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Aghajani Mir M. Illuminating the pathogenic role of SARS-CoV-2: Insights into competing endogenous RNAs (ceRNAs) regulatory networks. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 122:105613. [PMID: 38844190 DOI: 10.1016/j.meegid.2024.105613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 05/20/2024] [Accepted: 05/31/2024] [Indexed: 06/10/2024]
Abstract
The appearance of SARS-CoV-2 in 2019 triggered a significant economic and health crisis worldwide, with heterogeneous molecular mechanisms that contribute to its development are not yet fully understood. Although substantial progress has been made in elucidating the mechanisms behind SARS-CoV-2 infection and therapy, it continues to rank among the top three global causes of mortality due to infectious illnesses. Non-coding RNAs (ncRNAs), being integral components across nearly all biological processes, demonstrate effective importance in viral pathogenesis. Regarding viral infections, ncRNAs have demonstrated their ability to modulate host reactions, viral replication, and host-pathogen interactions. However, the complex interactions of different types of ncRNAs in the progression of COVID-19 remains understudied. In recent years, a novel mechanism of post-transcriptional gene regulation known as "competing endogenous RNA (ceRNA)" has been proposed. Long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and viral ncRNAs function as ceRNAs, influencing the expression of associated genes by sequestering shared microRNAs. Recent research on SARS-CoV-2 has revealed that disruptions in specific ceRNA regulatory networks (ceRNETs) contribute to the abnormal expression of key infection-related genes and the establishment of distinctive infection characteristics. These findings present new opportunities to delve deeper into the underlying mechanisms of SARS-CoV-2 pathogenesis, offering potential biomarkers and therapeutic targets. This progress paves the way for a more comprehensive understanding of ceRNETs, shedding light on the intricate mechanisms involved. Further exploration of these mechanisms holds promise for enhancing our ability to prevent viral infections and develop effective antiviral treatments.
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Affiliation(s)
- Mahsa Aghajani Mir
- Deputy of Research and Technology, Babol University of Medical Sciences, Babol, Iran.
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2
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Adams SK, Ducharme GE, Loveday EK. All the single cells: if you like it then you should put some virus on it. J Virol 2024; 98:e0127323. [PMID: 38904395 DOI: 10.1128/jvi.01273-23] [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: 06/22/2024] Open
Abstract
Across a rich 70-year history, single-cell virology has revealed the impact of host and pathogen heterogeneity during virus infections. Recent technological innovations have enabled higher-resolution analyses of cellular and viral heterogeneity. Furthermore, single-cell analysis has revealed extreme phenotypes and provided additional insights into host-pathogen dynamics. Using a single-cell approach to explore fundamental virology questions, contemporary researchers have contributed to a revival of interest in single-cell virology with increased insights and enthusiasm.
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Affiliation(s)
- Sophia K Adams
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
| | - Grace E Ducharme
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, Montana, USA
| | - Emma K Loveday
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, Montana, USA
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3
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Ramirez-Martínez G. Editorial: Reviews in virus and host. Front Cell Infect Microbiol 2024; 14:1445721. [PMID: 39040599 PMCID: PMC11261525 DOI: 10.3389/fcimb.2024.1445721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2024] [Accepted: 06/25/2024] [Indexed: 07/24/2024] Open
Affiliation(s)
- Gustavo Ramirez-Martínez
- Laboratorio de Inmunobiología y Genética, Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
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4
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Fu CF, Li JL, Chen JW, Liang H, Zhao WR, He SY, Ma XW, Yang XF, Wang HL. Mechanism and therapeutic potential of traditional Chinese medicine extracts in sepsis. Front Pharmacol 2024; 15:1365639. [PMID: 39021837 PMCID: PMC11251979 DOI: 10.3389/fphar.2024.1365639] [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: 01/04/2024] [Accepted: 06/03/2024] [Indexed: 07/20/2024] Open
Abstract
Sepsis is a complex syndrome characterized by multi-organ dysfunction, due to the presence of harmful microorganisms in blood which could cause mortality. Complications associated with sepsis involve multiple organ dysfunction. The pathogenesis of sepsis remains intricate, with limited treatment options and high mortality rates. Traditional Chinese medicine (TCM) has consistently demonstrated to have a potential on various disease management. Its complements include reduction of oxidative stress, inhibiting inflammatory pathways, regulating immune responses, and improving microcirculation. Traditional Chinese medicine can mitigate or even treat sepsis in a human system. This review examines progress on the use of TCM extracts for treating sepsis through different pharmacological action and its mechanisms. The potential targets of TCM extracts and active ingredients for the treatment of sepsis and its complications have been elucidated through molecular biology research, network pharmacology prediction, molecular docking analysis, and visualization analysis. Our aim is to provide a theoretical basis and empirical support for utilizing TCM in the treatment of sepsis and its complications while also serving as a reference for future research and development of sepsis drugs.
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Affiliation(s)
- Chen-Fei Fu
- Heilongjiang University of Chinese Medicine, Harbin, China
| | - Jian-Long Li
- Heilongjiang University of Chinese Medicine, Harbin, China
| | | | - Hao Liang
- Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Wen-Rui Zhao
- Hongqi Hospital Affiliated to Mudanjiang Medical University, Mudanjiang, China
| | - Shi-Yu He
- Shenzhen Pingle Orthopedic Hospital, Shenzhen, China
| | - Xiao-Wei Ma
- Hongqi Hospital Affiliated to Mudanjiang Medical University, Mudanjiang, China
| | - Xiao-Fan Yang
- Hongqi Hospital Affiliated to Mudanjiang Medical University, Mudanjiang, China
| | - He-Lin Wang
- Donghuashi Community Health Service Center, Beijing, China
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5
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Zath GK, Thomas MM, Loveday EK, Bikos DA, Sanche S, Ke R, Brooke CB, Chang CB. Influenza A viral burst size from thousands of infected single cells using droplet quantitative PCR (dqPCR). PLoS Pathog 2024; 20:e1012257. [PMID: 38950082 PMCID: PMC11244780 DOI: 10.1371/journal.ppat.1012257] [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: 08/22/2023] [Revised: 07/12/2024] [Accepted: 05/13/2024] [Indexed: 07/03/2024] Open
Abstract
An important aspect of how viruses spread and infect is the viral burst size, or the number of new viruses produced by each infected cell. Surprisingly, this value remains poorly characterized for influenza A virus (IAV), commonly known as the flu. In this study, we screened tens of thousands of cells using a microfluidic method called droplet quantitative PCR (dqPCR). The high-throughput capability of dqPCR enabled the measurement of a large population of infected cells producing progeny virus. By measuring the fully assembled and successfully released viruses from these infected cells, we discover that the viral burst sizes for both the seasonal H3N2 and the 2009 pandemic H1N1 strains vary significantly, with H3N2 ranging from 101 to 104 viruses per cell, and H1N1 ranging from 101 to 103 viruses per cell. Some infected cells produce average numbers of new viruses, while others generate extensive number of viruses. In fact, we find that only 10% of the single-cell infections are responsible for creating a significant portion of all the viruses. This small fraction produced approximately 60% of new viruses for H3N2 and 40% for H1N1. On average, each infected cell of the H3N2 flu strain produced 709 new viruses, whereas for H1N1, each infected cell produced 358 viruses. This novel method reveals insights into the flu virus and can lead to improved strategies for managing and preventing the spread of viruses.
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Affiliation(s)
- Geoffrey K. Zath
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, United States of America
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, Montana, United States of America
| | - Mallory M. Thomas
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, United States of America
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota, United States of America
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, United States of America
| | - Emma K. Loveday
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, United States of America
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, Montana, United States of America
| | - Dimitri A. Bikos
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, United States of America
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, Montana, United States of America
| | - Steven Sanche
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Ruian Ke
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Christopher B. Brooke
- Department of Microbiology, University of Illinois, Urbana-Champaign, Urbana, Illinois, United States of America
| | - Connie B. Chang
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota, United States of America
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6
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Li S, Bu J, Pan X, Li Q, Zuo X, Xiao G, Du J, Zhang LK, Xia B, Gao Z. SARS-CoV-2 envelope protein-derived extracellular vesicles act as potential media for viral spillover. J Med Virol 2024; 96:e29782. [PMID: 39011762 DOI: 10.1002/jmv.29782] [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: 02/15/2024] [Revised: 06/13/2024] [Accepted: 06/25/2024] [Indexed: 07/17/2024]
Abstract
Extracellular vesicles (EVs) are shown to be a novel viral transmission model capable of increasing a virus's tropism. According to our earlier research, cells infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) or transfected with envelope protein plasmids generate a novel type of EVs that are micrometer-sized and able to encase virus particles. Here, we showed the capacity of these EVs to invade various animals both in vitro and in vivo independent of the angiotensin-converting enzyme 2 receptor. First, via macropinocytosis, intact EVs produced from Vero E6 (monkey) cells were able to enter cells from a variety of animals, including cats, dogs, bats, hamsters, and minks, and vice versa. Second, when given to zebrafish with cutaneous wounds, the EVs showed favorable stability in aqueous environments and entered the fish. Moreover, infection of wild-type (WT) mice with heterogeneous EVs carrying SARS-CoV-2 particles led to a strong cytokine response and a notable amount of lung damage. Conversely, free viral particles did not infect WT mice. These results highlight the variety of processes behind viral transmission and cross-species evolution by indicating that EVs may be possible vehicles for SARS-CoV-2 spillover and raising risk concerns over EVs' potential for viral gene transfer.
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Affiliation(s)
- Shuangqu Li
- Stake Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jiwen Bu
- State Key Laboratory of Neuroscience, Institute of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Xiaoyan Pan
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Qiguang Li
- Stake Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoli Zuo
- Stake Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Gengfu Xiao
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Jiulin Du
- State Key Laboratory of Neuroscience, Institute of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Lei-Ke Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, China
- Hubei Jiangxia Laboratory, Wuhan, Hubei, China
| | - Bingqing Xia
- Stake Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhaobing Gao
- Stake Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- Zhongshan Institute of Drug Discovery, Institution for Drug Discovery Innovation, 22 Chinese Academy of Science, Zhongshan, China
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7
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Kalemera MD, Maher AK, Dominguez-Villar M, Maertens GN. Cell Culture Evaluation Hints Widely Available HIV Drugs Are Primed for Success if Repurposed for HTLV-1 Prevention. Pharmaceuticals (Basel) 2024; 17:730. [PMID: 38931397 PMCID: PMC11206710 DOI: 10.3390/ph17060730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 05/15/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024] Open
Abstract
With an estimated 10 million people infected, the deltaretrovirus human T-cell lymphotropic virus type 1 (HTLV-1) is the second most prevalent pathogenic retrovirus in humans after HIV-1. Like HIV-1, HTLV-1 overwhelmingly persists in a host via a reservoir of latently infected CD4+ T cells. Although most patients are asymptomatic, HTLV-1-associated pathologies are often debilitating and include adult T-cell leukaemia/lymphoma (ATLL), which presents in mature adulthood and is associated with poor prognosis with short overall survival despite treatment. Curiously, the strongest indicator for the development of ATLL is the acquisition of HTLV-1 through breastfeeding. There are no therapeutic or preventative regimens for HTLV-1. However, antiretrovirals (ARVs), which target the essential retrovirus enzymes, have been developed for and transformed HIV therapy. As the architectures of retroviral enzyme active sites are highly conserved, some HIV-specific compounds are active against HTLV-1. Here, we expand on our work, which showed that integrase strand transfer inhibitors (INSTIs) and some nucleoside reverse transcriptase inhibitors (NRTIs) block HTLV-1 transmission in cell culture. Specifically, we find that dolutegravir, the INSTI currently recommended as the basis of all new combination antiretroviral therapy prescriptions, and the latest prodrug formula of the NRTI tenofovir, tenofovir alafenamide, also potently inhibit HTLV-1 infection. Our results, if replicated in a clinical setting, could see transmission rates of HTLV-1 and future caseloads of HTLV-1-associated pathologies like ATLL dramatically cut via the simple repurposing of already widely available HIV pills in HTLV-1 endemic areas. Considering our findings with the old medical saying "it is better to prevent than cure", we highly recommend the inclusion of INSTIs and tenofovir prodrugs in upcoming HTLV-1 clinical trials as potential prophylactics.
