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Nambulli S, Escriou N, Rennick LJ, Demers MJ, Tilston-Lunel NL, McElroy AK, Barbeau DJ, Crossland NA, Hoehl RM, Schrauf S, White AG, Borish HJ, Tomko JA, Frye LJ, Scanga CA, Flynn JL, Martin A, Gerke C, Hartman AL, Duprex WP. A measles-vectored vaccine candidate expressing prefusion-stabilized SARS-CoV-2 spike protein brought to phase I/II clinical trials: protection of African green monkeys from COVID-19 disease. J Virol 2024; 98:e0176223. [PMID: 38563762 DOI: 10.1128/jvi.01762-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 03/01/2024] [Indexed: 04/04/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged at the end of 2019 and is responsible for the largest human pandemic in 100 years. Thirty-four vaccines are currently approved for use worldwide, and approximately 67% of the world population has received a complete primary series of one, yet countries are dealing with new waves of infections, variant viruses continue to emerge, and breakthrough infections are frequent secondary to waning immunity. Here, we evaluate a measles virus (MV)-vectored vaccine expressing a stabilized prefusion SARS-CoV-2 spike (S) protein (MV-ATU3-S2PΔF2A; V591) with demonstrated immunogenicity in mouse models (see companion article [J. Brunet, Z. Choucha, M. Gransagne, H. Tabbal, M.-W. Ku et al., J Virol 98:e01693-23, 2024, https://doi.org/10.1128/jvi.01693-23]) in an established African green monkey model of disease. Animals were vaccinated with V591 or the control vaccine (an equivalent MV-vectored vaccine with an irrelevant antigen) intramuscularly using a prime/boost schedule, followed by challenge with an early pandemic isolate of SARS-CoV-2 at 56 days post-vaccination. Pre-challenge, only V591-vaccinated animals developed S-specific antibodies that had virus-neutralizing activity as well as S-specific T cells. Following the challenge, V591-vaccinated animals had lower infectious virus and viral (v) RNA loads in mucosal secretions and stopped shedding virus in these secretions earlier. vRNA loads were lower in these animals in respiratory and gastrointestinal tract tissues at necropsy. This correlated with a lower disease burden in the lungs as quantified by PET/CT at early and late time points post-challenge and by pathological analysis at necropsy.IMPORTANCESevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the largest human pandemic in 100 years. Even though vaccines are currently available, countries are dealing with new waves of infections, variant viruses continue to emerge, breakthrough infections are frequent, and vaccine hesitancy persists. This study uses a safe and effective measles vaccine as a platform for vaccination against SARS-CoV-2. The candidate vaccine was used to vaccinate African green monkeys (AGMs). All vaccinated AGMs developed robust antigen-specific immune responses. After challenge, these AGMs produced less virus in mucosal secretions, for a shorter period, and had a reduced disease burden in the lungs compared to control animals. At necropsy, lower levels of viral RNA were detected in tissue samples from vaccinated animals, and the lungs of these animals lacked the histologic hallmarks of SARS-CoV-2 disease observed exclusively in the control AGMs.
