1
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Xu X, Nielsen BF, Sneppen K. Self-inhibiting percolation and viral spreading in epithelial tissue. eLife 2024; 13:RP94056. [PMID: 38941138 PMCID: PMC11213566 DOI: 10.7554/elife.94056] [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] [Indexed: 06/29/2024] Open
Abstract
SARS-CoV-2 induces delayed type-I/III interferon production, allowing it to escape the early innate immune response. The delay has been attributed to a deficiency in the ability of cells to sense viral replication upon infection, which in turn hampers activation of the antiviral state in bystander cells. Here, we introduce a cellular automaton model to investigate the spatiotemporal spreading of viral infection as a function of virus and host-dependent parameters. The model suggests that the considerable person-to-person heterogeneity in SARS-CoV-2 infections is a consequence of high sensitivity to slight variations in biological parameters near a critical threshold. It further suggests that within-host viral proliferation can be curtailed by the presence of remarkably few cells that are primed for IFN production. Thus, the observed heterogeneity in defense readiness of cells reflects a remarkably cost-efficient strategy for protection.
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Affiliation(s)
- Xiaochan Xu
- Niels Bohr Institute, University of CopenhagenCopenhagenDenmark
- Novo Nordisk Foundation Center for Stem Cell Medicine, reNEW, University of CopenhagenCopenhagenDenmark
| | - Bjarke Frost Nielsen
- PandemiX Center, Department of Science and Environment, Roskilde UniversityRoskildeDenmark
- High Meadows Environmental Institute, Princeton UniversityPrincetonUnited States
| | - Kim Sneppen
- Niels Bohr Institute, University of CopenhagenCopenhagenDenmark
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2
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Waman VP, Ashford P, Lam SD, Sen N, Abbasian M, Woodridge L, Goldtzvik Y, Bordin N, Wu J, Sillitoe I, Orengo CA. Predicting human and viral protein variants affecting COVID-19 susceptibility and repurposing therapeutics. Sci Rep 2024; 14:14208. [PMID: 38902252 PMCID: PMC11190248 DOI: 10.1038/s41598-024-61541-1] [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: 11/07/2023] [Accepted: 05/07/2024] [Indexed: 06/22/2024] Open
Abstract
The COVID-19 disease is an ongoing global health concern. Although vaccination provides some protection, people are still susceptible to re-infection. Ostensibly, certain populations or clinical groups may be more vulnerable. Factors causing these differences are unclear and whilst socioeconomic and cultural differences are likely to be important, human genetic factors could influence susceptibility. Experimental studies indicate SARS-CoV-2 uses innate immune suppression as a strategy to speed-up entry and replication into the host cell. Therefore, it is necessary to understand the impact of variants in immunity-associated human proteins on susceptibility to COVID-19. In this work, we analysed missense coding variants in several SARS-CoV-2 proteins and their human protein interactors that could enhance binding affinity to SARS-CoV-2. We curated a dataset of 19 SARS-CoV-2: human protein 3D-complexes, from the experimentally determined structures in the Protein Data Bank and models built using AlphaFold2-multimer, and analysed the impact of missense variants occurring in the protein-protein interface region. We analysed 468 missense variants from human proteins and 212 variants from SARS-CoV-2 proteins and computationally predicted their impacts on binding affinities for the human viral protein complexes. We predicted a total of 26 affinity-enhancing variants from 13 human proteins implicated in increased binding affinity to SARS-CoV-2. These include key-immunity associated genes (TOMM70, ISG15, IFIH1, IFIT2, RPS3, PALS1, NUP98, AXL, ARF6, TRIMM, TRIM25) as well as important spike receptors (KREMEN1, AXL and ACE2). We report both common (e.g., Y13N in IFIH1) and rare variants in these proteins and discuss their likely structural and functional impact, using information on known and predicted functional sites. Potential mechanisms associated with immune suppression implicated by these variants are discussed. Occurrence of certain predicted affinity-enhancing variants should be monitored as they could lead to increased susceptibility and reduced immune response to SARS-CoV-2 infection in individuals/populations carrying them. Our analyses aid in understanding the potential impact of genetic variation in immunity-associated proteins on COVID-19 susceptibility and help guide drug-repurposing strategies.
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Affiliation(s)
- Vaishali P Waman
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Paul Ashford
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Su Datt Lam
- Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Malaysia
| | - Neeladri Sen
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Mahnaz Abbasian
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Laurel Woodridge
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Yonathan Goldtzvik
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Nicola Bordin
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Jiaxin Wu
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Ian Sillitoe
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Christine A Orengo
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK.
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3
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Lundrigan E, Toudic C, Pennock E, Pezacki JP. SARS-CoV-2 Protein Nsp9 Is Involved in Viral Evasion through Interactions with Innate Immune Pathways. ACS OMEGA 2024; 9:26428-26438. [PMID: 38911767 PMCID: PMC11191075 DOI: 10.1021/acsomega.4c02631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 04/13/2024] [Accepted: 04/23/2024] [Indexed: 06/25/2024]
Abstract
The suppression of the host's innate antiviral immune response by SARS-CoV-2, a contributing factor to the severity of disease, has been considerably studied in recent years. Many of these studies have focused on the actions of the structural proteins of the virus because of their accessibility to host immunological components. However, less is known about SARS-CoV-2 nonstructural and accessory proteins in relation to viral evasion. Herein, we study SARS-CoV-2 nonstructural proteins Orf3a, Orf6, and Nsp9 in a mimicked virus-infected state using poly(I:C), a synthetic analog of viral dsRNA, that elicits the antiviral immune response. Through genome-wide expression profiling, we determined that Orf3a, Orf6, and Nsp9 all modulate the host antiviral signaling transcriptome to varying extents, uniquely suppressing aspects of innate immune signaling. Our data suggest that SARS-CoV-2 Nsp9 hinders viral detection through suppression of RIG-I expression and antagonizes the interferon antiviral cascade by downregulating NF-kB and TBK1. Our data point to unique molecular mechanisms through which the different SARS-CoV-2 proteins suppress immune signaling and promote viral evasion. Nsp9 in particular acts on major elements of the host antiviral pathways to impair the antiviral immune response.
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Affiliation(s)
- Eryn Lundrigan
- Department of Chemistry and
Biomolecular Sciences, University of Ottawa, Ottawa K1N 6N5, Canada
| | - Caroline Toudic
- Department of Chemistry and
Biomolecular Sciences, University of Ottawa, Ottawa K1N 6N5, Canada
| | - Emily Pennock
- Department of Chemistry and
Biomolecular Sciences, University of Ottawa, Ottawa K1N 6N5, Canada
| | - John Paul Pezacki
- Department of Chemistry and
Biomolecular Sciences, University of Ottawa, Ottawa K1N 6N5, Canada
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4
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Li X, Mi Z, Liu Z, Rong P. SARS-CoV-2: pathogenesis, therapeutics, variants, and vaccines. Front Microbiol 2024; 15:1334152. [PMID: 38939189 PMCID: PMC11208693 DOI: 10.3389/fmicb.2024.1334152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 05/29/2024] [Indexed: 06/29/2024] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged in December 2019 with staggering economic fallout and human suffering. The unique structure of SARS-CoV-2 and its underlying pathogenic mechanism were responsible for the global pandemic. In addition to the direct damage caused by the virus, SARS-CoV-2 triggers an abnormal immune response leading to a cytokine storm, culminating in acute respiratory distress syndrome and other fatal diseases that pose a significant challenge to clinicians. Therefore, potential treatments should focus not only on eliminating the virus but also on alleviating or controlling acute immune/inflammatory responses. Current management strategies for COVID-19 include preventative measures and supportive care, while the role of the host immune/inflammatory response in disease progression has largely been overlooked. Understanding the interaction between SARS-CoV-2 and its receptors, as well as the underlying pathogenesis, has proven to be helpful for disease prevention, early recognition of disease progression, vaccine development, and interventions aimed at reducing immunopathology have been shown to reduce adverse clinical outcomes and improve prognosis. Moreover, several key mutations in the SARS-CoV-2 genome sequence result in an enhanced binding affinity to the host cell receptor, or produce immune escape, leading to either increased virus transmissibility or virulence of variants that carry these mutations. This review characterizes the structural features of SARS-CoV-2, its variants, and their interaction with the immune system, emphasizing the role of dysfunctional immune responses and cytokine storm in disease progression. Additionally, potential therapeutic options are reviewed, providing critical insights into disease management, exploring effective approaches to deal with the public health crises caused by SARS-CoV-2.
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Affiliation(s)
- Xi Li
- Department of Radiology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Ze Mi
- Department of Radiology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Zhenguo Liu
- Department of Infectious Disease, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Pengfei Rong
- Department of Radiology, The Third Xiangya Hospital, Central South University, Changsha, China
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5
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Ku D, Yang Y, Park Y, Jang D, Lee N, Lee YK, Lee K, Lee J, Han YB, Jang S, Choi SR, Ha YJ, Choi YS, Jeong WJ, Lee YJ, Lee KJ, Cha S, Kim Y. SLIRP promotes autoimmune diseases by amplifying antiviral signaling via positive feedback regulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.28.587146. [PMID: 38915695 PMCID: PMC11195051 DOI: 10.1101/2024.03.28.587146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
The abnormal innate immune response is a prominent feature underlying autoimmune diseases. One emerging factor that can trigger dysregulated immune activation is cytosolic mitochondrial double-stranded RNAs (mt-dsRNAs). However, the mechanism by which mt-dsRNAs stimulate immune responses remains poorly understood. Here, we discover SRA stem-loop interacting RNA binding protein (SLIRP) as a key amplifier of mt-dsRNA-triggered antiviral signals. In autoimmune diseases, SLIRP is commonly upregulated, and targeted knockdown of SLIRP dampens the interferon response. We find that the activation of melanoma differentiation-associated gene 5 (MDA5) by exogenous dsRNAs upregulates SLIRP, which then stabilizes mt-dsRNAs and promotes their cytosolic release to activate MDA5 further, augmenting the interferon response. Furthermore, the downregulation of SLIRP partially rescues the abnormal interferon-stimulated gene expression in autoimmune patients' primary cells and makes cells vulnerable to certain viral infections. Our study unveils SLIRP as a pivotal mediator of interferon response through positive feedback amplification of antiviral signaling.
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6
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Zhang K, Eldin P, Ciesla JH, Briant L, Lentini JM, Ramos J, Cobb J, Munger J, Fu D. Proteolytic cleavage and inactivation of the TRMT1 tRNA modification enzyme by SARS-CoV-2 main protease. eLife 2024; 12:RP90316. [PMID: 38814682 PMCID: PMC11139479 DOI: 10.7554/elife.90316] [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] [Indexed: 05/31/2024] Open
Abstract
Nonstructural protein 5 (Nsp5) is the main protease of SARS-CoV-2 that cleaves viral polyproteins into individual polypeptides necessary for viral replication. Here, we show that Nsp5 binds and cleaves human tRNA methyltransferase 1 (TRMT1), a host enzyme required for a prevalent post-transcriptional modification in tRNAs. Human cells infected with SARS-CoV-2 exhibit a decrease in TRMT1 protein levels and TRMT1-catalyzed tRNA modifications, consistent with TRMT1 cleavage and inactivation by Nsp5. Nsp5 cleaves TRMT1 at a specific position that matches the consensus sequence of SARS-CoV-2 polyprotein cleavage sites, and a single mutation within the sequence inhibits Nsp5-dependent proteolysis of TRMT1. The TRMT1 cleavage fragments exhibit altered RNA binding activity and are unable to rescue tRNA modification in TRMT1-deficient human cells. Compared to wild-type human cells, TRMT1-deficient human cells infected with SARS-CoV-2 exhibit reduced levels of intracellular viral RNA. These findings provide evidence that Nsp5-dependent cleavage of TRMT1 and perturbation of tRNA modification patterns contribute to the cellular pathogenesis of SARS-CoV-2 infection.
