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Basu S, Kayal T, Patro PP, Patnaik A. JN.1: ongoing considerations of the shifting landscape of SARS-CoV-2 variants. Future Microbiol 2024; 19:559-562. [PMID: 38629923 DOI: 10.2217/fmb-2024-0010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 02/26/2024] [Indexed: 07/04/2024] Open
Affiliation(s)
- Soumya Basu
- Molecular Biotechnology Laboratory, Department of Biotechnology, NIST University, Berhampur, Odisha, 761008, India
| | - Titirsha Kayal
- Department of Microbiology, Indira Gandhi Government Medical College & Hospital (IGGMC&H), Nagpur, Maharashtra, 440018, India
| | - Ponoop Prasad Patro
- Molecular Biotechnology Laboratory, Department of Biotechnology, NIST University, Berhampur, Odisha, 761008, India
| | - Amit Patnaik
- Molecular Biotechnology Laboratory, Department of Biotechnology, NIST University, Berhampur, Odisha, 761008, India
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2
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Hsieh MK, Klauda JB. Multiscale Molecular Dynamics Simulations of the Homodimer Accessory Protein ORF7b of SARS-CoV-2. J Phys Chem B 2024; 128:150-162. [PMID: 38147592 DOI: 10.1021/acs.jpcb.3c07105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2023]
Abstract
The SARS-CoV-2 ORF7b protein has drawn attention for its potential role in viral pathogenesis, but its structural details and lateral membrane associations remain elusive. In this study, we conducted multiscale molecular dynamics simulations to provide detailed molecular insights of the protein's dimerization, which is crucial for unraveling its structural model of protein-protein interface important to regulating cellular immune response. To gain a deeper understanding of homodimer configurations, we employed a machine learning algorithm for structural-based clustering. Clusters were categorized into three distinct groups for both parallel and antiparallel orientations, highlighting the influence of the initial monomer conformation on dimer configurations. Analysis of hydrogen bonding and π-π and π-cation stacking interactions within clusters revealed variations in interactions between clusters. In parallel dimers, weak stacking interactions in the transmembrane (TM) region were observed. In contrast, antiparallel dimers exhibited strong hydrogen bonding and stacking interactions contributing to tight dimeric packing, both within and outside the TM domain. Overall, our study provides a comprehensive view of the structural dynamics of ORF7b homodimerization in both parallel and antiparallel orientations. These findings shed light on the molecular interactions involved in ORF7b dimerization, which are crucial for understanding its potential roles in SARS-CoV-2 pathogenesis. This knowledge could inform future research and therapeutic strategies targeting this viral protein.
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Affiliation(s)
- Min-Kang Hsieh
- Department of Chemical and Biomolecular Engineering, University of Maryland College Park, College Park, Maryland 20742, United States
| | - Jeffery B Klauda
- Department of Chemical and Biomolecular Engineering, University of Maryland College Park, College Park, Maryland 20742, United States
- Institute for Physical Science and Technology, Biophysics Program, University of Maryland College Park, College Park, Maryland 20742, United States
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3
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Stewart H, Lu Y, O’Keefe S, Valpadashi A, Cruz-Zaragoza LD, Michel HA, Nguyen SK, Carnell GW, Lukhovitskaya N, Milligan R, Adewusi Y, Jungreis I, Lulla V, Matthews DA, High S, Rehling P, Emmott E, Heeney JL, Davidson AD, Edgar JR, Smith GL, Firth AE. The SARS-CoV-2 protein ORF3c is a mitochondrial modulator of innate immunity. iScience 2023; 26:108080. [PMID: 37860693 PMCID: PMC10583119 DOI: 10.1016/j.isci.2023.108080] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 08/06/2023] [Accepted: 09/25/2023] [Indexed: 10/21/2023] Open
Abstract
The SARS-CoV-2 genome encodes a multitude of accessory proteins. Using comparative genomic approaches, an additional accessory protein, ORF3c, has been predicted to be encoded within the ORF3a sgmRNA. Expression of ORF3c during infection has been confirmed independently by ribosome profiling. Despite ORF3c also being present in the 2002-2003 SARS-CoV, its function has remained unexplored. Here we show that ORF3c localizes to mitochondria, where it inhibits innate immunity by restricting IFN-β production, but not NF-κB activation or JAK-STAT signaling downstream of type I IFN stimulation. We find that ORF3c is inhibitory after stimulation with cytoplasmic RNA helicases RIG-I or MDA5 or adaptor protein MAVS, but not after TRIF, TBK1 or phospho-IRF3 stimulation. ORF3c co-immunoprecipitates with the antiviral proteins MAVS and PGAM5 and induces MAVS cleavage by caspase-3. Together, these data provide insight into an uncharacterized mechanism of innate immune evasion by this important human pathogen.
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Affiliation(s)
- Hazel Stewart
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Yongxu Lu
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Sarah O’Keefe
- Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, Manchester, UK
| | - Anusha Valpadashi
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | | | | | | | - George W. Carnell
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | | | - Rachel Milligan
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, Bristol, UK
| | - Yasmin Adewusi
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Irwin Jungreis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA
| | - Valeria Lulla
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - David A. Matthews
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, Bristol, UK
| | - Stephen High
- Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, Manchester, UK
| | - Peter Rehling
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Edward Emmott
- Centre for Proteome Research, Department of Biochemistry & Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Jonathan L. Heeney
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Andrew D. Davidson
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, Bristol, UK
| | - James R. Edgar
- Department of Pathology, University of Cambridge, Cambridge, UK
| | | | - Andrew E. Firth
- Department of Pathology, University of Cambridge, Cambridge, UK
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4
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Daniels A, Fletcher S, Kerr HEM, Kratzel A, Pinto RM, Kriplani N, Craig N, Hastie CJ, Davies P, Digard P, Thiel V, Tait-Burkard C. One for all-human kidney Caki-1 cells are highly susceptible to infection with corona- and other respiratory viruses. J Virol 2023; 97:e0055523. [PMID: 37668370 PMCID: PMC10537734 DOI: 10.1128/jvi.00555-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 07/05/2023] [Indexed: 09/06/2023] Open
Abstract
In vitro investigations of host-virus interactions are reliant on suitable cell and tissue culture models. Results are only as good as the model they are generated in. However, choosing cell models for in vitro work often depends on availability and previous use alone. Despite the vast increase in coronavirus research over the past few years, scientists are still heavily reliant on: non-human, highly heterogeneous or not fully differentiated, or naturally unsusceptible cells requiring overexpression of receptors and other accessory factors. Complex primary or stem cell models are highly representative of human tissues but are expensive and time-consuming to develop and maintain with limited suitability for high-throughput experiments.Using tissue-specific expression patterns, we identified human kidney cells as an ideal target for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and broader coronavirus infection. We show the use of the well-characterized human kidney cell line Caki-1 for infection with three human coronaviruses (hCoVs): Betacoronaviruses SARS-CoV-2 and Middle Eastern respiratory syndrome coronavirus and Alphacoronavirus hCoV 229E. Caki-1 cells show equal or superior susceptibility to all three coronaviruses when compared to other commonly used cell lines for the cultivation of the respective virus. Antibody staining against SARS-CoV-2 N protein shows comparable replication rates. A panel of 26 custom antibodies shows the location of SARS-CoV-2 proteins during replication using immunocytochemistry. In addition, Caki-1 cells were found to be susceptible to two other human respiratory viruses, influenza A virus and respiratory syncytial virus, making them an ideal model for cross-comparison for a broad range of respiratory viruses. IMPORTANCE Cell lines remain the backbone of virus research, but results are only as good as their originating model. Despite increased research into human coronaviruses following the COVID-19 pandemic, researchers continue to rely on suboptimal cell line models of: non-human origin, incomplete differentiation, or lacking active interferon responses. We identified the human kidney Caki-1 cell line as a potential target for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). This cell line could be shown to be infectable with a wide range of coronaviruses including common cold virus hCoV-229E, epidemic virus MERS-CoV, and SARS-CoV-2 as well as other important respiratory viruses influenza A virus and respiratory syncytial virus. We could show the localization of 26 SARS-CoV-2 proteins in Caki-1 cells during natural replication and the cells are competent of forming a cellular immune response. Together, this makes Caki-1 cells a unique tool for cross-virus comparison in one cell line.
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Affiliation(s)
- Alison Daniels
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
- Infection Medicine, University of Edinburgh, Little France Crescent, United Kingdom
| | - Sarah Fletcher
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Holly E. M. Kerr
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Annika Kratzel
- Institute of Virology and Immunology (IVI), Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Rute Maria Pinto
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Nisha Kriplani
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Nicky Craig
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - C. James Hastie
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Paul Davies
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Paul Digard
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Volker Thiel
- Institute of Virology and Immunology (IVI), Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Christine Tait-Burkard
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
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5
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Emslander Q, Krey K, Hamad S, Maidl S, Oubraham L, Hesse J, Henrici A, Austen K, Mergner J, Grass V, Pichlmair A. MDM2 Influences ACE2 Stability and SARS-CoV-2 Uptake. Viruses 2023; 15:1763. [PMID: 37632105 PMCID: PMC10459000 DOI: 10.3390/v15081763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/20/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
Angiotensin-converting enzyme 2 (ACE2) is the central entry receptor for SARS-CoV-2. However, surprisingly little is known about the effects of host regulators on ACE2 localization, expression, and the associated influence on SARS-CoV-2 infection. Here we identify that ACE2 expression levels are regulated by the E3 ligase MDM2 and that MDM2 levels indirectly influence infection with SARS-CoV-2. Genetic depletion of MDM2 elevated ACE2 expression levels, which strongly promoted infection with all SARS-CoV-2 isolates tested. SARS-CoV-2 spike-pseudotyped viruses and the uptake of non-replication-competent virus-like particles showed that MDM2 affects the viral uptake process. MDM2 ubiquitinates Lysine 788 of ACE2 to induce proteasomal degradation, and degradation of this residue led to higher ACE2 expression levels and superior virus particle uptake. Our study illustrates that cellular regulators of ACE2 stability, such as MDM2, play an important role in defining the infection capabilities of SARS-CoV-2.
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Affiliation(s)
- Quirin Emslander
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany (S.H.)
| | - Karsten Krey
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany (S.H.)
| | - Sabri Hamad
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany (S.H.)
| | - Susanne Maidl
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany (S.H.)
| | - Lila Oubraham
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany (S.H.)
| | - Joshua Hesse
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany (S.H.)
| | - Alexander Henrici
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany (S.H.)
| | - Katharina Austen
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany (S.H.)
| | - Julia Mergner
- BayBioMS@MRI—Bavarian Center for Biomolecular Mass Spectrometry at Klinikum Rechts der Isar, Technical University of Munich, 81675 Munich, Germany
| | - Vincent Grass
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany (S.H.)
| | - Andreas Pichlmair
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany (S.H.)
- German Centre for Infection Research (DZIF), Partner site Munich, 81675 Munich, Germany
- Center of Immunology of Viral Infection (CiViA), Aarhus University, 8000 Aarhus, Denmark
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6
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Carrera JM, Aktepe TE, Earnest L, Christiansen D, Wheatley AK, Tan HX, Chung AW, Collett S, McPherson K, Torresi J, Mackenzie JM, Simmons CP. Adenovirus vector produced Zika virus-like particles induce a long-lived neutralising antibody response in mice. Vaccine 2023:S0264-410X(23)00757-0. [PMID: 37391311 DOI: 10.1016/j.vaccine.2023.06.068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 06/18/2023] [Accepted: 06/21/2023] [Indexed: 07/02/2023]
Abstract
Countermeasures against Zika virus (ZIKV) epidemics are urgently needed. In this study we generated a ZIKV virus-like particle (VLP) based vaccine candidate and assessed the immunogenicity of these particles in mice. The ZIKV-VLPs were morphologically similar to ZIKV by electron microscopy and were recognized by anti-Flavivirus neutralising antibodies. We observed that a single dose of unadjuvanted ZIKV-VLPs, or inactivated ZIKV, generated an immune response that lasted over 6 months, but did not neutralize ZIKV infection of cells in vitro. However, when we co-administered the ZIKV VLPs with either Aluminium hydroxide (Alhydrogel®; Alum), AddaVax or Pam2Cys we observed that Alum was the most effective in a single dose regime, since it not only produced antibodies that neutralized the virus, but also generated a greater number of antigen-specific memory B cells. We additionally observed that the generation of the neutralising antibodies persisted for up to 6 months. Our results suggest that a single dose ZIKV VLPs could be a suitable single dose vaccine candidate for use in outbreak settings.
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Affiliation(s)
- Julio M Carrera
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty for Infection and Immunity, Parkville, Melbourne, VIC 3010, Australia; Institute of Vector-Borne Diseases, Monash University, Clayton, VIC 3800, Australia
| | - Turgut E Aktepe
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty for Infection and Immunity, Parkville, Melbourne, VIC 3010, Australia
| | - Linda Earnest
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty for Infection and Immunity, Parkville, Melbourne, VIC 3010, Australia
| | - Dale Christiansen
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty for Infection and Immunity, Parkville, Melbourne, VIC 3010, Australia
| | - Adam K Wheatley
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty for Infection and Immunity, Parkville, Melbourne, VIC 3010, Australia
| | - Hyon-Xhi Tan
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty for Infection and Immunity, Parkville, Melbourne, VIC 3010, Australia
| | - Amy W Chung
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty for Infection and Immunity, Parkville, Melbourne, VIC 3010, Australia
| | - Simon Collett
- School of Science, College of Science, Engineering and Health, RMIT University, Melbourne, VIC 3000, Australia
| | - Kirsty McPherson
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty for Infection and Immunity, Parkville, Melbourne, VIC 3010, Australia
| | - Joseph Torresi
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty for Infection and Immunity, Parkville, Melbourne, VIC 3010, Australia
| | - Jason M Mackenzie
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty for Infection and Immunity, Parkville, Melbourne, VIC 3010, Australia.
| | - Cameron P Simmons
- Institute of Vector-Borne Diseases, Monash University, Clayton, VIC 3800, Australia.
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7
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Si F, Song S, Yu R, Li Z, Wei W, Wu C. Coronavirus accessory protein ORF3 biology and its contribution to viral behavior and pathogenesis. iScience 2023; 26:106280. [PMID: 36945252 PMCID: PMC9972675 DOI: 10.1016/j.isci.2023.106280] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023] Open
Abstract
Coronavirus porcine epidemic diarrhea virus (PEDV) is classified in the genus Alphacoronavirus, family Coronaviridae that encodes the only accessory protein, ORF3 protein. However, how ORF3 contributes to viral pathogenicity, adaptability, and replication is obscure. In this review, we summarize current knowledge and identify gaps in many aspects of ORF3 protein in PEDV, with emphasis on its unique biological features, including membrane topology, Golgi retention mechanism, potential intrinsic disordered property, functional motifs, protein glycosylation, and codon usage phenotypes related to genetic evolution and gene expression. In addition, we propose intriguing questions related to ORF3 protein that we hope to stimulate further studies and encourage collaboration among virologists worldwide to provide constructive knowledge about the unique characteristics and biological functions of ORF3 protein, by which their potential role in clarifying viral behavior and pathogenesis can be possible.