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MESH Headings
- Animals
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/genetics
- Chlorocebus aethiops
- SARS-CoV-2/immunology
- SARS-CoV-2/genetics
- COVID-19/prevention & control
- COVID-19/immunology
- COVID-19/virology
- Measles virus/immunology
- Measles virus/genetics
- COVID-19 Vaccines/immunology
- Humans
- Antibodies, Viral/immunology
- Antibodies, Viral/blood
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/blood
- Genetic Vectors
- Vero Cells
- Pandemics/prevention & control
- Female
- Betacoronavirus/immunology
- Betacoronavirus/genetics
- Pneumonia, Viral/prevention & control
- Pneumonia, Viral/virology
- Pneumonia, Viral/immunology
- Coronavirus Infections/prevention & control
- Coronavirus Infections/immunology
- Coronavirus Infections/virology
- Coronavirus Infections/veterinary
- Viral Vaccines/immunology
- Viral Vaccines/genetics
- Viral Vaccines/administration & dosage
- Disease Models, Animal
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Affiliation(s)
- Sham Nambulli
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Nicolas Escriou
- Département de Santé Globale, Institut Pasteur, Université de Paris Cite, Paris, France
| | - Linda J Rennick
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Matthew J Demers
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Natasha L Tilston-Lunel
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Anita K McElroy
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Division of Pediatric Infectious Disease, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Dominique J Barbeau
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Division of Pediatric Infectious Disease, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Nicholas A Crossland
- National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, Massachusetts, USA
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Ryan M Hoehl
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Sabrina Schrauf
- Themis Bioscience GmbH, a subsidiary of Merck & Co., Inc., Rahway, New Jersey, USA
| | - Alexander G White
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - H Jacob Borish
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Jaime A Tomko
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Lonnie J Frye
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Charles A Scanga
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - JoAnne L Flynn
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Annette Martin
- CNRS UMR3569, Génétique Moléculaire des Virus à ARN, Institut Pasteur, Université de Paris, Paris, France
| | - Christiane Gerke
- Vaccine Programs, Institut Pasteur, Université de Paris Cite, Innovation Office, Paris, France
| | - Amy L Hartman
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Infectious Diseases and Microbiology, University of Pittsburgh School of Public Health, Pittsburgh, Pennsylvania, USA
| | - W Paul Duprex
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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2
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Schmitz KS, Rennick LJ, Tilston-Lunel NL, Comvalius AD, Laksono BM, Geers D, van Run P, de Vries RD, de Swart RL, Duprex WP. Rational attenuation of canine distemper virus (CDV) to develop a morbillivirus animal model that mimics measles in humans. J Virol 2024; 98:e0185023. [PMID: 38415596 PMCID: PMC10949419 DOI: 10.1128/jvi.01850-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 02/05/2024] [Indexed: 02/29/2024] Open
Abstract
Morbilliviruses are members of the family Paramyxoviridae and are known for their ability to cause systemic disease in a variety of mammalian hosts. The prototypic morbillivirus, measles virus (MeV), infects humans and still causes morbidity and mortality in unvaccinated children and young adults. Experimental infection studies in non-human primates have contributed to the understanding of measles pathogenesis. However, ethical restrictions call for the development of new animal models. Canine distemper virus (CDV) infects a wide range of animals, including ferrets, and its pathogenesis shares many features with measles. However, wild-type CDV infection is almost always lethal, while MeV infection is usually self-limiting. Here, we made five recombinant CDVs, predicted to be attenuated, and compared their pathogenesis to the non-attenuated recombinant CDV in a ferret model. Three viruses were insufficiently attenuated based on clinical signs, fatality, and systemic infection, while one virus was too attenuated. The last candidate virus caused a self-limiting infection associated with transient viremia and viral dissemination to all lymphoid tissues, was shed transiently from the upper respiratory tract, and did not result in acute neurological signs. Additionally, an in-depth phenotyping of the infected white blood cells showed lower infection percentages in all lymphocyte subsets when compared to the non-attenuated CDV. In conclusion, infection models using this candidate virus mimic measles and can be used to study pathogenesis-related questions and to test interventions for morbilliviruses in a natural host species.IMPORTANCEMorbilliviruses are transmitted via the respiratory route but cause systemic disease. The viruses use two cellular receptors to infect myeloid, lymphoid, and epithelial cells. Measles virus (MeV) remains an important cause of morbidity and mortality in humans, requiring animal models to study pathogenesis or intervention strategies. Experimental MeV infections in non-human primates are restricted by ethical and practical constraints, and animal morbillivirus infections in natural host species have been considered as alternatives. Inoculation of ferrets with wild-type canine distemper virus (CDV) has been used for this purpose, but in most cases, the virus overwhelms the immune system and causes highly lethal disease. Introduction of an additional transcription unit and an additional attenuating point mutation in the polymerase yielded a candidate virus that caused self-limiting disease with transient viremia and virus shedding. This rationally attenuated CDV strain can be used for experimental morbillivirus infections in ferrets that reflect measles in humans.