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Affiliation(s)
- Kejia Zhang
- Department of Biology, Center for RNA Biology, University of RochesterRochesterUnited States
| | - Patrick Eldin
- Institut de Recherche en Infectiologie de Montpellier (IRIM), CNRS, UMR 9004, Université de MontpellierMontpellierFrance
| | - Jessica H Ciesla
- Department of Biochemistry and Biophysics, University of Rochester Medical CenterRochesterUnited States
| | - Laurence Briant
- Institut de Recherche en Infectiologie de Montpellier (IRIM), CNRS, UMR 9004, Université de MontpellierMontpellierFrance
| | - Jenna M Lentini
- Department of Biology, Center for RNA Biology, University of RochesterRochesterUnited States
| | - Jillian Ramos
- Department of Biology, Center for RNA Biology, University of RochesterRochesterUnited States
| | - Justin Cobb
- Department of Biology, Center for RNA Biology, University of RochesterRochesterUnited States
| | - Joshua Munger
- Department of Biochemistry and Biophysics, University of Rochester Medical CenterRochesterUnited States
| | - Dragony Fu
- Department of Biology, Center for RNA Biology, University of RochesterRochesterUnited States
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7
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Zhang Y, Chen S, Tian Y, Fu X. Host factors of SARS-CoV-2 in infection, pathogenesis, and long-term effects. Front Cell Infect Microbiol 2024; 14:1407261. [PMID: 38846354 PMCID: PMC11155306 DOI: 10.3389/fcimb.2024.1407261] [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: 03/26/2024] [Accepted: 05/08/2024] [Indexed: 06/09/2024] Open
Abstract
SARS-CoV-2 is the causative virus of the devastating COVID-19 pandemic that results in an unparalleled global health and economic crisis. Despite unprecedented scientific efforts and therapeutic interventions, the fight against COVID-19 continues as the rapid emergence of different SARS-CoV-2 variants of concern and the increasing challenge of long COVID-19, raising a vast demand to understand the pathomechanisms of COVID-19 and its long-term sequelae and develop therapeutic strategies beyond the virus per se. Notably, in addition to the virus itself, the replication cycle of SARS-CoV-2 and clinical severity of COVID-19 is also governed by host factors. In this review, we therefore comprehensively overview the replication cycle and pathogenesis of SARS-CoV-2 from the perspective of host factors and host-virus interactions. We sequentially outline the pathological implications of molecular interactions between host factors and SARS-CoV-2 in multi-organ and multi-system long COVID-19, and summarize current therapeutic strategies and agents targeting host factors for treating these diseases. This knowledge would be key for the identification of new pathophysiological aspects and mechanisms, and the development of actionable therapeutic targets and strategies for tackling COVID-19 and its sequelae.
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Affiliation(s)
| | | | - Yan Tian
- Department of Endocrinology and Metabolism, Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Medical School, West China Hospital and Cancer Center, Sichuan University and Collaborative Innovation Center of Biotherapy, Sichuan, Chengdu, China
| | - Xianghui Fu
- Department of Endocrinology and Metabolism, Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Medical School, West China Hospital and Cancer Center, Sichuan University and Collaborative Innovation Center of Biotherapy, Sichuan, Chengdu, China
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8
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Bishop CR, Yan K, Nguyen W, Rawle DJ, Tang B, Larcher T, Suhrbier A. Microplastics dysregulate innate immunity in the SARS-CoV-2 infected lung. Front Immunol 2024; 15:1382655. [PMID: 38803494 PMCID: PMC11128561 DOI: 10.3389/fimmu.2024.1382655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 04/24/2024] [Indexed: 05/29/2024] Open
Abstract
Introduction Global microplastic (MP) pollution is now well recognized, with humans and animals consuming and inhaling MPs on a daily basis, with a growing body of concern surrounding the potential impacts on human health. Methods Using a mouse model of mild COVID-19, we describe herein the effects of azide-free 1 μm polystyrene MP beads, co-delivered into lungs with a SARS-CoV-2 omicron BA.5 inoculum. The effect of MPs on the host response to SARS-CoV-2 infection was analysed using histopathology and RNA-Seq at 2 and 6 days post-infection (dpi). Results Although infection reduced clearance of MPs from the lung, virus titres and viral RNA levels were not significantly affected by MPs, and overt MP-associated clinical or histopathological changes were not observed. However, RNA-Seq of infected lungs revealed that MP exposure suppressed innate immune responses at 2 dpi and increased pro-inflammatory signatures at 6 dpi. The cytokine profile at 6 dpi showed a significant correlation with the 'cytokine release syndrome' signature observed in some COVID-19 patients. Discussion The findings are consistent with the recent finding that MPs can inhibit phagocytosis of apoptotic cells via binding of Tim4. They also add to a growing body of literature suggesting that MPs can dysregulate inflammatory processes in specific disease settings.
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Affiliation(s)
- Cameron R. Bishop
- Inflammation Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Kexin Yan
- Inflammation Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Wilson Nguyen
- Inflammation Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Daniel J. Rawle
- Inflammation Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Bing Tang
- Inflammation Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Thibaut Larcher
- Institut National de Recherche Agronomique, Unité Mixte de Recherche, Oniris, Nantes, France
| | - Andreas Suhrbier
- Inflammation Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- Australian Infectious Disease Research Centre, Global Virus Network (GVN) Center of Excellence, Brisbane, QLD, Australia
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9
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Urbanowicz K, Opielka M, Stegmann KM, Dickmanns A, Dobbelstein M, Peters GJ, Smoleński RT. Evaluation of N4-hydroxycytidine incorporation into nucleic acids of SARS-CoV-2-infected host cells by direct measurement with liquid chromatography-mass spectrometry. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2024:1-9. [PMID: 38741480 DOI: 10.1080/15257770.2024.2346550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 04/16/2024] [Indexed: 05/16/2024]
Abstract
Molnupiravir, an orally administered prodrug of β-d-N4-hydroxycytidine (NHC), is incorporated into newly synthesized RNA by viral RNA-dependent RNA polymerase (RdRp). It is used for treatment of SARS-CoV-2 infections. Incorporation of NHC triphosphate into viral RNA inhibits replication of the virus, at least in part by introducing deleterious mutations. However, there is limited information on NHC incorporation into host RNA and reports on the risk of mutagenicity that molnupiravir/NHC pose to the host are conflicting. We used two liquid chromatography-mass spectrometry (LC-MS) methods to evaluate the incorporation of NHC into RNA and DNA of host Vero E6 cells in a SARS-CoV-2 infection model. To test this, host and viral RNA were degraded to their ribonucleosides, while host DNA was degraded to deoxyribonucleosides. Subsequently, nucleic acid constituents were analyzed by LC-MS, which offers specific, direct, and quantitative determination of incorporation. Our findings revealed concentration dependent NHC incorporation into host cell RNA in both infected and uninfected cell cultures, reaching a maximum of 1 in 7,093 bases. Analysis of host DNA revealed no presence of deoxy-N4-hydroxycytidine down to a detection limit of 1 in 133,000 bases. Our findings therefore suggest minimal to no NHC incorporation into host DNA, indicating a low probability of significant host cell mutagenicity associated with its use.
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Affiliation(s)
| | - Mikolaj Opielka
- Department of Biochemistry, Medical University of Gdansk, Gdansk, Poland
| | - Kim M Stegmann
- Department of Molecular Oncology, Göttingen Center of Molecular Biosciences, University of Göttingen, Göttingen, Germany
| | - Antje Dickmanns
- Department of Molecular Oncology, Göttingen Center of Molecular Biosciences, University of Göttingen, Göttingen, Germany
| | - Matthias Dobbelstein
- Department of Molecular Oncology, Göttingen Center of Molecular Biosciences, University of Göttingen, Göttingen, Germany
| | - Godefridus J Peters
- Department of Biochemistry, Medical University of Gdansk, Gdansk, Poland
- Laboratory of Medical Oncology, Amsterdam University Medical Centers, Cancer Center Amsterdam, Vrije Unversteit Amsterdam, Amsterdam, the Netherlands
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10
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Steiner S, Kratzel A, Barut GT, Lang RM, Aguiar Moreira E, Thomann L, Kelly JN, Thiel V. SARS-CoV-2 biology and host interactions. Nat Rev Microbiol 2024; 22:206-225. [PMID: 38225365 DOI: 10.1038/s41579-023-01003-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2023] [Indexed: 01/17/2024]
Abstract
The zoonotic emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the ensuing coronavirus disease 2019 (COVID-19) pandemic have profoundly affected our society. The rapid spread and continuous evolution of new SARS-CoV-2 variants continue to threaten global public health. Recent scientific advances have dissected many of the molecular and cellular mechanisms involved in coronavirus infections, and large-scale screens have uncovered novel host-cell factors that are vitally important for the virus life cycle. In this Review, we provide an updated summary of the SARS-CoV-2 life cycle, gene function and virus-host interactions, including recent landmark findings on general aspects of coronavirus biology and newly discovered host factors necessary for virus replication.
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Affiliation(s)
- Silvio Steiner
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Annika Kratzel
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - G Tuba Barut
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Reto M Lang
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Etori Aguiar Moreira
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Lisa Thomann
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Jenna N Kelly
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
- European Virus Bioinformatics Center, Jena, Germany
| | - Volker Thiel
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland.
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland.
- European Virus Bioinformatics Center, Jena, Germany.
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11
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Vajdi M, Karimi A, Hassanizadeh S, Farhangi MA, Bagherniya M, Askari G, Roufogalis BD, Davies NM, Sahebkar A. Effect of polyphenols against complications of COVID-19: current evidence and potential efficacy. Pharmacol Rep 2024; 76:307-327. [PMID: 38498260 DOI: 10.1007/s43440-024-00585-6] [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: 09/23/2023] [Revised: 03/01/2024] [Accepted: 03/03/2024] [Indexed: 03/20/2024]
Abstract
The COVID-19 pandemic that started in 2019 and resulted in significant morbidity and mortality continues to be a significant global health challenge, characterized by inflammation, oxidative stress, and immune system dysfunction.. Developing therapies for preventing or treating COVID-19 remains an important goal for pharmacology and drug development research. Polyphenols are effective against various viral infections and can be extracted and isolated from plants without losing their therapeutic potential. Researchers have developed methods for separating and isolating polyphenols from complex matrices. Polyphenols are effective in treating common viral infections, including COVID-19, and can also boost immunity. Polyphenolic-based antiviral medications can mitigate SARS-CoV-2 enzymes vital to virus replication and infection. Individual polyphenolic triterpenoids, flavonoids, anthraquinonoids, and tannins may also inhibit the SARS-CoV-2 protease. Polyphenol pharmacophore structures identified to date can explain their action and lead to the design of novel anti-COVID-19 compounds. Polyphenol-containing mixtures offer the advantages of a well-recognized safety profile with few known severe side effects. However, studies to date are limited, and further animal studies and randomized controlled trials are needed in future studies. The purpose of this study was to review and present the latest findings on the therapeutic impact of plant-derived polyphenols on COVID-19 infection and its complications. Exploring alternative approaches to traditional therapies could aid in developing novel drugs and remedies against coronavirus infection.
