100 results on '"Yount B"'
Search Results
2. A Neptune Orbiter Concept Using Drag Modulated Aerocaptue (DMA) and the Adaptable, Deployable Entry and Placement Technology (ADEPT)
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Wercinski, P, Austin, A, Nelessen, A, Strauss, B, Hogstrom, K, Landau, D, Luthman, E, Ravich, J, Lobbia, M, Allen, G, Cassell, A, Prabhu, D, Yount, B, and Venkatapathy, E
- Subjects
Engineering (General) - Abstract
Conceptual Neptune orbiter was designed for the purpose of assessing mission feasibilityBuilt off of the 2017 Pre-Decadal Study, but adapted for drag modulation aerocapture.Science payload includes: Narrow Angle camera, Doppler Imager, Magnetometer, Atmospheric Probe (w/ ASI, Nephelometer, Mass Spectrometer). Baseline concept of operations releases probe prior to orbit insertion, but investigations are ongoing to assess the feasibility of bringing the probe to orbit before release.
- Published
- 2019
3. MHV Subgenomic Negative Strand Function
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Baric, R. S., Curtis, K. M., Yount, B., Lavi, Ehud, editor, Weiss, Susan R., editor, and Hingley, Susan T., editor
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- 2001
- Full Text
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4. ADEPT Sounding Rocket One (SR-1)Flight Experiment Overview
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Wercinski, Paul, Smith, B, Yount, B, Cassell, A, Kruger, C, Brivkalns, C, Makino, A, Duttta, S, Ghassemieh, S, Wu, S, Battazzo, S, Nishioka, O, and Venkatapathy, E
- Subjects
Launch Vehicles And Launch Operations ,Engineering (General) - Abstract
The SR-1 flight experiment will demonstrate most of the primary end-to-end mission stages including: launch in a stowed configuration, separation and deployment in exo-atmospheric conditions, and passive ballistic re-entry of a 70-degree half-angle faceted cone geometry.
- Published
- 2017
5. Adaptable, Deployable Entry and Placement Technology (ADEPT) Overview of FY15 Accomplishments
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Wercinski, P, Brivkalns, C, Cassell, A, Chen, Y.-K, Boghozian, T, Chinnapongse, R, Gasch, M, Kruger, C, Makino, A, Milos, F, Nishioka, O, Smith, B, Squire, T, Venkatapathy, E, Yount, B, and Zarchi, K
- Subjects
Fluid Mechanics And Thermodynamics ,Astrodynamics ,Lunar And Planetary Science And Exploration - Abstract
ADEPT is an atmospheric entry architecture for missions to most planetary bodies with atmospheres: Current Technology development project funded under STMD Game Changing Development Program (FY12 start); stowed inside the launch vehicle shroud and deployed in space prior to entry; low ballistic coefficient (less than 50 kilograms per square meter) provides a benign deceleration and thermal environment to the payload; High-temperature ribs support three dimensional woven carbon fabric to generate drag and withstand high heating.
- Published
- 2015
6. Nano-ADEPT Aeroloads Wind Tunnel Test
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Smith, Brandon, Cassell, A, Yount, B, Kruger, C, Brivkalns, C, Makino, A, Zarchi, K, McDaniel, R, Venkatapathy, E, and Swanson, G
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Spacecraft Design, Testing And Performance - Abstract
Analysis completed since the test suggests that all test objectives were met– This claim will be verified in the coming weeks as the data is examined further– Final disposition of test objective success will be documented in a final reportsubmitted to NASA stakeholders (early August 2015)– Expect conference paper in early 2016• Data products and observations made during testing will be used to refinecomputational models of Nano-ADEPT• Carbon fabric relaxed from its pre-test state during the test– System-level tolerance for relaxation will be driven by destination-specific andmission-specific aerothermal and aerodynamic requirements• Bonus experiment of asymmetric shape demonstrates that an asymmetricdeployable blunt body can be used to generate measureable lift– With a strut actuation system and a robust GN&C algorithm, this effect could beused to steer a blunt body at hypersonic speeds to aid precision landing
- Published
- 2015
7. Deployment Testing of the ADEPT Ground Test Article
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Yount, B. C, Kruger, C. E, Cassell, A. M, and Kazemba, C. D
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Spacecraft Design, Testing And Performance - Published
- 2014
8. Adaptable, Deployable Entry and Placement Technology (ADEPT) for Future Mars Missions
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Wercinski, P, Venkatapathy, E, Gage, P, Prabhu, D, Smith, B, Cassell, A, Yount, B, and Allen, G
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Spacecraft Design, Testing And Performance - Abstract
The concept of a mechanically deploy- able hypersonic decelerator, developed initially for high mass (40 MT) human Mars missions, is currently funded by OCT for technology maturation. The ADEPT (Adaptive, Deployable Entry and Placement Technology) project has broad, game-changing applicability to in situ science missions to Venus, Mars, and the Outer Planets.
- Published
- 2013
9. Cryo-electron microscopy structure of mouse coronavirus spike protein complexed with its murine receptor
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Shang, J., primary, Wan, Y.S., additional, Liu, C., additional, Yount, B., additional, Gully, K., additional, Yang, Y., additional, Auerbach, A., additional, Peng, G.Q., additional, Baric, R., additional, and Li, F., additional
- Published
- 2020
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10. Further Evidence for Bats as the Evolutionary Source of Middle East Respiratory Syndrome Coronavirus
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Anthony, S. J., primary, Gilardi, K., additional, Menachery, V. D., additional, Goldstein, T., additional, Ssebide, B., additional, Mbabazi, R., additional, Navarrete-Macias, I., additional, Liang, E., additional, Wells, H., additional, Hicks, A., additional, Petrosov, A., additional, Byarugaba, D. K., additional, Debbink, K., additional, Dinnon, K. H., additional, Scobey, T., additional, Randell, S. H., additional, Yount, B. L., additional, Cranfield, M., additional, Johnson, C. K., additional, Baric, R. S., additional, Lipkin, W. I., additional, and Mazet, J. A. K., additional
- Published
- 2017
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11. Characterization of Blockade Antibody Responses in GII.2.1976 Snow Mountain Virus-Infected Subjects
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Donaldson, E. F., Lindesmith, L. C., Yount, B., Baric, R. S., and Swanstrom, J.
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fluids and secretions ,viruses ,virus diseases - Abstract
Snow Mountain virus (GII.2.1976) is the prototype strain of GII.2 noroviruses (NoVs), which cause an estimated 8% of norovirus outbreaks, yet little is known about the immunobiology of these viruses. To define the human immune response induced by SMV infection and the antigenic relationship between different GII.2 strains that have circulated between 1976 and 2010, we developed a panel of four GII.2 variant virus-like particles (VLPs) and compared their antigenicities by enzyme immunoassay (EIA) and surrogate antibody neutralization (blockade) assays. Volunteers infected with GII.2.1976 developed a mean 167-fold increase in blockade response against the homotypic VLP by day 8 postchallenge. Blockade extended cross-genotype activity in some individuals but not cross-genogroup activity. Polyclonal sera from GII.2.1976-infected volunteers blocked GII.2.1976 significantly better than they blocked GII.2.2002, GII.2.2008, and GII.2.2010, suggesting that blockade epitopes within the GII.2 strains have evolved in the past decade. To potentially map these epitope changes, we developed mouse monoclonal antibodies (MAbs) against GII.2.1976 VLPs and compared their reactivities to a panel of norovirus VLPs. One MAb had broad cross-genogroup EIA reactivity to a nonblockade, linear, conserved epitope. Six MAbs recognized conformational epitopes exclusive to the GII.2 strains. Two MAbs recognized GII.2 blockade epitopes, and both blocked the entire panel of GII.2 variants. These data indicate that the GII.2 strains, unlike the predominant GII.4 strains, have undergone only a limited amount of evolution in blockade epitopes between 1976 and 2010 and indicate that the GII.2-protective component of a multivalent norovirus vaccine may not require frequent reformulation.
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- 2014
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12. A New Quaternary Structure Epitope on Dengue Virus Serotype 2 Is the Target of Durable Type-Specific Neutralizing Antibodies
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Gallichotte, E. N., primary, Widman, D. G., additional, Yount, B. L., additional, Wahala, W. M., additional, Durbin, A., additional, Whitehead, S., additional, Sariol, C. A., additional, Crowe, J. E., additional, de Silva, A. M., additional, and Baric, R. S., additional
- Published
- 2015
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13. Systemic, Mucosal, and Heterotypic Immune Induction in Mice Inoculated with Venezuelan Equine Encephalitis Replicons Expressing Norwalk Virus-Like Particles
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Harrington, P. R., Johnston, R. E., Davis, N., Baric, R. S., Moe, C., and Yount, B.