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Affiliation(s)
| | - Linda J. Rennick
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Natasha L. Tilston-Lunel
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | | | | | - Daryl Geers
- Department of Viroscience, Erasmus MC, Rotterdam, the Netherlands
| | - Peter van Run
- Department of Viroscience, Erasmus MC, Rotterdam, the Netherlands
| | - Rory D. de Vries
- Department of Viroscience, Erasmus MC, Rotterdam, the Netherlands
| | - Rik L. de Swart
- Department of Viroscience, Erasmus MC, Rotterdam, the Netherlands
| | - W. Paul Duprex
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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3
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Rennick LJ, Duprex WP, Tilston-Lunel NL. Generation of Defective Interfering Particles of Morbilliviruses Using Reverse Genetics. Methods Mol Biol 2024; 2808:57-70. [PMID: 38743362 DOI: 10.1007/978-1-0716-3870-5_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
RNA viruses generate defective genomes naturally during virus replication. Defective genomes that interfere with the infection dynamics either through resource competition or by interferon stimulation are known as defective interfering (DI) genomes. DI genomes can be successfully packaged into virus-like-particles referred to as defective interfering particles (DIPs). Such DIPs can sustainably coexist with the full-length virus particles and have been shown to negatively impact virus replication in vitro and in vivo. Here, we describe a method to generate a clonal DI genome population by reverse genetics. This method is applicable to other RNA viruses and will enable assessment of DIPs for their antiviral properties.
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Affiliation(s)
- Linda J Rennick
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - W Paul Duprex
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
- Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Natasha L Tilston-Lunel
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, USA
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4
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Nambulli S, Xiang Y, Tilston-Lunel NL, Rennick LJ, Sang Z, Klimstra WB, Reed DS, Crossland NA, Shi Y, Duprex WP. Inhalable Nanobody (PiN-21) prevents and treats SARS-CoV-2 infections in Syrian hamsters at ultra-low doses. Sci Adv 2021; 7:eabh0319. [PMID: 34039613 PMCID: PMC8153718 DOI: 10.1126/sciadv.abh0319] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 04/05/2021] [Indexed: 05/18/2023]
Abstract
Globally, there is an urgency to develop effective, low-cost therapeutic interventions for coronavirus disease 2019 (COVID-19). We previously generated the stable and ultrapotent homotrimeric Pittsburgh inhalable Nanobody 21 (PiN-21). Using Syrian hamsters that model moderate to severe COVID-19 disease, we demonstrate the high efficacy of PiN-21 to prevent and treat SARS-CoV-2 infection. Intranasal delivery of PiN-21 at 0.6 mg/kg protects infected animals from weight loss and substantially reduces viral burdens in both lower and upper airways compared to control. Aerosol delivery of PiN-21 facilitates deposition throughout the respiratory tract and dose minimization to 0.2 mg/kg. Inhalation treatment quickly reverses animals' weight loss after infection, decreases lung viral titers by 6 logs leading to drastically mitigated lung pathology, and prevents viral pneumonia. Combined with the marked stability and low production cost, this innovative therapy may provide a convenient and cost-effective option to mitigate the ongoing pandemic.
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Affiliation(s)
- Sham Nambulli
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yufei Xiang
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Natasha L Tilston-Lunel
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Linda J Rennick
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Zhe Sang
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA
- University of Pittsburgh-Carnegie Mellon University Program in Computational Biology, Pittsburgh, PA, USA
| | - William B Klimstra
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Douglas S Reed
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Nicholas A Crossland
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Yi Shi
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA.