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Affiliation(s)
- Mahdi Vajdi
- Department of Community Nutrition, School of Nutrition and Food Science, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Arash Karimi
- Traditional Medicine and Hydrotherapy Research Center, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Shirin Hassanizadeh
- Department of Community Nutrition, School of Nutrition and Food Science, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mahdieh Abbasalizad Farhangi
- Department of Community Nutrition, Faculty of Nutrition and Food Science, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Bagherniya
- Department of Community Nutrition, Food Security Research Center, School of Nutrition and Food Science, Isfahan University of Medical Sciences, Isfahan, Iran
- Anesthesia and Critical Care Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Gholamreza Askari
- Department of Community Nutrition, Food Security Research Center, School of Nutrition and Food Science, Isfahan University of Medical Sciences, Isfahan, Iran
- Anesthesia and Critical Care Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Basil D Roufogalis
- Discipline of Pharmacology, School of Medical Sciences, University of Sydney, Sydney, NSW, Australia
- NICM Health Research Institute, Western Sydney University, Penrith, NSW, Australia
| | - Neal M Davies
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Amirhossein Sahebkar
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
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Baker PJ, Bohrer AC, Castro E, Amaral EP, Snow-Smith M, Torres-Juárez F, Gould ST, Queiroz ATL, Fukutani ER, Jordan CM, Khillan JS, Cho K, Barber DL, Andrade BB, Johnson RF, Hilligan KL, Mayer-Barber KD. The inflammatory microenvironment of the lung at the time of infection governs innate control of SARS-CoV-2 replication. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.27.586885. [PMID: 38585846 PMCID: PMC10996686 DOI: 10.1101/2024.03.27.586885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
SARS-CoV-2 infection leads to vastly divergent clinical outcomes ranging from asymptomatic infection to fatal disease. Co-morbidities, sex, age, host genetics and vaccine status are known to affect disease severity. Yet, how the inflammatory milieu of the lung at the time of SARS-CoV-2 exposure impacts the control of viral replication remains poorly understood. We demonstrate here that immune events in the mouse lung closely preceding SARS-CoV-2 infection significantly impact viral control and we identify key innate immune pathways required to limit viral replication. A diverse set of pulmonary inflammatory stimuli, including resolved antecedent respiratory infections with S. aureus or influenza, ongoing pulmonary M. tuberculosis infection, ovalbumin/alum-induced asthma or airway administration of defined TLR ligands and recombinant cytokines, all establish an antiviral state in the lung that restricts SARS-CoV-2 replication upon infection. In addition to antiviral type I interferons, the broadly inducible inflammatory cytokines TNFα and IL-1 precondition the lung for enhanced viral control. Collectively, our work shows that SARS-CoV-2 may benefit from an immunologically quiescent lung microenvironment and suggests that heterogeneity in pulmonary inflammation that precedes or accompanies SARS-CoV-2 exposure may be a significant factor contributing to the population-wide variability in COVID-19 disease outcomes.
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Affiliation(s)
- Paul J. Baker
- Inflammation and Innate Immunity Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
- Current Address: Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia
| | - Andrea C. Bohrer
- Inflammation and Innate Immunity Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
| | - Ehydel Castro
- Inflammation and Innate Immunity Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
| | - Eduardo P. Amaral
- Inflammation and Innate Immunity Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
| | - Maryonne Snow-Smith
- Inflammation and Innate Immunity Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
- Human Eosinophil Section, Laboratory of Parasitic Diseases, NIAID, NIH, Bethesda, Maryland 20892, USA
| | - Flor Torres-Juárez
- Inflammation and Innate Immunity Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
| | - Sydnee T. Gould
- T Lymphocyte Biology Section, Laboratory of Parasitic Diseases, NIAID, NIH, Bethesda, Maryland 20892, USA
- Current Address: Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Artur T. L. Queiroz
- Multinational Organization Network Sponsoring Translational and Epidemiological Research Initiative, Salvador, Bahia 41810-710, Brazil
- Laboratory of Clinical and Translational Research, Gonçalo Moniz Institute, Oswaldo Cruz Foundation, Salvador, Bahia 40296-710, Brazil
| | - Eduardo R. Fukutani
- Multinational Organization Network Sponsoring Translational and Epidemiological Research Initiative, Salvador, Bahia 41810-710, Brazil
- Laboratory of Clinical and Translational Research, Gonçalo Moniz Institute, Oswaldo Cruz Foundation, Salvador, Bahia 40296-710, Brazil
| | - Cassandra M. Jordan
- Inflammation and Innate Immunity Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
| | - Jaspal S. Khillan
- Mouse Genetics and Gene Modification Section, Comparative Medicine Branch, NIAID, NIH, Rockville, Maryland 20852, USA
| | - Kyoungin Cho
- Mouse Genetics and Gene Modification Section, Comparative Medicine Branch, NIAID, NIH, Rockville, Maryland 20852, USA
| | - Daniel L. Barber
- T Lymphocyte Biology Section, Laboratory of Parasitic Diseases, NIAID, NIH, Bethesda, Maryland 20892, USA
| | - Bruno B. Andrade
- Multinational Organization Network Sponsoring Translational and Epidemiological Research Initiative, Salvador, Bahia 41810-710, Brazil
- Laboratory of Clinical and Translational Research, Gonçalo Moniz Institute, Oswaldo Cruz Foundation, Salvador, Bahia 40296-710, Brazil
| | - Reed F. Johnson
- SCV2 Virology Core, Laboratory of Viral Diseases, NIAID, NIH, Bethesda, Maryland 20892, USA
| | - Kerry L. Hilligan
- Malaghan Institute of Medical Research, Wellington 6012, New Zealand
| | - Katrin D. Mayer-Barber
- Inflammation and Innate Immunity Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
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Guo J, Lai Y, Yang Z, Song W, Zhou J, Li Z, Su W, Xiao S, Fang L. Coinfection and Nonrandom Recombination Drive the Evolution of Swine Enteric Coronaviruses. Emerg Microbes Infect 2024:2332653. [PMID: 38517703 DOI: 10.1080/22221751.2024.2332653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2024]
Abstract
Coinfection with multiple viruses is a common phenomenon in clinical settings and is a crucial driver of viral evolution. Although numerous studies have demonstrated viral recombination arising from coinfections of different strains of a specific species, the role of coinfections of different species or genera during viral evolution is rarely investigated. Here, we analyzed coinfections of and recombination events between four different swine enteric coronaviruses that infect the jejunum and ileum in pigs, including porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), and swine acute diarrhea syndrome coronavirus (SADS-CoV), and a deltacoronavirus, porcine deltacoronavirus (PDCoV). Various coinfection patterns were observed in 4,468 fecal and intestinal tissue samples collected from pigs in a 4-year survey. PEDV/PDCoV was the most frequent coinfection. However, recombination analyses have only detected events involving PEDV/TGEV and SADS-CoV/TGEV, indicating that inter-species recombination among coronaviruses is most likely to occur within the same genus. We also analyzed recombination events within the newly identified genus Deltacoronavirus and found that sparrows have played a unique host role in the recombination history of the deltacoronaviruses. The emerging virus PDCoV, which can infect humans, has a different recombination history. In summary, our study demonstrates that swine enteric coronaviruses are a valuable model for investigating the relationship between viral coinfection and recombination, which provide new insights into both inter- and intraspecies recombination events among swine enteric coronaviruses, and extend our understanding of the relationship between coronavirus coinfection and recombination.
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Affiliation(s)
- Jiahui Guo
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University. Wuhan, Hubei, 430070, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, China
| | - Yinan Lai
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University. Wuhan, Hubei, 430070, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, China
| | - Zhixiang Yang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University. Wuhan, Hubei, 430070, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, China
| | - Wenbo Song
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University. Wuhan, Hubei, 430070, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, China
| | - Junwei Zhou
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University. Wuhan, Hubei, 430070, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, China
| | - Zhuang Li
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University. Wuhan, Hubei, 430070, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, China
| | - Wen Su
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University. Wuhan, Hubei, 430070, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University. Wuhan, Hubei, 430070, China
| | - Shaobo Xiao
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University. Wuhan, Hubei, 430070, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, China
| | - Liurong Fang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University. Wuhan, Hubei, 430070, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, China
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14
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Shi Y, Zhen X, Zhang Y, Li Y, Koo S, Saiding Q, Kong N, Liu G, Chen W, Tao W. Chemically Modified Platforms for Better RNA Therapeutics. Chem Rev 2024; 124:929-1033. [PMID: 38284616 DOI: 10.1021/acs.chemrev.3c00611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2024]
Abstract
RNA-based therapies have catalyzed a revolutionary transformation in the biomedical landscape, offering unprecedented potential in disease prevention and treatment. However, despite their remarkable achievements, these therapies encounter substantial challenges including low stability, susceptibility to degradation by nucleases, and a prominent negative charge, thereby hindering further development. Chemically modified platforms have emerged as a strategic innovation, focusing on precise alterations either on the RNA moieties or their associated delivery vectors. This comprehensive review delves into these platforms, underscoring their significance in augmenting the performance and translational prospects of RNA-based therapeutics. It encompasses an in-depth analysis of various chemically modified delivery platforms that have been instrumental in propelling RNA therapeutics toward clinical utility. Moreover, the review scrutinizes the rationale behind diverse chemical modification techniques aiming at optimizing the therapeutic efficacy of RNA molecules, thereby facilitating robust disease management. Recent empirical studies corroborating the efficacy enhancement of RNA therapeutics through chemical modifications are highlighted. Conclusively, we offer profound insights into the transformative impact of chemical modifications on RNA drugs and delineates prospective trajectories for their future development and clinical integration.
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Affiliation(s)
- Yesi Shi
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, National Innovation Platform for Industry-Education Integration in Vaccine Research, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Xueyan Zhen
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Yiming Zhang
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Yongjiang Li
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Seyoung Koo
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Qimanguli Saiding
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Na Kong
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou 310058, China
| | - Gang Liu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, National Innovation Platform for Industry-Education Integration in Vaccine Research, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Wei Chen
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Wei Tao
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
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15
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Kong X, Wang W, Zhong Y, Wang N, Bai K, Wu Y, Qi Q, Zhang Y, Liu X, Xie J. Recent advances in the exploration and discovery of SARS-CoV-2 inhibitory peptides from edible animal proteins. Front Nutr 2024; 11:1346510. [PMID: 38389797 PMCID: PMC10883054 DOI: 10.3389/fnut.2024.1346510] [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: 12/01/2023] [Accepted: 01/22/2024] [Indexed: 02/24/2024] Open
Abstract
The severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), which causes the coronavirus disease 2019 (COVID-19), is spreading worldwide. Although the COVID-19 epidemic has passed its peak of transmission, the harm it has caused deserves our attention. Scientists are striving to develop medications that can effectively treat COVID-19 symptoms without causing any adverse reactions. SARS-CoV-2 inhibitory peptides derived from animal proteins have a wide range of functional activities in addition to safety. Identifying animal protein sources is crucial to obtaining SARS-CoV-2 inhibitory peptides from animal sources. This review aims to reveal the mechanisms of action of these peptides on SARS-CoV-2 and the possibility of animal proteins as a material source of SARS-CoV-2 inhibitory peptides. Also, it introduces the utilization of computer-aided design methods, phage display, and drug delivery strategies in the research on SARS-CoV-2 inhibitor peptides from animal proteins. In order to identify new antiviral peptides and boost their efficiency, we recommend investigating the interaction between SARS-CoV-2 inhibitory peptides from animal protein sources and non-structural proteins (Nsps) using a variety of technologies, including computer-aided drug approaches, phage display techniques, and drug delivery techniques. This article provides useful information for the development of novel anti-COVID-19 drugs.
