1
|
Vránová L, Poláková I, Vaníková Š, Saláková M, Musil J, Vaníčková M, Vencálek O, Holub M, Bohoněk M, Řezáč D, Dresler J, Tachezy R, Šmahel M. Multiparametric analysis of the specific immune response against SARS-CoV-2. Infect Dis (Lond) 2024; 56:851-869. [PMID: 38805304 DOI: 10.1080/23744235.2024.2358379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Revised: 04/24/2024] [Accepted: 05/17/2024] [Indexed: 05/30/2024] Open
Abstract
BACKGROUND SARS-CoV-2, which causes COVID-19, has killed more than 7 million people worldwide. Understanding the development of postinfectious and postvaccination immune responses is necessary for effective treatment and the introduction of appropriate antipandemic measures. OBJECTIVES We analysed humoral and cell-mediated anti-SARS-CoV-2 immune responses to spike (S), nucleocapsid (N), membrane (M), and open reading frame (O) proteins in individuals collected up to 1.5 years after COVID-19 onset and evaluated immune memory. METHODS Peripheral blood mononuclear cells and serum were collected from patients after COVID-19. Sampling was performed in two rounds: 3-6 months after infection and after another year. Most of the patients were vaccinated between samplings. SARS-CoV-2-seronegative donors served as controls. ELISpot assays were used to detect SARS-CoV-2-specific T and B cells using peptide pools (S, NMO) or recombinant proteins (rS, rN), respectively. A CEF peptide pool consisting of selected viral epitopes was applied to assess the antiviral T-cell response. SARS-CoV-2-specific antibodies were detected via ELISA and a surrogate virus neutralisation assay. RESULTS We confirmed that SARS-CoV-2 infection induces the establishment of long-term memory IgG+ B cells and memory T cells. We also found that vaccination enhanced the levels of anti-S memory B and T cells. Multivariate comparison also revealed the benefit of repeated vaccination. Interestingly, the T-cell response to CEF was lower in patients than in controls. CONCLUSION This study supports the importance of repeated vaccination for enhancing immunity and suggests a possible long-term perturbation of the overall antiviral immune response caused by SARS-CoV-2 infection.
Collapse
Affiliation(s)
- Lucie Vránová
- Department of Genetics and Microbiology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Ingrid Poláková
- Department of Genetics and Microbiology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Šárka Vaníková
- Department of Immunomonitoring and Flow Cytometry, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Martina Saláková
- Department of Genetics and Microbiology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Jan Musil
- Department of Immunomonitoring and Flow Cytometry, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Marie Vaníčková
- Department of Genetics and Microbiology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Ondřej Vencálek
- Department of Mathematical Analysis and Applications of Mathematics, Faculty of Science, Palacky University in Olomouc, Olomouc, Czech Republic
| | - Michal Holub
- Department of Infectious Diseases, First Faculty of Medicine, Military University Hospital Prague and Charles University, Prague, Czech Republic
| | - Miloš Bohoněk
- Department of Hematology and Blood Transfusion, Military University Hospital Prague, Prague, Czech Republic
- Faculty of Biomedical Engineering, Czech Technical University, Prague, Czech Republic
| | - David Řezáč
- Department of Infectious Diseases, First Faculty of Medicine, Military University Hospital Prague and Charles University, Prague, Czech Republic
| | - Jiří Dresler
- Military Health Institute, Military Medical Agency, Prague, Czech Republic
| | - Ruth Tachezy
- Department of Genetics and Microbiology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Michal Šmahel
- Department of Genetics and Microbiology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| |
Collapse
|
2
|
Wouters C, Sachithanandham J, Akin E, Pieterse L, Fall A, Truong TT, Bard JD, Yee R, Sullivan DJ, Mostafa HH, Pekosz A. SARS-CoV-2 Variants from Long-Term, Persistently Infected Immunocompromised Patients Have Altered Syncytia Formation, Temperature-Dependent Replication, and Serum Neutralizing Antibody Escape. Viruses 2024; 16:1436. [PMID: 39339912 PMCID: PMC11437501 DOI: 10.3390/v16091436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2024] [Revised: 09/01/2024] [Accepted: 09/02/2024] [Indexed: 09/30/2024] Open
Abstract
SARS-CoV-2 infection of immunocompromised individuals often leads to prolonged detection of viral RNA and infectious virus in nasal specimens, presumably due to the lack of induction of an appropriate adaptive immune response. Mutations identified in virus sequences obtained from persistently infected patients bear signatures of immune evasion and have some overlap with sequences present in variants of concern. We characterized virus isolates obtained greater than 100 days after the initial COVID-19 diagnosis from two COVID-19 patients undergoing immunosuppressive cancer therapy, wand compared them to an isolate from the start of the infection. Isolates from an individual who never mounted an antibody response specific to SARS-CoV-2 despite the administration of convalescent plasma showed slight reductions in plaque size and some showed temperature-dependent replication attenuation on human nasal epithelial cell culture compared to the virus that initiated infection. An isolate from another patient-who did mount a SARS-CoV-2 IgM response-showed temperature-dependent changes in plaque size as well as increased syncytia formation and escape from serum-neutralizing antibodies. Our results indicate that not all virus isolates from immunocompromised COVID-19 patients display clear signs of phenotypic change, but increased attention should be paid to monitoring virus evolution in this patient population.
Collapse
Affiliation(s)
- Camille Wouters
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Jaiprasath Sachithanandham
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Elgin Akin
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Lisa Pieterse
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Amary Fall
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Thao T Truong
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA 90027, USA
| | - Jennifer Dien Bard
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA 90027, USA
- Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Rebecca Yee
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA 90027, USA
- Department of Pathology, The George Washington University School of Medicine and Health Sciences, Washington, DC 20052, USA
| | - David J Sullivan
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Heba H Mostafa
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| |
Collapse
|
3
|
Lebeau G, Paulo-Ramos A, Hoareau M, El Safadi D, Meilhac O, Krejbich-Trotot P, Roche M, Viranaicken W. Metabolic Dependency Shapes Bivalent Antiviral Response in Host Cells in Response to Poly:IC: The Role of Glutamine. Viruses 2024; 16:1391. [PMID: 39339867 PMCID: PMC11436187 DOI: 10.3390/v16091391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2024] [Revised: 08/24/2024] [Accepted: 08/28/2024] [Indexed: 09/30/2024] Open
Abstract
The establishment of effective antiviral responses within host cells is intricately related to their metabolic status, shedding light on immunometabolism. In this study, we investigated the hypothesis that cellular reliance on glutamine metabolism contributes to the development of a potent antiviral response. We evaluated the antiviral response in the presence or absence of L-glutamine in the culture medium, revealing a bivalent response hinging on cellular metabolism. While certain interferon-stimulated genes (ISGs) exhibited higher expression in an oxidative phosphorylation (OXPHOS)-dependent manner, others were surprisingly upregulated in a glycolytic-dependent manner. This metabolic dichotomy was influenced in part by variations in interferon-β (IFN-β) expression. We initially demonstrated that the presence of L-glutamine induced an enhancement of OXPHOS in A549 cells. Furthermore, in cells either stimulated by poly:IC or infected with dengue virus and Zika virus, a marked increase in ISGs expression was observed in a dose-dependent manner with L-glutamine supplementation. Interestingly, our findings unveiled a metabolic dependency in the expression of specific ISGs. In particular, genes such as ISG54, ISG12 and ISG15 exhibited heightened expression in cells cultured with L-glutamine, corresponding to higher OXPHOS rates and IFN-β signaling. Conversely, the expression of viperin and 2'-5'-oligoadenylate synthetase 1 was inversely related to L-glutamine concentration, suggesting a glycolysis-dependent regulation, confirmed by inhibition experiments. This study highlights the intricate interplay between cellular metabolism, especially glutaminergic and glycolytic, and the establishment of the canonical antiviral response characterized by the expression of antiviral effectors, potentially paving the way for novel strategies to modulate antiviral responses through metabolic interventions.
Collapse
Affiliation(s)
- Grégorie Lebeau
- PIMIT—Processus Infectieux en Milieu Insulaire Tropical, INSERM UMR 1187, CNRS 9192, IRD 249, Plateforme CYROI, Université de La Réunion, 97490 Sainte-Clotilde, France
- Diabète Athérothrombose Réunion Océan Indien (DéTROI), INSERM UMR 1188, Campus Santé de Terre Sainte, Université de La Réunion, 97410 Saint-Pierre, France
| | - Aurélie Paulo-Ramos
- Diabète Athérothrombose Réunion Océan Indien (DéTROI), INSERM UMR 1188, Campus Santé de Terre Sainte, Université de La Réunion, 97410 Saint-Pierre, France
| | - Mathilde Hoareau
- Diabète Athérothrombose Réunion Océan Indien (DéTROI), INSERM UMR 1188, Campus Santé de Terre Sainte, Université de La Réunion, 97410 Saint-Pierre, France
| | - Daed El Safadi
- PIMIT—Processus Infectieux en Milieu Insulaire Tropical, INSERM UMR 1187, CNRS 9192, IRD 249, Plateforme CYROI, Université de La Réunion, 97490 Sainte-Clotilde, France
| | - Olivier Meilhac
- Diabète Athérothrombose Réunion Océan Indien (DéTROI), INSERM UMR 1188, Campus Santé de Terre Sainte, Université de La Réunion, 97410 Saint-Pierre, France
| | - Pascale Krejbich-Trotot
- PIMIT—Processus Infectieux en Milieu Insulaire Tropical, INSERM UMR 1187, CNRS 9192, IRD 249, Plateforme CYROI, Université de La Réunion, 97490 Sainte-Clotilde, France
| | - Marjolaine Roche
- PIMIT—Processus Infectieux en Milieu Insulaire Tropical, INSERM UMR 1187, CNRS 9192, IRD 249, Plateforme CYROI, Université de La Réunion, 97490 Sainte-Clotilde, France
| | - Wildriss Viranaicken
- PIMIT—Processus Infectieux en Milieu Insulaire Tropical, INSERM UMR 1187, CNRS 9192, IRD 249, Plateforme CYROI, Université de La Réunion, 97490 Sainte-Clotilde, France
- Diabète Athérothrombose Réunion Océan Indien (DéTROI), INSERM UMR 1188, Campus Santé de Terre Sainte, Université de La Réunion, 97410 Saint-Pierre, France
| |
Collapse
|
4
|
Ding J, Zhang Q, Jiang J, Zhou N, Yu Z, Wang Z, Meng X, Daggumati L, Liu T, Wang F, Lu Z, Yang X, Yang Z, Zhang H, Thorek DLJ, Du P, Zhu H. Preclinical Evaluation and Pilot Clinical Study of 18F-Labeled Inhibitor Peptide for Noninvasive Positron Emission Tomography Mapping of Angiotensin Converting Enzyme 2. ACS Pharmacol Transl Sci 2024; 7:1758-1769. [PMID: 38898955 PMCID: PMC11184604 DOI: 10.1021/acsptsci.3c00337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 05/08/2024] [Accepted: 05/14/2024] [Indexed: 06/21/2024]
Abstract
Angiotensin-converting enzyme 2 (ACE2) is the main molecular target for coronavirus SARS-CoV-2 to enter cells. Molecularly specific tracers that bind to ACE2 with high affinity can be used to determine the tissue distribution of this important receptor, noninvasively. A novel targeting PET imaging probe, [18F]AlF-DX600-BCH, was developed to detect the in vivo expression of ACE2 and monitor response to therapy. Preclinical experiments, including biodistribution, PET imaging, and tissue section analysis, were conducted after tests of in vitro and in vivo stability and pharmacokinetics. The agent was advanced to clinical evaluation in 10 volunteers who received [18F]AlF-DX600-BCH PET/CT at 1 and 2 h after injection (NCT04542863). Preclinical results of both biodistribution and PET demonstrated [18F]AlF-DX600-BCH accumulation in rat kidney (standardized uptake value; SUVkidney/normal > 50), along with specific uptake in testes (SUVtestis/normal > 10) tissues. Kidney, gastrointestinal, and bronchial cell labeling were correlated to ACE2 positive by immunohistochemistry (IHC) staining. In clinical imaging, significant tracer accumulation was predominantly observed in the urinary and reproductive system (SUVrenal cortex = 32.00, SUVtestis = 4.56), and the conjunctiva and nasal mucosa saw elevated uptake in several cases. This work is the first report of a radioisotope probe, [18F]AlF-DX600-BCH, targeting ACE2 with promising preliminary preclinical and translational outlook, thereby demonstrating the potential of noninvasive mapping of ACE2.
Collapse
Affiliation(s)
- Jin Ding
- Key
Laboratory of Carcinogenesis and Translational Research (Ministry
of Education/Beijing), NMPA Key Laboratory for Research and Evaluation
of Radiopharmaceuticals (National Medical Products Administration),
Department of Nuclear Medicine, Peking University
Cancer Hospital & Institute, No. 52 Fucheng Road, Beijing 100142, China
| | - Qian Zhang
- Key
Laboratory of Carcinogenesis and Translational Research (Ministry
of Education/Beijing), NMPA Key Laboratory for Research and Evaluation
of Radiopharmaceuticals (National Medical Products Administration),
Department of Nuclear Medicine, Peking University
Cancer Hospital & Institute, No. 52 Fucheng Road, Beijing 100142, China
- Guizhou
University School of Medicine, Guiyang, 550025 Guizhou, China
| | - Jinquan Jiang
- Department
of Radiology, People’s Hospital of
Deyang City, Deyang, 618000 Sichuan, China
| | - Nina Zhou
- Key
Laboratory of Carcinogenesis and Translational Research (Ministry
of Education/Beijing), NMPA Key Laboratory for Research and Evaluation
of Radiopharmaceuticals (National Medical Products Administration),
Department of Nuclear Medicine, Peking University
Cancer Hospital & Institute, No. 52 Fucheng Road, Beijing 100142, China
| | - Ziyu Yu
- Key
Laboratory of Carcinogenesis and Translational Research (Ministry
of Education/Beijing), Department of Urology, Peking University Cancer Hospital & Institute, No. 52 Fucheng Road, 100142 Beijing, China
| | - Zilei Wang
- Key
Laboratory of Carcinogenesis and Translational Research (Ministry
of Education/Beijing), NMPA Key Laboratory for Research and Evaluation
of Radiopharmaceuticals (National Medical Products Administration),
Department of Nuclear Medicine, Peking University
Cancer Hospital & Institute, No. 52 Fucheng Road, Beijing 100142, China
| | - Xiangxi Meng
- Key
Laboratory of Carcinogenesis and Translational Research (Ministry
of Education/Beijing), NMPA Key Laboratory for Research and Evaluation
of Radiopharmaceuticals (National Medical Products Administration),
Department of Nuclear Medicine, Peking University
Cancer Hospital & Institute, No. 52 Fucheng Road, Beijing 100142, China
| | - Lasya Daggumati
- Department
of Radiology, Washington University in St.
Louis School of Medicine, St. Louis, Missouri 63110, United States
| | - Teli Liu
- Key
Laboratory of Carcinogenesis and Translational Research (Ministry
of Education/Beijing), NMPA Key Laboratory for Research and Evaluation
of Radiopharmaceuticals (National Medical Products Administration),
Department of Nuclear Medicine, Peking University
Cancer Hospital & Institute, No. 52 Fucheng Road, Beijing 100142, China
| | - Feng Wang
- Key
Laboratory of Carcinogenesis and Translational Research (Ministry
of Education/Beijing), NMPA Key Laboratory for Research and Evaluation
of Radiopharmaceuticals (National Medical Products Administration),
Department of Nuclear Medicine, Peking University
Cancer Hospital & Institute, No. 52 Fucheng Road, Beijing 100142, China
| | - Zhihao Lu
- Key
Laboratory of Carcinogenesis and Translational Research (Ministry
of Education/Beijing), Department of Gastro-intestinal oncology, Peking University Cancer Hospital & Institute, No. 52 Fucheng Road, 100142 Beijing, China
| | - Xing Yang
- Department
of Nuclear Medicine, Peking University First
Hospital, No. 8 Xishiku Street, 100034 Beijing, China
| | - Zhi Yang
- Key
Laboratory of Carcinogenesis and Translational Research (Ministry
of Education/Beijing), NMPA Key Laboratory for Research and Evaluation
of Radiopharmaceuticals (National Medical Products Administration),
Department of Nuclear Medicine, Peking University
Cancer Hospital & Institute, No. 52 Fucheng Road, Beijing 100142, China
| | - Hanwen Zhang
- Department
of Radiology, Washington University in St.
Louis School of Medicine, St. Louis, Missouri 63110, United States
| | - Daniel L. J. Thorek
- Department
of Radiology, Washington University in St.