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Affiliation(s)
| | | | | | - Goedele N. Maertens
- Department of Infectious Disease, Imperial College London, London W2 1PG, UK; (M.D.K.); (A.K.M.); (M.D.-V.)
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8
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Hagan MF, Zandi R, Uetrecht C. Overview of the 2023 Physical Virology Gordon Research Conference-Viruses at Multiple Levels of Complexity. Viruses 2024; 16:895. [PMID: 38932189 PMCID: PMC11209351 DOI: 10.3390/v16060895] [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: 05/27/2024] [Accepted: 05/29/2024] [Indexed: 06/28/2024] Open
Abstract
This review accompanies the Special Issue on the subject of physical virology, which features work presented at the recent Gordon Research Conference (GRC) on this topic [...].
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Affiliation(s)
- Michael F. Hagan
- Martin Fisher School of Physics, Brandeis University, Waltham, MA 02453, USA
| | - Roya Zandi
- Department of Physics and Astronomy, University of California Riverside, Riverside, CA 92521, USA
| | - Charlotte Uetrecht
- CSSB Centre for Structural Systems Biology, Deutsches Elektronen Synchrotron DESY, Leibniz Institute of Virology (LIV), 22607 Hamburg, Germany
- Institute of Chemistry and Metabolomics, University Lübeck, 23562 Lübeck, Germany
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9
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Browning AP, Jenner AL, Baker RE, Maini PK. Smoothing in linear multicompartment biological processes subject to stochastic input. Phys Rev E 2024; 109:054405. [PMID: 38907461 DOI: 10.1103/physreve.109.054405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 04/01/2024] [Indexed: 06/24/2024]
Abstract
Many physical and biological systems rely on the progression of material through multiple independent stages. In viral replication, for example, virions enter a cell to undergo a complex process comprising several disparate stages before the eventual accumulation and release of replicated virions. While such systems may have some control over the internal dynamics that make up this progression, a challenge for many is to regulate behavior under what are often highly variable external environments acting as system inputs. In this work, we study a simple analog of this problem through a linear multicompartment model subject to a stochastic input in the form of a mean-reverting Ornstein-Uhlenbeck process, a type of Gaussian process. By expressing the system as a multidimensional Gaussian process, we derive several closed-form analytical results relating to the covariances and autocorrelations of the system, quantifying the smoothing effect discrete compartments afford multicompartment systems. Semianalytical results demonstrate that feedback and feedforward loops can enhance system robustness, and simulation results probe the intractable problem of the first passage time distribution, which has specific relevance to eventual cell lysis in the viral replication cycle. Finally, we demonstrate that the smoothing seen in the process is a consequence of the discreteness of the system, and does not manifest in systems with continuous transport. While we make progress through analysis of a simple linear problem, many of our insights are applicable more generally, and our work enables future analysis into multicompartment processes subject to stochastic inputs.
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Affiliation(s)
| | - Adrianne L Jenner
- School of Mathematical Sciences, Queensland University of Technology, Brisbane 4000, Australia
| | - Ruth E Baker
- Mathematical Institute, University of Oxford, Oxford OX2 6GG, United Kingdom
| | - Philip K Maini
- Mathematical Institute, University of Oxford, Oxford OX2 6GG, United Kingdom
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10
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Pereira TA, Espósito BP. Can iron chelators ameliorate viral infections? Biometals 2024; 37:289-304. [PMID: 38019378 DOI: 10.1007/s10534-023-00558-x] [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: 08/29/2023] [Accepted: 10/25/2023] [Indexed: 11/30/2023]
Abstract
The redox reactivity of iron is a double-edged sword for cell functions, being either essential or harmful depending on metal concentration and location. Deregulation of iron homeostasis is associated with several clinical conditions, including viral infections. Clinical studies as well as in silico, in vitro and in vivo models show direct effects of several viruses on iron levels. There is support for the strategy of iron chelation as an alternative therapy to inhibit infection and/or viral replication, on the rationale that iron is required for the synthesis of some viral proteins and genes. In addition, abnormal iron levels can affect signaling immune response. However, other studies report different effects of viral infections on iron homeostasis, depending on the class and genotype of the virus, therefore making it difficult to predict whether iron chelation would have any benefit. This review brings general aspects of the relationship between iron homeostasis and the nonspecific immune response to viral infections, along with its relevance to the progress or inhibition of the inflammatory process, in order to elucidate situations in which the use of iron chelators could be efficient as antivirals.
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11
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Xue Y, Ma Y, Sun Z, Liu X, Zhang M, Zhang J, Xi N. Identification and Measurement of Biomarkers at Single Microorganism Level for In Situ Monitoring Deep Ultraviolet Disinfection Process. IEEE Trans Nanobioscience 2024; 23:242-251. [PMID: 37676797 DOI: 10.1109/tnb.2023.3312754] [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: 09/09/2023]
Abstract
Since the COVID-19 disease has been further aggravated, the prevention of pathogen transmission becomes a vital issue to restrain casualties. Recent research outcomes have shown the possibilities of the viruses existing on inanimate surfaces up to few days, which carry the risk of touch propagation of the disease. Deep ultraviolet germicide irradiation (UVGI) with the wavelength of 255-280nm has been verified to efficiently disinfect various types of bacteria and virus, which could prevent the aggravation of pandemic spread. Even though considerable experiments and approaches have been applied to evaluate the disinfection effects, there are only few reports about how the individual bio-organism behaves after ultraviolet C (UVC) irradiation, especially in the aspect of mechanical changes. Furthermore, since the standard pathway of virus transmission and reproduction requires the host cell to assemble and transport newly generated virus, the dynamic response of infectious cell is always the vital aspect of virology study. In this work, high power LEDs array has been established with 270nm UVC irradiation to evaluate disinfection capability on various types of bio-organism, and incubator embedded atomic force microscopy (AFM) is used to investigate the single bacterium and virus under UVGI. The real-time tracking of the living Vero cells infected with adenovirus has also been presented in this study. The results show that after sufficient UVGI, the outer shell of bacteria and viruses remain intact in structure, however the bio-organisms lost the capability of reproduction and normal metabolism. The experiment results also indicate that once the host cell is infected with adenovirus, the rapid production of newborn virus capsid will gradually destroy the cellular normal metabolism and lose mechanical integrity.
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12
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Stergiopoulos GM, Iankov I, Galanis E. Personalizing Oncolytic Immunovirotherapy Approaches. Mol Diagn Ther 2024; 28:153-168. [PMID: 38150172 DOI: 10.1007/s40291-023-00689-4] [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] [Accepted: 12/03/2023] [Indexed: 12/28/2023]
Abstract
Development of successful cancer therapeutics requires exploration of the differences in genetics, metabolism, and interactions with the immune system among malignant and normal cells. The clinical observation of spontaneous tumor regression following natural infection with microorganism has created the premise of their use as cancer therapeutics. Oncolytic viruses (OVs) originate from viruses with attenuated virulence in humans, well-characterized vaccine strains of known human pathogens, or engineered replication-deficient viral vectors. Their selectivity is based on receptor expression level and post entry restriction factors that favor replication in the tumor, while keeping the normal cells unharmed. Clinical trials have demonstrated a wide range of patient responses to virotherapy, with subgroups of patients significantly benefiting from OV administration. Tumor-specific gene signatures, including antiviral interferon-stimulated gene (ISG) expression profile, have demonstrated a strong correlation with tumor permissiveness to infection. Furthermore, the combination of OVs with immunotherapeutics, including anticancer vaccines and immune checkpoint inhibitors [ICIs, such as anti-PD-1/PD-L1 or anti-CTLA-4 and chimeric antigen receptor (CAR)-T or CAR-NK cells], could synergistically improve the therapeutic outcome. Creating response prediction algorithms represents an important step for the transition to individualized immunovirotherapy approaches in the clinic. Integrative predictors could include tumor mutational burden (TMB), inflammatory gene signature, phenotype of tumor-infiltrating lymphocytes, tumor microenvironment (TME), and immune checkpoint receptor expression on both immune and target cells. Additionally, the gut microbiota has recently been recognized as a systemic immunomodulatory factor and could further be used in the optimization of individualized immunovirotherapy algorithms.
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Affiliation(s)
| | - Ianko Iankov
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA.
| | - Evanthia Galanis
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA.
- Department of Oncology, Mayo Clinic, Rochester, MN, USA.
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13
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Vanderpas J, Dramaix M, Coppieters Y. Wording the trajectory of the three-year COVID-19 epidemic in a general population - Belgium. BMC Public Health 2024; 24:638. [PMID: 38424526 PMCID: PMC10903008 DOI: 10.1186/s12889-024-17951-x] [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: 07/27/2023] [Accepted: 02/01/2024] [Indexed: 03/02/2024] Open
Abstract
The trajectory of COVID-19 epidemic waves in the general population of Belgium was analysed by defining quantitative criteria for epidemic waves from March 2020 to early 2023. Peaks and starting/ending times characterised nine waves numerated I to IX based on the daily reported incidence number (symbol INCID) and three "endemic" interval periods between the first four waves. The SIR compartmental model was applied to the first epidemic wave by fitting the daily prevalence pool (symbol I) calculated as the sum of the daily incidence rate and estimated number of subjects still infectious from the previous days. The basic reproductive number R0 was calculated based on the exponential growth rate during the early phase and on medical literature knowledge of the time of generation of SARS-CoV-2 infection. The first COVID-19 wave was well fitted by an open SIR model. According to this approach, dampened recurrent epidemic waves evolving through an endemic state would have been expected. This was not the case with the subsequent epidemic waves being characterised by new variants of concern (VOC). Evidence-based observations: 1) each epidemic wave affected less than a fifth of the general population; 2) the Vth epidemic wave (VOC Omicron) presented the greatest amplitude. The lack of recurrence of the same VOC during successive epidemic waves strongly suggests that a VOC has a limited persistence, disappearing from the population well before the expected proportion of the theoretical susceptible cohort being maximally infected. Fitting the theoretical SIR model, a limited persistence of VOCs in a population could explain that new VOCs replace old ones, even if the new VOC has a lower transmission rate than the preceding one. In conclusion, acquisition of potential defective mutations in VOC during an epidemic wave is a potential factor explaining the absence of resurgence of a same VOC during successive waves. Such an hypothesis is open to discussion and to rebuttal. A modified SIR model with epidemic waves of variable amplitude related not only to R0 and public health measures but also to acquisition of defective fitting in virus within a population should be tested.
