bertrand Aigle
- Dynamique des Génomes et Adaptation Microbienne, University of Lorraine, Vandœuvre-lès-Nancy, France
| | | | - Lars Jelsbak
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Christian Sohlenkamp
- Centro de Ciencias Genómicas, Universidad Nacional Autonoma de Mexico, Cuernavaca, Mexico
| | - Pavel Pevzner
- Center for Computational Mass Spectrometry, UC San Diego, La Jolla, United States.,Computer Science and Engineering, UC San Diego, La Jolla, United States
| | - Anna Edlund
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, United States.,School of Dentistry, UC Los Angeles, Los Angeles, United States
| | - Jeffrey McLean
- Department of Periodontics, University of Washington, Seattle, United States.,School of Dentistry, UC Los Angeles, Los Angeles, United States
| | - Jörn Piel
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Brian T Murphy
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois Chicago, Chicago, United States
| | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Chih-Chuang Liaw
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Yu-Liang Yang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Hans-Ulrich Humpf
- Institute of Food Chemistry, University of Münster, Münster, Germany
| | - Maria Maansson
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Robert A Keyzers
- School of Chemical & Physical Sciences, and Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
| | - Amy C Sims
- Gillings School of Global Public Health, Department of Epidemiology, UNC Chapel Hill, Chapel Hill, United States
| | - Andrew R Johnson
- Department of Chemistry, Indiana University, Bloomington, United States
| | | | - Brian E Sedio
- Smithsonian Tropical Research Institute, Ancón, Panama.,Center for Drug Discovery and Biodiversity, INDICASAT, City of Knowledge, Panama
| | - Andreas Klitgaard
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Charles B Larson
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States.,Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Cristopher A Boya P
- Center for Drug Discovery and Biodiversity, INDICASAT, City of Knowledge, Panama
| | | | - David J Gonzalez
- Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.,Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Denise B Silva
- School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil.,Centro de Ciencias Biologicas e da Saude, Universidade Fderal de Mato Grosso do Sul, Campo Grande, Brazil
| | - Lucas M Marques
- School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil
| | - Daniel P Demarque
- School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil
| | - Egle Pociute
- Sirenas Marine Discovery, San Diego, United States
| | - Ellis C O'Neill
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Enora Briand
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States.,UMR CNRS 6553 ECOBIO, University of Rennes 1, Rennes Cedex, France
| | | | - Eve A Granatosky
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, United States
| | - Evgenia Glukhov
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Florian Ryffel
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | | | - Hosein Mohimani
- Center for Computational Mass Spectrometry, UC San Diego, La Jolla, United States
| | - Jenan J Kharbush
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Yi Zeng
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, United States
| | | | - Kenji L Kurita
- PBSci-Chemistry & Biochemistry Department, UC Santa Cruz, Santa Cruz, United States
| | - Pep Charusanti
- Department of Bioengineering, UC San Diego, La Jolla, United States
| | - Kerry L McPhail
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, United States
| | | | - Lisa Vuong
- Sirenas Marine Discovery, San Diego, United States
| | - Maryam Elfeki
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois Chicago, Chicago, United States
| | - Matthew F Traxler
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, United States
| | - Niclas Engene
- Department of Biological Sciences, Florida International University, Miami, United States
| | - Nobuhiro Koyama
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Oliver B Vining
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, United States
| | - Ralph Baric
- Gillings School of Global Public Health, Department of Epidemiology, UNC Chapel Hill, Chapel Hill, United States
| | - Ricardo R Silva
- School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil
| | - Samantha J Mascuch
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Sophie Tomasi
- Produits naturels - Synthèses - Chimie Médicinale, University of Rennes 1, Rennes Cedex, France
| | - Stefan Jenkins
- Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, United States
| | | | - Thomas Hoffman
- Department of Pharmaceutical Biotechnology, Helmholtz Institute for Pharmaceutical Research Saarland, Saarbrücken, Germany
| | - Vinayak Agarwal
- Center for Oceans and Human Health, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Philip G Williams
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, United States
| | - Jingqui Dai
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, United States
| | - Ram Neupane
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, United States
| | - Joshua Gurr
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, United States
| | - Andrés M C Rodríguez
- School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil
| | - Anne Lamsa
- Division of Biological Sciences, UC San Diego, La Jolla, United States
| | - Chen Zhang
- Department of Nanoengineering, UC San Diego, La Jolla, United States
| | - Kathleen Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Brendan M Duggan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Jehad Almaliti
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Pierre-Marie Allard
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
| | - Prasad Phapale
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Louis-Felix Nothias
- Institut de Chimie des Substances Naturelles, CNRS-ICSN, UPR 2301, Labex CEBA, University of Paris-Saclay, Gif-sur-Yvette, France
| | - Theodore Alexandrov
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Marc Litaudon
- Institut de Chimie des Substances Naturelles, CNRS-ICSN, UPR 2301, Labex CEBA, University of Paris-Saclay, Gif-sur-Yvette, France
| | - Jean-Luc Wolfender
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
| | - Jennifer E Kyle
- Biological Sciences, Pacific Northwest National Laboratory, Richland, United States
| | - Thomas O Metz
- Biological Sciences, Pacific Northwest National Laboratory, Richland, United States
| | - Tyler Peryea
- National Center for Advancing Translational Sciences, National Institute of Health, Rockville, United States
| | - Dac-Trung Nguyen
- National Center for Advancing Translational Sciences, National Institute of Health, Rockville, United States
| | - Danielle VanLeer
- National Center for Advancing Translational Sciences, National Institute of Health, Rockville, United States
| | - Paul Shinn
- National Center for Advancing Translational Sciences, National Institute of Health, Rockville, United States
| | - Ajit Jadhav
- National Center for Advancing Translational Sciences, National Institute of Health, Rockville, United States
| | - Rolf Müller
- Department of Pharmaceutical Biotechnology, Helmholtz Institute for Pharmaceutical Research Saarland, Saarbrücken, Germany
| | - Katrina M Waters
- Biological Sciences, Pacific Northwest National Laboratory, Richland, United States
| | - Wenyuan Shi
- School of Dentistry, UC Los Angeles, Los Angeles, United States
| | - Xueting Liu
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Lixin Zhang
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Rob Knight
- Department of Pediatrics, UC San Diego, La Jolla, United States
| | - Paul R Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | | | - Kit Pogliano
- Division of Biological Sciences, UC San Diego, La Jolla, United States
| | - Roger G Linington
- PBSci-Chemistry & Biochemistry Department, UC Santa Cruz, Santa Cruz, United States
| | - Marcelino Gutiérrez
- Center for Drug Discovery and Biodiversity, INDICASAT, City of Knowledge, Panama
| | - Norberto P Lopes
- School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil
| | - William H Gerwick
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.,Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Bradley S Moore
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.,Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States.,Center for Oceans and Human Health, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.,Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States.,Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Nuno Bandeira
- Center for Computational Mass Spectrometry, UC San Diego, La Jolla, United States.,Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.,Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
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Green R, Wilkins C, Thomas S, Sekine A, Ireton RC, Ferris MT, Hendrick DM, Voss K, de Villena FPM, Baric R, Heise M, Gale M. Identifying protective host gene expression signatures within the spleen during West Nile virus infection in the collaborative cross model. Genom Data 2016; 10:114-117. [PMID: 27843766 PMCID: PMC5097955 DOI: 10.1016/j.gdata.2016.10.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Revised: 10/10/2016] [Accepted: 10/13/2016] [Indexed: 10/25/2022]
Abstract
Flaviviruses are hematophagous arthropod-viruses that pose global challenges to human health. Like Zika virus, West Nile Virus (WNV) is a flavivirus for which no approved vaccine exists [1]. The role host genetics play in early detection and response to WNV still remains largely unexplained. In order to capture the impact of genetic variation on innate immune responses, we studied gene expression following WNV infection using the collaborative cross (CC). The CC is a mouse genetics resource composed of hundreds of independently bred, octo-parental recombinant inbred mouse lines [2]. To accurately capture the host immune gene expression signatures of West Nile infection, we used the nanostring platform to evaluate expression in spleen tissue isolated from CC mice infected with WNV over a time course of 4, 7, and 12 days' post-infection [3]. Nanostring is a non-amplification based digital method to quantitate gene expression that uses color-coded molecular barcodes to detect hundreds of transcripts in a sample. Using this approach, we identified unique gene signatures in spleen tissue at days 4, 7, and 12 following WNV infection, which delineated distinct differences between asymptomatic and symptomatic CC lines. We also identified novel immune genes. Data was deposited into the Gene Expression Omnibus under accession GSE86000.
