1
|
Espinoza-Ascurra G, Gonzales-Graus I, Meléndez-Marón M, Cabrera R. Prevalence and factors associated with depression in healthcare personnel during the SARS-CoV-2 pandemic in the Department of Piura, Peru. Rev Colomb Psiquiatr (Engl Ed) 2024; 53:63-72. [PMID: 38653662 DOI: 10.1016/j.rcpeng.2021.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 11/07/2021] [Indexed: 04/25/2024]
Abstract
INTRODUCTION The COVID-19 pandemic has increased the magnitude of mental illnesses such as depression, not only in the general population, but also in healthcare personnel. However, in Peru the prevalence, and the associated factors for developing depression in healthcare personnel, are not known. The objective was to determine the prevalence and identify the factors associated with depression in healthcare personnel, in the context of the SARS-CoV-2 pandemic. METHODS An analytical cross-sectional study was carried out from May to September in healthcare establishments. A sample of 136 health workers were included and a survey was applied to collect the data. Depression as a dependent variable was measured using the Zung self-report scale. To identify the associated factors, the bivariate and multivariate analysis was performed by logistic regression with STATA v 14. RESULTS The prevalence of depression was 8.8% (95%CI, 4.64-14.90). Having a family member or friend who had died from COVID-19 was associated with depression (OR = 6.78; 95%CI, 1.39-32.90; p = 0.017). Whereas the use of personal protective equipment was found to be a protective factor against developing depression (OR = 0.03; 95%CI, 0.004-0.32; p = 0.003). CONCLUSIONS Approximately 1 in 10 healthcare professionals and technicians developed depression during the COVID-19 pandemic in this study. In addition, having relatives or friends who had died from COVID-19 was negatively associated with depression and use of personal protective equipment was identified as a protective factor.
Collapse
Affiliation(s)
| | | | - Mónica Meléndez-Marón
- Subregión de Salud Luciano Castillo Colona, Dirección Regional de Salud Piura, Sullana, Peru
| | - Rufino Cabrera
- Escuela de Medicina, Universidad Peruana de Ciencias Aplicadas, Lima, Peru
| |
Collapse
|
2
|
Akbari B, Ahmadi E, Zabihi MR, Zamir MR, Shaker MS, Noorbakhsh F. SARS-CoV-2 helicase might interfere with cellular nonsense-mediated RNA decay: insights from a bioinformatics study. BMC Genom Data 2023; 24:68. [PMID: 37980504 PMCID: PMC10657555 DOI: 10.1186/s12863-023-01173-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 11/10/2023] [Indexed: 11/20/2023] Open
Abstract
BACKGROUND Viruses employ diverse strategies to interfere with host defense mechanisms, including the production of proteins that mimic or resemble host proteins. This study aimed to analyze the similarities between SARS-CoV-2 and human proteins, investigate their impact on virus-host interactions, and elucidate underlying mechanisms. RESULTS Comparing the proteins of SARS-CoV-2 with human and mammalian proteins revealed sequence and structural similarities between viral helicase with human UPF1. The latter is a protein that is involved in nonsense-mediated RNA decay (NMD), an mRNA surveillance pathway which also acts as a cellular defense mechanism against viruses. Protein sequence similarities were also observed between viral nsp3 and human Poly ADP-ribose polymerase (PARP) family of proteins. Gene set enrichment analysis on transcriptomic data derived from SARS-CoV-2 positive samples illustrated the enrichment of genes belonging to the NMD pathway compared with control samples. Moreover, comparing transcriptomic data from SARS-CoV-2-infected samples with transcriptomic data derived from UPF1 knockdown cells demonstrated a significant overlap between datasets. CONCLUSIONS These findings suggest that helicase/UPF1 sequence and structural similarity might have the ability to interfere with the NMD pathway with pathogenic and immunological implications.
Collapse
Affiliation(s)
- Behnia Akbari
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Ehsan Ahmadi
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Zabihi
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mina Roshan Zamir
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mina Sadeghi Shaker
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Farshid Noorbakhsh
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
- Shefa Neuroscience Research Center, Khatam Alanbia Hospital, Tehran, Iran.
| |
Collapse
|
3
|
Woo PCY, de Groot RJ, Haagmans B, Lau SKP, Neuman BW, Perlman S, Sola I, van der Hoek L, Wong ACP, Yeh SH. ICTV Virus Taxonomy Profile: Coronaviridae 2023. J Gen Virol 2023; 104. [PMID: 37097842 DOI: 10.1099/jgv.0.001843] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Abstract
The family Coronaviridae includes viruses with positive-sense RNA genomes of 22-36 kb that are expressed through a nested set of 3' co-terminal subgenomic mRNAs. Members of the subfamily Orthocoronavirinae are characterized by 80-160 nm diameter, enveloped virions with spike projections. The orthocoronaviruses, severe acute respiratory syndrome coronavirus and Middle East respiratory syndrome-related coronavirus are extremely pathogenic for humans and in the last two decades have been responsible for the SARS and MERS epidemics. Another orthocoronavirus, severe acute respiratory syndrome coronavirus 2, was responsible for the recent global COVID-19 pandemic. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Coronaviridae which is available at www.ictv.global/report/coronaviridae.
Collapse
Affiliation(s)
- Patrick C Y Woo
- PhD Program in Translational Medicine and Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan, ROC
| | - Raoul J de Groot
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Bart Haagmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam, Netherlands
| | - Susanna K P Lau
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, PR China
| | - Benjamin W Neuman
- Department of Biology, Texas A&M University, College Station, Texas, 77843, USA
| | - Stanley Perlman
- Departments of Microbiology and Immunology, and Pediatrics, University of Iowa, Iowa City, IA 52242, USA
| | - Isabel Sola
- Department of Molecular and Cell Biology, National Center for Biotechnology-Spanish, National Research Council (CNB-CSIC), Madrid, Spain
| | - Lia van der Hoek
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, Laboratory of Experimental Virology, Location University of Amsterdam, 1105 AZ Amsterdam, Netherlands
| | - Antonio C P Wong
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, PR China
| | - Shiou-Hwei Yeh
- Department of Microbiology, College of Medicine, National Taiwan University, Taipei, Taiwan, ROC
| |
Collapse
|
4
|
Chaturvedi A, Borkar K, Priyakumar UD, Vinod P. PREHOST: Host prediction of coronaviridae family using machine learning. Heliyon 2023; 9:e13646. [PMID: 36816252 PMCID: PMC9922161 DOI: 10.1016/j.heliyon.2023.e13646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 02/05/2023] [Accepted: 02/06/2023] [Indexed: 02/13/2023] Open
Abstract
Coronavirus, a zoonotic virus capable of transmitting infections from animals to humans, emerged as a pandemic recently. In such circumstances, it is essential to understand the virus's origin. In this study, we present a novel machine-learning pipeline PreHost for host prediction of the family, Coronaviridae. We leverage the complete viral genome and sequences at the protein level (spike protein, membrane protein, and nucleocapsid protein). Compared with the current state-of-the-art approaches, the random forest model attained high accuracy and recall scores of 99.91% and 0.98, respectively, for genome sequences. In addition to the spike protein sequences, our study shows membrane and nucleocapsid protein sequences can be utilized to predict the host of viruses. We also identified important sites in the viral sequences that help distinguish between different host classes. The host prediction pipeline PreHost will cater as a valuable tool to take effective measures to govern the transmission of future viruses.
Collapse
|
5
|
Baldisserotto C, Gentili V, Rizzo R, Di Donna C, Ardondi L, Maietti A, Pancaldi S. Characterization of Neochloris oleoabundans under Different Cultivation Modes and First Results on Bioactivity of Its Extracts against HCoV-229E Virus. Plants (Basel) 2022; 12:26. [PMID: 36616154 PMCID: PMC9823352 DOI: 10.3390/plants12010026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/14/2022] [Accepted: 12/17/2022] [Indexed: 06/17/2023]
Abstract
Microalgae are proposed in several biotechnological fields because of their ability to produce biomass enriched in high-value compounds according to cultivation conditions. Regarding the health sector, an emerging area focuses on natural products exploitable against viruses. This work deals with the characterization of the green microalga Neochloris oleoabundans cultivated under autotrophic and mixotrophic conditions as a source of whole aqueous extracts, tested as antivirals against HCoV-229E (Coronaviridae family). Glucose was employed for mixotrophic cultures. Growth and maximum quantum yield of photosystem II were monitored for both cultivations. Algae extracts for antiviral tests were prepared using cultures harvested at the early stationary phase of growth. Biochemical and morphological analyses of algae indicated a different content of the most important classes of bioactive compounds with antiviral properties (lipids, exo-polysaccharides, and total phenolics, proteins and pigments). To clarify which phase of HCoV-229E infection on MRC-5 fibroblast cells was affected by N. oleoabundans extracts, four conditions were tested. Extracts gave excellent results, mainly against the first steps of virus infection. Notwithstanding the biochemical profile of algae/extracts deserves further investigation, the antiviral effect may have been mainly promoted by the combination of proteins/pigments/phenolics for the extract derived from autotrophic cultures and of proteins/acidic exo-polysaccharides/lipids in the case of mixotrophic ones.
Collapse
Affiliation(s)
- Costanza Baldisserotto
- Department of Environmental and Prevention Sciences, University of Ferrara, C.so Ercole I d’Este, 32, 44121 Ferrara, Italy
| | - Valentina Gentili
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Via Luigi Borsari, 46, 44121 Ferrara, Italy
| | - Roberta Rizzo
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Via Luigi Borsari, 46, 44121 Ferrara, Italy
| | - Chiara Di Donna
- Department of Environmental and Prevention Sciences, University of Ferrara, C.so Ercole I d’Este, 32, 44121 Ferrara, Italy
| | - Luna Ardondi
- Department of Environmental and Prevention Sciences, University of Ferrara, C.so Ercole I d’Este, 32, 44121 Ferrara, Italy
| | - Annalisa Maietti
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Via Luigi Borsari, 46, 44121 Ferrara, Italy
| | - Simonetta Pancaldi
- Department of Environmental and Prevention Sciences, University of Ferrara, C.so Ercole I d’Este, 32, 44121 Ferrara, Italy
| |
Collapse
|
6
|
Violet-Lozano L, Haach V, Barboza CM, Dos Santos J, Gomes BF, de Cassia Pardo de Souza T, Junior PC, Arns CW, de Carvalho Ruthner Batista HB, Roehe PM, Franco AC. No molecular evidence for influenza A virus and coronavirus in bats belonging to the families Phyllostomidae, Vespertilionidae, and Molossidae in the state of São Paulo, Brazil. Braz J Microbiol 2023; 54:523-9. [PMID: 36422849 DOI: 10.1007/s42770-022-00878-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 11/16/2022] [Indexed: 11/25/2022] Open
Abstract
This study aimed to evaluate, by molecular methods, the presence of influenza A virus (IAV) and coronavirus in non-hematophagous bats collected in the state of São Paulo, Brazil. Samples of lung tissue and small intestine from 105 bats belonging to three families (Phyllostomidae, Vespertilionidae, and Molossidae) were collected in 22 municipalities in the state of São Paulo. Genetic identification of bats species was performed by amplification and sequencing of a fragment of 710 bp of the mitochondrial COI gene. In the detection of IAV, genomes were performed by RT-PCR, aiming at the amplification of a 245-bp fragment of the IAV matrix (M) protein gene. For coronaviruses, two fragments of 602 and 440 bp corresponding to segments along the gene encoding the RNA-dependent RNA polymerase (RdRp) were targeted. The detection limit for each of the PCRs was also determined. All samples analyzed here were negative for both viruses, and the lower limit of detection of the PCRs for the amplification of influenza virus A and coronavirus was estimated at 3.5 × 103 and 4.59 genomic copies per microliter, respectively. Although bats have been shown to harbor a large number of pathogens, the results of the present study support the theory that virus circulation in bats in the wild often occurs at low viral loads and that our understanding of the complex infectious dynamics of these viruses in wild conditions is still limited.
Collapse
|
7
|
Kumar S, Dutta D, Ravichandiran V, Sukla S. Monoclonal antibodies: a remedial approach to prevent SARS-CoV-2 infection. 3 Biotech 2022; 12:227. [PMID: 35982759 PMCID: PMC9383686 DOI: 10.1007/s13205-022-03281-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 07/26/2022] [Indexed: 11/07/2022] Open
Abstract
SARS-CoV-2, the newly emerged virus of the Coronaviridae family is causing havoc worldwide. The novel coronavirus 2019 was first reported in Wuhan, China marked as the third highly infectious pathogenic virus of the twenty-first century. The typical manifestations of COVID-19 include cough, sore throat, fever, fatigue, loss of sense of taste and difficulties in breathing. Large numbers of SARS-CoV-2 infected patients have mild to moderate symptoms, however severe and life-threatening cases occur in about 5-10% of infections with an approximately 2% mortality rate. For the treatment of SARS-CoV-2, the use of neutralizing monoclonal antibodies (mAbs) could be one approach. The receptor binding domain (RBD) and N-terminal domain (NTD) situated on the peak of the spike protein (S-Protein) of SARS-CoV-2 are immunogenic in nature, therefore, can be targeted by neutralizing monoclonal antibodies. Several bioinformatics approaches highlight the identification of novel SARS-CoV-2 epitopes which can be targeted for the development of COVID-19 therapeutics. Here we present a summary of neutralizing mAbs isolated from COVID-19 infected patients which are anticipated to be a better therapeutic alternative against SARS-CoV-2. However, provided the vast escalation of the disease worldwide affecting people from all strata, affording expensive mAb therapy will not be feasible. Hence other strategies are also being employed to find suitable vaccine candidates and antivirals against SARS-CoV-2 that can be made easily available to the population.
