1
|
Pauciullo S, Riccio A, Santopolo S, Albecka A, Papa G, James LC, Piacentini S, Lanzilli G, Rossi A, Santoro MG. Human coronaviruses activate and hijack the host transcription factor HSF1 to enhance viral replication. Cell Mol Life Sci 2024; 81:386. [PMID: 39243335 DOI: 10.1007/s00018-024-05370-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Revised: 07/16/2024] [Accepted: 07/17/2024] [Indexed: 09/09/2024]
Abstract
Organisms respond to proteotoxic-stress by activating the heat-shock response, a cellular defense mechanism regulated by a family of heat-shock factors (HSFs); among six human HSFs, HSF1 acts as a proteostasis guardian regulating severe stress-driven transcriptional responses. Herein we show that human coronaviruses (HCoV), both low-pathogenic seasonal-HCoVs and highly-pathogenic SARS-CoV-2 variants, are potent inducers of HSF1, promoting HSF1 serine-326 phosphorylation and triggering a powerful and distinct HSF1-driven transcriptional-translational response in infected cells. Despite the coronavirus-mediated shut-down of the host translational machinery, selected HSF1-target gene products, including HSP70, HSPA6 and AIRAP, are highly expressed in HCoV-infected cells. Using silencing experiments and a direct HSF1 small-molecule inhibitor we show that, intriguingly, HCoV-mediated activation of the HSF1-pathway, rather than representing a host defense response to infection, is hijacked by the pathogen and is essential for efficient progeny particles production. The results open new scenarios for the search of innovative antiviral strategies against coronavirus infections.
Collapse
Affiliation(s)
- Silvia Pauciullo
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Anna Riccio
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Silvia Santopolo
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Anna Albecka
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Guido Papa
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Leo C James
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Sara Piacentini
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | | | - Antonio Rossi
- Institute of Translational Pharmacology, CNR, Rome, Italy
| | - M Gabriella Santoro
- Department of Biology, University of Rome Tor Vergata, Rome, Italy.
- Institute of Translational Pharmacology, CNR, Rome, Italy.
| |
Collapse
|
2
|
De Greve H, Fioravanti A. Single domain antibodies from camelids in the treatment of microbial infections. Front Immunol 2024; 15:1334829. [PMID: 38827746 PMCID: PMC11140111 DOI: 10.3389/fimmu.2024.1334829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 04/29/2024] [Indexed: 06/04/2024] Open
Abstract
Infectious diseases continue to pose significant global health challenges. In addition to the enduring burdens of ailments like malaria and HIV, the emergence of nosocomial outbreaks driven by antibiotic-resistant pathogens underscores the ongoing threats. Furthermore, recent infectious disease crises, exemplified by the Ebola and SARS-CoV-2 outbreaks, have intensified the pursuit of more effective and efficient diagnostic and therapeutic solutions. Among the promising options, antibodies have garnered significant attention due to their favorable structural characteristics and versatile applications. Notably, nanobodies (Nbs), the smallest functional single-domain antibodies of heavy-chain only antibodies produced by camelids, exhibit remarkable capabilities in stable antigen binding. They offer unique advantages such as ease of expression and modification and enhanced stability, as well as improved hydrophilicity compared to conventional antibody fragments (antigen-binding fragments (Fab) or single-chain variable fragments (scFv)) that can aggregate due to their low solubility. Nanobodies directly target antigen epitopes or can be engineered into multivalent Nbs and Nb-fusion proteins, expanding their therapeutic potential. This review is dedicated to charting the progress in Nb research, particularly those derived from camelids, and highlighting their diverse applications in treating infectious diseases, spanning both human and animal contexts.
Collapse
Affiliation(s)
- Henri De Greve
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Antonella Fioravanti
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
- VIB-VUB Center for Structural Biology, Vrije Universiteit Brussel, Brussels, Belgium
- Fondazione ParSeC – Parco delle Scienze e della Cultura, Prato, Italy
| |
Collapse
|
3
|
Mancusi A, Proroga YTR, Maiolino P, Marrone R, D’Emilio C, Girardi S, Egidio M, Boni A, Vicenza T, Suffredini E, Power K. Droplet Digital RT-PCR (dd RT-PCR) Detection of SARS-CoV-2 in Honey Bees and Honey Collected in Apiaries across the Campania Region. Viruses 2024; 16:729. [PMID: 38793611 PMCID: PMC11126096 DOI: 10.3390/v16050729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/28/2024] [Accepted: 05/02/2024] [Indexed: 05/26/2024] Open
Abstract
Coronaviruses (CoVs), a subfamily of Orthocoronavirinae, are viruses that sometimes present a zoonotic character. Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is responsible for the recent outbreak of COVID-19, which, since its outbreak in 2019, has caused about 774,593,066 confirmed cases and 7,028,881 deaths. Aereosols are the main route of transmission among people; however, viral droplets can contaminate surfaces and fomites as well as particulate matter (PM) in suspensions of natural and human origin. Honey bees are well known bioindicators of the presence of pollutants and PMs in the environment as they can collect a great variety of substances during their foraging activities. The aim of this study was to evaluate the possible role of honey bees as bioindicators of the prevalence SARS-CoV-2. In this regard, 91 samples of honey bees and 6 of honey were collected from different apiaries of Campania region (Southern Italy) in four time periods from September 2020 to June 2022 and were analyzed with Droplet Digital RT-PCR for SARS-CoV-2 target genes Orf1b and N. The screening revealed the presence of SARS-CoV-2 in 12/91 in honey bee samples and in 2/6 honey samples. These results suggest that honey bees could also be used as indicators of outbreaks of airborne pathogens such as SARS-CoV-2.