Louis School of Medicine, St. Louis, Missouri 63110, United States
| | - Peng Du
- Key
Laboratory of Carcinogenesis and Translational Research (Ministry
of Education/Beijing), Department of Urology, Peking University Cancer Hospital & Institute, No. 52 Fucheng Road, 100142 Beijing, China
| | - Hua Zhu
- Key
Laboratory of Carcinogenesis and Translational Research (Ministry
of Education/Beijing), NMPA Key Laboratory for Research and Evaluation
of Radiopharmaceuticals (National Medical Products Administration),
Department of Nuclear Medicine, Peking University
Cancer Hospital & Institute, No. 52 Fucheng Road, Beijing 100142, China
| |
Collapse
|
5
|
Solstad AD, Denz PJ, Kenney AD, Mahfooz NS, Speaks S, Gong Q, Robinson RT, Long ME, Forero A, Yount JS, Hemann EA. IFN-λ uniquely promotes CD8 T cell immunity against SARS-CoV-2 relative to type I IFN. JCI Insight 2024; 9:e171830. [PMID: 38973611 PMCID: PMC11383353 DOI: 10.1172/jci.insight.171830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 05/15/2024] [Indexed: 07/09/2024] Open
Abstract
Optimization of protective immune responses against SARS-CoV-2 remains an urgent worldwide priority. In this regard, type III IFN (IFN-λ) restricts SARS-CoV-2 infection in vitro, and treatment with IFN-λ limits infection, inflammation, and pathogenesis in murine models. Furthermore, IFN-λ has been developed for clinical use to limit COVID-19 severity. However, whether endogenous IFN-λ signaling has an effect on SARS-CoV-2 antiviral immunity and long-term immune protection in vivo is unknown. In this study, we identified a requirement for IFN-λ signaling in promoting viral clearance and protective immune programming in SARS-CoV-2 infection of mice. Expression of both IFN and IFN-stimulated gene (ISG) in the lungs were minimally affected by the absence of IFN-λ signaling and correlated with transient increases in viral titers. We found that IFN-λ supported the generation of protective CD8 T cell responses against SARS-CoV-2 by facilitating accumulation of CD103+ DC in lung draining lymph nodes (dLN). IFN-λ signaling specifically in DCs promoted the upregulation of costimulatory molecules and the proliferation of CD8 T cells. Intriguingly, antigen-specific CD8 T cell immunity to SARS-CoV-2 was independent of type I IFN signaling, revealing a nonredundant function of IFN-λ. Overall, these studies demonstrate a critical role for IFN-λ in protective innate and adaptive immunity upon infection with SARS-CoV-2 and suggest that IFN-λ serves as an immune adjuvant to support CD8 T cell immunity.
Collapse
Affiliation(s)
- Abigail D Solstad
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
| | - Parker J Denz
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
| | - Adam D Kenney
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
| | - Najmus S Mahfooz
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
| | - Samuel Speaks
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Qiaoke Gong
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Richard T Robinson
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
| | - Matthew E Long
- Dorothy M. Davis Heart and Lung Research Institute and
- Department of Internal Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Adriana Forero
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
- Dorothy M. Davis Heart and Lung Research Institute and
| | - Jacob S Yount
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
| | - Emily A Hemann
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
- Dorothy M. Davis Heart and Lung Research Institute and
| |
Collapse
|
6
|
Patel P, Kaushik N, Acharya TR, Choi EH, Kaushik NK. Surface air gas discharge plasma: An ecofriendly virus inactivation approach to enhance CPRRs mediated antiviral genes expression against airborne bio-contaminant (human Coronavirus-229E). ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 347:123700. [PMID: 38452839 DOI: 10.1016/j.envpol.2024.123700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/28/2024] [Accepted: 02/29/2024] [Indexed: 03/09/2024]
Abstract
Emerging bio-contaminants (airborne viruses) exploits and manipulate host (human) metabolism to produce new viral particles, evading the host's immune defences and leading to infections. Non-thermal plasma, operating at atmospheric pressure and ambient temperature, is explored for virus inactivation, generating RONS that interact and denatures viral proteins. However, various factors affecting virus survival influence the efficacy of non-thermal plasma. Glucose analogue 2-DG, a metabolic modifier used in this study, disrupts the glycolysis pathway viruses rely on, creating an unfavourable environment for replication. Here, airborne HCoV-229E bio-contaminant was treated with plasma for inactivation, and the presence of RONS was analysed. Metabolically altered lung cells were subsequently exposed to the treated airborne viruses. Cytopathic effect, spike protein, and cell death were evaluated via flow cytometry and confocal microscopy, and CPRRs mediated antiviral gene expression was evaluated using PCR. Gas plasma-treated viruses led to reduced virus proliferation in unaltered lung cells, although few virus particles survived the exposure, as confirmed by biological assessment (cytopathic effects and live/dead staining). A combination approach of gas plasma-treated viruses and altered lung cells displayed drastic virus reduction compared to the control group, established through confocal microscopy and flow cytometry. Furthermore, altered lung cell enhances gene transcription responsible for innate immunity when exposed to the gas plasma-treated virus, thereby impeding airborne virus propagation. This study demonstrates the significance of a surface air gas plasma and metabolic alteration approach in enhancing genes targeted towards antiviral innate immunity and tackling outbreaks of emerging bio-contaminants of concerns (airborne viruses).
Collapse
Affiliation(s)
- Paritosh Patel
- Plasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul, 01897, South Korea
| | - Neha Kaushik
- Department of Biotechnology, College of Engineering, The University of Suwon, Hwaseong, 18323, South Korea
| | - Tirtha Raj Acharya
- Plasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul, 01897, South Korea
| | - Eun Ha Choi
- Plasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul, 01897, South Korea
| | - Nagendra Kumar Kaushik
- Plasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul, 01897, South Korea.
| |
Collapse
|
7
|
Shi G, Li T, Lai KK, Johnson RF, Yewdell JW, Compton AA. Omicron Spike confers enhanced infectivity and interferon resistance to SARS-CoV-2 in human nasal tissue. Nat Commun 2024; 15:889. [PMID: 38291024 PMCID: PMC10828397 DOI: 10.1038/s41467-024-45075-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 01/11/2024] [Indexed: 02/01/2024] Open
Abstract
Omicron emerged following COVID-19 vaccination campaigns, displaced previous SARS-CoV-2 variants of concern worldwide, and gave rise to lineages that continue to spread. Here, we show that Omicron exhibits increased infectivity in primary adult upper airway tissue relative to Delta. Using recombinant forms of SARS-CoV-2 and nasal epithelial cells cultured at the liquid-air interface, we show that mutations unique to Omicron Spike enable enhanced entry into nasal tissue. Unlike earlier variants of SARS-CoV-2, our findings suggest that Omicron enters nasal cells independently of serine transmembrane proteases and instead relies upon metalloproteinases to catalyze membrane fusion. Furthermore, we demonstrate that this entry pathway unlocked by Omicron Spike enables evasion from constitutive and interferon-induced antiviral factors that restrict SARS-CoV-2 entry following attachment. Therefore, the increased transmissibility exhibited by Omicron in humans may be attributed not only to its evasion of vaccine-elicited adaptive immunity, but also to its superior invasion of nasal epithelia and resistance to the cell-intrinsic barriers present therein.
Collapse
Affiliation(s)
- Guoli Shi
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Tiansheng Li
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Kin Kui Lai
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Reed F Johnson
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Jonathan W Yewdell
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Alex A Compton
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA.
| |
Collapse
|
8
|
Zaidi AK, Singh RB. SARS-CoV-2 variant biology and immune evasion. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 202:45-66. [PMID: 38237990 DOI: 10.1016/bs.pmbts.2023.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
This chapter discusses the SARS-CoV-2 variants and their immune evasion strategies, shedding light on the dynamic nature of the COVID-19 pandemic. The ecological dynamics and viral evolution of SARS-CoV-2 are explored, considering carriers of infection, individual immunity profiles, and human movement as key factors in the emergence and dissemination of variants. The chapter discusses SARS-CoV-2 mutation, including mutation rate, substitution rate, and recombination, influencing genetic diversity and evolution. Transmission bottlenecks are highlighted as determinants of dominant variants during viral spread. The evolution phases of the pandemic are outlined, from limited early evolution to the emergence of notable changes like the D614G substitution and variants with heavy mutations. Variants of Concern (VOCs), including Alpha, Beta, Gamma, and the recent Omicron variant, are examined, with insights into inter-lineage and intra-lineage dynamics. The origin of VOCs and the Omicron variant is explored, alongside the role of the furin cleavage site (FCS) in variant emergence. The impact of structural and non-structural proteins on viral infectivity is assessed, as well as innate immunity evasion strategies employed by SARS-CoV-2 variants. The chapter concludes by considering future possibilities, including ongoing virus evolution, the need for surveillance, vaccine development, and public health measures.
Collapse
Affiliation(s)
| | - Rohan Bir Singh
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, United States; Department of Population, Policy and Practice, Greater Ormond Street Institute of Child Health, University College London, United Kingdom; Discipline of Ophthalmology and Visual Sciences, Adelaide Medical School, University of Adelaide, Australia.
| |
Collapse
|
9
|
Bhargava A, Szachnowski U, Chazal M, Foretek D, Caval V, Aicher SM, Pipoli da Fonseca J, Jeannin P, Beauclair G, Monot M, Morillon A, Jouvenet N. Transcriptomic analysis of sorted lung cells revealed a proviral activity of the NF-κB pathway toward SARS-CoV-2. iScience 2023; 26:108449. [PMID: 38213785 PMCID: PMC10783605 DOI: 10.1016/j.isci.2023.108449] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 09/30/2023] [Accepted: 11/10/2023] [Indexed: 01/13/2024] Open
Abstract
Investigations of cellular responses to viral infection are commonly performed on mixed populations of infected and uninfected cells or using single-cell RNA sequencing, leading to inaccurate and low-resolution gene expression interpretations. Here, we performed deep polyA+ transcriptome analyses and novel RNA profiling of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infected lung epithelial cells, sorted based on the expression of the viral spike (S) protein. Infection caused a massive reduction in mRNAs and long non-coding RNAs (lncRNAs), including transcripts coding for antiviral factors, such as interferons (IFNs). This absence of IFN signaling probably explained the poor transcriptomic response of bystander cells co-cultured with S+ ones. NF-κB pathway and the inflammatory response escaped the global shutoff in S+ cells. Functional investigations revealed the proviral function of the NF-κB pathway and the antiviral activity of CYLD, a negative regulator of the pathway. Thus, our transcriptomic analysis on sorted cells revealed additional genes that modulate SARS-CoV-2 replication in lung cells.
Collapse
Affiliation(s)
- Anvita Bhargava
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Virus sensing and signaling Unit, 75015 Paris, France
| | - Ugo Szachnowski
- CNRS UMR3244, Sorbonne University, PSL University, Institut Curie, Centre de Recherche, 75005 Paris, France
| | - Maxime Chazal
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Virus sensing and signaling Unit, 75015 Paris, France
| | - Dominika Foretek
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Virus sensing and signaling Unit, 75015 Paris, France
- CNRS UMR3244, Sorbonne University, PSL University, Institut Curie, Centre de Recherche, 75005 Paris, France
| | - Vincent Caval
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Virus sensing and signaling Unit, 75015 Paris, France
| | - Sophie-Marie Aicher
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Virus sensing and signaling Unit, 75015 Paris, France
| | | | - Patricia Jeannin
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Unité Épidémiologie et Physiopathologie des Virus Oncogènes, 75015 Paris, France
| | - Guillaume Beauclair
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91190 Gif-sur-Yvette, France
| | - Marc Monot
- Institut Pasteur, Université de Paris, Biomics Platform, C2RT, 75015 Paris, France
| | - Antonin Morillon
- CNRS UMR3244, Sorbonne University, PSL University, Institut Curie, Centre de Recherche, 75005 Paris, France
| | - Nolwenn Jouvenet
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Virus sensing and signaling Unit, 75015 Paris, France
| |
Collapse
|
10
|
Mathew DS, Pandya T, Pandya H, Vaghela Y, Subbian S. An Overview of SARS-CoV-2 Etiopathogenesis and Recent Developments in COVID-19 Vaccines. Biomolecules 2023; 13:1565. [PMID: 38002247 PMCID: PMC10669259 DOI: 10.3390/biom13111565] [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: 09/25/2023] [Revised: 10/18/2023] [Accepted: 10/21/2023] [Indexed: 11/26/2023] Open
Abstract
The Coronavirus disease-2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has significantly impacted the health and socioeconomic status of humans worldwide. Pulmonary infection of SARS-CoV-2 results in exorbitant viral replication and associated onset of inflammatory cytokine storm and disease pathology in various internal organs. However, the etiopathogenesis of SARS-CoV-2 infection is not fully understood. Currently, there are no targeted therapies available to cure COVID-19, and most patients are treated empirically with anti-inflammatory and/or anti-viral drugs, based on the disease symptoms. Although several types of vaccines are currently implemented to control COVID-19 and prevent viral dissemination, the emergence of new variants of SARS-CoV-2 that can evade the vaccine-induced protective immunity poses challenges to current vaccination strategies and highlights the necessity to develop better and improved vaccines. In this review, we summarize the etiopathogenesis of SARS-CoV-2 and elaborately discuss various types of vaccines and vaccination strategies, focusing on those vaccines that are currently in use worldwide to combat COVID-19 or in various stages of clinical development to use in humans.
Collapse
Affiliation(s)
- Dona Susan Mathew
- Department of Microbiology, Amrita Institute of Medical Science and Research Centre, Amrita Vishwa Vidyapeetham, Kochi 608204, India;
| | - Tirtha Pandya
- Public Health Research Institute (PHRI) Center, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA; (T.P.); (H.P.); (Y.V.)
| | - Het Pandya
- Public Health Research Institute (PHRI) Center, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA; (T.P.); (H.P.); (Y.V.)
| | - Yuzen Vaghela
- Public Health Research Institute (PHRI) Center, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA; (T.P.); (H.P.); (Y.V.)
| | - Selvakumar Subbian
- Public Health Research Institute (PHRI) Center, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA; (T.P.); (H.P.); (Y.V.)
| |
Collapse
|
11
|
Shi G, Li T, Lai KK, Johnson RF, Yewdell JW, Compton AA. Omicron Spike confers enhanced infectivity and interferon resistance to SARS-CoV-2 in human nasal tissue. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.06.539698. [PMID: 37425811 PMCID: PMC10327209 DOI: 10.1101/2023.05.06.539698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Omicron emerged following COVID-19 vaccination campaigns, displaced previous SARS-CoV-2 variants of concern worldwide, and gave rise to lineages that continue to spread. Here, we show that Omicron exhibits increased infectivity in primary adult upper airway tissue relative to Delta. Using recombinant forms of SARS-CoV-2 and nasal epithelial cells cultured at the liquid-air interface, enhanced infectivity maps to the step of cellular entry and evolved recently through mutations unique to Omicron Spike. Unlike earlier variants of SARS-CoV-2, Omicron enters nasal cells independently of serine transmembrane proteases and instead relies upon metalloproteinases to catalyze membrane fusion. This entry pathway unlocked by Omicron Spike enables evasion of constitutive and interferon-induced antiviral factors that restrict SARS-CoV-2 entry following attachment. Therefore, the increased transmissibility exhibited by Omicron in humans may be attributed not only to its evasion of vaccine-elicited adaptive immunity, but also to its superior invasion of nasal epithelia and resistance to the cell-intrinsic barriers present therein.
Collapse
Affiliation(s)
- Guoli Shi
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD
| | - Tiansheng Li
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD
| | - Kin Kui Lai
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD
| | - Reed F. Johnson
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD
| | - Jonathan W Yewdell
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD
| | - Alex A Compton
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD
| |
Collapse
|
12
|
Ben Geoffrey AS, Gracia J. A Bayesian walker coupled with a computational workflow that generates the micro-evolution of SARS-CoV-2 and makes predictions of new mutations that can emerge. J Biomol Struct Dyn 2023:1-9. [PMID: 37771150 DOI: 10.1080/07391102.2023.2263798] [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: 11/29/2022] [Accepted: 09/22/2023] [Indexed: 09/30/2023]
Abstract
In this work, a Bayesian walker was constructed that generates mutations that are more prone as per UNIPROT variant data. The Bayesian walker was used to search the mutational landscape of Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2) and a computational workflow was followed to evaluate whether a particular mutation would satisfy natural selection's fitness criteria. For SARS-CoV-2, the empirical known fitness criteria derived from SARS-CoV-2 micro-evolution data is 3-fold criteria. Mutations that have emerged on the Spike protein of SARS-CoV-2 are ones that preserve the structural integrity of the Spike, retain, or increase infectivity and are Immune evasive as per literature reports. Based on the molecular mechanism of infectivity and Immune evasion of SARS-CoV-2, a molecular modelling workflow was adopted to investigate the evolutionary feasibility of the mutations generated by the walker, to check whether the mutations satisfy the 3-fold fitness criteria for SARS-CoV-2 micro-evolution. It was found that the walker (mutation generator) coupled with the computational workflow to evaluate the evolutionary fitness of the generated mutations, re-generated the mutants corresponding to the Alpha, Beta and Gamma variants of SARS-CoV-2 demonstrating the ability of the methodology to generate the micro-evolution of SARS-CoV-2. Having demonstrated the ability of the methodology to generate the micro-evolution of SARS-CoV-2, the computational methodology was used to make predictions for new mutants that could emerge.Communicated by Ramaswamy H. Sarma.