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Affiliation(s)
- Fusheng Si
- Institute of Animal Science and Veterinary Medicine, Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai Engineering Research Center of Breeding Pig, Shanghai 201106, P.R. China
| | - Shuai Song
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture of Rural Affairs, and Key Laboratory of Animal Disease Prevention of Guangdong Province, Guangzhou 510640, P.R. China
| | - Ruisong Yu
- Institute of Animal Science and Veterinary Medicine, Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai Engineering Research Center of Breeding Pig, Shanghai 201106, P.R. China
| | - Zhen Li
- Institute of Animal Science and Veterinary Medicine, Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai Engineering Research Center of Breeding Pig, Shanghai 201106, P.R. China
| | - Wenqiang Wei
- Department of Microbiology, School of Basic Medical Sciences, Henan University, Kaifeng, Henan 475004, P.R. China
| | - Chao Wu
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO 63110, USA
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8
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Pisanic N, Antar AAR, Kruczynski KL, Gregory Rivera M, Dhakal S, Spicer K, Randad PR, Pekosz A, Klein SL, Betenbaugh MJ, Detrick B, Clarke W, Thomas DL, Manabe YC, Heaney CD. Methodological approaches to optimize multiplex oral fluid SARS-CoV-2 IgG assay performance and correlation with serologic and neutralizing antibody responses. J Immunol Methods 2023; 514:113440. [PMID: 36773929 PMCID: PMC9911157 DOI: 10.1016/j.jim.2023.113440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 01/25/2023] [Accepted: 02/07/2023] [Indexed: 02/11/2023]
Abstract
BACKGROUND Oral fluid (hereafter, saliva) is a non-invasive and attractive alternative to blood for SARS-CoV-2 IgG testing; however, the heterogeneity of saliva as a matrix poses challenges for immunoassay performance. OBJECTIVES To optimize performance of a magnetic microparticle-based multiplex immunoassay (MIA) for SARS-CoV-2 IgG measurement in saliva, with consideration of: i) threshold setting and validation across different MIA bead batches; ii) sample qualification based on salivary total IgG concentration; iii) calibration to U.S. SARS-CoV-2 serological standard binding antibody units (BAU); and iv) correlations with blood-based SARS-CoV-2 serological and neutralizing antibody (nAb) assays. METHODS The salivary SARS-CoV-2 IgG MIA included 2 nucleocapsid (N), 3 receptor-binding domain (RBD), and 2 spike protein (S) antigens. Gingival crevicular fluid (GCF) swab saliva samples were collected before December 2019 (n = 555) and after molecular test-confirmed SARS-CoV-2 infection from 113 individuals (providing up to 5 repeated-measures; n = 398) and used to optimize and validate MIA performance (total n = 953). Combinations of IgG responses to N, RBD and S and total salivary IgG concentration (μg/mL) as a qualifier of nonreactive samples were optimized and validated, calibrated to the U.S. SARS-CoV-2 serological standard, and correlated with blood-based SARS-CoV-2 IgG ELISA and nAb assays. RESULTS The sum of signal to cutoff (S/Co) to all seven MIA SARS-CoV-2 antigens and disqualification of nonreactive saliva samples with ≤15 μg/mL total IgG led to correct classification of 62/62 positives (sensitivity [Se] = 100.0%; 95% confidence interval [CI] = 94.8%, 100.0%) and 108/109 negatives (specificity [Sp] = 99.1%; 95% CI = 97.3%, 100.0%) at 8-million beads coupling scale and 80/81 positives (Se = 98.8%; 95% CI = 93.3%, 100.0%] and 127/127 negatives (Sp = 100%; 95% CI = 97.1%, 100.0%) at 20-million beads coupling scale. Salivary SARS-CoV-2 IgG crossed the MIA cutoff of 0.1 BAU/mL on average 9 days post-COVID-19 symptom onset and peaked around day 30. Among n = 30 matched saliva and plasma samples, salivary SARS-CoV-2 MIA IgG levels correlated with corresponding-antigen plasma ELISA IgG (N: ρ = 0.76, RBD: ρ = 0.83, S: ρ = 0.82; all p < 0.001). Correlations of plasma SARS-CoV-2 nAb assay area under the curve (AUC) with salivary MIA IgG (N: ρ = 0.68, RBD: ρ = 0.78, S: ρ = 0.79; all p < 0.001) and with plasma ELISA IgG (N: ρ = 0.76, RBD: ρ = 0.79, S: ρ = 0.76; p < 0.001) were similar. CONCLUSIONS A salivary SARS-CoV-2 IgG MIA produced consistently high Se (> 98.8%) and Sp (> 99.1%) across two bead coupling scales and correlations with nAb responses that were similar to blood-based SARS-CoV-2 IgG ELISA data. This non-invasive salivary SARS-CoV-2 IgG MIA could increase engagement of vulnerable populations and improve broad understanding of humoral immunity (kinetics and gaps) within the evolving context of booster vaccination, viral variants and waning immunity.
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Affiliation(s)
- Nora Pisanic
- Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA.
| | - Annukka A R Antar
- Division of Infectious Diseases, Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Kate L Kruczynski
- Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Magdielis Gregory Rivera
- Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Santosh Dhakal
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Kristoffer Spicer
- Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Pranay R Randad
- Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Andrew Pekosz
- Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA; Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Sabra L Klein
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA; Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Michael J Betenbaugh
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Barbara Detrick
- Department of Pathology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - William Clarke
- Department of Pathology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - David L Thomas
- Division of Infectious Diseases, Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA; Department of Pathology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Yukari C Manabe
- Division of Infectious Diseases, Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA; Department of Pathology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Christopher D Heaney
- Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA; Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA; Department of International Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA.
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9
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Severe acute respiratory syndrome coronaviruses contributing to mitochondrial dysfunction: Implications for post-COVID complications. Mitochondrion 2023; 69:43-56. [PMID: 36690315 PMCID: PMC9854144 DOI: 10.1016/j.mito.2023.01.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 01/03/2023] [Accepted: 01/03/2023] [Indexed: 01/21/2023]
Abstract
Mitochondria play a central role in oxidative phosphorylation (OXPHOS), bioenergetics linked with ATP production, fatty acids biosynthesis, calcium signaling, cell cycle regulation, apoptosis, and innate immune response. Severe acute respiratory syndrome-associated coronavirus (SARS-CoV) infection manipulates the host cellular machinery for its survival and replication in the host cell. The infectiaon causes perturbed the cellular metabolism that favours viral replication leading to mitochondrial dysfunction and chronic inflammation. By localizing to the mitochondria, SARS CoV proteins increase reactive oxygen species (ROS) levels, perturbation of Ca2+ signaling, changes in mtDNA copy number, mitochondrial membrane potential (MMP), mitochondrial mass, and induction of mitophagy. These proteins also influence the fusion and fission kinetics, size, structure, and distribution of mitochondria in the infected host cells. This results in compromised bioenergetics, altered metabolism, and innate immune signaling, and hence can be a key player in determining the outcome of SARS-CoV infection. SARS-CoV infection contributes to stress and activates apoptotic pathways. This review summarizes how mitochondrial function and dynamics are affected by SARS-CoV and how the mitochondria-SARS-CoV interaction benefits viral survival and growth by evading innate host immunity. We also highlight how the SARS-CoV-mediated mitochondrial dysfunction contributes to post-COVID complications. Besides, a discussion on targeting virus-mitochondria interactions as a therapeutic strategy is presented.
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10
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Sarkar M, Saha S. Modeling of SARS-CoV-2 Virus Proteins: Implications on Its Proteome. Methods Mol Biol 2023; 2627:265-299. [PMID: 36959453 DOI: 10.1007/978-1-0716-2974-1_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Abstract
COronaVIrus Disease 19 (COVID-19) is a severe acute respiratory syndrome (SARS) caused by a group of beta coronaviruses, SARS-CoV-2. The SARS-CoV-2 virus is similar to previous SARS- and MERS-causing strains and has infected nearly six hundred and fifty million people all over the globe, while the death toll has crossed the six million mark (as of December, 2022). In this chapter, we look at how computational modeling approaches of the viral proteins could help us understand the various processes in the viral life cycle inside the host, an understanding of which might provide key insights in mitigating this and future threats. This understanding helps us identify key targets for the purpose of drug discovery and vaccine development.
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Affiliation(s)
- Manish Sarkar
- Hochschule für Technik und Wirtschaft (HTW) Berlin, Berlin, Germany
- MedInsights SAS, Paris, France
| | - Soham Saha
- MedInsights, Veuilly la Poterie, France.
- MedInsights SAS, Paris, France.
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11
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Guo C, Tsai SJ, Ai Y, Li M, Anaya E, Pekosz A, Cox A, Gould SJ. The D614G mutation redirects SARS-CoV-2 spike to lysosomes and suppresses deleterious traits of the furin cleavage site insertion mutation. SCIENCE ADVANCES 2022; 8:eade5085. [PMID: 36563151 PMCID: PMC9788772 DOI: 10.1126/sciadv.ade5085] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 11/21/2022] [Indexed: 06/16/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) egress occurs by lysosomal exocytosis. We show that the Spike D614G mutation enhances Spike trafficking to lysosomes, drives Spike-mediated reprogramming of lysosomes, and reduces cell surface Spike expression by ~3-fold. D614G is not a human-specific adaptation. Rather, it is an adaptation to the earlier furin cleavage site insertion (FCSI) mutation that occurred at the genesis of SARS-CoV-2. While advantageous to the virus, furin cleavage of spike has deleterious effects on spike structure and function, inhibiting its trafficking to lysosomes and impairing its infectivity by the transmembrane serine protease 2(TMPRSS2)-independent, endolysosomal pathway. D614G restores spike trafficking to lysosomes and enhances the earliest events in SARS-CoV-2 infectivity, while spike mutations that restore SARS-CoV-2's TMPRSS2-independent infectivity restore spike's trafficking to lysosomes. Together, these and other results show that D614G is an intragenic suppressor of deleterious traits linked to the FCSI and lend additional support to the endolysosomal model of SARS-CoV-2 egress and entry.
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Affiliation(s)
- Chenxu Guo
- Department of Biological Chemistry, Johns Hopkins University, School of Medicine, 725 North Wolfe Street, Baltimore, MD, 21205, USA
| | - Shang-Jui Tsai
- Department of Biological Chemistry, Johns Hopkins University, School of Medicine, 725 North Wolfe Street, Baltimore, MD, 21205, USA
| | - Yiwei Ai
- Department of Biological Chemistry, Johns Hopkins University, School of Medicine, 725 North Wolfe Street, Baltimore, MD, 21205, USA
| | - Maggie Li
- Department of Microbiology and Immunology, Johns Hopkins University, School of Public Health, 615 North Wolfe Street, Baltimore, MD 21205, USA
| | - Eduardo Anaya
- Department of Microbiology and Immunology, Johns Hopkins University, School of Public Health, 615 North Wolfe Street, Baltimore, MD 21205, USA
| | - Andrew Pekosz
- Department of Microbiology and Immunology, Johns Hopkins University, School of Public Health, 615 North Wolfe Street, Baltimore, MD 21205, USA
| | - Andrea Cox
- Department of Medicine, Department of Microbiology and Immunology, Johns Hopkins University, School of Medicine, 725 North Wolfe Street, Baltimore, MD, 21205, USA
| | - Stephen J. Gould
- Department of Biological Chemistry, Johns Hopkins University, School of Medicine, 725 North Wolfe Street, Baltimore, MD, 21205, USA
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12
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Hassan SS, Kodakandla V, Redwan EM, Lundstrom K, Choudhury PP, Serrano-Aroca Á, Azad GK, Aljabali AAA, Palu G, Abd El-Aziz TM, Barh D, Uhal BD, Adadi P, Takayama K, Bazan NG, Tambuwala M, Sherchan SP, Lal A, Chauhan G, Baetas-da-Cruz W, Uversky VN. Non-uniform aspects of the SARS-CoV-2 intraspecies evolution reopen question of its origin. Int J Biol Macromol 2022; 222:972-993. [PMID: 36174872 PMCID: PMC9511875 DOI: 10.1016/j.ijbiomac.2022.09.184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 05/04/2022] [Accepted: 09/20/2022] [Indexed: 12/01/2022]
Abstract
Several hypotheses have been presented on the origin of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) from its identification as the agent causing the current coronavirus disease 19 (COVID-19) pandemic. So far, no solid evidence has been found to support any hypothesis on the origin of this virus, and the issue continue to resurface over and over again. Here we have unfolded a pattern of distribution of several mutations in the SARS-CoV-2 proteins in 24 geo-locations across different continents. The results showed an evenly uneven distribution of the unique protein variants, distinct mutations, unique frequency of common conserved residues, and mutational residues across these 24 geo-locations. Furthermore, ample mutations were identified in the evolutionarily conserved invariant regions in the SARS-CoV-2 proteins across almost all geo-locations studied. This pattern of mutations potentially breaches the law of evolutionary conserved functional units of the beta-coronavirus genus. These mutations may lead to several novel SARS-CoV-2 variants with a high degree of transmissibility and virulence. A thorough investigation on the origin and characteristics of SARS-CoV-2 needs to be conducted in the interest of science and for the preparation of meeting the challenges of potential future pandemics.
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Affiliation(s)
- Sk Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, Paschim Medinipur, 721140, West Bengal, India.
| | - Vaishnavi Kodakandla
- Department of Life sciences, Sophia College For Women, University of Mumbai, Bhulabhai Desai Road, Mumbai 400026, India
| | - Elrashdy M Redwan
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia; Therapeutic and Protective Proteins Laboratory, Protein Research Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications, New Borg EL-Arab 21934, Alexandria, Egypt.
| | | | - Pabitra Pal Choudhury
- Indian Statistical Institute, Applied Statistics Unit, 203 B T Road, Kolkata 700108, India
| | - Ángel Serrano-Aroca
- Biomaterials and Bioengineering Lab, Centro de Investigacion Traslacional San Alberto Magno, Universidad Cat'olica de Valencia San Vicente Martir, c/Guillem de Castro, 94, 46001 Valencia, Valencia, Spain.
| | | | - Alaa A A Aljabali
- Department of Pharmaceutics and Pharmaceutical Technology, Yarmouk University, Faculty of Pharmacy, Irbid 566, Jordan.
| | - Giorgio Palu
- Department of Molecular Medicine, University of Padova, Via Gabelli 63, 35121 Padova, Italy.
| | - Tarek Mohamed Abd El-Aziz
- Zoology Department, Faculty of Science, Minia University, El-Minia 61519, Egypt; Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229-3900, USA.
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, WB, India; Departamento de Geńetica, Ecologia e Evolucao, Instituto de Cíencias Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Bruce D Uhal
- Department of Physiology, Michigan State University, East Lansing, MI 48824, USA
| | - Parise Adadi
- Department of Food Science, University of Otago, Dunedin 9054, New Zealand
| | - Kazuo Takayama
- Center for iPS Cell Research and Application, Kyoto University, Kyoto 6068507, Japan.
| | - Nicolas G Bazan
- Neuroscience Center of Excellence, School of Medicine, LSU Health New Orleans, New Orleans, LA 70112, USA.
| | - Murtaza Tambuwala
- School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine BT52 1SA, Northern Ireland, UK.
| | - Samendra P Sherchan
- Lincoln Medical School, University of Lincoln, Brayford Pool Campus, Lincoln LN6 7TS, UK.
| | - Amos Lal
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN, USA
| | - Gaurav Chauhan
- School of Engineering and Sciences, Tecnologico de Monterrey, Av. Eugenio Garza Sada 2501 Sur, 64849 Monterrey, Nuevo León, Mexico.
| | - Wagner Baetas-da-Cruz
- Translational Laboratory in Molecular Physiology, Centre for Experimental Surgery, College of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Vladimir N Uversky
- Department of Molecular Medicineand USF Health Byrd Alzheimer's Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA; Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Institutskiy pereulok, 9, Dolgoprudny 141700, Russia.
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13
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Surya W, Queralt-Martin M, Mu Y, Aguilella VM, Torres J. SARS-CoV-2 accessory protein 7b forms homotetramers in detergent. Virol J 2022; 19:193. [PMID: 36414943 PMCID: PMC9680129 DOI: 10.1186/s12985-022-01920-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 11/04/2022] [Indexed: 11/23/2022] Open
Abstract
A global pandemic is underway caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The SARS-CoV-2 genome, like its predecessor SARS-CoV, contains open reading frames that encode accessory proteins involved in virus-host interactions active during infection and which likely contribute to pathogenesis. One of these accessory proteins is 7b, with only 44 (SARS-CoV) and 43 (SARS-CoV-2) residues. It has one predicted transmembrane domain fully conserved, which suggests a functional role, whereas most variability is contained in the predicted cytoplasmic C-terminus. In SARS-CoV, 7b protein is expressed in infected cells, and the transmembrane domain was necessary and sufficient for Golgi localization. Also, anti-p7b antibodies have been found in the sera of SARS-CoV convalescent patients. In the present study, we have investigated the hypothesis that SARS-2 7b protein forms oligomers with ion channel activity. We show that in both SARS viruses 7b is almost completely α-helical and has a single transmembrane domain. In SDS, 7b forms various oligomers, from monomers to tetramers, but only monomers when exposed to reductants. Combination of SDS gel electrophoresis and analytical ultracentrifugation (AUC) in both equilibrium and velocity modes suggests a dimer-tetramer equilibrium, but a monomer-dimer-tetramer equilibrium in the presence of reductant. This data suggests that although disulfide-linked dimers may be present, they are not essential to form tetramers. Inclusion of pentamers or higher oligomers in the SARS-2 7b model were detrimental to fit quality. Preliminary models of this association was generated with AlphaFold2, and two alternative models were exposed to a molecular dynamics simulation in presence of a model lipid membrane. However, neither of the two models provided any evident pathway for ions. To confirm this, SARS-2 p7b was studied using Planar Bilayer Electrophysiology. Addition of p7b to model membranes produced occasional membrane permeabilization, but this was not consistent with bona fide ion channels made of a tetrameric assembly of α-helices.