Collapse
Affiliation(s)
- Andrea Mancusi
- Department of Food Security Coordination, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute No. 2, 80055 Portici, Italy; (A.M.); (Y.T.R.P.); (S.G.)
| | - Yolande Thérèse Rose Proroga
- Department of Food Security Coordination, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute No. 2, 80055 Portici, Italy; (A.M.); (Y.T.R.P.); (S.G.)
| | - Paola Maiolino
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, 80137 Naples, Italy; (P.M.); (R.M.); (C.D.)
| | - Raffaele Marrone
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, 80137 Naples, Italy; (P.M.); (R.M.); (C.D.)
| | - Claudia D’Emilio
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, 80137 Naples, Italy; (P.M.); (R.M.); (C.D.)
| | - Santa Girardi
- Department of Food Security Coordination, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute No. 2, 80055 Portici, Italy; (A.M.); (Y.T.R.P.); (S.G.)
| | - Marica Egidio
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, 80137 Naples, Italy; (P.M.); (R.M.); (C.D.)
| | - Arianna Boni
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (A.B.); (T.V.); (E.S.)
| | - Teresa Vicenza
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (A.B.); (T.V.); (E.S.)
| | - Elisabetta Suffredini
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (A.B.); (T.V.); (E.S.)
| | - Karen Power
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy;
| |
Collapse
|
4
|
Lauber C, Zhang X, Vaas J, Klingler F, Mutz P, Dubin A, Pietschmann T, Roth O, Neuman BW, Gorbalenya AE, Bartenschlager R, Seitz S. Deep mining of the Sequence Read Archive reveals major genetic innovations in coronaviruses and other nidoviruses of aquatic vertebrates. PLoS Pathog 2024; 20:e1012163. [PMID: 38648214 PMCID: PMC11065284 DOI: 10.1371/journal.ppat.1012163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 05/02/2024] [Accepted: 03/31/2024] [Indexed: 04/25/2024] Open
Abstract
Virus discovery by genomics and metagenomics empowered studies of viromes, facilitated characterization of pathogen epidemiology, and redefined our understanding of the natural genetic diversity of viruses with profound functional and structural implications. Here we employed a data-driven virus discovery approach that directly queries unprocessed sequencing data in a highly parallelized way and involves a targeted viral genome assembly strategy in a wide range of sequence similarity. By screening more than 269,000 datasets of numerous authors from the Sequence Read Archive and using two metrics that quantitatively assess assembly quality, we discovered 40 nidoviruses from six virus families whose members infect vertebrate hosts. They form 13 and 32 putative viral subfamilies and genera, respectively, and include 11 coronaviruses with bisegmented genomes from fishes and amphibians, a giant 36.1 kilobase coronavirus genome with a duplicated spike glycoprotein (S) gene, 11 tobaniviruses and 17 additional corona-, arteri-, cremega-, nanhypo- and nangoshaviruses. Genome segmentation emerged in a single evolutionary event in the monophyletic lineage encompassing the subfamily Pitovirinae. We recovered the bisegmented genome sequences of two coronaviruses from RNA samples of 69 infected fishes and validated the presence of poly(A) tails at both segments using 3'RACE PCR and subsequent Sanger sequencing. We report a genetic linkage between accessory and structural proteins whose phylogenetic relationships and evolutionary distances are incongruent with the phylogeny of replicase proteins. We rationalize these observations in a model of inter-family S recombination involving at least five ancestral corona- and tobaniviruses of aquatic hosts. In support of this model, we describe an individual fish co-infected with members from the families Coronaviridae and Tobaniviridae. Our results expand the scale of the known extraordinary evolutionary plasticity in nidoviral genome architecture and call for revisiting fundamentals of genome expression, virus particle biology, host range and ecology of vertebrate nidoviruses.
Collapse
Affiliation(s)
- Chris Lauber
- Institute for Experimental Virology, TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany
- Cluster of Excellence 2155 RESIST, Hannover, Germany
| | - Xiaoyu Zhang
- Institute for Experimental Virology, TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany
| | - Josef Vaas
- Division of Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research, Heidelberg, Germany
| | - Franziska Klingler
- Division of Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research, Heidelberg, Germany
| | - Pascal Mutz
- Division of Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Arseny Dubin
- Marine Evolutionary Biology, Zoological Institute, Kiel University, Kiel, Germany
| | - Thomas Pietschmann
- Institute for Experimental Virology, TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany
- Cluster of Excellence 2155 RESIST, Hannover, Germany
| | - Olivia Roth
- Marine Evolutionary Biology, Zoological Institute, Kiel University, Kiel, Germany
| | - Benjamin W. Neuman
- Department of Biology and Texas A&M Global Health Research Complex, Texas A&M University, College Station, Texas, United States
| | - Alexander E. Gorbalenya
- Leiden University Center of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
- Faculty of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Ralf Bartenschlager
- Division of Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research, Heidelberg, Germany
| | - Stefan Seitz
- Division of Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research, Heidelberg, Germany
| |
Collapse
|
5
|
Park KS, Park TI, Lee JE, Hwang SY, Choi A, Pack SP. Aptamers and Nanobodies as New Bioprobes for SARS-CoV-2 Diagnostic and Therapeutic System Applications. BIOSENSORS 2024; 14:146. [PMID: 38534253 DOI: 10.3390/bios14030146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/10/2024] [Accepted: 03/12/2024] [Indexed: 03/28/2024]
Abstract
The global challenges posed by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic have underscored the critical importance of innovative and efficient control systems for addressing future pandemics. The most effective way to control the pandemic is to rapidly suppress the spread of the virus through early detection using a rapid, accurate, and easy-to-use diagnostic platform. In biosensors that use bioprobes, the binding affinity of molecular recognition elements (MREs) is the primary factor determining the dynamic range of the sensing platform. Furthermore, the sensitivity relies mainly on bioprobe quality with sufficient functionality. This comprehensive review investigates aptamers and nanobodies recently developed as advanced MREs for SARS-CoV-2 diagnostic and therapeutic applications. These bioprobes might be integrated into organic bioelectronic materials and devices, with promising enhanced sensitivity and specificity. This review offers valuable insights into advancing biosensing technologies for infectious disease diagnosis and treatment using aptamers and nanobodies as new bioprobes.