Collapse
Affiliation(s)
- Sonu Kumar
- Department of Pharmacology and Toxicology, National Institute of Pharmaceuticals Education and Research, 168, Maniktala Main Road, Kolkata, 700054 West Bengal India
| | - Debrupa Dutta
- Department of Pharmacology and Toxicology, National Institute of Pharmaceuticals Education and Research, 168, Maniktala Main Road, Kolkata, 700054 West Bengal India
| | - Velayutham Ravichandiran
- Department of Natural Products, National Institute of Pharmaceuticals Education and Research, 168, Maniktala Main Road, Kolkata, 700054 West Bengal India
| | - Soumi Sukla
- Department of Pharmacology and Toxicology, National Institute of Pharmaceuticals Education and Research, 168, Maniktala Main Road, Kolkata, 700054 West Bengal India
| |
Collapse
|
8
|
Abstract
Virus infection is a process that requires combined contributions from both virus and host factors. For this process to be efficient within the crowded host environment, viruses have evolved ways to manipulate and reorganize host structures to produce cellular microenvironments. Positive-strand RNA virus replication and assembly occurs in association with cytoplasmic membranes, causing a reorganization of these membranes to create microenvironments that support viral processes. Similarities between virus-induced membrane domains and cellular organelles have led to the description of these structures as virus replication organelles (vRO). Electron microscopy analysis of vROs in positive-strand RNA virus infected cells has revealed surprising morphological similarities between genetically diverse virus species. For all positive-strand RNA viruses, vROs can be categorized into two groups: those that make invaginations into the cellular membranes (In-vRO), and those that cause the production of protrusions from cellular membranes (Pr-vRO), most often in the form of double membrane vesicles (DMVs). In this review, we will discuss the current knowledge on the structure and biogenesis of these two different vRO classes as well as comparing morphology and function of vROs between various positive-strand RNA viruses. Finally, we will discuss recent studies describing pharmaceutical intervention in vRO formation as an avenue to control virus infection.
Collapse
Affiliation(s)
- Christopher John Neufeldt
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Mirko Cortese
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| |
Collapse
|
9
|
Hernández S, Feracci M, De Jesus CT, El Kazzi P, Kaci R, Garlatti L, Mondielli C, Bailly F, Cotelle P, Touret F, de Lamballerie X, Coutard B, Decroly E, Canard B, Ferron F, Alvarez K. Identification of potent inhibitors of arenavirus and SARS-CoV-2 exoribonucleases by fluorescence polarization assay. Antiviral Res 2022; 204:105364. [PMID: 35716929 PMCID: PMC9212739 DOI: 10.1016/j.antiviral.2022.105364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 06/08/2022] [Accepted: 06/13/2022] [Indexed: 01/17/2023]
Abstract
Viral exoribonucleases are uncommon in the world of RNA viruses. To date, they have only been identified in the Arenaviridae and the Coronaviridae families. The exoribonucleases of these viruses play a crucial role in the pathogenicity and interplay with host innate immune response. Moreover, coronaviruses exoribonuclease is also involved in a proofreading mechanism ensuring the genetic stability of the viral genome. Because of their key roles in virus life cycle, they constitute attractive target for drug design. Here we developed a sensitive, robust and reliable fluorescence polarization assay to measure the exoribonuclease activity and its inhibition in vitro. The effectiveness of the method was validated on three different viral exoribonucleases, including SARS-CoV-2, Lymphocytic Choriomeningitis and Machupo viruses. We performed a screening of a focused library consisting of 113 metal chelators. Hit compounds were recovered with an IC50 at micromolar level. We confirmed 3 hits in SARS-CoV-2 infected Vero-E6 cells.
Collapse
Affiliation(s)
- Sergio Hernández
- Université Aix-Marseille, Architecture et Fonction des Macromolécules Biologiques (AFMB) – UMR7257 CNRS – Case 932, 163 avenue de Luminy, Marseille CEDEX 09, 13288, France
| | - Mikael Feracci
- Université Aix-Marseille, Architecture et Fonction des Macromolécules Biologiques (AFMB) – UMR7257 CNRS – Case 932, 163 avenue de Luminy, Marseille CEDEX 09, 13288, France
| | - Carolina Trajano De Jesus
- Université Aix-Marseille, Architecture et Fonction des Macromolécules Biologiques (AFMB) – UMR7257 CNRS – Case 932, 163 avenue de Luminy, Marseille CEDEX 09, 13288, France
| | - Priscila El Kazzi
- Université Aix-Marseille, Architecture et Fonction des Macromolécules Biologiques (AFMB) – UMR7257 CNRS – Case 932, 163 avenue de Luminy, Marseille CEDEX 09, 13288, France
| | - Rafik Kaci
- Université Aix-Marseille, Architecture et Fonction des Macromolécules Biologiques (AFMB) – UMR7257 CNRS – Case 932, 163 avenue de Luminy, Marseille CEDEX 09, 13288, France
| | - Laura Garlatti
- Université Aix-Marseille, Architecture et Fonction des Macromolécules Biologiques (AFMB) – UMR7257 CNRS – Case 932, 163 avenue de Luminy, Marseille CEDEX 09, 13288, France
| | - Clemence Mondielli
- Evotec (France) SAS, Campus Curie, 195 route d’Espagne, 31036, Toulouse CEDEX, France
| | - Fabrice Bailly
- Univ Lille, INSERM, CHU Lille, UMR-S 1172, Lille Neuroscience and Cognition Research Center, F-59000, Lille, France
| | - Philippe Cotelle
- Univ Lille, INSERM, CHU Lille, UMR-S 1172, Lille Neuroscience and Cognition Research Center, F-59000, Lille, France,ENSCL-Centrale Lille, CS 90108, F-59652, Villeneuve d’Ascq, France
| | - Franck Touret
- Unité des Virus Émergents (UVE: Aix-Marseille University -IRD 190-Inserm 1207-IHU Méditerranée Infection), Marseille, France
| | - Xavier de Lamballerie
- Unité des Virus Émergents (UVE: Aix-Marseille University -IRD 190-Inserm 1207-IHU Méditerranée Infection), Marseille, France
| | - Bruno Coutard
- Unité des Virus Émergents (UVE: Aix-Marseille University -IRD 190-Inserm 1207-IHU Méditerranée Infection), Marseille, France
| | - Etienne Decroly
- Université Aix-Marseille, Architecture et Fonction des Macromolécules Biologiques (AFMB) – UMR7257 CNRS – Case 932, 163 avenue de Luminy, Marseille CEDEX 09, 13288, France
| | - Bruno Canard
- Université Aix-Marseille, Architecture et Fonction des Macromolécules Biologiques (AFMB) – UMR7257 CNRS – Case 932, 163 avenue de Luminy, Marseille CEDEX 09, 13288, France
| | - François Ferron
- Université Aix-Marseille, Architecture et Fonction des Macromolécules Biologiques (AFMB) – UMR7257 CNRS – Case 932, 163 avenue de Luminy, Marseille CEDEX 09, 13288, France,Corresponding author. AFMB, Case 932, 163 avenue de Luminy, 13288, Marseille Cedex 9, France
| | - Karine Alvarez
- Université Aix-Marseille, Architecture et Fonction des Macromolécules Biologiques (AFMB) – UMR7257 CNRS – Case 932, 163 avenue de Luminy, Marseille CEDEX 09, 13288, France,Corresponding author. AFMB, Case 932, 163 avenue de Luminy, 13288, Marseille Cedex 9, France
| |
Collapse
|
10
|
Abstract
Recombination is a common evolutionary tool for RNA viruses, and coronaviruses are no exception. We review here the evidence for recombination in SARS-CoV-2 and reconcile nomenclature for recombinants, discuss their origin and fitness, and speculate how recombinants could make a difference in the future of the COVID-19 pandemics.
Collapse
Affiliation(s)
- Daniele Focosi
- North-Western Tuscany Blood Bank, Pisa University Hospital, 56124 Pisa, Italy
| | - Fabrizio Maggi
- Department of Medicine and Surgery, University of Insubria, 21100 Varese, Italy
| |
Collapse
|
11
|
Kesheh MM, Shavandi S, Haeri Moghaddam N, Ramezani M, Ramezani F. Effect of herbal compounds on coronavirus; a systematic review and meta-analysis. Virol J 2022; 19:87. [PMID: 35597998 PMCID: PMC9123756 DOI: 10.1186/s12985-022-01808-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 04/28/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The new coronavirus (COVID-19) has been transmitted exponentially. Numerous studies have been performed in recent years that have shown the inhibitory effect of plant extracts or plant-derived compounds on the coronavirus family. In this study, we want to use systematic review and meta-analysis to answer the question, which herbal compound has been more effective? MAIN BODY The present study is based on the guidelines for conducting meta-analyzes. An extensive search was conducted in the electronic database, and based on the inclusion and exclusion criteria, articles were selected and data screening was done. Quality control of articles was performed. Data analysis was carried out in STATA software. CONCLUSION Due to the variety of study methods, definitive conclusions are not possible. However, in this study, we attempted to gather all the available evidence on the effect of plant compounds on SARS-COV-2 to be used for the development and use of promising antiviral agents against this virus and other coronaviruses. Trypthantrin, Sambucus extract, S. cusia extract, Boceprevir and Indigole B, dioica agglutinin urtica had a good effect on reducing the virus titer. Also among the compounds that had the greatest effect on virus inhibition, Saikosaponins B2, SaikosaponinsD, SaikosaponinsA and Phillyrin, had an acceptable selectivity index greater than 10. Andrographolide showed the highest selectivity index on SARS-COV-2. Our study confirmed insufficient data to support alkaloid compounds against SARS-COV-2, and the small number of studies that used alkaloid compounds was a limitation. It is recommended to investigate the effect of more alkaloid compounds against Corona virus.
Collapse
Affiliation(s)
- Mina Mobini Kesheh
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Sara Shavandi
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Niloofar Haeri Moghaddam
- Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | | | - Fatemeh Ramezani
- Physiology Research Center, Iran University of Medical Sciences, Tehran, Iran.
| |
Collapse
|
12
|
Abstract
The current outbreak of coronavirus disease-2019 (COVID-19) caused by SARS-CoV-2 poses unparalleled challenges to global public health. SARS-CoV-2 is a Betacoronavirus, one of four genera belonging to the Coronaviridae subfamily Orthocoronavirinae. Coronaviridae, in turn, are members of the order Nidovirales, a group of enveloped, positive-stranded RNA viruses. Here we present a systematic phylogenetic and evolutionary study based on protein domain architecture, encompassing the entire proteomes of all Orthocoronavirinae, as well as other Nidovirales. This analysis has revealed that the genomic evolution of Nidovirales is associated with extensive gains and losses of protein domains. In Orthocoronavirinae, the sections of the genomes that show the largest divergence in protein domains are found in the proteins encoded in the amino-terminal end of the polyprotein (PP1ab), the spike protein (S), and many of the accessory proteins. The diversity among the accessory proteins is particularly striking, as each subgenus possesses a set of accessory proteins that is almost entirely specific to that subgenus. The only notable exception to this is ORF3b, which is present and orthologous over all Alphacoronaviruses. In contrast, the membrane protein (M), envelope small membrane protein (E), nucleoprotein (N), as well as proteins encoded in the central and carboxy-terminal end of PP1ab (such as the 3C-like protease, RNA-dependent RNA polymerase, and Helicase) show stable domain architectures across all Orthocoronavirinae. This comprehensive analysis of the Coronaviridae domain architecture has important implication for efforts to develop broadly cross-protective coronavirus vaccines.