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viruses ,virus diseases ,biochemical phenomena, metabolism, and nutrition ,complex mixtures - Abstract
Norwalk-like viruses (NLVs) are a diverse group of single-stranded, nonenveloped, positive-polarity RNA viruses and are the leading cause of epidemic acute gastroenteritis in the United States. In this study, the major capsid gene of Norwalk virus, the prototype NLV, has been cloned and expressed in mammalian cells using a Venezuelan equine encephalitis (VEE) replicon expression system. Upon infection of baby hamster kidney (BHK) cells with VEE replicon particles (VRPs), the Norwalk virus capsid proteins self-assemble to generate high titers of Norwalk virus-like particles (VLPs) that are morphologically and antigenically analogous to wild-type Norwalk virus. Mice inoculated subcutaneously with VRPs expressing the Norwalk virus capsid protein (VRP-NV1) developed systemic and mucosal immune responses to Norwalk VLPs, as well as heterotypic antibody responses to the major capsid protein from another genogroup I NLV strain (NCFL) isolated from a recent outbreak. A second Norwalk virus capsid clone (NV2) containing three amino acid codon mutations from the NV1 clone was also expressed using VEE replicons (VRP-NV2), but upon infection of BHK cells failed to confer VLP self-assembly. Mice inoculated with VRP-NV2 elicited reduced systemic and mucosal immune responses to Norwalk VLPs, demonstrating the importance and potential utility of endogenous VLP presentation for maximum immune induction. Inoculation with either VRP-NV1 or VRP-NV2 resulted in serum antibody responses far superior to the induction in mice dosed orally with VLPs that were prepared using the VEE-NV1 replicon construct, a regimen similar to current models for NLV vaccination. Expression of NLV VLPs in mammalian cells offers a powerful approach for the design of novel NLV vaccines, either alone or in combination with current vaccination models.
- Published
- 2002
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14. Subgenomic Negative-Strand RNA Function during Mouse Hepatitis Virus Infection
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Baric, R. S. and Yount, B.
- Abstract
Mouse hepatitis virus (MHV)-infected cells contain full-length and subgenomic-length positive- and negative-strand RNAs. The origin and function of the subgenomic negative-strand RNAs is controversial. In this report we demonstrate that the synthesis and molar ratios of subgenomic negative strands are similar in alternative host cells, suggesting that these RNAs function as important mediators of positive-strand synthesis. Using kinetic labeling experiments, we show that the full-length and subgenomic-length replicative form RNAs rapidly accumulate and then saturate with label, suggesting that the subgenomic-length negative strands are the principal mediators of positive-strand synthesis. Using cycloheximide, which preferentially inhibits negative-strand and to a lesser extent positive-strand synthesis, we demonstrate that cycloheximide treatment equally inhibits full-length and subgenomic-length negative-strand synthesis. Importantly, following treatment, previously transcribed negative strands remain in transcriptionally active complexes even in the absence of new negative-strand synthesis. These findings indicate that the subgenomic-length negative strands are the principal templates of positive-strand synthesis during MHV infection.
- Published
- 2000
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15. Strategy for Systematic Assembly of Large RNA and DNA Genomes: Transmissible Gastroenteritis Virus Model
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Yount, B., Baric, R. S., and Curtis, K. M.
- Abstract
A systematic method was developed to assemble functional full-length genomes of large RNA and DNA viruses. Coronaviruses contain the largest single-stranded positive-polarity RNA genome in nature. The ∼30-kb genome, coupled with regions of genomic instability, has hindered the development of a full-length infectious cDNA construct. We have assembled a full-length infectious construct of transmissible gastroenteritis virus (TGEV), an important pathogen in swine. Using a novel approach, six adjoining cDNA subclones that span the entire TGEV genome were isolated. Each clone was engineered with unique flanking interconnecting junctions which determine a precise systematic assembly with only the adjacent cDNA subclones, resulting in an intact TGEV cDNA construct of ∼28.5 kb in length. Transcripts derived from the full-length TGEV construct were infectious, and progeny virions were serially passaged in permissive host cells. Viral antigen production and subgenomic mRNA synthesis were evident during infection and throughout passage. Plaque-purified virus derived from the infectious construct replicated efficiently and displayed similar plaque morphology in permissive host cells. Host range phenotypes of the molecularly cloned and wild-type viruses were similar in cells of swine and feline origin. The recombinant viruses were sequenced across the unique interconnecting junctions, conclusively demonstrating the marker mutations and restriction sites that were engineered into the component clones. Full-length infectious constructs of TGEV will permit the precise genetic modification of the coronavirus genome. The method that we have designed to generate an infectious cDNA construct of TGEV could theoretically be used to precisely reconstruct microbial or eukaryotic genomes approaching several million base pairs in length.
- Published
- 2000
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16. Venus In Situ Explorer Mission design using a mechanically deployed aerodynamic decelerator
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Smith, B., primary, Venkatapathy, E., additional, Wercinski, P., additional, Yount, B., additional, Prabhu, D., additional, Gage, P., additional, Glaze, L., additional, and Baker, C., additional
- Published
- 2013
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17. Episodic evolution mediates interspecies transfer of a murine coronavirus
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Baric, R S, primary, Yount, B, additional, Hensley, L, additional, Peel, S A, additional, and Chen, W, additional
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- 1997
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18. Agricultural risk factors for t(14;18) subtypes of non-Hodgkin's lymphoma.
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Schroeder, Jane C., Olshan, Andrew F., Baric, Ralph, Dent, Georgette A., Weinberg, Clarice R., Yount, Boyd, Cerhan, James R., Lynch, Charles F., Schuman, Leonard M., Tolbert, Paige E., Rothman, Nathaniel, P Cantor, Kenneth, Blair, Aaron, Schroeder, J C, Olshan, A F, Baric, R, Dent, G A, Weinberg, C R, Yount, B, and Cerhan, J R
- Published
- 2001
19. Radiologic Assessment of Pulmonary Arterial Pressure and Blood Volume in Chronic, Diffuse, Interstitial Pulmonary Diseases
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AUSTIN, JOHN H. M., YOUNT, B GERALD, THOMAS, HENRY M., and ENSON, YALE
- Abstract
Chronic, diffuse, interstitial pulmonary diseases may cause an increase in mean pulmonary arterial pressure
- Published
- 1979
20. A New Quaternary Structure Epitope on Dengue Virus Serotype 2 Is the Target of Durable Type-Specific Neutralizing Antibodies
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Widman, D. G., Baric, R. S., Wahala, W. M., Gallichotte, E. N., Yount, B. L., Durbin, A., Crowe, J. E., Sariol, C. A., Whitehead, S., and de Silva, A. M.
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3. Good health - Abstract
Dengue virus serotype 2 (DENV2) is widespread and responsible for severe epidemics. While primary DENV2 infections stimulate serotype-specific protective responses, a leading vaccine failed to induce a similar protective response. Using human monoclonal antibodies (hMAbs) isolated from dengue cases and structure-guided design of a chimeric DENV, here we describe the major site on the DENV2 envelope (E) protein targeted by neutralizing antibodies. DENV2-specific neutralizing hMAb 2D22 binds to a quaternary structure epitope. We engineered and recovered a recombinant DENV4 that displayed the 2D22 epitope. DENV2 neutralizing antibodies in people exposed to infection or a live vaccine tracked with the 2D22 epitope on the DENV4/2 chimera. The chimera remained sensitive to DENV4 antibodies, indicating that the major neutralizing epitopes on DENV2 and -4 are at different sites. The ability to transplant a complex epitope between DENV serotypes demonstrates a hitherto underappreciated structural flexibility in flaviviruses, which could be harnessed to develop new vaccines and diagnostics. IMPORTANCE Dengue virus causes fever and dengue hemorrhagic fever. Dengue serotype 2 (DENV2) is widespread and frequently responsible for severe epidemics. Natural DENV2 infections stimulate serotype-specific neutralizing antibodies, but a leading DENV vaccine did not induce a similar protective response. While groups have identified epitopes of single monoclonal antibodies (MAbs), the molecular basis of DENV2 neutralization by polyclonal human immune sera is unknown. Using a recombinant DENV displaying serotype 2 epitopes, here we map the main target of DENV2 polyclonal neutralizing antibodies induced by natural infection and a live DENV2 vaccine candidate. Proper display of the epitope required the assembly of viral envelope proteins into higher-order structures present on intact virions. Despite the complexity of the epitope, it was possible to transplant the epitope between DENV serotypes. Our findings have immediate implications for evaluating dengue vaccines in the pipeline as well as designing next-generation vaccines.
21. Parks promoting physical activity: Synthesis of findings from interventions in seven National Parks
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Hoehner, C. M., Brownson, R. C., Allen, D., Gramann, J., Behrens, T. K., Myron Floyd, Leahy, J., Liddle, J. B., Smaldone, D., Spain, D. D., Tardona, D. R., Ruthmann, N. P., Seiler, R. L., and Yount, B. W.
22. The oral nucleoside prodrug GS-5245 is efficacious against SARS-CoV-2 and other endemic, epidemic, and enzootic coronaviruses.