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Affiliation(s)
- Richard Green
- Department of Immunology, Center for Innate Immunity and Immune Disease (CIIID), University of Washington, Seattle, Washington, USA
| | - Courtney Wilkins
- Department of Immunology, Center for Innate Immunity and Immune Disease (CIIID), University of Washington, Seattle, Washington, USA
| | - Sunil Thomas
- Department of Immunology, Center for Innate Immunity and Immune Disease (CIIID), University of Washington, Seattle, Washington, USA
| | - Aimee Sekine
- Department of Immunology, Center for Innate Immunity and Immune Disease (CIIID), University of Washington, Seattle, Washington, USA
| | - Renee C Ireton
- Department of Immunology, Center for Innate Immunity and Immune Disease (CIIID), University of Washington, Seattle, Washington, USA
| | - Martin T Ferris
- Department of Epidemiology, University of North Carolina at Chapel Hill, North Carolina, USA
| | - Duncan M Hendrick
- Department of Immunology, Center for Innate Immunity and Immune Disease (CIIID), University of Washington, Seattle, Washington, USA
| | - Kathleen Voss
- Department of Immunology, Center for Innate Immunity and Immune Disease (CIIID), University of Washington, Seattle, Washington, USA
| | | | - Ralph Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, North Carolina, USA
| | - Mark Heise
- Department of Epidemiology, University of North Carolina at Chapel Hill, North Carolina, USA
| | - Michael Gale
- Department of Immunology, Center for Innate Immunity and Immune Disease (CIIID), University of Washington, Seattle, Washington, USA
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34
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Wang M, Carver JJ, Phelan VV, Sanchez LM, Garg N, Peng Y, Nguyen DD, Watrous J, Kapono CA, Luzzatto-Knaan T, Porto C, Bouslimani A, Melnik AV, Meehan MJ, Liu WT, Crüsemann M, Boudreau PD, Esquenazi E, Sandoval-Calderón M, Kersten RD, Pace LA, Quinn RA, Duncan KR, Hsu CC, Floros DJ, Gavilan RG, Kleigrewe K, Northen T, Dutton RJ, Parrot D, Carlson EE, Aigle B, Michelsen CF, Jelsbak L, Sohlenkamp C, Pevzner P, Edlund A, McLean J, Piel J, Murphy BT, Gerwick L, Liaw CC, Yang YL, Humpf HU, Maansson M, Keyzers RA, Sims AC, Johnson AR, Sidebottom AM, Sedio BE, Klitgaard A, Larson CB, P CAB, Torres-Mendoza D, Gonzalez DJ, Silva DB, Marques LM, Demarque DP, Pociute E, O'Neill EC, Briand E, Helfrich EJN, Granatosky EA, Glukhov E, Ryffel F, Houson H, Mohimani H, Kharbush JJ, Zeng Y, Vorholt JA, Kurita KL, Charusanti P, McPhail KL, Nielsen KF, Vuong L, Elfeki M, Traxler MF, Engene N, Koyama N, Vining OB, Baric R, Silva RR, Mascuch SJ, Tomasi S, Jenkins S, Macherla V, Hoffman T, Agarwal V, Williams PG, Dai J, Neupane R, Gurr J, Rodríguez AMC, Lamsa A, Zhang C, Dorrestein K, Duggan BM, Almaliti J, Allard PM, Phapale P, Nothias LF, Alexandrov T, Litaudon M, Wolfender JL, Kyle JE, Metz TO, Peryea T, Nguyen DT, VanLeer D, Shinn P, Jadhav A, Müller R, Waters KM, Shi W, Liu X, Zhang L, Knight R, Jensen PR, Palsson BO, Pogliano K, Linington RG, Gutiérrez M, Lopes NP, Gerwick WH, Moore BS, Dorrestein PC, Bandeira N. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nat Biotechnol 2016. [PMID: 27504778 DOI: 10.1038/nbt.3597.sharing] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry (MS) techniques are well-suited to high-throughput characterization of NP, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social Molecular Networking (GNPS; http://gnps.ucsd.edu), an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of 'living data' through continuous reanalysis of deposited data.
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Affiliation(s)
- Mingxun Wang
- Computer Science and Engineering, UC San Diego, La Jolla, United States.,Center for Computational Mass Spectrometry, UC San Diego, La Jolla, United States
| | - Jeremy J Carver
- Computer Science and Engineering, UC San Diego, La Jolla, United States.,Center for Computational Mass Spectrometry, UC San Diego, La Jolla, United States
| | - Vanessa V Phelan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Laura M Sanchez
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Neha Garg
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Yao Peng
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, United States
| | - Don Duy Nguyen
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, United States
| | - Jeramie Watrous
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Clifford A Kapono
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, United States
| | - Tal Luzzatto-Knaan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Carla Porto
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Amina Bouslimani
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Alexey V Melnik
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Michael J Meehan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Wei-Ting Liu
- Department of Microbiology and Immunology, Stanford University, Palo Alto, United States
| | - Max Crüsemann
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Paul D Boudreau
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | | | | | | | - Laura A Pace
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Robert A Quinn
- Biology Department, San Diego State University, San Diego, United States
| | - Katherine R Duncan
- Scottish Association for Marine Science, Scottish Marine Institute, Oban, United Kingdom.,Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Cheng-Chih Hsu
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, United States
| | - Dimitrios J Floros
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, United States
| | - Ronnie G Gavilan
- Center for Drug Discovery and Biodiversity, INDICASAT, City of Knowledge, Panama
| | - Karin Kleigrewe
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Trent Northen
- Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Rachel J Dutton
- FAS Center for Systems Biology, Harvard, Cambridge, United States
| | - Delphine Parrot
- Produits naturels - Synthèses - Chimie Médicinale, University of Rennes 1, Rennes Cedex, France
| | - Erin E Carlson
- Chemistry, University of Minnesota, Minneapolis, United States
| | - Bertrand Aigle
- Dynamique des Génomes et Adaptation Microbienne, University of Lorraine, Vandœuvre-lès-Nancy, France
| | | | - Lars Jelsbak
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Christian Sohlenkamp
- Centro de Ciencias Genómicas, Universidad Nacional Autonoma de Mexico, Cuernavaca, Mexico
| | - Pavel Pevzner
- Center for Computational Mass Spectrometry, UC San Diego, La Jolla, United States.,Computer Science and Engineering, UC San Diego, La Jolla, United States
| | - Anna Edlund
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, United States.,School of Dentistry, UC Los Angeles, Los Angeles, United States
| | - Jeffrey McLean
- Department of Periodontics, University of Washington, Seattle, United States.,School of Dentistry, UC Los Angeles, Los Angeles, United States
| | - Jörn Piel
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Brian T Murphy
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois Chicago, Chicago, United States
| | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Chih-Chuang Liaw
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Yu-Liang Yang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Hans-Ulrich Humpf
- Institute of Food Chemistry, University of Münster, Münster, Germany
| | - Maria Maansson
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Robert A Keyzers
- School of Chemical & Physical Sciences, and Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
| | - Amy C Sims
- Gillings School of Global Public Health, Department of Epidemiology, UNC Chapel Hill, Chapel Hill, United States
| | - Andrew R Johnson
- Department of Chemistry, Indiana University, Bloomington, United States
| | | | - Brian E Sedio
- Smithsonian Tropical Research Institute, Ancón, Panama.,Center for Drug Discovery and Biodiversity, INDICASAT, City of Knowledge, Panama
| | - Andreas Klitgaard
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Charles B Larson
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States.,Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Cristopher A Boya P
- Center for Drug Discovery and Biodiversity, INDICASAT, City of Knowledge, Panama
| | | | - David J Gonzalez
- Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.,Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Denise B Silva
- School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil.,Centro de Ciencias Biologicas e da Saude, Universidade Fderal de Mato Grosso do Sul, Campo Grande, Brazil
| | - Lucas M Marques
- School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil
| | - Daniel P Demarque
- School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil
| | - Egle Pociute
- Sirenas Marine Discovery, San Diego, United States
| | - Ellis C O'Neill
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Enora Briand