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Affiliation(s)
- Xiaoyue Kong
- College of Food and Health, Zhejiang Agriculture and Forestry University, Hangzhou, China
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, China
| | - Wei Wang
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, China
| | - Yizhi Zhong
- Department of Anesthesiology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Nan Wang
- College of Biology and Environmental Engineering, Zhejiang Shuren University, Hangzhou, China
| | - Kaiwen Bai
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, China
| | - Yi Wu
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, China
| | - Qianhui Qi
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, China
| | - Yu Zhang
- Institute of Quality and Standard for Agriculture Products, Zhejiang Academy of Agricultural Science, Hangzhou, China
| | - Xingquan Liu
- College of Food and Health, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Junran Xie
- Department of Anesthesiology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
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16
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Sievers BL, Cheng MTK, Csiba K, Meng B, Gupta RK. SARS-CoV-2 and innate immunity: the good, the bad, and the "goldilocks". Cell Mol Immunol 2024; 21:171-183. [PMID: 37985854 PMCID: PMC10805730 DOI: 10.1038/s41423-023-01104-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 11/01/2023] [Indexed: 11/22/2023] Open
Abstract
An ancient conflict between hosts and pathogens has driven the innate and adaptive arms of immunity. Knowledge about this interplay can not only help us identify biological mechanisms but also reveal pathogen vulnerabilities that can be leveraged therapeutically. The humoral response to SARS-CoV-2 infection has been the focus of intense research, and the role of the innate immune system has received significantly less attention. Here, we review current knowledge of the innate immune response to SARS-CoV-2 infection and the various means SARS-CoV-2 employs to evade innate defense systems. We also consider the role of innate immunity in SARS-CoV-2 vaccines and in the phenomenon of long COVID.
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Affiliation(s)
| | - Mark T K Cheng
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Kata Csiba
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Bo Meng
- Department of Medicine, University of Cambridge, Cambridge, UK.
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK.
| | - Ravindra K Gupta
- Department of Medicine, University of Cambridge, Cambridge, UK.
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK.
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17
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Wellford SA, Moseman EA. Olfactory immune response to SARS-CoV-2. Cell Mol Immunol 2024; 21:134-143. [PMID: 38143247 PMCID: PMC10806031 DOI: 10.1038/s41423-023-01119-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 12/04/2023] [Indexed: 12/26/2023] Open
Abstract
Numerous pathogens can infect the olfactory tract, yet the pandemic caused by SARS-CoV-2 has strongly emphasized the importance of the olfactory mucosa as an immune barrier. Situated in the nasal passages, the olfactory mucosa is directly exposed to the environment to sense airborne odorants; however, this also means it can serve as a direct route of entry from the outside world into the brain. As a result, olfactotropic infections can have serious consequences, including dysfunction of the olfactory system, CNS invasion, dissemination to the lower respiratory tract, and transmission between individuals. Recent research has shown that a distinctive immune response is needed to protect this neuronal and mucosal tissue. A better understanding of innate, adaptive, and structural immune barriers in the olfactory mucosa is needed to develop effective therapeutics and vaccines against olfactotropic microbes such as SARS-CoV-2. Here, we summarize the ramifications of SARS-CoV-2 infection of the olfactory mucosa, review the subsequent immune response, and discuss important areas of future research for olfactory immunity to infectious disease.
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Affiliation(s)
- Sebastian A Wellford
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, NC, USA
| | - E Ashley Moseman
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, NC, USA.
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18
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Höft MA, Burgers WA, Riou C. The immune response to SARS-CoV-2 in people with HIV. Cell Mol Immunol 2024; 21:184-196. [PMID: 37821620 PMCID: PMC10806256 DOI: 10.1038/s41423-023-01087-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 09/12/2023] [Indexed: 10/13/2023] Open
Abstract
This review examines the intersection of the HIV and SARS-CoV-2 pandemics. People with HIV (PWH) are a heterogeneous group that differ in their degree of immune suppression, immune reconstitution, and viral control. While COVID-19 in those with well-controlled HIV infection poses no greater risk than that for HIV-uninfected individuals, people with advanced HIV disease are more vulnerable to poor COVID-19 outcomes. COVID-19 vaccines are effective and well tolerated in the majority of PWH, though reduced vaccine efficacy, breakthrough infections and faster waning of vaccine effectiveness have been demonstrated in PWH. This is likely a result of suboptimal humoral and cellular immune responses after vaccination. People with advanced HIV may also experience prolonged infection that may give rise to new epidemiologically significant variants, but initiation or resumption of antiretroviral therapy (ART) can effectively clear persistent infection. COVID-19 vaccine guidelines reflect these increased risks and recommend prioritization for vaccination and additional booster doses for PWH who are moderately to severely immunocompromised. We recommend continued research and monitoring of PWH with SARS-CoV-2 infection, especially in areas with a high HIV burden.
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Affiliation(s)
- Maxine A Höft
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Wendy A Burgers
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.
- Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa.
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Cape Town, South Africa.
| | - Catherine Riou
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.
- Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa.
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Cape Town, South Africa.
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19
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Zhang K, Eldin P, Ciesla JH, Briant L, Lentini JM, Ramos J, Cobb J, Munger J, Fu D. Proteolytic cleavage and inactivation of the TRMT1 tRNA modification enzyme by SARS-CoV-2 main protease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.02.10.527147. [PMID: 37502865 PMCID: PMC10370084 DOI: 10.1101/2023.02.10.527147] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Nonstructural protein 5 (Nsp5) is the main protease of SARS-CoV-2 that cleaves viral polyproteins into individual polypeptides necessary for viral replication. Here, we show that Nsp5 binds and cleaves human tRNA methyltransferase 1 (TRMT1), a host enzyme required for a prevalent post-transcriptional modification in tRNAs. Human cells infected with SARS-CoV-2 exhibit a decrease in TRMT1 protein levels and TRMT1-catalyzed tRNA modifications, consistent with TRMT1 cleavage and inactivation by Nsp5. Nsp5 cleaves TRMT1 at a specific position that matches the consensus sequence of SARS-CoV-2 polyprotein cleavage sites, and a single mutation within the sequence inhibits Nsp5-dependent proteolysis of TRMT1. The TRMT1 cleavage fragments exhibit altered RNA binding activity and are unable to rescue tRNA modification in TRMT1-deficient human cells. Compared to wildtype human cells, TRMT1-deficient human cells infected with SARS-CoV-2 exhibit reduced levels of intracellular viral RNA. These findings provide evidence that Nsp5-dependent cleavage of TRMT1 and perturbation of tRNA modification patterns contribute to the cellular pathogenesis of SARS-CoV-2 infection.
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Affiliation(s)
- Kejia Zhang
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Patrick Eldin
- Institut de Recherche en Infectiologie de Montpellier (IRIM), CNRS, UMR 9004, Université de Montpellier, 1919 Route de Mende, 34293, Montpellier Cedex 5, France
| | - Jessica H. Ciesla
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Laurence Briant
- Institut de Recherche en Infectiologie de Montpellier (IRIM), CNRS, UMR 9004, Université de Montpellier, 1919 Route de Mende, 34293, Montpellier Cedex 5, France
| | - Jenna M. Lentini
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Jillian Ramos
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Justin Cobb
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Joshua Munger
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Dragony Fu
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, NY, 14627, USA
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20
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Lu W, Wang L, Xing J. Editorial: Antiviral innate immune sensing, regulation, and viral immune evasion. Front Immunol 2024; 14:1358542. [PMID: 38239347 PMCID: PMC10794728 DOI: 10.3389/fimmu.2023.1358542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 12/26/2023] [Indexed: 01/22/2024] Open
Affiliation(s)
- Wenting Lu
- Department of Surgery and Immunobiology and Transplant Science Center, Houston Methodist Research Institute, Houston Methodist, Houston, TX, United States
| | - Ling Wang
- Department of Surgery and Immunobiology and Transplant Science Center, Houston Methodist Research Institute, Houston Methodist, Houston, TX, United States
- Department of Obstetrics and Gynecology, The Second Hospital of Jilin University, Changchun, China
| | - Junji Xing
- Department of Surgery and Immunobiology and Transplant Science Center, Houston Methodist Research Institute, Houston Methodist, Houston, TX, United States
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston Methodist, Houston, TX, United States
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21
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Gremese E, Tolusso B, Bruno D, Paglionico AM, Perniola S, Ferraccioli G, Alivernini S. COVID-19 illness: Different comorbidities may require different immunological therapeutic targets. Eur J Clin Invest 2023; 53:e14096. [PMID: 37724937 DOI: 10.1111/eci.14096] [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: 01/25/2023] [Revised: 07/02/2023] [Accepted: 07/26/2023] [Indexed: 09/21/2023]
Abstract
BACKGROUND The SARS-CoV-2 pandemic has led to more than 6,870.000 deaths worldwide. Despite recent therapeutic advances, deaths in Intensive Care Units still range between 34 and 72%, comprising substantial unmet need as we move to an endemic phase. The general agreement is that in the first few days of infection, antiviral drugs and neutralizing monoclonal antibodies should be adopted. When the patient is hospitalized and develops severe pneumonia, progressing to a systemic disease, immune modifying therapy with corticosteroids is indicated. Such interventions, however, are less effective in the context of comorbidities (e.g., diabetes, hypertension, heart failure, atrial fibrillation, obesity and central nervous system-CNS diseases) which are by themselves associated with poor outcomes. Such comorbidities comprise common and some distinct underlying inflammatory pathobiology regulated by differential cytokine taxonomy. METHODS Searching in the PubMed database, literature pertaining to the biology underlying the different comorbidities, and the data from the studies related to various immunological treatments for the Covid-19 disease were carefully analyzed. RESULTS Several experimental and clinical data have demonstrated that hypertension and atrial fibrillation present an IL-6 dependent signature, whereas diabetes, obesity, heart failure and CNS diseases may exhibit an IL-1a/b predominant signature. Distinct selective cytokine targeting may offer advantage in treating severe COVID-19 illness based on single or multiple associated comorbidities. When the patient does not immediately respond, a broader target range through JAKs pathway inhibitors may be indicated. CONCLUSIONS Herein, we discuss the biological background associated with distinct comorbidities which might impact the SARS-CoV-2 infection course and how these should to be addressed to improve the current therapeutic outcome.