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Affiliation(s)
- Jean Vanderpas
- Centre de recherche Epidémiologie, biostatistiques, recherche clinique, School of Public Health, Université libre de Bruxelles (ULB), Route de Lennik 808, 596, 1070, Brussels, CP, Belgium.
| | - Michèle Dramaix
- Centre de recherche Epidémiologie, biostatistiques, recherche clinique, School of Public Health, Université libre de Bruxelles (ULB), Route de Lennik 808, 596, 1070, Brussels, CP, Belgium
| | - Yves Coppieters
- Centre de recherche Epidémiologie, biostatistiques, recherche clinique, School of Public Health, Université libre de Bruxelles (ULB), Route de Lennik 808, 596, 1070, Brussels, CP, Belgium
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14
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Lomont JP, Smith JP. In situ process analytical technology for real time viable cell density and cell viability during live-virus vaccine production. Int J Pharm 2024; 649:123630. [PMID: 38040394 DOI: 10.1016/j.ijpharm.2023.123630] [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: 09/15/2023] [Revised: 11/13/2023] [Accepted: 11/19/2023] [Indexed: 12/03/2023]
Abstract
Viable cell density (VCD) and cell viability (CV) are key performance indicators of cell culture processes in biopharmaceutical production of biologics and vaccines. Traditional methods for monitoring VCD and CV involve offline cell counting assays that are both labor intensive and prone to high variability, resulting in sparse sampling and uncertainty in the obtained data. Process analytical technology (PAT) approaches offer a means to address these challenges. Specifically, in situ probe-based measurements of dielectric spectroscopy (also commonly known as capacitance) can characterize VCD and CV continuously in real time throughout an entire process, enabling robust process characterization. In this work, we propose in situ dielectric spectroscopy as a PAT tool for real time analysis of live-virus vaccine (LVV) production. Dielectric spectroscopy was collected across 25 discreet frequencies, offering a thorough evaluation of the proposed technology. Correlation of this PAT methodology to traditional offline cell counting assays was performed, in which VCD and CV were both successfully predicted using dielectric spectroscopy. Both univariate and multivariate data analysis approaches were evaluated for their potential to establish correlation between the in situ dielectric spectroscopy and offline measurements. Univariate analysis strategies are presented for optimal single frequency selection. Multivariate analysis, in the form of partial least squares (PLS) regression, produced significantly higher correlations between dielectric spectroscopy and offline VCD and CV data, as compared to univariate analysis. Specifically, by leveraging multivariate analysis of dielectric information from all 25 spectroscopic frequencies measured, PLS models performed significantly better than univariate models. This is particularly evident during cell death, where tracking VCD and CV have historically presented the greatest challenge. The results of this work demonstrate the potential of both single and multiple frequency dielectric spectroscopy measurements for enabling robust LVV process characterization, suggesting that broader application of in situ dielectric spectroscopy as a PAT tool in LVV processes can provide significantly improved process understanding. To the best of our knowledge, this is the first report of in situ dielectric spectroscopy with multivariate analysis to successfully predict VCD and CV in real time during live virus-based vaccine production.
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Affiliation(s)
- Justin P Lomont
- Analytical Research & Development, MRL, Merck & Co., Inc., West Point, PA 19486, USA.
| | - Joseph P Smith
- Process Research & Development, MRL, Merck & Co., Inc., West Point, PA 19486, USA.
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15
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Xiong L, Li Y, Zeng K, Wei Y, Li H, Ji X. Revealing viral diversity in the Napahai plateau wetland based on metagenomics. Antonie Van Leeuwenhoek 2023; 117:3. [PMID: 38153618 DOI: 10.1007/s10482-023-01912-2] [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: 08/30/2023] [Accepted: 11/22/2023] [Indexed: 12/29/2023]
Abstract
We focused on exploring the diversity of viruses in the Napahai plateau wetland, a unique ecosystem located in Yunnan, China. While viruses in marine environments have been extensively studied for their influence on microbial metabolism and biogeochemical cycles, little is known about their composition and function in plateau wetlands. Metagenomic analysis was employed to investigate the viral diversity and biogeochemical impacts in the Napahai wetland. It revealed that the Caudoviricetes and Malgrandaviricetes class level was the most abundant viral category based on phylogenetic analysis. Additionally, a gene-sharing network highlighted the presence of numerous unexplored viruses and demonstrated their unique characteristics and significant variation within the viral community of the Napahai wetland. Furthermore, the study identified the auxiliary metabolic genes (AMGs). AMGs provide phages with additional functions, such as protection against host degradation and involvement in metabolic pathways, such as the pentose phosphate pathway and DNA biosynthesis. The viruses in the Napahai wetland were found to influence carbon, nitrogen, sulfur, and amino acid metabolism, indirectly contributing to biogeochemical cycling through these AMGs. Overall, the research sheds light on the diverse and unique viral communities in the Napahai plateau wetland and emphasizes the significant roles of viruses in microbial ecology. The findings contribute to a deeper understanding of the characteristics and ecological functions of viral communities in plateau wetland ecosystems.
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Affiliation(s)
- Lingling Xiong
- Faculty of Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Yanmei Li
- Faculty of Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Kun Zeng
- Faculty of Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Yunlin Wei
- Faculty of Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Haiyan Li
- Medical School, Kunming University of Science and Technology, Kunming, 650500, China.
| | - Xiuling Ji
- Faculty of Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China.
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16
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Zhao L, Song R, Liu Y. Glycolytic metabolite phosphoenolpyruvate protects host from viral infection through promoting AATK expression. Eur J Immunol 2023; 53:e2350536. [PMID: 37724936 DOI: 10.1002/eji.202350536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 08/23/2023] [Accepted: 09/18/2023] [Indexed: 09/21/2023]
Abstract
Viral infections can result in metabolism rewiring of host cells, which in turn affects the viral lifecycle. Phosphoenolpyruvate (PEP), a metabolic intermediate in the glycolytic pathway, plays important roles in several biological processes including anti-tumor T cell immunity. However, whether PEP might participate in modulating viral infection remains largely unknown. Here, we demonstrate that PEP generally inhibits viral replication via upregulation of apoptosis-associated tyrosine kinase (AATK) expression. Targeted metabolomic analyses have shown that the intracellular level of PEP was increased upon viral infection. PEP treatment significantly restricted viral infection and hence declined subsequent inflammatory response both in vitro and in vivo. Besides, PEP took inhibitory effect on the stage of viral replication and also decreased the mortality of mice with viral infection. Mechanistically, PEP significantly promoted the expression of AATK. Knockdown of AATK led to enhanced viral replication and consequent increased levels of cytokines. Moreover, AATK deficiency disabled the antiviral effect of PEP. Together, our study reveals a previously unknown role of PEP in broadly inhibiting viral replication by promoting AATK expression, highlighting the potential application of activation or upregulation of the PEP-AATK axis in controlling viral infections.
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Affiliation(s)
- Lu Zhao
- Department of Immunology, Center for Immunotherapy, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Renjie Song
- Department of Immunology, Center for Immunotherapy, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Yang Liu
- Department of Immunology, Center for Immunotherapy, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
- Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences, Suzhou, China
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17
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Moore DS. On the evolution of epigenetics via exaptation: A developmental systems perspective. Ann N Y Acad Sci 2023; 1529:21-32. [PMID: 37750405 DOI: 10.1111/nyas.15065] [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] [Indexed: 09/27/2023]
Abstract
Evolution and development are interrelated processes influenced by genomic, epigenetic, and environmental factors. Epigenetic processes serve critical roles in development and operate as intermediaries that connect the genome to the rest of the world. Therefore, it is of interest to consider the evolution of epigenetic processes. The developmental systems perspective offers a distinctive, coherent, integrative way to understand the relationships between evolution, epigenetics, development, and the effects of experienced contexts. By adopting this perspective, this paper draws attention to the role of exaptation in the evolution of epigenetics in the RNA world and addresses the role of epigenetics in the later evolution of developmental processes such as cellular differentiation, learning, and memory. In so doing, the paper considers the appearance and functions of epigenetics in evolutionary history-sketching a pathway by which epigenetic processes might have evolved via exaptation and then contributed to the later development and evolution of phenotypes.
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Affiliation(s)
- David S Moore
- Psychology Field Group, Pitzer College, Claremont, California, USA
- Division of Behavioral & Organizational Sciences, Claremont Graduate University, Claremont, California, USA
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18
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Bruurs LJM, Müller M, Schipper JG, Rabouw HH, Boersma S, van Kuppeveld FJM, Tanenbaum ME. Antiviral responses are shaped by heterogeneity in viral replication dynamics. Nat Microbiol 2023; 8:2115-2129. [PMID: 37814072 PMCID: PMC10627821 DOI: 10.1038/s41564-023-01501-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 09/01/2023] [Indexed: 10/11/2023]
Abstract
Antiviral signalling, which can be activated in host cells upon virus infection, restricts virus replication and communicates infection status to neighbouring cells. The antiviral response is heterogeneous, both quantitatively (efficiency of response activation) and qualitatively (transcribed antiviral gene set). To investigate the basis of this heterogeneity, we combined Virus Infection Real-time IMaging (VIRIM), a live-cell single-molecule imaging method, with real-time readouts of the dsRNA sensing pathway to analyse the response of human cells to encephalomyocarditis virus (EMCV) infection. We find that cell-to-cell heterogeneity in viral replication rates early in infection affect the efficiency of antiviral response activation, with lower replication rates leading to more antiviral response activation. Furthermore, we show that qualitatively distinct antiviral responses can be linked to the strength of the antiviral signalling pathway. Our analyses identify variation in early viral replication rates as an important parameter contributing to heterogeneity in antiviral response activation.
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Grants
- ERC starting grant (EU/ERC-677936 RNAREG), NWO klein-2 grant (OCENW.KLEIN.344), Howard Hughes Medical Institute international research scholar grant (HHMI/IRS 55008747), Oncode Institute
- ERC starting grant (EU/ERC-677936 RNAREG), NWO klein-2 grant (OCENW.KLEIN.344), Oncode Institute
- NWO klein-2 grant (OCENW.KLEIN.344), NWO VICI (91812628)
- NWO VICI (91812628), ERC starting grant (EU/ERC-677936 RNAREG), Oncode Institute
- ERC starting grant (EU/ERC-677936 RNAREG), Howard Hughes Medical Institute international research scholar grant (HHMI/IRS 55008747), Oncode Institute
- Howard Hughes Medical Institute international research scholar grant (HHMI/IRS 55008747), Oncode Institute
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Affiliation(s)
- Lucas J M Bruurs
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Micha Müller
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jelle G Schipper
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Huib H Rabouw
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Sanne Boersma
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Frank J M van Kuppeveld
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Marvin E Tanenbaum
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands.
- Department of Bionanoscience, Delft University of Technology, Delft, the Netherlands.
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19
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Morabito KM, Cassetti MC, DeRocco AJ, Deschamps AM, Pierson TC. Viral Prototypes for Pandemic Preparedness: The Road Ahead. J Infect Dis 2023; 228:S460-S464. [PMID: 37849396 PMCID: PMC10582320 DOI: 10.1093/infdis/jiad267] [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: 10/19/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic demonstrated how rapidly vaccines and monoclonal antibodies (mAbs) could be deployed when the field is prepared to respond to a novel virus, serving as proof of concept that the prototype pathogen approach is feasible. This success was built upon decades of foundational research, including the characterization of protective antigens and coronavirus immunity leading to the development and validation of a generalizable vaccine approach for multiple coronaviruses. For other virus families of pandemic concern, the field is less prepared. The articles in this special issue have highlighted research gaps that need to be addressed to accelerate the development of effective vaccines and mAbs, to identify generalizable vaccine and mAb strategies, and to increase preparedness against other pandemic threats. Successful implementation of the prototype pathogen approach will require a systematic, multidisciplinary, coordinated approach with expertise and crosstalk among researchers of different virus families.
