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Quantifying dose-, strain-, and tissue-specific kinetics of parainfluenza virus infection. PLoS Comput Biol 2021; 17:e1009299. [PMID: 34383757 PMCID: PMC8384156 DOI: 10.1371/journal.pcbi.1009299] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 08/24/2021] [Accepted: 07/23/2021] [Indexed: 11/25/2022] Open
Abstract
Human parainfluenza viruses (HPIVs) are a leading cause of acute respiratory infection hospitalization in children, yet little is known about how dose, strain, tissue tropism, and individual heterogeneity affects the processes driving growth and clearance kinetics. Longitudinal measurements are possible by using reporter Sendai viruses, the murine counterpart of HPIV 1, that express luciferase, where the insertion location yields a wild-type (rSeV-luc(M-F*)) or attenuated (rSeV-luc(P-M)) phenotype. Bioluminescence from individual animals suggests that there is a rapid increase in expression followed by a peak, biphasic clearance, and resolution. However, these kinetics vary between individuals and with dose, strain, and whether the infection was initiated in the upper and/or lower respiratory tract. To quantify the differences, we translated the bioluminescence measurements from the nasopharynx, trachea, and lung into viral loads and used a mathematical model together a nonlinear mixed effects approach to define the mechanisms distinguishing each scenario. The results confirmed a higher rate of virus production with the rSeV-luc(M-F*) virus compared to its attenuated counterpart, and suggested that low doses result in disproportionately fewer infected cells. The analyses indicated faster infectivity and infected cell clearance rates in the lung and that higher viral doses, and concomitantly higher infected cell numbers, resulted in more rapid clearance. This parameter was also highly variable amongst individuals, which was particularly evident during infection in the lung. These critical differences provide important insight into distinct HPIV dynamics, and show how bioluminescence data can be combined with quantitative analyses to dissect host-, virus-, and dose-dependent effects. Human parainfluenza viruses (HPIVs) cause acute respiratory infections and can lead to the hospitalization of children. HPIV infection severity may vary due to dose, strain, patient, and whether the infection initiates within the upper or lower respiratory tract. There is a need to determine how the rates of virus spread and clearance change in different infection scenarios in order to better understand varying clinical manifestations. The significance of our research is in identifying the dominant mechanisms driving strain-, dose-, and tissue-specific HPIV infection kinetics, and in pairing bioluminescence data with quantitative analyses to determine how the same virus can yield patient-specific outcomes. This work enhances our understanding of HPIV infection and broadens our knowledge viral dynamics in the upper and lower respiratory tracts.
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Cox RM, Sourimant J, Toots M, Yoon JJ, Ikegame S, Govindarajan M, Watkinson RE, Thibault P, Makhsous N, Lin MJ, Marengo JR, Sticher Z, Kolykhalov AA, Natchus MG, Greninger AL, Lee B, Plemper RK. Orally efficacious broad-spectrum allosteric inhibitor of paramyxovirus polymerase. Nat Microbiol 2020; 5:1232-1246. [PMID: 32661315 PMCID: PMC7529989 DOI: 10.1038/s41564-020-0752-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 06/09/2020] [Indexed: 12/13/2022]
Abstract
Paramyxoviruses such as human parainfluenza virus type-3 (HPIV3) and measles virus (MeV) are a substantial health threat. In a high-throughput screen for inhibitors of HPIV3 (a major cause of acute respiratory infection), we identified GHP-88309-a non-nucleoside inhibitor of viral polymerase activity that possesses unusual broad-spectrum activity against diverse paramyxoviruses including respiroviruses (that is, HPIV1 and HPIV3) and morbilliviruses (that is, MeV). Resistance profiles of distinct target viruses overlapped spatially, revealing a conserved binding site in the central cavity of the viral polymerase (L) protein that was validated by photoaffinity labelling-based target mapping. Mechanistic characterization through viral RNA profiling and in vitro MeV polymerase assays identified a block in the initiation phase of the viral polymerase. GHP-88309 showed nanomolar potency against HPIV3 isolates in well-differentiated human airway organoid cultures, was well tolerated (selectivity index > 7,111) and orally bioavailable, and provided complete protection against lethal infection in a Sendai virus mouse surrogate model of human HPIV3 disease when administered therapeutically 48 h after infection. Recoverees had acquired robust immunoprotection against reinfection, and viral resistance coincided with severe attenuation. This study provides proof of the feasibility of a well-behaved broad-spectrum allosteric antiviral and describes a chemotype with high therapeutic potential that addresses major obstacles of anti-paramyxovirus drug development.