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Affiliation(s)
- Elisa Gremese
- Clinical Immunology Unit, Fondazione Policlinico Universitario A. Gemelli-IRCCS, Rome, Italy
- Catholic University of the Sacred Heart, Rome, Italy
- Immunology Core Facility, GSTEP, Fondazione Policlinico Universitario A. Gemelli-IRCCS, Rome, Italy
| | - Barbara Tolusso
- Immunology Core Facility, GSTEP, Fondazione Policlinico Universitario A. Gemelli-IRCCS, Rome, Italy
| | - Dario Bruno
- Clinical Immunology Unit, Fondazione Policlinico Universitario A. Gemelli-IRCCS, Rome, Italy
| | - Anna Maria Paglionico
- Clinical Immunology Unit, Fondazione Policlinico Universitario A. Gemelli-IRCCS, Rome, Italy
| | - Simone Perniola
- Clinical Immunology Unit, Fondazione Policlinico Universitario A. Gemelli-IRCCS, Rome, Italy
| | | | - Stefano Alivernini
- Catholic University of the Sacred Heart, Rome, Italy
- Immunology Core Facility, GSTEP, Fondazione Policlinico Universitario A. Gemelli-IRCCS, Rome, Italy
- Rheumatology Unit, Fondazione Policlinico Universitario A. Gemelli-IRCCS, Rome, Italy
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22
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Flagg M, Goldin K, Pérez-Pérez L, Singh M, Williamson BN, Pruett N, Hoang CD, de Wit E. Low level of tonic interferon signalling is associated with enhanced susceptibility to SARS-CoV-2 variants of concern in human lung organoids. Emerg Microbes Infect 2023; 12:2276338. [PMID: 37883246 PMCID: PMC10732190 DOI: 10.1080/22221751.2023.2276338] [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: 06/22/2023] [Accepted: 10/23/2023] [Indexed: 10/28/2023]
Abstract
There is tremendous heterogeneity in the severity of COVID-19 disease in the human population, and the mechanisms governing the development of severe disease remain incompletely understood. The emergence of SARS-CoV-2 variants of concern (VOC) Delta (B.1.617.2) and Omicron (B.1.1.529) further compounded this heterogeneity. Virus replication and host cell damage in the distal lung is often associated with severe clinical disease, making this an important site to consider when evaluating pathogenicity of SARS-CoV-2 VOCs. Using distal human lung organoids (hLOs) derived from multiple human donors, we compared the fitness and pathogenicity of SARS-CoV-2 VOC Delta and Omicron, along with an ancestral clade B variant D614G, and evaluated donor-dependent differences in susceptibility to infection. We observed substantial attenuation of Omicron in hLOs and demonstrated enhanced susceptibility to Omicron and D614G replication in hLOs from one donor. Transcriptomic analysis revealed that increased susceptibility to SARS-CoV-2 infection in these hLOs was associated with reduced tonic interferon signaling activity at baseline. We show that hLOs can be used to model heterogeneity of SARS-CoV-2 pathogenesis in humans, and propose that variability in tonic interferon signaling set point may impact susceptibility to SARS-CoV-2 VOCs and subsequent COVID-19 disease progression.
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Affiliation(s)
- Meaghan Flagg
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Kerry Goldin
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Lizzette Pérez-Pérez
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Manmeet Singh
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Brandi N. Williamson
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Nathanael Pruett
- Thoracic Surgery Branch, Division of Intramural Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Chuong D. Hoang
- Thoracic Surgery Branch, Division of Intramural Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Emmie de Wit
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
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23
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Parums DV. Editorial: Factors Driving New Variants of SARS-CoV-2, Immune Escape, and Resistance to Antiviral Treatments as the End of the COVID-19 Pandemic is Declared. Med Sci Monit 2023; 29:e942960. [PMID: 37908161 PMCID: PMC10626992 DOI: 10.12659/msm.942960] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 10/23/2023] [Indexed: 11/02/2023] Open
Abstract
On May 5, 2023, the Director-General of the World Health Organization (WHO) advised the transition to long-term management of the COVID-19 pandemic and that COVID-19 is now an established and ongoing health issue that is no longer a public health emergency of international concern (PHEIC). The WHO decision was based on an analysis of the decreasing trend in mortality, the decline in hospital admissions and Intensive Care Unit (ICU) admissions from COVID-19, and the increasing levels of population immunity to SARS-CoV-2. This Editorial aims to highlight what is known of the factors that drive new variants, subvariants, and lineages of SARS-CoV-2 associated with immune escape to previous infection or vaccines and resistance to antiviral treatments as the end of the COVID-19 pandemic is declared.
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Affiliation(s)
- Dinah V Parums
- Science Editor, Medical Science Monitor, International Scientific Information, Inc., Melville, NY, USA
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24
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O’Neil JD, Bolimowska OO, Clayton SA, Tang T, Daley KK, Lara-Reyna S, Warner J, Martin CS, Mahida RY, Hardy RS, Arthur JSC, Clark AR. Dexamethasone impairs the expression of antimicrobial mediators in lipopolysaccharide-activated primary macrophages by inhibiting both expression and function of interferon β. Front Immunol 2023; 14:1190261. [PMID: 37942320 PMCID: PMC10628473 DOI: 10.3389/fimmu.2023.1190261] [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: 03/20/2023] [Accepted: 10/11/2023] [Indexed: 11/10/2023] Open
Abstract
Glucocorticoids potently inhibit expression of many inflammatory mediators, and have been widely used to treat both acute and chronic inflammatory diseases for more than seventy years. However, they can have several unwanted effects, amongst which immunosuppression is one of the most common. Here we used microarrays and proteomic approaches to characterise the effect of dexamethasone (a synthetic glucocorticoid) on the responses of primary mouse macrophages to a potent pro-inflammatory agonist, lipopolysaccharide (LPS). Gene ontology analysis revealed that dexamethasone strongly impaired the lipopolysaccharide-induced antimicrobial response, which is thought to be driven by an autocrine feedback loop involving the type I interferon IFNβ. Indeed, dexamethasone strongly and dose-dependently inhibited the expression of IFNβ by LPS-activated macrophages. Unbiased proteomic data also revealed an inhibitory effect of dexamethasone on the IFNβ-dependent program of gene expression, with strong down-regulation of several interferon-induced antimicrobial factors. Surprisingly, dexamethasone also inhibited the expression of several antimicrobial genes in response to direct stimulation of macrophages with IFNβ. We tested a number of hypotheses based on previous publications, but found that no single mechanism could account for more than a small fraction of the broad suppressive impact of dexamethasone on macrophage type I interferon signaling, underlining the complexity of this pathway. Preliminary experiments indicated that dexamethasone exerted similar inhibitory effects on primary human monocyte-derived or alveolar macrophages.
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Affiliation(s)
- John D. O’Neil
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, United Kingdom
| | - Oliwia O. Bolimowska
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, United Kingdom
| | - Sally A. Clayton
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, United Kingdom
| | - Tina Tang
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, United Kingdom
| | - Kalbinder K. Daley
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, United Kingdom
| | - Samuel Lara-Reyna
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Jordan Warner
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Claire S. Martin
- School of Biomedical Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Rahul Y. Mahida
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, United Kingdom
| | - Rowan S. Hardy
- School of Biomedical Sciences, University of Birmingham, Birmingham, United Kingdom
| | | | - Andrew R. Clark
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, United Kingdom
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25
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Burkart SS, Schweinoch D, Frankish J, Sparn C, Wüst S, Urban C, Merlo M, Magalhães VG, Piras A, Pichlmair A, Willemsen J, Kaderali L, Binder M. High-resolution kinetic characterization of the RIG-I-signaling pathway and the antiviral response. Life Sci Alliance 2023; 6:e202302059. [PMID: 37558422 PMCID: PMC10412806 DOI: 10.26508/lsa.202302059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 07/24/2023] [Accepted: 07/27/2023] [Indexed: 08/11/2023] Open
Abstract
RIG-I recognizes viral dsRNA and activates a cell-autonomous antiviral response. Upon stimulation, it triggers a signaling cascade leading to the production of type I and III IFNs. IFNs are secreted and signal to elicit the expression of IFN-stimulated genes, establishing an antiviral state of the cell. The topology of this pathway has been studied intensively, however, its exact dynamics are less understood. Here, we employed electroporation to synchronously activate RIG-I, enabling us to characterize cell-intrinsic innate immune signaling at a high temporal resolution. Employing IFNAR1/IFNLR-deficient cells, we could differentiate primary RIG-I signaling from secondary signaling downstream of the IFN receptors. Based on these data, we developed a comprehensive mathematical model capable of simulating signaling downstream of dsRNA recognition by RIG-I and the feedback and signal amplification by IFN. We further investigated the impact of viral antagonists on signaling dynamics. Our work provides a comprehensive insight into the signaling events that occur early upon virus infection and opens new avenues to study and disentangle the complexity of the host-virus interface.
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Affiliation(s)
- Sandy S Burkart
- Research Group "Dynamics of Early Viral Infection and the Innate Antiviral Response", Division Virus-Associated Carcinogenesis (F170), German Cancer Research Center, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Darius Schweinoch
- Institute of Bioinformatics & Center for Functional Genomics of Microbes, University Medicine Greifswald, Greifswald, Germany
| | - Jamie Frankish
- Research Group "Dynamics of Early Viral Infection and the Innate Antiviral Response", Division Virus-Associated Carcinogenesis (F170), German Cancer Research Center, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Carola Sparn
- Research Group "Dynamics of Early Viral Infection and the Innate Antiviral Response", Division Virus-Associated Carcinogenesis (F170), German Cancer Research Center, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Sandra Wüst
- Research Group "Dynamics of Early Viral Infection and the Innate Antiviral Response", Division Virus-Associated Carcinogenesis (F170), German Cancer Research Center, Heidelberg, Germany
| | - Christian Urban
- Technical University of Munich, School of Medicine, Institute of Virology, Munich, Germany
| | - Marta Merlo
- Research Group "Dynamics of Early Viral Infection and the Innate Antiviral Response", Division Virus-Associated Carcinogenesis (F170), German Cancer Research Center, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Vladimir G Magalhães
- Research Group "Dynamics of Early Viral Infection and the Innate Antiviral Response", Division Virus-Associated Carcinogenesis (F170), German Cancer Research Center, Heidelberg, Germany
| | - Antonio Piras
- Technical University of Munich, School of Medicine, Institute of Virology, Munich, Germany
| | - Andreas Pichlmair
- Technical University of Munich, School of Medicine, Institute of Virology, Munich, Germany
- German Center for Infection Research (DZIF), Munich Partner Site, Munich, Germany
| | - Joschka Willemsen
- Research Group "Dynamics of Early Viral Infection and the Innate Antiviral Response", Division Virus-Associated Carcinogenesis (F170), German Cancer Research Center, Heidelberg, Germany
| | - Lars Kaderali
- Institute of Bioinformatics & Center for Functional Genomics of Microbes, University Medicine Greifswald, Greifswald, Germany
| | - Marco Binder
- Research Group "Dynamics of Early Viral Infection and the Innate Antiviral Response", Division Virus-Associated Carcinogenesis (F170), German Cancer Research Center, Heidelberg, Germany
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26
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Eberhardt N, Noval MG, Kaur R, Amadori L, Gildea M, Sajja S, Das D, Cilhoroz B, Stewart O, Fernandez DM, Shamailova R, Guillen AV, Jangra S, Schotsaert M, Newman JD, Faries P, Maldonado T, Rockman C, Rapkiewicz A, Stapleford KA, Narula N, Moore KJ, Giannarelli C. SARS-CoV-2 infection triggers pro-atherogenic inflammatory responses in human coronary vessels. NATURE CARDIOVASCULAR RESEARCH 2023; 2:899-916. [PMID: 38076343 PMCID: PMC10702930 DOI: 10.1038/s44161-023-00336-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 08/23/2023] [Indexed: 12/19/2023]
Abstract
Patients with coronavirus disease 2019 (COVID-19) present increased risk for ischemic cardiovascular complications up to 1 year after infection. Although the systemic inflammatory response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection likely contributes to this increased cardiovascular risk, whether SARS-CoV-2 directly infects the coronary vasculature and attendant atherosclerotic plaques remains unknown. Here we report that SARS-CoV-2 viral RNA is detectable and replicates in coronary lesions taken at autopsy from severe COVID-19 cases. SARS-CoV-2 targeted plaque macrophages and exhibited a stronger tropism for arterial lesions than adjacent perivascular fat, correlating with macrophage infiltration levels. SARS-CoV-2 entry was increased in cholesterol-loaded primary macrophages and dependent, in part, on neuropilin-1. SARS-CoV-2 induced a robust inflammatory response in cultured macrophages and human atherosclerotic vascular explants with secretion of cytokines known to trigger cardiovascular events. Our data establish that SARS-CoV-2 infects coronary vessels, inducing plaque inflammation that could trigger acute cardiovascular complications and increase the long-term cardiovascular risk.