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Affiliation(s)
- Kaitlyn M Morabito
- Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - M Cristina Cassetti
- Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Amanda J DeRocco
- Office of the Director, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Anne M Deschamps
- Office of the Director, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Theodore C Pierson
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
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20
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Li J, Zhao Y, Dai Y, Zhao J. Identification of γ-Fagarine as a novel antiviral agent against respiratory virus (hMPV) infection. Virus Res 2023; 336:199223. [PMID: 37734492 PMCID: PMC10522984 DOI: 10.1016/j.virusres.2023.199223] [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: 06/11/2023] [Revised: 09/12/2023] [Accepted: 09/13/2023] [Indexed: 09/23/2023]
Abstract
Human metapneumovirus (hMPV) causes significant upper and lower respiratory disease in all age groups worldwide. However, there is no licensed drugs or vaccine available against hMPV. γ-Fagarine, an alkaloid isolated from the root of zanthoxylum, has been reported to be effective in the treatment of cancer, inflammatory diseases and antivirals. However, little is known about the inhibitory effect of γ-Fagarine against respiratory virus infection and the mechanism. In this study, we aim to investigate the effect of γ-Fagarine on hMPV infection and explore its underlying molecular mechanisms. Vero-E6 and 16HBE cells were used as cell models. Virus replication and microcosm character were explored in Vero-E6 cells. Then, the antiviral activities were investigated by quantitative real-time PCR (RT-qPCR), western blotting (WB), and indirect immunofluorescence assays (IFAs) in Vero-E6 and 16HBE. Potential mechanisms of γ-Fagarine related to HSPG and lysosome pH were assessed in 16HBE cells. Lastly, a virus-infected mouse model was established and antiviral assay in vivo was conducted. γ-Fagarine showed no toxicity toward Vero-E6 cells and 16HBE cells but demonstrated anti-hMPV activity. Virus titers of γ-Fagarine group were reduced to 33% and 45% of the hMPV groups, respectively. Besides, mechanistic studies revealed that γ-Fagarine could inhibit hMPV by dual mechanisms of direct restraining virus binding with HSPG and influencing lysosome pH. Furthermore, oral delivery of γ-Fagarine to hMPV-infected mice at a dosage of 25 mg/kg reduced the hMPV load in lung tissues. After γ-Fagarine treatment, pathological damage caused by viral infection was also ameliorated. These findings suggest that γ-Fagarine has antiviral effects in vitro and in vivo, which are associated with its ability to restrain virus binding with HSPG and influence lysosome pH, thus indicating that γ-Fagarine has the potential to serve as a candidate to fight against hMPV infection and other respiratory viruses such as influenza viruses and SARS-CoV-2.
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Affiliation(s)
- Jinhua Li
- Department of Pharmacognosy, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Yao Zhao
- Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing 400014, China
| | - Ying Dai
- Translational Chinese Medicine Key Laboratory of Sichuan Province, Sichuan Academy of Chinese Medicine Sciences, Sichuan Institute for Translational Chinese Medicine, Chengdu, Sichuan 610041, China
| | - Junning Zhao
- Department of Pharmacognosy, West China School of Pharmacy, Sichuan University, Chengdu 610041, China; National Key Laboratory of Drug Regulatory Science, National Medical Products Administration (NMPA), Beijing 100038, China.
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21
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Ezz Eldin RR, Saleh MA, Alwarsh SA, Rushdi A, Althoqapy AA, El Saeed HS, Abo Elmaaty A. Design and Synthesis of Novel 5-((3-(Trifluoromethyl)piperidin-1-yl)sulfonyl)indoline-2,3-dione Derivatives as Promising Antiviral Agents: In Vitro, In Silico, and Structure-Activity Relationship Studies. Pharmaceuticals (Basel) 2023; 16:1247. [PMID: 37765055 PMCID: PMC10534365 DOI: 10.3390/ph16091247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 07/29/2023] [Accepted: 08/01/2023] [Indexed: 09/29/2023] Open
Abstract
Herein, a series of new isatin derivatives was designed and synthesized (1-9) as broad-spectrum antiviral agents. Consequently, the antiviral activities of the synthesized compounds (1-9) were pursued against three viruses, namely influenza virus (H1N1), herpes simplex virus 1 (HSV-1), and coxsackievirus B3 (COX-B3). In particular, compounds 9, 5, and 4 displayed the highest antiviral activity against H1N1, HSV-1, and COX-B3 with IC50 values of 0.0027, 0.0022, and 0.0092 µM, respectively. Compound 7 was the safest, with a CC50 value of 315,578.68 µM. Moreover, a quantitative PCR (real-time PCR) assay was carried out for the most relevant compounds. The selected compounds exhibited a decrease in viral gene expression. Additionally, the conducted in silico studies emphasized the binding affinities of the synthesized compounds and their reliable pharmacokinetic properties as well. Finally, a structure-antiviral activity relationship study was conducted to anticipate the antiviral activity change upon future structural modification.
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Affiliation(s)
- Rogy R. Ezz Eldin
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Port Said University, Port Said 42526, Egypt
| | - Marwa A. Saleh
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo 11651, Egypt; (M.A.S.); (H.S.E.S.)
| | - Sefat A. Alwarsh
- Department of Science, Prince Sultan Military College of Health Sciences, Dhahran 31932, Saudi Arabia;
| | - Areej Rushdi
- Department of Medical Microbiology and Immunology, Faculty of Medicine for Girls, Al-Azhar University, Cairo 11651, Egypt; (A.R.); (A.A.A.)
| | - Azza Ali Althoqapy
- Department of Medical Microbiology and Immunology, Faculty of Medicine for Girls, Al-Azhar University, Cairo 11651, Egypt; (A.R.); (A.A.A.)
| | - Hoda S. El Saeed
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo 11651, Egypt; (M.A.S.); (H.S.E.S.)
| | - Ayman Abo Elmaaty
- Medicinal Chemistry Department, Faculty of Pharmacy, Port Said University, Port Said 42526, Egypt
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22
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Sun YQ, Chen JJ, Liu MC, Zhang YY, Wang T, Che TL, Li TT, Liu YN, Teng AY, Wu BZ, Hong XG, Xu Q, Lv CL, Jiang BG, Liu W, Fang LQ. Mapping global zoonotic niche and interregional transmission risk of monkeypox: a retrospective observational study. Global Health 2023; 19:58. [PMID: 37592305 PMCID: PMC10436417 DOI: 10.1186/s12992-023-00959-0] [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: 06/19/2023] [Accepted: 07/31/2023] [Indexed: 08/19/2023] Open
Abstract
BACKGROUND Outbreaks of monkeypox have been ongoing in non-endemic countries since May 2022. A thorough assessment of its global zoonotic niche and potential transmission risk is lacking. METHODS We established an integrated database on global monkeypox virus (MPXV) occurrence during 1958 - 2022. Phylogenetic analysis was performed to examine the evolution of MPXV and effective reproductive number (Rt) was estimated over time to examine the dynamic of MPXV transmissibility. The potential ecological drivers of zoonotic transmission and inter-regional transmission risks of MPXV were examined. RESULTS As of 24 July 2022, a total of 49 432 human patients with MPXV infections have been reported in 78 countries. Based on 525 whole genome sequences, two main clades of MPXV were formed, of which Congo Basin clade has a higher transmissibility than West African clade before the 2022-monkeypox, estimated by the overall Rt (0.81 vs. 0.56), and the latter significantly increased in the recent decade. Rt of 2022-monkeypox varied from 1.14 to 4.24 among the 15 continuously epidemic countries outside Africa, with the top three as Peru (4.24, 95% CI: 2.89-6.71), Brazil (3.45, 95% CI: 1.62-7.00) and the United States (2.44, 95% CI: 1.62-3.60). The zoonotic niche of MPXV was associated with the distributions of Graphiurus lorraineus and Graphiurus crassicaudatus, the richness of Rodentia, and four ecoclimatic indicators. Besides endemic areas in Africa, more areas of South America, the Caribbean States, and Southeast and South Asia are ecologically suitable for the occurrence of MPXV once the virus has invaded. Most of Western Europe has a high-imported risk of monkeypox from Western Africa, whereas France and the United Kingdom have a potential imported risk of Congo Basin clade MPXV from Central Africa. Eleven of the top 15 countries with a high risk of MPXV importation from the main countries of 2022-monkeypox outbreaks are located at Europe with the highest risk in Italy, Ireland and Poland. CONCLUSIONS The suitable ecological niche for MPXV is not limited to Africa, and the transmissibility of MPXV was significantly increased during the 2022-monkeypox outbreaks. The imported risk is higher in Europe, both from endemic areas and currently epidemic countries. Future surveillance and targeted intervention programs are needed in its high-risk areas informed by updated prediction.
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Affiliation(s)
- Yan-Qun Sun
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dong-Da Street, Fengtai District, Beijing, 100071, China
- Nanjing Municipal Center for Disease Control and Prevention, Affiliated Nanjing Center for Disease Control and Prevention of Nanjing Medical University, Nanjing, China
| | - Jin-Jin Chen
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dong-Da Street, Fengtai District, Beijing, 100071, China
| | - Mei-Chen Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dong-Da Street, Fengtai District, Beijing, 100071, China
- School of Public Health, Anhui Medical University, Hefei, 230032, China
| | - Yuan-Yuan Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dong-Da Street, Fengtai District, Beijing, 100071, China
| | - Tao Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dong-Da Street, Fengtai District, Beijing, 100071, China
| | - Tian-Le Che
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dong-Da Street, Fengtai District, Beijing, 100071, China
| | - Ting-Ting Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dong-Da Street, Fengtai District, Beijing, 100071, China
- School of Public Health, Guizhou Medical University, Guiyang, 550025, China
| | - Yan-Ning Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dong-Da Street, Fengtai District, Beijing, 100071, China
| | - Ai-Ying Teng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dong-Da Street, Fengtai District, Beijing, 100071, China
| | - Bing-Zheng Wu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dong-Da Street, Fengtai District, Beijing, 100071, China
| | - Xue-Geng Hong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dong-Da Street, Fengtai District, Beijing, 100071, China
| | - Qiang Xu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dong-Da Street, Fengtai District, Beijing, 100071, China
| | - Chen-Long Lv
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dong-Da Street, Fengtai District, Beijing, 100071, China
| | - Bao-Gui Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dong-Da Street, Fengtai District, Beijing, 100071, China
| | - Wei Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dong-Da Street, Fengtai District, Beijing, 100071, China.
| | - Li-Qun Fang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dong-Da Street, Fengtai District, Beijing, 100071, China.
- School of Public Health, Anhui Medical University, Hefei, 230032, China.
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23
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Andronico LA, Jung SR, Fujimoto BS, Chiu DT. Improving Multicolor Colocalization in Single-Vesicle Flow Cytometry with Vesicle Transit Time. Anal Chem 2023; 95:10492-10497. [PMID: 37403691 PMCID: PMC10357400 DOI: 10.1021/acs.analchem.3c01197] [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: 03/18/2023] [Accepted: 06/21/2023] [Indexed: 07/06/2023]
Abstract
Immunophenotyping of vesicles, such as extracellular vesicles (EVs), is essential to understanding their origin and biological role. We previously described a custom-built flow analyzer that utilizes a gravity-driven flow, high numerical aperture objective, and micrometer-sized flow channels to reach the sensitivity needed for fast multidimensional analysis of the surface proteins of EVs, even down to the smallest EVs (e.g., ∼30-40 nm). It is difficult to flow focus small EVs, and thus, the transiting EVs exhibit a distribution in particle velocities due to the laminar flow. This distribution of vesicle velocities leads to potentially incorrect results when immunophenotyping nanometer-sized vesicles using cross-correlation analysis (Xcorr), as the order of appearance of the vesicles might not be the same at different spatially offset laser excitation regions. Here, we describe an alternative cross-correlation analysis strategy (Scorr), which uses information on particle transit time across the laser excitation beam width to improve multicolor colocalization in single-vesicle immunoprofiling. We tested the performance of the algorithm for colocalization analysis of multicolor nanobeads and EVs experimentally and via simulations and found that Scorr improved both the efficiency and accuracy of colocalization versus Xcorr. As shown from Monte Carlo simulations, Scorr provided an ∼1.2-4.7-fold increase in the number of colocalized peaks and ensured negligible colocalization of peaks. In silico results were in good agreement with experimental data, which showed an increase in colocalized peaks of ∼1.3-2.5-fold and ∼1.2-2-fold for multicolor beads and EVs, respectively.