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Martinez DR, Moreira FR, Catanzaro NJ, Diefenbacher MV, Zweigart MR, Gully KL, De la Cruz G, Brown AJ, Adams LE, Yount B, Baric TJ, Mallory ML, Conrad H, May SR, Dong S, Scobey DT, Nguyen C, Montgomery SA, Perry JK, Babusis D, Barrett KT, Nguyen AH, Nguyen AQ, Kalla R, Bannister R, Feng JY, Cihlar T, Baric RS, Mackman RL, Bilello JP, Schäfer A, and Sheahan TP
- Subjects
- Animals, Humans, Mice, Administration, Oral, Chlorocebus aethiops, Vero Cells, COVID-19 Drug Treatment, COVID-19 virology, Virus Replication drug effects, Nucleosides pharmacology, Nucleosides therapeutic use, Nucleosides chemistry, Coronavirus Infections drug therapy, Coronavirus Infections virology, Female, Disease Models, Animal, SARS-CoV-2 drug effects, Prodrugs pharmacology, Prodrugs therapeutic use, Antiviral Agents pharmacology, Antiviral Agents therapeutic use
- Abstract
Despite the wide availability of several safe and effective vaccines that prevent severe COVID-19, the persistent emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) that can evade vaccine-elicited immunity remains a global health concern. In addition, the emergence of SARS-CoV-2 VOCs that can evade therapeutic monoclonal antibodies underscores the need for additional, variant-resistant treatment strategies. Here, we characterize the antiviral activity of GS-5245, obeldesivir (ODV), an oral prodrug of the parent nucleoside GS-441524, which targets the highly conserved viral RNA-dependent RNA polymerase (RdRp). We show that GS-5245 is broadly potent in vitro against alphacoronavirus HCoV-NL63, SARS-CoV, SARS-CoV-related bat-CoV RsSHC014, Middle East respiratory syndrome coronavirus (MERS-CoV), SARS-CoV-2 WA/1, and the highly transmissible SARS-CoV-2 BA.1 Omicron variant. Moreover, in mouse models of SARS-CoV, SARS-CoV-2 (WA/1 and Omicron B1.1.529), MERS-CoV, and bat-CoV RsSHC014 pathogenesis, we observed a dose-dependent reduction in viral replication, body weight loss, acute lung injury, and pulmonary function with GS-5245 therapy. Last, we demonstrate that a combination of GS-5245 and main protease (M
pro ) inhibitor nirmatrelvir improved outcomes in vivo against SARS-CoV-2 compared with the single agents. Together, our data support the clinical evaluation of GS-5245 against coronaviruses that cause or have the potential to cause human disease.- Published
- 2024
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23. Homotypic antibodies target novel E glycoprotein domains after natural DENV 3 infection/vaccination.
- Author
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Munt JE, Henein S, Adams C, Young E, Hou YJ, Conrad H, Zhu D, Dong S, Kose N, Yount B, Meganck RM, Tse LPV, Kuan G, Balmaseda A, Ricciardi MJ, Watkins DI, Crowe JE Jr, Harris E, DeSilva AM, and Baric RS
- Subjects
- Humans, Antibodies, Viral, Antibodies, Neutralizing, Viral Envelope Proteins genetics, Glycoproteins, Vaccination, Dengue Virus, Dengue Vaccines, Dengue
- Abstract
The envelope (E) glycoprotein is the primary target of type-specific (TS) neutralizing antibodies (nAbs) after infection with any of the four distinct dengue virus serotypes (DENV1-4). nAbs can be elicited to distinct structural E domains (EDs) I, II, or III. However, the relative contribution of these domain-specific antibodies is unclear. To identify the primary DENV3 nAb targets in sera after natural infection or vaccination, chimeric DENV1 recombinant encoding DENV3 EDI, EDII, or EDIII were generated. DENV3 EDII is the principal target of TS polyclonal nAb responses and encodes two or more neutralizing epitopes. In contrast, some were individuals vaccinated with a DENV3 monovalent vaccine-elicited serum TS nAbs targeting each ED in a subject-dependent fashion, with an emphasis on EDI and EDIII. Vaccine responses were also sensitive to DENV3 genotypic variation. This DENV1/3 panel allows the measurement of serum ED TS nAbs, revealing differences in TS nAb immunity after natural infection or vaccination., Competing Interests: Declaration of interests R.S.B. and E.H. have served on the Scientific Advisory Boards for Takeda vaccines, VaxArt, and Invivyd Therapeutics and has collaborations with Gilead, Janssen Pharmaceuticals, Pardas Biosciences, and Chimerix. A.M.D. has served as an unpaid consultant for Moderna and Takeda vaccines and is an unpaid member of Merck’s dengue vaccine Scientific Advisory Board, and R.S.B. and A.M.D. are inventors on pending and approved flavivirus vaccine and diagnostic patents filed by the University of North Carolina at Chapel Hill. A.M.D. is co-directing a partnership program between UNC and Moderna to develop flavivirus vaccines. UNC has applied for a patent related to the chimeric viruses. J.E.C. has served as a consultant for Takeda vaccines, Sanofi Pasteur, Pfizer, and Novavax; is on the Scientific Advisory Boards of CompuVax and Meissa Vaccines; and is a Founder of IDBiologics, Inc., (Copyright © 2023 Elsevier Inc. All rights reserved.)
- Published
- 2023
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24. Dengue virus 4/2 envelope domain chimeric virus panel maps type-specific responses against dengue serotype 2.
- Author
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Zhu DR, Rajesh AJ, Meganck RM, Young EF, Munt JE, Tse VL, Yount B Jr, Conrad H, White L, Henein S, DeSilva AM, and Baric RS
- Subjects
- Humans, Antibodies, Viral, Viral Envelope Proteins genetics, Serogroup, Antibodies, Neutralizing, Dengue Virus, Dengue
- Abstract
Importance: The four dengue virus (DENV) serotypes infect several hundred million people each year. Although primary infection is generally mild, subsequent infection by differing serotypes increases the risk for symptomatic disease ranging from fever to life-threatening shock. Despite the availability of licensed vaccines, a comprehensive understanding of antibodies that target the viral envelope protein and protect from infection remains incomplete. In this manuscript, we develop a panel of recombinant viruses that graft each envelope domain of DENV2 onto the DENV4 envelope glycoprotein, revealing protein interactions important for virus viability. Furthermore, we map neutralizing antibody responses after primary DENV2 natural infection and a human challenge model to distinct domains on the viral envelope protein. The panel of recombinant viruses provides a new tool for dissecting the E domain-specific targeting of protective antibody responses, informing future DENV vaccine design., Competing Interests: The authors declare no conflict of interest.
- Published
- 2023
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25. Adjuvant-dependent effects on the safety and efficacy of inactivated SARS-CoV-2 vaccines during heterologous infection by a SARS-related coronavirus.
- Author
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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 3rd, 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, and Baxter V
- 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., Competing Interests: Declarations of Interest / Conflicts of Interest RSB has served on the Scientific Advisory Boards for Takeda vaccines, VaxArt and Invivyd Therapeutics, and has collaborations with Gilead, Janssen Pharmaceuticals, Pardas Biosciences, and Chimerix. RSB, KHD III and SRL are listed as inventors on patents pertaining to the mouse-adapted SARS-CoV-2 viruses (MA10 and MA10-B.1.351; Patent number 11,225,508) and the SARS-CoV-2 nanoLuciferase viruses (SARS-CoV-2-nLuc and B.1.351-nLuc; Patent number 11,492,379) used in this study. In accordance with the Nature Portfolio Competing interests policy, this section is also stated at the end of this manuscript.- Published
- 2023
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26. Host range, transmissibility and antigenicity of a pangolin coronavirus.
- Author
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Hou YJ, Chiba S, Leist SR, Meganck RM, Martinez DR, Schäfer A, Catanzaro NJ, Sontake V, West A, Edwards CE, Yount B, Lee RE, Gallant SC, Zost SJ, Powers J, Adams L, Kong EF, Mattocks M, Tata A, Randell SH, Tata PR, Halfmann P, Crowe JE Jr, Kawaoka Y, and Baric RS
- Subjects
- Cricetinae, Humans, Animals, Mice, Host Specificity, Pangolins, SARS-CoV-2 genetics, Antibodies, Viral, COVID-19 Vaccines, Mice, Inbred BALB C, COVID-19 prevention & control, Severe acute respiratory syndrome-related coronavirus
- Abstract
The pathogenic and cross-species transmission potential of SARS-CoV-2-related coronaviruses (CoVs) remain poorly characterized. Here we recovered a wild-type pangolin (Pg) CoV GD strain including derivatives encoding reporter genes using reverse genetics. In primary human cells, PgCoV replicated efficiently but with reduced fitness and showed less efficient transmission via airborne route compared with SARS-CoV-2 in hamsters. PgCoV was potently inhibited by US Food and Drug Administration approved drugs, and neutralized by COVID-19 patient sera and SARS-CoV-2 therapeutic antibodies in vitro. A pan-Sarbecovirus antibody and SARS-CoV-2 S2P recombinant protein vaccine protected BALB/c mice from PgCoV infection. In K18-hACE2 mice, PgCoV infection caused severe clinical disease, but mice were protected by a SARS-CoV-2 human antibody. Efficient PgCoV replication in primary human cells and hACE2 mice, coupled with a capacity for airborne spread, highlights an emergence potential. However, low competitive fitness, pre-immune humans and the benefit of COVID-19 countermeasures should impede its ability to spread globally in human populations., (© 2023. The Author(s).)
- Published
- 2023
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27. Efficacy of the oral nucleoside prodrug GS-5245 (Obeldesivir) against SARS-CoV-2 and coronaviruses with pandemic potential.