Collapse
Affiliation(s)
- Christian M Zmasek
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA, 92037, USA
| | - Elliot J Lefkowitz
- Department of Microbiology, UAB School of Medicine, Birmingham, AL, 35294, USA
| | - Anna Niewiadomska
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA, 92037, USA
| | - Richard H Scheuermann
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA, 92037, USA; Department of Pathology, University of California, San Diego, CA, 92093, USA; Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA; Global Virus Network, Baltimore MD, 21201, USA.
| |
Collapse
|
13
|
Allen RA, Williams CL, Penrod Y, McCloskey C, Carpenter-Azevedo K, Huard RC, King E, Terence Dunn S. A pyrosequencing protocol for rapid identification of SARS-CoV-2 variants. J Med Virol 2022; 94:3661-3668. [PMID: 35416308 PMCID: PMC9088475 DOI: 10.1002/jmv.27770] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 03/18/2022] [Accepted: 04/09/2022] [Indexed: 11/25/2022]
Abstract
Next‐generation sequencing (NGS) is the primary method used to monitor the distribution and emergence of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) variants around the world; however, it is costly and time‐consuming to perform and is not widely available in low‐resourced geographical regions. Pyrosequencing has the potential to augment surveillance efforts by providing information on specific targeted mutations for rapid identification of circulating and emerging variants. The current study describes the development of a reverse transcription (RT)‐PCR‐pyrosequencing assay targeting >65 spike protein gene (S) mutations of SARS‐CoV‐2, which permits differentiation of commonly reported variants currently circulating in the United States with a high degree of confidence. Variants typed using the assay included B.1.1.7 (Alpha), B.1.1.529 (Omicron), B.1.351 (Beta), B.1.375, B.1.427/429 (Epsilon), B.1.525 (Eta), B.1.526.1 (Iota), B.1.617.1 (Kappa), B.1.617.2 (Delta), B.1.621 (Mu), P1 (Gamma), and B.1.1 variants, all of which were confirmed by the NGS data. An electronic typing tool was developed to aid in the identification of variants based on mutations detected by pyrosequencing. The assay could provide an important typing tool for rapid identification of candidate patients for monoclonal antibody therapies and a method to supplement SARS‐CoV‐2 surveillance efforts by identification of circulating variants and novel emerging lineages.
Collapse
Affiliation(s)
| | - Christopher L Williams
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Yvonne Penrod
- OU Health Laboratories, Oklahoma City, Oklahoma, USA
| | | | | | - Richard C Huard
- Rhode Island Department of Health (RIDOH) Laboratories, Providence, Rhode Island, USA
| | - Ewa King
- Rhode Island Department of Health (RIDOH) Laboratories, Providence, Rhode Island, USA
| | - S Terence Dunn
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| |
Collapse
|
14
|
He WT, Bollen N, Xu Y, Zhao J, Dellicour S, Yan Z, Gong W, Zhang C, Zhang L, Lu M, Lai A, Suchard MA, Ji X, Tu C, Lemey P, Baele G, Su S. Phylogeography reveals association between swine trade and the spread of porcine epidemic diarrhea virus in China and across the world. Mol Biol Evol 2021; 39:6482749. [PMID: 34951645 PMCID: PMC8826572 DOI: 10.1093/molbev/msab364] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The ongoing SARS (severe acute respiratory syndrome)-CoV (coronavirus)-2 pandemic has exposed major gaps in our knowledge on the origin, ecology, evolution, and spread of animal coronaviruses. Porcine epidemic diarrhea virus (PEDV) is a member of the genus Alphacoronavirus in the family Coronaviridae that may have originated from bats and leads to significant hazards and widespread epidemics in the swine population. The role of local and global trade of live swine and swine-related products in disseminating PEDV remains unclear, especially in developing countries with complex swine production systems. Here, we undertake an in-depth phylogeographic analysis of PEDV sequence data (including 247 newly sequenced samples) and employ an extension of this inference framework that enables formally testing the contribution of a range of predictor variables to the geographic spread of PEDV. Within China, the provinces of Guangdong and Henan were identified as primary hubs for the spread of PEDV, for which we estimate live swine trade to play a very important role. On a global scale, the United States and China maintain the highest number of PEDV lineages. We estimate that, after an initial introduction out of China, the United States acted as an important source of PEDV introductions into Japan, Korea, China, and Mexico. Live swine trade also explains the dispersal of PEDV on a global scale. Given the increasingly global trade of live swine, our findings have important implications for designing prevention and containment measures to combat a wide range of livestock coronaviruses.
Collapse
Affiliation(s)
- Wan-Ting He
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, China Nanjing
| | - Nena Bollen
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Belgium Leuven
| | - Yi Xu
- China animal disease control center, Ministry of Agriculture, China Beijing
| | - Jin Zhao
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, China Nanjing
| | - Simon Dellicour
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Belgium Leuven.,Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Belgium CP160/12 50, av. FD Roosevelt, 1050 Bruxelles
| | - Ziqing Yan
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, China Nanjing
| | - Wenjie Gong
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, China Changchun, Jilin
| | - Cheng Zhang
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, China Nanjing
| | - Letian Zhang
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, China Nanjing
| | - Meng Lu
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, China Nanjing
| | - Alexander Lai
- School of Science, Technology, Engineering, and Mathematics, Kentucky State University, United States Frankfort, Kentucky
| | - Marc A Suchard
- Department of Biostatistics, Fielding School of Public Health, and Departments of Biomathematics and Human Genetics, David Geffen School of Medicine, University of California Los Angeles Los Angeles, CA
| | - Xiang Ji
- Department of Mathematics, School of Science & Engineering, Tulane University New Orleans, LA
| | - Changchun Tu
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, China Changchun, Jilin
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Belgium Leuven
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Belgium Leuven
| | - Shuo Su
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, China Nanjing
| |
Collapse
|
15
|
Espinoza-Ascurra G, Gonzales-Graus I, Meléndez-Marón M, Cabrera R. [Prevalence and factors associated with depression in health personnel during the SARS-CoV-2 pandemic in the department of Piura, Peru]. Rev Colomb Psiquiatr 2021:S0034-7450(21)00179-7. [PMID: 34931095 PMCID: PMC8673821 DOI: 10.1016/j.rcp.2021.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 11/07/2021] [Indexed: 01/08/2023]
Abstract
INTRODUCTION The COVID-19 pandemic has increased the magnitude of mental illnesses such as depression, not only in the general population, but also in health personnel. However, in Peru the prevalence is not known and the associated factors for developing depression in health personnel are not known. OBJECTIVE To determine the prevalence and identify the factors associated with depression in health personnel, in the context of the SARS-CoV-2 pandemic. MATERIAL AND METHOD An analytical cross-sectional study was carried out between the months of May-September in health establishments. A sample of 136 health workers were included and a survey was applied to collect the data. Depression as a dependent variable was measured using the Zung self-report scale. To identify the associated factors, the bivariate and multivariate analysis was performed by logistic regression with STATA v 14. RESULTS The prevalence of depression was 8.8% CI 95% (4.64-14.90), likewise, the antecedent of having a family member or friend died from COVID-19 with a p value of 0.017 and OR of 6.78 (CI: 1.39-32.90). On the other hand, the use of personal protective equipment (PPE) was found to be a protective factor against the development of depression with p value 0.003 and OR of 0.03 (CI: 0.004-0.32). CONCLUSIONS Approximately 1 in 10 among health professionals and technicians developed depression during the SARS-CoV-2 pandemic in this study. In addition, the history of having relatives or friends killed by COVID-19 was negatively associated with depression and the use of PPE was identified as a protective factor for depression.
Collapse
Affiliation(s)
| | | | - Mónica Meléndez-Marón
- Subregión de Salud Luciano Castillo Colona, Dirección Regional de Salud Piura, Sullana, Perú
| | - Rufino Cabrera
- Escuela de Medicina, Universidad Peruana de Ciencias Aplicadas, Lima, Perú
| |
Collapse
|
16
|
Nefedova E, Koptev V, Bobikova AS, Cherepushkina V, Mironova T, Afonyushkin V, Shkil N, Donchenko N, Kozlova Y, Sigareva N, Davidova N, Bogdanchikova N, Pestryakov A, Toledano-Magaña Y. The Infectious Bronchitis Coronavirus Pneumonia Model Presenting a Novel Insight for the SARS-CoV-2 Dissemination Route. Vet Sci 2021; 8:239. [PMID: 34679068 PMCID: PMC8540477 DOI: 10.3390/vetsci8100239] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/10/2021] [Accepted: 10/12/2021] [Indexed: 12/13/2022] Open
Abstract
Infectious bronchitis (IB) of chickens is a highly contagious disease characterized by damage of the respiratory system and reproductive organs in young animals caused by a virus of the genus Gamma coronavirus. The condition of the respiratory system caused by the IB virus in chickens has many similarities with the pathology of the respiratory system caused by SARS-CoV-2 in humans. The effectiveness of virucidal drugs (Argovit, Triviron, Ecocid, and lauric acid monoglyceride) was tested on chickens inoculated with a tenfold dose of a vaccine strain based on the attenuated virus H120 against IB of chickens. On the 6th day after inoculation, inflammatory changes in the intestines, lungs, and thymus were observed in the control group. The experimental groups were characterized by less pronounced inflammatory reactions and a lower proportion of thymus and lung probes containing genomic IB virus RNA. Since the virucidal activity of four orally administrated formulations was possible only in the intestine, the experimental data indirectly confirmed the hypothesis of the possibility of the predominant accumulation of coronaviruses in the intestine and subsequent lung damage due to the hematogenous redistribution of viral particles and IBV antigens. It was suggested that other coronaviruses including SARS-CoV-2 can implement a similar mechanism.
Collapse
Affiliation(s)
- Ekaterina Nefedova
- Siberian Federal Scientific Center of Agro-BioTechnologies of Russian Academy of Sciences, Novosibirsk Region, Novosibirsk District, 630501 Krasnoobsk, Russia; (E.N.); (V.K.); (A.S.B.); (V.C.); (T.M.); (V.A.); (N.S.); (N.D.); (N.D.)
| | - Vyacheslav Koptev
- Siberian Federal Scientific Center of Agro-BioTechnologies of Russian Academy of Sciences, Novosibirsk Region, Novosibirsk District, 630501 Krasnoobsk, Russia; (E.N.); (V.K.); (A.S.B.); (V.C.); (T.M.); (V.A.); (N.S.); (N.D.); (N.D.)
| | - Anna S. Bobikova
- Siberian Federal Scientific Center of Agro-BioTechnologies of Russian Academy of Sciences, Novosibirsk Region, Novosibirsk District, 630501 Krasnoobsk, Russia; (E.N.); (V.K.); (A.S.B.); (V.C.); (T.M.); (V.A.); (N.S.); (N.D.); (N.D.)
- Molecular Biology Department, Federal State Budgetary Educational Institution Higher Education Novosibirsk State Agrarian University, 630090 Novosibirsk, Russia;
| | - Viktoria Cherepushkina
- Siberian Federal Scientific Center of Agro-BioTechnologies of Russian Academy of Sciences, Novosibirsk Region, Novosibirsk District, 630501 Krasnoobsk, Russia; (E.N.); (V.K.); (A.S.B.); (V.C.); (T.M.); (V.A.); (N.S.); (N.D.); (N.D.)
| | - Tatyana Mironova
- Siberian Federal Scientific Center of Agro-BioTechnologies of Russian Academy of Sciences, Novosibirsk Region, Novosibirsk District, 630501 Krasnoobsk, Russia; (E.N.); (V.K.); (A.S.B.); (V.C.); (T.M.); (V.A.); (N.S.); (N.D.); (N.D.)
- Molecular Biology Department, Federal State Budgetary Educational Institution Higher Education Novosibirsk State Agrarian University, 630090 Novosibirsk, Russia;
| | - Vasily Afonyushkin
- Siberian Federal Scientific Center of Agro-BioTechnologies of Russian Academy of Sciences, Novosibirsk Region, Novosibirsk District, 630501 Krasnoobsk, Russia; (E.N.); (V.K.); (A.S.B.); (V.C.); (T.M.); (V.A.); (N.S.); (N.D.); (N.D.)
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia;
| | - Nikolai Shkil
- Siberian Federal Scientific Center of Agro-BioTechnologies of Russian Academy of Sciences, Novosibirsk Region, Novosibirsk District, 630501 Krasnoobsk, Russia; (E.N.); (V.K.); (A.S.B.); (V.C.); (T.M.); (V.A.); (N.S.); (N.D.); (N.D.)
| | - Nikolai Donchenko
- Siberian Federal Scientific Center of Agro-BioTechnologies of Russian Academy of Sciences, Novosibirsk Region, Novosibirsk District, 630501 Krasnoobsk, Russia; (E.N.); (V.K.); (A.S.B.); (V.C.); (T.M.); (V.A.); (N.S.); (N.D.); (N.D.)
| | - Yulia Kozlova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia;
| | - Natalia Sigareva
- Molecular Biology Department, Federal State Budgetary Educational Institution Higher Education Novosibirsk State Agrarian University, 630090 Novosibirsk, Russia;
| | - Natalia Davidova
- Siberian Federal Scientific Center of Agro-BioTechnologies of Russian Academy of Sciences, Novosibirsk Region, Novosibirsk District, 630501 Krasnoobsk, Russia; (E.N.); (V.K.); (A.S.B.); (V.C.); (T.M.); (V.A.); (N.S.); (N.D.); (N.D.)
| | - Nina Bogdanchikova
- Centro de Nanociencias y Nanotecnología, Universidad Nacional Autónoma de México, Ensenada 22860, BC, Mexico
| | - Alexey Pestryakov
- Research School of Chemistry & Applied Biomedical Sciences, National Research Tomsk Polytechnic University, 634050 Tomsk, Russia;
| | - Yanis Toledano-Magaña
- Escuela de Ciencias de la Salud Unidad Valle Dorado, Universidad Autónoma de Baja California, Ensenada 22890, BC, Mexico
| |
Collapse
|
17
|
Van Borm S, Steensels M, Mathijs E, Vandenbussche F, van den Berg T, Lambrecht B. Metagenomic sequencing determines complete infectious bronchitis virus (avian Gammacoronavirus) vaccine strain genomes and associated viromes in chicken clinical samples. Virus Genes 2021; 57:529-540. [PMID: 34626348 PMCID: PMC8501334 DOI: 10.1007/s11262-021-01872-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 09/24/2021] [Indexed: 12/24/2022]
Abstract
Infectious bronchitis virus (IBV, genus Gammacoronavirus) causes an economically important and highly contagious disease in chicken. Random primed RNA sequencing was applied to two IBV positive clinical samples and one in ovo-passaged virus. The virome of a cloacal swab pool was dominated by IBV (82% of viral reads) allowing de novo assembly of a GI-13 lineage complete genome with 99.95% nucleotide identity to vaccine strain 793B. In addition, substantial read counts (16% of viral reads) allowed the assembly of a near-complete chicken astrovirus genome, while lower read counts identified the presence of chicken calicivirus and avian leucosis virus. Viral reads in a respiratory/intestinal tissue pool were distributed between IBV (22.53%), Sicinivirus (Picornaviridae, 24%), and avian leucosis virus (37.04%). A complete IBV genome with 99.95% nucleotide identity to vaccine strain H120 (lineage GI-1), as well as a near-complete avian leucosis virus genome and a partial Sicinivirus genome were assembled from the tissue sample data. Lower read counts identified chicken calicivirus, Avibirnavirus (infectious bursal disease virus, assembling to 98.85% of segment A and 69.66% of segment B closely related to D3976/1 from Germany, 2017) and avian orthoreovirus, while three avian orthoavulavirus 1 reads confirmed prior real-time RT-PCR result. IBV sequence variation analysis identified both fixed and minor frequency variations in the tissue sample compared to its in ovo-passaged virus. Metagenomic methods allow the determination of complete coronavirus genomes from clinical chicken samples while providing additional insights in RNA virus sequence diversity and coinfecting viruses potentially contributing to pathogenicity.