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Affiliation(s)
- Luca A. Andronico
- Department
of Women’s and Children’s Health (KBH), Karolinska Institutet, Solna 17177, Sweden
| | - Seung-Ryoung Jung
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Bryant S. Fujimoto
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Daniel T. Chiu
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
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24
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Chen HC. A systematic review of the barcoding strategy that contributes to COVID-19 diagnostics at a population level. Front Mol Biosci 2023; 10:1141534. [PMID: 37496777 PMCID: PMC10366608 DOI: 10.3389/fmolb.2023.1141534] [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: 01/10/2023] [Accepted: 06/30/2023] [Indexed: 07/28/2023] Open
Abstract
The outbreak of SARS-CoV-2 has made us more alert to the importance of viral diagnostics at a population level to rapidly control the spread of the disease. The critical question would be how to scale up testing capacity and perform a diagnostic test in a high-throughput manner with robust results and affordable costs. Here, the latest 26 articles using barcoding technology for COVID-19 diagnostics and biologically-relevant studies are reviewed. Barcodes are molecular tags, that allow proceeding an array of samples at once. To date, barcoding technology followed by high-throughput sequencing has been made for molecular diagnostics for SARS-CoV-2 infections because it can synchronously analyze up to tens of thousands of clinical samples within a short diagnostic time. Essentially, this technology can also be used together with different biotechnologies, allowing for investigation with resolution of single molecules. In this Mini-Review, I first explain the general principle of the barcoding strategy and then put forward recent studies using this technology to accomplish COVID-19 diagnostics and basic research. In the meantime, I provide the viewpoint to improve the current COVID-19 diagnostic strategy with potential solutions. Finally, and importantly, two practical ideas about how barcodes can be further applied in studying SARS-CoV-2 to accelerate our understanding of this virus are proposed.
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Zannella C, Chianese A, Annunziata G, Ambrosino A, De Filippis A, Tenore GC, Novellino E, Stornaiuolo M, Galdiero M. Antiherpetic Activity of Taurisolo ®, a Grape Pomace Polyphenolic Extract. Microorganisms 2023; 11:1346. [PMID: 37317320 DOI: 10.3390/microorganisms11051346] [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: 04/23/2023] [Revised: 05/15/2023] [Accepted: 05/18/2023] [Indexed: 06/16/2023] Open
Abstract
Herpes simplex virus (HSV) is widespread in the population, causing oral or genital ulcers and, rarely, severe complications such as encephalitis, keratitis, and neonatal herpes. Current available anti-HSV drugs are acyclovir and its derivatives, although long-term therapy with these agents can lead to drug resistance. Thus, the discovery of novel antiherpetic compounds merits additional studies. In recent decades, much scientific effort has been invested in the discovery of new synthetic or natural compounds with promising antiviral properties. In our study, we tested the antiviral potential of a novel polyphenol-based nutraceutical formulation (named Taurisolo®) consisting of a water polyphenol extract of grape pomace. The evaluation of the antiviral activity was carried out by using HSV-1 and HSV-2 in plaque assay experiments to understand the mechanism of action of the extract. Results were confirmed by real-time PCR, transmission electron microscope (TEM), and fluorescence microscope. Taurisolo® was able to block the viral infection by acting on cells when added together with the virus and also when the virus was pretreated with the extract, demonstrating an inhibitory activity directed to the early phases of HSV-1 and HSV-2 infection. Altogether, these data evidence for the first time the potential use of Taurisolo® as a topical formulation for both preventing and healing herpes lesions.
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Affiliation(s)
- Carla Zannella
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Annalisa Chianese
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Giuseppe Annunziata
- Department of Pharmacy, University of Naples Federico II, 80131 Naples, Italy
| | - Annalisa Ambrosino
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Anna De Filippis
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Gian Carlo Tenore
- Department of Pharmacy, University of Naples Federico II, 80131 Naples, Italy
| | - Ettore Novellino
- Department of Medicine and Surgery, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Mariano Stornaiuolo
- Department of Pharmacy, University of Naples Federico II, 80131 Naples, Italy
| | - Massimiliano Galdiero
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
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26
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Bhalla N, Payam AF. Addressing the Silent Spread of Monkeypox Disease with Advanced Analytical Tools. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2206633. [PMID: 36517107 DOI: 10.1002/smll.202206633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Indexed: 06/17/2023]
Abstract
Monkeypox disease is caused by a virus which belongs to the orthopoxvirus genus of the poxviridae family. This disease has recently spread out to several non-endemic countries. While some cases have been linked to travel from endemic regions, more recent infections are thought to have spread in the community without any travel links, raising the risks of a wider outbreak. This state of public health represents a highly unusual event which requires urgent surveillance. In this context, the opportunities and technological challenges of current bio/chemical sensors, nanomaterials, nanomaterial characterization instruments, and artificially intelligent biosystems collectively called "advanced analytical tools" are reviewed here, which will allow early detection, characterization, and inhibition of the monkeypox virus (MPXV) in the community and limit its expansion from endemic to pandemic. A summary of background information is also provided from biological and epidemiological perspective of monkeypox to support the scientific case for its holistic management using advanced analytical tools.
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Affiliation(s)
- Nikhil Bhalla
- Nanotechnology and Integrated Bioengineering Centre (NIBEC), School of Engineering, Ulster University, York St., BT15 1ED Belfast, Northern Ireland, UK
- Healthcare Technology Hub, Ulster University, York St., BT15 1ED Belfast, Northern Ireland, UK
| | - Amir Farokh Payam
- Nanotechnology and Integrated Bioengineering Centre (NIBEC), School of Engineering, Ulster University, York St., BT15 1ED Belfast, Northern Ireland, UK
- Healthcare Technology Hub, Ulster University, York St., BT15 1ED Belfast, Northern Ireland, UK
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27
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Shirogane Y, Harada H, Hirai Y, Takemoto R, Suzuki T, Hashiguchi T, Yanagi Y. Collective fusion activity determines neurotropism of an en bloc transmitted enveloped virus. SCIENCE ADVANCES 2023; 9:eadf3731. [PMID: 36706187 PMCID: PMC9882980 DOI: 10.1126/sciadv.adf3731] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 12/29/2022] [Indexed: 06/09/2023]
Abstract
Measles virus (MeV), which is usually non-neurotropic, sometimes persists in the brain and causes subacute sclerosing panencephalitis (SSPE) several years after acute infection, serving as a model for persistent viral infections. The persisting MeVs have hyperfusogenic mutant fusion (F) proteins that likely enable cell-cell fusion at synapses and "en bloc transmission" between neurons. We here show that during persistence, F protein fusogenicity is generally enhanced by cumulative mutations, yet mutations paradoxically reducing the fusogenicity may be selected alongside the wild-type (non-neurotropic) MeV genome. A mutant F protein having SSPE-derived substitutions exhibits lower fusogenicity than the hyperfusogenic F protein containing some of those substitutions, but by the wild-type F protein coexpression, the fusogenicity of the former F protein is enhanced, while that of the latter is nearly abolished. These findings advance the understanding of the long-term process of MeV neuropathogenicity and provide critical insight into the genotype-phenotype relationships of en bloc transmitted viruses.
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Affiliation(s)
- Yuta Shirogane
- Department of Virology, Faculty of Medicine, Kyushu University, Fukuoka, Japan
| | - Hidetaka Harada
- Department of Virology, Faculty of Medicine, Kyushu University, Fukuoka, Japan
| | - Yuichi Hirai
- Department of Virology, Faculty of Medicine, Kyushu University, Fukuoka, Japan
| | - Ryuichi Takemoto
- Department of Virology, Faculty of Medicine, Kyushu University, Fukuoka, Japan
| | - Tateki Suzuki
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Takao Hashiguchi
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Yusuke Yanagi
- National Research Center for the Control and Prevention of Infectious Diseases, Nagasaki University, Nagasaki, Japan
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28
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Juhas M. The World of Microorganisms. BRIEF LESSONS IN MICROBIOLOGY 2023:1-16. [DOI: 10.1007/978-3-031-29544-7_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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29
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Karpuzcu BA, Türk E, Ibrahim AH, Karabulut OC, Süzek BE. Machine Learning Methods for Virus-Host Protein-Protein Interaction Prediction. Methods Mol Biol 2023; 2690:401-417. [PMID: 37450162 DOI: 10.1007/978-1-0716-3327-4_31] [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] [Indexed: 07/18/2023]
Abstract
The attachment of a virion to a respective cellular receptor on the host organism occurring through the virus-host protein-protein interactions (PPIs) is a decisive step for viral pathogenicity and infectivity. Therefore, a vast number of wet-lab experimental techniques are used to study virus-host PPIs. Taking the great number and enormous variety of virus-host PPIs and the cost as well as labor of laboratory work, however, computational approaches toward analyzing the available interaction data and predicting previously unidentified interactions have been on the rise. Among them, machine-learning-based models are getting increasingly more attention with a great body of resources and tools proposed recently.In this chapter, we first provide the methodology with major steps toward the development of a virus-host PPI prediction tool. Next, we discuss the challenges involved and evaluate several existing machine-learning-based virus-host PPI prediction tools. Finally, we describe our experience with several ensemble techniques as utilized on available prediction results retrieved from individual PPI prediction tools. Overall, based on our experience, we recognize there is still room for the development of new individual and/or ensemble virus-host PPI prediction tools that leverage existing tools.
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Affiliation(s)
- Betül Asiye Karpuzcu
- Bioinformatics Graduate Program, Graduate School of Natural and Applied Sciences, Muğla Sıtkı Koçman University, Muğla, Turkey
| | - Erdem Türk
- Bioinformatics Graduate Program, Graduate School of Natural and Applied Sciences, Muğla Sıtkı Koçman University, Muğla, Turkey
- Department of Computer Engineering, Faculty of Engineering, Muğla Sıtkı Koçman University, Muğla, Turkey
| | - Ahmad Hassan Ibrahim
- Bioinformatics Graduate Program, Graduate School of Natural and Applied Sciences, Muğla Sıtkı Koçman University, Muğla, Turkey
| | - Onur Can Karabulut
- Bioinformatics Graduate Program, Graduate School of Natural and Applied Sciences, Muğla Sıtkı Koçman University, Muğla, Turkey
| | - Barış Ethem Süzek
- Bioinformatics Graduate Program, Graduate School of Natural and Applied Sciences, Muğla Sıtkı Koçman University, Muğla, Turkey.
- Department of Computer Engineering, Faculty of Engineering, Muğla Sıtkı Koçman University, Muğla, Turkey.