- Author
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Martinez DR, Moreira FR, Zweigart MR, Gully KL, De la Cruz G, Brown AJ, Adams LE, Catanzaro N, Yount B, Baric TJ, Mallory ML, Conrad H, May SR, Dong S, Scobey DT, Montgomery SA, Perry J, Babusis D, Barrett KT, Nguyen AH, Nguyen AQ, Kalla R, Bannister R, Bilello JP, Feng JY, Cihlar T, Baric RS, Mackman RL, Schäfer A, and Sheahan TP
- Abstract
Despite the wide availability of several safe and effective vaccines that can prevent severe COVID-19 disease, the emergence of SARS-CoV-2 variants of concern (VOC) that can partially evade vaccine immunity remains a global health concern. In addition, the emergence of highly mutated and neutralization-resistant SARS-CoV-2 VOCs such as BA.1 and BA.5 that can partially or fully evade (1) many therapeutic monoclonal antibodies in clinical use underlines the need for additional effective treatment strategies. Here, we characterize the antiviral activity of GS-5245, Obeldesivir (ODV), an oral prodrug of the parent nucleoside GS-441524, which targets the highly conserved RNA-dependent viral RNA polymerase (RdRp). Importantly, we show that GS-5245 is broadly potent in vitro against alphacoronavirus HCoV-NL63, severe acute respiratory syndrome coronavirus (SARS-CoV), SARS-CoV-related Bat-CoV RsSHC014, Middle East Respiratory Syndrome coronavirus (MERS-CoV), SARS-CoV-2 WA/1, and the highly transmissible SARS-CoV-2 BA.1 Omicron variant in vitro and highly effective as antiviral therapy in mouse models of SARS-CoV, SARS-CoV-2 (WA/1), MERS-CoV and Bat-CoV RsSHC014 pathogenesis. In all these models of divergent coronaviruses, we observed protection and/or significant reduction of disease metrics such as weight loss, lung viral replication, acute lung injury, and degradation in pulmonary function in GS-5245-treated mice compared to vehicle controls. Finally, we demonstrate that GS-5245 in combination with the main protease (M
pro ) inhibitor nirmatrelvir had increased efficacy in vivo against SARS-CoV-2 compared to each single agent. Altogether, our data supports the continuing clinical evaluation of GS-5245 in humans infected with COVID-19, including as part of a combination antiviral therapy, especially in populations with the most urgent need for more efficacious and durable interventions., Competing Interests: DECLARATION OF INTERESTS These authors are employees of Gilead Sciences and hold stock in Gilead Sciences: D.B., A.N., K.T.B., R.B, J.P.B., J.Y.F., T.C., R.L.M.- Published
- 2023
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28. A live dengue virus vaccine carrying a chimeric envelope glycoprotein elicits dual DENV2-DENV4 serotype-specific immunity.
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Young E, Yount B, Pantoja P, Henein S, Meganck RM, McBride J, Munt JE, Baric TJ, Zhu D, Scobey T, Dong S, Tse LV, Martinez MI, Burgos AG, Graham RL, White L, DeSilva A, Sariol CA, and Baric RS
- Subjects
- Male, Humans, Antibodies, Viral, Serogroup, Viral Envelope Proteins genetics, Antibodies, Neutralizing, Dengue Virus genetics, Dengue
- Abstract
The four dengue virus serotypes co-circulate globally and cause significant human disease. Dengue vaccine development is challenging because some virus-specific antibodies are protective, while others are implicated in enhanced viral replication and more severe disease. Current dengue tetravalent vaccines contain four live attenuated serotypes formulated to theoretically induce balanced protective immunity. Among the number of vaccine candidates in clinical trials, only Dengvaxia is licensed for use in DENV seropositive individuals. To simplify live-virus vaccine design, we identify co-evolutionary constraints inherent in flavivirus virion assembly and design chimeric viruses to replace domain II (EDII) of the DENV2 envelope (E) glycoprotein with EDII from DENV4. The chimeric DENV2/4EDII virus replicates efficiently in vitro and in vivo. In male macaques, a single inoculation of DENV2/4EDII induces type-specific neutralizing antibodies to both DENV2 and DENV4, thereby providing a strategy to simplify DENV vaccine design by utilizing a single bivalent E glycoprotein immunogen for two DENV serotypes., (© 2023. The Author(s).)
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- 2023
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29. Prediction of sepsis onset in hospital admissions using survival analysis.
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DeShon B, Dummitt B, Allen J, and Yount B
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- Humans, Retrospective Studies, Survival Analysis, Hospitals, Emergency Service, Hospital, Intensive Care Units, Shock, Septic diagnosis, Sepsis diagnosis
- Abstract
To determine the efficacy of modern survival analysis methods for predicting sepsis onset in ICU, emergency, medical/surgical, and TCU departments. We performed a retrospective analysis on ICU, med/surg, ED, and TCU cases from multiple Mercy Health hospitals from August 2018 to March 2020. Patients in these departments were monitored by the Mercy Virtual vSepsis team and sepsis cases were determined and documented in the Mercy EHR via a rule-based engine utilizing clinical data. We used survival-based modeling methods to predict sepsis onset in these cases. The three survival methods that were used to predict the onset of severe sepsis and septic shock produced AUC values > 0.85 and each provided a median lead time of > 20 h prior to disease onset. This methodology improves upon previous work by demonstrating excellent model performance when generalizing survival-based prediction methods to both severe sepsis and septic shock as well as non-ICU departments.IRB InformationTrial Registration ID: 1,532,327-1.Trial Effective Date: 12/02/2019., (© 2022. The Author(s), under exclusive licence to Springer Nature B.V.)
- Published
- 2022
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30. A broadly cross-reactive antibody neutralizes and protects against sarbecovirus challenge in mice.
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Martinez DR, Schäfer A, Gobeil S, Li D, De la Cruz G, Parks R, Lu X, Barr M, Stalls V, Janowska K, Beaudoin E, Manne K, Mansouri K, Edwards RJ, Cronin K, Yount B, Anasti K, Montgomery SA, Tang J, Golding H, Shen S, Zhou T, Kwong PD, Graham BS, Mascola JR, Montefiori DC, Alam SM, Sempowski G, Sempowski GD, Khurana S, Wiehe K, Saunders KO, Acharya P, Haynes BF, and Baric RS
- Subjects
- Animals, Antibodies, Neutralizing, Antibodies, Viral, Humans, Mice, Spike Glycoprotein, Coronavirus, COVID-19, SARS-CoV-2
- Abstract
Severe acute respiratory syndrome coronaviruses 1 (SARS-CoV) and 2 (SARS-CoV-2), including SARS-CoV-2 variants of concern, can cause deadly infections. The mortality associated with sarbecovirus infection underscores the importance of developing broadly effective countermeasures against them, which could be key in the prevention and mitigation of current and future zoonotic events. Here, we demonstrate the neutralization of SARS-CoV; bat coronaviruses WIV-1 and RsSHC014; and SARS-CoV-2 variants D614G, B.1.1.7, B.1.351, P.1, B.1.429, B.1.526, B.1.617.1, and B.1.617.2 by a receptor binding domain (RBD)–specific human antibody, DH1047. Prophylactic and therapeutic treatment with DH1047 was protective against SARS-CoV, WIV-1, RsSHC014, and SARS-CoV-2 B.1.351 infection in mice. Binding and structural analysis showed high affinity binding of DH1047 to an epitope that is highly conserved among sarbecoviruses. Thus, DH1047 is a broadly protective antibody that can prevent infection and mitigate outbreaks caused by SARS-related strains and SARS-CoV-2 variants. Our results also suggest that the conserved RBD epitope bound by DH1047 is a rational target for a universal sarbecovirus vaccine.
- Published
- 2022
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31. Outcomes Associated With Social Distancing Policies in St Louis, Missouri, During the Early Phase of the COVID-19 Pandemic.
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Geng EH, Schwab J, Foraker R, Fox B, Hoehner CM, Schootman M, Mody A, Powderly W, Yount B, Woeltje K, and Petersen M
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- Bayes Theorem, Female, Hospital Mortality trends, Humans, Male, Missouri, Pandemics, SARS-CoV-2, COVID-19 mortality, Health Policy, Hospitalization statistics & numerical data, Physical Distancing
- Abstract
Importance: In the absence of a national strategy in response to the COVID-19 pandemic, many public health decisions fell to local elected officials and agencies. Outcomes of such policies depend on a complex combination of local epidemic conditions and demographic features as well as the intensity and timing of such policies and are therefore unclear., Objective: To use a decision analytical model of the COVID-19 epidemic to investigate potential outcomes if actual policies enacted in March 2020 (during the first wave of the epidemic) in the St Louis region of Missouri had been delayed., Design, Setting, and Participants: A previously developed, publicly available, open-source modeling platform (Local Epidemic Modeling for Management & Action, version 2.1) designed to enable localized COVID-19 epidemic projections was used. The compartmental epidemic model is programmed in R and Stan, uses bayesian inference, and accepts user-supplied demographic, epidemiologic, and policy inputs. Hospital census data for 1.3 million people from St Louis City and County from March 14, 2020, through July 15, 2020, were used to calibrate the model., Exposures: Hypothetical delays in actual social distancing policies (which began on March 13, 2020) by 1, 2, or 4 weeks. Sensitivity analyses were conducted that explored plausible spontaneous behavior change in the absence of social distancing policies., Main Outcomes and Measures: Hospitalizations and deaths., Results: A model of 1.3 million residents of the greater St Louis, Missouri, area found an initial reproductive number (indicating transmissibility of an infectious agent) of 3.9 (95% credible interval [CrI], 3.1-4.5) in the St Louis region before March 15, 2020, which fell to 0.93 (95% CrI, 0.88-0.98) after social distancing policies were implemented between March 15 and March 21, 2020. By June 15, a 1-week delay in policies would have increased cumulative hospitalizations from an observed actual number of 2246 hospitalizations to 8005 hospitalizations (75% CrI: 3973-15 236 hospitalizations) and increased deaths from an observed actual number of 482 deaths to a projected 1304 deaths (75% CrI, 656-2428 deaths). By June 15, a 2-week delay would have yielded 3292 deaths (75% CrI, 2104-4905 deaths)-an additional 2810 deaths or a 583% increase beyond what was actually observed. Sensitivity analyses incorporating a range of spontaneous behavior changes did not avert severe epidemic projections., Conclusions and Relevance: The results of this decision analytical model study suggest that, in the St Louis region, timely social distancing policies were associated with improved population health outcomes, and small delays may likely have led to a COVID-19 epidemic similar to the most heavily affected areas in the US. These findings indicate that an open-source modeling platform designed to accept user-supplied local and regional data may provide projections tailored to, and more relevant for, local settings.