Collapse
Affiliation(s)
- Steven Van Borm
- Department of Animal Infectious Diseases, Sciensano, Brussels, Belgium.
| | - Mieke Steensels
- Department of Animal Infectious Diseases, Sciensano, Brussels, Belgium
| | - Elisabeth Mathijs
- Department of Animal Infectious Diseases, Sciensano, Brussels, Belgium
| | | | | | | |
Collapse
|
18
|
Ayipo YO, Yahaya SN, Alananzeh WA, Babamale HF, Mordi MN. Pathomechanisms, therapeutic targets and potent inhibitors of some beta-coronaviruses from bench-to-bedside. Infect Genet Evol 2021; 93:104944. [PMID: 34052418 PMCID: PMC8159710 DOI: 10.1016/j.meegid.2021.104944] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 04/22/2021] [Accepted: 05/26/2021] [Indexed: 01/07/2023]
Abstract
Since the emergence of their primitive strains, the complexity surrounding their pathogenesis, constant genetic mutation and translation are contributing factors to the scarcity of a successful vaccine for coronaviruses till moment. Although, the recent announcement of vaccine breakthrough for COVID-19 renews the hope, however, there remains a major challenge of accessibility to urgently match the rapid global therapeutic demand for curtailing the pandemic, thereby creating an impetus for further search. The reassessment of results from a stream of experiments is of enormous importance in identifying bona fide lead-like candidates to fulfil this quest. This review comprehensively highlights the common pathomechanisms and pharmacological targets of HCoV-OC43, SARS-CoV-1, MERS-CoV and SARS-CoV-2, and potent therapeutic potentials from basic and clinical experimental investigations. The implicated targets for the prevention and treatment include the viral proteases (Mpro, PLpro, 3CLpro), viral structural proteins (S- and N-proteins), non-structural proteins (nsp 3, 8, 10, 14, 16), accessory protein (ns12.9), viroporins (3a, E, 8a), enzymes (RdRp, TMPRSS2, ADP-ribosyltransferase, MTase, 2'-O-MTase, TATase, furin, cathepsin, deamidated human triosephosphate isomerase), kinases (MAPK, ERK, PI3K, mTOR, AKT, Abl2), interleukin-6 receptor (IL-6R) and the human host receptor, ACE2. Notably among the 109 overviewed inhibitors include quercetin, eriodictyol, baicalin, luteolin, melatonin, resveratrol and berberine from natural products, GC373, NP164 and HR2P-M2 from peptides, 5F9, m336 and MERS-GD27 from specific human antibodies, imatinib, remdesivir, ivermectin, chloroquine, hydroxychloroquine, nafamostat, interferon-β and HCQ from repurposing libraries, some iron chelators and traditional medicines. This review represents a model for further translational studies for effective anti-CoV therapeutic designs.
Collapse
Affiliation(s)
- Yusuf Oloruntoyin Ayipo
- Centre for Drug Research, Universiti Sains Malaysia, USM, 11800 Pulau Pinang, Malaysia,Department of Chemistry, Kwara State University, P. M. B. 1530, Malete, Ilorin, Nigeria
| | - Sani Najib Yahaya
- Centre for Drug Research, Universiti Sains Malaysia, USM, 11800 Pulau Pinang, Malaysia
| | - Waleed A. Alananzeh
- Centre for Drug Research, Universiti Sains Malaysia, USM, 11800 Pulau Pinang, Malaysia
| | | | - Mohd Nizam Mordi
- Centre for Drug Research, Universiti Sains Malaysia, USM, 11800 Pulau Pinang, Malaysia,Corresponding author
| |
Collapse
|
19
|
Güttler T, Aksu M, Dickmanns A, Stegmann KM, Gregor K, Rees R, Taxer W, Rymarenko O, Schünemann J, Dienemann C, Gunkel P, Mussil B, Krull J, Teichmann U, Groß U, Cordes VC, Dobbelstein M, Görlich D. Neutralization of SARS-CoV-2 by highly potent, hyperthermostable, and mutation-tolerant nanobodies. EMBO J 2021; 40:e107985. [PMID: 34302370 PMCID: PMC8420576 DOI: 10.15252/embj.2021107985] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 07/06/2021] [Accepted: 07/13/2021] [Indexed: 11/09/2022] Open
Abstract
Monoclonal anti-SARS-CoV-2 immunoglobulins represent a treatment option for COVID-19. However, their production in mammalian cells is not scalable to meet the global demand. Single-domain (VHH) antibodies (also called nanobodies) provide an alternative suitable for microbial production. Using alpaca immune libraries against the receptor-binding domain (RBD) of the SARS-CoV-2 Spike protein, we isolated 45 infection-blocking VHH antibodies. These include nanobodies that can withstand 95°C. The most effective VHH antibody neutralizes SARS-CoV-2 at 17-50 pM concentration (0.2-0.7 µg per liter), binds the open and closed states of the Spike, and shows a tight RBD interaction in the X-ray and cryo-EM structures. The best VHH trimers neutralize even at 40 ng per liter. We constructed nanobody tandems and identified nanobody monomers that tolerate the K417N/T, E484K, N501Y, and L452R immune-escape mutations found in the Alpha, Beta, Gamma, Epsilon, Iota, and Delta/Kappa lineages. We also demonstrate neutralization of the Beta strain at low-picomolar VHH concentrations. We further discovered VHH antibodies that enforce native folding of the RBD in the E. coli cytosol, where its folding normally fails. Such "fold-promoting" nanobodies may allow for simplified production of vaccines and their adaptation to viral escape-mutations.
Collapse
Affiliation(s)
- Thomas Güttler
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Metin Aksu
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Antje Dickmanns
- Institute of Molecular Oncology, GZMB, University Medical Center, Göttingen, Germany
| | - Kim M Stegmann
- Institute of Molecular Oncology, GZMB, University Medical Center, Göttingen, Germany
| | - Kathrin Gregor
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Renate Rees
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Waltraud Taxer
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Oleh Rymarenko
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Jürgen Schünemann
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Christian Dienemann
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Philip Gunkel
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Bianka Mussil
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Jens Krull
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Ulrike Teichmann
- Animal facility, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Uwe Groß
- Institute of Medical Microbiology and Virology, University Medical Center, Göttingen, Germany
| | - Volker C Cordes
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Matthias Dobbelstein
- Institute of Molecular Oncology, GZMB, University Medical Center, Göttingen, Germany
| | - Dirk Görlich
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| |
Collapse
|
20
|
Bagherani N, Smoller BR. Hypothesis: Designation of Liposomal Scavenger System for Fighting against 2019-nCoV. Infect Disord Drug Targets 2021; 22:e150621194093. [PMID: 34132188 DOI: 10.2174/1871526521666210615141036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 02/18/2021] [Accepted: 03/05/2021] [Indexed: 11/22/2022]
Abstract
2019 novel coronavirus (2019-nCoV), also known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) or COVID-19 virus, is a member of the family Coronaviridae, which is responsible for the current pandemic of disease COVID-19. It is the seventh member of the family Coronaviridae, which infects humans, after 229E, OC43, NL63, HKU1, SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV). Fever, dry cough and severe pneumonia are seen as common symptoms at the early stages of COVID-19. Some cases progress to acute respiratory stress syndrome, septic shock, organ failure, and death. The development of an effective treatment or vaccination for treating or preventing this lethal condition is an urgent need in order to fight this crisis. Up to now, some effective vaccines with different efficacy profiles have been introduced. Herein, we have theoretically designed a scavenger system for gathering 2019-nCoVs, breaking them, and re-introducing them to the immune system.
Collapse
Affiliation(s)
- Nooshin Bagherani
- Department of Molecular Medicine, School of Advanced Medical Science, Tehran University of Medical School, Tehran, Iran
| | - Bruce R Smoller
- Department of Pathology, Professor, Department of Dermatology, University of Rochester, School of Medicine and Dentistry, United States
| |
Collapse
|
21
|
Miller AK, Mifsud JCO, Costa VA, Grimwood RM, Kitson J, Baker C, Brosnahan CL, Pande A, Holmes EC, Gemmell NJ, Geoghegan JL. Slippery when wet: cross-species transmission of divergent coronaviruses in bony and jawless fish and the evolutionary history of the Coronaviridae. Virus Evol 2021; 7:veab050. [PMID: 34527280 PMCID: PMC8244743 DOI: 10.1093/ve/veab050] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/19/2021] [Accepted: 05/28/2021] [Indexed: 01/31/2023] Open
Abstract
The Nidovirales comprise a genetically diverse group of positive-sense single-stranded RNA virus families that infect a range of invertebrate and vertebrate hosts. Recent metagenomic studies have identified nido-like virus sequences, particularly those related to the Coronaviridae, in a range of aquatic hosts including fish, amphibians, and reptiles. We sought to identify additional members of the Coronaviridae in both bony and jawless fish through a combination of total RNA sequencing (meta-transcriptomics) and data mining of published RNA sequencing data and from this reveal more of the long-term patterns and processes of coronavirus evolution. Accordingly, we identified a number of divergent viruses that fell within the Letovirinae subfamily of the Coronaviridae, including those in a jawless fish-the pouched lamprey. By mining fish transcriptome data, we identified additional virus transcripts matching these viruses in bony fish from both marine and freshwater environments. These new viruses retained sequence conservation in the RNA-dependant RNA polymerase across the Coronaviridae but formed a distinct and diverse phylogenetic group. Although there are broad-scale topological similarities between the phylogenies of the major groups of coronaviruses and their vertebrate hosts, the evolutionary relationship of viruses within the Letovirinae does not mirror that of their hosts. For example, the coronavirus found in the pouched lamprey fell within the phylogenetic diversity of bony fish letoviruses, indicative of past host switching events. Hence, despite possessing a phylogenetic history that likely spans the entire history of the vertebrates, coronavirus evolution has been characterised by relatively frequent cross-species transmission, particularly in hosts that reside in aquatic habitats.
Collapse
Affiliation(s)
| | | | | | - Rebecca M Grimwood
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand
| | - Jane Kitson
- Kitson Consulting Ltd 9 Black Road, Invercargill 9879, Invercargill/Waihopai, New Zealand
| | - Cindy Baker
- National Institute of Water and Atmospheric Research, Hamilton 3216, New Zealand
| | - Cara L Brosnahan
- Animal Health Laboratory and Diagnostic and Surveillance Directorate, Ministry for Primary Industries, Upper Hutt 5018, New Zealand
| | - Anjali Pande
- National Institute of Water and Atmospheric Research, Hamilton 3216, New Zealand,Animal Health Laboratory and Diagnostic and Surveillance Directorate, Ministry for Primary Industries, Upper Hutt 5018, New Zealand
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, Johns Hopkins Drive, The University of Sydney, Sydney, NSW 2006, Australia
| | - Neil J Gemmell
- Department of Anatomy, University of Otago, Dunedin 9016, New Zealand
| | | |
Collapse
|
22
|
Rossi G, Galosi L, Gavazza A, Cerquetella M, Mangiaterra S. Therapeutic approaches to coronavirus infection according to "One Health" concept. Res Vet Sci 2021; 136:81-88. [PMID: 33588098 PMCID: PMC7871813 DOI: 10.1016/j.rvsc.2021.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 02/03/2021] [Accepted: 02/06/2021] [Indexed: 12/16/2022]
Abstract
Coronaviridae constantly infect human and animals causing respiratory, gastroenteric or systemic diseases. Over time, these viruses have shown a marked ability to mutate, jumping over the human-animal barrier, thus becoming from enzootic to zoonotic. In the last years, numerous therapeutic protocols have been developed, mainly for severe acute respiratory syndromes in humans. The aim of this review is to summarize drugs or other approaches used in coronavirus infections focusing on different roles of these molecules or bacterial products on viral adhesion and replication or in modulating the host's immune system. Within the "One Health" concept, the study of viral pathogenic role and possible therapeutic approaches in both humans and animals is essential to protect public health.