Collapse
Affiliation(s)
- Ki Sung Park
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
| | - Tae-In Park
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
| | - Jae Eon Lee
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
| | - Seo-Yeong Hwang
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
| | - Anna Choi
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
| | - Seung Pil Pack
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
| |
Collapse
|
6
|
Collins CP, Longo DL, Murphy WJ. The immunobiology of SARS-CoV-2 infection and vaccine responses: potential influences of cross-reactive memory responses and aging on efficacy and off-target effects. Front Immunol 2024; 15:1345499. [PMID: 38469293 PMCID: PMC10925677 DOI: 10.3389/fimmu.2024.1345499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 02/12/2024] [Indexed: 03/13/2024] Open
Abstract
Immune responses to both SARS-CoV-2 infection and its associated vaccines have been highly variable within the general population. The increasing evidence of long-lasting symptoms after resolution of infection, called post-acute sequelae of COVID-19 (PASC) or "Long COVID," suggests that immune-mediated mechanisms are at play. Closely related endemic common human coronaviruses (hCoV) can induce pre-existing and potentially cross-reactive immunity, which can then affect primary SARS-CoV-2 infection, as well as vaccination responses. The influence of pre-existing immunity from these hCoVs, as well as responses generated from original CoV2 strains or vaccines on the development of new high-affinity responses to CoV2 antigenic viral variants, needs to be better understood given the need for continuous vaccine adaptation and application in the population. Due in part to thymic involution, normal aging is associated with reduced naïve T cell compartments and impaired primary antigen responsiveness, resulting in a reliance on the pre-existing cross-reactive memory cell pool which may be of lower affinity, restricted in diversity, or of shorter duration. These effects can also be mediated by the presence of down-regulatory anti-idiotype responses which also increase in aging. Given the tremendous heterogeneity of clinical data, utilization of preclinical models offers the greatest ability to assess immune responses under a controlled setting. These models should now involve prior antigen/viral exposure combined with incorporation of modifying factors such as age on immune responses and effects. This will also allow for mechanistic dissection and understanding of the different immune pathways involved in both SARS-CoV-2 pathogen and potential vaccine responses over time and how pre-existing memory responses, including potential anti-idiotype responses, can affect efficacy as well as potential off-target effects in different tissues as well as modeling PASC.
Collapse
Affiliation(s)
- Craig P. Collins
- Graduate Program in Immunology, University of California (UC) Davis, Davis, CA, United States
| | - Dan L. Longo
- Harvard Medical School, Brigham and Women’s Hospital, Boston, MA, United States
| | - William J. Murphy
- Departments of Dermatology and Internal Medicine (Hematology/Oncology), University of California (UC) Davis School of Medicine, Sacramento, CA, United States
| |
Collapse
|
7
|
Jin X, Zhang M, Fu B, Li M, Yang J, Zhang Z, Li C, Zhang H, Wu H, Xue W, Liu Y. Structure-Based Discovery of the SARS-CoV-2 Main Protease Noncovalent Inhibitors from Traditional Chinese Medicine. J Chem Inf Model 2024; 64:1319-1330. [PMID: 38346323 DOI: 10.1021/acs.jcim.3c01327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Traditional Chinese medicine (TCM) has been extensively employed for the treatment of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, there is demand for discovering more SARS-CoV-2 Mpro inhibitors with diverse scaffolds to optimize anti-SARS-CoV-2 lead compounds. In this study, comprehensive in silico and in vitro assays were utilized to determine the potential inhibitors from TCM compounds against SARS-CoV-2 Mpro, which is an important therapeutic target for SARS-CoV-2. The ensemble docking analysis of 18263 TCM compounds against 15 SARS-CoV-2 Mpro conformations identified 19 TCM compounds as promising candidates. Further in vitro testing validated three compounds as inhibitors of SARS-CoV-2 Mpro and showed IC50 values of 4.64 ± 0.11, 7.56 ± 0.78, and 11.16 ± 0.26 μM, with EC50 values of 12.25 ± 1.68, 15.58 ± 0.77, and 29.32 ± 1.25 μM, respectively. Molecular dynamics (MD) simulations indicated that the three complexes remained stable over the last 100 ns of production run. An analysis of the binding mode revealed that the active compounds occupy different subsites (S1, S2, S3, and S4) of the active site of SARS-CoV-2 Mpro via specific poses through noncovalent interactions with key amino acids (e.g., HIS 41, ASN 142, GLY 143, MET 165, GLU 166, or GLN 189). Overall, this study provides evidence indicating that the three natural products obtained from TCM could be further used for anti-COVID-19 research, justifying the investigation of Chinese herbal medicinal ingredients as bioactive constituents for therapeutic targets.
Collapse
Affiliation(s)
- Xiaojie Jin
- College of Pharmacy, Gansu University of Chinese Medicine, Lanzhou 730000, China
- Gansu University Key Laboratory for Molecular Medicine and Chinese Medicine Prevention and Treatment of Major Diseases, Gansu University of Chinese Medicine, Lanzhou 730000, China
- Key Laboratory of Dunhuang Medicine, Ministry of Education, Gansu University of Chinese Medicine, Lanzhou 730000, China
| | - Min Zhang
- College of Pharmacy, Gansu University of Chinese Medicine, Lanzhou 730000, China
| | - Beibei Fu
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Mi Li
- College of Pharmacy, Gansu University of Chinese Medicine, Lanzhou 730000, China
| | - Jingyi Yang
- School of Pharmaceutical Sciences and Innovative Drug Research Centre, Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Chongqing University, Chongqing 401331, China
| | - Zhiming Zhang
- Gansu Provincial Hospital of TCM, Lanzhou 730000, China
| | - Chenghao Li
- Medical College, Yangzhou University, Yangzhou 225000, China
| | - Huijuan Zhang
- College of Pharmacy, Gansu University of Chinese Medicine, Lanzhou 730000, China
| | - Haibo Wu
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Weiwei Xue
- School of Pharmaceutical Sciences and Innovative Drug Research Centre, Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Chongqing University, Chongqing 401331, China
| | - Yongqi Liu
- Gansu University Key Laboratory for Molecular Medicine and Chinese Medicine Prevention and Treatment of Major Diseases, Gansu University of Chinese Medicine, Lanzhou 730000, China
- Key Laboratory of Dunhuang Medicine, Ministry of Education, Gansu University of Chinese Medicine, Lanzhou 730000, China
| |
Collapse
|
8
|
Park KS, Choi A, Park TI, Pack SP. Fluorometric and Colorimetric Method for SARS-CoV-2 Detection Using Designed Aptamer Display Particles. BIOSENSORS 2024; 14:113. [PMID: 38534220 DOI: 10.3390/bios14030113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 02/16/2024] [Accepted: 02/17/2024] [Indexed: 03/28/2024]
Abstract
SARS-CoV-2, the virus responsible for the COVID-19 pandemic, has spurred the urgent need for practical diagnostics with high sensitivity and selectivity. Although advanced diagnostic tools have emerged to efficiently control pandemics, they still have costly limitations owing to their reliance on antibodies or enzymes and require high-tech equipment. Therefore, there is still a need to develop rapid and low-cost diagnostics with high sensitivity and selectivity. In this study, we generated aptamer display particles (AdP), enabling easy fabrication of a SARS-CoV-2 detection matrix through particle PCR, and applied it to diagnosis using fluorometric and colorimetric assays. We designed two AdPs, C1-AdP and C4-AdP, displayed with SpS1-C1 and SpS1-C4 aptamers, respectively, and showed their high binding ability against SARS-CoV-2 spike protein with a concentration-dependent fluorescence increase. This enabled detection even at low concentrations (0.5 nM). To validate its use as a diagnostic tool for SARS-CoV-2, we designed a sandwich-type assay using two AdPs and high-quality aptamers targeting SARS-CoV-2 pseudoviruses. The fluorometric assay achieved a detection limit of 3.9 × 103 pseudoviruses/mL. The colorimetric assay using an amplification approach exhibited higher sensitivity, with a detection limit of 1 × 101 pseudoviruses/mL, and a broad range of over four orders of magnitude was observed.