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States.,UMR CNRS 6553 ECOBIO, University of Rennes 1, Rennes Cedex, France
| | | | - Eve A Granatosky
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, United States
| | - Evgenia Glukhov
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Florian Ryffel
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | | | - Hosein Mohimani
- Center for Computational Mass Spectrometry, UC San Diego, La Jolla, United States
| | - Jenan J Kharbush
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Yi Zeng
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, United States
| | | | - Kenji L Kurita
- PBSci-Chemistry & Biochemistry Department, UC Santa Cruz, Santa Cruz, United States
| | - Pep Charusanti
- Department of Bioengineering, UC San Diego, La Jolla, United States
| | - Kerry L McPhail
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, United States
| | | | - Lisa Vuong
- Sirenas Marine Discovery, San Diego, United States
| | - Maryam Elfeki
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois Chicago, Chicago, United States
| | - Matthew F Traxler
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, United States
| | - Niclas Engene
- Department of Biological Sciences, Florida International University, Miami, United States
| | - Nobuhiro Koyama
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Oliver B Vining
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, United States
| | - Ralph Baric
- Gillings School of Global Public Health, Department of Epidemiology, UNC Chapel Hill, Chapel Hill, United States
| | - Ricardo R Silva
- School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil
| | - Samantha J Mascuch
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Sophie Tomasi
- Produits naturels - Synthèses - Chimie Médicinale, University of Rennes 1, Rennes Cedex, France
| | - Stefan Jenkins
- Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, United States
| | | | - Thomas Hoffman
- Department of Pharmaceutical Biotechnology, Helmholtz Institute for Pharmaceutical Research Saarland, Saarbrücken, Germany
| | - Vinayak Agarwal
- Center for Oceans and Human Health, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Philip G Williams
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, United States
| | - Jingqui Dai
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, United States
| | - Ram Neupane
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, United States
| | - Joshua Gurr
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, United States
| | - Andrés M C Rodríguez
- School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil
| | - Anne Lamsa
- Division of Biological Sciences, UC San Diego, La Jolla, United States
| | - Chen Zhang
- Department of Nanoengineering, UC San Diego, La Jolla, United States
| | - Kathleen Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Brendan M Duggan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Jehad Almaliti
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Pierre-Marie Allard
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
| | - Prasad Phapale
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Louis-Felix Nothias
- Institut de Chimie des Substances Naturelles, CNRS-ICSN, UPR 2301, Labex CEBA, University of Paris-Saclay, Gif-sur-Yvette, France
| | - Theodore Alexandrov
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Marc Litaudon
- Institut de Chimie des Substances Naturelles, CNRS-ICSN, UPR 2301, Labex CEBA, University of Paris-Saclay, Gif-sur-Yvette, France
| | - Jean-Luc Wolfender
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
| | - Jennifer E Kyle
- Biological Sciences, Pacific Northwest National Laboratory, Richland, United States
| | - Thomas O Metz
- Biological Sciences, Pacific Northwest National Laboratory, Richland, United States
| | - Tyler Peryea
- National Center for Advancing Translational Sciences, National Institute of Health, Rockville, United States
| | - Dac-Trung Nguyen
- National Center for Advancing Translational Sciences, National Institute of Health, Rockville, United States
| | - Danielle VanLeer
- National Center for Advancing Translational Sciences, National Institute of Health, Rockville, United States
| | - Paul Shinn
- National Center for Advancing Translational Sciences, National Institute of Health, Rockville, United States
| | - Ajit Jadhav
- National Center for Advancing Translational Sciences, National Institute of Health, Rockville, United States
| | - Rolf Müller
- Department of Pharmaceutical Biotechnology, Helmholtz Institute for Pharmaceutical Research Saarland, Saarbrücken, Germany
| | - Katrina M Waters
- Biological Sciences, Pacific Northwest National Laboratory, Richland, United States
| | - Wenyuan Shi
- School of Dentistry, UC Los Angeles, Los Angeles, United States
| | - Xueting Liu
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Lixin Zhang
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Rob Knight
- Department of Pediatrics, UC San Diego, La Jolla, United States
| | - Paul R Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | | | - Kit Pogliano
- Division of Biological Sciences, UC San Diego, La Jolla, United States
| | - Roger G Linington
- PBSci-Chemistry & Biochemistry Department, UC Santa Cruz, Santa Cruz, United States
| | - Marcelino Gutiérrez
- Center for Drug Discovery and Biodiversity, INDICASAT, City of Knowledge, Panama
| | - Norberto P Lopes
- School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil
| | - William H Gerwick
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.,Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Bradley S Moore
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.,Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States.,Center for Oceans and Human Health, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.,Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States.,Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Nuno Bandeira
- Center for Computational Mass Spectrometry, UC San Diego, La Jolla, United States.,Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.,Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
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35
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Beall A, Yount B, Lin CM, Hou Y, Wang Q, Saif L, Baric R. Characterization of a Pathogenic Full-Length cDNA Clone and Transmission Model for Porcine Epidemic Diarrhea Virus Strain PC22A. mBio 2016; 7:e01451-15. [PMID: 26733065 PMCID: PMC4724997 DOI: 10.1128/mbio.01451-15] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 11/10/2015] [Indexed: 01/18/2023] Open
Abstract
UNLABELLED Porcine epidemic diarrhea virus (PEDV) is a highly pathogenic alphacoronavirus. In the United States, highly virulent PEDV strains cause between 80 and 100% mortality in suckling piglets and are rapidly transmitted between animals and farms. To study the genetic factors that regulate pathogenesis and transmission, we developed a molecular clone of PEDV strain PC22A. The infectious-clone-derived PEDV (icPEDV) replicated as efficiently as the parental virus in cell culture and in pigs, resulting in lethal disease in vivo. Importantly, recombinant PEDV was rapidly transmitted to uninoculated pigs via indirect contact, demonstrating virulence and efficient transmission while replicating phenotypes seen in the wild-type virus. Using reverse genetics, we removed open reading frame 3 (ORF3) and replaced this region with a red fluorescent protein (RFP) gene to generate icPEDV-ΔORF3-RFP. icPEDV-ΔORF3-RFP replicated efficiently in vitro and in vivo, was efficiently transmitted among pigs, and produced lethal disease outcomes. However, the diarrheic scores in icPEDV-ΔORF3-RFP-infected pigs were lower than those in wild-type-virus- or icPEDV-infected pigs, and the virus formed smaller plaques than those of PC22A. Together, these data describe the development of a robust reverse-genetics platform for identifying genetic factors that regulate pathogenic outcomes and transmission efficiency in vivo, providing key infrastructural developments for developing and evaluating the efficacy of live attenuated vaccines and therapeutics in a clinical setting. IMPORTANCE Porcine epidemic diarrhea virus (PEDV) emerged in the United States in 2013 and has since killed 10% of U.S. farm pigs. Though the disease has been circulating internationally for decades, the lack of a rapid reverse-genetics platform for manipulating PEDV and identifying genetic factors that impact transmission and virulence has hindered the study of this important agricultural disease. Here, we present a DNA-based infectious-clone system that replicates the pathogenesis of circulating U.S. strain PC22A both in vitro and in piglets. This infectious clone can be used both to study the genetics, virulence, and transmission of PEDV coronavirus and to inform the creation of a live attenuated PEDV vaccine.