- University of Pittsburgh-Carnegie Mellon University Program in Computational Biology, Pittsburgh, PA, USA
| | - W Paul Duprex
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA, USA.
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, USA
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5
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Nambulli S, Xiang Y, Tilston-Lunel NL, Rennick LJ, Sang Z, Klimstra WB, Reed DS, Crossland NA, Shi Y, Duprex WP. Inhalable Nanobody (PiN-21) prevents and treats SARS-CoV-2 infections in Syrian hamsters at ultra-low doses. bioRxiv 2021. [PMID: 33655253 DOI: 10.1101/2021.02.23.432569] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Globally there is an urgency to develop effective, low-cost therapeutic interventions for coronavirus disease 2019 (COVID-19). We previously generated the stable and ultrapotent homotrimeric Pittsburgh inhalable Nanobody 21 (PiN-21). Using Syrian hamsters that model moderate to severe COVID-19 disease, we demonstrate the high efficacy of PiN-21 to prevent and treat SARS-CoV-2 infection. Intranasal delivery of PiN-21 at 0.6 mg/kg protects infected animals from weight loss and substantially reduces viral burdens in both lower and upper airways compared to control. Aerosol delivery of PiN-21 facilitates deposition throughout the respiratory tract and dose minimization to 0.2 mg/kg. Inhalation treatment quickly reverses animals' weight loss post-infection and decreases lung viral titers by 6 logs leading to drastically mitigated lung pathology and prevents viral pneumonia. Combined with the marked stability and low production cost, this novel therapy may provide a convenient and cost-effective option to mitigate the ongoing pandemic.
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6
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Klimstra WB, Tilston-Lunel NL, Nambulli S, Boslett J, McMillen CM, Gilliland T, Dunn MD, Sun C, Wheeler SE, Wells A, Hartman AL, McElroy AK, Reed DS, Rennick LJ, Duprex WP. SARS-CoV-2 growth, furin-cleavage-site adaptation and neutralization using serum from acutely infected hospitalized COVID-19 patients. J Gen Virol 2020; 101:1156-1169. [PMID: 32821033 PMCID: PMC7879561 DOI: 10.1099/jgv.0.001481] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 07/27/2020] [Indexed: 01/12/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), emerged at the end of 2019 and by mid-June 2020 the virus had spread to at least 215 countries, caused more than 8 000 000 confirmed infections and over 450 000 deaths, and overwhelmed healthcare systems worldwide. Like severe acute respiratory syndrome coronavirus (SARS-CoV), which emerged in 2002 and caused a similar disease, SARS-CoV-2 is a betacoronavirus. Both viruses use human angiotensin-converting enzyme 2 (hACE2) as a receptor to enter cells. However, the SARS-CoV-2 spike (S) glycoprotein has a novel insertion that generates a putative furin cleavage signal and this has been postulated to expand the host range. Two low-passage (P) strains of SARS-CoV-2 (Wash1 : P4 and Munich : P1) were cultured twice in Vero E6 cells and characterized virologically. Sanger and MinION sequencing demonstrated significant deletions in the furin cleavage signal of Wash1 : P6 and minor variants in the Munich : P3 strain. Cleavage of the S glycoprotein in SARS-CoV-2-infected Vero E6 cell lysates was inefficient even when an intact furin cleavage signal was present. Indirect immunofluorescence demonstrated that the S glycoprotein reached the cell surface. Since the S protein is a major antigenic target for the development of neutralizing antibodies, we investigated the development of neutralizing antibody titres in serial serum samples obtained from COVID-19 human patients. These were comparable regardless of the presence of an intact or deleted furin cleavage signal. These studies illustrate the need to characterize virus stocks meticulously prior to performing either in vitro or in vivo pathogenesis studies.