Collapse
|
13
|
Ju X, Wang Z, Wang P, Ren W, Yu Y, Yu Y, Yuan B, Song J, Zhang X, Zhang Y, Xu C, Tian B, Shi Y, Zhang R, Ding Q. SARS-CoV-2 main protease cleaves MAGED2 to antagonize host antiviral defense. mBio 2023; 14:e0137323. [PMID: 37439567 PMCID: PMC10470497 DOI: 10.1128/mbio.01373-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 06/02/2023] [Indexed: 07/14/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the agent causing the global pandemic of COVID-19. SARS-CoV-2 genome encodes a main protease (nsp5, also called Mpro) and a papain-like protease (nsp3, also called PLpro), which are responsible for processing viral polyproteins to assemble a functional replicase complex. In this study, we found that Mpro of SARS-CoV-2 can cleave human MAGED2 and other mammalian orthologs at Gln-263. Moreover, SARS-CoV and MERS-CoV Mpro can also cleave human MAGED2, suggesting MAGED2 cleavage by Mpro is an evolutionarily conserved mechanism of coronavirus infection in mammals. Intriguingly, Mpro from Beta variant cleaves MAGED2 more efficiently than wild type, but Omicron Mpro is opposite. Further studies show that MAGED2 inhibits SARS-CoV-2 infection at viral replication step. Mechanistically, MAGED2 is associated with SARS-CoV-2 nucleocapsid protein through its N-terminal region in an RNA-dependent manner, and this disrupts the interaction between SARS-CoV-2 nucleocapsid protein and viral genome, thus inhibiting viral replication. When MAGED2 is cleaved by Mpro, the N-terminal of MAGED2 will translocate into the nucleus, and the truncated MAGED2 is unable to suppress SARS-CoV-2 replication. This work not only discovers the antiviral function of MAGED2 but also provides new insights into how SARS-CoV-2 Mpro antagonizes host antiviral response. IMPORTANCE Host factors that restrict severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection remain elusive. Here, we found that MAGED2 can be cleaved by SARS-CoV-2 main protease (Mpro) at Gln-263. SARS-CoV and MERS-CoV Mpro can also cleave MAGED2, and MAGED2 from multiple species can be cleaved by SARS-CoV-2 Mpro. Mpro from Beta variant cleaves MAGED2 more efficiently efficiently than wild type, but Omicron is the opposite. MAGED2 depletion enhances SARS-CoV-2 infection, suggesting its inhibitory role in SARS-CoV-2 infection. Mechanistically, MAGED2 restricts SARS-CoV-2 replication by disrupting the interaction between nucleocapsid and viral genomes. When MAGED2 is cleaved, its N-terminal will translocate into the nucleus. In this way, Mpro relieves MAGED2' inhibition on viral replication. This study improves our understanding of complex viral-host interaction and provides novel targets to treat SARS-CoV-2 infection.
Collapse
Affiliation(s)
- Xiaohui Ju
- School of Medicine, Tsinghua University, Beijing, China
| | - Ziqiao Wang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Biosafety Level 3 Laboratory, Fudan University, Shanghai, China
| | - Pengcheng Wang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Biosafety Level 3 Laboratory, Fudan University, Shanghai, China
| | - Wenlin Ren
- School of Medicine, Tsinghua University, Beijing, China
| | - Yanying Yu
- School of Medicine, Tsinghua University, Beijing, China
| | - Yin Yu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Biosafety Level 3 Laboratory, Fudan University, Shanghai, China
| | - Bin Yuan
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jingwei Song
- School of Medicine, Tsinghua University, Beijing, China
| | - Xiaochun Zhang
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Yu Zhang
- School of Medicine, Tsinghua University, Beijing, China
| | - Chang Xu
- School of Medicine, Tsinghua University, Beijing, China
| | - Boxue Tian
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Yi Shi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Rong Zhang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Biosafety Level 3 Laboratory, Fudan University, Shanghai, China
| | | |
Collapse
|
14
|
Smith JR, Dowling JW, McFadden MI, Karp A, Schwerk J, Woodward JJ, Savan R, Forero A. MEF2A suppresses stress responses that trigger DDX41-dependent IFN production. Cell Rep 2023; 42:112805. [PMID: 37467105 PMCID: PMC10652867 DOI: 10.1016/j.celrep.2023.112805] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 05/17/2023] [Accepted: 06/27/2023] [Indexed: 07/21/2023] Open
Abstract
Cellular stress in the form of disrupted transcription, loss of organelle integrity, or damage to nucleic acids can elicit inflammatory responses by activating signaling cascades canonically tasked with controlling pathogen infections. These stressors must be kept in check to prevent unscheduled activation of interferon, which contributes to autoinflammation. This study examines the role of the transcription factor myocyte enhancing factor 2A (MEF2A) in setting the threshold of transcriptional stress responses to prevent R-loop accumulation. Increases in R-loops lead to the induction of interferon and inflammatory responses in a DEAD-box helicase 41 (DDX41)-, cyclic GMP-AMP synthase (cGAS)-, and stimulator of interferon genes (STING)-dependent manner. The loss of MEF2A results in the activation of ATM and RAD3-related (ATR) kinase, which is also necessary for the activation of STING. This study identifies the role of MEF2A in sustaining transcriptional homeostasis and highlights the role of ATR in positively regulating R-loop-associated inflammatory responses.
Collapse
Affiliation(s)
- Julian R Smith
- Department of Immunology, University of Washington, Seattle, WA 98109, USA
| | - Jack W Dowling
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Matthew I McFadden
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, OH 43210, USA; Biomedical Sciences Graduate Program, The Ohio State University, Columbus, OH 43210, USA
| | - Andrew Karp
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, OH 43210, USA; Discovery PREP, The Ohio State University, Columbus, OH 43210, USA
| | - Johannes Schwerk
- Department of Immunology, University of Washington, Seattle, WA 98109, USA
| | - Joshua J Woodward
- Department of Microbiology, University of Washington, Seattle, WA 98109, USA
| | - Ram Savan
- Department of Immunology, University of Washington, Seattle, WA 98109, USA
| | - Adriana Forero
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, OH 43210, USA; Cancer Biology Program, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA; Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA.
| |
Collapse
|
15
|
Lin Y, Sun Q, Zhang B, Zhao W, Shen C. The regulation of lncRNAs and miRNAs in SARS-CoV-2 infection. Front Cell Dev Biol 2023; 11:1229393. [PMID: 37576600 PMCID: PMC10416254 DOI: 10.3389/fcell.2023.1229393] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 07/20/2023] [Indexed: 08/15/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) was a global endemic that continues to cause a large number of severe illnesses and fatalities. There is increasing evidence that non-coding RNAs (ncRNAs) are crucial regulators of viral infection and antiviral immune response and the role of non-coding RNAs in SARS-CoV-2 infection has now become the focus of scholarly inquiry. After SARS-CoV-2 infection, some ncRNAs' expression levels are regulated to indirectly control the expression of antiviral genes and viral gene replication. However, some other ncRNAs are hijacked by SARS-CoV-2 in order to help the virus evade the immune system by suppressing the expression of type I interferon (IFN-1) and controlling cytokine levels. In this review, we summarize the recent findings of long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) among non-coding RNAs in SARS-CoV-2 infection and antiviral response, discuss the potential mechanisms of actions, and prospects for the detection, treatment, prevention and future directions of SARS-CoV-2 infection research.
Collapse
Affiliation(s)
| | | | | | - Wei Zhao
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Chenguang Shen
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| |
Collapse
|
16
|
Sacchi A, Giannessi F, Sabatini A, Percario ZA, Affabris E. SARS-CoV-2 Evasion of the Interferon System: Can We Restore Its Effectiveness? Int J Mol Sci 2023; 24:ijms24119353. [PMID: 37298304 DOI: 10.3390/ijms24119353] [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: 03/31/2023] [Revised: 05/12/2023] [Accepted: 05/22/2023] [Indexed: 06/12/2023] Open
Abstract
Type I and III Interferons (IFNs) are the first lines of defense in microbial infections. They critically block early animal virus infection, replication, spread, and tropism to promote the adaptive immune response. Type I IFNs induce a systemic response that impacts nearly every cell in the host, while type III IFNs' susceptibility is restricted to anatomic barriers and selected immune cells. Both IFN types are critical cytokines for the antiviral response against epithelium-tropic viruses being effectors of innate immunity and regulators of the development of the adaptive immune response. Indeed, the innate antiviral immune response is essential to limit virus replication at the early stages of infection, thus reducing viral spread and pathogenesis. However, many animal viruses have evolved strategies to evade the antiviral immune response. The Coronaviridae are viruses with the largest genome among the RNA viruses. Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) caused the coronavirus disease 2019 (COVID-19) pandemic. The virus has evolved numerous strategies to contrast the IFN system immunity. We intend to describe the virus-mediated evasion of the IFN responses by going through the main phases: First, the molecular mechanisms involved; second, the role of the genetic background of IFN production during SARS-CoV-2 infection; and third, the potential novel approaches to contrast viral pathogenesis by restoring endogenous type I and III IFNs production and sensitivity at the sites of infection.
Collapse
Affiliation(s)
- Alessandra Sacchi
- Laboratory of Molecular Virology and Antimicrobial Immunity, Department of Science, Roma Tre University, 00146 Rome, Italy
| | - Flavia Giannessi
- Laboratory of Molecular Virology and Antimicrobial Immunity, Department of Science, Roma Tre University, 00146 Rome, Italy
| | - Andrea Sabatini
- Laboratory of Molecular Virology and Antimicrobial Immunity, Department of Science, Roma Tre University, 00146 Rome, Italy
| | - Zulema Antonia Percario
- Laboratory of Molecular Virology and Antimicrobial Immunity, Department of Science, Roma Tre University, 00146 Rome, Italy
| | - Elisabetta Affabris
- Laboratory of Molecular Virology and Antimicrobial Immunity, Department of Science, Roma Tre University, 00146 Rome, Italy
| |
Collapse
|
17
|
Mohandas S, Jagannathan P, Henrich TJ, Sherif ZA, Bime C, Quinlan E, Portman MA, Gennaro M, Rehman J. Immune mechanisms underlying COVID-19 pathology and post-acute sequelae of SARS-CoV-2 infection (PASC). eLife 2023; 12:e86014. [PMID: 37233729 PMCID: PMC10219649 DOI: 10.7554/elife.86014] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 05/18/2023] [Indexed: 05/27/2023] Open
Abstract
With a global tally of more than 500 million cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections to date, there are growing concerns about the post-acute sequelae of SARS-CoV-2 infection (PASC), also known as long COVID. Recent studies suggest that exaggerated immune responses are key determinants of the severity and outcomes of the initial SARS-CoV-2 infection as well as subsequent PASC. The complexity of the innate and adaptive immune responses in the acute and post-acute period requires in-depth mechanistic analyses to identify specific molecular signals as well as specific immune cell populations which promote PASC pathogenesis. In this review, we examine the current literature on mechanisms of immune dysregulation in severe COVID-19 and the limited emerging data on the immunopathology of PASC. While the acute and post-acute phases may share some parallel mechanisms of immunopathology, it is likely that PASC immunopathology is quite distinct and heterogeneous, thus requiring large-scale longitudinal analyses in patients with and without PASC after an acute SARS-CoV-2 infection. By outlining the knowledge gaps in the immunopathology of PASC, we hope to provide avenues for novel research directions that will ultimately lead to precision therapies which restore healthy immune function in PASC patients.
Collapse
Affiliation(s)
- Sindhu Mohandas
- Division of Infectious Diseases, Children’s Hospital Los Angeles, Keck School of Medicine, University of Southern CaliforniaLos AngelesUnited States
| | - Prasanna Jagannathan
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford UniversityStanfordUnited States
| | - Timothy J Henrich
- Division of Experimental Medicine, University of California, San FranciscoSan FranciscoUnited States
| | - Zaki A Sherif
- Department of Biochemistry & Molecular Biology, Howard University College of MedicineWashingtonUnited States
| | - Christian Bime
- Division of Pulmonary, Allergy, Critical Care & Sleep Medicine, Department of Medicine, University of Arizona College of MedicineTucsonUnited States
| | - Erin Quinlan
- National Center for Complementary and Integrative Health, National Institutes of HealthBethesdaUnited States
| | - Michael A Portman
- Seattle Children’s Hospital, Division of Pediatric Cardiology, Department of Pediatrics, University of WashingtonSeattleUnited States
| | - Marila Gennaro
- Public Health Research Institute and Department of Medicine, Rutgers New Jersey Medical SchoolNewarkUnited States
| | - Jalees Rehman
- Department of Biochemistry and Molecular Genetics, University of Illinois, College of MedicineChicagoUnited States
| |
Collapse
|
18
|
Maffia-Bizzozero S, Cevallos C, Lenicov FR, Freiberger RN, Lopez CAM, Guano Toaquiza A, Sviercz F, Jarmoluk P, Bustos C, D’Addario AC, Quarleri J, Delpino MV. Viable SARS-CoV-2 Omicron sub-variants isolated from autopsy tissues. Front Microbiol 2023; 14:1192832. [PMID: 37283920 PMCID: PMC10240073 DOI: 10.3389/fmicb.2023.1192832] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 05/08/2023] [Indexed: 06/08/2023] Open
Abstract
Introduction Pulmonary and extrapulmonary manifestations have been described after infection with SARS-CoV-2, the causative agent of coronavirus disease 2019 (COVID-19). The virus is known to persist in multiple organs due to its tropism for several tissues. However, previous reports were unable to provide definitive information about whether the virus is viable and transmissible. It has been hypothesized that the persisting reservoirs of SARS-CoV-2 in tissues could be one of the multiple potentially overlapping causes of long COVID. Methods In the present study, we investigated autopsy materials obtained from 21 cadaveric donors with documented first infection or reinfection at the time of death. The cases studied included recipients of different formulations of COVID-19 vaccines. The aim was to find the presence of SARS-CoV-2 in the lungs, heart, liver, kidneys, and intestines. We used two technical approaches: the detection and quantification of viral genomic RNA using RT-qPCR, and virus infectivity using permissive in vitro Vero E6 culture. Results All tissues analyzed showed the presence of SARS-CoV-2 genomic RNA but at dissimilar levels ranging from 1.01 × 102 copies/mL to 1.14 × 108 copies/mL, even among those cases who had been COVID-19 vaccinated. Importantly, different amounts of replication-competent virus were detected in the culture media from the studied tissues. The highest viral load were measured in the lung (≈1.4 × 106 copies/mL) and heart (≈1.9 × 106 copies/mL) samples. Additionally, based on partial Spike gene sequences, SARS-CoV-2 characterization revealed the presence of multiple Omicron sub-variants exhibiting a high level of nucleotide and amino acid identity among them. Discussion These findings highlight that SARS-CoV-2 can spread to multiple tissue locations such as the lungs, heart, liver, kidneys, and intestines, both after primary infection and after reinfections with the Omicron variant, contributing to extending knowledge about the pathogenesis of acute infection and understanding the sequelae of clinical manifestations that are observed during post-acute COVID-19.