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Affiliation(s)
- Wahyu Surya
- grid.59025.3b0000 0001 2224 0361School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551 Singapore
| | - Maria Queralt-Martin
- grid.9612.c0000 0001 1957 9153Laboratory of Molecular Biophysics, Department of Physics, Universitat Jaume I, 12080 Castelló, Spain
| | - Yuguang Mu
- grid.59025.3b0000 0001 2224 0361School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551 Singapore
| | - Vicente M. Aguilella
- grid.9612.c0000 0001 1957 9153Laboratory of Molecular Biophysics, Department of Physics, Universitat Jaume I, 12080 Castelló, Spain
| | - Jaume Torres
- grid.59025.3b0000 0001 2224 0361School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551 Singapore
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14
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García-García T, Fernández-Rodríguez R, Redondo N, de Lucas-Rius A, Zaldívar-López S, López-Ayllón BD, Suárez-Cárdenas JM, Jiménez-Marín Á, Montoya M, Garrido JJ. Impairment of antiviral immune response and disruption of cellular functions by SARS-CoV-2 ORF7a and ORF7b. iScience 2022; 25:105444. [PMID: 36310646 PMCID: PMC9597514 DOI: 10.1016/j.isci.2022.105444] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 09/20/2022] [Accepted: 10/21/2022] [Indexed: 11/09/2022] Open
Abstract
SARS-CoV-2, the causative agent of the present COVID-19 pandemic, possesses eleven accessory proteins encoded in its genome, and some have been implicated in facilitating infection and pathogenesis through their interaction with cellular components. Among these proteins, accessory protein ORF7a and ORF7b functions are poorly understood. In this study, A549 cells were transduced to express ORF7a and ORF7b, respectively, to explore more in depth the role of each accessory protein in the pathological manifestation leading to COVID-19. Bioinformatic analysis and integration of transcriptome results identified defined canonical pathways and functional groupings revealing that after expression of ORF7a or ORF7b, the lung cells are potentially altered to create conditions more favorable for SARS-CoV-2, by inhibiting the IFN-I response, increasing proinflammatory cytokines release, and altering cell metabolic activity and adhesion. Based on these results, it is plausible to suggest that ORF7a or ORF7b could be used as biomarkers of progression in this pandemic.
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Affiliation(s)
- Tránsito García-García
- Immunogenomics and Molecular Pathogenesis Group, UIC Zoonoses and Emergent Diseases ENZOEM, Department of Genetics, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), GA-14 Research Group, Córdoba, Spain
| | - Raúl Fernández-Rodríguez
- Immunogenomics and Molecular Pathogenesis Group, UIC Zoonoses and Emergent Diseases ENZOEM, Department of Genetics, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), GA-14 Research Group, Córdoba, Spain
| | - Natalia Redondo
- Molecular Biomedicine Department, Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid 28040, Spain
| | - Ana de Lucas-Rius
- Molecular Biomedicine Department, Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid 28040, Spain
| | - Sara Zaldívar-López
- Immunogenomics and Molecular Pathogenesis Group, UIC Zoonoses and Emergent Diseases ENZOEM, Department of Genetics, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), GA-14 Research Group, Córdoba, Spain
| | - Blanca Dies López-Ayllón
- Molecular Biomedicine Department, Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid 28040, Spain
| | - José M. Suárez-Cárdenas
- Immunogenomics and Molecular Pathogenesis Group, UIC Zoonoses and Emergent Diseases ENZOEM, Department of Genetics, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), GA-14 Research Group, Córdoba, Spain
| | - Ángeles Jiménez-Marín
- Immunogenomics and Molecular Pathogenesis Group, UIC Zoonoses and Emergent Diseases ENZOEM, Department of Genetics, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), GA-14 Research Group, Córdoba, Spain
| | - María Montoya
- Molecular Biomedicine Department, Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid 28040, Spain
- Corresponding author
| | - Juan J. Garrido
- Immunogenomics and Molecular Pathogenesis Group, UIC Zoonoses and Emergent Diseases ENZOEM, Department of Genetics, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), GA-14 Research Group, Córdoba, Spain
- Corresponding author
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15
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Cruz CAK, Medina PMB. Temporal changes in the accessory protein mutations of SARS-CoV-2 variants and their predicted structural and functional effects. J Med Virol 2022; 94:5189-5200. [PMID: 35764775 PMCID: PMC9349927 DOI: 10.1002/jmv.27964] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 06/22/2022] [Accepted: 06/26/2022] [Indexed: 12/15/2022]
Abstract
Emerging variants enable the continuous spread of SARS-CoV-2 in humans. The factors contributing to behavioral differences in variants remain elusive despite associations with several Spike protein mutations. Exploring accessory proteins may provide a wider understanding of these differences since these proteins may affect viral processes that occur beyond infection. Various bioinformatics tools were utilized to identify significant accessory protein mutations and determine their structural and functional effects over time. The ViruClust web application was used to retrieve accessory protein amino acid sequences and determine mutation frequencies in these sequences across time. The structural and functional effects of the mutations were determined using Missense3D and PROVEAN, respectively. The accessory and Spike protein mutations were compared using mutation densities. Q57H and T151I of ORF3a; T21I and W27L of ORF6; G38V, V82A, and T120I of ORF7a; S31P and T40I of ORF7b; and R52I, C61F, and I121L of ORF8 were highly frequent in most variants of concern and were within known functional domains. Thus, these are good candidates for further experimental evaluation. Among the accessory proteins, ORF6 and ORF8 were highlighted because of their strong and weak correlation with Spike protein mutations, respectively.
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Affiliation(s)
- Christian Alfredo K. Cruz
- Biological Models Laboratory, Department of Biochemistry and Molecular Biology, College of MedicineUniversity of the Philippines ManilaManila, Metro ManilaPhilippines
| | - Paul Mark B. Medina
- Biological Models Laboratory, Department of Biochemistry and Molecular Biology, College of MedicineUniversity of the Philippines ManilaManila, Metro ManilaPhilippines
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16
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Mohler K, Moen J, Rogulina S, Rinehart J. Cell type-independent profiling of interactions between intracellular pathogens and the human phosphoproteome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.09.27.509702. [PMID: 36203552 PMCID: PMC9536036 DOI: 10.1101/2022.09.27.509702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Interactions between proteins from intracellular pathogens and host proteins in an infected cell are often mediated by post-translational modifications encoded in the host proteome. Identifying protein modifications, such as phosphorylation, that dictate these interactions remains a defining challenge in unraveling the molecular mechanisms of pathogenesis. We have developed a platform in engineered bacteria that displays over 110,000 phosphorylated human proteins coupled to a fluorescent reporter system capable of identifying the host-pathogen interactome of phosphoproteins (H-PIP). This resource broadly enables cell-type independent interrogation and discovery of proteins from intracellular pathogens capable of binding phosphorylated human proteins. As an example of the H-PIP platform, we generated a unique, high-resolution SARS-CoV-2 interaction network which expanded our knowledge of viral protein function and identified understudied areas of host pathology.
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17
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Debnath P, Khan U, Khan MS. Characterization and Structural Prediction of Proteins in SARS-CoV-2 Bangladeshi Variant Through Bioinformatics. Microbiol Insights 2022; 15:11786361221115595. [PMID: 35966939 PMCID: PMC9373114 DOI: 10.1177/11786361221115595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 06/30/2022] [Indexed: 11/15/2022] Open
Abstract
The renowned respiratory disease induced by the severe acute respiratory
syndrome-coronavirus-2 (SARS-CoV-2) has become a global epidemic in just less
than a year by the first half of 2020. The subsequent efficient human-to-human
transmission of this virus eventually affected millions of people worldwide. The
most devastating thing is that the infection rate is continuously uprising and
resulting in significant mortality especially among the older age population and
those with health co-morbidities. This enveloped, positive-sense RNA virus is
chiefly responsible for the infection of the upper respiratory system. The
virulence of the SARS-CoV-2 is mostly regulated by its proteins such as entry to
the host cell through fusion mechanism, fusion of infected cells with
neighboring uninfected cells to spread virus, inhibition of host gene
expression, cellular differentiation, apoptosis, mitochondrial biogenesis, etc.
But very little is known about the protein structures and functionalities.
Therefore, the main purpose of this study is to learn more about these proteins
through bioinformatics approaches. In this study, ORF10, ORF7b, ORF7a, ORF6,
membrane glycoprotein, and envelope protein have been selected from a
Bangladeshi Corona-virus strain G039392 and a number of bioinformatics tools
(MEGA-X-V10.1.7, PONDR, ProtScale, ProtParam, SCRIBER, NetSurfP v2.0, IntFOLD,
UCSF Chimera, and PyMol) and strategies were implemented for multiple sequence
alignment and phylogeny analysis with 9 different variants, predicting
hydropathicity, amino acid compositions, protein-binding propensity, protein
disorders, and 2D and 3D protein modeling. Selected proteins were characterized
as highly flexible, structurally and electrostatically extremely stable,
ordered, biologically active, hydrophobic, and closely related to proteins of
different variants. This detailed information regarding the characterization and
structure of proteins of SARS-CoV-2 Bangladeshi variant was performed for the
first time ever to unveil the deep mechanism behind the virulence features. And
this robust appraisal also paves the future way for molecular docking, vaccine
development targeting these characterized proteins.
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Affiliation(s)
- Pinky Debnath
- Chemical Biotechnology Department, Technical University of Munich, Straubing, Germany
| | - Umama Khan
- Biotechnology and Genetic Engineering Discipline, Khulna University, Bangladesh
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18
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Okura T, Shirato K, Kakizaki M, Sugimoto S, Matsuyama S, Tanaka T, Kume Y, Chishiki M, Ono T, Moriishi K, Sonoyama M, Hosoya M, Hashimoto K, Maenaka K, Takeda M. Hydrophobic Alpha-Helical Short Peptides in Overlapping Reading Frames of the Coronavirus Genome. Pathogens 2022; 11:pathogens11080877. [PMID: 36014999 PMCID: PMC9415614 DOI: 10.3390/pathogens11080877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/28/2022] [Accepted: 08/01/2022] [Indexed: 02/04/2023] Open
Abstract
In this study, we show that the coronavirus (CoV) genome may encode many functional hydrophobic alpha-helical peptides (HAHPs) in overlapping reading frames of major coronaviral proteins throughout the entire viral genome. These HAHPs can theoretically be expressed from non-canonical sub-genomic (sg)RNAs that are synthesized in substantial amounts in infected cells. We selected and analyzed five and six HAHPs encoded in the S gene regions of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and Middle East respiratory syndrome coronavirus (MERS-CoV), respectively. Two and three HAHPs derived from SARS-CoV-2 and MERS-CoV, respectively, specifically interacted with both the SARS-CoV-2 and MERS-CoV S proteins and inhibited their membrane fusion activity. Furthermore, one of the SARS-CoV-2 HAHPs specifically inhibited viral RNA synthesis by accumulating at the site of viral RNA synthesis. Our data show that a group of HAHPs in the coronaviral genome potentially has a regulatory role in viral propagation.
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Affiliation(s)
- Takashi Okura
- Department of Virology 3, National Institute of Infectious Diseases, Musashimurayama 208-0011, Tokyo, Japan; (T.O.); (K.S.); (M.K.); (S.S.)
| | - Kazuya Shirato
- Department of Virology 3, National Institute of Infectious Diseases, Musashimurayama 208-0011, Tokyo, Japan; (T.O.); (K.S.); (M.K.); (S.S.)
| | - Masatoshi Kakizaki
- Department of Virology 3, National Institute of Infectious Diseases, Musashimurayama 208-0011, Tokyo, Japan; (T.O.); (K.S.); (M.K.); (S.S.)
| | - Satoko Sugimoto
- Department of Virology 3, National Institute of Infectious Diseases, Musashimurayama 208-0011, Tokyo, Japan; (T.O.); (K.S.); (M.K.); (S.S.)
- Management Department of Biosafety, Laboratory Animal, and Pathogen Bank, National Institute of Infectious Diseases, Musashimurayama 208-0011, Tokyo, Japan
| | - Shutoku Matsuyama
- Center for Influenza and Respiratory Virus Research, National Institute of Infectious Diseases, Musashimurayama 208-0011, Tokyo, Japan;
| | - Tomohisa Tanaka
- Department of Microbiology, Faculty of Medicine, Graduate Faculty of Interdisciplinary Research, University of Yamanashi, Chuo 409-3898, Yamanashi, Japan; (T.T.); (K.M.)
| | - Yohei Kume
- Department of Pediatrics, School of Medicine, Fukushima Medical University, Fukushima 960-1295, Fukushima, Japan; (Y.K.); (M.C.); (T.O.); (M.H.); (K.H.)
| | - Mina Chishiki
- Department of Pediatrics, School of Medicine, Fukushima Medical University, Fukushima 960-1295, Fukushima, Japan; (Y.K.); (M.C.); (T.O.); (M.H.); (K.H.)
| | - Takashi Ono
- Department of Pediatrics, School of Medicine, Fukushima Medical University, Fukushima 960-1295, Fukushima, Japan; (Y.K.); (M.C.); (T.O.); (M.H.); (K.H.)
| | - Kohji Moriishi
- Department of Microbiology, Faculty of Medicine, Graduate Faculty of Interdisciplinary Research, University of Yamanashi, Chuo 409-3898, Yamanashi, Japan; (T.T.); (K.M.)
- Center for Life Science Research, University of Yamanashi, Chuo 409-3898, Yamanashi, Japan
- Division of Hepatitis Virology, Institute for Genetic Medicine, Hokkaido University, Sapporo 060-0808, Hokkaido, Japan
| | - Masashi Sonoyama
- Division of Molecular Science, Graduate School of Science and Technology, Gunma University, Kiryu 376-8515, Gunma, Japan;
- Gunma University Center for Food Science and Wellness (GUCFW), Gunma University, Kiryu 376-8515, Gunma, Japan
- Gunma University Initiative for Advanced Research (GIAR), Gunma University, Kiryu 376-8515, Gunma, Japan
| | - Mitsuaki Hosoya
- Department of Pediatrics, School of Medicine, Fukushima Medical University, Fukushima 960-1295, Fukushima, Japan; (Y.K.); (M.C.); (T.O.); (M.H.); (K.H.)
| | - Koichi Hashimoto
- Department of Pediatrics, School of Medicine, Fukushima Medical University, Fukushima 960-1295, Fukushima, Japan; (Y.K.); (M.C.); (T.O.); (M.H.); (K.H.)
| | - Katsumi Maenaka
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Hokkaido, Japan;
- Center for Research and Education on Drug Discovery, Hokkaido University, Sapporo 060-0812, Hokkaido, Japan
- Global Station for Biosurfaces and Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Hokkaido, Japan
| | - Makoto Takeda
- Department of Virology 3, National Institute of Infectious Diseases, Musashimurayama 208-0011, Tokyo, Japan; (T.O.); (K.S.); (M.K.); (S.S.)