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Affiliation(s)
- Natalia Eberhardt
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
| | - Maria Gabriela Noval
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
| | - Ravneet Kaur
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
| | - Letizia Amadori
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
| | - Michael Gildea
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
| | - Swathy Sajja
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
| | - Dayasagar Das
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
| | - Burak Cilhoroz
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
| | - O’Jay Stewart
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dawn M. Fernandez
- Department of Medicine, Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Roza Shamailova
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
| | - Andrea Vasquez Guillen
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
| | - Sonia Jangra
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael Schotsaert
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jonathan D. Newman
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
| | - Peter Faries
- Department of Surgery, Vascular Division, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Thomas Maldonado
- Department of Surgery, Vascular Division, New York University Langone Health, New York, NY, USA
| | - Caron Rockman
- Department of Surgery, Vascular Division, New York University Langone Health, New York, NY, USA
| | - Amy Rapkiewicz
- Department of Pathology, NYU Winthrop Hospital, Long Island School of Medicine, New York, NY, USA
| | - Kenneth A. Stapleford
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
| | - Navneet Narula
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Kathryn J. Moore
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
| | - Chiara Giannarelli
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, New York University School of Medicine, New York, NY, USA
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27
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Shafqat A, Omer MH, Albalkhi I, Alabdul Razzak G, Abdulkader H, Abdul Rab S, Sabbah BN, Alkattan K, Yaqinuddin A. Neutrophil extracellular traps and long COVID. Front Immunol 2023; 14:1254310. [PMID: 37828990 PMCID: PMC10565006 DOI: 10.3389/fimmu.2023.1254310] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 09/06/2023] [Indexed: 10/14/2023] Open
Abstract
Post-acute COVID-19 sequelae, commonly known as long COVID, encompasses a range of systemic symptoms experienced by a significant number of COVID-19 survivors. The underlying pathophysiology of long COVID has become a topic of intense research discussion. While chronic inflammation in long COVID has received considerable attention, the role of neutrophils, which are the most abundant of all immune cells and primary responders to inflammation, has been unfortunately overlooked, perhaps due to their short lifespan. In this review, we discuss the emerging role of neutrophil extracellular traps (NETs) in the persistent inflammatory response observed in long COVID patients. We present early evidence linking the persistence of NETs to pulmonary fibrosis, cardiovascular abnormalities, and neurological dysfunction in long COVID. Several uncertainties require investigation in future studies. These include the mechanisms by which SARS-CoV-2 brings about sustained neutrophil activation phenotypes after infection resolution; whether the heterogeneity of neutrophils seen in acute SARS-CoV-2 infection persists into the chronic phase; whether the presence of autoantibodies in long COVID can induce NETs and protect them from degradation; whether NETs exert differential, organ-specific effects; specifically which NET components contribute to organ-specific pathologies, such as pulmonary fibrosis; and whether senescent cells can drive NET formation through their pro-inflammatory secretome in long COVID. Answering these questions may pave the way for the development of clinically applicable strategies targeting NETs, providing relief for this emerging health crisis.
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Affiliation(s)
- Areez Shafqat
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Mohamed H. Omer
- School of Medicine, Cardiff University, Cardiff, United Kingdom
| | | | | | | | | | | | - Khaled Alkattan
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
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28
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Tardivat Y, Sosnowski P, Tidu A, Westhof E, Eriani G, Martin F. SARS-CoV-2 NSP1 induces mRNA cleavages on the ribosome. Nucleic Acids Res 2023; 51:8677-8690. [PMID: 37503833 PMCID: PMC10484668 DOI: 10.1093/nar/gkad627] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 07/10/2023] [Accepted: 07/17/2023] [Indexed: 07/29/2023] Open
Abstract
In severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the non-structural protein NSP1 inhibits translation of host mRNAs by binding to the mRNA entry channel of the ribosome and, together with the 5'-untranslated region (UTR) of the viral mRNAs, allows the evasion of that inhibition. Here, we show that NSP1 mediates endonucleolytic cleavages of both host and viral mRNAs in the 5'UTR, but with different cleavage patterns. The first pattern is observed in host mRNAs with cleavages interspersed regularly and close to the 5' cap (6-11 nt downstream of the cap). Those cleavage positions depend more on the position relative to the 5' cap than on the sequence itself. The second cleavage pattern occurs at high NSP1 concentrations and only in SARS-CoV-2 RNAs, with the cleavages clustered at positions 45, 46 and 49. Both patterns of cleavage occur with the mRNA and NSP1 bound to the ribosome, with the SL1 hairpin at the 5' end sufficient to protect from NSP1-mediated degradation at low NSP1 concentrations. We show further that the N-terminal domain of NSP1 is necessary and sufficient for efficient cleavage. We suggest that in the ribosome-bound NSP1 protein the catalytic residues of the N-terminal domain are unmasked by the remodelling of the α1- and α2-helices of the C-terminal domain.
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Affiliation(s)
- Yann Tardivat
- Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, Architecture et Réactivité de l’ARN, CNRS UPR9002, 2, allée Konrad Roentgen, F-67084 Strasbourg, France
| | - Piotr Sosnowski
- Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, Architecture et Réactivité de l’ARN, CNRS UPR9002, 2, allée Konrad Roentgen, F-67084 Strasbourg, France
| | - Antonin Tidu
- Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, Architecture et Réactivité de l’ARN, CNRS UPR9002, 2, allée Konrad Roentgen, F-67084 Strasbourg, France
| | - Eric Westhof
- Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, Architecture et Réactivité de l’ARN, CNRS UPR9002, 2, allée Konrad Roentgen, F-67084 Strasbourg, France
| | - Gilbert Eriani
- Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, Architecture et Réactivité de l’ARN, CNRS UPR9002, 2, allée Konrad Roentgen, F-67084 Strasbourg, France
| | - Franck Martin
- Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, Architecture et Réactivité de l’ARN, CNRS UPR9002, 2, allée Konrad Roentgen, F-67084 Strasbourg, France
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29
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Lee JD, Menasche BL, Mavrikaki M, Uyemura MM, Hong SM, Kozlova N, Wei J, Alfajaro MM, Filler RB, Müller A, Saxena T, Posey RR, Cheung P, Muranen T, Heng YJ, Paulo JA, Wilen CB, Slack FJ. Differences in syncytia formation by SARS-CoV-2 variants modify host chromatin accessibility and cellular senescence via TP53. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.31.555625. [PMID: 37693555 PMCID: PMC10491142 DOI: 10.1101/2023.08.31.555625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
COVID-19 remains a significant public health threat due to the ability of SARS-CoV-2 variants to evade the immune system and cause breakthrough infections. Although pathogenic coronaviruses such as SARS-CoV-2 and MERS-CoV lead to severe respiratory infections, how these viruses affect the chromatin proteomic composition upon infection remains largely uncharacterized. Here we used our recently developed integrative DNA And Protein Tagging (iDAPT) methodology to identify changes in host chromatin accessibility states and chromatin proteomic composition upon infection with pathogenic coronaviruses. SARS-CoV-2 infection induces TP53 stabilization on chromatin, which contributes to its host cytopathic effect. We mapped this TP53 stabilization to the SARS-CoV-2 spike and its propensity to form syncytia, a consequence of cell-cell fusion. Differences in SARS-CoV-2 spike variant-induced syncytia formation modify chromatin accessibility, cellular senescence, and inflammatory cytokine release via TP53. Our findings suggest that differences in syncytia formation alter senescence-associated inflammation, which varies among SARS-CoV-2 variants.
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30
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Abaeva IS, Arhab Y, Miścicka A, Hellen CUT, Pestova TV. In vitro reconstitution of SARS-CoV-2 Nsp1-induced mRNA cleavage reveals the key roles of the N-terminal domain of Nsp1 and the RRM domain of eIF3g. Genes Dev 2023; 37:844-860. [PMID: 37821106 PMCID: PMC10620056 DOI: 10.1101/gad.350829.123] [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: 05/25/2023] [Accepted: 09/19/2023] [Indexed: 10/13/2023]
Abstract
SARS CoV-2 nonstructural protein 1 (Nsp1) is the major pathogenesis factor that inhibits host translation using a dual strategy of impairing initiation and inducing endonucleolytic cleavage of cellular mRNAs. To investigate the mechanism of cleavage, we reconstituted it in vitro on β-globin, EMCV IRES, and CrPV IRES mRNAs that use unrelated initiation mechanisms. In all instances, cleavage required Nsp1 and only canonical translational components (40S subunits and initiation factors), arguing against involvement of a putative cellular RNA endonuclease. Requirements for initiation factors differed for these mRNAs, reflecting their requirements for ribosomal attachment. Cleavage of CrPV IRES mRNA was supported by a minimal set of components consisting of 40S subunits and eIF3g's RRM domain. The cleavage site was located in the coding region 18 nt downstream from the mRNA entrance, indicating that cleavage occurs on the solvent side of the 40S subunit. Mutational analysis identified a positively charged surface on Nsp1's N-terminal domain (NTD) and a surface above the mRNA-binding channel on eIF3g's RRM domain that contain residues essential for cleavage. These residues were required for cleavage on all three mRNAs, highlighting general roles of the Nsp1 NTD and eIF3g's RRM domain in cleavage per se, irrespective of the mode of ribosomal attachment.