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Affiliation(s)
- William B. Klimstra
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Natasha L. Tilston-Lunel
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Sham Nambulli
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - James Boslett
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Cynthia M. McMillen
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Theron Gilliland
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Matthew D. Dunn
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Chengun Sun
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Sarah E. Wheeler
- Department of Pathology, University of Pittsburgh School of Public Health, Pittsburgh, Pennsylvania, USA
| | - Alan Wells
- Department of Pathology, University of Pittsburgh School of Public Health, Pittsburgh, Pennsylvania, USA
| | - Amy L. Hartman
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Infectious Diseases and Microbiology, University of Pittsburgh School of Public Health, Pittsburgh, Pennsylvania, USA
| | - Anita K. McElroy
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Division of Pediatric Infectious Disease, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Douglas S. Reed
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Linda J. Rennick
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - W. Paul Duprex
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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7
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Klimstra WB, Tilston-Lunel NL, Nambulli S, Boslett J, McMillen CM, Gilliland T, Dunn MD, Sun C, Wheeler SE, Wells A, Hartman AL, McElroy AK, Reed DS, Rennick LJ, Duprex WP. SARS-CoV-2 growth, furin-cleavage-site adaptation and neutralization using serum from acutely infected, hospitalized COVID-19 patients. bioRxiv 2020. [PMID: 32607507 PMCID: PMC7325173 DOI: 10.1101/2020.06.19.154930] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
SARS-CoV-2, the causative agent of COVID-19, emerged at the end of 2019 and by mid-June 2020, the virus has spread to at least 215 countries, caused more than 8,000,000 confirmed infections and over 450,000 deaths, and overwhelmed healthcare systems worldwide. Like SARS-CoV, which emerged in 2002 and caused a similar disease, SARS-CoV-2 is a betacoronavirus. Both viruses use human angiotensin-converting enzyme 2 (hACE2) as a receptor to enter cells. However, the SARS-CoV-2 spike (S) glycoprotein has a novel insertion that generates a putative furin cleavage signal and this has been postulated to expand the host range. Two low passage (P) strains of SARS-CoV-2 (Wash1: P4 and Munich: P1) were cultured twice in Vero-E6 cells and characterized virologically. Sanger and MinION sequencing demonstrated significant deletions in the furin cleavage signal of Wash1: P6 and minor variants in the Munich: P3 strain. Cleavage of the S glycoprotein in SARS-CoV-2-infected Vero-E6 cell lysates was inefficient even when an intact furin cleavage signal was present. Indirect immunofluorescence demonstrated the S glycoprotein reached the cell surface. Since the S protein is a major antigenic target for the development of neutralizing antibodies we investigated the development of neutralizing antibody titers in serial serum samples obtained from COVID-19 human patients. These were comparable regardless of the presence of an intact or deleted furin cleavage signal. These studies illustrate the need to characterize virus stocks meticulously prior to performing either in vitro or in vivo pathogenesis studies.
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Affiliation(s)
- William B Klimstra
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Natasha L Tilston-Lunel
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Sham Nambulli
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - James Boslett
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Cynthia M McMillen
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Theron Gilliland
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Matthew D Dunn
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Chengqun Sun
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Sarah E Wheeler
- Department of Pathology, University of Pittsburgh School of Public Health, Pittsburgh, Pennsylvania, USA
| | - Alan Wells
- Department of Pathology, University of Pittsburgh School of Public Health, Pittsburgh, Pennsylvania, USA
| | - Amy L Hartman
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Infectious Diseases and Microbiology, University of Pittsburgh School of Public Health, Pittsburgh, Pennsylvania, USA
| | - Anita K McElroy
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,University of Pittsburgh, Division of Pediatric Infectious Disease, Pittsburgh, Pennsylvania, USA
| | - Douglas S Reed
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Linda J Rennick
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - W Paul Duprex
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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8
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Tilston-Lunel NL, Hughes J, Acrani GO, da Silva DEA, Azevedo RSS, Rodrigues SG, Vasconcelos PFC, Nunes MRT, Elliott RM. Genetic analysis of members of the species Oropouche virus and identification of a novel M segment sequence. J Gen Virol 2015; 96:1636-50. [PMID: 25735305 PMCID: PMC4635451 DOI: 10.1099/vir.0.000108] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Oropouche virus (OROV) is a public health threat in South America, and in particular in northern Brazil, causing frequent outbreaks of febrile illness. Using a combination of deep sequencing and Sanger sequencing approaches, we determined the complete genome sequences of eight clinical isolates that were obtained from patient sera during an Oropouche fever outbreak in Amapa state, northern Brazil, in 2009. We also report the complete genome sequences of two OROV reassortants isolatd from two marmosets in Minas Gerais state, south-east Brazil, in 2012 that contained a novel M genome segment. Interestingly, all 10 isolates possessed a 947 nt S segment that lacked 11 residues in the S-segment 3′ UTR compared with the recently redetermined Brazilian prototype OROV strain BeAn19991. OROV maybe circulating more widely in Brazil and in the non-human primate population than previously appreciated, and the identification of yet another reassortant highlights the importance of bunyavirus surveillance in South America.