- Correspondence:
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19
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Brandolini M, Dirani G, Taddei F, Zannoli S, Denicolò A, Arfilli V, Battisti A, Manera M, Mancini A, Grumiro L, Marino MM, Gatti G, Fantini M, Semprini S, Sambri V. Mutational induction in SARS-CoV-2 major lineages by experimental exposure to neutralising sera. Sci Rep 2022; 12:12479. [PMID: 35864211 PMCID: PMC9302871 DOI: 10.1038/s41598-022-16533-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 07/12/2022] [Indexed: 11/24/2022] Open
Abstract
The ongoing evolution of SARS-CoV-2 and the emergence of new viral variants bearing specific escape mutations responsible for immune evasion from antibody neutralisation has required a more accurate characterisation of the immune response as one of the evolutive forces behind viral adaptation to a largely immunised human population. In this work, culturing in the presence of neutralising sera vigorously promoted mutagenesis leading to the acquisition of known escape mutations on the spike as well as new presumptive escape mutations on structural proteins whose role as target of the neutralizing antibody response might have been thus far widely neglected. From this perspective, this study, in addition to tracing the past evolution of the species back to interactions with neutralising antibody immune response, also offers a glimpse into future evolutive scenarios.
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Affiliation(s)
- Martina Brandolini
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522, Cesena, Italy
| | - Giorgio Dirani
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522, Cesena, Italy
| | - Francesca Taddei
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522, Cesena, Italy
| | - Silvia Zannoli
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522, Cesena, Italy
| | - Agnese Denicolò
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522, Cesena, Italy
| | - Valentina Arfilli
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522, Cesena, Italy
| | - Arianna Battisti
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522, Cesena, Italy
| | - Martina Manera
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522, Cesena, Italy
| | - Andrea Mancini
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522, Cesena, Italy
| | - Laura Grumiro
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522, Cesena, Italy
| | - Maria Michela Marino
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522, Cesena, Italy
| | - Giulia Gatti
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522, Cesena, Italy
| | - Michela Fantini
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522, Cesena, Italy
| | - Simona Semprini
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522, Cesena, Italy
| | - Vittorio Sambri
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522, Cesena, Italy.
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES)-Alma Mater Studiorum, University of Bologna, 40138, Bologna, Italy.
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20
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Functional mutations of SARS-CoV-2: implications to viral transmission, pathogenicity and immune escape. Chin Med J (Engl) 2022; 135:1213-1222. [PMID: 35788093 PMCID: PMC9337262 DOI: 10.1097/cm9.0000000000002158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The pandemic of coronavirus disease 2019 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to major public health challenges globally. The increasing viral lineages identified indicate that the SARS-CoV-2 genome is evolving at a rapid rate. Viral genomic mutations may cause antigenic drift or shift, which are important ways by which SARS-CoV-2 escapes the human immune system and changes its transmissibility and virulence. Herein, we summarize the functional mutations in SARS-CoV-2 genomes to characterize its adaptive evolution to inform the development of vaccination, treatment as well as control and intervention measures.
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21
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Hardick J, Gallagher N, Sachithanandham J, Fall A, Siddiqui Z, Pekosz A, Manabe YC, Mostafa HH. Evaluation of Four Point of Care (POC) Antigen Assays for the Detection of the SARS-CoV-2 Variant Omicron. Microbiol Spectr 2022; 10:e0102522. [PMID: 35616382 PMCID: PMC9241858 DOI: 10.1128/spectrum.01025-22] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 05/06/2022] [Indexed: 12/29/2022] Open
Abstract
Ensuring SARS-CoV-2 diagnostics that can reliably detect emerging variants has been an ongoing challenge. Due to the rapid spread of the Omicron variant, point-of-care (POC) antigen tests have become more widely used. This study aimed at (i) comparing the analytical sensitivity (LOD) of 4 POC antigen assays, BD Veritor, Abbott BinaxNow, Orasure InteliSwab and Quidel QuickVue, for the Omicron versus the Delta variant and (ii) verifying the reproducible detection of Omicron by the 4 antigen assays. The LOD for all four assays were evaluated using Omicron and Delta virus stocks quantified for infectivity and genome copies. The four assays detected all replicates of Omicron and Delta dilutions at 104 and 105 TCID50/mL, respectively. We quantified both viral stocks using droplet digital PCR (ddPCR), which revealed that the Omicron stock had equivalent copies of the N gene to Delta at a one log lower infectious virus. The Abbott BinaxNow and Orasure InteliSwab had the highest analytical sensitivity for Omicron while the Orasure InteliSwab and the Quidel QuickVue had the highest analytical sensitivity for Delta. When 14 SARS-CoV-2 real-time PCR positive nasal/nasopharyngeal swab samples (12 Omicron and 2 Delta, mean Ct = 19.1), were tested by the four assays, only the QuickVue detected all samples. Antigen test positivity correlated with recovery of infectious virus on cell culture in 9 out of 13 tested specimens from symptomatic, asymptomatic, unvaccinated, and vaccinated individuals. Although our study confirms the reduced analytical sensitivity of antigen testing compared to molecular methods, the Omicron variant was detectable by the four evaluated rapid antigen tests. IMPORTANCE In the manuscript, we report an evaluation of the capability of 4 point of care (POC) antigen assays, the BD Veritor, Abbott BinaxNow, Orasure InteliSwab and Quidel QuickVue to detect the Omicron variant of SARS-CoV-2, and we compared their analytical sensitivity for Omicron versus Delta. In this analysis we found that all four assays detected Omicron and Delta at 104 and 105 TCID50/mL, respectively. We further quantified the viral stocks used by droplet digital (ddPCR) and found that the Omicron stock had equivalent copies of the N gene to Delta at a one log lower infectious virus titer and that an increased RNA to infectious virus ratio may be contributing to discrepancies in limit of detection in Omicron compared to Delta. We evaluated 14 SARS-CoV-2 real-time PCR positive nasal/nasopharyngeal swab samples (12 Omicron and 2 Delta), with an average cycle threshold value of 19.1, and only the QuickVue showed 100% agreement.
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Affiliation(s)
- Justin Hardick
- Department of Medicine, Division of Infectious Diseases, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Nicholas Gallagher
- Department of Pathology, Division of Medical Microbiology, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | | | - Amary Fall
- Department of Pathology, Division of Medical Microbiology, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Zishan Siddiqui
- Department of Medicine, Division of Hospital Medicine, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Andrew Pekosz
- Department of Medicine, Division of Infectious Diseases, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Yukari C. Manabe
- Department of Medicine, Division of Infectious Diseases, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Heba H. Mostafa
- Department of Pathology, Division of Medical Microbiology, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
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22
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Lyu L, Feng R, Zhang M, Xie X, Liao Y, Zhou Y, Guo X, Su B, Dorsett Y, Chen L. Subgenomic RNA profiling suggests novel mechanism in coronavirus gene regulation and host adaption. Life Sci Alliance 2022; 5:5/8/e202101347. [PMID: 35470238 PMCID: PMC9039346 DOI: 10.26508/lsa.202101347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 04/11/2022] [Accepted: 04/11/2022] [Indexed: 11/24/2022] Open
Abstract
CORONATATOR, developed to analyze the subgenomic RNA of coronavirus, was applied on large number of sequencing data sets from coronaviruses, and shed light on viral gene regulation. Fundamental to viral biology is identification and annotation of viral genes and their function. Determining the level of coronavirus gene expression is inherently difficult due to the positive stranded RNA genome and the identification of subgenomic RNAs (sgRNAs) that are required for expression of most viral genes. We developed a bioinformatic pipeline to analyze metatranscriptomic data from 20 independent studies encompassing 588 individual samples and 10 coronavirus species. This comparative analysis defined a core sgRNA repertoire for SARS-CoV-2 and found novel sgRNAs that could encode functional short peptides. Relevant to coronavirus infectivity and transmission, we also observed that the ratio of Spike sgRNA to Nucleocapsid one is highest in SARS-CoV-2, among the β-coronaviruses examined. Furthermore, the adjustment of this ratio can be made by modifications to the viral RNA replication machinery, representing a form of viral gene regulation that may be involved in host adaption.
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Affiliation(s)
- Lin Lyu
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ru Feng
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mingnan Zhang
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaoqing Xie
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yinjing Liao
- College of Chemistry, Sichuan University, Chengdu, China
| | - Yanjiao Zhou
- Department of Medicine, University of Connecticut Health, Farmington, CT, USA
| | - Xiaokui Guo
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bing Su
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yair Dorsett
- Department of Medicine, University of Connecticut Health, Farmington, CT, USA
| | - Lei Chen
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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23
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Ugolini C, Mulroney L, Leger A, Castelli M, Criscuolo E, Williamson MK, Davidson AD, Almuqrin A, Giambruno R, Jain M, Frigè G, Olsen H, Tzertzinis G, Schildkraut I, Wulf MG, Corrêa IR, Ettwiller L, Clementi N, Clementi M, Mancini N, Birney E, Akeson M, Nicassio F, Matthews D, Leonardi T. Nanopore ReCappable sequencing maps SARS-CoV-2 5' capping sites and provides new insights into the structure of sgRNAs. Nucleic Acids Res 2022; 50:3475-3489. [PMID: 35244721 PMCID: PMC8989550 DOI: 10.1093/nar/gkac144] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 02/05/2022] [Accepted: 02/16/2022] [Indexed: 01/09/2023] Open
Abstract
The SARS-CoV-2 virus has a complex transcriptome characterised by multiple, nested subgenomic RNAsused to express structural and accessory proteins. Long-read sequencing technologies such as nanopore direct RNA sequencing can recover full-length transcripts, greatly simplifying the assembly of structurally complex RNAs. However, these techniques do not detect the 5' cap, thus preventing reliable identification and quantification of full-length, coding transcript models. Here we used Nanopore ReCappable Sequencing (NRCeq), a new technique that can identify capped full-length RNAs, to assemble a complete annotation of SARS-CoV-2 sgRNAs and annotate the location of capping sites across the viral genome. We obtained robust estimates of sgRNA expression across cell lines and viral isolates and identified novel canonical and non-canonical sgRNAs, including one that uses a previously un-annotated leader-to-body junction site. The data generated in this work constitute a useful resource for the scientific community and provide important insights into the mechanisms that regulate the transcription of SARS-CoV-2 sgRNAs.
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Affiliation(s)
- Camilla Ugolini
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, 20139 Milano, Italy
| | - Logan Mulroney
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, 20139 Milano, Italy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
- Biomolecular Engineering Department, UC Santa Cruz, CA 95064, USA
| | - Adrien Leger
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Matteo Castelli
- Laboratory of Microbiology and Virology, Vita-Salute San Raffaele University; via Olgettina 58, 20132 Milan, Italy
| | - Elena Criscuolo
- Laboratory of Microbiology and Virology, Vita-Salute San Raffaele University; via Olgettina 58, 20132 Milan, Italy
| | - Maia Kavanagh Williamson
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University Walk, University of Bristol, Bristol BS8 1TD, UK
| | - Andrew D Davidson
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University Walk, University of Bristol, Bristol BS8 1TD, UK
| | - Abdulaziz Almuqrin
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University Walk, University of Bristol, Bristol BS8 1TD, UK
- Department of Clinical Laboratory Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Roberto Giambruno
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, 20139 Milano, Italy
| | - Miten Jain
- Biomolecular Engineering Department, UC Santa Cruz, CA 95064, USA
| | - Gianmaria Frigè
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, 20139 Milano, Italy
| | - Hugh Olsen
- Biomolecular Engineering Department, UC Santa Cruz, CA 95064, USA
| | | | | | | | | | | | - Nicola Clementi
- Laboratory of Microbiology and Virology, Vita-Salute San Raffaele University; via Olgettina 58, 20132 Milan, Italy
- Laboratory of Medical Microbiology and Virology, IRCCS San Raffaele Scientific Institute; via Olgettina 60, 20132 Milan, Italy
| | - Massimo Clementi
- Laboratory of Microbiology and Virology, Vita-Salute San Raffaele University; via Olgettina 58, 20132 Milan, Italy
- Laboratory of Medical Microbiology and Virology, IRCCS San Raffaele Scientific Institute; via Olgettina 60, 20132 Milan, Italy
| | - Nicasio Mancini
- Laboratory of Microbiology and Virology, Vita-Salute San Raffaele University; via Olgettina 58, 20132 Milan, Italy
- Laboratory of Medical Microbiology and Virology, IRCCS San Raffaele Scientific Institute; via Olgettina 60, 20132 Milan, Italy
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Mark Akeson
- Biomolecular Engineering Department, UC Santa Cruz, CA 95064, USA
| | - Francesco Nicassio
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, 20139 Milano, Italy
| | - David A Matthews
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University Walk, University of Bristol, Bristol BS8 1TD, UK
| | - Tommaso Leonardi
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, 20139 Milano, Italy
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24
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Karaba AH, Zhu X, Liang T, Wang KH, Rittenhouse AG, Akinde O, Eby Y, Ruff JE, Blankson JN, Abedon AT, Alejo JL, Cox AL, Bailey JR, Thompson EA, Klein SL, Warren DS, Garonzik-Wang JM, Boyarsky BJ, Sitaras I, Pekosz A, Segev DL, Tobian AA, Werbel WA. A third dose of SARS-CoV-2 vaccine increases neutralizing antibodies against variants of concern in solid organ transplant recipients. Am J Transplant 2022; 22:1253-1260. [PMID: 34951746 PMCID: PMC8983554 DOI: 10.1111/ajt.16933] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/30/2021] [Accepted: 12/18/2021] [Indexed: 01/25/2023]
Abstract
Vaccine-induced SARS-CoV-2 antibody responses are attenuated in solid organ transplant recipients (SOTRs) and breakthrough infections are more common. Additional SARS-CoV-2 vaccine doses increase anti-spike IgG in some SOTRs, but it is uncertain whether neutralization of variants of concern (VOCs) is enhanced. We tested 47 SOTRs for clinical and research anti-spike IgG, pseudoneutralization (ACE2 blocking), and live-virus neutralization (nAb) against VOCs before and after a third SARS-CoV-2 vaccine dose (70% mRNA, 30% Ad26.COV2.S) with comparison to 15 healthy controls after two mRNA vaccine doses. We used correlation analysis to compare anti-spike IgG assays and focused on thresholds associated with neutralization. A third SARS-CoV-2 vaccine dose increased median total anti-spike (1.6-fold), pseudoneutralization against VOCs (2.5-fold vs. Delta), and neutralizing antibodies (1.4-fold against Delta). However, neutralization activity was significantly lower than healthy controls (p < .001); 32% of SOTRs had zero detectable nAb against Delta after third vaccination compared to 100% for controls. Correlation with nAb was seen at anti-spike IgG >4 Log10 (AU/ml) on the Euroimmun ELISA and >4 Log10 (AU/ml) on the MSD research assay. These findings highlight benefits of a third vaccine dose for some SOTRs and the need for alternative strategies to improve protection in a significant subset of this population.
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Affiliation(s)
- Andrew H. Karaba
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Xianming Zhu
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Tao Liang
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Kristy H. Wang
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Alex G. Rittenhouse
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Olivia Akinde
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Yolanda Eby
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jessica E. Ruff
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Joel N. Blankson
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Aura T. Abedon
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jennifer L. Alejo
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Andrea L. Cox
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland
- Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Justin R. Bailey
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Elizabeth A. Thompson
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Sabra L. Klein
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland
| | - Daniel S. Warren
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Brian J. Boyarsky
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ioannis Sitaras
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland
| | - Andrew Pekosz
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland
| | - Dorry L. Segev
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Aaron A.R. Tobian
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - William A. Werbel
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
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25
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Zhang D, Zhu L, Wang Y, Li P, Gao Y. Translational Control of COVID-19 and Its Therapeutic Implication. Front Immunol 2022; 13:857490. [PMID: 35422818 PMCID: PMC9002053 DOI: 10.3389/fimmu.2022.857490] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/07/2022] [Indexed: 12/19/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of COVID-19, which has broken out worldwide for more than two years. However, due to limited treatment, new cases of infection are still rising. Therefore, there is an urgent need to understand the basic molecular biology of SARS-CoV-2 to control this virus. SARS-CoV-2 replication and spread depend on the recruitment of host ribosomes to translate viral messenger RNA (mRNA). To ensure the translation of their own mRNAs, the SARS-CoV-2 has developed multiple strategies to globally inhibit the translation of host mRNAs and block the cellular innate immune response. This review provides a comprehensive picture of recent advancements in our understanding of the molecular basis and complexity of SARS-CoV-2 protein translation. Specifically, we summarize how this viral infection inhibits host mRNA translation to better utilize translation elements for translation of its own mRNA. Finally, we discuss the potential of translational components as targets for therapeutic interventions.