Collapse
Affiliation(s)
- Ki Sung Park
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
| | - Anna Choi
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
| | - Tae-In Park
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
| | - Seung Pil Pack
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
| |
Collapse
|
9
|
Park CH, Yang J, Lee HS, Kim TH, Eun LY. Characteristics of Teenagers Presenting with Chest Pain after COVID-19 mRNA Vaccination. J Clin Med 2023; 12:4421. [PMID: 37445457 DOI: 10.3390/jcm12134421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/14/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023] Open
Abstract
In this study, we evaluated the clinical and radiological manifestations of teenagers presenting with chest pain after coronavirus disease 2019 (COVID-19) messenger RNA (mRNA) vaccination. We retrospectively enrolled 61 teenage patients, aged 13 to 19 years, who underwent echocardiography and cardiac magnetic resonance imaging (CMR) for chest pain after COVID-19 mRNA vaccination, from November 2021 to April 2022. Medical records, laboratory results, echocardiographic, and CMR findings were analyzed. The mean age of the participants was 14.4 ± 1.9 years, with a male:female ratio of 28:33. Among the sixty-one patients with chest pain after COVID-19 vaccination, only two (3.3%) were diagnosed as confirmed myocarditis, and almost all of them recovered with conservative treatments. However, on CMR, 24 (39.3%) presented with mild myocardial abnormalities; 22 (36.1%) showed myocardial edema, and 19 (31.1%) were found to have a myocardial injury. Multivariate logistic analyses revealed that older age and female sex were significantly associated with myocardial abnormalities. In teenagers who present with chest pain after COVID-19 mRNA vaccination, confirmed myocarditis is uncommon. However, myocardial abnormalities on CMR might occur frequently, and females in their late teens might be more vulnerable to myocardial abnormalities.
Collapse
Affiliation(s)
- Chul Hwan Park
- Department of Radiology and Research Institute of Radiological Science, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul 06273, Republic of Korea
| | - Juyeon Yang
- Biostatistics Collaboration Unit, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Hye Sun Lee
- Biostatistics Collaboration Unit, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Tae Hoon Kim
- Department of Radiology and Research Institute of Radiological Science, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul 06273, Republic of Korea
| | - Lucy Youngmin Eun
- Department of Pediatrics, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul 06273, Republic of Korea
| |
Collapse
|
10
|
Strine MS, Cai WL, Wei J, Alfajaro MM, Filler RB, Biering SB, Sarnik S, Chow RD, Patil A, Cervantes KS, Collings CK, DeWeirdt PC, Hanna RE, Schofield K, Hulme C, Konermann S, Doench JG, Hsu PD, Kadoch C, Yan Q, Wilen CB. DYRK1A promotes viral entry of highly pathogenic human coronaviruses in a kinase-independent manner. PLoS Biol 2023; 21:e3002097. [PMID: 37310920 PMCID: PMC10263356 DOI: 10.1371/journal.pbio.3002097] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 03/29/2023] [Indexed: 06/15/2023] Open
Abstract
Identifying host genes essential for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has the potential to reveal novel drug targets and further our understanding of Coronavirus Disease 2019 (COVID-19). We previously performed a genome-wide CRISPR/Cas9 screen to identify proviral host factors for highly pathogenic human coronaviruses. Few host factors were required by diverse coronaviruses across multiple cell types, but DYRK1A was one such exception. Although its role in coronavirus infection was previously undescribed, DYRK1A encodes Dual Specificity Tyrosine Phosphorylation Regulated Kinase 1A and is known to regulate cell proliferation and neuronal development. Here, we demonstrate that DYRK1A regulates ACE2 and DPP4 transcription independent of its catalytic kinase function to support SARS-CoV, SARS-CoV-2, and Middle East Respiratory Syndrome Coronavirus (MERS-CoV) entry. We show that DYRK1A promotes DNA accessibility at the ACE2 promoter and a putative distal enhancer, facilitating transcription and gene expression. Finally, we validate that the proviral activity of DYRK1A is conserved across species using cells of nonhuman primate and human origin. In summary, we report that DYRK1A is a novel regulator of ACE2 and DPP4 expression that may dictate susceptibility to multiple highly pathogenic human coronaviruses.