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Affiliation(s)
- Natasha L Tilston-Lunel
- 1MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow G61 1QH, Scotland, UK 2Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews KY16 9ST, Scotland, UK
| | - Joseph Hughes
- 1MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow G61 1QH, Scotland, UK
| | - Gustavo Olszanski Acrani
- 1MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow G61 1QH, Scotland, UK 3Department of Cell and Molecular Biology, University of Sao Paulo School of Medicine, 3900, Av Bandeirantes, Ribeirão Preto, SP 14049-900, Brazil
| | - Daisy E A da Silva
- 4Center for Technological Innovation, Instituto Evandro Chagas, Ananindeua, Brazil
| | - Raimunda S S Azevedo
- 5Department of Arbovirology and Hemorrhagic Fevers, Instituto Evandro Chagas, Ananindeua, Brazil
| | - Sueli G Rodrigues
- 5Department of Arbovirology and Hemorrhagic Fevers, Instituto Evandro Chagas, Ananindeua, Brazil
| | - Pedro F C Vasconcelos
- 5Department of Arbovirology and Hemorrhagic Fevers, Instituto Evandro Chagas, Ananindeua, Brazil
| | - Marcio R T Nunes
- 4Center for Technological Innovation, Instituto Evandro Chagas, Ananindeua, Brazil
| | - Richard M Elliott
- 1MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow G61 1QH, Scotland, UK
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Acrani GO, Tilston-Lunel NL, Spiegel M, Weidmann M, Dilcher M, Andrade da Silva DE, Nunes MRT, Elliott RM. Establishment of a minigenome system for Oropouche virus reveals the S genome segment to be significantly longer than reported previously. J Gen Virol 2014; 96:513-523. [PMID: 25491420 DOI: 10.1099/jgv.0.000005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Oropouche virus (OROV) is a medically important orthobunyavirus, which causes frequent outbreaks of a febrile illness in the northern parts of Brazil. However, despite being the cause of an estimated half a million human infections since its first isolation in Trinidad in 1955, details of the molecular biology of this tripartite, negative-sense RNA virus remain limited. We have determined the complete nucleotide sequence of the Brazilian prototype strain of OROV, BeAn 19991, and found a number of differences compared with sequences in the database. Most notable were that the S segment contained an additional 204 nt at the 3' end and that there was a critical nucleotide mismatch at position 9 within the base-paired terminal panhandle structure of each genome segment. In addition, we obtained the complete sequence of the Trinidadian prototype strain TRVL-9760 that showed similar characteristics to the BeAn 19991 strain. By using a T7 RNA polymerase-driven minigenome system, we demonstrated that cDNA clones of the BeAn 19991 L and S segments expressed functional proteins, and also that the newly determined terminal untranslated sequences acted as functional promoters in the minigenome assay. By co-transfecting a cDNA to the viral glycoproteins, virus-like particles were generated that packaged a minigenome and were capable of infecting naive cells.