Collapse
Affiliation(s)
- Giacomo Rossi
- Corresponding author at: School of Biosciences and Veterinary Medicine, University of Camerino, Via Circonvallazione 93/95 – 62024, Matelica (MC), Italy
| | | | | | | | | |
Collapse
|
23
|
Barik S. Systematizing the genomic order and relatedness in the open reading frames (ORFs) of the coronaviruses. Infect Genet Evol 2021; 92:104858. [PMID: 33848683 PMCID: PMC8053407 DOI: 10.1016/j.meegid.2021.104858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 04/05/2021] [Accepted: 04/07/2021] [Indexed: 11/16/2022]
Abstract
The coronaviruses (CoVs), including SARS-CoV-2, the agent of the ongoing deadly CoVID-19 pandemic (Coronavirus disease-2019), represent a highly complex and diverse class of RNA viruses with large genomes, complex gene repertoire, and intricate transcriptional and translational mechanisms. The 3′-terminal one-third of the genome encodes four structural proteins, namely spike, envelope, membrane, and nucleocapsid, interspersed with genes for accessory proteins that are largely nonstructural and called ‘open reading frame’ (ORF) proteins with alphanumerical designations, but not in a consistent or sequential order. Here, I report a comparative study of these ORF proteins, mainly encoded in two gene clusters, i.e. between the Spike and the Envelope genes, and between the Membrane and the Nucleocapsid genes. For brevity and focus, a greater emphasis was placed on the first cluster, collectively designated as the ‘orf3 region’ for ease of referral. Overall, an apparently diverse set of ORFs, such as ORF3a, ORF3b, ORF3c, ORF3d, ORF4 and ORF5, but not necessarily numbered in that order on all CoV genomes, were analyzed along with other ORFs. Unexpectedly, the gene order or naming of the ORFs were never fully conserved even within the members of one Genus. These studies also unraveled hitherto unrecognized orf genes in alternative translational frames, encoding potentially novel polypeptides as well as some that are highly similar to known ORFs. Finally, several options of an inclusive and systematic numbering are proposed not only for the orf3 region but also for the other orf genes in the viral genome in an effort to regularize the apparently confusing names and orders. Regardless of the ultimate acceptability of one system over the others, this treatise is hoped to initiate an informed discourse in this area.
Collapse
|
24
|
Mazzocco G, Niemiec I, Myronov A, Skoczylas P, Kaczmarczyk J, Sanecka-Duin A, Gruba K, Król P, Drwal M, Szczepanik M, Pyrc K, Stȩpniak P. AI Aided Design of Epitope-Based Vaccine for the Induction of Cellular Immune Responses Against SARS-CoV-2. Front Genet 2021; 12:602196. [PMID: 33841493 PMCID: PMC8027494 DOI: 10.3389/fgene.2021.602196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 01/28/2021] [Indexed: 12/17/2022] Open
Abstract
The heavy burden imposed by the COVID-19 pandemic on our society triggered the race toward the development of therapies or preventive strategies. Among these, antibodies and vaccines are particularly attractive because of their high specificity, low probability of drug-drug interaction, and potentially long-standing protective effects. While the threat at hand justifies the pace of research, the implementation of therapeutic strategies cannot be exempted from safety considerations. There are several potential adverse events reported after the vaccination or antibody therapy, but two are of utmost importance: antibody-dependent enhancement (ADE) and cytokine storm syndrome (CSS). On the other hand, the depletion or exhaustion of T-cells has been reported to be associated with worse prognosis in COVID-19 patients. This observation suggests a potential role of vaccines eliciting cellular immunity, which might simultaneously limit the risk of ADE and CSS. Such risk was proposed to be associated with FcR-induced activation of proinflammatory macrophages (M1) by Fu et al. (2020) and Iwasaki and Yang (2020). All aspects of the newly developed vaccine (including the route of administration, delivery system, and adjuvant selection) may affect its effectiveness and safety. In this work we use a novel in silico approach (based on AI and bioinformatics methods) developed to support the design of epitope-based vaccines. We evaluated the capabilities of our method for predicting the immunogenicity of epitopes. Next, the results of our approach were compared with other vaccine-design strategies reported in the literature. The risk of immuno-toxicity was also assessed. The analysis of epitope conservation among other Coronaviridae was carried out in order to facilitate the selection of peptides shared across different SARS-CoV-2 strains and which might be conserved in emerging zootic coronavirus strains. Finally, the potential applicability of the selected epitopes for the development of a vaccine eliciting cellular immunity for COVID-19 was discussed, highlighting the benefits and challenges of such an approach.
Collapse
Affiliation(s)
| | | | - Alexander Myronov
- Ardigen, Krakow, Poland
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
| | | | | | | | - Katarzyna Gruba
- Ardigen, Krakow, Poland
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
| | | | | | - Marian Szczepanik
- Department of Medical Biology, Faculty of Health Sciences, Jagiellonian University Medical College, Krakow, Poland
| | - Krzysztof Pyrc
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | | |
Collapse
|
25
|
Ji D, Juhas M, Tsang CM, Kwok CK, Li Y, Zhang Y. Discovery of G-quadruplex-forming sequences in SARS-CoV-2. Brief Bioinform 2021; 22:1150-1160. [PMID: 32484220 PMCID: PMC7314185 DOI: 10.1093/bib/bbaa114] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 05/10/2020] [Accepted: 05/12/2020] [Indexed: 12/28/2022] Open
Abstract
The outbreak caused by the novel coronavirus SARS-CoV-2 has been declared a global health emergency. G-quadruplex structures in genomes have long been considered essential for regulating a number of biological processes in a plethora of organisms. We have analyzed and identified 25 four contiguous GG runs (G2NxG2NyG2NzG2) in the SARS-CoV-2 RNA genome, suggesting putative G-quadruplex-forming sequences (PQSs). Detailed analysis of SARS-CoV-2 PQSs revealed their locations in the open reading frames of ORF1 ab, spike (S), ORF3a, membrane (M) and nucleocapsid (N) genes. Identical PQSs were also found in the other members of the Coronaviridae family. The top-ranked PQSs at positions 13385 and 24268 were confirmed to form RNA G-quadruplex structures in vitro by multiple spectroscopic assays. Furthermore, their direct interactions with viral helicase (nsp13) were determined by microscale thermophoresis. Molecular docking model suggests that nsp13 distorts the G-quadruplex structure by allowing the guanine bases to be flipped away from the guanine quartet planes. Targeting viral helicase and G-quadruplex structure represents an attractive approach for potentially inhibiting the SARS-CoV-2 virus.
Collapse
Affiliation(s)
- Danyang Ji
- Department of Chemistry, City University of Hong Kong, China
| | - Mario Juhas
- universities of Oxford, Cambridge and Zurich. Currently, he works at the University of Fribourg. His work spans microbiology and synthetic biology
| | - Chi Man Tsang
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, China
| | - Chun Kit Kwok
- Department of Chemistry, City University of Hong Kong, China, and Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China
| | - Yongshu Li
- Department of Anatomical and Cellular Pathology at The Chinese University of Hong Kong
| | - Yang Zhang
- College of Science, Harbin Institute of Technology Shenzhen
| |
Collapse
|
26
|
Pennarossa G, Fazeli A, Ledda S, Gandolfi F, Brevini TAL. Use of Virus-Mimicking Nanoparticles to Investigate Early Infection Events in Upper Airway 3D Models. Methods Mol Biol 2021; 2273:131-8. [PMID: 33604849 DOI: 10.1007/978-1-0716-1246-0_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
The current coronavirus disease-19 (COVID-19) pandemic, caused by "severe acute respiratory syndrome coronavirus 2" (SARS-CoV-2), underscores the threat posed by newly emerging viruses. The understanding of the mechanisms driving early infection events, that are crucial for the exponential spread of the disease, is mandatory and can be significantly implemented generating 3D in vitro models as experimental platforms to investigate the infection substrates and how the virus invades and ravages the tissues.We here describe a protocol for the creation of a synthetic hydrogel-based 3D culture system that mimics in vitro the complex architectures and mechanical cues distinctive of the upper airway epithelia. We then expose the in vitro generated 3D nasal and tracheal epithelia to gold nanoparticles (AuNPs) that display the typical shape and size distinctive of SARS-CoV-2 and of the majority of Coronaviridae presently known.The infection platform here described provides an efficient and highly physiological in vitro model that reproduces the host-pathogen early interactions, using virus-mimicking nanoparticles, and offers a flexible tool to study virus entry into the cell. At the same time, it reduces the risk of accidental infection/spillovers for researchers, which represents a crucial aspect when dealing with a virus that is highly contagious, virulent, and even deadly.
Collapse
|
27
|
Mulabbi EN, Tweyongyere R, Byarugaba DK. The history of the emergence and transmission of human coronaviruses. Onderstepoort J Vet Res 2021; 88:e1-e8. [PMID: 33567843 PMCID: PMC7876959 DOI: 10.4102/ojvr.v88i1.1872] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 09/25/2020] [Indexed: 12/15/2022] Open
Abstract
Human coronaviruses are known respiratory pathogens associated with a range of respiratory illnesses, and there are considerable morbidity and hospitalisation amongst immune-compromised individuals of all age groups. The emergence of a highly pathogenic human coronavirus in China in 2019 has confirmed the long-held opinion that these viruses are important emerging and re-emerging pathogens. In this review article, we trace the discovery and emergence of coronaviruses (CoVs) over time since they were first reported. The review article will enrich our understanding on the host range, diversity and evolution, transmission of human CoVs and the threat posed by these viruses circulating in animal populations but overtime have spilled over to humans because of the increased proximity between humans and animals.
Collapse
Affiliation(s)
- Elijah N Mulabbi
- Department of Veterinary Medicine, Faculty of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala.
| | | | | |
Collapse
|
28
|
Arena F, Pollini S, Rossolini GM, Margaglione M. Summary of the Available Molecular Methods for Detection of SARS-CoV-2 during the Ongoing Pandemic. Int J Mol Sci 2021; 22:ijms22031298. [PMID: 33525651 PMCID: PMC7865767 DOI: 10.3390/ijms22031298] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 01/24/2021] [Accepted: 01/25/2021] [Indexed: 12/25/2022] Open
Abstract
Since early 2020, the COVID-19 pandemic has caused an excess in morbidity and mortality rates worldwide. Containment strategies rely firstly on rapid and sensitive laboratory diagnosis, with molecular detection of the viral genome in respiratory samples being the gold standard. The reliability of diagnostic protocols could be affected by SARS-CoV-2 genetic variability. In fact, mutations occurring during SARS-CoV-2 genomic evolution can involve the regions targeted by the diagnostic probes. Following a review of the literature and an in silico analysis of the most recently described virus variants (including the UK B 1.1.7 and the South Africa 501Y.V2 variants), we conclude that the described genetic variability should have minimal or no effect on the sensitivity of existing diagnostic protocols for SARS-CoV-2 genome detection. However, given the continuous emergence of new variants, the situation should be monitored in the future, and protocols including multiple targets should be preferred.
Collapse
Affiliation(s)
- Fabio Arena
- Department of Clinical and Experimental Medicine, University of Foggia, 71122 Foggia, Italy;
- IRCCS Don Carlo Gnocchi Foundation, 50143 Florence, Italy
- Correspondence: ; Tel.: +39-0881-588064
| | - Simona Pollini
- Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy; (S.P.); (G.M.R.)
- Clinical Microbiology and Virology Unit, Florence Careggi University Hospital, 50134 Florence, Italy
| | - Gian Maria Rossolini
- Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy; (S.P.); (G.M.R.)