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Affiliation(s)
- Dejiu Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Lei Zhu
- College of Basic Medical, Qingdao Binhai University, Qingdao, China
| | - Yin Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Yanyan Gao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
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26
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Park HS, Shapiro JR, Sitaras I, Woldemeskel BA, Garliss CC, Dziedzic A, Sachithanandham J, Jedlicka AE, Caputo CA, Rousseau KE, Thakar M, Suwanmanee S, Hauk P, Aliyu L, Majewska NI, Koley S, Patel B, Broderick P, Mosnaim G, Heath SL, Spivak ES, Shenoy A, Bloch EM, Gniadek TJ, Shoham S, Casadevall A, Hanley D, Cox AL, Laeyendecker O, Betenbaugh MJ, Cramer SM, Mostafa HH, Pekosz A, Blankson JN, Klein SL, Tobian AA, Sullivan D, Gebo KA. Adaptive immune responses in vaccinated patients with symptomatic SARS-CoV-2 Alpha infection. JCI Insight 2022; 7:e155944. [PMID: 35104245 PMCID: PMC8983140 DOI: 10.1172/jci.insight.155944] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 01/26/2022] [Indexed: 11/18/2022] Open
Abstract
Benchmarks for protective immunity from infection or severe disease after SARS-CoV-2 vaccination are still being defined. Here, we characterized virus neutralizing and ELISA antibody levels, cellular immune responses, and viral variants in 4 separate groups: healthy controls (HCs) weeks (early) or months (late) following vaccination in comparison with symptomatic patients with SARS-CoV-2 after partial or full mRNA vaccination. During the period of the study, most symptomatic breakthrough infections were caused by the SARS-CoV-2 Alpha variant. Neutralizing antibody levels in the HCs were sustained over time against the vaccine parent virus but decreased against the Alpha variant, whereas IgG titers and T cell responses against the parent virus and Alpha variant declined over time. Both partially and fully vaccinated patients with symptomatic infections had lower virus neutralizing antibody levels against the parent virus than the HCs, similar IgG antibody titers, and similar virus-specific T cell responses measured by IFN-γ. Compared with HCs, neutralization activity against the Alpha variant was lower in the partially vaccinated infected patients and tended to be lower in the fully vaccinated infected patients. In this cohort of breakthrough infections, parent virus neutralization was the superior predictor of breakthrough infections with the Alpha variant of SARS-CoV-2.
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Affiliation(s)
- Han-Sol Park
- W. Harry Feinstone Department of Molecular Microbiology and Immunology and
| | - Janna R. Shapiro
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Ioannis Sitaras
- W. Harry Feinstone Department of Molecular Microbiology and Immunology and
| | - Bezawit A. Woldemeskel
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Caroline C. Garliss
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Amanda Dziedzic
- W. Harry Feinstone Department of Molecular Microbiology and Immunology and
| | | | - Anne E. Jedlicka
- W. Harry Feinstone Department of Molecular Microbiology and Immunology and
| | | | - Kimberly E. Rousseau
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Manjusha Thakar
- W. Harry Feinstone Department of Molecular Microbiology and Immunology and
| | - San Suwanmanee
- W. Harry Feinstone Department of Molecular Microbiology and Immunology and
| | - Pricila Hauk
- Advanced Mammalian Biomanufacturing Innovation Center, Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Lateef Aliyu
- Advanced Mammalian Biomanufacturing Innovation Center, Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Natalia I. Majewska
- Advanced Mammalian Biomanufacturing Innovation Center, Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Sushmita Koley
- Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Bela Patel
- Critical Care Medicine, University of Texas Health, Houston, Texas, USA
| | | | - Giselle Mosnaim
- Division of Allergy and Immunology, Department of Medicine, Northshore University Health System, Evanston, Illinois, USA
| | - Sonya L. Heath
- Department of Medicine, Division of Infectious Diseases, University of Alabama Birmingham, Alabama, USA
| | - Emily S. Spivak
- Department of Medicine, Division of Infectious Diseases, University of Utah, Salt Lake City, Utah, USA
| | - Aarthi Shenoy
- Hematology Oncology, Medstar Washington Hospital Center, Washington, DC, USA
| | - Evan M. Bloch
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Thomas J. Gniadek
- Department of Pathology and Laboratory Medicine, Northshore University Health System, Evanston, Illinois, USA
| | - Shmuel Shoham
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Arturo Casadevall
- W. Harry Feinstone Department of Molecular Microbiology and Immunology and
| | - Daniel Hanley
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Andrea L. Cox
- W. Harry Feinstone Department of Molecular Microbiology and Immunology and
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Oliver Laeyendecker
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Michael J. Betenbaugh
- Advanced Mammalian Biomanufacturing Innovation Center, Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Steven M. Cramer
- Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Heba H. Mostafa
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology and
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Joel N. Blankson
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Sabra L. Klein
- W. Harry Feinstone Department of Molecular Microbiology and Immunology and
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Aaron A.R. Tobian
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - David Sullivan
- W. Harry Feinstone Department of Molecular Microbiology and Immunology and
| | - Kelly A. Gebo
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
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27
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Di Gioacchino A, Legendre R, Rahou Y, Najburg V, Charneau P, Greenbaum BD, Tangy F, van der Werf S, Cocco S, Komarova AV. sgDI-tector: defective interfering viral genome bioinformatics for detection of coronavirus subgenomic RNAs. RNA (NEW YORK, N.Y.) 2022; 28:277-289. [PMID: 34937774 PMCID: PMC8848934 DOI: 10.1261/rna.078969.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 12/07/2021] [Indexed: 06/14/2023]
Abstract
Coronavirus RNA-dependent RNA polymerases produce subgenomic RNAs (sgRNAs) that encode viral structural and accessory proteins. User-friendly bioinformatic tools to detect and quantify sgRNA production are urgently needed to study the growing number of next-generation sequencing (NGS) data of SARS-CoV-2. We introduced sgDI-tector to identify and quantify sgRNA in SARS-CoV-2 NGS data. sgDI-tector allowed detection of sgRNA without initial knowledge of the transcription-regulatory sequences. We produced NGS data and successfully detected the nested set of sgRNAs with the ranking M > ORF3a > N>ORF6 > ORF7a > ORF8 > S > E>ORF7b. We also compared the level of sgRNA production with other types of viral RNA products such as defective interfering viral genomes.
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Affiliation(s)
- Andrea Di Gioacchino
- Sorbonne Université, Université de Paris, Laboratoire de Physique de l'Ecole Normale Supérieure, PSL & CNRS UMR8063, 75005, Paris, France
| | - Rachel Legendre
- Institut Pasteur, Université de Paris, Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, 75015, Paris, France
| | - Yannis Rahou
- Institut Pasteur, Université de Paris, CNRS UMR3569, Génétique Moléculaire des Virus à ARN, F-75015 Paris, France
| | - Valérie Najburg
- Institut Pasteur, Université de Paris, Laboratory of Innovative Vaccines, 75015, Paris, France
| | - Pierre Charneau
- Institut Pasteur, Pasteur-TheraVectys joined unit, 75015, Paris, France
| | - Benjamin D Greenbaum
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York 10065, USA
- Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, Weill Cornell Medical College, New York 10065, USA
| | - Frédéric Tangy
- Institut Pasteur, Université de Paris, Laboratory of Innovative Vaccines, 75015, Paris, France
| | - Sylvie van der Werf
- Institut Pasteur, Université de Paris, CNRS UMR3569, Génétique Moléculaire des Virus à ARN, F-75015 Paris, France
| | - Simona Cocco
- Sorbonne Université, Université de Paris, Laboratoire de Physique de l'Ecole Normale Supérieure, PSL & CNRS UMR8063, 75005, Paris, France
| | - Anastassia V Komarova
- Institut Pasteur, Université de Paris, CNRS UMR3569, Génétique Moléculaire des Virus à ARN, F-75015 Paris, France
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28
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Mallick R, Duttaroy AK. Origin and Structural Biology of Novel Coronavirus (SARS-CoV-2). ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1352:1-13. [PMID: 35132591 DOI: 10.1007/978-3-030-85109-5_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
INTRODUCTION A recent rapid outbreak of infection around the globe has been caused by a novel coronavirus, now known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which was first identified in December 2019 in Wuhan city of Hubei province, People's Republic of China. METHODS We reviewed the currently available literature on coronaviruses. RESULTS Coronaviruses are a group of enveloped viruses with non-segmented, single-stranded, and positive-sense RNA genomes. Although 13 variation sites in open reading frames have been identified among SARS-CoV-2 strains, no mutation has been observed so far in envelop protein. The origin and structural biology of SARS-CoV-2 in details are discussed. CONCLUSIONS Origin and structural biology will help the researchers identify the virus's mechanism in the host and drug design. Currently, no clinical treatments or prevention strategies are available for any human coronavirus.
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Affiliation(s)
- Rahul Mallick
- Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Asim K Duttaroy
- Department of Nutrition, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway.
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29
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Malone B, Urakova N, Snijder EJ, Campbell EA. Structures and functions of coronavirus replication-transcription complexes and their relevance for SARS-CoV-2 drug design. Nat Rev Mol Cell Biol 2022; 23:21-39. [PMID: 34824452 PMCID: PMC8613731 DOI: 10.1038/s41580-021-00432-z] [Citation(s) in RCA: 184] [Impact Index Per Article: 92.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/22/2021] [Indexed: 02/08/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has killed millions of people and continues to cause massive global upheaval. Coronaviruses are positive-strand RNA viruses with an unusually large genome of ~30 kb. They express an RNA-dependent RNA polymerase and a cohort of other replication enzymes and supporting factors to transcribe and replicate their genomes. The proteins performing these essential processes are prime antiviral drug targets, but drug discovery is hindered by our incomplete understanding of coronavirus RNA synthesis and processing. In infected cells, the RNA-dependent RNA polymerase must coordinate with other viral and host factors to produce both viral mRNAs and new genomes. Recent research aiming to decipher and contextualize the structures, functions and interplay of the subunits of the SARS-CoV-2 replication and transcription complex proteins has burgeoned. In this Review, we discuss recent advancements in our understanding of the molecular basis and complexity of the coronavirus RNA-synthesizing machinery. Specifically, we outline the mechanisms and regulation of RNA translation, replication and transcription. We also discuss the composition of the replication and transcription complexes and their suitability as targets for antiviral therapy.
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Affiliation(s)
- Brandon Malone
- grid.134907.80000 0001 2166 1519Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY USA
| | - Nadya Urakova
- grid.10419.3d0000000089452978Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Eric J. Snijder
- grid.10419.3d0000000089452978Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Elizabeth A. Campbell
- grid.134907.80000 0001 2166 1519Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY USA
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30
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Amantadine has potential for the treatment of COVID-19 because it inhibits known and novel ion channels encoded by SARS-CoV-2. Commun Biol 2021; 4:1347. [PMID: 34853399 PMCID: PMC8636635 DOI: 10.1038/s42003-021-02866-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 11/02/2021] [Indexed: 12/16/2022] Open
Abstract
The dire need for COVID-19 treatments has inspired strategies of repurposing approved drugs. Amantadine has been suggested as a candidate, and cellular as well as clinical studies have indicated beneficial effects of this drug. We demonstrate that amantadine and hexamethylene-amiloride (HMA), but not rimantadine, block the ion channel activity of Protein E from SARS-CoV-2, a conserved viroporin among coronaviruses. These findings agree with their binding to Protein E as evaluated by solution NMR and molecular dynamics simulations. Moreover, we identify two novel viroporins of SARS-CoV-2; ORF7b and ORF10, by showing ion channel activity in a X. laevis oocyte expression system. Notably, amantadine also blocks the ion channel activity of ORF10, thereby providing two ion channel targets in SARS-CoV-2 for amantadine treatment in COVID-19 patients. A screen of known viroporin inhibitors on Protein E, ORF7b, ORF10 and Protein 3a from SARS-CoV-2 revealed inhibition of Protein E and ORF7b by emodin and xanthene, the latter also blocking Protein 3a. This illustrates a general potential of well-known ion channel blockers against SARS-CoV-2 and specifically a dual molecular basis for the promising effects of amantadine in COVID-19 treatment. Toft-Bertelsen et al. describe repurposing of anti-influenza drug amantadine and its derivatives for the treatment of SARS-CoV-2. They show that Amantadine, Emodin and Xanthene show significant blockage of ionchannels formed by SARS-CoV-2 which are crucial for its assembly and pathophysiology.
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31
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D’Souza AR, Buckingham AB, Salasc F, Ingemarsdotter CK, Iaconis G, Jarvis I, Groom HCT, Kenyon JC, Lever AML. Duplex formation between the template and the nascent strand in the transcription-regulating sequences is associated with the site of template switching in SARS - CoV-2. RNA Biol 2021; 18:148-156. [PMID: 34541994 PMCID: PMC8459930 DOI: 10.1080/15476286.2021.1975388] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 08/23/2021] [Accepted: 08/26/2021] [Indexed: 11/23/2022] Open
Abstract
Recently published transcriptomic data of the SARS-CoV-2 coronavirus show that there is a large variation in the frequency and steady state levels of subgenomic mRNA sequences. This variation is derived from discontinuous subgenomic RNA synthesis, where the polymerase switches template from a 3' proximal genome body sequence to a 5' untranslated leader sequence. This leads to a fusion between the common 5' leader sequence and a 3' proximal body sequence in the RNA product. This process revolves around a common core sequence (CS) that is present at both the template sites that make up the fusion junction. Base-pairing between the leader CS and the nascent complementary minus strand body CS, and flanking regions (together called the transcription regulating sequence, TRS) is vital for this template switching event. However, various factors can influence the site of template switching within the same TRS duplex. Here, we model the duplexes formed between the leader and complementary body TRS regions, hypothesizing the role of the stability of the TRS duplex in determining the major sites of template switching for the most abundant mRNAs. We indicate that the stability of secondary structures and the speed of transcription play key roles in determining the probability of template switching in the production of subgenomic RNAs. We speculate on the effect of reported variant nucleotide substitutions on our models.
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Affiliation(s)
- Aaron R. D’Souza
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | - Fanny Salasc
- Department of Medicine, University of Cambridge, Cambridge, UK
| | | | - Gennaro Iaconis
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Isobel Jarvis
- Department of Medicine, University of Cambridge, Cambridge, UK
| | | | - Julia C. Kenyon
- Department of Medicine, University of Cambridge, Cambridge, UK
- Homerton College, Cambridge, UK
- Department of Microbiology and Immunology, National University of Singapore, Singapore
| | - Andrew M. L. Lever
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Department of Medicine, University of Cambridge, Cambridge, UK
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32
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Karaba AH, Zhu X, Liang T, Wang KH, Rittenhouse AG, Akinde O, Eby Y, Ruff JE, Blankson JN, Abedon AT, Alejo JL, Cox AL, Bailey JR, Thompson EA, Klein SL, Warren DS, Garonzik-Wang JM, Boyarsky BJ, Sitaras I, Pekosz A, Segev DL, Tobian AAR, Werbel WA. A Third Dose of SARS-CoV-2 Vaccine Increases Neutralizing Antibodies Against Variants of Concern in Solid Organ Transplant Recipients. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.08.11.21261914. [PMID: 34671774 PMCID: PMC8528082 DOI: 10.1101/2021.08.11.21261914] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Vaccine-induced SARS-CoV-2 antibody responses are attenuated in solid organ transplant recipients (SOTRs) and breakthrough infections are more common. Additional SARS-CoV-2 vaccine doses increase anti-spike IgG in some SOTRs, but it is uncertain whether neutralization of variants of concern (VOCs) is enhanced. We tested 47 SOTRs for clinical and research anti-spike IgG, pseudoneutralization (ACE2 blocking), and live-virus neutralization (nAb) against VOCs before and after a third SARS-CoV-2 vaccine dose (70% mRNA, 30% Ad26.COV2.S) with comparison to 15 healthy controls after two mRNA vaccine doses. We used correlation analysis to compare anti-spike IgG assays and focused on thresholds associated with neutralizing activity. A third SARS-CoV-2 vaccine dose increased median anti-spike (1.6-fold) and receptor-binding domain (1.5-fold) IgG, as well as pseudoneutralization against VOCs (2.5-fold versus Delta). However, IgG and neutralization activity were significantly lower than healthy controls (p<0.001); 32% of SOTRs had zero detectable nAb against Delta after third vaccination. Correlation with nAb was seen at anti-spike IgG >4 AU on the clinical assay and >10^4 AU on the research assay. These findings highlight benefits of a third vaccine dose for some SOTRs and the need for alternative strategies to improve protection in a significant subset of this population.