Collapse
Affiliation(s)
- Madison S. Strine
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Wesley L. Cai
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States of America
| | - Jin Wei
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, United States of America
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei Province, China
| | - Mia Madel Alfajaro
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Renata B. Filler
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Scott B. Biering
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, California, United States of America
| | - Sylvia Sarnik
- University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Ryan D. Chow
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Ajinkya Patil
- Department of Pediatric Oncology, Dana–Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Program in Virology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Kasey S. Cervantes
- Department of Pediatric Oncology, Dana–Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Clayton K. Collings
- Department of Pediatric Oncology, Dana–Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Peter C. DeWeirdt
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Ruth E. Hanna
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Kevin Schofield
- Department of Chemistry and Biochemistry, College of Science, The University of Arizona, Tucson, Arizona, United States of America
| | - Christopher Hulme
- Department of Chemistry and Biochemistry, College of Science, The University of Arizona, Tucson, Arizona, United States of America
- Division of Drug Discovery and Development, Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, Arizona, United States of America
| | - Silvana Konermann
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, United States of America
- Arc Institute, Palo Alto, California, United States of America
| | - John G. Doench
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Patrick D. Hsu
- Arc Institute, Palo Alto, California, United States of America
- Department of Bioengineering, University of California, Berkeley, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, California, United States of America
- Center for Computational Biology, University of California, Berkeley, California, United States of America
| | - Cigall Kadoch
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Department of Pediatric Oncology, Dana–Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Qin Yan
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, United States of America
- Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Craig B. Wilen
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut, United States of America
| |
Collapse
|
11
|
Sekar RV, Oliva PJ, Woodside MT. Modelling the structures of frameshift-stimulatory pseudoknots from representative bat coronaviruses. PLoS Comput Biol 2023; 19:e1011124. [PMID: 37205708 DOI: 10.1371/journal.pcbi.1011124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 04/24/2023] [Indexed: 05/21/2023] Open
Abstract
Coronaviruses (CoVs) use -1 programmed ribosomal frameshifting stimulated by RNA pseudoknots in the viral genome to control expression of enzymes essential for replication, making CoV pseudoknots a promising target for anti-coronaviral drugs. Bats represent one of the largest reservoirs of CoVs and are the ultimate source of most CoVs infecting humans, including those causing SARS, MERS, and COVID-19. However, the structures of bat-CoV frameshift-stimulatory pseudoknots remain largely unexplored. Here we use a combination of blind structure prediction followed by all-atom molecular dynamics simulations to model the structures of eight pseudoknots that, together with the SARS-CoV-2 pseudoknot, are representative of the range of pseudoknot sequences in bat CoVs. We find that they all share some key qualitative features with the pseudoknot from SARS-CoV-2, notably the presence of conformers with two distinct fold topologies differing in whether or not the 5' end of the RNA is threaded through a junction, and similar conformations for stem 1. However, they differed in the number of helices present, with half sharing the 3-helix architecture of the SARS-CoV-2 pseudoknot but two containing 4 helices and two others only 2. These structure models should be helpful for future work studying bat-CoV pseudoknots as potential therapeutic targets.
Collapse
Affiliation(s)
| | | | - Michael T Woodside
- Department of Physics, University of Alberta, Edmonton, Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Canada
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Canada
| |
Collapse
|
12
|
Tangye SG. Impact of SARS-CoV-2 infection and COVID-19 on patients with inborn errors of immunity. J Allergy Clin Immunol 2023; 151:818-831. [PMID: 36522221 PMCID: PMC9746792 DOI: 10.1016/j.jaci.2022.11.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/02/2022] [Accepted: 11/04/2022] [Indexed: 12/15/2022]
Abstract
Since the arrival of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in December 2019, its characterization as a novel human pathogen, and the resulting coronavirus disease 2019 (COVID-19) pandemic, over 6.5 million people have died worldwide-a stark and sobering reminder of the fundamental and nonredundant roles of the innate and adaptive immune systems in host defense against emerging pathogens. Inborn errors of immunity (IEI) are caused by germline variants, typically in single genes. IEI are characterized by defects in development and/or function of cells involved in immunity and host defense, rendering individuals highly susceptible to severe, recurrent, and sometimes fatal infections, as well as immune dysregulatory conditions such as autoinflammation, autoimmunity, and allergy. The study of IEI has revealed key insights into the molecular and cellular requirements for immune-mediated protection against infectious diseases. Indeed, this has been exemplified by assessing the impact of SARS-CoV-2 infection in individuals with previously diagnosed IEI, as well as analyzing rare cases of severe COVID-19 in otherwise healthy individuals. This approach has defined fundamental aspects of mechanisms of disease pathogenesis, immunopathology in the context of infection with a novel pathogen, and therapeutic options to mitigate severe disease. This review summarizes these findings and illustrates how the study of these rare experiments of nature can inform key features of human immunology, which can then be leveraged to improve therapies for treating emerging and established infectious diseases.
Collapse
Affiliation(s)
- Stuart G Tangye
- Garvan Institute of Medical Research, Darlinghurst, Darlinghurst, Australia; St Vincent's Clinical School, University of New South Wales Sydney, Randwick, Randwick, Australia; Clinical Immunogenomics Research Consortium of Australasia (CIRCA).
| |
Collapse
|
13
|
An immunoinformatics approach to study the epitopes of SARS-CoV-2 helicase, Nsp13. VACUNAS 2023. [PMCID: PMC9977615 DOI: 10.1016/j.vacun.2023.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Introduction and objective. Vaccines are administered worldwide to control on-going coronavirus disease-19 (COVID-19) pandemic caused by SARS-CoV-2. Vaccine efficacy is largely contributed by the epitopes present on the viral proteins and their alteration might help emerging variants to escape host immune surveillance. Therefore, this study was designed to study SARS-CoV-2 Nsp13 protein, its epitopes and evolution. Methods Clustal Omega was used to identify mutations in Nsp13 protein. Secondary structure and disorder score was predicted by CFSSP and PONDR-VSL2 webservers. Protein stability was predicted by DynaMut webserver. B cell epitopes were predicted by IEDB DiscoTope 2.0 tools and their 3D structures were represented by discovery studio. Antigenicity and allergenicity of epitopes were predicted by Vaxijen2.0 and AllergenFPv.1.0. Physiochemical properties of epitopes were predicted by Toxinpred, HLP webserver tool. Results Our data revealed 182 mutations in Nsp13 among Indian SARS-CoV-2 isolates, which were characterised by secondary structure and per-residue disorderness, stability and dynamicity predictions. To correlate the functional impact of these mutations, we characterised the most prominent B cell and T cell epitopes contributed by Nsp13. Our data revealed twenty-one epitopes, which exhibited antigenicity, stability and interactions with MHC class-I and class-II molecules. Subsequently, the physiochemical properties of these epitopes were analysed. Furthermore, eighteen mutations reside in these Nsp13 epitopes. Conclusions We report appearance of eighteen mutations in the predicted twenty-one epitopes of Nsp13. Among these, at least seven epitopes closely matches with the functionally validated epitopes. Altogether, our study shows the pattern of evolution of Nsp13 epitopes and their probable implications.