Collapse
Affiliation(s)
| | - Cintia Cevallos
- Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Federico Remes Lenicov
- Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Rosa Nicole Freiberger
- Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Cinthya Alicia Marcela Lopez
- Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Alex Guano Toaquiza
- Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Franco Sviercz
- Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Patricio Jarmoluk
- Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | | | | | - Jorge Quarleri
- Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - M. Victoria Delpino
- Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| |
Collapse
|
19
|
Cowburn D, Rout M. Improving the hole picture: towards a consensus on the mechanism of nuclear transport. Biochem Soc Trans 2023; 51:871-886. [PMID: 37099395 PMCID: PMC10212546 DOI: 10.1042/bst20220494] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 04/04/2023] [Accepted: 04/06/2023] [Indexed: 04/27/2023]
Abstract
Nuclear pore complexes (NPCs) mediate the exchange of materials between the nucleoplasm and cytoplasm, playing a key role in the separation of nucleic acids and proteins into their required compartments. The static structure of the NPC is relatively well defined by recent cryo-EM and other studies. The functional roles of dynamic components in the pore of the NPC, phenylalanyl-glycyl (FG) repeat rich nucleoporins, is less clear because of our limited understanding of highly dynamic protein systems. These proteins form a 'restrained concentrate' which interacts with and concentrates nuclear transport factors (NTRs) to provide facilitated nucleocytoplasmic transport of cargoes. Very rapid on- and off-rates among FG repeats and NTRs supports extremely fast facilitated transport, close to the rate of macromolecular diffusion in cytoplasm, while complexes without specific interactions are entropically excluded, though details on several aspects of the transport mechanism and FG repeat behaviors remain to be resolved. However, as discussed here, new technical approaches combined with more advanced modeling methods will likely provide an improved dynamic description of NPC transport, potentially at the atomic level in the near future. Such advances are likely to be of major benefit in comprehending the roles the malfunctioning NPC plays in cancer, ageing, viral diseases, and neurodegeneration.
Collapse
Affiliation(s)
- David Cowburn
- Departments of Biochemistry and Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY 10461, U.S.A
| | - Michael Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, U.S.A
| |
Collapse
|
20
|
Ahmadi S, Bazargan M, Elahi R, Esmaeilzadeh A. Immune evasion of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2); molecular approaches. Mol Immunol 2023; 156:10-19. [PMID: 36857806 PMCID: PMC9684099 DOI: 10.1016/j.molimm.2022.11.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 11/04/2022] [Accepted: 11/22/2022] [Indexed: 11/25/2022]
Abstract
In December 2019, a new betacoronavirus, known as severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), caused an outbreak at the Wuhan seafood market in China. The disease was further named coronavirus disease 2019 (COVID-19). In March 2020, the World Health Organization (WHO) announced the disease to be a pandemic, as more cases were reported globally. SARS-CoV-2, like many other viruses, employs diverse strategies to elude the host immune response and/or counter immune responses. The infection outcome mainly depends on interactions between the virus and the host immune system. Inhibiting IFN production, blocking IFN signaling, enhancing IFN resistance, and hijacking the host's translation machinery to expedite the production of viral proteins are among the main immune evasion mechanisms of SARS-CoV-2. SARS-CoV-2 also downregulates the expression of MHC-I on infected cells, which is an additional immune-evasion mechanism of this virus. Moreover, antigenic modifications to the spike (S) protein, such as deletions, insertions, and also substitutions are essential for resistance to SARS-CoV-2 neutralizing antibodies. This review assesses the interaction between SARS-CoV-2 and host immune response and cellular and molecular approaches used by SARS-CoV-2 for immune evasion. Understanding the mechanisms of SARS-CoV-2 immune evasion is essential since it can improve the development of novel antiviral treatment options as well as vaccination methods.
Collapse
Affiliation(s)
- Shahrzad Ahmadi
- Virology Research Center, The National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Masih Daneshvari Hospital, Allergy and Immunology Subspecialty Lab, Tehran, Iran
| | - Mahsa Bazargan
- Virology Research Center, The National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Masih Daneshvari Hospital, Allergy and Immunology Subspecialty Lab, Tehran, Iran,Department of Immunology, School of Medicine, Sahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Reza Elahi
- M.D., School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Abdolreza Esmaeilzadeh
- Department of Immunology, Zanjan University of Medical Sciences, Zanjan, Iran; Cancer Gene Therapy Research Center (CGRC), Zanjan University of Medical Sciences, Zanjan, Iran.
| |
Collapse
|
21
|
Chen SC, Xu CT, Chang CF, Chao TY, Lin CC, Fu PW, Yu CH. Optimization of 5'UTR to evade SARS-CoV-2 Nonstructural protein 1-directed inhibition of protein synthesis in cells. Appl Microbiol Biotechnol 2023; 107:2451-2468. [PMID: 36843199 PMCID: PMC9968647 DOI: 10.1007/s00253-023-12442-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 02/09/2023] [Accepted: 02/13/2023] [Indexed: 02/28/2023]
Abstract
Maximizing the expression level of therapeutic proteins in cells is the general goal for DNA/mRNA therapies. It is particularly challenging to achieve efficient protein expression in the cellular contexts with inhibited translation machineries, such as in the presence of cellular Nonstructural protein 1 (Nsp1) of coronaviruses (CoVs) that has been reported to inhibit overall protein synthesis of host genes and exogenously delivered mRNAs/DNAs. In this study, we thoroughly examined the sequence and structure contexts of viral and non-viral 5'UTRs that determine the protein expression levels of exogenously delivered DNAs and mRNAs in cells expressing SARS-CoV-2 Nsp1. It was found that high 5'-proximal A/U content promotes an escape from Nsp1-directed inhibition of protein synthesis and results in selective protein expression. Furthermore, 5'-proximal Cs were found to significantly enhance the protein expression in an Nsp1-dependent manner, while Gs located at a specific window close to the 5'-end counteract such enhancement. The distinct protein expression levels resulted from different 5'UTRs were found correlated to Nsp1-induced mRNA degradations. These findings ultimately enabled rational designs for optimized 5'UTRs that lead to strong expression of exogenous proteins regardless of the translationally repressive Nsp1. On the other hand, we have also identified several 5'-proximal sequences derived from host genes that are capable of mediating the escapes. These results provided novel perspectives to the optimizations of 5'UTRs for DNA/mRNA therapies and/or vaccinations, as well as shedding light on the potential host escapees from Nsp1-directed translational shutoffs. KEY POINTS: • The 5'-proximal SL1 and 5a/b derived from SARS-CoV-2 genomic RNA promote exogenous protein synthesis in cells expressing Nsp1 comparing with non-specific 5'UTRs. • Specific 5'-proximal sequence contexts are the key determinants of the escapes from Nsp1-directed translational repression and thereby enhance protein expressions. • Systematic mutagenesis identified optimized 5'UTRs that strongly enhance protein expression and promote resistance to Nsp1-induced translational repression and RNA degradation.
Collapse
Affiliation(s)
- Shih-Cheng Chen
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- National Institute of Cancer Research, National Health Research Institutes, New Taipei, Taiwan
| | - Cui-Ting Xu
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chuan-Fu Chang
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ting-Yu Chao
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chia-Chi Lin
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Pei-Wen Fu
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chien-Hung Yu
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
| |
Collapse
|
22
|
Carabelli AM, Peacock TP, Thorne LG, Harvey WT, Hughes J, Peacock SJ, Barclay WS, de Silva TI, Towers GJ, Robertson DL. SARS-CoV-2 variant biology: immune escape, transmission and fitness. Nat Rev Microbiol 2023; 21:162-177. [PMID: 36653446 PMCID: PMC9847462 DOI: 10.1038/s41579-022-00841-7] [Citation(s) in RCA: 279] [Impact Index Per Article: 279.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2022] [Indexed: 01/19/2023]
Abstract
In late 2020, after circulating for almost a year in the human population, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exhibited a major step change in its adaptation to humans. These highly mutated forms of SARS-CoV-2 had enhanced rates of transmission relative to previous variants and were termed 'variants of concern' (VOCs). Designated Alpha, Beta, Gamma, Delta and Omicron, the VOCs emerged independently from one another, and in turn each rapidly became dominant, regionally or globally, outcompeting previous variants. The success of each VOC relative to the previously dominant variant was enabled by altered intrinsic functional properties of the virus and, to various degrees, changes to virus antigenicity conferring the ability to evade a primed immune response. The increased virus fitness associated with VOCs is the result of a complex interplay of virus biology in the context of changing human immunity due to both vaccination and prior infection. In this Review, we summarize the literature on the relative transmissibility and antigenicity of SARS-CoV-2 variants, the role of mutations at the furin spike cleavage site and of non-spike proteins, the potential importance of recombination to virus success, and SARS-CoV-2 evolution in the context of T cells, innate immunity and population immunity. SARS-CoV-2 shows a complicated relationship among virus antigenicity, transmission and virulence, which has unpredictable implications for the future trajectory and disease burden of COVID-19.
Collapse
Affiliation(s)
| | - Thomas P Peacock
- Department of Infectious Disease, St Mary's Medical School, Imperial College London, London, UK
| | - Lucy G Thorne
- Division of Infection and Immunity, University College London, London, UK
| | - William T Harvey
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Sharon J Peacock
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Cambridge, UK
| | - Wendy S Barclay
- Department of Infectious Disease, St Mary's Medical School, Imperial College London, London, UK
| | - Thushan I de Silva
- Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK
| | - Greg J Towers
- Division of Infection and Immunity, University College London, London, UK
| | - David L Robertson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK.
| |
Collapse
|
23
|
Qin Y, Zhang P, Deng S, Guo W, Zhang M, Liu H, Qiu R, Yao L. Red-grouper nervous necrosis virus B1 protein inhibits fish IFN response by targeting Ser5-phosphorylated RNA polymerase II to promote viral replication. FISH & SHELLFISH IMMUNOLOGY 2023; 134:108578. [PMID: 36740084 DOI: 10.1016/j.fsi.2023.108578] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 01/15/2023] [Accepted: 02/02/2023] [Indexed: 06/18/2023]
Abstract
Nervous necrosis virus (NNV) could infect more than 200 fish species worldwide, with almost 100% mortality in affected larvae and juvenile fish. Among different genotypes of NNV, the red-grouper nervous necrosis virus (RGNNV) genotype is the most widely reported with the highest number of susceptible species. Interferon (IFN) is a crucial antiviral cytokine and RGNNV needs to develop some efficient strategies to resist host IFN-stimulated antiviral immune. Although considerable researches on RGNNV, whether RGNNV B1 protein participates in regulating the host's IFN response remains unknown. Here, we reported that B1 protein acted as a transcript inhibition factor to suppress fish IFN production. We firstly found that ectopic expression of B1 protein significantly decreased IFN and IFN-stimulated genes (ISGs) mRNA levels and IFNφ1 promoter activity induced by polyinosinic:polycytidylic acid [poly (I:C)]. Further studies showed that B1 protein inhibited the IFNφ1 promoter activity stimulated by the key RIG-I-like receptors (RLRs) factors, including MDA5, MAVS, TBK1, IRF3, and IRF7 and decreased their protein levels. Moreover, B1 protein significantly inhibited the activity of constitutively active cytomegalovirus (CMV) promoter, which suggested that B1 protein was a transcription inhibitor. Western blot indicated that B1 protein decreased the Ser5 phosphorylation of RNA polymerase II (RNAP II) C-terminal domain (CTD). Together, our data demonstrated that RGNNV B1 protein was a host transcript antagonist, which intervened RNAP II Ser5-phosphorylation, inhibiting host IFN response and facilitating RGNNV replication.
Collapse
Affiliation(s)
- Yinghui Qin
- College of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, 473061, China; Key Laboratory of Ecological Security and Collaborative Innovation Centre of Water Security for Water Source Region of Mid-line of South-to-North Diversion Project of Henan Province, Nanyang, 473061, China; Henan Provincal Engineering and Technology Center of Health Products for Livestock and Poultry, Nanyang, 473061, China
| | - Peipei Zhang
- College of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, 473061, China; Key Laboratory of Ecological Security and Collaborative Innovation Centre of Water Security for Water Source Region of Mid-line of South-to-North Diversion Project of Henan Province, Nanyang, 473061, China; Henan Provincal Engineering and Technology Center of Health Products for Livestock and Poultry, Nanyang, 473061, China
| | - Si Deng
- College of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, 473061, China; Key Laboratory of Ecological Security and Collaborative Innovation Centre of Water Security for Water Source Region of Mid-line of South-to-North Diversion Project of Henan Province, Nanyang, 473061, China; Henan Provincal Engineering and Technology Center of Health Products for Livestock and Poultry, Nanyang, 473061, China
| | - Wenjing Guo
- College of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, 473061, China; Key Laboratory of Ecological Security and Collaborative Innovation Centre of Water Security for Water Source Region of Mid-line of South-to-North Diversion Project of Henan Province, Nanyang, 473061, China; Henan Provincal Engineering and Technology Center of Health Products for Livestock and Poultry, Nanyang, 473061, China
| | - Mengfan Zhang
- College of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, 473061, China; Key Laboratory of Ecological Security and Collaborative Innovation Centre of Water Security for Water Source Region of Mid-line of South-to-North Diversion Project of Henan Province, Nanyang, 473061, China; Henan Provincal Engineering and Technology Center of Health Products for Livestock and Poultry, Nanyang, 473061, China
| | - Haixiang Liu
- College of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, 473061, China; Key Laboratory of Ecological Security and Collaborative Innovation Centre of Water Security for Water Source Region of Mid-line of South-to-North Diversion Project of Henan Province, Nanyang, 473061, China; Henan Provincal Engineering and Technology Center of Health Products for Livestock and Poultry, Nanyang, 473061, China
| | - Reng Qiu
- College of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, 473061, China; Key Laboratory of Ecological Security and Collaborative Innovation Centre of Water Security for Water Source Region of Mid-line of South-to-North Diversion Project of Henan Province, Nanyang, 473061, China; Henan Provincal Engineering and Technology Center of Health Products for Livestock and Poultry, Nanyang, 473061, China
| | - Lunguang Yao
- College of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, 473061, China; Key Laboratory of Ecological Security and Collaborative Innovation Centre of Water Security for Water Source Region of Mid-line of South-to-North Diversion Project of Henan Province, Nanyang, 473061, China; Henan Provincal Engineering and Technology Center of Health Products for Livestock and Poultry, Nanyang, 473061, China.
| |
Collapse
|
24
|
Dumenil T, Le TT, Rawle DJ, Yan K, Tang B, Nguyen W, Bishop C, Suhrbier A. Warmer ambient air temperatures reduce nasal turbinate and brain infection, but increase lung inflammation in the K18-hACE2 mouse model of COVID-19. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 859:160163. [PMID: 36395835 PMCID: PMC9659553 DOI: 10.1016/j.scitotenv.2022.160163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 11/04/2022] [Accepted: 11/09/2022] [Indexed: 06/16/2023]
Abstract
Warmer climatic conditions have been associated with fewer COVID-19 cases. Herein we infected K18-hACE2 mice housed at the standard animal house temperature of ∼22 °C, or at ∼31 °C, which is considered to be thermoneutral for mice. On day 2 post infection, RNA-Seq analyses showed no significant differential gene expression lung in lungs of mice housed at the two temperatures, with almost identical viral loads and type I interferon responses. There was also no significant difference in viral loads in lungs on day 5, but RNA-Seq and histology analyses showed clearly elevated inflammatory signatures and infiltrates. Thermoneutrality thus promoted lung inflammation. On day 2 post infection mice housed at 31 °C showed reduced viral loads in nasal turbinates, consistent with increased mucociliary clearance at the warmer ambient temperature. These mice also had reduced virus levels in the brain, and an ensuing amelioration of weight loss and a delay in mortality. Warmer air temperatures may thus reduce infection of the upper respiratory track and the olfactory epithelium, resulting in reduced brain infection. Potential relevance for anosmia and neurological sequelae in COVID-19 patients is discussed.
Collapse
Affiliation(s)
- Troy Dumenil
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia
| | - Thuy T Le
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia
| | - Daniel J Rawle
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia
| | - Kexin Yan
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia
| | - Bing Tang
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia
| | - Wilson Nguyen
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia
| | - Cameron Bishop
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia
| | - Andreas Suhrbier
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia; Australian Infectious Disease Research Centre, GVN Center of Excellence, Brisbane, Queensland 4029, 4072, Australia.
| |
Collapse
|
25
|
Jernigan RJ, Logeswaran D, Doppler D, Nagaratnam N, Sonker M, Yang JH, Ketawala G, Martin-Garcia JM, Shelby ML, Grant TD, Mariani V, Tolstikova A, Sheikh MZ, Yung MC, Coleman MA, Zaare S, Kaschner EK, Rabbani MT, Nazari R, Zacks MA, Hayes B, Sierra RG, Hunter MS, Lisova S, Batyuk A, Kupitz C, Boutet S, Hansen DT, Kirian RA, Schmidt M, Fromme R, Frank M, Ros A, Chen JJL, Botha S, Fromme P. Room-temperature structural studies of SARS-CoV-2 protein NendoU with an X-ray free-electron laser. Structure 2023; 31:138-151.e5. [PMID: 36630960 PMCID: PMC9830665 DOI: 10.1016/j.str.2022.12.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 10/08/2022] [Accepted: 12/14/2022] [Indexed: 01/11/2023]
Abstract
NendoU from SARS-CoV-2 is responsible for the virus's ability to evade the innate immune system by cleaving the polyuridine leader sequence of antisense viral RNA. Here we report the room-temperature structure of NendoU, solved by serial femtosecond crystallography at an X-ray free-electron laser to 2.6 Å resolution. The room-temperature structure provides insight into the flexibility, dynamics, and other intrinsic properties of NendoU, with indications that the enzyme functions as an allosteric switch. Functional studies examining cleavage specificity in solution and in crystals support the uridine-purine cleavage preference, and we demonstrate that enzyme activity is fully maintained in crystal form. Optimizing the purification of NendoU and identifying suitable crystallization conditions set the benchmark for future time-resolved serial femtosecond crystallography studies. This could advance the design of antivirals with higher efficacy in treating coronaviral infections, since drugs that block allosteric conformational changes are less prone to drug resistance.