- Published
- 2021
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32. Chimeric spike mRNA vaccines protect against Sarbecovirus challenge in mice.
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Martinez DR, Schäfer A, Leist SR, De la Cruz G, West A, Atochina-Vasserman EN, Lindesmith LC, Pardi N, Parks R, Barr M, Li D, Yount B, Saunders KO, Weissman D, Haynes BF, Montgomery SA, and Baric RS
- Subjects
- Animals, Antibodies, Neutralizing immunology, Antibodies, Viral immunology, Betacoronavirus physiology, COVID-19 prevention & control, Coronavirus Infections immunology, Cross Protection, Cytokines blood, Female, Immunity, Heterologous, Immunogenicity, Vaccine, Liposomes, Lung pathology, Lung virology, Mice, Mice, Inbred BALB C, Nanoparticles, Protein Domains, Recombinant Fusion Proteins, Severe acute respiratory syndrome-related coronavirus immunology, Severe acute respiratory syndrome-related coronavirus physiology, SARS-CoV-2 immunology, SARS-CoV-2 physiology, Severe Acute Respiratory Syndrome prevention & control, Spike Glycoprotein, Coronavirus chemistry, Spike Glycoprotein, Coronavirus genetics, Virus Replication, mRNA Vaccines, Betacoronavirus immunology, COVID-19 Vaccines immunology, Coronavirus Infections prevention & control, Spike Glycoprotein, Coronavirus immunology, Vaccines, Synthetic immunology, Viral Vaccines immunology
- Abstract
The emergence of severe acute respiratory syndrome coronavirus (SARS-CoV) in 2003 and SARS-CoV-2 in 2019 highlights the need to develop universal vaccination strategies against the broader Sarbecovirus subgenus. Using chimeric spike designs, we demonstrate protection against challenge from SARS-CoV, SARS-CoV-2, SARS-CoV-2 B.1.351, bat CoV (Bt-CoV) RsSHC014, and a heterologous Bt-CoV WIV-1 in vulnerable aged mice. Chimeric spike messenger RNAs (mRNAs) induced high levels of broadly protective neutralizing antibodies against high-risk Sarbecoviruses. By contrast, SARS-CoV-2 mRNA vaccination not only showed a marked reduction in neutralizing titers against heterologous Sarbecoviruses, but SARS-CoV and WIV-1 challenge in mice resulted in breakthrough infections. Chimeric spike mRNA vaccines efficiently neutralized D614G, mink cluster five, and the UK B.1.1.7 and South African B.1.351 variants of concern. Thus, multiplexed-chimeric spikes can prevent SARS-like zoonotic coronavirus infections with pandemic potential., (Copyright © 2021 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.)
- Published
- 2021
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33. Prevention and therapy of SARS-CoV-2 and the B.1.351 variant in mice.
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Martinez DR, Schäfer A, Leist SR, Li D, Gully K, Yount B, Feng JY, Bunyan E, Porter DP, Cihlar T, Montgomery SA, Haynes BF, Baric RS, Nussenzweig MC, and Sheahan TP
- Subjects
- Animals, Antibodies, Monoclonal immunology, Antiviral Agents pharmacology, Humans, Mice, SARS-CoV-2 pathogenicity, Antibodies, Monoclonal pharmacology, SARS-CoV-2 drug effects, COVID-19 Drug Treatment
- Abstract
Improving clinical care for individuals infected with SARS-CoV-2 variants is a global health priority. Small-molecule antivirals like remdesivir (RDV) and biologics such as human monoclonal antibodies (mAbs) have demonstrated therapeutic efficacy against SARS-CoV-2, the causative agent of coronavirus disease 2019 (COVID-19). It is not known whether combination RDV/mAb will improve outcomes over single-agent therapies or whether antibody therapies will remain efficacious against variants. Here, we show that a combination of two mAbs in clinical trials, C144 and C135, have potent antiviral effects against even when initiated 48 h after infection and have therapeutic efficacy in vivo against the B.1.351 variant of concern (VOC). Combining RDV and antibodies provided a modest improvement in outcomes compared with single agents. These data support the continued use of RDV to treat SARS-CoV-2 infections and the continued clinical development of the C144 and C135 antibody combination to treat patients infected with SARS-CoV-2 variants., Competing Interests: Declaration of interests J.Y.F., E.B., D.P.P., and T.C. are employed by Gilead Sciences Inc., (Copyright © 2021 The Author(s). Published by Elsevier Inc. All rights reserved.)
- Published
- 2021
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34. Chimeric spike mRNA vaccines protect against Sarbecoviru s challenge in mice.
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Martinez DR, Schäfer A, Leist SR, De la Cruz G, West A, Atochina-Vasserman EN, Lindesmith LC, Pardi N, Parks R, Barr M, Li D, Yount B, Saunders KO, Weissman D, Haynes BF, Montgomery SA, and Baric RS
- Abstract
The emergence of SARS-CoV in 2003 and SARS-CoV-2 in 2019 highlights the need to develop universal vaccination strategies against the broader Sarbecovirus subgenus. Using chimeric spike designs, we demonstrate protection against challenge from SARS-CoV, SARS-CoV-2, SARS-CoV-2 B.1.351, bat CoV (Bt-CoV) RsSHC014, and a heterologous Bt-CoV WIV-1 in vulnerable aged mice. Chimeric spike mRNAs induced high levels of broadly protective neutralizing antibodies against high-risk Sarbecoviruses. In contrast, SARS-CoV-2 mRNA vaccination not only showed a marked reduction in neutralizing titers against heterologous Sarbecoviruses, but SARS-CoV and WIV-1 challenge in mice resulted in breakthrough infection. Chimeric spike mRNA vaccines efficiently neutralized D614G, UK B.1.1.7., mink cluster five, and the South African B.1.351 variant of concern. Thus, multiplexed-chimeric spikes can prevent SARS-like zoonotic coronavirus infections with pandemic potential., Competing Interests: Competing interests: The University of North Carolina at Chapel Hill has filed provisional patents for which D.R.M. and R.S.B are co-inventors (U.S. Provisional Application No. 63/106,247 filed on October 27th, 2020) for the chimeric vaccine constructs and their applications described in this study.
- Published
- 2021
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35. A broadly neutralizing antibody protects against SARS-CoV, pre-emergent bat CoVs, and SARS-CoV-2 variants in mice.
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Martinez DR, Schaefer A, Gobeil S, Li D, De la Cruz G, Parks R, Lu X, Barr M, Manne K, Mansouri K, Edwards RJ, Yount B, Anasti K, Montgomery SA, Shen S, Zhou T, Kwong PD, Graham BS, Mascola JR, Montefiori DC, Alam M, Sempowski GD, Wiehe K, Saunders KO, Acharya P, Haynes BF, and Baric RS
- Abstract
SARS-CoV in 2003, SARS-CoV-2 in 2019, and SARS-CoV-2 variants of concern (VOC) can cause deadly infections, underlining the importance of developing broadly effective countermeasures against Group 2B Sarbecoviruses, which could be key in the rapid prevention and mitigation of future zoonotic events. Here, we demonstrate the neutralization of SARS-CoV, bat CoVs WIV-1 and RsSHC014, and SARS-CoV-2 variants D614G, B.1.1.7, B.1.429, B1.351 by a receptor-binding domain (RBD)-specific antibody DH1047. Prophylactic and therapeutic treatment with DH1047 demonstrated protection against SARS-CoV, WIV-1, RsSHC014, and SARS-CoV-2 B1.351infection in mice. Binding and structural analysis showed high affinity binding of DH1047 to an epitope that is highly conserved among Sarbecoviruses. We conclude that DH1047 is a broadly neutralizing and protective antibody that can prevent infection and mitigate outbreaks caused by SARS-like strains and SARS-CoV-2 variants. Our results argue that the RBD conserved epitope bound by DH1047 is a rational target for pan Group 2B coronavirus vaccines., Competing Interests: Competing interests: Duke University has filed provisional patents for which B.F.H, K.O.S., D.L., and G.D.S., are inventors on a provisional U.S. patent for mAb DH1047 and its applications described in this study.
- Published
- 2021
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36. Antigenic Variation of the Dengue Virus 2 Genotypes Impacts the Neutralization Activity of Human Antibodies in Vaccinees.