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Affiliation(s)
- Andrew H Karaba
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Xianming Zhu
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Tao Liang
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Kristy H Wang
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Alex G Rittenhouse
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Olivia Akinde
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Yolanda Eby
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Jessica E Ruff
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Joel N Blankson
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Aura T Abedon
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Jennifer L Alejo
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Andrea L Cox
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21287, USA
- Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Justin R Bailey
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Elizabeth A Thompson
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Sabra L Klein
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21287, USA
| | - Daniel S Warren
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | | | - Brian J Boyarsky
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Ioannis Sitaras
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21287, USA
| | - Andrew Pekosz
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21287, USA
| | - Dorry L Segev
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Aaron A R Tobian
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - William A Werbel
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
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33
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O’Donoghue SI, Schafferhans A, Sikta N, Stolte C, Kaur S, Ho BK, Anderson S, Procter JB, Dallago C, Bordin N, Adcock M, Rost B. SARS-CoV-2 structural coverage map reveals viral protein assembly, mimicry, and hijacking mechanisms. Mol Syst Biol 2021; 17:e10079. [PMID: 34519429 PMCID: PMC8438690 DOI: 10.15252/msb.202010079] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 01/18/2023] Open
Abstract
We modeled 3D structures of all SARS-CoV-2 proteins, generating 2,060 models that span 69% of the viral proteome and provide details not available elsewhere. We found that ˜6% of the proteome mimicked human proteins, while ˜7% was implicated in hijacking mechanisms that reverse post-translational modifications, block host translation, and disable host defenses; a further ˜29% self-assembled into heteromeric states that provided insight into how the viral replication and translation complex forms. To make these 3D models more accessible, we devised a structural coverage map, a novel visualization method to show what is-and is not-known about the 3D structure of the viral proteome. We integrated the coverage map into an accompanying online resource (https://aquaria.ws/covid) that can be used to find and explore models corresponding to the 79 structural states identified in this work. The resulting Aquaria-COVID resource helps scientists use emerging structural data to understand the mechanisms underlying coronavirus infection and draws attention to the 31% of the viral proteome that remains structurally unknown or dark.
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MESH Headings
- Amino Acid Transport Systems, Neutral/chemistry
- Amino Acid Transport Systems, Neutral/genetics
- Amino Acid Transport Systems, Neutral/metabolism
- Angiotensin-Converting Enzyme 2/chemistry
- Angiotensin-Converting Enzyme 2/genetics
- Angiotensin-Converting Enzyme 2/metabolism
- Binding Sites
- COVID-19/genetics
- COVID-19/metabolism
- COVID-19/virology
- Computational Biology/methods
- Coronavirus Envelope Proteins/chemistry
- Coronavirus Envelope Proteins/genetics
- Coronavirus Envelope Proteins/metabolism
- Coronavirus Nucleocapsid Proteins/chemistry
- Coronavirus Nucleocapsid Proteins/genetics
- Coronavirus Nucleocapsid Proteins/metabolism
- Host-Pathogen Interactions/genetics
- Humans
- Mitochondrial Membrane Transport Proteins/chemistry
- Mitochondrial Membrane Transport Proteins/genetics
- Mitochondrial Membrane Transport Proteins/metabolism
- Mitochondrial Precursor Protein Import Complex Proteins
- Models, Molecular
- Molecular Mimicry
- Neuropilin-1/chemistry
- Neuropilin-1/genetics
- Neuropilin-1/metabolism
- Phosphoproteins/chemistry
- Phosphoproteins/genetics
- Phosphoproteins/metabolism
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- Protein Interaction Mapping/methods
- Protein Multimerization
- Protein Processing, Post-Translational
- SARS-CoV-2/chemistry
- SARS-CoV-2/genetics
- SARS-CoV-2/metabolism
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/metabolism
- Viral Matrix Proteins/chemistry
- Viral Matrix Proteins/genetics
- Viral Matrix Proteins/metabolism
- Viroporin Proteins/chemistry
- Viroporin Proteins/genetics
- Viroporin Proteins/metabolism
- Virus Replication
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Affiliation(s)
- Seán I O’Donoghue
- Garvan Institute of Medical ResearchDarlinghurstNSWAustralia
- CSIRO Data61CanberraACTAustralia
- School of Biotechnology and Biomolecular Sciences (UNSW)KensingtonNSWAustralia
| | - Andrea Schafferhans
- Garvan Institute of Medical ResearchDarlinghurstNSWAustralia
- Department of Bioengineering SciencesWeihenstephan‐Tr. University of Applied SciencesFreisingGermany
- Department of InformaticsBioinformatics & Computational BiologyTechnical University of MunichMunichGermany
| | - Neblina Sikta
- Garvan Institute of Medical ResearchDarlinghurstNSWAustralia
| | | | - Sandeep Kaur
- Garvan Institute of Medical ResearchDarlinghurstNSWAustralia
- School of Biotechnology and Biomolecular Sciences (UNSW)KensingtonNSWAustralia
| | - Bosco K Ho
- Garvan Institute of Medical ResearchDarlinghurstNSWAustralia
| | | | | | - Christian Dallago
- Department of InformaticsBioinformatics & Computational BiologyTechnical University of MunichMunichGermany
| | - Nicola Bordin
- Institute of Structural and Molecular BiologyUniversity College LondonLondonUK
| | | | - Burkhard Rost
- Department of InformaticsBioinformatics & Computational BiologyTechnical University of MunichMunichGermany
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34
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Dhakal S, Ruiz-Bedoya CA, Zhou R, Creisher PS, Villano JS, Littlefield K, Ruelas Castillo J, Marinho P, Jedlicka AE, Ordonez AA, Bahr M, Majewska N, Betenbaugh MJ, Flavahan K, Mueller ARL, Looney MM, Quijada D, Mota F, Beck SE, Brockhurst J, Braxton AM, Castell N, Stover M, D’Alessio FR, Metcalf Pate KA, Karakousis PC, Mankowski JL, Pekosz A, Jain SK, Klein SL. Sex Differences in Lung Imaging and SARS-CoV-2 Antibody Responses in a COVID-19 Golden Syrian Hamster Model. mBio 2021; 12:e0097421. [PMID: 34253053 PMCID: PMC8406232 DOI: 10.1128/mbio.00974-21] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/10/2021] [Indexed: 12/15/2022] Open
Abstract
In the coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), more severe outcomes are reported in males than in females, including hospitalizations and deaths. Animal models can provide an opportunity to mechanistically interrogate causes of sex differences in the pathogenesis of SARS-CoV-2. Adult male and female golden Syrian hamsters (8 to 10 weeks of age) were inoculated intranasally with 105 50% tissue culture infective dose (TCID50) of SARS-CoV-2/USA-WA1/2020 and euthanized at several time points during the acute (i.e., virus actively replicating) and recovery (i.e., after the infectious virus has been cleared) phases of infection. There was no mortality, but infected male hamsters experienced greater morbidity, losing a greater percentage of body mass, developed more extensive pneumonia as noted on chest computed tomography, and recovered more slowly than females. Treatment of male hamsters with estradiol did not alter pulmonary damage. Virus titers in respiratory tissues, including nasal turbinates, trachea, and lungs, and pulmonary cytokine concentrations, including interferon-β (IFN-β) and tumor necrosis factor-α (TNF-α), were comparable between the sexes. However, during the recovery phase of infection, females mounted 2-fold greater IgM, IgG, and IgA responses against the receptor-binding domain of the spike protein (S-RBD) in both plasma and respiratory tissues. Female hamsters also had significantly greater IgG antibodies against whole-inactivated SARS-CoV-2 and mutant S-RBDs as well as virus-neutralizing antibodies in plasma. The development of an animal model to study COVID-19 sex differences will allow for a greater mechanistic understanding of the SARS-CoV-2-associated sex differences seen in the human population. IMPORTANCE Men experience more severe outcomes from coronavirus disease 2019 (COVID-19) than women. Golden Syrian hamsters were used to explore sex differences in the pathogenesis of a human isolate of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). After inoculation, male hamsters experienced greater sickness, developed more severe lung pathology, and recovered more slowly than females. Sex differences in disease could not be reversed by estradiol treatment in males and were not explained by either virus replication kinetics or the concentrations of inflammatory cytokines in the lungs. During the recovery period, antiviral antibody responses in the respiratory tract and plasma, including to newly emerging SARS-CoV-2 variants, were greater in female than in male hamsters. Greater lung pathology during the acute phase combined with lower antiviral antibody responses during the recovery phase of infection in males than in females illustrate the utility of golden Syrian hamsters as a model to explore sex differences in the pathogenesis of SARS-CoV-2 and vaccine-induced immunity and protection.
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Affiliation(s)
- Santosh Dhakal
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Camilo A. Ruiz-Bedoya
- Department of Pediatrics, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Ruifeng Zhou
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Patrick S. Creisher
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Jason S. Villano
- Department of Molecular and Comparative Pathobiology, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Kirsten Littlefield
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | | | - Paula Marinho
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Anne E. Jedlicka
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Alvaro A. Ordonez
- Department of Pediatrics, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Melissa Bahr
- Department of Pediatrics, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Natalia Majewska
- Advanced Mammalian Biomanufacturing Innovation Center, Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Michael J. Betenbaugh
- Advanced Mammalian Biomanufacturing Innovation Center, Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Kelly Flavahan
- Department of Pediatrics, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Alice R. L. Mueller
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Monika M. Looney
- Department of Medicine, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Darla Quijada
- Department of Medicine, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Filipa Mota
- Department of Pediatrics, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Sarah E. Beck
- Department of Molecular and Comparative Pathobiology, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Jacqueline Brockhurst
- Department of Molecular and Comparative Pathobiology, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Alicia M. Braxton
- Department of Molecular and Comparative Pathobiology, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Natalie Castell
- Department of Molecular and Comparative Pathobiology, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Mitchel Stover
- Department of Molecular and Comparative Pathobiology, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Franco R. D’Alessio
- Department of Medicine, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Kelly A. Metcalf Pate
- Department of Molecular and Comparative Pathobiology, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Petros C. Karakousis
- Department of Medicine, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Joseph L. Mankowski
- Department of Molecular and Comparative Pathobiology, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Department of Molecular and Comparative Pathobiology, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Sanjay K. Jain
- Department of Pediatrics, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Sabra L. Klein
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
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35
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A high-resolution temporal atlas of the SARS-CoV-2 translatome and transcriptome. Nat Commun 2021; 12:5120. [PMID: 34433827 PMCID: PMC8387416 DOI: 10.1038/s41467-021-25361-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 08/02/2021] [Indexed: 12/15/2022] Open
Abstract
COVID-19 is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which infected >200 million people resulting in >4 million deaths. However, temporal landscape of the SARS-CoV-2 translatome and its impact on the human genome remain unexplored. Here, we report a high-resolution atlas of the translatome and transcriptome of SARS-CoV-2 for various time points after infecting human cells. Intriguingly, substantial amount of SARS-CoV-2 translation initiates at a novel translation initiation site (TIS) located in the leader sequence, termed TIS-L. Since TIS-L is included in all the genomic and subgenomic RNAs, the SARS-CoV-2 translatome may be regulated by a sophisticated interplay between TIS-L and downstream TISs. TIS-L functions as a strong translation enhancer for ORF S, and as translation suppressors for most of the other ORFs. Our global temporal atlas provides compelling insight into unique regulation of the SARS-CoV-2 translatome and helps comprehensively evaluate its impact on the human genome. Here, Kim et al. apply various sequencing techniques (RPF-seq, QTI-seq, mRNA-seq, sRNA-seq) to unravel the high-resolution, longitudinal translatome and transcriptome of SARS-CoV-2. They identify a translation initiation site in the leader sequence of all genomic and subgenomic RNAs and show its relevance for the SARS-CoV-2 translatome.
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Contribution of SARS-CoV-2 Accessory Proteins to Viral Pathogenicity in K18 Human ACE2 Transgenic Mice. J Virol 2021; 95:e0040221. [PMID: 34133899 PMCID: PMC8354228 DOI: 10.1128/jvi.00402-21] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the viral pathogen responsible for the current coronavirus disease 2019 (COVID-19) pandemic. As of 19 May 2021, John Hopkins University’s COVID-19 tracking platform reported 3.3 million deaths associated with SARS-CoV-2 infection. Currently, the World Health Organization has granted emergency use listing (EUL) to six COVID-19 vaccine candidates. However, much of the pathogenesis observed during SARS-CoV-2 infection remains elusive. To gain insight into the contribution of individual accessory open reading frame (ORF) proteins in SARS-CoV-2 pathogenesis, we used our recently described reverse-genetics system approach to successfully engineer recombinant SARS-CoV-2 (rSARS-CoV-2) constructs; we removed individual viral ORF3a, −6, −7a, −7b, and −8 proteins from them, and we characterized the resulting recombinant viruses in vitro and in vivo. Our results indicate differences in plaque morphology, with ORF-deficient (ΔORF) viruses producing smaller plaques than those of the wild type (rSARS-CoV-2/WT). However, growth kinetics of ΔORF viruses were like those of rSARS-CoV-2/WT. Interestingly, infection of K18 human angiotensin-converting enzyme 2 (hACE2) transgenic mice with the ΔORF rSARS-CoV-2s identified ORF3a and ORF6 as the major contributors of viral pathogenesis, while ΔORF7a, ΔORF7b, and ΔORF8 rSARS-CoV-2s induced pathology comparable to that of rSARS-CoV-2/WT. This study demonstrates the robustness of our reverse-genetics system to generate rSARS-CoV-2 constructs and the major role for ORF3a and ORF6 in viral pathogenesis, providing important information for the generation of attenuated forms of SARS-CoV-2 for their implementation as live attenuated vaccines for the treatment of SARS-CoV-2 infection and associated COVID-19. IMPORTANCE Despite great efforts put forward worldwide to combat the current coronavirus disease 2019 (COVID-19) pandemic, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to be a human health and socioeconomic threat. Insights into the pathogenesis of SARS-CoV-2 and the contribution of viral proteins to disease outcome remain elusive. Our study aims (i) to determine the contribution of SARS-CoV-2 accessory open reading frame (ORF) proteins to viral pathogenesis and disease outcome and (ii) to develop a synergistic platform combining our robust reverse-genetics system to generate recombinant SARS-CoV-2 constructs with a validated rodent model of infection and disease. We demonstrate that SARS-CoV-2 ORF3a and ORF6 contribute to lung pathology and ultimately disease outcome in K18 hACE2 transgenic mice, while ORF7a, ORF7b, and ORF8 have little impact on disease outcome. Moreover, our combinatory platform serves as a foundation for generating attenuated forms of the virus to develop live attenuated vaccines for the treatment of SARS-CoV-2.
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Abstract
CoVID-19 is a multi-symptomatic disease which has made a global impact due to its ability to spread rapidly, and its relatively high mortality rate. Beyond the heroic efforts to develop vaccines, which we do not discuss herein, the response of scientists and clinicians to this complex problem has reflected the need to detect CoVID-19 rapidly, to diagnose patients likely to show adverse symptoms, and to treat severe and critical CoVID-19. Here we aim to encapsulate these varied and sometimes conflicting approaches and the resulting data in terms of chemistry and biology. In the process we highlight emerging concepts, and potential future applications that may arise out of this immense effort.