Collapse
Affiliation(s)
- Rebecca J Jernigan
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Dhenugen Logeswaran
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Diandra Doppler
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Nirupa Nagaratnam
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA
| | - Mukul Sonker
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Jay-How Yang
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA
| | - Gihan Ketawala
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Jose M Martin-Garcia
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA
| | - Megan L Shelby
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
| | - Thomas D Grant
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, 955 Main Street, Buffalo, NY 14203, USA
| | - Valerio Mariani
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | | | - Michelle Z Sheikh
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA
| | - Mimi Cho Yung
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
| | - Matthew A Coleman
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
| | - Sahba Zaare
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; Fulton School of Electrical, Computer, and Energy Engineering, Arizona State University, Tempe, AZ 85287, USA; Department of Physics, Arizona State University, Tempe, AZ 85287-1504, USA
| | - Emily K Kaschner
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Mohammad Towshif Rabbani
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA
| | - Reza Nazari
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA
| | - Michele A Zacks
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA
| | - Brandon Hayes
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Raymond G Sierra
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Mark S Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Stella Lisova
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Alexander Batyuk
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Christopher Kupitz
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Sebastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Debra T Hansen
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA
| | - Richard A Kirian
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; Department of Physics, Arizona State University, Tempe, AZ 85287-1504, USA
| | - Marius Schmidt
- Department of Physics, University of Wisconsin-Milwaukee, 3135 N. Maryland Avenue, Milwaukee, WI 53211, USA
| | - Raimund Fromme
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Matthias Frank
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
| | - Alexandra Ros
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Julian J-L Chen
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Sabine Botha
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; Department of Physics, Arizona State University, Tempe, AZ 85287-1504, USA.
| | - Petra Fromme
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA.
| |
Collapse
|
26
|
Zhu J, Chen T, Mao X, Fang Y, Sun H, Wei DQ, Ji G. Machine learning of flow cytometry data reveals the delayed innate immune responses correlate with the severity of COVID-19. Front Immunol 2023; 14:974343. [PMID: 36845115 PMCID: PMC9951775 DOI: 10.3389/fimmu.2023.974343] [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: 06/21/2022] [Accepted: 01/04/2023] [Indexed: 01/27/2023] Open
Abstract
Introduction The COVID-19 pandemic has posed a major burden on healthcare and economic systems across the globe for over 3 years. Even though vaccines are available, the pathogenesis is still unclear. Multiple studies have indicated heterogeneity of immune responses to SARS-CoV-2, and potentially distinct patient immune types that might be related to disease features. However, those conclusions are mainly inferred by comparing the differences of pathological features between moderate and severe patients, some immunological features may be subjectively overlooked. Methods In this study, the relevance scores(RS), reflecting which features play a more critical role in the decision-making process, between immunological features and the COVID-19 severity are objectively calculated through neural network, where the input features include the immune cell counts and the activation marker concentrations of particular cell, and these quantified characteristic data are robustly generated by processing flow cytometry data sets containing the peripheral blood information of COVID-19 patients through PhenoGraph algorithm. Results Specifically, the RS between immune cell counts and COVID-19 severity with time indicated that the innate immune responses in severe patients are delayed at the early stage, and the continuous decrease of classical monocytes in peripherial blood is significantly associated with the severity of disease. The RS between activation marker concentrations and COVID-19 severity suggested that the down-regulation of IFN-γ in classical monocytes, Treg, CD8 T cells, and the not down-regulation of IL_17a in classical monocytes, Tregs are highly correlated with the occurrence of severe disease. Finally, a concise dynamic model of immune responses in COVID-19 patients was generalized. Discussion These results suggest that the delayed innate immune responses in the early stage, and the abnormal expression of IL-17a and IFN-γ in classical monocytes, Tregs, and CD8 T cells are primarily responsible for the severity of COVID-19.
Collapse
Affiliation(s)
- Jing Zhu
- National Key Laboratory for Shock Wave and Detonation Physics Research, Institute of Fluid Physics, Chinese Academy of Engineering Physics, Mianyang, China
| | - Tunan Chen
- Department of Neurosurgery and Key Laboratory of Neurotrauma, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqin, China
| | - Xueying Mao
- State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint Laboratory of International Cooperation in Metabolic and Developmental, Sciences, Ministry of Education and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yitian Fang
- State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint Laboratory of International Cooperation in Metabolic and Developmental, Sciences, Ministry of Education and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Heqi Sun
- State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint Laboratory of International Cooperation in Metabolic and Developmental, Sciences, Ministry of Education and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Dong-Qing Wei
- State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint Laboratory of International Cooperation in Metabolic and Developmental, Sciences, Ministry of Education and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Peng Cheng Laboratory, Shenzhen, China
| | - Guangfu Ji
- National Key Laboratory for Shock Wave and Detonation Physics Research, Institute of Fluid Physics, Chinese Academy of Engineering Physics, Mianyang, China
| |
Collapse
|
27
|
Mukherjee SB, Mukherjee S, Detroja R, Frenkel-Morgenstern M. The landscape of differential splicing and transcript alternations in severe COVID-19 infection. FEBS J 2023. [PMID: 36628954 DOI: 10.1111/febs.16723] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 10/25/2022] [Accepted: 01/09/2023] [Indexed: 01/12/2023]
Abstract
Viral infections can modulate the widespread alternations of cellular splicing, favouring viral replication within the host cells by overcoming host immune responses. However, how SARS-CoV-2 induces host cell differential splicing and affects the landscape of transcript alternation in severe COVID-19 infection remains elusive. Understanding the differential splicing and transcript alternations in severe COVID-19 infection may improve our molecular insights into the SARS-CoV-2 pathogenesis. In this study, we analysed the publicly available blood and lung transcriptome data of severe COVID-19 patients, blood transcriptome data of recovered COVID-19 patients at 12-, 16- and 24-week postinfection and healthy controls. We identified a significant transcript isoform switching in the individual blood and lung RNA-seq data of severe COVID-19-infected patients and 25 common genes that alter their transcript isoform in both blood and lung samples. Altered transcripts show significant loss of the open reading frame, functional domains and switch from coding to noncoding transcript, impacting normal cellular functions. Furthermore, we identified the expression of several novel recurrent chimeric transcripts in the blood samples from severe COVID-19 patients. Moreover, the analysis of the isoform switching into blood samples from recovered COVID-19 patients highlights that there is no significant isoform switching in 16- and 24-week postinfection, and the levels of expressed chimeric transcripts are reduced. This finding emphasizes that SARS-CoV-2 severe infection induces widespread splicing in the host cells, which could help the virus alter the host immune responses and facilitate the viral replication within the host and the efficient translation of viral proteins.
Collapse
Affiliation(s)
- Sunanda Biswas Mukherjee
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Sumit Mukherjee
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel.,National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Rajesh Detroja
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel.,Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Milana Frenkel-Morgenstern
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| |
Collapse
|
28
|
Escudero-Pérez B, Lawrence P, Castillo-Olivares J. Immune correlates of protection for SARS-CoV-2, Ebola and Nipah virus infection. Front Immunol 2023; 14:1156758. [PMID: 37153606 PMCID: PMC10158532 DOI: 10.3389/fimmu.2023.1156758] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 03/20/2023] [Indexed: 05/09/2023] Open
Abstract
Correlates of protection (CoP) are biological parameters that predict a certain level of protection against an infectious disease. Well-established correlates of protection facilitate the development and licensing of vaccines by assessing protective efficacy without the need to expose clinical trial participants to the infectious agent against which the vaccine aims to protect. Despite the fact that viruses have many features in common, correlates of protection can vary considerably amongst the same virus family and even amongst a same virus depending on the infection phase that is under consideration. Moreover, the complex interplay between the various immune cell populations that interact during infection and the high degree of genetic variation of certain pathogens, renders the identification of immune correlates of protection difficult. Some emerging and re-emerging viruses of high consequence for public health such as SARS-CoV-2, Nipah virus (NiV) and Ebola virus (EBOV) are especially challenging with regards to the identification of CoP since these pathogens have been shown to dysregulate the immune response during infection. Whereas, virus neutralising antibodies and polyfunctional T-cell responses have been shown to correlate with certain levels of protection against SARS-CoV-2, EBOV and NiV, other effector mechanisms of immunity play important roles in shaping the immune response against these pathogens, which in turn might serve as alternative correlates of protection. This review describes the different components of the adaptive and innate immune system that are activated during SARS-CoV-2, EBOV and NiV infections and that may contribute to protection and virus clearance. Overall, we highlight the immune signatures that are associated with protection against these pathogens in humans and could be used as CoP.
Collapse
Affiliation(s)
- Beatriz Escudero-Pérez
- WHO Collaborating Centre for Arbovirus and Haemorrhagic Fever Reference and Research, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Luebeck-Borstel-Reims, Braunschweig, Germany
- *Correspondence: Beatriz Escudero-Pérez, ; Javier Castillo-Olivares,
| | - Philip Lawrence
- CONFLUENCE: Sciences et Humanités (EA 1598), Université Catholique de Lyon (UCLy), Lyon, France
| | - Javier Castillo-Olivares
- Laboratory of Viral Zoonotics, University of Cambridge, Cambridge, United Kingdom
- *Correspondence: Beatriz Escudero-Pérez, ; Javier Castillo-Olivares,
| |
Collapse
|
29
|
Akaishi T, Fujiwara K, Ishii T. Genetic Recombination Sites Away from the Insertion/Deletion Hotspots in SARS-Related Coronaviruses. TOHOKU J EXP MED 2023; 259:17-26. [PMID: 36351613 DOI: 10.1620/tjem.2022.j093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/29/2023]
Affiliation(s)
| | - Kei Fujiwara
- Department of Gastroenterology and Metabolism, Nagoya City University
| | - Tadashi Ishii
- Department of Education and Support for Regional Medicine, Tohoku University
| |
Collapse
|
30
|
Buchynskyi M, Kamyshna I, Lyubomirskaya K, Moshynets O, Kobyliak N, Oksenych V, Kamyshnyi A. Efficacy of interferon alpha for the treatment of hospitalized patients with COVID-19: A meta-analysis. Front Immunol 2023; 14:1069894. [PMID: 36776844 PMCID: PMC9909279 DOI: 10.3389/fimmu.2023.1069894] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 01/12/2023] [Indexed: 01/27/2023] Open
Abstract
Introduction IFN-α intervention may block SARS-CoV-2 replication and normalize the deregulated innate immunity of COVID-19. Aim This meta-analysis aimed to investigate the efficacy of interferon IFN-α-containing regimens when treating patients with moderate-to-severe COVID-19. Material and methods PubMed, SCOPUS, and ClinicalTrials.gov were searched from inception to 15 January 2022. A systematic literature search was conducted by applying relevant terms for 'COVID-19' and 'interferon-α'. The primary outcome enclosed the all-cause hospital mortality. The secondary outcomes constituted the length of hospital stay; hospital discharge; nucleic acid negative conversion. Results Eleven studies are enclosed in the meta-analysis. No significant difference in the all-cause mortality rate was found between the study and control groups (OR 0.2; 95% CI 0.05-1.2; I2 = 96%). The implementation of interferon did not influence such outcomes as the length of hospital stay (OR 0.9; 95% CІ, 0.3-2.6; I2 = 91%), nucleic acid negative conversion (OR 0.8; 95% CI, 0.04-17.2; I2 = 94%). Nevertheless, IFN-α treatment resulted in a higher number of patients discharged from the hospital (OR 26.6; 95% CІ, 2.7-254.3; I2 = 95%). Conclusions Thus, IFN-α does not benefit the survival of hospitalized COVID-19 patients but may increase the number of patients discharged from the hospital. Systematic review registration www.crd.york.ac.uk/prospero, identifier (CRD42022374589).
Collapse
Affiliation(s)
- Mykhailo Buchynskyi
- Department of Microbiology, Virology, and Immunology, I. Horbachevsky Ternopil National Medical University, Ternopil, Ukraine
| | - Iryna Kamyshna
- Department of Medical Rehabilitation, I. Horbachevsky Ternopil National Medical University, Ternopil, Ukraine
| | - Katerina Lyubomirskaya
- Department of Obstetrics and Gynecology, Zaporizhzhia State Medical University, Zaporizhzhia, Ukraine
| | - Olena Moshynets
- Biofilm Study Group, Department of Cell Regulatory Mechanisms, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kiev, Ukraine
| | - Nazarii Kobyliak
- Endocrinology Department, Bogomolets National Medical University, Kyiv, Ukraine.,Medical Laboratory CSD, Kyiv, Ukraine
| | | | - Aleksandr Kamyshnyi
- Department of Microbiology, Virology, and Immunology, I. Horbachevsky Ternopil National Medical University, Ternopil, Ukraine
| |
Collapse
|
31
|
Shi G, Chiramel AI, Li T, Lai KK, Kenney AD, Zani A, Eddy AC, Majdoul S, Zhang L, Dempsey T, Beare PA, Kar S, Yewdell JW, Best SM, Yount JS, Compton AA. Rapalogs downmodulate intrinsic immunity and promote cell entry of SARS-CoV-2. J Clin Invest 2022; 132:e160766. [PMID: 36264642 PMCID: PMC9753997 DOI: 10.1172/jci160766] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 10/18/2022] [Indexed: 12/24/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in immunocompromised individuals is associated with prolonged virus shedding and evolution of viral variants. Rapamycin and its analogs (rapalogs, including everolimus, temsirolimus, and ridaforolimus) are FDA approved as mTOR inhibitors for the treatment of human diseases, including cancer and autoimmunity. Rapalog use is commonly associated with an increased susceptibility to infection, which has been traditionally explained by impaired adaptive immunity. Here, we show that exposure to rapalogs increased susceptibility to SARS-CoV-2 infection in tissue culture and in immunologically naive rodents by antagonizing the cell-intrinsic immune response. We identified 1 rapalog (ridaforolimus) that was less potent in this regard and demonstrated that rapalogs promote spike-mediated entry into cells, by triggering the degradation of the antiviral proteins IFITM2 and IFITM3 via an endolysosomal remodeling program called microautophagy. Rapalogs that increased virus entry inhibited mTOR-mediated phosphorylation of the transcription factor TFEB, which facilitated its nuclear translocation and triggered microautophagy. In rodent models of infection, injection of rapamycin prior to and after virus exposure resulted in elevated SARS-CoV-2 replication and exacerbated viral disease, while ridaforolimus had milder effects. Overall, our findings indicate that preexisting use of certain rapalogs may elevate host susceptibility to SARS-CoV-2 infection and disease by activating lysosome-mediated suppression of intrinsic immunity.