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Affiliation(s)
- Irina S Abaeva
- Department of Cell Biology, State University of New York Downstate Health Sciences University, Brooklyn, New York 11203, USA
| | - Yani Arhab
- Department of Cell Biology, State University of New York Downstate Health Sciences University, Brooklyn, New York 11203, USA
| | - Anna Miścicka
- Department of Cell Biology, State University of New York Downstate Health Sciences University, Brooklyn, New York 11203, USA
| | - Christopher U T Hellen
- Department of Cell Biology, State University of New York Downstate Health Sciences University, Brooklyn, New York 11203, USA
| | - Tatyana V Pestova
- Department of Cell Biology, State University of New York Downstate Health Sciences University, Brooklyn, New York 11203, USA
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31
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Salvagno GL, Pighi L, Henry BM, Valentini M, Tonin B, Bragantini D, Gianfilippi G, De Nitto S, Plebani M, Lippi G. Assessment of humoral and cellular immunity after bivalent BNT162b2 vaccination and potential association with reactogenicity. Clin Chem Lab Med 2023; 61:1343-1348. [PMID: 36722026 DOI: 10.1515/cclm-2023-0055] [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: 01/14/2023] [Accepted: 01/20/2023] [Indexed: 02/02/2023]
Abstract
OBJECTIVES This study investigated the feasibility and clinical value of using a novel, automated and high-throughput SARS-CoV-2 Interferon Gamma Release Assay (IGRA), combined with total anti-SARS-CoV-2 antibodies assessment, for evaluating the immune response after bivalent BNT162b2 vaccination. METHODS A cohort of healthcare workers, who already underwent primary vaccination and boosting with monovalent BNT162b2 vaccine, received a booster dose of the new BNT162b2 bivalent formulation. Blood samples were taken immediately before vaccination (T0) and 1 month afterwards (T1). Humoral and cellular immunity were assayed with Roche Elecsys Anti-SARS-CoV-2 and Roche Elecsys IGRA SARS-CoV-2, respectively. RESULTS The study population consisted of 51 subjects (median age: 43 years; 51% females). Total anti-SARS-CoV-2 antibodies and IGRA SARS-CoV-2 values increased at T1 from 9,050 to 25,000 BAU/mL (p<0.001), and from 0.44 to 0.78 IU/mL (p=0.385), accounting for median increase of 2.0 and 1.6 folds, respectively. Increased T1 values of total anti-SARS-CoV-2 antibodies and IGRA SARS-CoV-2 were recorded in 100% and 68.6% subjects, respectively. In those with baseline values below the median, post-vaccine levels displayed larger increases of 3.3 and 5.1 folds for anti-SARS-CoV-2 total antibodies and IGRA SARS-CoV-2, respectively. The variation of total anti-SARS-CoV-2 antibodies was inversely associated with their T0 values (r=-0.97; p<0.001), whilst that of IGRA SARS-CoV-2 was inversely associated with its T0 value (r=-0.58; p<0.001). No other signifcant associations were found with demographical or clinical variables, including side effects. CONCLUSIONS The bivalent BNT162b2 vaccine booster enhances humoral and cellular immunity against SARS-CoV-2, especially in recipients with lower baseline biological protection.
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Affiliation(s)
- Gian Luca Salvagno
- Section of Clinical Biochemistry, University of Verona, Verona, Italy
- Service of Laboratory Medicine, Pederzoli Hospital, Peschiera del Garda, Italy
| | - Laura Pighi
- Section of Clinical Biochemistry, University of Verona, Verona, Italy
- Service of Laboratory Medicine, Pederzoli Hospital, Peschiera del Garda, Italy
| | - Brandon M Henry
- Clinical Laboratory, Division of Nephrology and Hypertension, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Myriam Valentini
- Service of Laboratory Medicine, Pederzoli Hospital, Peschiera del Garda, Italy
| | - Beatrice Tonin
- Medical Direction, Pederzoli Hospital, Peschiera del Garda, Italy
| | - Damiano Bragantini
- Infectious Diseases Unit, Pederzoli Hospital, Peschiera del Garda, Italy
| | | | - Simone De Nitto
- Section of Clinical Biochemistry, University of Verona, Verona, Italy
- Service of Laboratory Medicine, Pederzoli Hospital, Peschiera del Garda, Italy
| | - Mario Plebani
- Department of Medicine, University of Padova, Padova, Italy
| | - Giuseppe Lippi
- Section of Clinical Biochemistry, University of Verona, Verona, Italy
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Dwivedi R, Farrag M, Sharma P, Shi D, Shami AA, Misra SK, Ray P, Shukla J, Zhang F, Linhardt RJ, Sharp JS, Tandon R, Pomin VH. The Sea Cucumber Thyonella gemmata Contains a Low Anticoagulant Sulfated Fucan with High Anti-SARS-CoV-2 Actions against Wild-Type and Delta Variants. JOURNAL OF NATURAL PRODUCTS 2023; 86:1463-1475. [PMID: 37306476 PMCID: PMC10401483 DOI: 10.1021/acs.jnatprod.3c00151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
In this work, we isolated two new sulfated glycans from the body wall of the sea cucumber Thyonella gemmata: one fucosylated chondroitin sulfate (TgFucCS) (17.5 ± 3.5% kDa) and one sulfated fucan (TgSF) (383.3 ± 2.1% kDa). NMR results showed the TgFucCS backbone composed of [→3)-β-N-acetylgalactosamine-(1→4)-β-glucuronic acid-(1→] with 70% 4-sulfated and 30% 4,6-disulfated GalNAc units and one-third of the GlcA units decorated at the C3 position with branching α-fucose (Fuc) units either 4-sulfated (65%) or 2,4-disulfated (35%) and the TgSF structure composed of a tetrasaccharide repeating unit of [→3)-α-Fuc2,4S-(1→2)-α-Fuc4S-(1→3)-α-Fuc2S-(1→3)-α-Fuc2S-(1→]n. Inhibitory properties of TgFucCS and TgSF were investigated using SARS-CoV-2 pseudovirus coated with S-proteins of the wild-type (Wuhan-Hu-1) or the delta (B.1.617.2) strains and in four different anticoagulant assays, comparatively with unfractionated heparin. Molecular binding to coagulation (co)-factors and S-proteins was investigated by competitive surface plasmon resonance spectroscopy. Among the two sulfated glycans tested, TgSF showed significant anti-SARS-CoV-2 activity against both strains together with low anticoagulant properties, indicating a good candidate for future studies in drug development.
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Affiliation(s)
- Rohini Dwivedi
- Department of BioMolecular Sciences, University of Mississippi, Oxford, Mississippi 38677, United States
| | - Marwa Farrag
- Department of BioMolecular Sciences, University of Mississippi, Oxford, Mississippi 38677, United States
- Department of Pharmacognosy, Faculty of Pharmacy, Assiut University, Assiut 71515, Egypt
| | - Poonam Sharma
- Center for Immunology and Microbial Research, Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi 39216, United States
| | - Deling Shi
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Anter A Shami
- Department of BioMolecular Sciences, University of Mississippi, Oxford, Mississippi 38677, United States
| | - Sandeep K Misra
- Department of BioMolecular Sciences, University of Mississippi, Oxford, Mississippi 38677, United States
| | - Priya Ray
- Center for Immunology and Microbial Research, Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi 39216, United States
| | - Jayanti Shukla
- Center for Immunology and Microbial Research, Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi 39216, United States
| | - Fuming Zhang
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Robert J Linhardt
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Joshua S Sharp
- Department of BioMolecular Sciences, University of Mississippi, Oxford, Mississippi 38677, United States
- Department of Chemistry and Biochemistry, University of Mississippi, Oxford, Mississippi 38677, United States
- Research Institute of Pharmaceutical Sciences, School of Pharmacy, University of Mississippi, Oxford, Mississippi 38677, United States
| | - Ritesh Tandon
- Department of BioMolecular Sciences, University of Mississippi, Oxford, Mississippi 38677, United States
- Center for Immunology and Microbial Research, Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi 39216, United States
- Department of Medicine, University of Mississippi Medical Center, Jackson, Mississippi 39216, United States
| | - Vitor H Pomin
- Department of BioMolecular Sciences, University of Mississippi, Oxford, Mississippi 38677, United States
- Research Institute of Pharmaceutical Sciences, School of Pharmacy, University of Mississippi, Oxford, Mississippi 38677, United States
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Maurina SF, O’Sullivan JP, Sharma G, Pineda Rodriguez DC, MacFadden A, Cendali F, Henen MA, Kieft JS, Glasgow A, Steckelberg AL. An evolutionarily conserved strategy for ribosome binding and inhibition by β-coronavirus non-structural protein 1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.07.544141. [PMID: 37333070 PMCID: PMC10274807 DOI: 10.1101/2023.06.07.544141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
An important pathogenicity factor of SARS-CoV-2 and related coronaviruses is Nsp1, which suppresses host gene expression and stunts antiviral signaling. SARS-CoV-2 Nsp1 binds the ribosome to inhibit translation through mRNA displacement and induces degradation of host mRNAs through an unknown mechanism. Here we show that Nsp1-dependent host shutoff is conserved in diverse coronaviruses, but only Nsp1 from β-CoV inhibits translation through ribosome binding. The C-terminal domain of all β-CoV Nsp1s confers high-affinity ribosome-binding despite low sequence conservation. Modeling of interactions of four Nsp1s to the ribosome identified few absolutely conserved amino acids that, together with an overall conservation in surface charge, form the β-CoV Nsp1 ribosome-binding domain. Contrary to previous models, the Nsp1 ribosome-binding domain is an inefficient translation inhibitor. Instead, the Nsp1-CTD likely functions by recruiting Nsp1's N-terminal "effector" domain. Finally, we show that a viral cis -acting RNA element has co-evolved to fine-tune SARS-CoV-2 Nsp1 function, but does not provide similar protection against Nsp1 from related viruses. Together, our work provides new insight into the diversity and conservation of ribosome-dependent host-shutoff functions of Nsp1, knowledge that could aide future efforts in pharmacological targeting of Nsp1 from SARS-CoV-2, but also related human-pathogenic β-coronaviruses. Our study also exemplifies how comparing highly divergent Nsp1 variants can help to dissect the different modalities of this multi-functional viral protein.
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Affiliation(s)
- Stephanie F. Maurina
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - John P. O’Sullivan
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Geetika Sharma
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | | | - Andrea MacFadden
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Francesca Cendali
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Morkos A. Henen
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Jeffrey S. Kieft
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
- RNA BioScience Initiative, University of Colorado School of Medicine, Aurora, CO, USA
- Current address: New York Structural Biology Center, New York, NY, USA
| | - Anum Glasgow
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Anna-Lena Steckelberg
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
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Bellucci G, Albanese A, Rizzi C, Rinaldi V, Salvetti M, Ristori G. The value of Interferon β in multiple sclerosis and novel opportunities for its anti-viral activity: a narrative literature review. Front Immunol 2023; 14:1161849. [PMID: 37334371 PMCID: PMC10275407 DOI: 10.3389/fimmu.2023.1161849] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 05/24/2023] [Indexed: 06/20/2023] Open
Abstract
Interferon-beta (IFN-β) for Multiple Sclerosis (MS) is turning 30. The COVID-19 pandemic rejuvenated the interest in interferon biology in health and disease, opening translational opportunities beyond neuroinflammation. The antiviral properties of this molecule are in accord with the hypothesis of a viral etiology of MS, for which a credible culprit has been identified in the Epstein-Barr Virus. Likely, IFNs are crucial in the acute phase of SARS-CoV-2 infection, as demonstrated by inherited and acquired impairments of the interferon response that predispose to a severe COVID-19 course. Accordingly, IFN-β exerted protection against SARS-CoV-2 in people with MS (pwMS). In this viewpoint, we summarize the evidence on IFN-β mechanisms of action in MS with a focus on its antiviral properties, especially against EBV. We synopsize the role of IFNs in COVID-19 and the opportunities and challenges of IFN-β usage for this condition. Finally, we leverage the lessons learned in the pandemic to suggest a role of IFN-β in long-COVID-19 and in special MS subpopulations.