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Affiliation(s)
- Anne Beall
- University of North Carolina Chapel Hill, Chapel Hill, North Carolina, USA
| | - Boyd Yount
- University of North Carolina Chapel Hill, Chapel Hill, North Carolina, USA
| | - Chun-Ming Lin
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio, USA
| | - Yixuan Hou
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio, USA
| | - Qiuhong Wang
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio, USA
| | - Linda Saif
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio, USA
| | - Ralph Baric
- University of North Carolina Chapel Hill, Chapel Hill, North Carolina, USA
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Aevermann BD, Pickett BE, Kumar S, Klem EB, Agnihothram S, Askovich PS, Bankhead A, Bolles M, Carter V, Chang J, Clauss TRW, Dash P, Diercks AH, Eisfeld AJ, Ellis A, Fan S, Ferris MT, Gralinski LE, Green RR, Gritsenko MA, Hatta M, Heegel RA, Jacobs JM, Jeng S, Josset L, Kaiser SM, Kelly S, Law GL, Li C, Li J, Long C, Luna ML, Matzke M, McDermott J, Menachery V, Metz TO, Mitchell H, Monroe ME, Navarro G, Neumann G, Podyminogin RL, Purvine SO, Rosenberger CM, Sanders CJ, Schepmoes AA, Shukla AK, Sims A, Sova P, Tam VC, Tchitchek N, Thomas PG, Tilton SC, Totura A, Wang J, Webb-Robertson BJ, Wen J, Weiss JM, Yang F, Yount B, Zhang Q, McWeeney S, Smith RD, Waters KM, Kawaoka Y, Baric R, Aderem A, Katze MG, Scheuermann RH. A comprehensive collection of systems biology data characterizing the host response to viral infection. Sci Data 2014; 1:140033. [PMID: 25977790 PMCID: PMC4410982 DOI: 10.1038/sdata.2014.33] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Accepted: 08/15/2014] [Indexed: 12/13/2022] Open
Abstract
The Systems Biology for Infectious Diseases Research program was established by
the U.S. National Institute of Allergy and Infectious Diseases to investigate
host-pathogen interactions at a systems level. This program generated 47
transcriptomic and proteomic datasets from 30 studies that investigate
in vivo and in vitro host responses to
viral infections. Human pathogens in the Orthomyxoviridae and
Coronaviridae families, especially pandemic H1N1 and avian
H5N1 influenza A viruses and severe acute respiratory syndrome coronavirus
(SARS-CoV), were investigated. Study validation was demonstrated via
experimental quality control measures and meta-analysis of independent
experiments performed under similar conditions. Primary assay results are
archived at the GEO and PeptideAtlas public repositories, while processed
statistical results together with standardized metadata are publically available
at the Influenza Research Database (www.fludb.org) and the Virus Pathogen
Resource (www.viprbrc.org). By comparing data from mutant versus wild-type
virus and host strains, RNA versus protein differential expression, and
infection with genetically similar strains, these data can be used to further
investigate genetic and physiological determinants of host responses to viral
infection.
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Affiliation(s)
| | | | - Sanjeev Kumar
- Northrop Grumman Information Systems, Health IT , Rockville, MD 20850, USA
| | - Edward B Klem
- Northrop Grumman Information Systems, Health IT , Rockville, MD 20850, USA
| | - Sudhakar Agnihothram
- Department of Epidemiology, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599-7400, USA
| | | | - Armand Bankhead
- Oregon Clinical & Translational Research Institute , Portland, Oregon 97239-3098, USA ; Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health Sciences University , Portland, Oregon 97239-3098, USA
| | - Meagen Bolles
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599-7290, USA
| | - Victoria Carter
- Department of Microbiology, University of Washington , Seattle, WA 98195, USA
| | - Jean Chang
- Department of Microbiology, University of Washington , Seattle, WA 98195, USA
| | - Therese R W Clauss
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Pradyot Dash
- Department of Immunology, St. Jude Children's Research Hospital , Memphis, TN 38105-3678, USA
| | - Alan H Diercks
- Seattle Biomedical Research Institute , Seattle, WA 98109, USA
| | - Amie J Eisfeld
- School of Veterinary Medicine, Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison , Madison, WI 53706, USA
| | - Amy Ellis
- School of Veterinary Medicine, Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison , Madison, WI 53706, USA
| | - Shufang Fan
- School of Veterinary Medicine, Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison , Madison, WI 53706, USA
| | - Martin T Ferris
- Department of Genetics, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599-7264, USA
| | - Lisa E Gralinski
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599-7290, USA
| | - Richard R Green
- Department of Microbiology, University of Washington , Seattle, WA 98195, USA
| | - Marina A Gritsenko
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Masato Hatta
- School of Veterinary Medicine, Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison , Madison, WI 53706, USA
| | - Robert A Heegel
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Jon M Jacobs
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Sophia Jeng
- Oregon Clinical & Translational Research Institute , Portland, Oregon 97239-3098, USA
| | - Laurence Josset
- Department of Microbiology, University of Washington , Seattle, WA 98195, USA
| | - Shari M Kaiser
- Seattle Biomedical Research Institute , Seattle, WA 98109, USA
| | - Sara Kelly
- Department of Microbiology, University of Washington , Seattle, WA 98195, USA
| | - G Lynn Law
- Department of Microbiology, University of Washington , Seattle, WA 98195, USA
| | - Chengjun Li
- Division of Animal influenza, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences , Harbin, Heilongjiang Province 150001, China
| | - Jiangning Li
- Seattle Biomedical Research Institute , Seattle, WA 98109, USA
| | - Casey Long
- Department of Epidemiology, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599-7400, USA
| | - Maria L Luna
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Melissa Matzke
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Jason McDermott
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Vineet Menachery
- Department of Epidemiology, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599-7400, USA
| | - Thomas O Metz
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Hugh Mitchell
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Matthew E Monroe
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Garnet Navarro
- Seattle Biomedical Research Institute , Seattle, WA 98109, USA
| | - Gabriele Neumann
- School of Veterinary Medicine, Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison , Madison, WI 53706, USA
| | | | - Samuel O Purvine
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory , Richland, WA 99354, USA
| | | | - Catherine J Sanders
- Department of Immunology, St. Jude Children's Research Hospital , Memphis, TN 38105-3678, USA
| | - Athena A Schepmoes
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Anil K Shukla
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Amy Sims
- Department of Epidemiology, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599-7400, USA
| | - Pavel Sova
- Department of Microbiology, University of Washington , Seattle, WA 98195, USA
| | - Vincent C Tam
- Seattle Biomedical Research Institute , Seattle, WA 98109, USA
| | - Nicolas Tchitchek
- Department of Microbiology, University of Washington , Seattle, WA 98195, USA
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital , Memphis, TN 38105-3678, USA
| | - Susan C Tilton
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Allison Totura
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599-7290, USA
| | - Jing Wang
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | | | - Ji Wen
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Jeffrey M Weiss
- Department of Microbiology, University of Washington , Seattle, WA 98195, USA
| | - Feng Yang
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Boyd Yount
- Department of Epidemiology, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599-7400, USA
| | - Qibin Zhang
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Shannon McWeeney
- Oregon Clinical & Translational Research Institute , Portland, Oregon 97239-3098, USA ; Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health Sciences University , Portland, Oregon 97239-3098, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Katrina M Waters
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Yoshihiro Kawaoka
- School of Veterinary Medicine, Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison , Madison, WI 53706, USA
| | - Ralph Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599-7400, USA ; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599-7290, USA
| | - Alan Aderem
- Seattle Biomedical Research Institute , Seattle, WA 98109, USA
| | - Michael G Katze
- Department of Microbiology, University of Washington , Seattle, WA 98195, USA ; Washington National Primate Research Center, University of Washington , Seattle, WA 98195, USA
| | - Richard H Scheuermann
- J. Craig Venter Institute , La Jolla, CA 92037, USA ; Department of Pathology, University of California , San Diego, CA 92093, USA
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Debbink K, Costantini V, Swanstrom J, Agnihothram S, Vinjé J, Baric R, Lindesmith L. Human norovirus detection and production, quantification, and storage of virus-like particles. ACTA ACUST UNITED AC 2013; 31:15K.1.1-15K.1.45. [PMID: 24510290 DOI: 10.1002/9780471729259.mc15k01s31] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Human noroviruses constitute a significant worldwide disease burden. Each year, noroviruses cause over 267 million infections, deaths in over 200,000 children under the age of five, and over 50% of U.S. food-borne illness. Due to the absence of a tissue culture model or small animal model to study human norovirus, virus-like particles (VLPs) and ELISA-based biological assays have been used to answer questions about norovirus evolution and immunity as well to provide a potential vaccine platform. This chapter outlines the protocols for norovirus detection in stool, as well as norovirus VLP design, production, purification, and storage using a Venezuelan equine encephalitis virus (VEE)-based virus replicon particle (VRP) expression system.