Collapse
Affiliation(s)
- Guoli Shi
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute (NCI), NIH, Frederick, Maryland, USA
| | - Abhilash I. Chiramel
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Hamilton, Montana, USA
| | - Tiansheng Li
- Laboratory of Viral Diseases, NIAID, NIH, Bethesda, Maryland, USA
| | - Kin Kui Lai
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute (NCI), NIH, Frederick, Maryland, USA
| | - Adam D. Kenney
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, USA
| | - Ashley Zani
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, USA
| | - Adrian C. Eddy
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, USA
| | - Saliha Majdoul
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute (NCI), NIH, Frederick, Maryland, USA
| | - Lizhi Zhang
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, USA
| | - Tirhas Dempsey
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute (NCI), NIH, Frederick, Maryland, USA
| | - Paul A. Beare
- Laboratory of Bacteriology, Rocky Mountain Laboratories, NIAID, NIH, Hamilton, Montana, USA
| | | | | | - Sonja M. Best
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Hamilton, Montana, USA
| | - Jacob S. Yount
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, USA
| | - Alex A. Compton
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute (NCI), NIH, Frederick, Maryland, USA
| |
Collapse
|
32
|
Stein SR, Ramelli SC, Grazioli A, Chung JY, Singh M, Yinda CK, Winkler CW, Sun J, Dickey JM, Ylaya K, Ko SH, Platt AP, Burbelo PD, Quezado M, Pittaluga S, Purcell M, Munster VJ, Belinky F, Ramos-Benitez MJ, Boritz EA, Lach IA, Herr DL, Rabin J, Saharia KK, Madathil RJ, Tabatabai A, Soherwardi S, McCurdy MT, Peterson KE, Cohen JI, de Wit E, Vannella KM, Hewitt SM, Kleiner DE, Chertow DS. SARS-CoV-2 infection and persistence in the human body and brain at autopsy. Nature 2022; 612:758-763. [PMID: 36517603 PMCID: PMC9749650 DOI: 10.1038/s41586-022-05542-y] [Citation(s) in RCA: 376] [Impact Index Per Article: 188.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 11/08/2022] [Indexed: 12/15/2022]
Abstract
Coronavirus disease 2019 (COVID-19) is known to cause multi-organ dysfunction1-3 during acute infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), with some patients experiencing prolonged symptoms, termed post-acute sequelae of SARS-CoV-2 (refs. 4,5). However, the burden of infection outside the respiratory tract and time to viral clearance are not well characterized, particularly in the brain3,6-14. Here we carried out complete autopsies on 44 patients who died with COVID-19, with extensive sampling of the central nervous system in 11 of these patients, to map and quantify the distribution, replication and cell-type specificity of SARS-CoV-2 across the human body, including the brain, from acute infection to more than seven months following symptom onset. We show that SARS-CoV-2 is widely distributed, predominantly among patients who died with severe COVID-19, and that virus replication is present in multiple respiratory and non-respiratory tissues, including the brain, early in infection. Further, we detected persistent SARS-CoV-2 RNA in multiple anatomic sites, including throughout the brain, as late as 230 days following symptom onset in one case. Despite extensive distribution of SARS-CoV-2 RNA throughout the body, we observed little evidence of inflammation or direct viral cytopathology outside the respiratory tract. Our data indicate that in some patients SARS-CoV-2 can cause systemic infection and persist in the body for months.
Collapse
Affiliation(s)
- Sydney R. Stein
- grid.410305.30000 0001 2194 5650Emerging Pathogens Section, Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD USA ,grid.419681.30000 0001 2164 9667Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD USA
| | - Sabrina C. Ramelli
- grid.410305.30000 0001 2194 5650Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD USA
| | - Alison Grazioli
- grid.419635.c0000 0001 2203 7304Kidney Disease Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD USA
| | - Joon-Yong Chung
- grid.417768.b0000 0004 0483 9129Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
| | - Manmeet Singh
- grid.94365.3d0000 0001 2297 5165Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institute of Health, Hamilton, MT USA
| | - Claude Kwe Yinda
- grid.94365.3d0000 0001 2297 5165Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institute of Health, Hamilton, MT USA
| | - Clayton W. Winkler
- grid.94365.3d0000 0001 2297 5165Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institute of Health, Hamilton, MT USA
| | - Junfeng Sun
- grid.410305.30000 0001 2194 5650Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD USA
| | - James M. Dickey
- grid.410305.30000 0001 2194 5650Emerging Pathogens Section, Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD USA ,grid.419681.30000 0001 2164 9667Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD USA
| | - Kris Ylaya
- grid.417768.b0000 0004 0483 9129Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
| | - Sung Hee Ko
- grid.419681.30000 0001 2164 9667Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD USA
| | - Andrew P. Platt
- grid.410305.30000 0001 2194 5650Emerging Pathogens Section, Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD USA ,grid.419681.30000 0001 2164 9667Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD USA
| | - Peter D. Burbelo
- grid.419633.a0000 0001 2205 0568National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD USA
| | - Martha Quezado
- grid.417768.b0000 0004 0483 9129Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
| | - Stefania Pittaluga
- grid.417768.b0000 0004 0483 9129Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
| | - Madeleine Purcell
- grid.411024.20000 0001 2175 4264University of Maryland School of Medicine, Baltimore, MD USA
| | - Vincent J. Munster
- grid.94365.3d0000 0001 2297 5165Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institute of Health, Hamilton, MT USA
| | - Frida Belinky
- grid.419681.30000 0001 2164 9667Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD USA
| | - Marcos J. Ramos-Benitez
- grid.410305.30000 0001 2194 5650Emerging Pathogens Section, Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD USA ,grid.419681.30000 0001 2164 9667Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD USA ,grid.280785.00000 0004 0533 7286Postdoctoral Research Associate Training Program, National Institute of General Medical Sciences, National Institutes of Health, Bethesda, MD USA
| | - Eli A. Boritz
- grid.419681.30000 0001 2164 9667Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD USA
| | - Izabella A. Lach
- grid.410305.30000 0001 2194 5650Emerging Pathogens Section, Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD USA ,grid.419681.30000 0001 2164 9667Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD USA
| | - Daniel L. Herr
- grid.411024.20000 0001 2175 4264R Adams Cowley Shock Trauma Center, Department of Medicine and Program in Trauma, University of Maryland School of Medicine, Baltimore, MD USA
| | - Joseph Rabin
- grid.411024.20000 0001 2175 4264R Adams Cowley Shock Trauma Center, Department of Surgery and Program in Trauma, University of Maryland School of Medicine, Baltimore, MD USA
| | - Kapil K. Saharia
- grid.411024.20000 0001 2175 4264Department of Medicine, Division of Infectious Disease, University of Maryland School of Medicine, Baltimore, MD USA ,grid.411024.20000 0001 2175 4264Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD USA
| | - Ronson J. Madathil
- grid.411024.20000 0001 2175 4264Department of Surgery, Division of Cardiac Surgery, University of Maryland School of Medicine, Baltimore, MD USA
| | - Ali Tabatabai
- grid.411024.20000 0001 2175 4264Department of Medicine, Division of Pulmonary and Critical Care Medicine, University of Maryland School of Medicine, Baltimore, MD USA
| | - Shahabuddin Soherwardi
- grid.417209.90000 0004 0429 3816Hospitalist Department, TidalHealth Peninsula Regional, Salisbury, MD USA
| | - Michael T. McCurdy
- grid.411024.20000 0001 2175 4264Department of Medicine, Division of Pulmonary and Critical Care Medicine, University of Maryland School of Medicine, Baltimore, MD USA ,grid.416700.40000 0004 0440 9540Division of Critical Care Medicine, Department of Medicine, University of Maryland St. Joseph Medical Center, Towson, MD USA
| | | | - Karin E. Peterson
- grid.94365.3d0000 0001 2297 5165Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institute of Health, Hamilton, MT USA
| | - Jeffrey I. Cohen
- grid.419681.30000 0001 2164 9667Medical Virology Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD USA
| | - Emmie de Wit
- grid.94365.3d0000 0001 2297 5165Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institute of Health, Hamilton, MT USA
| | - Kevin M. Vannella
- grid.410305.30000 0001 2194 5650Emerging Pathogens Section, Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD USA ,grid.419681.30000 0001 2164 9667Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD USA
| | - Stephen M. Hewitt
- grid.417768.b0000 0004 0483 9129Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
| | - David E. Kleiner
- grid.417768.b0000 0004 0483 9129Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
| | - Daniel S. Chertow
- grid.410305.30000 0001 2194 5650Emerging Pathogens Section, Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD USA ,grid.419681.30000 0001 2164 9667Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD USA
| |
Collapse
|
33
|
Karami H, Karimi Z, Karami N. SARS-CoV-2 in brief: from virus to prevention. Osong Public Health Res Perspect 2022; 13:394-406. [PMID: 36617546 DOI: 10.24171/j.phrp.2022.0155] [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: 05/21/2022] [Accepted: 10/11/2022] [Indexed: 11/29/2022] Open
Abstract
The recent outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), ahighly transmissible virus with a likely animal origin, has posed major and unprecedentedchallenges to millions of lives across the affected nations of the world. This outbreak firstoccurred in China, and despite massive regional and global attempts shortly thereafter, itspread to other countries and caused millions of deaths worldwide. This review presents keyinformation about the characteristics of SARS-CoV-2 and its associated disease (namely,coronavirus disease 2019) and briefly discusses the origin of the virus. Herein, we also brieflysummarize the strategies used against viral spread and transmission.
Collapse
Affiliation(s)
- Hassan Karami
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Zeinab Karimi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Negin Karami
- Department of Nursing, School of Nursing, Alborz University of Medical Sciences, Karaj, Iran
| |
Collapse
|
34
|
Zandi M, Shafaati M, Kalantar-Neyestanaki D, Pourghadamyari H, Fani M, Soltani S, Kaleji H, Abbasi S. The role of SARS-CoV-2 accessory proteins in immune evasion. Biomed Pharmacother 2022; 156:113889. [PMID: 36265309 PMCID: PMC9574935 DOI: 10.1016/j.biopha.2022.113889] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/11/2022] [Accepted: 10/15/2022] [Indexed: 01/11/2023] Open
Abstract
Many questions on the SARS-CoV-2 pathogenesis remain to answer. The SARS-CoV-2 genome encodes some accessory proteins that are essential for infection. Notably, accessory proteins of SARS-CoV-2 play significant roles in affecting immune escape and viral pathogenesis. Therefore SARS-CoV-2 accessory proteins could be considered putative drug targets. IFN-I and IFN-III responses are the primary mechanisms of innate antiviral immunity in infection clearance. Previous research has shown that SARS-CoV-2 suppresses IFN-β by infecting host cells via ORF3a, ORF3b, ORF6, ORF7a, ORF7b, ORF8, and ORF9b. Furthermore, ORF3a, ORF7a, and ORF7b have a role in blocking IFNα signaling, and ORF8 represses IFNβ signaling. The ORF3a, ORF7a, and ORF7b disrupt the STAT1/2 phosphorylation. ORF3a, ORF6, ORF7a, and ORF7b could prevent the ISRE promoter activity. The main SARS-CoV-2 accessory proteins involved in immune evasion are discussed here for comprehensive learning on viral entry, replication, and transmission in vaccines and antiviral development.
Collapse
Affiliation(s)
- Milad Zandi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Shafaati
- Department of Microbiology, Faculty Science, Jahrom Branch, Islamic Azad University, Jahrom, Iran,Occupational Sleep Research Center, Baharloo Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Davood Kalantar-Neyestanaki
- Medical Mycology and Bacteriology Research Center, Kerman University of Medical Sciences, Kerman, Iran,Department of Medical Microbiology (Bacteriology & Virology), Afzalipour Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Hossein Pourghadamyari
- Student Research Committee, Kerman University of Medical Sciences, Kerman, Iran,Department of Clinical Biochemistry, Afzalipour School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Mona Fani
- Department of Pathobiology & Laboratory Sciences, School of Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Saber Soltani
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Hassan Kaleji
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Samaneh Abbasi
- Department of Microbiology, School of Medicine, Abadan University of Medical Sciences, Abadan, Iran,Corresponding author
| |
Collapse
|
35
|
Wolf C, Köppert S, Becza N, Kuerten S, Kirchenbaum GA, Lehmann PV. Antibody Levels Poorly Reflect on the Frequency of Memory B Cells Generated following SARS-CoV-2, Seasonal Influenza, or EBV Infection. Cells 2022; 11:cells11223662. [PMID: 36429090 PMCID: PMC9688940 DOI: 10.3390/cells11223662] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/14/2022] [Accepted: 11/15/2022] [Indexed: 11/19/2022] Open
Abstract
The scope of immune monitoring is to define the existence, magnitude, and quality of immune mechanisms operational in a host. In clinical trials and praxis, the assessment of humoral immunity is commonly confined to measurements of serum antibody reactivity without accounting for the memory B cell potential. Relying on fundamentally different mechanisms, however, passive immunity conveyed by pre-existing antibodies needs to be distinguished from active B cell memory. Here, we tested whether, in healthy human individuals, the antibody titers to SARS-CoV-2, seasonal influenza, or Epstein-Barr virus antigens correlated with the frequency of recirculating memory B cells reactive with the respective antigens. Weak correlations were found. The data suggest that the assessment of humoral immunity by measurement of antibody levels does not reflect on memory B cell frequencies and thus an individual's potential to engage in an anamnestic antibody response against the same or an antigenically related virus. Direct monitoring of the antigen-reactive memory B cell compartment is both required and feasible towards that goal.
Collapse
Affiliation(s)
- Carla Wolf
- Research and Development, Cellular Technology Ltd. (CTL), Shaker Heights, OH 44122, USA
- Institute of Anatomy and Cell Biology, Friedrich-Alexander University Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Sebastian Köppert
- Research and Development, Cellular Technology Ltd. (CTL), Shaker Heights, OH 44122, USA
- Institute of Anatomy and Cell Biology, Friedrich-Alexander University Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Noémi Becza
- Research and Development, Cellular Technology Ltd. (CTL), Shaker Heights, OH 44122, USA
| | - Stefanie Kuerten
- Institute of Anatomy and Cell Biology, Friedrich-Alexander University Erlangen-Nürnberg, 91054 Erlangen, Germany
- Institute of Neuroanatomy, Medical Faculty, University of Bonn, 53115 Bonn, Germany
| | - Greg A. Kirchenbaum
- Research and Development, Cellular Technology Ltd. (CTL), Shaker Heights, OH 44122, USA
| | - Paul V. Lehmann
- Research and Development, Cellular Technology Ltd. (CTL), Shaker Heights, OH 44122, USA
- Correspondence: ; Tel.: +1-(216)-791-5084
| |
Collapse
|
36
|
Host Protective Immunity against Severe Acute Respiratory Coronavirus 2 (SARS-CoV-2) and the COVID-19 Vaccine-Induced Immunity against SARS-CoV-2 and Its Variants. Viruses 2022; 14:v14112541. [PMID: 36423150 PMCID: PMC9697230 DOI: 10.3390/v14112541] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/14/2022] [Accepted: 11/15/2022] [Indexed: 11/19/2022] Open
Abstract
The world is now apparently at the last/recovery stage of the COVID-19 pandemic, starting from 29 December 2019, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). With the progression of time, several mutations have taken place in the original SARS-CoV-2 Wuhan strain, which have generated variants of concern (VOC). Therefore, combatting COVID-19 has required the development of COVID-19 vaccines using several platforms. The immunity induced by those vaccines is vital to study in order to assure total protection against SARS-CoV-2 and its emerging variants. Indeed, understanding and identifying COVID-19 protection mechanisms or the host immune responses are of significance in terms of designing both new and repurposed drugs as well as the development of novel vaccines with few to no side effects. Detecting the immune mechanisms for host protection against SARS-CoV-2 and its variants is crucial for the development of novel COVID-19 vaccines as well as to monitor the effectiveness of the currently used vaccines worldwide. Immune memory in terms of the production of neutralizing antibodies (NAbs) during reinfection is also very crucial to formulate the vaccine administration schedule/vaccine doses. The response of antigen-specific antibodies and NAbs as well as T cell responses, along with the protective cytokine production and the innate immunity generated upon COVID-19 vaccination, are discussed in the current review in comparison to the features of naturally induced protective immunity.
Collapse
|
37
|
Chavda VP, Bezbaruah R, Deka K, Nongrang L, Kalita T. The Delta and Omicron Variants of SARS-CoV-2: What We Know So Far. Vaccines (Basel) 2022; 10:1926. [PMID: 36423021 PMCID: PMC9698608 DOI: 10.3390/vaccines10111926] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 07/30/2023] Open
Abstract
The world has not yet completely overcome the fear of the havoc brought by SARS-CoV-2. The virus has undergone several mutations since its initial appearance in China in December 2019. Several variations (i.e., B.1.616.1 (Kappa variant), B.1.617.2 (Delta variant), B.1.617.3, and BA.2.75 (Omicron variant)) have emerged throughout the pandemic, altering the virus's capacity to spread, risk profile, and even symptoms. Humanity faces a serious threat as long as the virus keeps adapting and changing its fundamental function to evade the immune system. The Delta variant has two escape alterations, E484Q and L452R, as well as other mutations; the most notable of these is P681R, which is expected to boost infectivity, whereas the Omicron has about 60 mutations with certain deletions and insertions. The Delta variant is 40-60% more contagious in comparison to the Alpha variant. Additionally, the AY.1 lineage, also known as the "Delta plus" variant, surfaced as a result of a mutation in the Delta variant, which was one of the causes of the life-threatening second wave of coronavirus disease 2019 (COVID-19). Nevertheless, the recent Omicron variants represent a reminder that the COVID-19 epidemic is far from ending. The wave has sparked a fervor of investigation on why the variant initially appeared to propagate so much more rapidly than the other three variants of concerns (VOCs), whether it is more threatening in those other ways, and how its type of mutations, which induce minor changes in its proteins, can wreck trouble. This review sheds light on the pathogenicity, mutations, treatments, and impact on the vaccine efficacy of the Delta and Omicron variants of SARS-CoV-2.