- Clinical Microbiology and Virology Unit, Florence Careggi University Hospital, 50134 Florence, Italy
| | - Maurizio Margaglione
- Department of Clinical and Experimental Medicine, University of Foggia, 71122 Foggia, Italy;
| |
Collapse
|
29
|
Wong NA, Saier MH. The SARS-Coronavirus Infection Cycle: A Survey of Viral Membrane Proteins, Their Functional Interactions and Pathogenesis. Int J Mol Sci 2021; 22:1308. [PMID: 33525632 PMCID: PMC7865831 DOI: 10.3390/ijms22031308] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 02/07/2023] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is a novel epidemic strain of Betacoronavirus that is responsible for the current viral pandemic, coronavirus disease 2019 (COVID-19), a global health crisis. Other epidemic Betacoronaviruses include the 2003 SARS-CoV-1 and the 2009 Middle East Respiratory Syndrome Coronavirus (MERS-CoV), the genomes of which, particularly that of SARS-CoV-1, are similar to that of the 2019 SARS-CoV-2. In this extensive review, we document the most recent information on Coronavirus proteins, with emphasis on the membrane proteins in the Coronaviridae family. We include information on their structures, functions, and participation in pathogenesis. While the shared proteins among the different coronaviruses may vary in structure and function, they all seem to be multifunctional, a common theme interconnecting these viruses. Many transmembrane proteins encoded within the SARS-CoV-2 genome play important roles in the infection cycle while others have functions yet to be understood. We compare the various structural and nonstructural proteins within the Coronaviridae family to elucidate potential overlaps and parallels in function, focusing primarily on the transmembrane proteins and their influences on host membrane arrangements, secretory pathways, cellular growth inhibition, cell death and immune responses during the viral replication cycle. We also offer bioinformatic analyses of potential viroporin activities of the membrane proteins and their sequence similarities to the Envelope (E) protein. In the last major part of the review, we discuss complement, stimulation of inflammation, and immune evasion/suppression that leads to CoV-derived severe disease and mortality. The overall pathogenesis and disease progression of CoVs is put into perspective by indicating several stages in the resulting infection process in which both host and antiviral therapies could be targeted to block the viral cycle. Lastly, we discuss the development of adaptive immunity against various structural proteins, indicating specific vulnerable regions in the proteins. We discuss current CoV vaccine development approaches with purified proteins, attenuated viruses and DNA vaccines.
Collapse
Affiliation(s)
- Nicholas A. Wong
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA
| | - Milton H. Saier
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA
| |
Collapse
|
30
|
Nyayanit DA, Yadav PD, Kharde R, Cherian S. Natural Selection Plays an Important Role in Shaping the Codon Usage of Structural Genes of the Viruses Belonging to the Coronaviridae Family. Viruses 2020; 13:v13010003. [PMID: 33375017 PMCID: PMC7821998 DOI: 10.3390/v13010003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/10/2020] [Accepted: 11/11/2020] [Indexed: 02/06/2023] Open
Abstract
Viruses belonging to the Coronaviridae family have a single-stranded positive-sense RNA with a poly-A tail. The genome has a length of ~29.9 kbps, which encodes for genes that are essential for cell survival and replication. Different evolutionary constraints constantly influence the codon usage bias (CUB) of different genes. A virus optimizes its codon usage to fit the host environment on which it savors. This study is a comprehensive analysis of the CUB for the different genes encoded by viruses of the Coronaviridae family. Different methods including relative synonymous codon usage (RSCU), an Effective number of codons (ENc), parity plot 2, and Neutrality plot, were adopted to analyze the factors responsible for the genetic evolution of the Coronaviridae family. Base composition and RSCU analyses demonstrated the presence of A-ended and U-ended codons being preferred in the 3rd codon position and are suggestive of mutational selection. The lesser ENc value for the spike ‘S’ gene suggests a higher bias in the codon usage of this gene compared to the other structural genes. Parity plot 2 and neutrality plot analyses demonstrate the role and the extent of mutational and natural selection towards the codon usage pattern. It was observed that the structural genes of the Coronaviridae family analyzed in this study were at the least under 84% influence of natural selection, implying a major role of natural selection in shaping the codon usage.
Collapse
Affiliation(s)
- Dimpal A. Nyayanit
- Maximum Containment Facility, ICMR-National Institute of Virology, Sus Road, Pashan, Pune 411021, India; (D.A.N.); (P.D.Y.); (R.K.)
| | - Pragya D. Yadav
- Maximum Containment Facility, ICMR-National Institute of Virology, Sus Road, Pashan, Pune 411021, India; (D.A.N.); (P.D.Y.); (R.K.)
| | - Rutuja Kharde
- Maximum Containment Facility, ICMR-National Institute of Virology, Sus Road, Pashan, Pune 411021, India; (D.A.N.); (P.D.Y.); (R.K.)
| | - Sarah Cherian
- Bioinformatics Group, ICMR-National Institute of Virology, Pune 411001, India
- Correspondence: or ; Tel.: +91-20-260061213
| |
Collapse
|
31
|
Zandi K, Amblard F, Musall K, Downs-Bowen J, Kleinbard R, Oo A, Cao D, Liang B, Russell OO, McBrayer T, Bassit L, Kim B, Schinazi RF. Repurposing Nucleoside Analogs for Human Coronaviruses. Antimicrob Agents Chemother 2020; 65:e01652-20. [PMID: 33122172 DOI: 10.1128/AAC.01652-20] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 10/26/2020] [Indexed: 12/24/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is a serious illness caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2 or CoV-2). Some reports claimed certain nucleoside analogs to be active against CoV-2 and thus needed confirmation. Here, we evaluated a panel of compounds and identified novel nucleoside analogs with antiviral activity against CoV-2 and HCoV-OC43 while ruling out others. Of significance, sofosbuvir demonstrated no antiviral effect against CoV-2, and its triphosphate did not inhibit CoV-2 RNA polymerase.
Collapse
|
32
|
Abstract
As with many countries around the world, Thailand is currently experiencing restrictions to daily life as a consequence of the worldwide transmission of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). SARS-CoV-2 is the third respiratory syndrome coronavirus to be introduced into Thailand, following previous importation of cases of the severe acute respiratory syndrome coronavirus (SARS) and the Middle East respiratory syndrome coronavirus (MERS). Unlike SARS and MERS, SARS-CoV-2 was able to establish local transmission in Thailand. In addition to the imported coronaviruses, Thailand has a number of endemic coronaviruses that can affect livestock and pet species, can be found in bats, as well as four human coronaviruses that are mostly associated with the common cold. This article seeks to review what is known on both the endemic and imported coronaviruses in Thailand.
Collapse
Affiliation(s)
- Duncan R Smith
- Molecular Pathology Laboratory, Institute of Molecular Biosciences, Mahidol University, 25/25 Phutthamonthon Sai 4 Road, Salaya, Nakhon Pathom, 73170, Thailand.
| |
Collapse
|
33
|
Paladino L, Vitale AM, Caruso Bavisotto C, Conway de Macario E, Cappello F, Macario AJL, Gammazza AM. The Role of Molecular Chaperones in Virus Infection and Implications for Understanding and Treating COVID-19. J Clin Med 2020; 9:E3518. [PMID: 33143379 DOI: 10.3390/jcm9113518] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/24/2020] [Accepted: 10/28/2020] [Indexed: 12/14/2022] Open
Abstract
The COVID-19 pandemic made imperative the search for means to end it, which requires a knowledge of the mechanisms underpinning the multiplication and spread of its cause, the coronavirus SARS-CoV-2. Many viruses use members of the hosts’ chaperoning system to infect the target cells, replicate, and spread, and here we present illustrative examples. Unfortunately, the role of chaperones in the SARS-CoV-2 cycle is still poorly understood. In this review, we examine the interactions of various coronaviruses during their infectious cycle with chaperones in search of information useful for future research on SARS-CoV-2. We also call attention to the possible role of molecular mimicry in the development of autoimmunity and its widespread pathogenic impact in COVID-19 patients. Viral proteins share highly antigenic epitopes with human chaperones, eliciting anti-viral antibodies that crossreact with the chaperones. Both, the critical functions of chaperones in the infectious cycle of viruses and the possible role of these molecules in COVID-19 autoimmune phenomena, make clear that molecular chaperones are promising candidates for the development of antiviral strategies. These could consist of inhibiting-blocking those chaperones that are necessary for the infectious viral cycle, or those that act as autoantigens in the autoimmune reactions causing generalized destructive effects on human tissues.
Collapse
|
34
|
Zaragoza-Martínez F, Lucho-Constantino GG, Barrales-Cureño HJ. Overview of the current situation regarding the coronavirus. Rev Med Inst Mex Seguro Soc 2020; 58:S152-163. [PMID: 34695328 DOI: 10.24875/rmimss.m20000127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Coronaviruses (CoV) are pathogens that are transmitted to animals and humans; they spread around the world. Six types of coronavirus have been identified as causing human disease: four cause mild respiratory symptoms, while two types, the Middle East Respiratory Syndrome (MERS) and the Severe Acute Respiratory Syndrome (SARS), have caused epidemics with high mortality rates. Human coronaviruses cause common cold, lead to lower respiratory tract infections and are involved in pediatric gastroenteritis. Currently, the coronavirus SARS-CoV-2 has been transmitted between species, included humans, and is a very virulent respiratory virus, causing the disease known as COVID-19, which to date, has not an authorized medical treatment. The World Health Organization announced that the outbreak of COVID-19 has been upgraded from a health emergency to a pandemic. Therefore, the objectives of this paper are to mention the basic concepts of coronavirus (structure, genome, mutation and recombination), its epidemiological description, animal-human transmission mechanism, pathogenesis and therapeutics.
Collapse
Affiliation(s)
- Fabiola Zaragoza-Martínez
- Instituto Politécnico Nacional, Centro de Investigación y de Estudios Avanzados, Departamento de Biotecnología. Ciudad de México
| | | | - Hebert Jair Barrales-Cureño
- Universidad Michoacana de San Nicolás de Hidalgo, Instituto de Investigaciones Químico-Biológicas, Departamento de Biotecnología. Morelia, Michoacán. México
| |
Collapse
|
35
|
Encinas Pardilla MB, Caño Aguilar Á, Marcos Puig B, Sanz Lorenzana A, Rodríguez de la Torre I, Hernando López de la Manzanara P, Fernández Bernardo A, Martínez Pérez Ó. [Spanish registry of Covid-19 screening in asymptomatic pregnants.]. Rev Esp Salud Publica 2020; 94:e202009092. [PMID: 32945290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 07/13/2020] [Indexed: 06/11/2023] Open
Abstract
OBJECTIVE The Spanish registry of Covid-19 in Spanish pregnant women, made up of 100 centers, is created in response to the need to know the morbidity that Covid-19 generates in pregnant women and their newborns, to know the real incidence of the disease in this population group and to establish and monitor the package of measures to improve their care. The aim of this paper was the creation of a registry of pregnant women with Covid-19 infection in order to establish the interventions and measures necessary to improve the care of these patients during hospital admission. METHODS To prepare the registry, the main researcher of each center collected weekly / biweekly the number of total pregnant women screened, as well as the total number of positive and negative, sending these data to the responsible researchers so that it could be available in real time of the percentage of infected asymptomatic pregnant population and the evolution by weeks in the centers of each participating province. The data were analyzed using the linear regression test and the Mantel test. RESULTS As of May 31stsup> 2020, 16,308 screening tests were carried out in these hospitals, in which 338 pregnant women were positive, which translates into 2.07% (95% Confidence Interval: 1.86-2.30) of the asymptomatic pregnant women we attended in our centers were carriers of the virus and could develop the disease in subsequent days. CONCLUSIONS The Spanish epidemiological registry allows us to know the incidence of infection in pregnant women attended in the Spanish delivery centers, as well as the weekly and / or fortnightly evolution of the same, observing a significant decrease in the proportion of positive pregnant women over the total of screenings throughout this period, with an average of 6.5% in early April 2020 to an average of 0.93% positive in late May 2020.
Collapse
Affiliation(s)
- María Begoña Encinas Pardilla
- Profesor Honorario Facultad de Medicina. Universidad Autónoma de Madrid. Especialista en Obstetricia y Ginecología. Servicio de Obstetricia y Ginecología. Hospital Universitario Puerta de Hierro de Majadahonda. Madrid. España
| | - África Caño Aguilar
- Profesora Asociada en Ciencias de la Salud. Universidad de Granada. Facultativa Especialista de Área. Servicio de Obstetricia y Ginecología. Hospital Clínico Universitario San Cecilio. Granada. España
| | - Beatriz Marcos Puig
- Facultativo Especialista en Obstetricia y Ginecología. Servicio de Obstetricia y Ginecología. Hospital La Fe. Valencia. España
| | - Amelia Sanz Lorenzana
- Servicio de Obstetricia y Ginecología. Hospital Universitario Puerta de Hierro de Majadahonda. Madrid. España
| | | | | | - Ana Fernández Bernardo
- Facultativo Especialista en Obstetricia y Ginecología. Hospital Universitario Central de Asturias. Oviedo. España
| | - Óscar Martínez Pérez
- Especialista en Obstetricia y Ginecología. Hospital Puerta de Hierro de Majadahonda. Madrid. España. Profesor Asociado del Departamento de Obstetricia y Ginecología. Facultad de Medicina. Universidad Autónoma de Madrid. Cátedra de Simulación. Universidad Católica de Murcia
| |
Collapse
|
36
|
Ilias I, Jahaj E, Kokkoris S, Zervakis D, Temperikidis P, Magira E, Pratikaki M, Vassiliou AG, Routsi C, Kotanidou A, Dimopoulou I. Clinical Study of Hyperglycemia and SARS-CoV-2 Infection in Intensive Care Unit Patients. In Vivo 2020; 34:3029-3032. [PMID: 32871848 DOI: 10.21873/invivo.12136] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 06/29/2020] [Accepted: 06/30/2020] [Indexed: 12/20/2022]
Abstract
BACKGROUND/AIM Reports indicate that coronaviridae may inhibit insulin secretion. In this report we aimed to describe the course of glycemia in critically ill patients with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. PATIENTS AND METHODS We studied 36 SARS-CoV-2 patients (with no history of diabetes) in one intensive care unit (ICU). All the patients were admitted for hypoxemic respiratory failure; all but four required mechanical ventilation. The mean (±SD) age of the patients was 64.7 (9.7) years; 27 were men; the mean (±SD) duration of ICU stay was 12.9 (8.3 days). RESULTS Twenty of 36 patients presented with hyperglycemia; brief intravenous infusions of short-acting insulin were administered in six patients. As of May 29 2020, 11 patients had died (seven with hyperglycemia). In 17 patients the Hyperglycemia Index [HGI; defined as the area under the curve of (hyper)glycemia level*time (h) divided by the total time in the ICU] was <16.21 mg/dl (0.90 mmol/l), whereas in three patients the HGI was ≥16.21 mg/dl (0.90 mol/l) and <32.25 mg/dl (1.79 mmol/l). CONCLUSION In our series of ICU patients with SARS-CoV-2 infection, and no history of diabetes, a substantial number of patients had hyperglycemia, to a higher degree than would be expected by the stress of critical illness, lending credence to reports that speculated a tentative association between SARS-CoV-2 and hyperglycemia. This finding is important, since hyperglycemia can lead to further infectious complications.