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Affiliation(s)
- Gianmarco Bellucci
- Department of Neurosciences, Mental Health and Sensory Organs, Centre for Experimental Neurological Therapies (CENTERS), Sapienza University of Rome, Rome, Italy
| | - Angela Albanese
- Merck Serono S.p.A., An Affiliate of Merck KGaA, Rome, Italy
- Department of Health Sciences, University of Genoa, Genoa, Italy
| | - Caterina Rizzi
- Merck Serono S.p.A., An Affiliate of Merck KGaA, Rome, Italy
| | - Virginia Rinaldi
- Department of Neurosciences, Mental Health and Sensory Organs, Centre for Experimental Neurological Therapies (CENTERS), Sapienza University of Rome, Rome, Italy
| | - Marco Salvetti
- Department of Neurosciences, Mental Health and Sensory Organs, Centre for Experimental Neurological Therapies (CENTERS), Sapienza University of Rome, Rome, Italy
- Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Neurologico Mediterraneo Neuromed, Pozzilli, Italy
| | - Giovanni Ristori
- Department of Neurosciences, Mental Health and Sensory Organs, Centre for Experimental Neurological Therapies (CENTERS), Sapienza University of Rome, Rome, Italy
- Neuroimmunology Unit, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS) Fondazione Santa Lucia, Rome, Italy
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35
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Li G, Hilgenfeld R, Whitley R, De Clercq E. Therapeutic strategies for COVID-19: progress and lessons learned. Nat Rev Drug Discov 2023; 22:449-475. [PMID: 37076602 PMCID: PMC10113999 DOI: 10.1038/s41573-023-00672-y] [Citation(s) in RCA: 127] [Impact Index Per Article: 127.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/28/2023] [Indexed: 04/21/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has stimulated tremendous efforts to develop therapeutic strategies that target severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and/or human proteins to control viral infection, encompassing hundreds of potential drugs and thousands of patients in clinical trials. So far, a few small-molecule antiviral drugs (nirmatrelvir-ritonavir, remdesivir and molnupiravir) and 11 monoclonal antibodies have been marketed for the treatment of COVID-19, mostly requiring administration within 10 days of symptom onset. In addition, hospitalized patients with severe or critical COVID-19 may benefit from treatment with previously approved immunomodulatory drugs, including glucocorticoids such as dexamethasone, cytokine antagonists such as tocilizumab and Janus kinase inhibitors such as baricitinib. Here, we summarize progress with COVID-19 drug discovery, based on accumulated findings since the pandemic began and a comprehensive list of clinical and preclinical inhibitors with anti-coronavirus activities. We also discuss the lessons learned from COVID-19 and other infectious diseases with regard to drug repurposing strategies, pan-coronavirus drug targets, in vitro assays and animal models, and platform trial design for the development of therapeutics to tackle COVID-19, long COVID and pathogenic coronaviruses in future outbreaks.
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Affiliation(s)
- Guangdi Li
- Xiangya School of Public Health, Central South University; Hunan Children's Hospital, Changsha, China.
| | - Rolf Hilgenfeld
- Institute of Molecular Medicine & German Center for Infection Research (DZIF), University of Lübeck, Lübeck, Germany.
| | - Richard Whitley
- Department of Paediatrics, Microbiology, Medicine and Neurosurgery, University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Erik De Clercq
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium.
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36
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Abaeva IS, Arhab Y, Miścicka A, Hellen CUT, Pestova TV. In vitro reconstitution of SARS CoV-2 Nsp1-induced mRNA cleavage reveals the key roles of the N-terminal domain of Nsp1 and the RRM domain of eIF3g. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.25.542379. [PMID: 37292671 PMCID: PMC10245999 DOI: 10.1101/2023.05.25.542379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
SARS CoV-2 nonstructural protein 1 (Nsp1) is the major pathogenesis factor that inhibits host translation using a dual strategy of impairing initiation and inducing endonucleolytic cleavage of cellular mRNAs. To investigate the mechanism of cleavage, we reconstituted it in vitro on β-globin, EMCV IRES and CrPV IRES mRNAs that use unrelated initiation mechanisms. In all instances, cleavage required Nsp1 and only canonical translational components (40S subunits and initiation factors), arguing against involvement of a putative cellular RNA endonuclease. Requirements for initiation factors differed for these mRNAs, reflecting their requirements for ribosomal attachment. Cleavage of CrPV IRES mRNA was supported by a minimal set of components consisting of 40S subunits and eIF3g's RRM domain. The cleavage site was located in the coding region 18 nucleotides downstream from the mRNA entrance indicating that cleavage occurs on the solvent side of the 40S subunit. Mutational analysis identified a positively charged surface on Nsp1's N-terminal domain (NTD) and a surface above the mRNA-binding channel on eIF3g's RRM domain that contain residues essential for cleavage. These residues were required for cleavage on all three mRNAs, highlighting general roles of Nsp1-NTD and eIF3g's RRM domain in cleavage per se, irrespective of the mode of ribosomal attachment.
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Affiliation(s)
- Irina S. Abaeva
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - Yani Arhab
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - Anna Miścicka
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | | | - Tatyana V. Pestova
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
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37
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Rodriguez-Rodriguez BA, Ciabattoni GO, Duerr R, Valero-Jimenez AM, Yeung ST, Crosse KM, Schinlever AR, Bernard-Raichon L, Rodriguez Galvan J, McGrath ME, Vashee S, Xue Y, Loomis CA, Khanna KM, Cadwell K, Desvignes L, Frieman MB, Ortigoza MB, Dittmann M. A neonatal mouse model characterizes transmissibility of SARS-CoV-2 variants and reveals a role for ORF8. Nat Commun 2023; 14:3026. [PMID: 37230979 PMCID: PMC10211296 DOI: 10.1038/s41467-023-38783-0] [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: 10/21/2022] [Accepted: 05/15/2023] [Indexed: 05/27/2023] Open
Abstract
Small animal models have been a challenge for the study of SARS-CoV-2 transmission, with most investigators using golden hamsters or ferrets. Mice have the advantages of low cost, wide availability, less regulatory and husbandry challenges, and the existence of a versatile reagent and genetic toolbox. However, adult mice do not robustly transmit SARS-CoV-2. Here we establish a model based on neonatal mice that allows for transmission of clinical SARS-CoV-2 isolates. We characterize tropism, respiratory tract replication and transmission of ancestral WA-1 compared to variants Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), Omicron BA.1 and Omicron BQ.1.1. We identify inter-variant differences in timing and magnitude of infectious particle shedding from index mice, both of which shape transmission to contact mice. Furthermore, we characterize two recombinant SARS-CoV-2 lacking either the ORF6 or ORF8 host antagonists. The removal of ORF8 shifts viral replication towards the lower respiratory tract, resulting in significantly delayed and reduced transmission in our model. Our results demonstrate the potential of our neonatal mouse model to characterize viral and host determinants of SARS-CoV-2 transmission, while revealing a role for an accessory protein in this context.
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Affiliation(s)
| | - Grace O Ciabattoni
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Ralf Duerr
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY, 10016, USA
- Department of Medicine/Division of Infectious Diseases and Immunology, New York University Grossman School of Medicine, New York, NY, 10016, USA
- Vaccine Center, NYU Grossmann of Medicine, New York, NY, 10016, USA
| | - Ana M Valero-Jimenez
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Stephen T Yeung
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Keaton M Crosse
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Austin R Schinlever
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Lucie Bernard-Raichon
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Joaquin Rodriguez Galvan
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Marisa E McGrath
- Department of Microbiology and Immunology, Center for Pathogen Research, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Sanjay Vashee
- Department of Synthetic Biology and Bioenergy, J. Craig Venter Institute, Rockville, MD, 20850, USA
| | - Yong Xue
- Department of Synthetic Biology and Bioenergy, J. Craig Venter Institute, Rockville, MD, 20850, USA
| | - Cynthia A Loomis
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Kamal M Khanna
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY, 10016, USA
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, 10016, USA
| | - Ken Cadwell
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Ludovic Desvignes
- Department of Medicine/Division of Infectious Diseases and Immunology, New York University Grossman School of Medicine, New York, NY, 10016, USA
- High Containment Laboratories - Office of Science and Research, NYU Langone Health, New York, NY, 10016, USA
| | - Matthew B Frieman
- Department of Microbiology and Immunology, Center for Pathogen Research, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Mila B Ortigoza
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY, 10016, USA.
- Department of Medicine/Division of Infectious Diseases and Immunology, New York University Grossman School of Medicine, New York, NY, 10016, USA.
| | - Meike Dittmann
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY, 10016, USA.
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Duncan JKS, Xu D, Licursi M, Joyce MA, Saffran HA, Liu K, Gohda J, Tyrrell DL, Kawaguchi Y, Hirasawa K. Interferon regulatory factor 3 mediates effective antiviral responses to human coronavirus 229E and OC43 infection. Front Immunol 2023; 14:930086. [PMID: 37197656 PMCID: PMC10183588 DOI: 10.3389/fimmu.2023.930086] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 03/27/2023] [Indexed: 05/19/2023] Open
Abstract
Interferon regulatory factors (IRFs) are key elements of antiviral innate responses that regulate the transcription of interferons (IFNs) and IFN-stimulated genes (ISGs). While the sensitivity of human coronaviruses to IFNs has been characterized, antiviral roles of IRFs during human coronavirus infection are not fully understood. Type I or II IFN treatment protected MRC5 cells from human coronavirus 229E infection, but not OC43. Cells infected with 229E or OC43 upregulated ISGs, indicating that antiviral transcription is not suppressed. Antiviral IRFs, IRF1, IRF3 and IRF7, were activated in cells infected with 229E, OC43 or severe acute respiratory syndrome-associated coronavirus 2 (SARS-CoV-2). RNAi knockdown and overexpression of IRFs demonstrated that IRF1 and IRF3 have antiviral properties against OC43, while IRF3 and IRF7 are effective in restricting 229E infection. IRF3 activation effectively promotes transcription of antiviral genes during OC43 or 229E infection. Our study suggests that IRFs may be effective antiviral regulators against human coronavirus infection.
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Affiliation(s)
- Joseph K. Sampson Duncan
- Division of BioMedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, NL, Canada
| | - Danyang Xu
- Division of BioMedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, NL, Canada
| | - Maria Licursi
- Division of BioMedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, NL, Canada
| | - Michael A. Joyce
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, Canada
| | - Holly A. Saffran
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, Canada
| | - Kaiwen Liu
- Division of BioMedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, NL, Canada
| | - Jin Gohda
- Research Center for Asian Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - D. Lorne Tyrrell
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, Canada
| | - Yasushi Kawaguchi
- Research Center for Asian Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Division of Molecular Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Kensuke Hirasawa
- Division of BioMedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, NL, Canada
- *Correspondence: Kensuke Hirasawa,
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