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Martinez DR, Yount B, Nivarthi U, Munt JE, Delacruz MJ, Whitehead SS, Durbin AP, de Silva AM, and Baric RS
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- Antigenic Variation, Genotype, Humans, Antibodies, Neutralizing metabolism, Dengue Virus genetics, Vaccination methods
- Abstract
Dengue virus (DENV) infects an estimated 390 million people each year worldwide. As tetravalent DENV vaccines have variable efficacy against DENV serotype 2 (DENV2), we evaluated the role of genetic diversity within the pre-membrane (prM) and envelope (E) proteins of DENV2 on vaccine performance. We generated a recombinant DENV2 genotype variant panel with contemporary prM and E isolates that are representative of global genetic diversity. The DENV2 genotype variants differ in growth kinetics, morphology, and virion stability. Importantly, the DENV2 genotypic variants are differentially neutralized by monoclonal antibodies, polyclonal serum neutralizing antibodies from DENV2-infected human subjects, and vaccine-elicited antibody responses from the TV003 NIH DENV2 monovalent and DENV tetravalent vaccines. We conclude that DENV2 prM and E genetic diversity significantly modulates antibody neutralization activity. These findings have important implications for dengue vaccines, which are being developed under the assumption that intraserotype variation has minimal impact on neutralizing antibodies., Competing Interests: Declaration of Interests A.M.d.S. has consulted with Takeda, Merck, and GSK on developing DENV vaccine concepts. R.S.B. has consulted with Takeda on DENV and norovirus vaccine concepts. R.S.B. has had a sponsored program on norovirus vaccine development by Takeda. A.M.d.S. and R.S.B. are inventors on patents on DENV vaccines., (Copyright © 2020 The Author(s). Published by Elsevier Inc. All rights reserved.)
- Published
- 2020
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37. How real-world evidence can really deliver: a case study of data source development and use.
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Drozda J, Zeringue A, Dummitt B, Yount B, and Resnic F
- Abstract
Competing Interests: Competing interests: JPD has received grant support from Johnson and Johnson and Medtronic. His son is an employee of Boston Scientific Corporation. None declared by the other authors.
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- 2020
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38. Structure of mouse coronavirus spike protein complexed with receptor reveals mechanism for viral entry.
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Shang J, Wan Y, Liu C, Yount B, Gully K, Yang Y, Auerbach A, Peng G, Baric R, and Li F
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- Animals, Carcinoembryonic Antigen metabolism, Carcinoembryonic Antigen ultrastructure, Cell Line, Tumor, Cryoelectron Microscopy, HEK293 Cells, Humans, Membrane Fusion, Mice, Models, Molecular, Protein Binding, Protein Conformation, Protein Conformation, alpha-Helical, Protein Domains, Protein Multimerization, Proteolysis, Receptors, Virus metabolism, Receptors, Virus ultrastructure, Recombinant Proteins chemistry, Recombinant Proteins metabolism, Severe acute respiratory syndrome-related coronavirus chemistry, Spike Glycoprotein, Coronavirus metabolism, Spike Glycoprotein, Coronavirus ultrastructure, Virus Attachment, Carcinoembryonic Antigen chemistry, Murine hepatitis virus chemistry, Murine hepatitis virus physiology, Receptors, Virus chemistry, Spike Glycoprotein, Coronavirus chemistry, Virus Internalization
- 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., Competing Interests: The authors have declared that no competing interests exist.
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- 2020
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39. Beyond Neutralizing Antibody Levels: The Epitope Specificity of Antibodies Induced by National Institutes of Health Monovalent Dengue Virus Vaccines.
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Swanstrom JA, Nivarthi UK, Patel B, Delacruz MJ, Yount B, Widman DG, Durbin AP, Whitehead SS, De Silva AM, and Baric RS
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- Amino Acid Sequence, Dengue virology, Epitope Mapping methods, Humans, National Institutes of Health (U.S.), Serogroup, United States, Vaccination methods, Vaccines, Attenuated immunology, Viral Envelope Proteins immunology, Antibodies, Neutralizing immunology, Antibodies, Viral immunology, Dengue immunology, Dengue Vaccines immunology, Dengue Virus immunology, Epitopes immunology
- Abstract
Background: Dengue virus is an emerging mosquito-borne flavivirus responsible for considerable morbidity and mortality worldwide. The Division of Intramural Research, National Institute of Allergy and Infectious Diseases of the US National Institutes of Health (NIH) has developed live attenuated vaccines to each of the 4 serotypes of dengue virus (DENV1-4). While overall levels of DENV neutralizing antibodies (nAbs) in humans have been correlated with protection, these correlations vary depending on DENV serotype, prevaccination immunostatus, age, and study site. By combining both the level and molecular specificity of nAbs to each serotype, it may be possible to develop more robust correlates that predict long-term outcome., Methods: Using depletions and recombinant chimeric epitope transplant DENVs, we evaluate the molecular specificity and mapped specific epitopes and antigenic regions targeted by vaccine-induced nAbs in volunteers who received the NIH monovalent vaccines against each DENV serotype., Results: After monovalent vaccination, subjects developed high levels of nAbs that mainly targeted epitopes that are unique (type-specific) to each DENV serotype. The DENV1, 2, and 4 monovalent vaccines induced type-specific nAbs directed to quaternary structure envelope epitopes known to be targets of strongly neutralizing antibodies induced by wild-type DENV infections., Conclusions: Our results reported here on the molecular specificity of NIH vaccine-induced antibodies enable new strategies, beyond the absolute levels of nAbs, for determining correlates and mechanisms of protective immunity., (© The Author(s) 2019. Published by Oxford University Press for the Infectious Diseases Society of America.)
- Published
- 2019
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40. Antagonism of dsRNA-Induced Innate Immune Pathways by NS4a and NS4b Accessory Proteins during MERS Coronavirus Infection.
- Author
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Comar CE, Goldstein SA, Li Y, Yount B, Baric RS, and Weiss SR
- Subjects
- A549 Cells, Epithelial Cells virology, Gene Deletion, Humans, Immunity, Innate, Middle East Respiratory Syndrome Coronavirus immunology, Mutation, Viral Nonstructural Proteins genetics, Viral Regulatory and Accessory Proteins genetics, Virus Replication, Host-Pathogen Interactions, Immune Evasion, Middle East Respiratory Syndrome Coronavirus pathogenicity, RNA, Double-Stranded immunology, RNA, Viral immunology, Viral Nonstructural Proteins metabolism, Viral Regulatory and Accessory Proteins metabolism
- Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) was first identified in 2012 as a novel etiological agent of severe respiratory disease in humans. As during infection by other viruses, host sensing of viral double-stranded RNA (dsRNA) induces several antiviral pathways. These include interferon (IFN), oligoadenylate synthetase (OAS)-RNase L, and protein kinase R (PKR). Coronaviruses, including MERS-CoV, potently suppress the activation of these pathways, inducing only modest host responses. Our study describes the functions of two accessory proteins unique to MERS-CoV and related viruses, NS4a and NS4b, during infection in human airway epithelium-derived A549 cells. NS4a has been previously characterized as a dsRNA binding protein, while NS4b is a 2',5'-phosphodiesterase with structural and enzymatic similarity to NS2 encoded by mouse hepatitis virus (MHV). We found that deletion of NS4a results in increased interferon lambda ( IFNL1 ) expression, as does mutation of either the catalytic site or nuclear localization sequence of NS4b. All of the mutant viruses we tested exhibited slight decreases in replication. We previously reported that, like MHV NS2, NS4b antagonizes OAS-RNase L, but suppression of IFN is a previously unidentified function for viral phosphodiesterases. Unexpectedly, deletion of NS4a does not result in robust activation of the PKR or OAS-RNase L pathways. Therefore, MERS-CoV likely encodes other proteins that contribute to suppression or evasion of these antiviral innate immune pathways that should be an important focus of future work. This study provides additional insight into the complex interactions between MERS-CoV and the host immune response. IMPORTANCE Middle East respiratory syndrome coronavirus (MERS-CoV) is the second novel zoonotic coronavirus to emerge in the 21st century and cause outbreaks of severe respiratory disease. More than 2,200 cases and 800 deaths have been reported to date, yet there are no licensed vaccines or treatments. Coronaviruses encode unique accessory proteins that are not required for replication but most likely play roles in immune antagonism and/or pathogenesis. Our study describes the functions of MERS-CoV accessory proteins NS4a and NS4b during infection of a human airway-derived cell line. Loss of these accessory proteins during MERS-CoV infection leads to host antiviral activation and modestly attenuates replication. In the case of both NS4a and NS4b, we have identified roles during infection not previously described, yet the lack of robust activation suggests much remains to be learned about the interactions between MERS-CoV and the infected host., (Copyright © 2019 Comar et al.)
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- 2019
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41. Human Norovirus Epitope D Plasticity Allows Escape from Antibody Immunity without Loss of Capacity for Binding Cellular Ligands.