Collapse
Affiliation(s)
- Vivek P. Chavda
- Department of Pharmaceutics and Pharmaceutical Technology, L M College of Pharmacy, Ahmedabad 380008, Gujarat, India
| | - Rajashri Bezbaruah
- Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University, Dibrugarh 786004, Assam, India
| | - Kangkan Deka
- NETES Institute of Pharmaceutical Science, Mirza, Guwahati 781125, Assam, India
| | - Lawandashisha Nongrang
- Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University, Dibrugarh 786004, Assam, India
| | - Tutumoni Kalita
- Girijananda Chowdhury Institute of Pharmaceutical Science, Azara, Guwahati 781017, Assam, India
| |
Collapse
|
38
|
Noor R. How do the severe acute respiratory coronavirus 2 (SARS-CoV-2) and its variants escape the host protective immunity and mediate pathogenesis? BULLETIN OF THE NATIONAL RESEARCH CENTRE 2022; 46:255. [PMID: 36254244 PMCID: PMC9556142 DOI: 10.1186/s42269-022-00945-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 10/06/2022] [Indexed: 05/10/2023]
Abstract
Background To protect the global population from the ongoing COVID-19 pandemic caused by the severe acute respiratory β-coronavirus 2 (SARS-CoV-2), a number of vaccines are currently being used in three dosages (i.e., along with the booster dose) to induce the immunity required to combat the SARS-CoV-2 and its variants. So far, several antivirals and the commercial vaccines have been found to evoke the required humoral and cellular immunity within a huge population around world. However, an important aspect to consider is the avoidance mechanism of the host protective immunity by SARS-CoV-2 variants. Main body of the abstract Indeed, such an immune escape strategy has been noticed previously in case of SARS-CoV-1 and the Middle East Respiratory Syndrome coronavirus (MERS-CoV). Regarding the SARS-CoV-2 variants, the most important aspect on vaccine development is to determine whether the vaccine is actually capable to elicit the immune response or not, especially the viral spike (S) protein. Short conclusion Present review thus focused on such elicitation of immunity as well as pondered to the avoidance of host immunity by the SARS-CoV-2 Wuhan strain and its variants.
Collapse
Affiliation(s)
- Rashed Noor
- Department of Life Sciences (DLS), School of Environment and Life Sciences (SELS), Independent University, Bangladesh (IUB), Plot 16, Block B, Aftabuddin Ahmed Road, Bashundhara, Dhaka 1229 Bangladesh
| |
Collapse
|
39
|
Chiappelli F, Fotovat L. Virus interference in CoViD-19. Bioinformation 2022; 18:768-773. [PMID: 37426505 PMCID: PMC10326336 DOI: 10.6026/97320630018768] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 09/30/2022] [Accepted: 09/30/2022] [Indexed: 09/02/2023] Open
Abstract
Virus interference is one of the oldest concepts in immunology. Recent findings indicate that it may depend on the host's anti-viral cellular immune surveillance processes, as well as on sequence-specific gene silencing mechanism guided by double-stranded RNA. Other biological events, unrelated to some degree at least from immune-dependent IFN or RNA-dependent viral interference may be at play as well. We discuss these biological mechanisms in the context of of the Systemic Acute Respiratory Syndrome Corona virus2 (SARS-CoV2) virus responsible for Corona Virus Disease 2019 (CoViD-19).
Collapse
|
40
|
Lee SJ, Kim YJ, Ahn DG. Distinct Molecular Mechanisms Characterizing Pathogenesis of SARS-CoV-2. J Microbiol Biotechnol 2022; 32:1073-1085. [PMID: 36039385 PMCID: PMC9628960 DOI: 10.4014/jmb.2206.06064] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/18/2022] [Accepted: 08/20/2022] [Indexed: 01/18/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has continued for over 2 years, following the outbreak of coronavirus-19 (COVID-19) in 2019. It has resulted in enormous casualties and severe economic crises. The rapid development of vaccines and therapeutics against SARS-CoV-2 has helped slow the spread. In the meantime, various mutations in the SARS-CoV-2 have emerged to evade current vaccines and therapeutics. A better understanding of SARS-CoV-2 pathogenesis is a prerequisite for developing efficient, advanced vaccines and therapeutics. Since the outbreak of COVID-19, a tremendous amount of research has been conducted to unveil SARSCoV-2 pathogenesis, from clinical observations to biochemical analysis at the molecular level upon viral infection. In this review, we discuss the molecular mechanisms of SARS-CoV-2 propagation and pathogenesis, with an update on recent advances.
Collapse
Affiliation(s)
- Su Jin Lee
- Department of Convergent Research of Emerging Virus Infection, Therapeutics and Biotechnology Division, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea
| | - Yu-Jin Kim
- Department of Convergent Research of Emerging Virus Infection, Therapeutics and Biotechnology Division, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea
| | - Dae-Gyun Ahn
- Department of Convergent Research of Emerging Virus Infection, Therapeutics and Biotechnology Division, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea
| |
Collapse
|
41
|
Comparison of Homologous and Heterologous Booster SARS-CoV-2 Vaccination in Autoimmune Rheumatic and Musculoskeletal Patients. Int J Mol Sci 2022; 23:ijms231911411. [PMID: 36232710 PMCID: PMC9569441 DOI: 10.3390/ijms231911411] [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: 08/14/2022] [Revised: 09/17/2022] [Accepted: 09/22/2022] [Indexed: 11/16/2022] Open
Abstract
Vaccination against SARS-CoV-2 to prevent COVID-19 is highly recommended for immunocompromised patients with autoimmune rheumatic and musculoskeletal diseases (aiRMDs). Little is known about the effect of booster vaccination or infection followed by previously completed two-dose vaccination in aiRMDs. We determined neutralizing anti-SARS-CoV-2 antibody levels and applied flow cytometric immunophenotyping to quantify the SARS-CoV-2 reactive B- and T-cell mediated immunity in aiRMDs receiving homologous or heterologous boosters or acquired infection following vaccination. Patients receiving a heterologous booster had a higher proportion of IgM+ SARS-CoV-2 S+ CD19+CD27+ peripheral memory B-cells in comparison to those who acquired infection. Biologic therapy decreased the number of S+CD19+; S+CD19+CD27+IgG+; and S+CD19+CD27+IgM+ B-cells. The response rate to a booster event in cellular immunity was the highest in the S-, M-, and N-reactive CD4+CD40L+ T-cell subset. Patients with a disease duration of more than 10 years had higher proportions of CD8+TNF-α+ and CD8+IFN-γ+ T-cells in comparison to patients who were diagnosed less than 10 years ago. We detected neutralizing antibodies, S+ reactive peripheral memory B-cells, and five S-, M-, and N-reactive T-cells subsets in our patient cohort showing the importance of booster events. Biologic therapy and <10 years disease duration may confound anti-SARS-CoV-2 specific immunity in aiRMDs.
Collapse
|
42
|
Bencze D, Fekete T, Pázmándi K. Correlation between Type I Interferon Associated Factors and COVID-19 Severity. Int J Mol Sci 2022; 23:ijms231810968. [PMID: 36142877 PMCID: PMC9506204 DOI: 10.3390/ijms231810968] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/11/2022] [Accepted: 09/13/2022] [Indexed: 11/18/2022] Open
Abstract
Antiviral type I interferons (IFN) produced in the early phase of viral infections effectively inhibit viral replication, prevent virus-mediated tissue damages and promote innate and adaptive immune responses that are all essential to the successful elimination of viruses. As professional type I IFN producing cells, plasmacytoid dendritic cells (pDC) have the ability to rapidly produce waste amounts of type I IFNs. Therefore, their low frequency, dysfunction or decreased capacity to produce type I IFNs might increase the risk of severe viral infections. In accordance with that, declined pDC numbers and delayed or inadequate type I IFN responses could be observed in patients with severe coronavirus disease (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), as compared to individuals with mild or no symptoms. Thus, besides chronic diseases, all those conditions, which negatively affect the antiviral IFN responses lengthen the list of risk factors for severe COVID-19. In the current review, we would like to briefly discuss the role and dysregulation of pDC/type I IFN axis in COVID-19, and introduce those type I IFN-dependent factors, which account for an increased risk of COVID-19 severity and thus are responsible for the different magnitude of individual immune responses to SARS-CoV-2.
Collapse
Affiliation(s)
- Dóra Bencze
- Department of Immunology, Faculty of Medicine, University of Debrecen, 1 Egyetem Square, H-4032 Debrecen, Hungary
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, 1 Egyetem Square, H-4032 Debrecen, Hungary
| | - Tünde Fekete
- Department of Immunology, Faculty of Medicine, University of Debrecen, 1 Egyetem Square, H-4032 Debrecen, Hungary
| | - Kitti Pázmándi
- Department of Immunology, Faculty of Medicine, University of Debrecen, 1 Egyetem Square, H-4032 Debrecen, Hungary
- Correspondence: ; Tel./Fax: +36-52-417-159
| |
Collapse
|
43
|
Hossain A, Akter S, Rashid AA, Khair S, Alam ASMRU. Unique mutations in SARS-CoV-2 Omicron subvariants' non-spike proteins: Potential impacts on viral pathogenesis and host immune evasion. Microb Pathog 2022; 170:105699. [PMID: 35944840 PMCID: PMC9356572 DOI: 10.1016/j.micpath.2022.105699] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 07/27/2022] [Accepted: 07/28/2022] [Indexed: 12/20/2022]
Abstract
SARS-CoV-2 is the causative agent behind the ongoing COVID-19 pandemic. This virus is a cumulative outcome of mutations, leading to frequent emergence of new variants and their subvariants. Some of them are a matter of high concern, while others are variants of interest for studying the mutational effect. The major five variants of concern (VOCs) are Alpha (B.1.1.7), Beta (B.1.315), Gamma (P.1), Delta (B.1.617.2), and Omicron (B.1.1.529.*/BA.*). Omicron itself has >100 subvariants at present, among which BA.1 (21K), BA.2 (21L), BA.4 (22A), BA.5 (22B), and BA.2.12.1 (22C) are the dominant ones. Undoubtedly, these variants and sometimes their progeny subvariants have significant differences in their spike region that impart them the unique properties they harbor. But alongside, the mutations in their non-spike regions could also be responsible elements behind their characteristics, such as replication time, virulence, survival, host immune evasion, and such. There exists a probability that these mutations of non-spike proteins may also impart epistatic effects that are yet to be brought to light. The focus of this review encompasses the non-spike mutations of Omicron, especially in its widely circulating subvariants (BA.1, BA.2, BA.4, BA.5, and BA.2.12.1). The mutations such as in NSP3, NSP6, NSP13, M protein, ORF7b, and ORF9b are mentioned few of all, which might have led to the varying properties, including growth advantages, higher transmission rate, lower infectivity, and most importantly better host immune evasion through natural killer cell inactivation, autophagosome-lysosome fusion prevention, host protein synthesis disruption, and so on. This aspect of Omicron subvariants has not yet been explored. Further study of alteration of expression or interaction profile of these non-spike mutations bearing proteins, if present, can add a great deal of knowledge to the current understanding of the viral properties and thus effective prevention strategies.
Collapse
Affiliation(s)
- Anamica Hossain
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Shammi Akter
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Alfi Anjum Rashid
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Sabik Khair
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - A S M Rubayet Ul Alam
- Department of Microbiology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh.
| |
Collapse
|
44
|
Shi G, Chiramel AI, Li T, Lai KK, Kenney AD, Zani A, Eddy A, Majdoul S, Zhang L, Dempsey T, Beare PA, Kar S, Yewdell JW, Best SM, Yount JS, Compton AA. Rapalogs downmodulate intrinsic immunity and promote cell entry of SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2021.04.15.440067. [PMID: 33880473 PMCID: PMC8057238 DOI: 10.1101/2021.04.15.440067] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
SARS-CoV-2 infection in immunocompromised individuals is associated with prolonged virus shedding and evolution of viral variants. Rapamycin and its analogs (rapalogs, including everolimus, temsirolimus, and ridaforolimus) are FDA-approved as mTOR inhibitors for the treatment of human diseases, including cancer and autoimmunity. Rapalog use is commonly associated with increased susceptibility to infection, which has been traditionally explained by impaired adaptive immunity. Here, we show that exposure to rapalogs increases susceptibility to SARS-CoV-2 infection in tissue culture and in immunologically naive rodents by antagonizing the cell-intrinsic immune response. By identifying one rapalog (ridaforolimus) that is less potent in this regard, we demonstrate that rapalogs promote Spike-mediated entry into cells by triggering the degradation of antiviral proteins IFITM2 and IFITM3 via an endolysosomal remodeling program called microautophagy. Rapalogs that increase virus entry inhibit the mTOR-mediated phosphorylation of the transcription factor TFEB, which facilitates its nuclear translocation and triggers microautophagy. In rodent models of infection, injection of rapamycin prior to and after virus exposure resulted in elevated SARS-CoV-2 replication and exacerbated viral disease, while ridaforolimus had milder effects. Overall, our findings indicate that preexisting use of certain rapalogs may elevate host susceptibility to SARS-CoV-2 infection and disease by activating lysosome-mediated suppression of intrinsic immunity.
Collapse
Affiliation(s)
- Guoli Shi
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Abhilash I. Chiramel
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, Hamilton, MT, USA
| | - Tiansheng Li
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Kin Kui Lai
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Adam D. Kenney
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA
| | - Ashley Zani
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA
| | - Adrian Eddy
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA
| | - Saliha Majdoul
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Lizhi Zhang
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA
| | - Tirhas Dempsey
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Paul A. Beare
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, Hamilton, MT, USA
| | | | - Jonathan W. Yewdell
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Sonja M. Best
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, Hamilton, MT, USA
| | - Jacob S. Yount
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA
| | - Alex A. Compton
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| |
Collapse
|
45
|
Loucera C, Perez-Florido J, Casimiro-Soriguer CS, Ortuño FM, Carmona R, Bostelmann G, Martínez-González LJ, Muñoyerro-Muñiz D, Villegas R, Rodriguez-Baño J, Romero-Gomez M, Lorusso N, Garcia-León J, Navarro-Marí JM, Camacho-Martinez P, Merino-Diaz L, de Salazar A, Viñuela L, Lepe JA, Garcia F, Dopazo J. Assessing the Impact of SARS-CoV-2 Lineages and Mutations on Patient Survival. Viruses 2022; 14:1893. [PMID: 36146700 PMCID: PMC9500738 DOI: 10.3390/v14091893] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/20/2022] [Accepted: 08/24/2022] [Indexed: 12/29/2022] Open
Abstract
OBJECTIVES More than two years into the COVID-19 pandemic, SARS-CoV-2 still remains a global public health problem. Successive waves of infection have produced new SARS-CoV-2 variants with new mutations for which the impact on COVID-19 severity and patient survival is uncertain. METHODS A total of 764 SARS-CoV-2 genomes, sequenced from COVID-19 patients, hospitalized from 19th February 2020 to 30 April 2021, along with their clinical data, were used for survival analysis. RESULTS A significant association of B.1.1.7, the alpha lineage, with patient mortality (log hazard ratio (LHR) = 0.51, C.I. = [0.14,0.88]) was found upon adjustment by all the covariates known to affect COVID-19 prognosis. Moreover, survival analysis of mutations in the SARS-CoV-2 genome revealed 27 of them were significantly associated with higher mortality of patients. Most of these mutations were located in the genes coding for the S, ORF8, and N proteins. CONCLUSIONS This study illustrates how a combination of genomic and clinical data can provide solid evidence for the impact of viral lineage on patient survival.