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Affiliation(s)
- Robert M Cox
- Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Julien Sourimant
- Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Mart Toots
- Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Jeong-Joong Yoon
- Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Satoshi Ikegame
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Ruth E Watkinson
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Patricia Thibault
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Negar Makhsous
- Virology Division, Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Michelle J Lin
- Virology Division, Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Jose R Marengo
- Emory Institute for Drug Development, Emory University, Atlanta, GA, USA
| | - Zachary Sticher
- Emory Institute for Drug Development, Emory University, Atlanta, GA, USA
| | | | - Michael G Natchus
- Emory Institute for Drug Development, Emory University, Atlanta, GA, USA
| | - Alexander L Greninger
- Virology Division, Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Benhur Lee
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Richard K Plemper
- Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA.
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Rajaram S, Canaday LM, Ochayon DE, Rangel KM, Ali A, Gyurova IE, Krishnamurthy D, Fletcher JS, Reighard SD, Cox A, Weirauch MT, Kottyan LC, Deshmukh H, Zacharias WJ, Borchers MT, Waggoner SN. The Promise and Peril of Natural Killer Cell Therapies in Pulmonary Infection. Immunity 2020; 52:887-889. [PMID: 32405233 PMCID: PMC7219410 DOI: 10.1016/j.immuni.2020.04.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 04/23/2020] [Accepted: 04/24/2020] [Indexed: 02/06/2023]
Affiliation(s)
- Sanjeeth Rajaram
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Medical Sciences Undergraduate Program, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Laura M Canaday
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Immunology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - David E Ochayon
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kelly M Rangel
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Biomedical Research Technologies Program, University of Cincinnati College of Medicine, Cincinnati, OH, USA; Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Ayad Ali
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Immunology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH, USA; Medical Scientist Training Program, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Ivayla E Gyurova
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Pathobiology and Molecular Medicine Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Durga Krishnamurthy
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Jonathan S Fletcher
- Medical Scientist Training Program, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Seth D Reighard
- Medical Scientist Training Program, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Andrew Cox
- Department of Pediatrics, Pediatric Residency, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Immunology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH, USA; Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Leah C Kottyan
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Immunology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH, USA; Medical Scientist Training Program, University of Cincinnati College of Medicine, Cincinnati, OH, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA; Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Hitesh Deshmukh
- Immunology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH, USA; Medical Scientist Training Program, University of Cincinnati College of Medicine, Cincinnati, OH, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA; Division of Neonatology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Division of Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - William J Zacharias
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Medical Scientist Training Program, University of Cincinnati College of Medicine, Cincinnati, OH, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA; Division of Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Department of Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, USA; Department of Internal Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Michael T Borchers
- Department of Internal Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, USA; Cincinnati Veteran's Affairs Medical Center, Cincinnati, OH, USA
| | - Stephen N Waggoner
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Immunology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH, USA; Medical Scientist Training Program, University of Cincinnati College of Medicine, Cincinnati, OH, USA; Pathobiology and Molecular Medicine Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
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Masselli E, Vaccarezza M, Carubbi C, Pozzi G, Presta V, Mirandola P, Vitale M. NK cells: A double edge sword against SARS-CoV-2. Adv Biol Regul 2020; 77:100737. [PMID: 32773100 PMCID: PMC7292949 DOI: 10.1016/j.jbior.2020.100737] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 06/04/2020] [Indexed: 02/06/2023]
Abstract
Natural killer (NK) cells are pivotal effectors of the innate immunity protecting an individual from microbes. They are the first line of defense against invading viruses, given their substantial ability to directly target infected cells without the need for specific antigen presentation. By establishing cellular networks with a variety of cell types such as dendritic cells, NK cells can also amplify and modulate antiviral adaptive immune responses. In this review, we will examine the role of NK cells in SARS-COV2 infections causing the ongoing COVID19 pandemic, keeping in mind the controversial role of NK cells specifically in viral respiratory infections and in inflammatory-driven lung damage. We discuss lessons learnt from previous coronavirus outbreaks in humans (caused by SARS-CoV-1 and MERS-COV).