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Affiliation(s)
- Gustavo Olszanski Acrani
- Department of Cell and Molecular Biology, University of Sao Paulo School of Medicine, 3900, Av. Bandeirantes, Ribeirão Preto, SP 14049-900, Brazil.,MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow G61 1QH, Scotland, UK
| | - Natasha L Tilston-Lunel
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews KY16 9ST, Scotland, UK.,MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow G61 1QH, Scotland, UK
| | - Martin Spiegel
- Department of Virology, University Medical Center Göttingen, Kreuzbergring 57, 37075 Göttingen, Germany
| | - Manfred Weidmann
- Department of Virology, University Medical Center Göttingen, Kreuzbergring 57, 37075 Göttingen, Germany
| | - Meik Dilcher
- Department of Virology, University Medical Center Göttingen, Kreuzbergring 57, 37075 Göttingen, Germany
| | | | - Marcio R T Nunes
- Center for Technological Innovation, Instituto Evandro Chagas, Ananindeua, Brazil
| | - Richard M Elliott
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow G61 1QH, Scotland, UK
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10
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James JN, Hasan ZU, Ioerger TR, Brown AC, Personne Y, Carroll P, Ikeh M, Tilston-Lunel NL, Palavecino C, Sacchettini JC, Parish T. Deletion of SenX3-RegX3, a key two-component regulatory system of Mycobacterium smegmatis, results in growth defects under phosphate-limiting conditions. Microbiology (Reading) 2012; 158:2724-2731. [PMID: 22956756 DOI: 10.1099/mic.0.060319-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Two component regulatory systems are key elements in the control of bacterial gene expression in response to environmental perturbations. The SenX3-RegX3 system is implicated in the control of phosphate uptake in Mycobacterium smegmatis and Mycobacterium tuberculosis. regX3 is reported to be essential in M. smegmatis, but not in M. tuberculosis. We attempted to construct complete senX3-regX3 operon deletion strains of M. smegmatis; initially we found that the operon could only be deleted when another functional copy was provided. Using a strain in which the only functional copy of the operon was present on an integrating plasmid, we attempted to replace the functional copy with an empty vector. Surprisingly, we obtained strains in which the functional copy had been deleted from the chromosome at a low frequency. We deleted the senX3 gene in a similar fashion, but it was not possible to delete regX3 alone. To identify possible compensatory mutations we sequenced the whole genome of two deletion strains and the wild-type. A synonymous single nucleotide polymorphism (SNP) in a lipoprotein was found in all deletion strains, but not the parental strains, and a frameshift mutation in nhaA was identified in three of the four deletion strains. Operon deletion strains were more sensitive to phosphate limitation, showing a reduced ability to grow at lower phosphate concentrations. The M. tuberculosis operon was able to functionally complement the growth phenotype in M. smegmatis under phosphate-replete conditions, but not under low phosphate conditions, reinforcing the difference between the two species. Our data show that, in contrast with previous reports, it is possible to delete the operon in M. smegmatis, possibly due to the accumulation of compensatory mutations, and that the deletion does affect growth in phosphate.
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Affiliation(s)
- Jade N James
- Queen Mary University of London, Barts and the London, London, UK
| | | | - Thomas R Ioerger
- Department of Computer Science and Engineering, Texas A&M University, College Station, TX, USA
| | - Amanda C Brown
- Queen Mary University of London, Barts and the London, London, UK
| | - Yoann Personne
- Queen Mary University of London, Barts and the London, London, UK
| | - Paul Carroll
- Queen Mary University of London, Barts and the London, London, UK
| | - Melanie Ikeh
- Queen Mary University of London, Barts and the London, London, UK
| | | | | | - James C Sacchettini
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | - Tanya Parish
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, USA.,Queen Mary University of London, Barts and the London, London, UK
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