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30
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Zhou Y, Zhang W, Leblanc RM. Structure-Property-Activity Relationships in Carbon Dots. J Phys Chem B 2022; 126:10777-10796. [PMID: 36395361 DOI: 10.1021/acs.jpcb.2c06856] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Carbon dots (CDs) are one of the most versatile nanomaterials discovered in the 21st century. They possess many properties and thus hold potentials in diverse applications. While an increasing amount of attention has been given to these novel nanoparticles, the broad scientific community is actively engaged in exploring their limits. Recent studies on the fractionalization and assembly of CDs further push the limits beyond just CDs and demonstrate that CDs are both a mixture of heterogeneous fractions and promising building blocks for assembly of large carbon-based materials. With CDs moving forward toward both microscopic and macroscopic levels, a good understanding of the structure-property-activity relationships is essential to forecasting the future of CDs. Hence, in this Perspective, structure-property-activity relationships are highlighted based on the repeatedly verified findings in CDs. In addition, studies on CD fractionalization and assembly are briefly summarized in this Perspective. Eventually, these structure-property-activity relationships and controllability are essential for the development of CDs with desired properties for various applications especially in photochemistry, electrochemistry, nanomedicine, and surface chemistry. In summary, in our opinion, since 2004 until the present, history has witnessed a great development of CDs although there is still some room for more studies. Also, considering many attractive properties, structure-property-activity relationships, and the building block nature of CDs, a variety of carbon-based materials of interest can be constructed from CDs with control. They can help reduce blind trials in the development of carbon-based materials, which is of great significance in materials science, chemistry, and any fields related to the applications.
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Affiliation(s)
- Yiqun Zhou
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States.,C-Dots LLC, Miami, Florida 33136, United States.,Department of Biological Sciences, Florida International University, Miami, Florida 33199, United States
| | - Wei Zhang
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Roger M Leblanc
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
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Basnet S, Marahatha R, Shrestha A, Bhattarai S, Katuwal S, Sharma KR, Marasini BP, Dahal SR, Basnyat RC, Patching SG, Parajuli N. In Vitro and In Silico Studies for the Identification of Potent Metabolites of Some High-Altitude Medicinal Plants from Nepal Inhibiting SARS-CoV-2 Spike Protein. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27248957. [PMID: 36558090 PMCID: PMC9786757 DOI: 10.3390/molecules27248957] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 12/01/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
Despite ongoing vaccination programs against COVID-19 around the world, cases of infection are still rising with new variants. This infers that an effective antiviral drug against COVID-19 is crucial along with vaccinations to decrease cases. A potential target of such antivirals could be the membrane components of the causative pathogen, SARS-CoV-2, for instance spike (S) protein. In our research, we have deployed in vitro screening of crude extracts of seven ethnomedicinal plants against the spike receptor-binding domain (S1-RBD) of SARS-CoV-2 using an enzyme-linked immunosorbent assay (ELISA). Following encouraging in vitro results for Tinospora cordifolia, in silico studies were conducted for the 14 reported antiviral secondary metabolites isolated from T. cordifolia-a species widely cultivated and used as an antiviral drug in the Himalayan country of Nepal-using Genetic Optimization for Ligand Docking (GOLD), Molecular Operating Environment (MOE), and BIOVIA Discovery Studio. The molecular docking and binding energy study revealed that cordifolioside-A had a higher binding affinity and was the most effective in binding to the competitive site of the spike protein. Molecular dynamics (MD) simulation studies using GROMACS 5.4.1 further assayed the interaction between the potent compound and binding sites of the spike protein. It revealed that cordifolioside-A demonstrated better binding affinity and stability, and resulted in a conformational change in S1-RBD, hence hindering the activities of the protein. In addition, ADMET analysis of the secondary metabolites from T. cordifolia revealed promising pharmacokinetic properties. Our study thus recommends that certain secondary metabolites of T. cordifolia are possible medicinal candidates against SARS-CoV-2.
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Affiliation(s)
- Saroj Basnet
- Center for Drug Design and Molecular Simulation Division, Kathmandu 44600, Nepal
| | - Rishab Marahatha
- Central Department of Chemistry, Tribhuvan University, Kathmandu 44618, Nepal
- Department of Chemistry, Oklahoma State University, Still Water, OK 74078, USA
| | - Asmita Shrestha
- Central Department of Chemistry, Tribhuvan University, Kathmandu 44618, Nepal
| | - Salyan Bhattarai
- Paraza Pharma, Inc., 2525 Avenue Marie-Curie, Montreal, QC H4S 2E1, Canada
| | - Saurav Katuwal
- Central Department of Chemistry, Tribhuvan University, Kathmandu 44618, Nepal
| | - Khaga Raj Sharma
- Central Department of Chemistry, Tribhuvan University, Kathmandu 44618, Nepal
| | | | - Salik Ram Dahal
- Department of Chemistry, Oklahoma State University, Still Water, OK 74078, USA
- Oakridge National Laboratory, Bethel Valley Rd, Oak Ridge, TN 37830, USA
| | - Ram Chandra Basnyat
- Central Department of Chemistry, Tribhuvan University, Kathmandu 44618, Nepal
| | - Simon G. Patching
- Independent Researcher, Leeds LS2 9JT, UK
- Correspondence: (S.G.P.); (N.P.)
| | - Niranjan Parajuli
- Central Department of Chemistry, Tribhuvan University, Kathmandu 44618, Nepal
- Correspondence: (S.G.P.); (N.P.)
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32
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Ciaston I, Dobosz E, Potempa J, Koziel J. The subversion of toll-like receptor signaling by bacterial and viral proteases during the development of infectious diseases. Mol Aspects Med 2022; 88:101143. [PMID: 36152458 PMCID: PMC9924004 DOI: 10.1016/j.mam.2022.101143] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/29/2022] [Accepted: 09/09/2022] [Indexed: 02/05/2023]
Abstract
Toll-like receptors (TLRs) are pattern recognition receptors (PRRs) that respond to pathogen-associated molecular patterns (PAMPs). The recognition of specific microbial ligands by TLRs triggers an innate immune response and also promotes adaptive immunity, which is necessary for the efficient elimination of invading pathogens. Successful pathogens have therefore evolved strategies to subvert and/or manipulate TLR signaling. Both the impairment and uncontrolled activation of TLR signaling can harm the host, causing tissue destruction and allowing pathogens to proliferate, thus favoring disease progression. In this context, microbial proteases are key virulence factors that modify components of the TLR signaling pathway. In this review, we discuss the role of bacterial and viral proteases in the manipulation of TLR signaling, highlighting the importance of these enzymes during the development of infectious diseases.
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Affiliation(s)
- Izabela Ciaston
- Department of Microbiology Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Ewelina Dobosz
- Department of Microbiology Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Jan Potempa
- Department of Microbiology Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland; Department of Oral Health and Systemic Disease, University of Louisville School of Dentistry, University of Louisville, Louisville, KY, USA.
| | - Joanna Koziel
- Department of Microbiology Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland.
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33
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Zandi M, Hosseini F, Adli AH, Salmanzadeh S, Behboudi E, Halvaei P, Khosravi A, Abbasi S. State-of-the-art cerium nanoparticles as promising agents against human viral infections. Biomed Pharmacother 2022; 156:113868. [DOI: 10.1016/j.biopha.2022.113868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/10/2022] [Accepted: 10/13/2022] [Indexed: 11/02/2022] Open
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Abstract
Human genetics can inform the biology and epidemiology of coronavirus disease 2019 (COVID-19) by pinpointing causal mechanisms that explain why some individuals become more severely affected by the disease upon infection by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. Large-scale genetic association studies, encompassing both rare and common genetic variants, have used different study designs and multiple disease phenotype definitions to identify several genomic regions associated with COVID-19. Along with a multitude of follow-up studies, these findings have increased our understanding of disease aetiology and provided routes for management of COVID-19. Important emergent opportunities include the clinical translatability of genetic risk prediction, the repurposing of existing drugs, exploration of variable host effects of different viral strains, study of inter-individual variability in vaccination response and understanding the long-term consequences of SARS-CoV-2 infection. Beyond the current pandemic, these transferrable opportunities are likely to affect the study of many infectious diseases.
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Affiliation(s)
- Mari E K Niemi
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Mark J Daly
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- Broad Institute, Cambridge, MA, USA
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Andrea Ganna
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland.
- Broad Institute, Cambridge, MA, USA.
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
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35
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Li R, Qiao S, Zhang G. Reappraising host cellular factors involved in attachment and entry to develop antiviral strategies against porcine reproductive and respiratory syndrome virus. Front Microbiol 2022; 13:975610. [PMID: 35958155 PMCID: PMC9360752 DOI: 10.3389/fmicb.2022.975610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 07/08/2022] [Indexed: 11/13/2022] Open
Abstract
Porcine reproductive and respiratory syndrome (PRRS), caused by PRRS virus (PRRSV), is a highly contagious disease that brings tremendous economic losses to the global swine industry. As an intracellular obligate pathogen, PRRSV infects specific host cells to complete its replication cycle. PRRSV attachment to and entry into host cells are the first steps to initiate the replication cycle and involve multiple host cellular factors. In this review, we recapitulated recent advances on host cellular factors involved in PRRSV attachment and entry, and reappraised their functions in these two stages, which will deepen the understanding of PRRSV infection and provide insights to develop promising antiviral strategies against the virus.
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Affiliation(s)
| | - Songlin Qiao
- Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Gaiping Zhang
- Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, China
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36
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Reichling J. Antiviral and Virucidal Properties of Essential Oils and Isolated Compounds - A Scientific Approach. PLANTA MEDICA 2022; 88:587-603. [PMID: 34144626 DOI: 10.1055/a-1382-2898] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Essential oils and isolated essential oil compounds are known to exert various pharmacological effects, such as antibacterial, antifungal, antiviral, anti-inflammatory, anti-immunomodulatory, antioxidant, and wound healing effects. Based on selected articles, this review deals with the potential antiviral and virucidal activities of essential oils and essential oil compounds together with their mechanism of action as well as in silico studies involving viral and host cell-specific target molecules that are indispensable for virus cell adsorption, penetration, and replication. The reported in vitro and in vivo studies highlight the baseline data about the latest findings of essential oils and essential oil compounds antiviral and virucidal effects on enveloped and non-enveloped viruses, taking into account available biochemical and molecular biological tests. The results of many in vitro studies revealed that several essential oils and essential oil compounds from different medicinal and aromatic plants are potent antiviral and virucidal agents that inhibit viral progeny by blocking different steps of the viral infection/replication cycle of DNA and RNA viruses in various host cell lines. Studies in mice infected with viruses causing respiratory diseases showed that different essential oils and essential oil compounds were able to prolong the life of infected animals, reduce virus titers in brain and lung tissues, and significantly inhibit the synthesis of proinflammatory cytokines and chemokines. In addition, some in vitro studies on hydrophilic nano-delivery systems encapsulating essential oils/essential oil compounds exhibited a promising way to improve the chemical stability and enhance the water solubility, bioavailabilty, and antiviral efficacy of essential oils and essential oil compounds.
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Affiliation(s)
- Jürgen Reichling
- Formerly Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Heidelberg, Germany
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37
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Wang Y, Qiao X, Li Y, Yang Q, Wang L, Liu X, Wang H, Shen H. Role of the receptor for activated C kinase 1 during viral infection. Arch Virol 2022; 167:1915-1924. [PMID: 35763066 DOI: 10.1007/s00705-022-05484-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Accepted: 03/30/2022] [Indexed: 11/29/2022]
Abstract
Viruses can survive only in living cells, where they depend on the host's enzymatic system for survival and reproduction. Virus-host interactions are complex. On the one hand, hosts express host-restricted factors to protect the host cells from viral infections. On the other hand, viruses recruit certain host factors to facilitate their survival and transmission. The identification of host factors critical to viral infection is essential for comprehending the pathogenesis of contagion and developing novel antiviral therapies that specifically target the host. Receptor for activated C kinase 1 (RACK1), an evolutionarily conserved host factor that exists in various eukaryotic organisms, is a promising target for antiviral therapy. This review primarily summarizes the roles of RACK1 in regulating different viral life stages, particularly entry, replication, translation, and release.