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Affiliation(s)
- Elena Masselli
- Department of Medicine and Surgery, Anatomy Unit, University of Parma, Via Gramsci 14, 43126, Parma, Italy; University Hospital of Parma, AOU-PR, Via Gramsci 14, 43126, Parma, Italy
| | - Mauro Vaccarezza
- School of Pharmacy and Biomedical Sciences, Faculty of Health Sciences, Curtin University, Bentley, Perth, WA, 6102, Australia
| | - Cecilia Carubbi
- Department of Medicine and Surgery, Anatomy Unit, University of Parma, Via Gramsci 14, 43126, Parma, Italy
| | - Giulia Pozzi
- Department of Medicine and Surgery, Anatomy Unit, University of Parma, Via Gramsci 14, 43126, Parma, Italy
| | - Valentina Presta
- Department of Medicine and Surgery, Anatomy Unit, University of Parma, Via Gramsci 14, 43126, Parma, Italy
| | - Prisco Mirandola
- Department of Medicine and Surgery, Anatomy Unit, University of Parma, Via Gramsci 14, 43126, Parma, Italy.
| | - Marco Vitale
- Department of Medicine and Surgery, Anatomy Unit, University of Parma, Via Gramsci 14, 43126, Parma, Italy; University Hospital of Parma, AOU-PR, Via Gramsci 14, 43126, Parma, Italy.
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Directed Evolution of an Influenza Reporter Virus To Restore Replication and Virulence and Enhance Noninvasive Bioluminescence Imaging in Mice. J Virol 2018; 92:JVI.00593-18. [PMID: 29899096 DOI: 10.1128/jvi.00593-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 06/06/2018] [Indexed: 02/06/2023] Open
Abstract
Reporter viruses provide a powerful tool to study infection, yet incorporating a nonessential gene often results in virus attenuation and genetic instability. Here, we used directed evolution of a luciferase-expressing pandemic H1N1 (pH1N1) 2009 influenza A virus in mice to restore replication kinetics and virulence, increase the bioluminescence signal, and maintain reporter gene expression. An unadapted pH1N1 virus with NanoLuc luciferase inserted into the 5' end of the PA gene segment grew to titers 10-fold less than those of the wild type in MDCK cells and in DBA/2 mice and was less virulent. For 12 rounds, we propagated DBA/2 lung samples with the highest bioluminescence-to-titer ratios. Every three rounds, we compared in vivo replication, weight loss, mortality, and bioluminescence. Mouse-adapted virus after 9 rounds (MA-9) had the highest relative bioluminescence signal and had wild-type-like fitness and virulence in DBA/2 mice. Using reverse genetics, we discovered fitness was restored in virus rPB2-MA9/PA-D479N by a combination of PA-D479N and PB2-E158G amino acid mutations and PB2 noncoding mutations C1161T and C1977T. rPB2-MA9/PA-D479N has increased mRNA transcription, which helps restore wild-type-like phenotypes in DBA/2 and BALB/c mice. Overall, the results demonstrate that directed evolution that maximizes foreign-gene expression while maintaining genetic stability is an effective method to restore wild-type-like in vivo fitness of a reporter virus. Virus rPB2-MA9/PA-D479N is expected to be a useful tool for noninvasive imaging of pH1N1 influenza virus infection and clearance while analyzing virus-host interactions and developing new therapeutics and vaccines.IMPORTANCE Influenza viruses contribute to 290,000 to 650,000 deaths globally each year. Infection is studied in mice to learn how the virus causes sickness and to develop new drugs and vaccines. During experiments, scientists have needed to euthanize groups of mice at different times to measure the amount of infectious virus in mouse tissues. By inserting a foreign gene that causes infected cells to light up, scientists could see infection spread in living mice. Unfortunately, adding an extra gene not needed by the virus slowed it down and made it weaker. Here, we used a new strategy to restore the fitness and lethality of an influenza reporter virus; we adapted it to mouse lungs and selected for variants that had the greatest light signal. The adapted virus can be used to study influenza virus infection, immunology, and disease in living mice. The strategy can also be used to adapt other viruses.
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