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Affiliation(s)
| | - Yimon Aye
- Swiss Federal Institute of Technology in Lausanne (EPFL)1015LausanneSwitzerland
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38
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Kim C, Mahasenan KV, Bhardwaj A, Wiest O, Chang M, Mobashery S. Production of Proteins of the SARS-CoV-2 Proteome for Drug Discovery. ACS OMEGA 2021; 6:19983-19994. [PMID: 34337272 PMCID: PMC8315141 DOI: 10.1021/acsomega.1c02984] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 07/06/2021] [Indexed: 05/09/2023]
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the causative agent of the coronavirus disease of 2019 (COVID-19). Its genome encodes two open reading frames for two large proteins, PP1a and PP1ab. Within the two polypeptide stretches, there are two proteases that process the large proteins into 15 discrete proteins essential for the assembly of the virion during its replication. We describe herein the cloning of the genes for these discrete proteins optimized for expression in Escherichia coli, production of the proteins, and their purification to homogeneity. These included all but six: NSP6, which possesses eight transmembrane regions, and five that are small proteins/peptides (E, ORF3b, ORF6, ORF7b, and ORF10). These proteins are intended for experimental validation of small-molecule binders as molecular template hits. The proof of concept was established with the ADP-ribosylhydrolase (ARH) domain of NSP3 in discovery of small-molecule templates that could serve as the basis for further optimization. The hit molecules include one submicromolar and a few low-micromolar binders to the ARH domain. Availability of these proteins in soluble forms opens up the opportunity for discoveries of novel templates with the potential for anti-COVID-19 pharmaceuticals.
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Shemesh M, Aktepe TE, Deerain JM, McAuley JL, Audsley MD, David CT, Purcell DFJ, Urin V, Hartmann R, Moseley GW, Mackenzie JM, Schreiber G, Harari D. SARS-CoV-2 suppresses IFNβ production mediated by NSP1, 5, 6, 15, ORF6 and ORF7b but does not suppress the effects of added interferon. PLoS Pathog 2021; 17:e1009800. [PMID: 34437657 PMCID: PMC8389490 DOI: 10.1371/journal.ppat.1009800] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 07/14/2021] [Indexed: 12/16/2022] Open
Abstract
Type I Interferons (IFN-Is) are a family of cytokines which play a major role in inhibiting viral infection. Resultantly, many viruses have evolved mechanisms in which to evade the IFN-I response. Here we tested the impact of expression of 27 different SARS-CoV-2 genes in relation to their effect on IFN production and activity using three independent experimental methods. We identified six gene products; NSP6, ORF6, ORF7b, NSP1, NSP5 and NSP15, which strongly (>10-fold) blocked MAVS-induced (but not TRIF-induced) IFNβ production. Expression of the first three of these SARS-CoV-2 genes specifically blocked MAVS-induced IFNβ-promoter activity, whereas all six genes induced a collapse in IFNβ mRNA levels, corresponding with suppressed IFNβ protein secretion. Five of these six genes furthermore suppressed MAVS-induced activation of IFNλs, however with no effect on IFNα or IFNγ production. In sharp contrast, SARS-CoV-2 infected cells remained extremely sensitive to anti-viral activity exerted by added IFN-Is. None of the SARS-CoV-2 genes were able to block IFN-I signaling, as demonstrated by robust activation of Interferon Stimulated Genes (ISGs) by added interferon. This, despite the reduced levels of STAT1 and phospho-STAT1, was likely caused by broad translation inhibition mediated by NSP1. Finally, we found that a truncated ORF7b variant that has arisen from a mutant SARS-CoV-2 strain harboring a 382-nucleotide deletion associating with mild disease (Δ382 strain identified in Singapore & Taiwan in 2020) lost its ability to suppress type I and type III IFN production. In summary, our findings support a multi-gene process in which SARS-CoV-2 blocks IFN-production, with ORF7b as a major player, presumably facilitating evasion of host detection during early infection. However, SARS-CoV-2 fails to suppress IFN-I signaling thus providing an opportunity to exploit IFN-Is as potential therapeutic antiviral drugs.
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Affiliation(s)
- Maya Shemesh
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Turgut E. Aktepe
- Department of Microbiology and Immunology, University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, Parkville, Melbourne, Victoria, Australia
| | - Joshua M. Deerain
- Department of Microbiology and Immunology, University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, Parkville, Melbourne, Victoria, Australia
| | - Julie L. McAuley
- Department of Microbiology and Immunology, University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, Parkville, Melbourne, Victoria, Australia
| | - Michelle D. Audsley
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Victoria, Australia
| | - Cassandra T. David
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Victoria, Australia
| | - Damian F. J. Purcell
- Department of Microbiology and Immunology, University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, Parkville, Melbourne, Victoria, Australia
| | - Victoria Urin
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Rune Hartmann
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Gregory W. Moseley
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Victoria, Australia
| | - Jason M. Mackenzie
- Department of Microbiology and Immunology, University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, Parkville, Melbourne, Victoria, Australia
| | - Gideon Schreiber
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Daniel Harari
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
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40
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Redondo N, Zaldívar-López S, Garrido JJ, Montoya M. SARS-CoV-2 Accessory Proteins in Viral Pathogenesis: Knowns and Unknowns. Front Immunol 2021; 12:708264. [PMID: 34305949 PMCID: PMC8293742 DOI: 10.3389/fimmu.2021.708264] [Citation(s) in RCA: 163] [Impact Index Per Article: 54.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 06/22/2021] [Indexed: 12/23/2022] Open
Abstract
There are still many unanswered questions concerning viral SARS-CoV-2 pathogenesis in COVID-19. Accessory proteins in SARS-CoV-2 consist of eleven viral proteins whose roles during infection are still not completely understood. Here, a review on the current knowledge of SARS-CoV-2 accessory proteins is summarized updating new research that could be critical in understanding SARS-CoV-2 interaction with the host. Some accessory proteins such as ORF3b, ORF6, ORF7a and ORF8 have been shown to be important IFN-I antagonists inducing an impairment in the host immune response. In addition, ORF3a is involved in apoptosis whereas others like ORF9b and ORF9c interact with cellular organelles leading to suppression of the antiviral response in infected cells. However, possible roles of ORF7b and ORF10 are still awaiting to be described. Also, ORF3d has been reassigned. Relevant information on the knowns and the unknowns in these proteins is analyzed, which could be crucial for further understanding of SARS-CoV-2 pathogenesis and to design strategies counteracting their actions evading immune responses in COVID-19.
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Affiliation(s)
- Natalia Redondo
- Molecular Biomedicine Department, Centro de Investigaciones Biológicas Margarita Salas (CIB-CSIC), Madrid, Spain
| | - Sara Zaldívar-López
- Animal Breeding and Genomics Group, Department of Genetics, Faculty of Veterinary Medicine, University of Córdoba, Córdoba, Spain
- Immunogenomics and Molecular Pathogenesis GA14 Group, Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
| | - Juan J. Garrido
- Animal Breeding and Genomics Group, Department of Genetics, Faculty of Veterinary Medicine, University of Córdoba, Córdoba, Spain
- Immunogenomics and Molecular Pathogenesis GA14 Group, Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
| | - Maria Montoya
- Molecular Biomedicine Department, Centro de Investigaciones Biológicas Margarita Salas (CIB-CSIC), Madrid, Spain
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41
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In silico analysis of the aggregation propensity of the SARS-CoV-2 proteome: Insight into possible cellular pathologies. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2021; 1869:140693. [PMID: 34237472 PMCID: PMC8256665 DOI: 10.1016/j.bbapap.2021.140693] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/29/2021] [Accepted: 06/30/2021] [Indexed: 12/12/2022]
Abstract
The SARS-CoV-2 virus causes the coronavirus disease 19 emerged in 2020. The pandemic triggered a turmoil in public health and is having a tremendous social and economic impact around the globe. Upon entry into host cells, the SARS-CoV-2 virus hijacks cellular machineries to produce and maintain its own proteins, spreading the infection. Although the disease is known for prominent respiratory symptoms, accumulating evidence is also demonstrating the involvement of the central nervous system, with possible mid- and long-term neurological consequences. In this study, we conducted a detailed bioinformatic analysis of the SARS-CoV-2 proteome aggregation propensity by using several complementary computational tools. Our study identified 10 aggregation prone proteins in the reference SARS-CoV-2 strain: the non-structural proteins Nsp4, Nsp6 and Nsp7 as well as ORF3a, ORF6, ORF7a, ORF7b, ORF10, CovE and CovM. By searching for the available mutants of each protein, we have found that most proteins are conserved, while ORF3a and ORF7b are variable and characterized by the occurrence of a large number of mutants with increased aggregation propensity. The geographical distribution of the mutants revealed interesting differences in the localization of aggregation-prone mutants of each protein. Aggregation-prone mutants of ORF7b were found in 7 European countries, whereas those of ORF3a in only 2. Aggregation-prone sequences of ORF7b, but not of ORF3a, were identified in Australia, India, Nepal, China, and Thailand. Our results are important for future analysis of a possible correlation between higher transmissibility and infection, as well as the presence of neurological symptoms with aggregation propensity of SARS-CoV-2 proteins.
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42
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Srivastava V, Ahmad A. New perspective towards therapeutic regimen against SARS-CoV-2 infection. J Infect Public Health 2021; 14:852-862. [PMID: 34118735 PMCID: PMC8152204 DOI: 10.1016/j.jiph.2021.05.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 05/05/2021] [Accepted: 05/16/2021] [Indexed: 12/23/2022] Open
Abstract
The ongoing enormous loss of human life owing to Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), has led to a global crisis ranging from the collapse of health - care systems to socio-economic instability. As SARS-CoV-2 is a novel virus, very little information is available from researchers and therefore, a rigorous effort is required to decode its pathogenicity. There are no licenced treatment options available for treating SARS-CoV-2 infections and the development of a new antiviral drug targeting coronavirus cannot happen soon. Consequently, drug repurposing is a promising solution for combating the present pandemic. In this review, we have thoroughly discussed all the proteins encoded by the SARS-CoV-2 genome; their importance in pathogenicity and their potential role in drug discovery. Also, the budding threat of co-infections by other pathogenic microbes has been highlighted. Furthermore, the advances made in the medicinal field for the treatment and prevention of this viral infection is explained. Altogether, this review will provide some insightful discussions about this infectious disease and will meet certain of the knowledge gaps which exist by presenting an exhaustive and extensive scientific report on the ongoing mission for COVID-19 drug discovery.
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Affiliation(s)
- Vartika Srivastava
- Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2193, South Africa
| | - Aijaz Ahmad
- Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2193, South Africa; Infection Control, Charlotte Maxeke Johannesburg Academic Hospital, National Health Laboratory Service, Johannesburg, 2193, South Africa.
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43
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Gorkhali R, Koirala P, Rijal S, Mainali A, Baral A, Bhattarai HK. Structure and Function of Major SARS-CoV-2 and SARS-CoV Proteins. Bioinform Biol Insights 2021; 15:11779322211025876. [PMID: 34220199 PMCID: PMC8221690 DOI: 10.1177/11779322211025876] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 05/25/2021] [Indexed: 01/20/2023] Open
Abstract
SARS-CoV-2 virus, the causative agent of COVID-19 pandemic, has a genomic organization consisting of 16 nonstructural proteins (nsps), 4 structural proteins, and 9 accessory proteins. Relative of SARS-CoV-2, SARS-CoV, has genomic organization, which is very similar. In this article, the function and structure of the proteins of SARS-CoV-2 and SARS-CoV are described in great detail. The nsps are expressed as a single or two polyproteins, which are then cleaved into individual proteins using two proteases of the virus, a chymotrypsin-like protease and a papain-like protease. The released proteins serve as centers of virus replication and transcription. Some of these nsps modulate the host’s translation and immune systems, while others help the virus evade the host immune system. Some of the nsps help form replication-transcription complex at double-membrane vesicles. Others, including one RNA-dependent RNA polymerase and one exonuclease, help in the polymerization of newly synthesized RNA of the virus and help minimize the mutation rate by proofreading. After synthesis of the viral RNA, it gets capped. The capping consists of adding GMP and a methylation mark, called cap 0 and additionally adding a methyl group to the terminal ribose called cap1. Capping is accomplished with the help of a helicase, which also helps remove a phosphate, two methyltransferases, and a scaffolding factor. Among the structural proteins, S protein forms the receptor of the virus, which latches on the angiotensin-converting enzyme 2 receptor of the host and N protein binds and protects the genomic RNA of the virus. The accessory proteins found in these viruses are small proteins with immune modulatory roles. Besides functions of these proteins, solved X-ray and cryogenic electron microscopy structures related to the function of the proteins along with comparisons to other coronavirus homologs have been described in the article. Finally, the rate of mutation of SARS-CoV-2 residues of the proteome during the 2020 pandemic has been described. Some proteins are mutated more often than other proteins, but the significance of these mutation rates is not fully understood.
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Affiliation(s)
- Ritesh Gorkhali
- Department of Biotechnology, Kathmandu University, Dhulikhel, Nepal
| | | | - Sadikshya Rijal
- Department of Biotechnology, Kathmandu University, Dhulikhel, Nepal
| | - Ashmita Mainali
- Department of Biotechnology, Kathmandu University, Dhulikhel, Nepal
| | - Adesh Baral
- Department of Biotechnology, Kathmandu University, Dhulikhel, Nepal
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44
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Jungreis I, Sealfon R, Kellis M. SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. Nat Commun 2021; 12:2642. [PMID: 33976134 PMCID: PMC8113528 DOI: 10.1038/s41467-021-22905-7] [Citation(s) in RCA: 110] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 03/28/2021] [Indexed: 02/03/2023] Open
Abstract
Despite its clinical importance, the SARS-CoV-2 gene set remains unresolved, hindering dissection of COVID-19 biology. We use comparative genomics to provide a high-confidence protein-coding gene set, characterize evolutionary constraint, and prioritize functional mutations. We select 44 Sarbecovirus genomes at ideally-suited evolutionary distances, and quantify protein-coding evolutionary signatures and overlapping constraint. We find strong protein-coding signatures for ORFs 3a, 6, 7a, 7b, 8, 9b, and a novel alternate-frame gene, ORF3c, whereas ORFs 2b, 3d/3d-2, 3b, 9c, and 10 lack protein-coding signatures or convincing experimental evidence of protein-coding function. Furthermore, we show no other conserved protein-coding genes remain to be discovered. Mutation analysis suggests ORF8 contributes to within-individual fitness but not person-to-person transmission. Cross-strain and within-strain evolutionary pressures agree, except for fewer-than-expected within-strain mutations in nsp3 and S1, and more-than-expected in nucleocapsid, which shows a cluster of mutations in a predicted B-cell epitope, suggesting immune-avoidance selection. Evolutionary histories of residues disrupted by spike-protein substitutions D614G, N501Y, E484K, and K417N/T provide clues about their biology, and we catalog likely-functional co-inherited mutations. Previously reported RNA-modification sites show no enrichment for conservation. Here we report a high-confidence gene set and evolutionary-history annotations providing valuable resources and insights on SARS-CoV-2 biology, mutations, and evolution.
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Affiliation(s)
- Irwin Jungreis
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Rachel Sealfon
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA
| | - Manolis Kellis
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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45
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Morgenlander WR, Henson SN, Monaco DR, Chen A, Littlefield K, Bloch EM, Fujimura E, Ruczinski I, Crowley AR, Natarajan H, Butler SE, Weiner JA, Li MZ, Bonny TS, Benner SE, Balagopal A, Sullivan D, Shoham S, Quinn TC, Eshleman SH, Casadevall A, Redd AD, Laeyendecker O, Ackerman ME, Pekosz A, Elledge SJ, Robinson M, Tobian AA, Larman HB. Antibody responses to endemic coronaviruses modulate COVID-19 convalescent plasma functionality. J Clin Invest 2021; 131:146927. [PMID: 33571169 DOI: 10.1172/jci146927] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 02/03/2021] [Indexed: 12/23/2022] Open
Abstract
SARS-CoV-2 (CoV2) antibody therapies, including COVID-19 convalescent plasma (CCP), monoclonal antibodies, and hyperimmune globulin, are among the leading treatments for individuals with early COVID-19 infection. The functionality of convalescent plasma varies greatly, but the association of antibody epitope specificities with plasma functionality remains uncharacterized. We assessed antibody functionality and reactivities to peptides across the CoV2 and the 4 endemic human coronavirus (HCoV) genomes in 126 CCP donations. We found strong correlation between plasma functionality and polyclonal antibody targeting of CoV2 spike protein peptides. Antibody reactivity to many HCoV spike peptides also displayed strong correlation with plasma functionality, including pan-coronavirus cross-reactive epitopes located in a conserved region of the fusion peptide. After accounting for antibody cross-reactivity, we identified an association between greater alphacoronavirus NL63 antibody responses and development of highly neutralizing antibodies against CoV2. We also found that plasma preferentially reactive to the CoV2 spike receptor binding domain (RBD), versus the betacoronavirus HKU1 RBD, had higher neutralizing titer. Finally, we developed a 2-peptide serosignature that identifies plasma donations with high anti-spike titer, but that suffer from low neutralizing activity. These results suggest that analysis of coronavirus antibody fine specificities may be useful for selecting desired therapeutics and understanding the complex immune responses elicited by CoV2 infection.