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Affiliation(s)
- Yan Wang
- School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Xiaorong Qiao
- School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Yuhan Li
- School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Qingru Yang
- School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Lulu Wang
- School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Xiaolan Liu
- School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Hua Wang
- School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Hongxing Shen
- School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.
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38
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Hill JM, Lukiw WJ. microRNA, the Innate-Immune System and SARS-CoV-2. Front Cell Infect Microbiol 2022; 12:887800. [PMID: 35782132 PMCID: PMC9245018 DOI: 10.3389/fcimb.2022.887800] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 05/02/2022] [Indexed: 12/31/2022] Open
Abstract
The single-stranded viral RNA (ssvRNA) known as the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that causes COVID-19 can be effectively inactivated by a number of natural ribonucleic acid-based host cell defenses. One of the most important of these defenses includes the actions of a class of small non-coding RNAs (sncRNAs) known as microRNAs (miRNAs). Via base-pair complementarity miRNAs are capable of specifically targeting ssvRNA sequences such as SARS-CoV-2 promoting its inactivation and neutralization. RNA-sequencing and bioinformatics analysis indicate that multiple naturally-occurring human miRNAs have extensive complementarity to the SARS-CoV-2 ssvRNA genome. Since miRNA abundance, speciation, and complexity vary significantly amongst human individuals, this may in part explain the variability in the innate-immune and pathophysiological response of different individuals to SARS-CoV-2 and overall susceptibility to ssvRNA-mediated viral infection.
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Affiliation(s)
- James M. Hill
- Louisiana State University (LSU) Neuroscience Center, Louisiana State University Health Science Center, New Orleans, LA, United States
- Department of Ophthalmology, LSU Health Science Center, New Orleans, LA, United States
- Department of Pharmacology, Louisiana State University (LSU) Health Science Center, New Orleans, LA, United States
- Department of Microbiology, Louisiana State University (LSU) Health Science Center, New Orleans, LA, United States
| | - Walter J. Lukiw
- Louisiana State University (LSU) Neuroscience Center, Louisiana State University Health Science Center, New Orleans, LA, United States
- Department of Ophthalmology, LSU Health Science Center, New Orleans, LA, United States
- Department Neurology, Louisiana State University Health Science Center, New Orleans, LA, United States
- *Correspondence: Walter J. Lukiw,
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Chu Q, Li J, Chen J, Yuan Z. HBV induced the discharge of intrinsic antiviral miRNAs in HBV-replicating hepatocytes via extracellular vesicles to facilitate its replication. J Gen Virol 2022; 103. [PMID: 35604380 DOI: 10.1099/jgv.0.001744] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Hepatitis B virus (HBV), which can cause chronic hepatitis B, has sophisticated machinery to establish persistent infection. Here, we report a novel mechanism whereby HBV changed miRNA packaging into extracellular vesicles (EVs) to facilitate replication. Disruption of the miRNA machinery in hepatocytes enhanced HBV replication, indicating an intrinsic miRNA-mediated antiviral state. Interference with EV release only decreased HBV replication if there was normal miRNA biogenesis, suggesting a possible link between HBV replication and EV-associated miRNAs. Microarray and qPCR analyses revealed that HBV replication changed miRNA expression in EVs. EV incubation, transfection of miRNA mimics and inhibitors, and functional pathway and network analyses showed that EV miRNAs are associated with antiviral function, suggesting that to promote survival HBV coopts EVs to excrete anti-HBV intracellular miRNAs. These data suggest a novel mechanism by which HBV maintains its replication, which has therapeutic implications.
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Affiliation(s)
- Qiaofang Chu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, PR China
| | - Jianhua Li
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, PR China
| | - Jieliang Chen
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, PR China
| | - Zhenghong Yuan
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, PR China
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Khan F, Tabassum N, Bamunuarachchi NI, Kim YM. Phloroglucinol and Its Derivatives: Antimicrobial Properties toward Microbial Pathogens. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:4817-4838. [PMID: 35418233 DOI: 10.1021/acs.jafc.2c00532] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Phloroglucinol (PG) is a natural product isolated from plants, algae, and microorganisms. Aside from that, the number of PG derivatives has expanded due to the discovery of their potential biological roles. Aside from its diverse biological activities, PG and its derivatives have been widely utilized to treat microbial infections caused by bacteria, fungus, and viruses. The rapid emergence of antimicrobial-resistant microbial infections necessitates the chemical synthesis of numerous PG derivatives in order to meet the growing demand for drugs. This review focuses on the use of PG and its derivatives to control microbial infection and the underlying mechanism of action. Furthermore, as future perspectives, some of the various alternative strategies, such as the use of PG and its derivatives in conjugation, nanoformulation, antibiotic combination, and encapsulation, have been thoroughly discussed. This review will enable the researcher to investigate the possible antibacterial properties of PG and its derivatives, either free or in the form of various formulations.
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Affiliation(s)
- Fazlurrahman Khan
- Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Republic of Korea
| | - Nazia Tabassum
- Industry 4.0 Convergence Bionics Engineering, Pukyong National University, Busan 48513, Republic of Korea
| | | | - Young-Mog Kim
- Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Republic of Korea
- Department of Food Science and Technology, Pukyong National University, Busan 48513, Republic of Korea
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41
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Xue Y, Liu C, Andrews G, Wang J, Ge Y. Recent advances in carbon quantum dots for virus detection, as well as inhibition and treatment of viral infection. NANO CONVERGENCE 2022; 9:15. [PMID: 35366117 PMCID: PMC8976173 DOI: 10.1186/s40580-022-00307-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 03/17/2022] [Indexed: 05/28/2023]
Abstract
In the last decade, carbon quantum dots (CQDs), as a novel class of carbon-based nanomaterials, have received increasing attention due to their distinct properties. CQDs are ultimately small nanoparticles with an average size below 10 nm, possessing high water solubility, alluring photoluminescence, photostability, excellent biocompatibility, low/none toxicity, environmental friendliness, and high sustainability, etc. In history, there are intermittent threats from viruses to humans, animals and plants worldwide, resulting in enormous crises and impacts on our life, environment, economy and society. Some recent studies have unveiled that certain types of CQDs exhibited high and potent antiviral activities against various viruses such as human coronavirus, arterivirus, norovirus and herpesvirus. Moreover, they have been successfully explored and developed for different virus detections including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This article exclusively overviews and discusses the recent progress of designing, synthesizing, modifying/functionalizing and developing CQDs towards effective virus detection as well as the inhibition and treatment of viral infection. Their mechanisms and applications against various pathogenic viruses are addressed. The latest outcomes for combating the coronavirus disease 2019 (COVID-19) utilizing CQDs are also highlighted. It can be envisaged that CQDs could further benefit the development of virus detectors and antiviral agents with added broad-spectrum activity and cost-effective production.
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Affiliation(s)
- Yuxiang Xue
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Edinburgh, EH9 3HL, UK
| | - Chenchen Liu
- Department of Metabolism, Digestion and Reproductive, Faculty of Medicine, Imperial College London, London, SW7 2AZ, UK
| | - Gavin Andrews
- School of Pharmacy, Queen's University Belfast, Belfast, BT9 7BL, UK
| | - Jinyan Wang
- College of Basic Medical Science, China Medical University, Shenyang, 110122, China
| | - Yi Ge
- School of Pharmacy, Queen's University Belfast, Belfast, BT9 7BL, UK.
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42
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Iron–sulfur clusters as inhibitors and catalysts of viral replication. Nat Chem 2022; 14:253-266. [DOI: 10.1038/s41557-021-00882-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 12/15/2021] [Indexed: 12/11/2022]
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Mueller Brown K, Le Sage V, French AJ, Jones JE, Padovani GH, Avery AJ, Schultz-Cherry S, Rosch JW, Hiller NL, Lakdawala SS. Secondary infection with Streptococcus pneumoniae decreases influenza virus replication and is linked to severe disease. FEMS MICROBES 2022; 3:xtac007. [PMID: 35392116 PMCID: PMC8981988 DOI: 10.1093/femsmc/xtac007] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/31/2022] [Accepted: 03/02/2022] [Indexed: 11/29/2022] Open
Abstract
Secondary bacterial infection is a common complication in severe influenza virus infections. During the H1N1 pandemic of 2009, increased mortality was observed among healthy young adults due to secondary bacterial pneumonia, one of the most frequent bacterial species being Streptococcus pneumoniae (Spn). Previous studies in mice and ferrets have suggested a synergistic relationship between Spn and influenza viruses. In this study, the ferret model was used to examine whether secondary Spn infection (strains BHN97 and D39) influence replication and airborne transmission of the 2009 pandemic H1N1 virus (H1N1pdm09). Secondary infection with Spn after H1N1pdm09 infection consistently resulted in a significant decrease in viral titers in the ferret nasal washes. While secondary Spn infection appeared to negatively impact influenza virus replication, animals precolonized with Spn were equally susceptible to H1N1pdm09 airborne transmission. In line with previous work, ferrets with preceding H1N1pdm09 and secondary Spn infection had increased bacterial loads and more severe clinical symptoms as compared to animals infected with H1N1pdm09 or Spn alone. Interestingly, the donor animals that displayed the most severe clinical symptoms had reduced airborne transmission of H1N1pdm09. Based on these data, we propose an asymmetrical relationship between these two pathogens, rather than a synergistic one, since secondary bacterial infection enhances Spn colonization and pathogenesis but decreases viral titers.
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Affiliation(s)
- Karina Mueller Brown
- Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA
| | - Valerie Le Sage
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 450 Technology Drive, Bridgeside Point II, Pittsburgh, PA 15219, USA
| | - Andrea J French
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 450 Technology Drive, Bridgeside Point II, Pittsburgh, PA 15219, USA
| | - Jennifer E Jones
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 450 Technology Drive, Bridgeside Point II, Pittsburgh, PA 15219, USA
| | - Gabriella H Padovani
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 450 Technology Drive, Bridgeside Point II, Pittsburgh, PA 15219, USA
| | - Annika J Avery
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 450 Technology Drive, Bridgeside Point II, Pittsburgh, PA 15219, USA
| | - Stacey Schultz-Cherry
- Department of Infectious Diseases, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Jason W Rosch
- Department of Infectious Diseases, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - N Luisa Hiller
- Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA
| | - Seema S Lakdawala
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 450 Technology Drive, Bridgeside Point II, Pittsburgh, PA 15219, USA
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Hu S, Yin F, Nie L, Wang Y, Qin J, Chen J. Estrogen and Estrogen Receptor Modulators: Potential Therapeutic Strategies for COVID-19 and Breast Cancer. Front Endocrinol (Lausanne) 2022; 13:829879. [PMID: 35399920 PMCID: PMC8985365 DOI: 10.3389/fendo.2022.829879] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 02/21/2022] [Indexed: 01/08/2023] Open
Abstract
Owing to the ongoing coronavirus disease 2019 (COVID-19) pandemic, we need to pay a particular focus on the impact of coronavirus infection on breast cancer patients. Approximately 70% of breast cancer patients express estrogen receptor (ER), and intervention therapy for ER has been the primary treatment strategy to prevent the development and metastasis of breast cancer. Recent studies have suggested that selective estrogen receptor modulators (SERMs) are a potential therapeutic strategy for COVID-19. With its anti-ER and anti-viral combined functions, SERMs may be an effective treatment for COVID-19 in patients with breast cancer. In this review, we explore the latent effect of SERMs, especially tamoxifen, and the mechanism between ER and virus susceptibility.