Collapse
Affiliation(s)
- Ioannis Ilias
- Department of Endocrinology, Diabetes and Metabolism, Elena Venizelou Hospital, Athens, Greece
| | - Edison Jahaj
- 1 Department of Critical Care & Pulmonary Services, Medical School, National & Kapodistrian University of Athens, Evangelismos Hospital, Athens, Greece
| | - Stylianos Kokkoris
- 1 Department of Critical Care & Pulmonary Services, Medical School, National & Kapodistrian University of Athens, Evangelismos Hospital, Athens, Greece
| | - Dimitrios Zervakis
- 1 Department of Critical Care & Pulmonary Services, Medical School, National & Kapodistrian University of Athens, Evangelismos Hospital, Athens, Greece
| | - Prodromos Temperikidis
- 1 Department of Critical Care & Pulmonary Services, Medical School, National & Kapodistrian University of Athens, Evangelismos Hospital, Athens, Greece
| | - Eleni Magira
- 1 Department of Critical Care & Pulmonary Services, Medical School, National & Kapodistrian University of Athens, Evangelismos Hospital, Athens, Greece
| | - Maria Pratikaki
- 1 Department of Critical Care & Pulmonary Services, Medical School, National & Kapodistrian University of Athens, Evangelismos Hospital, Athens, Greece
| | - Alice G Vassiliou
- 1 Department of Critical Care & Pulmonary Services, Medical School, National & Kapodistrian University of Athens, Evangelismos Hospital, Athens, Greece
| | - Christina Routsi
- 1 Department of Critical Care & Pulmonary Services, Medical School, National & Kapodistrian University of Athens, Evangelismos Hospital, Athens, Greece
| | - Anastasia Kotanidou
- 1 Department of Critical Care & Pulmonary Services, Medical School, National & Kapodistrian University of Athens, Evangelismos Hospital, Athens, Greece
| | - Ioanna Dimopoulou
- 1 Department of Critical Care & Pulmonary Services, Medical School, National & Kapodistrian University of Athens, Evangelismos Hospital, Athens, Greece
| |
Collapse
|
37
|
Milewska A, Kula-Pacurar A, Wadas J, Suder A, Szczepanski A, Dabrowska A, Owczarek K, Marcello A, Ochman M, Stacel T, Rajfur Z, Sanak M, Labaj P, Branicki W, Pyrc K. Replication of Severe Acute Respiratory Syndrome Coronavirus 2 in Human Respiratory Epithelium. J Virol 2020; 94:e00957-20. [PMID: 32434888 DOI: 10.1128/JVI.00957-20] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 05/18/2020] [Indexed: 01/08/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged by the end of 2019 and rapidly spread in 2020. At present, it is of utmost importance to understand the biology of the virus, rapidly assess the treatment potential of existing drugs, and develop new active compounds. While some animal models for such studies are under development, most of the research is carried out in Vero E6 cells. Here, we propose fully differentiated human airway epithelium cultures as a model for studies on SARS-CoV-2. Currently, there are four seasonal coronaviruses associated with relatively mild respiratory tract disease in humans. However, there is also a plethora of animal coronaviruses which have the potential to cross the species border. This regularly results in the emergence of new viruses in humans. In 2002, severe acute respiratory syndrome coronavirus (SARS-CoV) emerged and rapidly disappeared in May 2003. In 2012, Middle East respiratory syndrome coronavirus (MERS-CoV) was identified as a possible threat to humans, but its pandemic potential so far is minimal, as human-to-human transmission is ineffective. The end of 2019 brought us information about severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emergence, and the virus rapidly spread in 2020, causing an unprecedented pandemic. At present, studies on the virus are carried out using a surrogate system based on the immortalized simian Vero E6 cell line. This model is convenient for diagnostics, but it has serious limitations and does not allow for understanding of the biology and evolution of the virus. Here, we show that fully differentiated human airway epithelium cultures constitute an excellent model to study infection with the novel human coronavirus SARS-CoV-2. We observed efficient replication of the virus in the tissue, with maximal replication at 2 days postinfection. The virus replicated in ciliated cells and was released apically. IMPORTANCE Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged by the end of 2019 and rapidly spread in 2020. At present, it is of utmost importance to understand the biology of the virus, rapidly assess the treatment potential of existing drugs, and develop new active compounds. While some animal models for such studies are under development, most of the research is carried out in Vero E6 cells. Here, we propose fully differentiated human airway epithelium cultures as a model for studies on SARS-CoV-2.
Collapse
|
38
|
Abstract
COVID-19 is the first known pandemic caused by a coronavirus, SARS-CoV-2, which is the third virus in the family Coronaviridae to cause fatal infections in humans after SARS-CoV and MERS-CoV. Animals are involved in the COVID-19 pandemic. This review summarizes the role of animals as reservoirs, natural hosts and experimental models. SARS-CoV-2 originated from animal reservoir, most likely bats and/or pangolins. Anthroponotic transmission has been reported in cats, dogs, tigers, lions and minks. As of now, there is no a strong evidence for natural animal-to-human transmission or sustained animal-to-animal transmission of SARS-CoV-2. Experimental infections conducted by several research groups have shown that monkeys, hamsters, ferrets, cats, tree shrews, transgenic mice and fruit bats were permissive, while dogs, pigs and poultry were resistant. There is an urgent need to understand the zoonotic potential of different viruses in animals, particularly in bats, before they transmit to humans. Vaccines or antivirals against SARS-CoV-2 should be evaluated not only for humans, but also for the protection of companion animals (particularly cats) and susceptible zoo and farm animals.
Collapse
Affiliation(s)
- Ahmed S. Abdel-Moneim
- Microbiology Department, Virology Division, College of Medicine, Taif University, Al-Taif 21944, Saudi Arabia; or
- Virology Department, Faculty of Veterinary Medicine, Beni-Suef University, Beni-Suef 62511, Egypt
| | - Elsayed M. Abdelwhab
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald-Insel Riems, Germany
| |
Collapse
|
39
|
Lvov DK, Alkhovsky SV. [Source of the COVID-19 pandemic: ecology and genetics of coronaviruses (Betacoronavirus: Coronaviridae) SARS-CoV, SARS-CoV-2 (subgenus Sarbecovirus), and MERS-CoV (subgenus Merbecovirus).]. Vopr Virusol 2020; 65:62-70. [PMID: 32515561 DOI: 10.36233/0507-4088-2020-65-2-62-70] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 04/29/2020] [Indexed: 01/12/2023]
Abstract
Since the early 2000s, three novel zooanthroponous coronaviruses (Betacoronavirus) have emerged. The first outbreak of infection (SARS) caused by SARS-CoV virus occurred in the fall of 2002 in China (Guangdong Province). A second outbreak (MERS) associated with the new MERS-CoV virus appeared in Saudi Arabia in autumn 2012. The third epidemic, which turned into a COVID-19 pandemic caused by SARS-CoV-2 virus, emerged in China (Hubei Province) in the autumn 2019. This review focuses on ecological and genetic aspects that lead to the emergence of new human zoanthroponous coronaviruses. The main mechanism of adaptation of zoonotic betacoronaviruses to humans is to changes in the receptor-binding domain of surface protein (S), as a result of which it gains the ability to bind human cellular receptors of epithelial cells in respiratory and gastrointestinal tract. This process is caused by the high genetic diversity and variability combined with frequent recombination, during virus circulation in their natural reservoir - bats (Microchiroptera, Chiroptera). Appearance of SARS-CoV, SARS-CoV-2 (subgenus Sarbecovirus), and MERS (subgenus Merbecovirus) viruses is a result of evolutionary events occurring in bat populations with further transfer of viruses to the human directly or through the intermediate vertebrate hosts, ecologically connected with bats. This review is based on the report at the meeting «Coronavirus - a global challenge to science» of the Scientific Council «Life Science» of the Russian Academy of Science: Lvov D.K., Alkhovsky S.V., Burtseva E.I. COVID-19 pandemic sources: origin, biology and genetics of coronaviruses of SARS-CoV, SARS-CoV-2, MERS-CoV (Conference hall of Presidium of RAS, 14 Leninsky Prospect, Moscow, Russia. April 16, 2020).
Collapse
Affiliation(s)
- D K Lvov
- D.I. Ivanovsky Institute of Virology of National Research Centre for Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya, Moscow, 123098, Russia
| | - S V Alkhovsky
- D.I. Ivanovsky Institute of Virology of National Research Centre for Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya, Moscow, 123098, Russia
| |
Collapse
|
40
|
Mani JS, Johnson JB, Steel JC, Broszczak DA, Neilsen PM, Walsh KB, Naiker M. Natural product-derived phytochemicals as potential agents against coronaviruses: A review. Virus Res 2020; 284:197989. [PMID: 32360300 PMCID: PMC7190535 DOI: 10.1016/j.virusres.2020.197989] [Citation(s) in RCA: 243] [Impact Index Per Article: 60.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 04/24/2020] [Accepted: 04/24/2020] [Indexed: 12/19/2022]
Abstract
Coronaviruses are responsible for a growing economic, social and mortality burden, as the causative agent of diseases such as severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), avian infectious bronchitis virus (IBV) and COVID-19. However, there is a lack of effective antiviral agents for many coronavirus strains. Naturally existing compounds provide a wealth of chemical diversity, including antiviral activity, and thus may have utility as therapeutic agents against coronaviral infections. The PubMed database was searched for papers including the keywords coronavirus, SARS or MERS, as well as traditional medicine, herbal, remedy or plants, with 55 primary research articles identified. The overwhelming majority of publications focussed on polar compounds. Compounds that show promise for the inhibition of coronavirus in humans include scutellarein, silvestrol, tryptanthrin, saikosaponin B2, quercetin, myricetin, caffeic acid, psoralidin, isobavachalcone, and lectins such as griffithsin. Other compounds such as lycorine may be suitable if a therapeutic level of antiviral activity can be achieved without exceeding toxic plasma concentrations. It was noted that the most promising small molecules identified as coronavirus inhibitors contained a conjugated fused ring structure with the majority being classified as being polyphenols.
Collapse
Affiliation(s)
- Janice S Mani
- School of Health, Medical and Applied Sciences, CQUniversity, Bruce Hwy, North Rockhampton, QLD, Australia
| | - Joel B Johnson
- School of Health, Medical and Applied Sciences, CQUniversity, Bruce Hwy, North Rockhampton, QLD, Australia
| | - Jason C Steel
- School of Health, Medical and Applied Sciences, CQUniversity, Bruce Hwy, North Rockhampton, QLD, Australia
| | - Daniel A Broszczak
- Institute of Health & Biomedical Innovation (Q-Block), Queensland University of Technology, Kelvin Grove Campus, QLD, Australia
| | - Paul M Neilsen
- School of Health, Medical and Applied Sciences, CQUniversity, Bruce Hwy, North Rockhampton, QLD, Australia
| | - Kerry B Walsh
- School of Health, Medical and Applied Sciences, CQUniversity, Bruce Hwy, North Rockhampton, QLD, Australia
| | - Mani Naiker
- School of Health, Medical and Applied Sciences, CQUniversity, Bruce Hwy, North Rockhampton, QLD, Australia; Centre for Indigenous Health Equity Research, CQUniversity, Bruce Hwy, North Rockhampton, QLD, Australia.
| |
Collapse
|
41
|
Rahimi F, Talebi Bezmin Abadi A. Practical Strategies Against the Novel Coronavirus and COVID-19-the Imminent Global Threat. Arch Med Res 2020; 51:280-281. [PMID: 32229157 PMCID: PMC7270650 DOI: 10.1016/j.arcmed.2020.03.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 03/17/2020] [Indexed: 01/22/2023]
Abstract
The last month of 2019 harbingered the emergence of a viral outbreak that is now a major public threat globally. COVID-19 was first diagnosed and confirmed in a couple of cases with unknown pneumonia; the patients lived in, or travelled to, Wuhan, the capital of China's Hubei province. People now face a complex challenge that deserves urgent intervention by all involved in medical healthcare globally. Conventional antiviral therapies or vaccines are the most referred means of tackling the virus, but we think establishing these ideal management strategies is presently far-fetched. In-house isolation or quarantine of suspected cases to keep hospital admissions manageable and prevent in-hospital spread of the virus, and promoting general awareness about transmission routes are the practical strategies used to tackle the spread of COVID-19. Cases with weakened or compromised immune systems—for example, elderly individuals, young children, and those with pre-existing conditions such as diabetes, cancer, hypertension, and chronic respiratory diseases—are particularly more susceptible to COVID-19. Hopefully, cumulative data using whole-genome sequencing of the SARS-CoV-2 genome in parallel with mathematical modeling will help the molecular biologists to understand unknown features of the pathogenesis and epidemiology of COVID-19.