Collapse
|
14
|
Heparan Sulfate and Enoxaparin Interact at the Interface of the Spike Protein of HCoV-229E but Not with HCoV-OC43. Viruses 2023; 15:v15030663. [PMID: 36992372 PMCID: PMC10056857 DOI: 10.3390/v15030663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 11/20/2022] [Accepted: 01/05/2023] [Indexed: 03/05/2023] Open
Abstract
It is known that the spike protein of human coronaviruses can bind to a secondary receptor, or coreceptor, to facilitate the virus entry. While HCoV-229E uses human aminopeptidase N (hAPN) as a receptor, HCoV-OC43 binds to 9-O-acetyl-sialic acid (9-O-Ac-Sia), which is linked in a terminal way to the oligosaccharides that decorate glycoproteins and gangliosides on the surface of the host cell. Thus, evaluating the possible inhibitory activity of heparan sulfate, a linear polysaccharide found in animal tissues, and enoxaparin sodium on these viral strains can be considered attractive. Therefore, our study also aims to evaluate these molecules’ antiviral activity as possible adsorption inhibitors against non-SARS-CoV. Once the molecules’ activity was verified in in vitro experiments, the binding was studied by molecular docking and molecular dynamic simulations confirming the interactions at the interface of the spike proteins.
Collapse
|
15
|
Jaiswal D, Kumar U, Gaur V, Salunke DM. Epitope-directed anti-SARS-CoV-2 scFv engineered against the key spike protein region could block membrane fusion. Protein Sci 2023; 32:e4575. [PMID: 36691733 PMCID: PMC9926471 DOI: 10.1002/pro.4575] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 01/17/2023] [Accepted: 01/20/2023] [Indexed: 01/25/2023]
Abstract
The newly emerged SARS-CoV-2 causing coronavirus disease (COVID-19) resulted in >500 million infections. A great deal about the molecular processes of virus infection in the host is getting uncovered. Two sequential proteolytic cleavages of viral spike protein by host proteases are prerequisites for the entry of the virus into the host cell. The first cleavage occurs at S1/S2 site by the furin protease, and the second cleavage at a fusion activation site, the S2' site, by the TMPRSS2 protease. S2' cleavage site is present in the S2 domain of spike protein followed by a fusion peptide. Given the S2' site to be conserved among all the SARS-CoV-2 variants, we chose an S2' epitope encompassing the S2' cleavage site and generated single-chain antibodies (scFvs) through an exhaustive phage display library screening. Crystal structure of a scFv in complex with S2' epitope was determined. Incidentally, S2' epitope in the scFv bound structure adopts an alpha-helical conformation equivalent to the conformation of the epitope in the spike protein. Furthermore, these scFvs can bind to the spike protein expressed either in vitro or on the mammalian cell surface. We illustrate a molecular model based on structural and biochemical insights into the antibody-S2' epitope interaction emphasizing scFvs mediated blocking of virus entry into the host cell by restricting the access of TMPRSS2 protease and consequently inhibiting the S2' cleavage competitively.
Collapse
Affiliation(s)
- Deepika Jaiswal
- International Centre for Genetic Engineering and BiotechnologyNew DelhiDelhiIndia
| | - Ujjwal Kumar
- International Centre for Genetic Engineering and BiotechnologyNew DelhiDelhiIndia
| | - Vineet Gaur
- National Institute of Plant Genome ResearchNew DelhiDelhiIndia
| | - Dinakar M. Salunke
- International Centre for Genetic Engineering and BiotechnologyNew DelhiDelhiIndia
| |
Collapse
|
16
|
Gong HH, Worley MJ, Carver KA, Goldstein DR, Deng JC. Neutrophils drive pulmonary vascular leakage in MHV-1 infection of susceptible A/J mice. Front Immunol 2023; 13:1089064. [PMID: 36685578 PMCID: PMC9853883 DOI: 10.3389/fimmu.2022.1089064] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 12/15/2022] [Indexed: 01/07/2023] Open
Abstract
Background Lung inflammation, neutrophil infiltration, and pulmonary vascular leakage are pathological hallmarks of acute respiratory distress syndrome (ARDS) which can lethally complicate respiratory viral infections. Despite similar comorbidities, however, infections in some patients may be asymptomatic while others develop ARDS as seen with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections for example. Methods In this study, we infected resistant C57BL/6 and susceptible A/J strains of mice with pulmonary administration of murine hepatitis virus strain 1 (MHV-1) to determine mechanisms underlying susceptibility to pulmonary vascular leakage in a respiratory coronavirus infection model. Results A/J animals displayed increased lung injury parameters, pulmonary neutrophil influx, and deficient recruitment of other leukocytes early in the infection. Moreover, under basal conditions, A/J neutrophils overexpressed primary granule protein genes for myeloperoxidase and multiple serine proteases. During infection, myeloperoxidase and elastase protein were released in the bronchoalveolar spaces at higher concentrations compared to C57BL/6 mice. In contrast, genes from other granule types were not differentially expressed between these 2 strains. We found that depletion of neutrophils led to mitigation of lung injury in infected A/J mice while having no effect in the C57BL/6 mice, demonstrating that an altered neutrophil phenotype and recruitment profile is a major driver of lung immunopathology in susceptible mice. Conclusions These results suggest that host susceptibility to pulmonary coronaviral infections may be governed in part by underlying differences in neutrophil phenotypes, which can vary between mice strains, through mechanisms involving primary granule proteins as mediators of neutrophil-driven lung injury.