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Affiliation(s)
- Kari Debbink
- University of North Carolina, Chapel Hill, North Carolina
| | | | | | | | - Jan Vinjé
- Centers for Disease Control, Atlanta, Georgia
| | - Ralph Baric
- University of North Carolina, Chapel Hill, North Carolina
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38
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Tchitchek N, Eisfeld AJ, Tisoncik-Go J, Josset L, Gralinski LE, Bécavin C, Tilton SC, Webb-Robertson BJ, Ferris MT, Totura AL, Li C, Neumann G, Metz TO, Smith RD, Waters KM, Baric R, Kawaoka Y, Katze MG. Specific mutations in H5N1 mainly impact the magnitude and velocity of the host response in mice. BMC Syst Biol 2013; 7:69. [PMID: 23895213 PMCID: PMC3750405 DOI: 10.1186/1752-0509-7-69] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 06/27/2013] [Indexed: 11/10/2022]
Abstract
BACKGROUND Influenza infection causes respiratory disease that can lead to death. The complex interplay between virus-encoded and host-specific pathogenicity regulators - and the relative contributions of each toward viral pathogenicity - is not well-understood. RESULTS By analyzing a collection of lung samples from mice infected by A/Vietnam/1203/2004 (H5N1; VN1203), we characterized a signature of transcripts and proteins associated with the kinetics of the host response. Using a new geometrical representation method and two criteria, we show that inoculation concentrations and four specific mutations in VN1203 mainly impact the magnitude and velocity of the host response kinetics, rather than specific sets of up- and down- regulated genes. We observed analogous kinetic effects using lung samples from mice infected with A/California/04/2009 (H1N1), and we show that these effects correlate with morbidity and viral titer. CONCLUSIONS We have demonstrated the importance of the kinetics of the host response to H5N1 pathogenesis and its relationship with clinical disease severity and virus replication. These kinetic properties imply that time-matched comparisons of 'omics profiles to viral infections give limited views to differentiate host-responses. Moreover, these results demonstrate that a fast activation of the host-response at the earliest time points post-infection is critical for protective mechanisms against fast replicating viruses.
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Affiliation(s)
- Nicolas Tchitchek
- Department of Microbiology, University of Washington, Seattle, WA 98195 USA
| | - Amie J Eisfeld
- School of Veterinary Medicine, Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Laurence Josset
- Department of Microbiology, University of Washington, Seattle, WA 98195 USA
| | - Lisa E Gralinski
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Christophe Bécavin
- Unité des Interactions Bactéries-Cellules, Institut Pasteur, 75015 Paris, France
| | - Susan C Tilton
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | | | - Martin T Ferris
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Allison L Totura
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Chengjun Li
- School of Veterinary Medicine, Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison, Madison, WI, USA
| | - Gabriele Neumann
- School of Veterinary Medicine, Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison, Madison, WI, USA
| | - Thomas O Metz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Katrina M Waters
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ralph Baric
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yoshihiro Kawaoka
- School of Veterinary Medicine, Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison, Madison, WI, USA
| | - Michael G Katze
- Department of Microbiology, University of Washington, Seattle, WA 98195 USA
- Washington National Primate Research Center, University of Washington, Seattle, WA, USA
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Abstract
Most new emerging viruses are derived from strains circulating in zoonotic reservoirs. Coronaviruses, which had an established potential for cross-species transmission within domesticated animals, suddenly became relevant with the unexpected emergence of the highly pathogenic human SARS-CoV strain from zoonotic reservoirs in 2002. SARS-CoV infected approximately 8000 people worldwide before public health measures halted the epidemic. Supported by robust time-ordered sequence variation, structural biology, well-characterized patient pools, and biological data, the emergence of SARS-CoV represents one of the best-studied natural models of viral disease emergence from zoonotic sources. This review article summarizes previous and more recent advances into the molecular and structural characteristics, with particular emphasis on host–receptor interactions, that drove this remarkable virus disease outbreak in human populations.
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Affiliation(s)
- Meagan Bolles
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Eric Donaldson
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Ralph Baric
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
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40
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Varshney B, Agnihotram S, Tan YJ, Baric R, Lal SK. SARS coronavirus 3b accessory protein modulates transcriptional activity of RUNX1b. PLoS One 2012; 7:e29542. [PMID: 22253733 PMCID: PMC3257236 DOI: 10.1371/journal.pone.0029542] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Accepted: 11/30/2011] [Indexed: 12/12/2022] Open
Abstract
Background The causative agent of severe acute respiratory syndrome, SARS coronavirus (SARS-CoV) genome encodes several unique group specific accessory proteins with unknown functions. Among them, accessory protein 3b (also known as ORF4) was lately identified as one of the viral interferon antagonist. Recently our lab uncovered a new role for 3b in upregulation of AP-1 transcriptional activity and its downstream genes. Thus, we believe that 3b might play an important role in SARS-CoV pathogenesis and therefore is of considerable interest. The current study aims at identifying novel host cellular interactors of the 3b protein. Methodology/Principal Findings In this study, using yeast two-hybrid and co-immunoprecipitation techniques, we have identified a host transcription factor RUNX1b (Runt related transcription factor, isoform b) as a novel interacting partner for SARS-CoV 3b protein. Chromatin immunoprecipitaion (ChIP) and reporter gene assays in 3b expressing jurkat cells showed recruitment of 3b on the RUNX1 binding element that led to an increase in RUNX1b transactivation potential on the IL2 promoter. Kinase assay and pharmacological inhibitor treatment implied that 3b also affect RUNX1b transcriptional activity by regulating its ERK dependent phosphorylation levels. Additionally, mRNA levels of MIP-1α, a RUNX1b target gene upregulated in SARS-CoV infected monocyte-derived dendritic cells, were found to be elevated in 3b expressing U937 monocyte cells. Conclusions/Significance These results unveil a novel interaction of SARS-CoV 3b with the host factor, RUNX1b, and speculate its physiological relevance in upregulating cytokines and chemokine levels in state of SARS virus infection.
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Affiliation(s)
- Bhavna Varshney
- Virology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Sudhakar Agnihotram
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Yee-Joo Tan
- Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Ralph Baric
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Sunil K. Lal
- Virology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
- * E-mail:
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Frieman M, Basu D, Matthews K, Taylor J, Jones G, Pickles R, Baric R, Engel DA. Yeast based small molecule screen for inhibitors of SARS-CoV. PLoS One 2011; 6:e28479. [PMID: 22164298 PMCID: PMC3229576 DOI: 10.1371/journal.pone.0028479] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Accepted: 11/09/2011] [Indexed: 11/18/2022] Open
Abstract
Severe acute respiratory coronavirus (SARS-CoV) emerged in 2002, resulting in roughly 8000 cases worldwide and 10% mortality. The animal reservoirs for SARS-CoV precursors still exist and the likelihood of future outbreaks in the human population is high. The SARS-CoV papain-like protease (PLP) is an attractive target for pharmaceutical development because it is essential for virus replication and is conserved among human coronaviruses. A yeast-based assay was established for PLP activity that relies on the ability of PLP to induce a pronounced slow-growth phenotype when expressed in S. cerevisiae. Induction of the slow-growth phenotype was shown to take place over a 60-hour time course, providing the basis for conducting a screen for small molecules that restore growth by inhibiting the function of PLP. Five chemical suppressors of the slow-growth phenotype were identified from the 2000 member NIH Diversity Set library. One of these, NSC158362, potently inhibited SARS-CoV replication in cell culture without toxic effects on cells, and it specifically inhibited SARS-CoV replication but not influenza virus replication. The effect of NSC158362 on PLP protease, deubiquitinase and anti-interferon activities was investigated but the compound did not alter these activities. Another suppressor, NSC158011, demonstrated the ability to inhibit PLP protease activity in a cell-based assay. The identification of these inhibitors demonstrated a strong functional connection between the PLP-based yeast assay, the inhibitory compounds, and SARS-CoV biology. Furthermore the data with NSC158362 suggest a novel mechanism for inhibition of SARS-CoV replication that may involve an unknown activity of PLP, or alternatively a direct effect on a cellular target that modifies or bypasses PLP function in yeast and mammalian cells.