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Lindesmith LC, Brewer-Jensen PD, Mallory ML, Yount B, Collins MH, Debbink K, Graham RL, and Baric RS
- Subjects
- Antibodies, Viral metabolism, Caliciviridae Infections virology, Capsid Proteins chemistry, Capsid Proteins immunology, Child, Epitopes genetics, Feces virology, Humans, Immunity, Herd, Ligands, Norovirus genetics, Norovirus immunology, Protein Binding, Antibodies, Blocking metabolism, Caliciviridae Infections immunology, Capsid Proteins genetics, Epitopes immunology, INDEL Mutation, Norovirus isolation & purification
- Abstract
Emergent strains of human norovirus seed pandemic waves of disease. These new strains have altered ligand binding and antigenicity characteristics. Study of viral variants isolated from immunosuppressed patients with long-term norovirus infection indicates that initial virus in vivo evolution occurs at the same antigenic sites as in pandemic strains. Here, cellular ligand binding and antigenicity of two cocirculating strains isolated from a patient with long-term norovirus infection were characterized. The isolated GII.4 viruses differed from previous strains and from each other at known blockade antibody epitopes. One strain had a unique sequence in epitope D, including loss of an insertion at residue 394, corresponding to a decreased relative affinity for carbohydrate ligands. Replacement of 394 with alanine or restoration of the contemporary strain epitope D consensus sequence STT improved ligand binding relative affinity. However, monoclonal antibody blockade of binding potency was only gained for the consensus sequence, not by the alanine insertion. In-depth study of unique changes in epitope D indicated that ligand binding, but not antibody blockade of ligand binding, is maintained despite sequence diversity, allowing escape from blockade antibodies without loss of capacity for binding cellular ligands. IMPORTANCE Human norovirus causes ∼20% of all acute gastroenteritis and ∼200,000 deaths per year, primarily in young children. Most epidemic and all pandemic waves of disease over the past 30 years have been caused by type GII.4 human norovirus strains. The capsid sequence of GII.4 strains is changing over time, resulting in viruses with altered ligand and antibody binding characteristics. The carbohydrate binding pocket of these strains does not vary over time. Here, utilizing unique viral sequences, we study how residues in GII.4 epitope D balance the dual roles of variable antibody binding site and cellular ligand binding stabilization domain, demonstrating that amino acid changes in epitope D can result in loss of antibody binding without ablating ligand binding. This flexibility in epitope D likely contributes to GII.4 strain persistence by both allowing escape from antibody-mediated herd immunity and maintenance of cellular ligand binding and infectivity., (Copyright © 2019 Lindesmith et al.)
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- 2019
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42. The Human Sodium Iodide Symporter as a Reporter Gene for Studying Middle East Respiratory Syndrome Coronavirus Pathogenesis.
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Chefer S, Seidel J, Cockrell AS, Yount B, Solomon J, Hagen KR, Liu DX, Huzella LM, Kumar MR, Postnikova E, Bohannon JK, Lackemeyer MG, Cooper K, Endlich-Frazier A, Sharma H, Thomasson D, Bartos C, Sayre PJ, Sims A, Dyall J, Holbrook MR, Jahrling PB, Baric RS, and Johnson RF
- Subjects
- Animals, Chlorocebus aethiops, Disease Models, Animal, Genomic Instability, Mice, Transgenic, Middle East Respiratory Syndrome Coronavirus genetics, Mutagenesis, Insertional, Symporters genetics, Vero Cells, Coronavirus Infections pathology, Genes, Reporter, Middle East Respiratory Syndrome Coronavirus growth & development, Single Photon Emission Computed Tomography Computed Tomography methods, Symporters metabolism
- Abstract
Single photon emission computed tomography (SPECT) is frequently used in oncology and cardiology to evaluate disease progression and/or treatment efficacy. Such technology allows for real-time evaluation of disease progression and when applied to studying infectious diseases may provide insight into pathogenesis. Insertion of a SPECT-compatible reporter gene into a virus may provide insight into mechanisms of pathogenesis and viral tropism. The human sodium iodide symporter (hNIS), a SPECT and positron emission tomography reporter gene, was inserted into Middle East respiratory syndrome coronavirus (MERS-CoV), a recently emerged virus that can cause severe respiratory disease and death in afflicted humans to obtain a quantifiable and sensitive marker for viral replication to further MERS-CoV animal model development. The recombinant virus was evaluated for fitness, stability, and reporter gene functionality. The recombinant and parental viruses demonstrated equal fitness in terms of peak titer and replication kinetics, were stable for up to six in vitro passages, and were functional. Further in vivo evaluation indicated variable stability, but resolution limits hampered in vivo functional evaluation. These data support the further development of hNIS for monitoring infection in animal models of viral disease. IMPORTANCE Advanced medical imaging such as single photon emission computed tomography with computed tomography (SPECT/CT) enhances fields such as oncology and cardiology. Application of SPECT/CT, magnetic resonance imaging, and positron emission tomography to infectious disease may enhance pathogenesis studies and provide alternate biomarkers of disease progression. The experiments described in this article focus on insertion of a SPECT/CT-compatible reporter gene into MERS-CoV to demonstrate that a functional SPECT/CT reporter gene can be inserted into a virus.
- Published
- 2018
- Full Text
- View/download PDF
43. Using survival analysis to predict septic shock onset in ICU patients.
- Author
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Dummitt B, Zeringue A, Palagiri A, Veremakis C, Burch B, and Yount B
- Subjects
- APACHE, Critical Care, Female, Humans, Intensive Care Units, Male, Middle Aged, Missouri, Retrospective Studies, Sensitivity and Specificity, Survival Analysis, Critical Illness, Shock, Septic mortality
- Abstract
Purpose: To determine the efficacy of survival analysis for predicting septic shock onset in ICU patients., Materials and Methods: We performed a retrospective analysis on ICU cases from Mercy Hospital St. Louis from 2012 to 2016. As part of the procedure for inclusion in the Apache Outcomes database, each case is reviewed by critical care clinicians to identify septic shock patients as well as the time of septic shock onset. We used survival analysis to predict septic shock onset in these cases and employed lagging to compensate for uncertainties in septic shock onset time., Results: Survival analysis was highly effective at predicting septic shock onset, producing AUC values of >0.87. The methodology was robust to lag times as well as the specific method of survival analysis used., Conclusions: This methodology has the potential to be implemented in the ICU for real time prediction and can be used as a building block to expand the approach to other hospital wards or care environments., (Copyright © 2018 Elsevier Inc. All rights reserved.)
- Published
- 2018
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44. Efficient Reverse Genetic Systems for Rapid Genetic Manipulation of Emergent and Preemergent Infectious Coronaviruses.
- Author
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Cockrell AS, Beall A, Yount B, and Baric R
- Subjects
- Animals, Chlorocebus aethiops, Communicable Diseases, Emerging transmission, Communicable Diseases, Emerging virology, Coronavirus Infections transmission, DNA, Complementary, Gene Expression Regulation, Viral, Genetic Engineering, Genome, Viral, Humans, Plasmids genetics, RNA, Viral, Recombination, Genetic, Transfection, Vero Cells, Coronavirus genetics, Coronavirus Infections virology, Reverse Genetics methods
- 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.
- Published
- 2017
- Full Text
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45. Middle East Respiratory Syndrome Coronavirus NS4b Protein Inhibits Host RNase L Activation.
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Thornbrough JM, Jha BK, Yount B, Goldstein SA, Li Y, Elliott R, Sims AC, Baric RS, Silverman RH, and Weiss SR
- Subjects
- Animals, Cricetinae, Humans, Immune Evasion, Mice, Nuclear Localization Signals, Viral Nonstructural Proteins genetics, Adenine Nucleotides metabolism, Endoribonucleases antagonists & inhibitors, Host-Pathogen Interactions, Middle East Respiratory Syndrome Coronavirus physiology, Oligoribonucleotides metabolism, Viral Nonstructural Proteins metabolism
- Abstract
Unlabelled: Middle East respiratory syndrome coronavirus (MERS-CoV) is the first highly pathogenic human coronavirus to emerge since severe acute respiratory syndrome coronavirus (SARS-CoV) in 2002. Like many coronaviruses, MERS-CoV carries genes that encode multiple accessory proteins that are not required for replication of the genome but are likely involved in pathogenesis. Evasion of host innate immunity through interferon (IFN) antagonism is a critical component of viral pathogenesis. The IFN-inducible oligoadenylate synthetase (OAS)-RNase L pathway activates upon sensing of viral double-stranded RNA (dsRNA). Activated RNase L cleaves viral and host single-stranded RNA (ssRNA), which leads to translational arrest and subsequent cell death, preventing viral replication and spread. Here we report that MERS-CoV, a lineage CBetacoronavirus, and related bat CoV NS4b accessory proteins have phosphodiesterase (PDE) activity and antagonize OAS-RNase L by enzymatically degrading 2',5'-oligoadenylate (2-5A), activators of RNase L. This is a novel function for NS4b, which has previously been reported to antagonize IFN signaling. NS4b proteins are distinct from lineage ABetacoronavirusPDEs and rotavirus gene-encoded PDEs, in having an amino-terminal nuclear localization signal (NLS) and are localized mostly to the nucleus. However, the expression level of cytoplasmic MERS-CoV NS4b protein is sufficient to prevent activation of RNase L. Finally, this is the first report of an RNase L antagonist expressed by a human or bat coronavirus and provides a specific mechanism by which this occurs. Our findings provide a potential mechanism for evasion of innate immunity by MERS-CoV while also identifying a potential target for therapeutic intervention., Importance: Middle East respiratory syndrome coronavirus (MERS-CoV) is the first highly pathogenic human coronavirus to emerge since severe acute respiratory syndrome coronavirus (SARS-CoV). MERS-CoV, like other coronaviruses, carries genes that encode accessory proteins that antagonize the host antiviral response, often the type I interferon response, and contribute to virulence. We found that MERS-CoV NS4b and homologs from related lineage C bat betacoronaviruses BtCoV-SC2013 (SC2013) and BtCoV-HKU5 (HKU5) are members of the 2H-phosphoesterase (2H-PE) enzyme family with phosphodiesterase (PDE) activity. Like murine coronavirus NS2, a previously characterized PDE, MERS NS4b, can antagonize activation of the OAS-RNase L pathway, an interferon-induced potent antiviral activity. Furthermore, MERS-CoV mutants with deletion of genes encoding accessory proteins NS3 to NS5 or NS4b alone or inactivation of the PDE can activate RNase L during infection of Calu-3 cells. Our report may offer a potential target for therapeutic intervention if NS4b proves to be critical to pathogenesis inin vivomodels of MERS-CoV infection., (Copyright © 2016 Thornbrough et al.)