Collapse
Affiliation(s)
- Henry H. Gong
- University of Michigan, Ann Arbor, MI, United States
- Research Service, Veterans Affairs (VA) Ann Arbor Healthcare System, Department of Veterans Affairs Health System, Ann Arbor, MI, United States
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Matthew J. Worley
- Research Service, Veterans Affairs (VA) Ann Arbor Healthcare System, Department of Veterans Affairs Health System, Ann Arbor, MI, United States
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Kyle A. Carver
- Research Service, Veterans Affairs (VA) Ann Arbor Healthcare System, Department of Veterans Affairs Health System, Ann Arbor, MI, United States
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Daniel R. Goldstein
- Division of Cardiology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Jane C. Deng
- University of Michigan, Ann Arbor, MI, United States
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States
- Medicine Service, Veterans Affairs (VA) Ann Arbor Healthcare System, Department of Veterans Affairs Health System, Ann Arbor, MI, United States
| |
Collapse
|
17
|
Chee J, Chern B, Loh WS, Mullol J, Wang DY. Pathophysiology of SARS-CoV-2 Infection of Nasal Respiratory and Olfactory Epithelia and Its Clinical Impact. Curr Allergy Asthma Rep 2023; 23:121-131. [PMID: 36598732 PMCID: PMC9811886 DOI: 10.1007/s11882-022-01059-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/10/2022] [Indexed: 01/05/2023]
Abstract
PURPOSE OF REVIEW While the predominant cause for morbidity and mortality with SARS-CoV-2 infection is the lower respiratory tract manifestations of the disease, the effects of SARS-CoV-2 infection on the sinonasal tract have also come to the forefront especially with the increased recognition of olfactory symptom. This review presents a comprehensive summary of the mechanisms of action of the SARS-CoV-2 virus, sinonasal pathophysiology of COVID-19, and the correlation with the clinical and epidemiological impact on olfactory dysfunction. RECENT FINDINGS ACE2 and TMPRSS2 receptors are key players in the mechanism of infection of SARS-CoV-2. They are present within both the nasal respiratory as well as olfactory epithelia. There are however differences in susceptibility between different groups of individuals, as well as between the different SARS-CoV-2 variants. The sinonasal cavity is an important route for SARS-CoV-2 infection. While the mechanism of infection of SARS-CoV-2 in nasal respiratory and olfactory epithelia is similar, there exist small but significant differences in the susceptibility of these epithelia and consequently clinical manifestations of the disease. Understanding the differences and nuances in sinonasal pathophysiology in COVID-19 would allow the clinician to predict and counsel patients suffering from COVID-19. Future research into molecular pathways and cytokine responses at different stages of infection and different variants of SARS-CoV-2 would evaluate the individual clinical phenotype, prognosis, and possibly response to vaccines and therapeutics.
Collapse
Affiliation(s)
- Jeremy Chee
- grid.410759.e0000 0004 0451 6143Department of Otolaryngology - Head & Neck Surgery, National University Health System, 1E Kent Ridge Road, Singapore, 119228 Singapore
| | - Beverlyn Chern
- grid.410759.e0000 0004 0451 6143Department of Otolaryngology - Head & Neck Surgery, National University Health System, 1E Kent Ridge Road, Singapore, 119228 Singapore
| | - Woei Shyang Loh
- grid.410759.e0000 0004 0451 6143Department of Otolaryngology - Head & Neck Surgery, National University Health System, 1E Kent Ridge Road, Singapore, 119228 Singapore ,grid.4280.e0000 0001 2180 6431Department of Otolaryngology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Joaquim Mullol
- grid.10403.360000000091771775Rhinology Unit & Smell Clinic, Department of Otorhinolaryngology, Hospital Clinic Barcelona, Universitat de Barcelona, IDIBAPS, CIBERES, Barcelona, Catalonia Spain
| | - De Yun Wang
- Department of Otolaryngology - Head & Neck Surgery, National University Health System, 1E Kent Ridge Road, Singapore, 119228, Singapore. .,Department of Otolaryngology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore. .,Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
| |
Collapse
|
18
|
Pagani I, Ghezzi S, Alberti S, Poli G, Vicenzi E. Origin and evolution of SARS-CoV-2. EUROPEAN PHYSICAL JOURNAL PLUS 2023; 138:157. [PMID: 36811098 PMCID: PMC9933829 DOI: 10.1140/epjp/s13360-023-03719-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 01/19/2023] [Indexed: 05/14/2023]
Abstract
SARS-CoV-2 is a novel coronavirus that emerged in China at the end of 2019 causing the severe disease known as coronavirus disease 2019 (COVID-19). SARS-CoV-2, as to the previously highly pathogenic human coronaviruses named SARS-CoV, the etiological agent of severe acute respiratory syndrome (SARS), has a zoonotic origin, although SARS-CoV-2 precise chain of animal-to-human transmission remains undefined. Unlike the 2002-2003 pandemic caused by SARS-CoV whose extinction from the human population was achieved in eight months, SARS-CoV-2 has been spreading globally in an immunologically naïve population in an unprecedented manner. The efficient infection and replication of SARS-CoV-2 has resulted in the emergence of viral variants that have become predominant posing concerns about their containment as they are more infectious with variable pathogenicity in respect to the original virus. Although vaccine availability is limiting severe disease and death caused by SARS-CoV-2 infection, its extinction is far to be close and predictable. In this regard, the emersion of the Omicron viral variant in November 2021 was characterized by humoral immune escape and it has reinforced the importance of the global monitoring of SARS-CoV-2 evolution. Given the importance of the SARS-CoV-2 zoonotic origin, it will also be crucial to monitor the animal-human interface to be better prepared to cope with future infections of pandemic potential.
Collapse
Affiliation(s)
- Isabel Pagani
- Viral Pathogenesis and Biosafety Unit, Division of Immunology, Transplantation, and Infectious Diseases, San Raffaele Scientific Institute, Via Olgettina, 58, Milan, Italy
| | - Silvia Ghezzi
- Viral Pathogenesis and Biosafety Unit, Division of Immunology, Transplantation, and Infectious Diseases, San Raffaele Scientific Institute, Via Olgettina, 58, Milan, Italy
| | - Simone Alberti
- Viral Pathogenesis and Biosafety Unit, Division of Immunology, Transplantation, and Infectious Diseases, San Raffaele Scientific Institute, Via Olgettina, 58, Milan, Italy
| | - Guido Poli
- Human Immuno-Virology (H.I.V.) Unit, Division of Immunology, Transplantation, and Infectious Diseases, San Raffaele Scientific Institute, Via Olgettina, 58, Milan, Italy
- Vita-Salute San Raffaele University School of Medicine, Via Olgettina, 58, Milan, Italy
| | - Elisa Vicenzi
- Viral Pathogenesis and Biosafety Unit, Division of Immunology, Transplantation, and Infectious Diseases, San Raffaele Scientific Institute, Via Olgettina, 58, Milan, Italy
| |
Collapse
|
19
|
Forni D, Cagliani R, Clerici M, Sironi M. Disease-causing human viruses: novelty and legacy. Trends Microbiol 2022; 30:1232-1242. [PMID: 35902319 DOI: 10.1016/j.tim.2022.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 07/01/2022] [Accepted: 07/04/2022] [Indexed: 01/13/2023]
Abstract
About 270 viruses are known to infect humans. Some of these viruses have been known for centuries, whereas others have recently emerged. During their evolutionary history, humans have moved out of Africa to populate the world. In historical times, human migrations resulted in the displacement of large numbers of people. All these events determined the movement and dispersal of human-infecting viruses. Technological advances have resulted in the characterization of the genetic variability of human viruses, both in extant and in archaeological samples. Field studies investigated the diversity of viruses hosted by other animals. In turn, these advances provided insight into the evolutionary history of human viruses back in time and defined the key events through which they originated and spread.