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Affiliation(s)
- Matthew Frieman
- Department of Microbiology and Immunology, University of Maryland, Baltimore, Maryland, United States of America
| | - Dipanwita Basu
- Department of Microbiology, University of Virginia School of Medicine, Charlottesville, Virginia, United States of America
| | - Krystal Matthews
- Department of Microbiology and Immunology, University of Maryland, Baltimore, Maryland, United States of America
| | - Justin Taylor
- Department of Microbiology and Immunology, University of Maryland, Baltimore, Maryland, United States of America
| | - Grant Jones
- Department of Microbiology and Immunology, University of Maryland, Baltimore, Maryland, United States of America
| | - Raymond Pickles
- Department of Microbiology and Immunology, Gene Therapy Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Ralph Baric
- School of Public Health, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Daniel A. Engel
- Department of Microbiology, University of Virginia School of Medicine, Charlottesville, Virginia, United States of America
- * E-mail:
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de Alwis R, Beltramello M, Messer WB, Sukupolvi-Petty S, Wahala WMPB, Kraus A, Olivarez NP, Pham Q, Brian J, Tsai WY, Wang WK, Halstead S, Kliks S, Diamond MS, Baric R, Lanzavecchia A, Sallusto F, de Silva AM. In-depth analysis of the antibody response of individuals exposed to primary dengue virus infection. PLoS Negl Trop Dis 2011; 5:e1188. [PMID: 21713020 PMCID: PMC3119640 DOI: 10.1371/journal.pntd.0001188] [Citation(s) in RCA: 162] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Accepted: 04/12/2011] [Indexed: 11/18/2022] Open
Abstract
Humans who experience a primary dengue virus (DENV) infection develop antibodies that preferentially neutralize the homologous serotype responsible for infection. Affected individuals also generate cross-reactive antibodies against heterologous DENV serotypes, which are non-neutralizing. Dengue cross-reactive, non-neutralizing antibodies can enhance infection of Fc receptor bearing cells and, potentially, exacerbate disease. The actual binding sites of human antibody on the DENV particle are not well defined. We characterized the specificity and neutralization potency of polyclonal serum antibodies and memory B-cell derived monoclonal antibodies (hMAbs) from 2 individuals exposed to primary DENV infections. Most DENV-specific hMAbs were serotype cross-reactive and weakly neutralizing. Moreover, many hMAbs bound to the viral pre-membrane protein and other sites on the virus that were not preserved when the viral envelope protein was produced as a soluble, recombinant antigen (rE protein). Nonetheless, by modifying the screening procedure to detect rare antibodies that bound to rE, we were able to isolate and map human antibodies that strongly neutralized the homologous serotype of DENV. Our MAbs results indicate that, in these two individuals exposed to primary DENV infections, a small fraction of the total antibody response was responsible for virus neutralization.
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Affiliation(s)
- Ruklanthi de Alwis
- Department of Microbiology and Immunology, and the Southeast Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | | | - William B. Messer
- Department of Microbiology and Immunology, and the Southeast Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Soila Sukupolvi-Petty
- Departments of Medicine, Molecular Microbiology, Pathology and Immunology, and the Midwest Regional Center for Biodefense and Emerging Infectious Diseases Research, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Wahala M. P. B. Wahala
- Department of Microbiology and Immunology, and the Southeast Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Annette Kraus
- Department of Microbiology and Immunology, and the Southeast Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Nicholas P. Olivarez
- Department of Microbiology and Immunology, and the Southeast Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Quang Pham
- Department of Microbiology and Immunology, and the Southeast Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - James Brian
- Departments of Medicine, Molecular Microbiology, Pathology and Immunology, and the Midwest Regional Center for Biodefense and Emerging Infectious Diseases Research, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Wen-Yang Tsai
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
| | - Wei-Kung Wang
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
| | - Scott Halstead
- Pediatric Dengue Vaccine Initiative, International Vaccine Institute, Seoul, Korea
| | - Srisakul Kliks
- Pediatric Dengue Vaccine Initiative, International Vaccine Institute, Seoul, Korea
| | - Michael S. Diamond
- Departments of Medicine, Molecular Microbiology, Pathology and Immunology, and the Midwest Regional Center for Biodefense and Emerging Infectious Diseases Research, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Ralph Baric
- Department of Microbiology and Immunology, and the Southeast Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | | | | | - Aravinda M. de Silva
- Department of Microbiology and Immunology, and the Southeast Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
- * E-mail:
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43
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Day CW, Baric R, Cai SX, Frieman M, Kumaki Y, Morrey JD, Smee DF, Barnard DL. A new mouse-adapted strain of SARS-CoV as a lethal model for evaluating antiviral agents in vitro and in vivo. Virology 2009; 395:210-22. [PMID: 19853271 PMCID: PMC2787736 DOI: 10.1016/j.virol.2009.09.023] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2009] [Revised: 06/26/2009] [Accepted: 09/16/2009] [Indexed: 12/17/2022]
Abstract
Severe acute respiratory syndrome (SARS) is a highly lethal emerging disease caused by coronavirus SARS-CoV. New lethal animal models for SARS were needed to facilitate antiviral research. We adapted and characterized a new strain of SARS-CoV (strain v2163) that was highly lethal in 5- to 6-week-old BALB/c mice. It had nine mutations affecting 10 amino acid residues. Strain v2163 increased IL-1alpha, IL-6, MIP-1alpha, MCP-1, and RANTES in mice, and high IL-6 expression correlated with mortality. The infection largely mimicked human disease, but lung pathology lacked hyaline membrane formation. In vitro efficacy against v2163 was shown with known inhibitors of SARS-CoV replication. In v2163-infected mice, Ampligen was fully protective, stinging nettle lectin (UDA) was partially protective, ribavirin was disputable and possibly exacerbated disease, and EP128533 was inactive. Ribavirin, UDA, and Ampligen decreased IL-6 expression. Strain v2163 provided a valuable model for anti-SARS research.
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Affiliation(s)
- Craig W Day
- Institute for Antiviral Research, Utah State University, UMC 5600, Logan, UT 84322-5600, USA
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Abstract
The modulation of the immune response is a common practice of many highly pathogenic viruses. The emergence of the highly pathogenic coronavirus severe acute respiratory virus (SARS-CoV) serves as a robust model system to elucidate the virus-host interactions that mediate severe end-stage lung disease in humans and animals. Coronaviruses encode the largest positive-sense RNA genome of approximately 30 kb, encode a variety of replicase and accessory open reading frames that are structurally unique, and encode novel enzymatic functions among RNA viruses. These viruses have broad or specific host ranges, suggesting the possibility of novel strategies for targeting and regulating host innate immune responses following virus infection. Using SARS-CoV as a model, we review the current literature on the ability of coronaviruses to interact with and modify the host intracellular environment during infection. These studies are revealing a rich set of novel viral proteins that engage, modify, and/or disrupt host cell signaling and nuclear import machinery for the benefit of virus replication.