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Affiliation(s)
- Shuying Hu
- Guangxi Health Commission Key Laboratory of Tumor Immunology and Receptor-Targeted Drug Basic Research, Guilin Medical University, Guilin, China
| | - Feiying Yin
- Guangxi Health Commission Key Laboratory of Tumor Immunology and Receptor-Targeted Drug Basic Research, Guilin Medical University, Guilin, China
- Laboratory of Environmental Pollution and Integrative Omics, Guilin Medical University, Guilin, China
| | - Litao Nie
- Laboratory of Environmental Pollution and Integrative Omics, Guilin Medical University, Guilin, China
| | - Yuqin Wang
- Laboratory of Environmental Pollution and Integrative Omics, Guilin Medical University, Guilin, China
| | - Jian Qin
- Department of Radiotherapy III, Clinical Oncology Canter, The People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- *Correspondence: Jian Qin, ; Jian Chen,
| | - Jian Chen
- Guangxi Health Commission Key Laboratory of Tumor Immunology and Receptor-Targeted Drug Basic Research, Guilin Medical University, Guilin, China
- Breast Center, the Second Affiliated Hospital of Guilin Medical University, Guilin, China
- *Correspondence: Jian Qin, ; Jian Chen,
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Vostinar AE, Skocelas KG, Lalejini A, Zaman L. Symbiosis in Digital Evolution: Past, Present, and Future. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.739047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Symbiosis, the living together of unlike organisms as symbionts, is ubiquitous in the natural world. Symbioses occur within and across all scales of life, from microbial to macro-faunal systems. Further, the interactions between symbionts are multimodal in both strength and type, can span from parasitic to mutualistic within one partnership, and persist over generations. Studying the ecological and evolutionary dynamics of symbiosis in natural or laboratory systems poses a wide range of challenges, including the long time scales at which symbioses evolve de novo, the limited capacity to experimentally control symbiotic interactions, the weak resolution at which we can quantify interactions, and the idiosyncrasies of current model systems. These issues are especially challenging when seeking to understand the ecological effects and evolutionary pressures on and of a symbiosis, such as how a symbiosis may shift between parasitic and mutualistic modes and how that shift impacts the dynamics of the partner population. In digital evolution, populations of computational organisms compete, mutate, and evolve in a virtual environment. Digital evolution features perfect data tracking and allows for experimental manipulations that are impractical or impossible in natural systems. Furthermore, modern computational power allows experimenters to observe thousands of generations of evolution in minutes (as opposed to several months or years), which greatly expands the range of possible studies. As such, digital evolution is poised to become a keystone technique in our methodological repertoire for studying the ecological and evolutionary dynamics of symbioses. Here, we review how digital evolution has been used to study symbiosis, and we propose a series of open questions that digital evolution is well-positioned to answer.
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46
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Laurini E, Marson D, Aulic S, Fermeglia A, Pricl S. Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. Sci Rep 2021; 11:20274. [PMID: 34642465 PMCID: PMC8511038 DOI: 10.1038/s41598-021-99827-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 09/30/2021] [Indexed: 12/22/2022] Open
Abstract
The purpose of this work is to provide an in silico molecular rationale of the role eventually played by currently circulating mutations in the receptor binding domain of the SARS-CoV-2 spike protein (S-RBDCoV‑2) in evading the immune surveillance effects elicited by the two Eli Lilly LY-CoV555/bamlanivimab and LY-CoV016/etesevimab monoclonal antibodies. The main findings from this study show that, compared to the wild-type SARS-CoV-2 spike protein, mutations E484A/G/K/Q/R/V, Q493K/L/R, S494A/P/R, L452R and F490S are predicted to be markedly resistant to neutralization by LY-CoV555, while mutations K417E/N/T, D420A/G/N, N460I/K/S/T, T415P, and Y489C/S are predicted to confer LY-CoV016 escaping advantage to the viral protein. A challenge of our global in silico results against relevant experimental data resulted in an overall 90% agreement. Thus, the results presented provide a molecular-based rationale for all relative experimental findings, constitute a fast and reliable tool for identifying and prioritizing all present and newly reported circulating spike SARS-CoV-2 variants with respect to antibody neutralization, and yield substantial structural information for the development of next-generation vaccines and monoclonal antibodies more resilient to viral evolution.
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Affiliation(s)
- Erik Laurini
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTS), DEA, University of Trieste, 34127, Trieste, Italy
| | - Domenico Marson
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTS), DEA, University of Trieste, 34127, Trieste, Italy
| | - Suzana Aulic
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTS), DEA, University of Trieste, 34127, Trieste, Italy
| | - Alice Fermeglia
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTS), DEA, University of Trieste, 34127, Trieste, Italy
| | - Sabrina Pricl
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTS), DEA, University of Trieste, 34127, Trieste, Italy.
- Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, 90-136, Lodz, Poland.
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Škubník J, Bejček J, Pavlíčková VS, Rimpelová S. Repurposing Cardiac Glycosides: Drugs for Heart Failure Surmounting Viruses. Molecules 2021; 26:molecules26185627. [PMID: 34577097 PMCID: PMC8469069 DOI: 10.3390/molecules26185627] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/13/2021] [Accepted: 09/14/2021] [Indexed: 12/21/2022] Open
Abstract
Drug repositioning is a successful approach in medicinal research. It significantly simplifies the long-term process of clinical drug evaluation, since the drug being tested has already been approved for another condition. One example of drug repositioning involves cardiac glycosides (CGs), which have, for a long time, been used in heart medicine. Moreover, it has been known for decades that CGs also have great potential in cancer treatment and, thus, many clinical trials now evaluate their anticancer potential. Interestingly, heart failure and cancer are not the only conditions for which CGs could be effectively used. In recent years, the antiviral potential of CGs has been extensively studied, and with the ongoing SARS-CoV-2 pandemic, this interest in CGs has increased even more. Therefore, here, we present CGs as potent and promising antiviral compounds, which can interfere with almost any steps of the viral life cycle, except for the viral attachment to a host cell. In this review article, we summarize the reported data on this hot topic and discuss the mechanisms of antiviral action of CGs, with reference to the particular viral life cycle phase they interfere with.
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48
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Okada Y, Yoshimura K, Toya S, Tsuchimochi M. Pathogenesis of taste impairment and salivary dysfunction in COVID-19 patients. JAPANESE DENTAL SCIENCE REVIEW 2021; 57:111-122. [PMID: 34257762 PMCID: PMC8266517 DOI: 10.1016/j.jdsr.2021.07.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 06/27/2021] [Accepted: 07/05/2021] [Indexed: 12/23/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is a highly transmissible pandemic disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The characteristics of the disease include a broad range of symptoms from mild to serious to death, with mild pneumonia to acute respiratory distress syndrome and complications in extrapulmonary organs. Taste impairment and salivary dysfunction are common early symptoms in COVID-19 patients. The mouth is a significant entry route for SARS-COV-2, similar to the nose and eyes. The cells of the oral epithelium, taste buds, and minor and major salivary glands express cell entry factors for SARS-COV-2, such as ACE2, TMPRSS2, and Furin. We describe the occurrence of taste impairment and salivary dysfunction in COVID-19 patients and show immunohistochemical findings regarding the cell entry factors in the oral tissue. We review and describe the pathogeneses of taste impairment and salivary dysfunction. Treatment for the oral disease is also described. Recently, it was reported that some people experience persistent and prolonged taste impairment and salivary dysfunction, described as post-COVID-19 syndrome or long COVID-19, after the acute illness of the infection has healed. To resolve these problems, it is important to understand the pathogenesis of oral complications. Recently, important advances have been reported in the understanding of gustatory impairment and salivary dysfunction. Although some progress has been made, considerable effort is still required for in-depth elucidation of the pathogenesis.
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Affiliation(s)
- Yasuo Okada
- Department of Pathology, The Nippon Dental University School of Life Dentistry at Niigata, 1-8 Hamaura-cho, Chuo-ku, Niigata 951-8580, Japan
| | - Ken Yoshimura
- Department of Anatomy, The Nippon Dental University School of Life Dentistry at Niigata, 1-8 Hamaura-cho, Chuo-ku, Niigata 951-8580, Japan
| | - Shuji Toya
- Oral and Maxillofacial Surgery, The Nippon Dental University Niigata Hospital, 1-8 Hamaura-cho, Chuo-ku, Niigata 951-8580, Japan
| | - Makoto Tsuchimochi
- The Nippon Dental University (Emeritus Professor), 1-9-20 Fujimi, Chiyoda-ku, Tokyo, 102-8159, Japan
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49
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Jaber N, Al-Remawi M, Al-Akayleh F, Al-Muhtaseb N, Al-Adham ISI, Collier PJ. A review of the antiviral activity of Chitosan, including patented applications and its potential use against COVID-19. J Appl Microbiol 2021; 132:41-58. [PMID: 34218488 PMCID: PMC8447037 DOI: 10.1111/jam.15202] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 06/29/2021] [Indexed: 12/13/2022]
Abstract
Chitosan is an abundant organic polysaccharide, which can be relatively easily obtained by chemical modification of animal or fungal source materials. Chitosan and its derivatives have been shown to exhibit direct antiviral activity, to be useful vaccine adjuvants and to have potential anti-SARS-CoV-2 activity. This thorough and timely review looks at the recent history of investigations into the role of chitosan and its derivatives as an antiviral agent and proposes a future application in the treatment of endemic SARS-CoV-2.
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Affiliation(s)
- Nisrein Jaber
- Faculty of Pharmacy, Al-Ahliyya Amman University, Amman, Jordan
| | - Mayyas Al-Remawi
- Faculty of Pharmacy & Medical Sciences, University of Petra, Amman, Jordan
| | - Faisal Al-Akayleh
- Faculty of Pharmacy & Medical Sciences, University of Petra, Amman, Jordan
| | - Najah Al-Muhtaseb
- Faculty of Pharmacy & Medical Sciences, University of Petra, Amman, Jordan
| | | | - Phillip J Collier
- Faculty of Pharmacy & Medical Sciences, University of Petra, Amman, Jordan
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50
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microRNA Heterogeneity, Innate-Immune Defense and the Efficacy of SARS-CoV-2 Infection-A Commentary. Noncoding RNA 2021; 7:ncrna7020037. [PMID: 34207055 PMCID: PMC8293307 DOI: 10.3390/ncrna7020037] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/07/2021] [Accepted: 06/13/2021] [Indexed: 12/12/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), a member of the genus Betacoronavirus in the family Coronaviridae, possesses an unusually large single-stranded viral RNA (ssvRNA) genome of about ~29,811 nucleotides (nt) that causes severe and acute respiratory distress and a highly lethal viral pneumonia known as COVID-19. COVID-19 also presents with multiple ancillary systemic diseases and often involves cardiovascular, inflammatory, and/or neurological complications. Pathological viral genomes consisting of ssvRNA, like cellular messenger RNA (mRNA), are susceptible to attack, destruction, neutralization, and/or modulation by naturally occurring small non-coding RNAs (sncRNAs) within the host cell, some of which are known as microRNAs (miRNAs). This paper proposes that the actions of the 2650 known human miRNAs and other sncRNAs form the basis for an under-recognized and unappreciated innate-immune regulator of ssvRNA viral genome activities and have implications for the efficiency of SARS-CoV-2 invasion, infection, and replication. Recent research indicates that both miRNA and mRNA abundance, speciation, and complexity varies widely amongst human individuals, and this may: (i) In part explain the variability in the innate-immune immunological and pathophysiological response of different human individuals to the initiation and progression of SARS-CoV-2 infection in multiple tissue types; and (ii) further support our understanding of human biochemical and genetic individuality and the variable resistance of individuals to ssvRNA-mediated viral infection and disease. This commentary will briefly address current findings and concepts in this fascinating research area of non-coding RNA and innate-immunity with special reference to natural host miRNAs, SARS-CoV-2, and the current COVID-19 pandemic.
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