Collapse
Affiliation(s)
- Farid Rahimi
- Research School of Biology, The Australian National University, Canberra, Australia
| | - Amin Talebi Bezmin Abadi
- Department of Bacteriology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran.
| |
Collapse
|
42
|
Abstract
The current rapid spread of the novel coronavirus (SARS-CoV-2) causing coronavirus disease 2019 (COVID-19) calls for a rapid response from the research community. Lithium is widely used to treat bipolar disorder, but has been shown to exhibit antiviral activity. This brief review took a systematic approach to identify six in vitro studies reporting on the influence of lithium on coronaviral infections. We propose mechanistic investigation of the influence of lithium - alone and with chloroquine - on the SARS-CoV-2 infection.
Collapse
Affiliation(s)
- Jan K Nowak
- Department of Pediatric Gastroenterology and Metabolic Diseases, Poznan University of Medical Sciences, Poznan, Poland
| | - Jarosław Walkowiak
- Department of Pediatric Gastroenterology and Metabolic Diseases, Poznan University of Medical Sciences, Poznan, Poland
| |
Collapse
|
43
|
Abstract
The current rapid spread of the novel coronavirus (SARS-CoV-2) causing coronavirus disease 2019 (COVID-19) calls for a rapid response from the research community. Lithium is widely used to treat bipolar disorder, but has been shown to exhibit antiviral activity. This brief review took a systematic approach to identify six
in vitro studies reporting on the influence of lithium on coronaviral infections. We propose mechanistic investigation of the influence of lithium – alone and with chloroquine – on the SARS-CoV-2 infection.
Collapse
Affiliation(s)
- Jan K Nowak
- Department of Pediatric Gastroenterology and Metabolic Diseases, Poznan University of Medical Sciences, Poznan, Poland
| | - Jarosław Walkowiak
- Department of Pediatric Gastroenterology and Metabolic Diseases, Poznan University of Medical Sciences, Poznan, Poland
| |
Collapse
|
44
|
Abstract
BACKGROUND Gallium has demonstrated strong anti-inflammatory activity in numerous animal studies, and has also demonstrated direct antiviral activity against the influenza A H1N1 virus and the human immunodeficiency virus (HIV). Gallium maltolate (GaM), a small metal-organic coordination complex, has been tested in several Phase 1 clinical trials, in which no dose-limiting or other serious toxicity was reported, even at high daily oral doses for several months at a time. For these reasons, GaM may be considered a potential candidate to treat coronavirus disease 2019 (COVID-19), which is caused by the SARS-CoV-2 virus and can result in severe, sometimes lethal, inflammatory reactions. In this study, we assessed the ability of GaM to inhibit the replication of SARS-CoV-2 in a culture of Vero E6 cells. METHODS The efficacy of GaM in inhibiting the replication of SARS-CoV-2 was determined in a screening assay using cultured Vero E6 cells. The cytotoxicity of GaM in uninfected cells was determined using the Cell Counting Kit-8 (CCK-8) colorimetric assay. RESULTS The results showed that GaM inhibits viral replication in a dose-dependent manner, with the concentration that inhibits replication by 50% (EC50) being about 14 µM. No cytotoxicity was observed at concentrations up to at least 200 µM. CONCLUSION The in vitro activity of GaM against SARS-CoV-2, together with GaM's known anti-inflammatory activity, provide justification for testing GaM in COVID-19 patients.
Collapse
Affiliation(s)
| | - Leike Zhang
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| |
Collapse
|
45
|
Abstract
Over the past few years, nucleosides have maintained a prominent role as one of the cornerstones of antiviral and anticancer therapeutics, and many approaches to nucleoside drug design have been pursued. One such approach involves flexibility in the sugar moiety of nucleosides, for example, in the highly successful anti-HIV and HBV drug tenofovir. In contrast, introduction of flexibility to the nucleobase scaffold has only more recently gained significance with the invention of our fleximers. The history, development, and some biological relevance for this innovative class of nucleosides are detailed herein.
Collapse
|
46
|
Nguyen THV, Lichière J, Canard B, Papageorgiou N, Attoumani S, Ferron F, Coutard B. Structure and oligomerization state of the C-terminal region of the Middle East respiratory syndrome coronavirus nucleoprotein. Acta Crystallogr D Struct Biol 2019; 75:8-15. [PMID: 30644840 PMCID: PMC7159728 DOI: 10.1107/s2059798318014948] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 10/22/2018] [Indexed: 12/16/2022]
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) is a human pathogen responsible for a severe respiratory illness that emerged in 2012. Structural information about the proteins that constitute the viral particle is scarce. In order to contribute to a better understanding of the nucleoprotein (N) in charge of RNA genome encapsidation, the structure of the C-terminal domain of N from MERS-CoV obtained using single-crystal X-ray diffraction is reported here at 1.97 Å resolution. The molecule is present as a dimer in the crystal structure and this oligomerization state is confirmed in solution, as measured by additional methods including small-angle X-ray scattering measurements. Comparisons with the structures of the C-terminal domains of N from other coronaviruses reveals a high degree of structural conservation despite low sequence conservation, and differences in electrostatic potential at the surface of the protein.
Collapse
Affiliation(s)
| | - Julie Lichière
- Aix-Marseille Université, AFMB UMR 7257, 13288 Marseilles, France
| | - Bruno Canard
- Aix-Marseille Université, AFMB UMR 7257, 13288 Marseilles, France
| | | | - Sarah Attoumani
- Aix-Marseille Université, AFMB UMR 7257, 13288 Marseilles, France
| | - François Ferron
- Aix-Marseille Université, AFMB UMR 7257, 13288 Marseilles, France
| | - Bruno Coutard
- Aix-Marseille Université, AFMB UMR 7257, 13288 Marseilles, France
| |
Collapse
|
47
|
Symes SJ, Allen JL, Mansell PD, Woodward KL, Bailey KE, Gilkerson JR, Browning GF. First detection of bovine noroviruses and detection of bovine coronavirus in Australian dairy cattle. Aust Vet J 2018; 96:203-208. [PMID: 29878330 PMCID: PMC7159654 DOI: 10.1111/avj.12695] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 07/31/2017] [Accepted: 08/22/2017] [Indexed: 01/20/2023]
Abstract
Background and objective Noroviruses have been recognised as a significant cause of neonatal enteritis in calves in many countries, but there has been no investigation of their occurrence in Australian cattle. This study aimed to establish whether bovine noroviruses could be detected in faecal samples from Australian dairy cattle. It also sought to determine whether bovine coronaviruses, also associated with neonatal enteritis in calves, could be detected in the same faecal samples. Methods A selection of faecal samples that were negative for rotaviruses from dairy farms located in three geographically distinct regions of Victoria were pooled and tested by reverse transcription‐PCR for the presence of noroviruses (genogroup III), neboviruses and bovine coronaviruses. Results and conclusion Genetically distinct genogroup III noroviruses were detected in two sample pools from different geographic regions and bovine coronavirus was detected in a third pool of samples. This is the first report of bovine norovirus infection in Australian cattle and suggests that future work is required to determine the significance of these agents as a cause of bovine enteric disease in Australia.
Collapse
Affiliation(s)
- S J Symes
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - J L Allen
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - P D Mansell
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Werribee, Victoria, Australia
| | | | - K E Bailey
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - J R Gilkerson
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - G F Browning
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia
| |
Collapse
|
48
|
Fehr AR, Jankevicius G, Ahel I, Perlman S. Viral Macrodomains: Unique Mediators of Viral Replication and Pathogenesis. Trends Microbiol 2018; 26:598-610. [PMID: 29268982 PMCID: PMC6003825 DOI: 10.1016/j.tim.2017.11.011] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 11/16/2017] [Accepted: 11/30/2017] [Indexed: 12/20/2022]
Abstract
Viruses from the Coronaviridae, Togaviridae, and Hepeviridae families all contain genes that encode a conserved protein domain, called a macrodomain; however, the role of this domain during infection has remained enigmatic. The recent discovery that mammalian macrodomain proteins enzymatically remove ADP-ribose, a common post-translation modification, from proteins has led to an outburst of studies describing both the enzymatic activity and function of viral macrodomains. These new studies have defined these domains as de-ADP-ribosylating enzymes, which indicates that these viruses have evolved to counteract antiviral ADP-ribosylation, likely mediated by poly-ADP-ribose polymerases (PARPs). Here, we comprehensively review this rapidly expanding field, describing the structures and enzymatic activities of viral macrodomains, and discussing their roles in viral replication and pathogenesis.
Collapse
Affiliation(s)
- Anthony R Fehr
- University of Iowa, Department of Microbiology and Immunology, Iowa City, IA 52242, USA; These authors contributed equally to this manuscript.
| | - Gytis Jankevicius
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK; These authors contributed equally to this manuscript
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Stanley Perlman
- University of Iowa, Department of Microbiology and Immunology, Iowa City, IA 52242, USA.
| |
Collapse
|
49
|
Abstract
The four endemic human coronaviruses HCoV-229E, -NL63, -OC43, and -HKU1 contribute a considerable share of upper and lower respiratory tract infections in adults and children. While their clinical representation resembles that of many other agents of the common cold, their evolutionary histories, and host associations could provide important insights into the natural history of past human pandemics. For two of these viruses, we have strong evidence suggesting an origin in major livestock species while primordial associations for all four viruses may have existed with bats and rodents. HCoV-NL63 and -229E may originate from bat reservoirs as assumed for many other coronaviruses, but HCoV-OC43 and -HKU1 seem more likely to have speciated from rodent-associated viruses. HCoV-OC43 is thought to have emerged from ancestors in domestic animals such as cattle or swine. The bovine coronavirus has been suggested to be a possible ancestor, from which HCoV-OC43 may have emerged in the context of a pandemic recorded historically at the end of the 19th century. New data suggest that HCoV-229E may actually be transferred from dromedary camels similar to Middle East respiratory syndrome (MERS) coronavirus. This scenario provides important ecological parallels to the present prepandemic pattern of host associations of the MERS coronavirus.
Collapse
Affiliation(s)
- Victor M Corman
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin, Germany; German Center for Infection Research (DZIF), Berlin, Germany
| | - Doreen Muth
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin, Germany; German Center for Infection Research (DZIF), Berlin, Germany
| | - Daniela Niemeyer
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin, Germany
| | - Christian Drosten
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin, Germany; German Center for Infection Research (DZIF), Berlin, Germany.
| |
Collapse
|
50
|
Milewska A, Nowak P, Owczarek K, Szczepanski A, Zarebski M, Hoang A, Berniak K, Wojarski J, Zeglen S, Baster Z, Rajfur Z, Pyrc K. Entry of Human Coronavirus NL63 into the Cell. J Virol 2018; 92:e01933-17. [PMID: 29142129 DOI: 10.1128/JVI.01933-17] [Citation(s) in RCA: 122] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 11/07/2017] [Indexed: 11/20/2022] Open
Abstract
The first steps of human coronavirus NL63 (HCoV-NL63) infection were previously described. The virus binds to target cells by use of heparan sulfate proteoglycans and interacts with the ACE2 protein. Subsequent events, including virus internalization and trafficking, remain to be elucidated. In this study, we mapped the process of HCoV-NL63 entry into the LLC-Mk2 cell line and ex vivo three-dimensional (3D) tracheobronchial tissue. Using a variety of techniques, we have shown that HCoV-NL63 virions require endocytosis for successful entry into the LLC-MK2 cells, and interaction between the virus and the ACE2 molecule triggers recruitment of clathrin. Subsequent vesicle scission by dynamin results in virus internalization, and the newly formed vesicle passes the actin cortex, which requires active cytoskeleton rearrangement. Finally, acidification of the endosomal microenvironment is required for successful fusion and release of the viral genome into the cytoplasm. For 3D tracheobronchial tissue cultures, we also observed that the virus enters the cell by clathrin-mediated endocytosis, but we obtained results suggesting that this pathway may be bypassed.IMPORTANCE Available data on coronavirus entry frequently originate from studies employing immortalized cell lines or undifferentiated cells. Here, using the most advanced 3D tissue culture system mimicking the epithelium of conductive airways, we systematically mapped HCoV-NL63 entry into susceptible cells. The data obtained allow for a better understanding of the infection process and may support development of novel treatment strategies.
Collapse
|