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Affiliation(s)
- William R Morgenlander
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Stephanie N Henson
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Daniel R Monaco
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Kirsten Littlefield
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Evan M Bloch
- Division of Transfusion Medicine, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Eric Fujimura
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, and Department of Genetics, Program in Virology, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Andrew R Crowley
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
| | - Harini Natarajan
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
| | - Savannah E Butler
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
| | - Joshua A Weiner
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire, USA
| | - Mamie Z Li
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, and Department of Genetics, Program in Virology, Harvard Medical School, Boston, Massachusetts, USA
| | - Tania S Bonny
- Division of Transfusion Medicine, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Sarah E Benner
- Division of Transfusion Medicine, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Ashwin Balagopal
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - David Sullivan
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA.,Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Shmuel Shoham
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Thomas C Quinn
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Division of Intramural Research, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Susan H Eshleman
- Division of Transfusion Medicine, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Arturo Casadevall
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Andrew D Redd
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Division of Intramural Research, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Oliver Laeyendecker
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Division of Intramural Research, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Margaret E Ackerman
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire, USA
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Stephen J Elledge
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, and Department of Genetics, Program in Virology, Harvard Medical School, Boston, Massachusetts, USA
| | - Matthew Robinson
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Aaron Ar Tobian
- Division of Transfusion Medicine, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - H Benjamin Larman
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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46
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Yadav R, Chaudhary JK, Jain N, Chaudhary PK, Khanra S, Dhamija P, Sharma A, Kumar A, Handu S. Role of Structural and Non-Structural Proteins and Therapeutic Targets of SARS-CoV-2 for COVID-19. Cells 2021; 10:cells10040821. [PMID: 33917481 PMCID: PMC8067447 DOI: 10.3390/cells10040821] [Citation(s) in RCA: 230] [Impact Index Per Article: 76.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 02/07/2023] Open
Abstract
Coronavirus belongs to the family of Coronaviridae, comprising single-stranded, positive-sense RNA genome (+ ssRNA) of around 26 to 32 kilobases, and has been known to cause infection to a myriad of mammalian hosts, such as humans, cats, bats, civets, dogs, and camels with varied consequences in terms of death and debilitation. Strikingly, novel coronavirus (2019-nCoV), later renamed as severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), and found to be the causative agent of coronavirus disease-19 (COVID-19), shows 88% of sequence identity with bat-SL-CoVZC45 and bat-SL-CoVZXC21, 79% with SARS-CoV and 50% with MERS-CoV, respectively. Despite key amino acid residual variability, there is an incredible structural similarity between the receptor binding domain (RBD) of spike protein (S) of SARS-CoV-2 and SARS-CoV. During infection, spike protein of SARS-CoV-2 compared to SARS-CoV displays 10-20 times greater affinity for its cognate host cell receptor, angiotensin-converting enzyme 2 (ACE2), leading proteolytic cleavage of S protein by transmembrane protease serine 2 (TMPRSS2). Following cellular entry, the ORF-1a and ORF-1ab, located downstream to 5' end of + ssRNA genome, undergo translation, thereby forming two large polyproteins, pp1a and pp1ab. These polyproteins, following protease-induced cleavage and molecular assembly, form functional viral RNA polymerase, also referred to as replicase. Thereafter, uninterrupted orchestrated replication-transcription molecular events lead to the synthesis of multiple nested sets of subgenomic mRNAs (sgRNAs), which are finally translated to several structural and accessory proteins participating in structure formation and various molecular functions of virus, respectively. These multiple structural proteins assemble and encapsulate genomic RNA (gRNA), resulting in numerous viral progenies, which eventually exit the host cell, and spread infection to rest of the body. In this review, we primarily focus on genomic organization, structural and non-structural protein components, and potential prospective molecular targets for development of therapeutic drugs, convalescent plasm therapy, and a myriad of potential vaccines to tackle SARS-CoV-2 infection.
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Affiliation(s)
- Rohitash Yadav
- Department of Pharmacology, All India Institute of Medical Sciences (AIIMS), Rishikesh 249203, India; (P.D.); (S.H.)
- Correspondence: ; Tel.: +91-94-1415-3849
| | | | - Neeraj Jain
- Department of Medical Oncology & Hematology, All India Institute of Medical Sciences (AIIMS), Rishikesh 249203, India;
| | - Pankaj Kumar Chaudhary
- Molecular Biology & Proteomics Laboratory, Department of Biotechnology, Indian Institute of Technology (IIT), Roorkee 247667, India;
| | - Supriya Khanra
- Uttaranchal Institute of Pharmaceutical Sciences, Dehradun 248007, India;
| | - Puneet Dhamija
- Department of Pharmacology, All India Institute of Medical Sciences (AIIMS), Rishikesh 249203, India; (P.D.); (S.H.)
| | - Ambika Sharma
- Department of Biochemistry, U.P. Pt. Deen Dayal Upadhyaya Veterinary Science University, Mathura 281001, India;
| | - Ashish Kumar
- Department of Biochemistry, All India Institute of Medical Sciences, Rishikesh 249203, India;
| | - Shailendra Handu
- Department of Pharmacology, All India Institute of Medical Sciences (AIIMS), Rishikesh 249203, India; (P.D.); (S.H.)
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47
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Dhakal S, Ruiz-Bedoya CA, Zhou R, Creisher P, Villano J, Littlefield K, Castillo J, Marinho P, Jedlicka A, Ordonez A, Majewska N, Betenbaugh M, Flavahan K, Mueller A, Looney M, Quijada D, Mota F, Beck SE, Brockhurst JK, Braxton A, Castell N, D'Alessio F, Metcalf Pate KA, Karakousis PC, Mankowski JL, Pekosz A, Jain SK, Klein SL. Sex differences in lung imaging and SARS-CoV-2 antibody responses in a COVID-19 golden Syrian hamster model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.04.02.438292. [PMID: 33821269 PMCID: PMC8020969 DOI: 10.1101/2021.04.02.438292] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
In the ongoing coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), more severe outcomes are reported in males compared with females, including hospitalizations and deaths. Animal models can provide an opportunity to mechanistically interrogate causes of sex differences in the pathogenesis of SARS-CoV-2. Adult male and female golden Syrian hamsters (8-10 weeks of age) were inoculated intranasally with 10 5 TCID 50 of SARS-CoV-2/USA-WA1/2020 and euthanized at several time points during the acute (i.e., virus actively replicating) and recovery (i.e., after the infectious virus has been cleared) phases of infection. There was no mortality, but infected male hamsters experienced greater morbidity, losing a greater percentage of body mass, developing more extensive pneumonia as noted on chest computed tomography, and recovering more slowly than females. Treatment of male hamsters with estradiol did not alter pulmonary damage. Virus titers in respiratory tissues, including nasal turbinates, trachea, and lungs, and pulmonary cytokine concentrations, including IFNb and TNFa, were comparable between the sexes. However, during the recovery phase of infection, females mounted two-fold greater IgM, IgG, and IgA responses against the receptor-binding domain of the spike protein (S-RBD) in both plasma and respiratory tissues. Female hamsters also had significantly greater IgG antibodies against whole inactivated SARS-CoV-2 and mutant S-RBDs, as well as virus neutralizing antibodies in plasma. The development of an animal model to study COVID-19 sex differences will allow for a greater mechanistic understanding of the SARS-CoV-2 associated sex differences seen in the human population.
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48
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Evans N, Martinez E, Petrosillo N, Nichols J, Islam E, Pruitt K, Almodovar S. SARS-CoV-2 and Human Immunodeficiency Virus: Pathogen Pincer Attack. HIV AIDS (Auckl) 2021; 13:361-375. [PMID: 33833585 PMCID: PMC8020331 DOI: 10.2147/hiv.s300055] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 02/22/2021] [Indexed: 12/16/2022] Open
Abstract
Paramount efforts worldwide are seeking to increase understanding of the basic virology of SARS-CoV-2, characterize the spectrum of complications associated with COVID-19, and develop vaccines that can protect from new and recurrent infections with SARS-CoV-2. While we continue learning about this new virus, it is clear that 1) the virus is spread via the respiratory route, primarily by droplets and contact with contaminated surfaces and fomites, as well as by aerosol formation during invasive respiratory procedures; 2) the airborne route is still controversial; and 3) that those infected can spread the virus without necessarily developing COVID-19 (ie, asymptomatic). With the number of SARS-CoV-2 infections increasing globally, the possibility of co-infections and/or co-morbidities is becoming more concerning. Co-infection with Human Immunodeficiency Virus (HIV) is one such example of polyparasitism of interest. This military-themed comparative review of SARS-CoV-2 and HIV details their virology and describes them figuratively as separate enemy armies. HIV, an old enemy dug into trenches in individuals already infected, and SARS-CoV-2 the new army, attempting to attack and capture territories, tissues and organs, in order to provide resources for their expansion. This analogy serves to aid in discussion of three main areas of focus and draw attention to how these viruses may cooperate to gain the upper hand in securing a host. Here we compare their target, the key receptors found on those tissues, viral lifecycles and tactics for immune response surveillance. The last focus is on the immune response to infection, addressing similarities in cytokines released. While the majority of HIV cases can be successfully managed with antiretroviral therapy nowadays, treatments for SARS-CoV-2 are still undergoing research given the novelty of this army.
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Affiliation(s)
- Nicholas Evans
- Texas Tech University Health Sciences Center, Department of Immunology & Molecular Microbiology, Lubbock, TX, USA
| | - Edgar Martinez
- Texas Tech University Health Sciences Center, Department of Immunology & Molecular Microbiology, Lubbock, TX, USA
| | - Nicola Petrosillo
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, Italy
| | - Jacob Nichols
- Texas Tech University Health Sciences Center, Department of Internal Medicine, Lubbock, TX, USA
| | - Ebtesam Islam
- Texas Tech University Health Sciences Center, Department of Internal Medicine, Lubbock, TX, USA
| | - Kevin Pruitt
- Texas Tech University Health Sciences Center, Department of Immunology & Molecular Microbiology, Lubbock, TX, USA
| | - Sharilyn Almodovar
- Texas Tech University Health Sciences Center, Department of Immunology & Molecular Microbiology, Lubbock, TX, USA
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49
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Haddad-Boubaker S, Othman H, Touati R, Ayouni K, Lakhal M, Ben Mustapha I, Ghedira K, Kharrat M, Triki H. In silico comparative study of SARS-CoV-2 proteins and antigenic proteins in BCG, OPV, MMR and other vaccines: evidence of a possible putative protective effect. BMC Bioinformatics 2021; 22:163. [PMID: 33771096 PMCID: PMC7995392 DOI: 10.1186/s12859-021-04045-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 02/22/2021] [Indexed: 12/15/2022] Open
Abstract
Background Coronavirus Disease 2019 (COVID-19) is a viral pandemic disease that may induce severe pneumonia in humans. In this paper, we investigated the putative implication of 12 vaccines, including BCG, OPV and MMR in the protection against COVID-19. Sequences of the main antigenic proteins in the investigated vaccines and SARS-CoV-2 proteins were compared to identify similar patterns. The immunogenic effect of identified segments was, then, assessed using a combination of structural and antigenicity prediction tools. Results A total of 14 highly similar segments were identified in the investigated vaccines. Structural and antigenicity prediction analysis showed that, among the identified patterns, three segments in Hepatitis B, Tetanus, and Measles proteins presented antigenic properties that can induce putative protective effect against COVID-19. Conclusions Our results suggest a possible protective effect of HBV, Tetanus and Measles vaccines against COVID-19, which may explain the variation of the disease severity among regions. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04045-3.
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Affiliation(s)
- Sondes Haddad-Boubaker
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institut Pasteur de Tunis, University of Tunis El Manar, 13 place Pasteur, BP74 1002 le Belvédère, Tunis, Tunisia. .,LR20IPT10 Laboratory of Virus, Host and Vectors, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia.
| | - Houcemeddine Othman
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Rabeb Touati
- LR99ES10 Human Genetics Laboratory, Faculty of Medicine of Tunis (FMT), University of Tunis El Manar, Tunis, Tunisia
| | - Kaouther Ayouni
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institut Pasteur de Tunis, University of Tunis El Manar, 13 place Pasteur, BP74 1002 le Belvédère, Tunis, Tunisia.,LR20IPT10 Laboratory of Virus, Host and Vectors, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Marwa Lakhal
- LR99ES10 Human Genetics Laboratory, Faculty of Medicine of Tunis (FMT), University of Tunis El Manar, Tunis, Tunisia
| | - Imen Ben Mustapha
- LR11-IPT02 Laboratory of Transmission, Control and Immunobiology of Infections, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Kais Ghedira
- LR16IPT09 Laboratory of Biomathematics, Biomathematics and Biostatistics, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Maher Kharrat
- LR99ES10 Human Genetics Laboratory, Faculty of Medicine of Tunis (FMT), University of Tunis El Manar, Tunis, Tunisia
| | - Henda Triki
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institut Pasteur de Tunis, University of Tunis El Manar, 13 place Pasteur, BP74 1002 le Belvédère, Tunis, Tunisia.,LR20IPT10 Laboratory of Virus, Host and Vectors, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
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50
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Zhou Z, Huang C, Zhou Z, Huang Z, Su L, Kang S, Chen X, Chen Q, He S, Rong X, Xiao F, Chen J, Chen S. Structural insight reveals SARS-CoV-2 ORF7a as an immunomodulating factor for human CD14 + monocytes. iScience 2021; 24:102187. [PMID: 33615195 PMCID: PMC7879101 DOI: 10.1016/j.isci.2021.102187] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 11/11/2020] [Accepted: 02/09/2021] [Indexed: 01/08/2023] Open
Abstract
Dysregulated immune cell responses have been linked to the severity of coronavirus disease 2019 (COVID-19), but the specific viral factors of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were currently unknown. Herein, we reveal that the Immunoglobulin-like fold ectodomain of the viral protein SARS-CoV-2 ORF7a interacts with high efficiency to CD14+ monocytes in human peripheral blood, compared to pathogenic protein SARS-CoV ORF7a. The crystal structure of SARS-CoV-2 ORF7a at 2.2 Å resolution reveals three remarkable changes on the amphipathic side of the four-stranded β-sheet, implying a potential functional interface of the viral protein. Importantly, SARS-CoV-2 ORF7a coincubation with CD14+ monocytes ex vivo triggered a decrease in HLA-DR/DP/DQ expression levels and upregulated significant production of proinflammatory cytokines, including IL-6, IL-1β, IL-8, and TNF-α. Our work demonstrates that SARS-CoV-2 ORF7a is an immunomodulating factor for immune cell binding and triggers dramatic inflammatory responses, providing promising therapeutic drug targets for pandemic COVID-19.
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Affiliation(s)
- Ziliang Zhou
- Molecular Imaging Center, Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai 519000, China
| | - Chunliu Huang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Zhechong Zhou
- Molecular Imaging Center, Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai 519000, China
| | - Zhaoxia Huang
- Molecular Imaging Center, Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai 519000, China
| | - Lili Su
- The Health Management Center, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai 519000, China
| | - Sisi Kang
- Molecular Imaging Center, Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai 519000, China
| | - Xiaoxue Chen
- Molecular Imaging Center, Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai 519000, China
| | - Qiuyue Chen
- Molecular Imaging Center, Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai 519000, China
| | - Suhua He
- Molecular Imaging Center, Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai 519000, China
| | - Xia Rong
- Institute of Clinical Transfusion, Guangzhou Blood Center, Guangzhou 510095, China
| | - Fei Xiao
- Molecular Imaging Center, Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai 519000, China
| | - Jun Chen
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
- Key Laboratory of Tropical Disease Control of the Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China
- Center for Precision Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Shoudeng Chen
- Molecular Imaging Center, Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai 519000, China
- Department of Experimental Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai 519000, China
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