- Published
- 2016
- Full Text
- View/download PDF
46. Characterization of a Pathogenic Full-Length cDNA Clone and Transmission Model for Porcine Epidemic Diarrhea Virus Strain PC22A.
- Author
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Beall A, Yount B, Lin CM, Hou Y, Wang Q, Saif L, and Baric R
- Subjects
- Animals, Cloning, Molecular, Coronavirus Infections pathology, Coronavirus Infections transmission, Coronavirus Infections virology, DNA, Complementary genetics, DNA, Viral genetics, Diarrhea pathology, Diarrhea virology, Gene Deletion, Luminescent Proteins genetics, Luminescent Proteins metabolism, Recombination, Genetic, Staining and Labeling, Survival Analysis, Swine, Swine Diseases pathology, United States, Virulence, Red Fluorescent Protein, Coronavirus Infections veterinary, Porcine epidemic diarrhea virus genetics, Porcine epidemic diarrhea virus pathogenicity, Reverse Genetics methods, Swine Diseases transmission, Swine Diseases virology
- 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., (Copyright © 2016 Beall et al.)
- Published
- 2016
- Full Text
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47. A comprehensive collection of systems biology data characterizing the host response to viral infection.
- Author
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Aevermann BD, Pickett BE, Kumar S, Klem EB, Agnihothram S, Askovich PS, Bankhead A 3rd, Bolles M, Carter V, Chang J, Clauss TR, 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, and Scheuermann RH
- Subjects
- Animals, Data Collection, Databases, Factual, Humans, Influenza, Human physiopathology, Mice, Orthomyxoviridae Infections physiopathology, Systems Biology, Host-Pathogen Interactions, Influenza A virus pathogenicity, Influenza A virus physiology, Influenza, Human virology, Orthomyxoviridae Infections virology
- 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.
- Published
- 2014
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48. Characterization of blockade antibody responses in GII.2.1976 Snow Mountain virus-infected subjects.
- Author
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Swanstrom J, Lindesmith LC, Donaldson EF, Yount B, and Baric RS
- Subjects
- Animals, Antibodies, Viral immunology, Caliciviridae Infections virology, Cross Reactions, Epitopes immunology, Genotype, Humans, Mice, Neutralization Tests, Norovirus classification, Norovirus genetics, Caliciviridae Infections immunology, Norovirus immunology
- Abstract
Snow Mountain virus (GII.2.1976) is the prototype strain of GII.2 noroviruses (NoVs), which cause an estimated 8% of norovirus outbreaks, yet little is known about the immunobiology of these viruses. To define the human immune response induced by SMV infection and the antigenic relationship between different GII.2 strains that have circulated between 1976 and 2010, we developed a panel of four GII.2 variant virus-like particles (VLPs) and compared their antigenicities by enzyme immunoassay (EIA) and surrogate antibody neutralization (blockade) assays. Volunteers infected with GII.2.1976 developed a mean 167-fold increase in blockade response against the homotypic VLP by day 8 postchallenge. Blockade extended cross-genotype activity in some individuals but not cross-genogroup activity. Polyclonal sera from GII.2.1976-infected volunteers blocked GII.2.1976 significantly better than they blocked GII.2.2002, GII.2.2008, and GII.2.2010, suggesting that blockade epitopes within the GII.2 strains have evolved in the past decade. To potentially map these epitope changes, we developed mouse monoclonal antibodies (MAbs) against GII.2.1976 VLPs and compared their reactivities to a panel of norovirus VLPs. One MAb had broad cross-genogroup EIA reactivity to a nonblockade, linear, conserved epitope. Six MAbs recognized conformational epitopes exclusive to the GII.2 strains. Two MAbs recognized GII.2 blockade epitopes, and both blocked the entire panel of GII.2 variants. These data indicate that the GII.2 strains, unlike the predominant GII.4 strains, have undergone only a limited amount of evolution in blockade epitopes between 1976 and 2010 and indicate that the GII.2-protective component of a multivalent norovirus vaccine may not require frequent reformulation.
- Published
- 2014
- Full Text
- View/download PDF
49. Evidence supporting a zoonotic origin of human coronavirus strain NL63.
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Huynh J, Li S, Yount B, Smith A, Sturges L, Olsen JC, Nagel J, Johnson JB, Agnihothram S, Gates JE, Frieman MB, Baric RS, and Donaldson EF
- Subjects
- Animals, Base Sequence, Bayes Theorem, Blotting, Western, Cell Line, Computational Biology, Feces virology, Fluorescent Antibody Technique, Humans, Likelihood Functions, Maryland, Models, Genetic, Molecular Sequence Data, Sequence Analysis, DNA, Virus Replication physiology, Chiroptera virology, Coronavirus Infections transmission, Coronavirus NL63, Human genetics, Evolution, Molecular, Phylogeny, Zoonoses virology
- Abstract
The relationship between bats and coronaviruses (CoVs) has received considerable attention since the severe acute respiratory syndrome (SARS)-like CoV was identified in the Chinese horseshoe bat (Rhinolophidae) in 2005. Since then, several bats throughout the world have been shown to shed CoV sequences, and presumably CoVs, in the feces; however, no bat CoVs have been isolated from nature. Moreover, there are very few bat cell lines or reagents available for investigating CoV replication in bat cells or for isolating bat CoVs adapted to specific bat species. Here, we show by molecular clock analysis that alphacoronavirus (α-CoV) sequences derived from the North American tricolored bat (Perimyotis subflavus) are predicted to share common ancestry with human CoV (HCoV)-NL63, with the most recent common ancestor between these viruses occurring approximately 563 to 822 years ago. Further, we developed immortalized bat cell lines from the lungs of this bat species to determine if these cells were capable of supporting infection with HCoVs. While SARS-CoV, mouse-adapted SARS-CoV (MA15), and chimeric SARS-CoVs bearing the spike genes of early human strains replicated inefficiently, HCoV-NL63 replicated for multiple passages in the immortalized lung cells from this bat species. These observations support the hypothesis that human CoVs are capable of establishing zoonotic-reverse zoonotic transmission cycles that may allow some CoVs to readily circulate and exchange genetic material between strains found in bats and other mammals, including humans.
- Published
- 2012
- Full Text
- View/download PDF
50. Development and characterization of a reverse genetic system for studying dengue virus serotype 3 strain variation and neutralization.
- Author
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Messer WB, Yount B, Hacker KE, Donaldson EF, Huynh JP, de Silva AM, and Baric RS
- Subjects
- Adult, Dengue immunology, Dengue virology, Genotype, Humans, Neutralization Tests, Viral Envelope Proteins genetics, Antibodies, Neutralizing blood, Antibodies, Viral blood, Dengue Virus genetics, Dengue Virus immunology, Genetic Variation, Reverse Genetics methods, Viral Envelope Proteins immunology
- Abstract
Dengue viruses (DENV) are enveloped single-stranded positive-sense RNA viruses transmitted by Aedes spp. mosquitoes. There are four genetically distinct serotypes designated DENV-1 through DENV-4, each further subdivided into distinct genotypes. The dengue scientific community has long contended that infection with one serotype confers lifelong protection against subsequent infection with the same serotype, irrespective of virus genotype. However this hypothesis is under increased scrutiny and the role of DENV genotypic variation in protection from repeated infection is less certain. As dengue vaccine trials move increasingly into field-testing, there is an urgent need to develop tools to better define the role of genotypic variation in DENV infection and immunity. To better understand genotypic variation in DENV-3 neutralization and protection, we designed and constructed a panel of isogenic, recombinant DENV-3 infectious clones, each expressing an envelope glycoprotein from a different DENV-3 genotype; Philippines 1982 (genotype I), Thailand 1995 (genotype II), Sri Lanka 1989 and Cuba 2002 (genotype III) and Puerto Rico 1977 (genotype IV). We used the panel to explore how natural envelope variation influences DENV-polyclonal serum interactions. When the recombinant viruses were tested in neutralization assays using immune sera from primary DENV infections, neutralization titers varied by as much as ∼19-fold, depending on the expressed envelope glycoprotein. The observed variability in neutralization titers suggests that relatively few residue changes in the E glycoprotein may have significant effects on DENV specific humoral immunity and influence antibody mediated protection or disease enhancement in the setting of both natural infection and vaccination. These genotypic differences are also likely to be important in temporal and spatial microevolution of DENV-3 in the background of heterotypic neutralization. The recombinant and synthetic tools described here are valuable for testing hypotheses on genetic determinants of DENV-3 immunopathogenesis.
- Published
- 2012
- Full Text
- View/download PDF
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