Collapse
Affiliation(s)
- Carlos Loucera
- Bioinformatics Area, Andalusian Public Foundation Progress and Health-FPS, 41013 Sevilla, Spain
- Institute of Biomedicine of Seville, IBiS, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Sevilla, Spain
| | - Javier Perez-Florido
- Bioinformatics Area, Andalusian Public Foundation Progress and Health-FPS, 41013 Sevilla, Spain
- Institute of Biomedicine of Seville, IBiS, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Sevilla, Spain
| | - Carlos S. Casimiro-Soriguer
- Bioinformatics Area, Andalusian Public Foundation Progress and Health-FPS, 41013 Sevilla, Spain
- Institute of Biomedicine of Seville, IBiS, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Sevilla, Spain
| | - Francisco M. Ortuño
- Bioinformatics Area, Andalusian Public Foundation Progress and Health-FPS, 41013 Sevilla, Spain
- Department of Computer Architecture and Computer Technology, University of Granada, 18011 Granada, Spain
| | - Rosario Carmona
- Bioinformatics Area, Andalusian Public Foundation Progress and Health-FPS, 41013 Sevilla, Spain
| | - Gerrit Bostelmann
- Bioinformatics Area, Andalusian Public Foundation Progress and Health-FPS, 41013 Sevilla, Spain
| | - L. Javier Martínez-González
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, 18016 Granada, Spain
| | - Dolores Muñoyerro-Muñiz
- Subdirección Técnica Asesora de Gestión de la Información, Servicio Andaluz de Salud, 41001 Sevilla, Spain
| | - Román Villegas
- Subdirección Técnica Asesora de Gestión de la Información, Servicio Andaluz de Salud, 41001 Sevilla, Spain
| | - Jesus Rodriguez-Baño
- Institute of Biomedicine of Seville, IBiS, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Sevilla, Spain
- Unidad Clínica de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen Macarena, 41009 Sevilla, Spain
- Departamento de Medicina, Universidad de Sevilla, C. San Fernando, 4, 41004 Sevilla, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), ISCIII, 28029 Madrid, Spain
| | - Manuel Romero-Gomez
- Institute of Biomedicine of Seville, IBiS, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Sevilla, Spain
- Departamento de Medicina, Universidad de Sevilla, C. San Fernando, 4, 41004 Sevilla, Spain
- Servicio de Aparato Digestivo, Hospital Universitario Virgen del Rocío, 41013 Sevilla, Spain
| | - Nicola Lorusso
- Dirección General de Salud Pública, Consejería de Salud y Familias, Junta de Andalucía, 41020 Sevilla, Spain
| | - Javier Garcia-León
- Departamento de Metafísica y Corrientes Actuales de la Filosofía, Ética y Filosofía Política, Universidad de Sevilla, 41004 Sevilla, Spain
| | - Jose M. Navarro-Marí
- Servicio de Microbiología, Hospital Virgen de las Nieves, 18014 Granada, Spain
- Instituto de Investigación Biosanitaria, ibs.GRANADA, 18012 Granada, Spain
| | - Pedro Camacho-Martinez
- Servicio de Microbiología, Unidad Clínica Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen del Rocío, 41013 Sevilla, Spain
| | - Laura Merino-Diaz
- Servicio de Microbiología, Unidad Clínica Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen del Rocío, 41013 Sevilla, Spain
| | - Adolfo de Salazar
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), ISCIII, 28029 Madrid, Spain
- Servicio de Microbiología, Hospital Universitario San Cecilio, 18016 Granada, Spain
| | - Laura Viñuela
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), ISCIII, 28029 Madrid, Spain
- Servicio de Microbiología, Hospital Universitario San Cecilio, 18016 Granada, Spain
| | | | - Jose A. Lepe
- Institute of Biomedicine of Seville, IBiS, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Sevilla, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), ISCIII, 28029 Madrid, Spain
- Servicio de Microbiología, Hospital Universitario San Cecilio, 18016 Granada, Spain
| | - Federico Garcia
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), ISCIII, 28029 Madrid, Spain
- Instituto de Investigación Biosanitaria, ibs.GRANADA, 18012 Granada, Spain
- Servicio de Microbiología, Hospital Universitario San Cecilio, 18016 Granada, Spain
| | - Joaquin Dopazo
- Bioinformatics Area, Andalusian Public Foundation Progress and Health-FPS, 41013 Sevilla, Spain
- Institute of Biomedicine of Seville, IBiS, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Sevilla, Spain
- FPS/ELIXIR-ES, Andalusian Public Foundation Progress and Health-FPS, 41013 Sevilla, Spain
| |
Collapse
|
46
|
Vaivode K, Verhovcova I, Skrastina D, Petrovska R, Kreismane M, Lapse D, Kalnina Z, Salmina K, Rubene D, Pjanova D. Bacteriophage-Derived Double-Stranded RNA Exerts Anti-SARS-CoV-2 Activity In Vitro and in Golden Syrian Hamsters In Vivo. Pharmaceuticals (Basel) 2022; 15:ph15091053. [PMID: 36145274 PMCID: PMC9504838 DOI: 10.3390/ph15091053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/18/2022] [Accepted: 08/22/2022] [Indexed: 01/08/2023] Open
Abstract
Bacteriophage-derived dsRNA, known as Larifan, is a nationally well-known broad-spectrum antiviral medication. This study aimed to ascertain the antiviral activity of Larifan against the novel SARS-CoV-2 virus. Larifan’s effect against SARS-CoV-2 in vitro was measured in human lung adenocarcinoma (Calu3) and primary human small airway epithelial cells (HSAEC), and in vivo in the SARS-CoV-2 infection model in golden Syrian hamsters. Larifan inhibited SARS-CoV-2 replication both in vitro and in vivo. Viral RNA copy numbers and titer of infectious virus in the supernatant of Calu3 cells dropped significantly: p = 0.0296 and p = 0.0286, respectively. A reduction in viral RNA copy number was also observed in HSAEC, especially when Larifan was added before infection (p = 0.0218). Larifan markedly reduced virus numbers in infected hamsters’ lungs post-infection, with a more pronounced effect after intranasal administration (p = 0.0032). The administration of Larifan also reduced the amount of infections virus titer in the lungs (p = 0.0039). Improvements in the infection-induced pathological lesion severity in the lungs of animals treated with Larifan were also demonstrated. The inhibition of SARS-CoV-2 replication in vitro and the reduction in the viral load in the lungs of infected hamsters treated with Larifan alongside the improved lung histopathology suggests a potential use of Larifan in also controlling the COVID-19 disease in humans.
Collapse
|
47
|
Alfi O, Hamdan M, Wald O, Yakirevitch A, Wandel O, Oiknine-Djian E, Gvili B, Knoller H, Rozendorn N, Golan Berman H, Adar S, Vorontsov O, Mandelboim M, Zakay-Rones Z, Oberbaum M, Panet A, Wolf DG. SARS-CoV-2 Omicron Induces Enhanced Mucosal Interferon Response Compared to other Variants of Concern, Associated with Restricted Replication in Human Lung Tissues. Viruses 2022; 14:v14071583. [PMID: 35891570 PMCID: PMC9318963 DOI: 10.3390/v14071583] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 02/07/2023] Open
Abstract
SARS-CoV-2 Omicron variant has been characterized by decreased clinical severity, raising the question of whether early variant-specific interactions within the mucosal surfaces of the respiratory tract could mediate its attenuated pathogenicity. Here, we employed ex vivo infection of native human nasal and lung tissues to investigate the local-mucosal susceptibility and innate immune response to Omicron compared to Delta and earlier SARS-CoV-2 variants of concern (VOC). We show that the replication of Omicron in lung tissues is highly restricted compared to other VOC, whereas it remains relatively unchanged in nasal tissues. Mechanistically, Omicron induced a much stronger antiviral interferon response in infected tissues compared to Delta and earlier VOC-a difference, which was most striking in the lung tissues, where the innate immune response to all other SARS-CoV-2 VOC was blunted. Notably, blocking the innate immune signaling restored Omicron replication in the lung tissues. Our data provide new insights to the reduced lung involvement and clinical severity of Omicron.
Collapse
Affiliation(s)
- Or Alfi
- Clinical Virology Unit, Hadassah Hebrew University Medical Center, Jerusalem 91120, Israel; (O.A.); (M.H.); (O.W.); (E.O.-D.); (O.V.)
- Department of Biochemistry, Institute for Medical Research Israel Canada, Faculty of Medicine, The Hebrew University, Jerusalem 9112102, Israel; (Z.Z.-R.); (A.P.)
- Lautenberg Center for General and Tumor Immunology, Faculty of Medicine, The Hebrew University, Jerusalem 9112102, Israel
| | - Marah Hamdan
- Clinical Virology Unit, Hadassah Hebrew University Medical Center, Jerusalem 91120, Israel; (O.A.); (M.H.); (O.W.); (E.O.-D.); (O.V.)
| | - Ori Wald
- Department of Cardiothoracic Surgery, Hadassah Hebrew University Medical Center, Jerusalem 91120, Israel;
| | - Arkadi Yakirevitch
- Department of Otorhinolaryngology, Sheba Medical Center, Ramat Gan 52621, Israel; (A.Y.); (B.G.); (H.K.); (N.R.)
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Ori Wandel
- Clinical Virology Unit, Hadassah Hebrew University Medical Center, Jerusalem 91120, Israel; (O.A.); (M.H.); (O.W.); (E.O.-D.); (O.V.)
| | - Esther Oiknine-Djian
- Clinical Virology Unit, Hadassah Hebrew University Medical Center, Jerusalem 91120, Israel; (O.A.); (M.H.); (O.W.); (E.O.-D.); (O.V.)
| | - Ben Gvili
- Department of Otorhinolaryngology, Sheba Medical Center, Ramat Gan 52621, Israel; (A.Y.); (B.G.); (H.K.); (N.R.)
| | - Hadas Knoller
- Department of Otorhinolaryngology, Sheba Medical Center, Ramat Gan 52621, Israel; (A.Y.); (B.G.); (H.K.); (N.R.)
| | - Noa Rozendorn
- Department of Otorhinolaryngology, Sheba Medical Center, Ramat Gan 52621, Israel; (A.Y.); (B.G.); (H.K.); (N.R.)
| | - Hadar Golan Berman
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University, Jerusalem 9112102, Israel; (H.G.B.); (S.A.)
| | - Sheera Adar
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University, Jerusalem 9112102, Israel; (H.G.B.); (S.A.)
| | - Olesya Vorontsov
- Clinical Virology Unit, Hadassah Hebrew University Medical Center, Jerusalem 91120, Israel; (O.A.); (M.H.); (O.W.); (E.O.-D.); (O.V.)
- Department of Biochemistry, Institute for Medical Research Israel Canada, Faculty of Medicine, The Hebrew University, Jerusalem 9112102, Israel; (Z.Z.-R.); (A.P.)
- Lautenberg Center for General and Tumor Immunology, Faculty of Medicine, The Hebrew University, Jerusalem 9112102, Israel
| | - Michal Mandelboim
- Central Virology Laboratory, Ministry of Health, Sheba Medical Center, Ramat Gan 52621, Israel;
- School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 6997801, Israel
| | - Zichria Zakay-Rones
- Department of Biochemistry, Institute for Medical Research Israel Canada, Faculty of Medicine, The Hebrew University, Jerusalem 9112102, Israel; (Z.Z.-R.); (A.P.)
| | - Menachem Oberbaum
- The Center for Integrative Complementary Medicine, Shaare Zedek Medical Center, Jerusalem 9103102, Israel;
| | - Amos Panet
- Department of Biochemistry, Institute for Medical Research Israel Canada, Faculty of Medicine, The Hebrew University, Jerusalem 9112102, Israel; (Z.Z.-R.); (A.P.)
| | - Dana G. Wolf
- Clinical Virology Unit, Hadassah Hebrew University Medical Center, Jerusalem 91120, Israel; (O.A.); (M.H.); (O.W.); (E.O.-D.); (O.V.)
- Lautenberg Center for General and Tumor Immunology, Faculty of Medicine, The Hebrew University, Jerusalem 9112102, Israel
- Correspondence:
| |
Collapse
|
48
|
Sarkar S, Runge B, Russell RW, Movellan KT, Calero D, Zeinalilathori S, Quinn CM, Lu M, Calero G, Gronenborn AM, Polenova T. Atomic-Resolution Structure of SARS-CoV-2 Nucleocapsid Protein N-Terminal Domain. J Am Chem Soc 2022; 144:10543-10555. [PMID: 35638584 PMCID: PMC9173677 DOI: 10.1021/jacs.2c03320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Indexed: 11/28/2022]
Abstract
The nucleocapsid (N) protein is one of the four structural proteins of the SARS-CoV-2 virus and plays a crucial role in viral genome organization and, hence, replication and pathogenicity. The N-terminal domain (NNTD) binds to the genomic RNA and thus comprises a potential target for inhibitor and vaccine development. We determined the atomic-resolution structure of crystalline NNTD by integrating solid-state magic angle spinning (MAS) NMR and X-ray diffraction. Our combined approach provides atomic details of protein packing interfaces as well as information about flexible regions as the N- and C-termini and the functionally important RNA binding, β-hairpin loop. In addition, ultrafast (100 kHz) MAS 1H-detected experiments permitted the assignment of side-chain proton chemical shifts not available by other means. The present structure offers guidance for designing therapeutic interventions against the SARS-CoV-2 infection.
Collapse
Affiliation(s)
- Sucharita Sarkar
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Brent Runge
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Ryan W. Russell
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Kumar Tekwani Movellan
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
| | - Daniel Calero
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Somayeh Zeinalilathori
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
| | - Caitlin M. Quinn
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
| | - Manman Lu
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Guillermo Calero
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Angela M. Gronenborn
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| |
Collapse
|
49
|
Smith AP, Williams EP, Plunkett TR, Selvaraj M, Lane LC, Zalduondo L, Xue Y, Vogel P, Channappanavar R, Jonsson CB, Smith AM. Time-Dependent Increase in Susceptibility and Severity of Secondary Bacterial Infections During SARS-CoV-2. Front Immunol 2022; 13:894534. [PMID: 35634338 PMCID: PMC9134015 DOI: 10.3389/fimmu.2022.894534] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 04/11/2022] [Indexed: 12/20/2022] Open
Abstract
Secondary bacterial infections can exacerbate SARS-CoV-2 infection, but their prevalence and impact remain poorly understood. Here, we established that a mild to moderate infection with the SARS-CoV-2 USA-WA1/2020 strain increased the risk of pneumococcal (type 2 strain D39) coinfection in a time-dependent, but sex-independent, manner in the transgenic K18-hACE2 mouse model of COVID-19. Bacterial coinfection increased lethality when the bacteria was initiated at 5 or 7 d post-virus infection (pvi) but not at 3 d pvi. Bacterial outgrowth was accompanied by neutrophilia in the groups coinfected at 7 d pvi and reductions in B cells, T cells, IL-6, IL-15, IL-18, and LIF were present in groups coinfected at 5 d pvi. However, viral burden, lung pathology, cytokines, chemokines, and immune cell activation were largely unchanged after bacterial coinfection. Examining surviving animals more than a week after infection resolution suggested that immune cell activation remained high and was exacerbated in the lungs of coinfected animals compared with SARS-CoV-2 infection alone. These data suggest that SARS-CoV-2 increases susceptibility and pathogenicity to bacterial coinfection, and further studies are needed to understand and combat disease associated with bacterial pneumonia in COVID-19 patients.
Collapse
Affiliation(s)
- Amanda P. Smith
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Evan P. Williams
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Taylor R. Plunkett
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Muneeswaran Selvaraj
- Department of Acute and Tertiary Care, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Lindey C. Lane
- College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Lillian Zalduondo
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Yi Xue
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Peter Vogel
- Animal Resources Center and Veterinary Pathology Core, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Rudragouda Channappanavar
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, United States
- Department of Acute and Tertiary Care, University of Tennessee Health Science Center, Memphis, TN, United States
- Institute for the Study of Host-Pathogen Systems, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Colleen B. Jonsson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, United States
- Institute for the Study of Host-Pathogen Systems, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Amber M. Smith
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN, United States
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, United States
- Institute for the Study of Host-Pathogen Systems, University of Tennessee Health Science Center, Memphis, TN, United States
| |
Collapse
|
50
|
The Evolutionary Dance between Innate Host Antiviral Pathways and SARS-CoV-2. Pathogens 2022; 11:pathogens11050538. [PMID: 35631059 PMCID: PMC9147806 DOI: 10.3390/pathogens11050538] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 04/29/2022] [Accepted: 04/30/2022] [Indexed: 02/04/2023] Open
Abstract
Compared to what we knew at the start of the SARS-CoV-2 global pandemic, our understanding of the interplay between the interferon signaling pathway and SARS-CoV-2 infection has dramatically increased. Innate antiviral strategies range from the direct inhibition of viral components to reprograming the host’s own metabolic pathways to block viral infection. SARS-CoV-2 has also evolved to exploit diverse tactics to overcome immune barriers and successfully infect host cells. Herein, we review the current knowledge of the innate immune signaling pathways triggered by SARS-CoV-2 with a focus on the type I interferon response, as well as the mechanisms by which SARS-CoV-2 impairs those defenses.
Collapse
|