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Affiliation(s)
- Matthew Frieman
- University of North Carolina, 210 McGaveran-Greenberg Hall, CB 7435, Chapel Hill, NC 27599, USA
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Enjuanes L, Dediego ML, Alvarez E, Deming D, Sheahan T, Baric R. Vaccines to prevent severe acute respiratory syndrome coronavirus-induced disease. Virus Res 2008; 133:45-62. [PMID: 17416434 PMCID: PMC2633062 DOI: 10.1016/j.virusres.2007.01.021] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2006] [Accepted: 01/04/2007] [Indexed: 01/19/2023]
Abstract
An important effort has been performed after the emergence of severe acute respiratory syndrome (SARS) epidemic in 2003 to diagnose and prevent virus spreading. Several types of vaccines have been developed including inactivated viruses, subunit vaccines, virus-like particles (VLPs), DNA vaccines, heterologous expression systems, and vaccines derived from SARS-CoV genome by reverse genetics. This review describes several aspects essential to develop SARS-CoV vaccines, such as the correlates of protection, virus serotypes, vaccination side effects, and bio-safeguards that can be engineered into recombinant vaccine approaches based on the SARS-CoV genome. The production of effective and safe vaccines to prevent SARS has led to the development of promising vaccine candidates, in contrast to the design of vaccines for other coronaviruses, that in general has been less successful. After preclinical trials in animal models, efficacy and safety evaluation of the most promising vaccine candidates described has to be performed in humans.
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Affiliation(s)
- Luis Enjuanes
- Centro Nacional de Biotecnología (CNB), CSIC, Campus Universidad Autónoma, Cantoblanco, Darwin 3, 28049 Madrid, Spain.
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Zhu Z, Chakraborti S, He Y, Roberts A, Sheahan T, Xiao X, Hensley LE, Prabakaran P, Rockx B, Sidorov IA, Corti D, Vogel L, Feng Y, Kim JO, Wang LF, Baric R, Lanzavecchia A, Curtis KM, Nabel GJ, Subbarao K, Jiang S, Dimitrov DS. Potent cross-reactive neutralization of SARS coronavirus isolates by human monoclonal antibodies. Proc Natl Acad Sci U S A 2007; 104:12123-8. [PMID: 17620608 PMCID: PMC1924550 DOI: 10.1073/pnas.0701000104] [Citation(s) in RCA: 240] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus (SARS-CoV) caused a worldwide epidemic in late 2002/early 2003 and a second outbreak in the winter of 2003/2004 by an independent animal-to-human transmission. The GD03 strain, which was isolated from an index patient of the second outbreak, was reported to resist neutralization by the human monoclonal antibodies (hmAbs) 80R and S3.1, which can potently neutralize isolates from the first outbreak. Here we report that two hmAbs, m396 and S230.15, potently neutralized GD03 and representative isolates from the first SARS outbreak (Urbani, Tor2) and from palm civets (SZ3, SZ16). These antibodies also protected mice challenged with the Urbani or recombinant viruses bearing the GD03 and SZ16 spike (S) glycoproteins. Both antibodies competed with the SARS-CoV receptor, ACE2, for binding to the receptor-binding domain (RBD), suggesting a mechanism of neutralization that involves interference with the SARS-CoV-ACE2 interaction. Two putative hot-spot residues in the RBD (Ile-489 and Tyr-491) were identified within the SARS-CoV spike that likely contribute to most of the m396-binding energy. Residues Ile-489 and Tyr-491 are highly conserved within the SARS-CoV spike, indicating a possible mechanism of the m396 cross-reactivity. Sequence analysis and mutagenesis data show that m396 might neutralize all zoonotic and epidemic SARS-CoV isolates with known sequences, except strains derived from bats. These antibodies exhibit cross-reactivity against isolates from the two SARS outbreaks and palm civets and could have potential applications for diagnosis, prophylaxis, and treatment of SARS-CoV infections.
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Affiliation(s)
- Zhongyu Zhu
- *Protein Interactions Group, Center for Cancer Research Nanobiology Program, and
- Basic Research Program, SAIC-Frederick, Inc., National Cancer Institute-Frederick, National Institutes of Health, Frederick, MD 21702
| | - Samitabh Chakraborti
- Basic Research Program, SAIC-Frederick, Inc., National Cancer Institute-Frederick, National Institutes of Health, Frederick, MD 21702
| | - Yuxian He
- Laboratory of Viral Immunology, Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY 10021
| | | | - Tim Sheahan
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599
| | - Xiaodong Xiao
- *Protein Interactions Group, Center for Cancer Research Nanobiology Program, and
| | - Lisa E. Hensley
- Virology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702
| | - Ponraj Prabakaran
- *Protein Interactions Group, Center for Cancer Research Nanobiology Program, and
| | - Barry Rockx
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599
| | - Igor A. Sidorov
- *Protein Interactions Group, Center for Cancer Research Nanobiology Program, and
| | - Davide Corti
- **Institute for Research in Biomedicine, Via Vela 6, CH 6500 Belllinzona, Switzerland; and
| | | | - Yang Feng
- *Protein Interactions Group, Center for Cancer Research Nanobiology Program, and
| | - Jae-Ouk Kim
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Lin-Fa Wang
- CSIRO Livestock Industries, Australian Animal Health Laboratory and Australian Biosecurity Cooperative Research Center for Emerging Infectious Diseases, Geelong, Victoria 3220, Australia
| | - Ralph Baric
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599
| | - Antonio Lanzavecchia
- **Institute for Research in Biomedicine, Via Vela 6, CH 6500 Belllinzona, Switzerland; and
| | - Kristopher M. Curtis
- Virology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702
| | - Gary J. Nabel
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | | | - Shibo Jiang
- Laboratory of Viral Immunology, Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY 10021
| | - Dimiter S. Dimitrov
- *Protein Interactions Group, Center for Cancer Research Nanobiology Program, and
- To whom correspondence should be addressed at:
Protein Interactions, Center for Cancer Research Nanobiology Program, National Cancer Institute, National Institutes of Health, P.O. Box B, Building 469, Room 150B, Frederick, MD 21702-1201. E-mail:
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Roberts A, Deming D, Paddock CD, Cheng A, Yount B, Vogel L, Herman BD, Sheahan T, Heise M, Genrich GL, Zaki SR, Baric R, Subbarao K. A mouse-adapted SARS-coronavirus causes disease and mortality in BALB/c mice. PLoS Pathog 2007; 3:e5. [PMID: 17222058 PMCID: PMC1769406 DOI: 10.1371/journal.ppat.0030005] [Citation(s) in RCA: 387] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2006] [Accepted: 11/15/2006] [Indexed: 12/11/2022] Open
Abstract
No single animal model for severe acute respiratory syndrome (SARS) reproduces all aspects of the human disease. Young inbred mice support SARS-coronavirus (SARS-CoV) replication in the respiratory tract and are available in sufficient numbers for statistical evaluation. They are relatively inexpensive and easily accessible, but their use in SARS research is limited because they do not develop illness following infection. Older (12- to 14-mo-old) BALB/c mice develop clinical illness and pneumonitis, but they can be hard to procure, and immune senescence complicates pathogenesis studies. We adapted the SARS-CoV (Urbani strain) by serial passage in the respiratory tract of young BALB/c mice. Fifteen passages resulted in a virus (MA15) that is lethal for mice following intranasal inoculation. Lethality is preceded by rapid and high titer viral replication in lungs, viremia, and dissemination of virus to extrapulmonary sites accompanied by lymphopenia, neutrophilia, and pathological changes in the lungs. Abundant viral antigen is extensively distributed in bronchial epithelial cells and alveolar pneumocytes, and necrotic cellular debris is present in airways and alveoli, with only mild and focal pneumonitis. These observations suggest that mice infected with MA15 die from an overwhelming viral infection with extensive, virally mediated destruction of pneumocytes and ciliated epithelial cells. The MA15 virus has six coding mutations associated with adaptation and increased virulence; when introduced into a recombinant SARS-CoV, these mutations result in a highly virulent and lethal virus (rMA15), duplicating the phenotype of the biologically derived MA15 virus. Intranasal inoculation with MA15 reproduces many aspects of disease seen in severe human cases of SARS. The availability of the MA15 virus will enhance the use of the mouse model for SARS because infection with MA15 causes morbidity, mortality, and pulmonary pathology. This virus will be of value as a stringent challenge in evaluation of the efficacy of vaccines and antivirals.
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Affiliation(s)
- Anjeanette Roberts
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Damon Deming
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Christopher D Paddock
- Infectious Disease Pathology Activity, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Aaron Cheng
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Boyd Yount
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Leatrice Vogel
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Brian D Herman
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Tim Sheahan
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Mark Heise
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Carolina Vaccine Institute, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Gillian L Genrich
- Infectious Disease Pathology Activity, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Sherif R Zaki
- Infectious Disease Pathology Activity, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Ralph Baric
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Carolina Vaccine Institute, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Kanta Subbarao
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- * To whom correspondence should be addressed. E-mail:
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von Brunn A, Teepe C, Simpson JC, Pepperkok R, Friedel CC, Zimmer R, Roberts R, Baric R, Haas J. Analysis of intraviral protein-protein interactions of the SARS coronavirus ORFeome. PLoS One 2007; 2:e459. [PMID: 17520018 PMCID: PMC1868897 DOI: 10.1371/journal.pone.0000459] [Citation(s) in RCA: 177] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2007] [Accepted: 04/21/2007] [Indexed: 12/13/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus (SARS-CoV) genome is predicted to encode 14 functional open reading frames, leading to the expression of up to 30 structural and non-structural protein products. The functions of a large number of viral ORFs are poorly understood or unknown. In order to gain more insight into functions and modes of action and interaction of the different proteins, we cloned the viral ORFeome and performed a genome-wide analysis for intraviral protein interactions and for intracellular localization. 900 pairwise interactions were tested by yeast-two-hybrid matrix analysis, and more than 65 positive non-redundant interactions, including six self interactions, were identified. About 38% of interactions were subsequently confirmed by CoIP in mammalian cells. Nsp2, nsp8 and ORF9b showed a wide range of interactions with other viral proteins. Nsp8 interacts with replicase proteins nsp2, nsp5, nsp6, nsp7, nsp8, nsp9, nsp12, nsp13 and nsp14, indicating a crucial role as a major player within the replication complex machinery. It was shown by others that nsp8 is essential for viral replication in vitro, whereas nsp2 is not. We show that also accessory protein ORF9b does not play a pivotal role for viral replication, as it can be deleted from the virus displaying normal plaque sizes and growth characteristics in Vero cells. However, it can be expected to be important for the virus-host interplay and for pathogenicity, due to its large number of interactions, by enhancing the global stability of the SARS proteome network, or play some unrealized role in regulating protein-protein interactions. The interactions identified provide valuable material for future studies.
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Affiliation(s)
- Albrecht von Brunn
- Genzentrum, Max-von-Pettenkofer-Institut, Lehrstuhl Virologie, Ludwig-Maximilians-Universität (LMU), München, Germany
- * To whom correspondence should be addressed. E-mail: (AvB); (JH)
| | - Carola Teepe
- Genzentrum, Max-von-Pettenkofer-Institut, Lehrstuhl Virologie, Ludwig-Maximilians-Universität (LMU), München, Germany
| | - Jeremy C. Simpson
- European Molecular Biology Laboratory (EMBL) Heidelberg, Heidelberg, Germany
| | - Rainer Pepperkok
- European Molecular Biology Laboratory (EMBL) Heidelberg, Heidelberg, Germany
| | - Caroline C. Friedel
- Institut für Informatik, Ludwig-Maximilians-Universität (LMU), München, Germany
| | - Ralf Zimmer
- Institut für Informatik, Ludwig-Maximilians-Universität (LMU), München, Germany
| | - Rhonda Roberts
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Ralph Baric
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jürgen Haas
- Genzentrum, Max-von-Pettenkofer-Institut, Lehrstuhl Virologie, Ludwig-Maximilians-Universität (LMU), München, Germany
- * To whom correspondence should be addressed. E-mail: (AvB); (JH)
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49
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Rockx B, Sheahan T, Donaldson E, Harkema J, Sims A, Heise M, Pickles R, Cameron M, Kelvin D, Baric R. Synthetic reconstruction of zoonotic and early human severe acute respiratory syndrome coronavirus isolates that produce fatal disease in aged mice. J Virol 2007; 81:7410-23. [PMID: 17507479 PMCID: PMC1933338 DOI: 10.1128/jvi.00505-07] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The severe acute respiratory syndrome (SARS) epidemic was characterized by high mortality rates in the elderly. The molecular mechanisms that govern enhanced susceptibility of elderly populations are not known, and robust animal models are needed that recapitulate the increased pathogenic phenotype noted with increasing age. Using synthetic biology and reverse genetics, we describe the construction of a panel of isogenic SARS coronavirus (SARS-CoV) strains bearing variant spike glycoproteins that are representative of zoonotic strains found in palm civets and raccoon dogs, as well as isolates spanning the early, middle, and late phases of the SARS-CoV epidemic. The recombinant viruses replicated efficiently in cell culture and demonstrated variable sensitivities to neutralization with antibodies. The human but not the zoonotic variants replicated efficiently in human airway epithelial cultures, supporting earlier hypotheses that zoonotic isolates are less pathogenic in humans but can evolve into highly pathogenic strains. All viruses replicated efficiently, but none produced clinical disease or death in young animals. In contrast, severe clinical disease, diffuse alveolar damage, hyaline membrane formation, alveolitis, and death were noted in 12-month-old mice inoculated with the palm civet HC/SZ/61/03 strain or early-human-phase GZ02 variants but not with related middle- and late-phase epidemic or raccoon dog strains. This panel of SARS-CoV recombinants bearing zoonotic and human epidemic spike glycoproteins will provide heterologous challenge models for testing vaccine efficacy against zoonotic reintroductions as well as provide the appropriate model system for elucidating the complex virus-host interactions that contribute to more-severe and fatal SARS-CoV disease and acute respiratory distress in the elderly.
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Affiliation(s)
- Barry Rockx
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27699-7435, USA
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50
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Roberts A, Lamirande EW, Vogel L, Jackson JP, Paddock CD, Guarner J, Zaki SR, Sheahan T, Baric R, Subbarao K. Animal models and vaccines for SARS-CoV infection. Virus Res 2007; 133:20-32. [PMID: 17499378 PMCID: PMC2323511 DOI: 10.1016/j.virusres.2007.03.025] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2006] [Revised: 03/28/2007] [Accepted: 03/29/2007] [Indexed: 01/04/2023]
Abstract
We summarize findings of SARS-CoV infections in several animal models each of which support viral replication in lungs accompanied by histopathological changes and/or clinical signs of illness to varying degrees. New findings are reported on SARS-CoV replication and associated pathology in two additional strains (C57BL/6 and 129S6) of aged mice. We also provide new comparative data on viral replication and associated pathology following infection of golden Syrian hamsters with various SARS-CoV strains and report the levels of neutralizing antibody titers following these infections and the cross-protective efficacy of infection with these strains in protecting against heterologous challenge. Finally, we summarize findings of a variety of vaccine approaches and discuss the available in vitro and in vivo data addressing the potential for disease enhancement following re-infection in animals previously vaccinated against or infected with SARS-CoV.
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Affiliation(s)
- Anjeanette Roberts
- Laboratory of Infectious Diseases, NIAID, NIH, Bethesda, MD, United States
| | | | - Leatrice Vogel
- Laboratory of Infectious Diseases, NIAID, NIH, Bethesda, MD, United States
| | - Jadon P. Jackson
- Laboratory of Infectious Diseases, NIAID, NIH, Bethesda, MD, United States
| | - Christopher D. Paddock
- Infectious Disease Pathology Activity, Centers for Disease Control & Prevention, Atlanta, GA, United States
| | - Jeannette Guarner
- Infectious Disease Pathology Activity, Centers for Disease Control & Prevention, Atlanta, GA, United States
| | - Sherif R. Zaki
- Infectious Disease Pathology Activity, Centers for Disease Control & Prevention, Atlanta, GA, United States
| | - Timothy Sheahan
- Departments of Epidemiology and Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, United States
| | - Ralph Baric
- Departments of Epidemiology and Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, United States
| | - Kanta Subbarao
- Laboratory of Infectious Diseases, NIAID, NIH, Bethesda, MD, United States
- Corresponding author. Tel.: +1 301 451 3839; fax: +1 301 496 8312.
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