Collapse
Affiliation(s)
- Diego Forni
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Rachele Cagliani
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Mario Clerici
- Department of Physiopathology and Transplantation, University of Milan, Milan, Italy; Don C. Gnocchi Foundation ONLUS, IRCCS, Milan, Italy
| | - Manuela Sironi
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy.
| |
Collapse
|
20
|
Lång M, Allard A, Blomqvist S, Iranto I, Vuorinen T, Tapio AH, Vainio J. Multicenter evaluation of the GenomEra SARS-CoV-2 assay kit. PLoS One 2022; 17:e0277925. [PMID: 36441674 PMCID: PMC9704634 DOI: 10.1371/journal.pone.0277925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 11/06/2022] [Indexed: 11/29/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) first emerged in late 2019, and quickly spread to every continent causing the global coronavirus disease 2019 (COVID-19) pandemic. Fast propagation of the disease presented numerous challenges to the health care industry in general and especially placed enormous pressure on laboratory testing. Throughout the pandemic, reverse transcription-PCR (RT-PCR)-based nucleic acid amplification tests have been the primary technique to identify acute infections caused by SARS-CoV-2. Since the start of the pandemic, there has been a constantly growing need for accurate and fast tests to enable timely protective and isolation means, as well as rapid therapeutic interventions. Here we present an evaluation of the GenomEra test for SARS-CoV-2. Analytical and clinical performance was evaluated in a multicenter setting with specimens analyzed using standard-of-care (SOC) techniques. Analytical sensitivity was assessed from spiked respiratory swab samples collected into different viral transport media, and in the best performer eSwab, the limit of detection was found to be 239 IU/mL in a heat processed sample. The GenomEra SARS-CoV-2 Assay Kit did not show specificity/cross-reactivity issues with common micro-organisms or other substances commonly found in respiratory specimens when analyzed both in vitro and in silico. Finally, the clinical performance was assessed in comparison to SOC techniques used at four institutions. Based on the analysis of 274 clinical specimens, the positive agreement of the GenomEra SARS-CoV-2 Assay Kit was 90.7%, and the negative agreement was 100%. The GenomEra SARS-CoV-2 Assay Kit provided accurate detection of SARS-CoV-2 with a short turnaround time in under 90 min.
Collapse
Affiliation(s)
- Mika Lång
- Fimlab Laboratories, Department of Clinical Microbiology, Tampere, Finland
- * E-mail:
| | - Annika Allard
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Soile Blomqvist
- Department of Health Security, Expert Microbiology Unit, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Irmeli Iranto
- Department of Health Security, Expert Microbiology Unit, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Tytti Vuorinen
- Department of Clinical Microbiology, Turku University Hospital and Institute of Biomedicine, University of Turku, Turku, Finland
| | | | | |
Collapse
|
21
|
Peng X, Kim J, Gupta G, Agaronyan K, Mankowski MC, Korde A, Takyar SS, Shin HJ, Habet V, Voth S, Audia JP, Chang D, Liu X, Wang L, Cai Y, Tian X, Ishibe S, Kang MJ, Compton S, Wilen CB, Dela Cruz CS, Sharma L. Coronavirus Lung Infection Impairs Host Immunity against Secondary Bacterial Infection by Promoting Lysosomal Dysfunction. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 209:1314-1322. [PMID: 36165196 PMCID: PMC9523490 DOI: 10.4049/jimmunol.2200198] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 07/21/2022] [Indexed: 11/06/2022]
Abstract
Postviral bacterial infections are a major health care challenge in coronavirus infections, including COVID-19; however, the coronavirus-specific mechanisms of increased host susceptibility to secondary infections remain unknown. In humans, coronaviruses, including SARS-CoV-2, infect lung immune cells, including alveolar macrophages, a phenotype poorly replicated in mouse models of SARS-CoV-2. To overcome this, we used a mouse model of native murine β-coronavirus that infects both immune and structural cells to investigate coronavirus-enhanced susceptibility to bacterial infections. Our data show that coronavirus infection impairs the host ability to clear invading bacterial pathogens and potentiates lung tissue damage in mice. Mechanistically, coronavirus limits the bacterial killing ability of macrophages by impairing lysosomal acidification and fusion with engulfed bacteria. In addition, coronavirus-induced lysosomal dysfunction promotes pyroptotic cell death and the release of IL-1β. Inhibition of cathepsin B decreased cell death and IL-1β release and promoted bacterial clearance in mice with postcoronavirus bacterial infection.
Collapse
Affiliation(s)
- Xiaohua Peng
- Department of Rehabilitation Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT
| | - Jooyoung Kim
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT
| | - Gayatri Gupta
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT
| | - Karen Agaronyan
- Howard Hughes Medical Institute and Department of Immunobiology, Yale University, New Haven, CT
| | | | - Asawari Korde
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT
| | - Shervin S Takyar
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT
| | - Hyeon Jun Shin
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT
| | - Victoria Habet
- Department of Pediatrics (Critical Care Medicine), Yale School of Medicine, New Haven, CT
| | - Sarah Voth
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT
| | - Jonathon P Audia
- Department of Microbiology and Immunology, University of South Alabama College of Medicine, Mobile, AL
| | - De Chang
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT
- College of Pulmonary and Critical Care Medicine, Chinese PLA General Hospital, Beijing, China
| | - Xinran Liu
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT
- Center for Cellular and Molecular Imaging, EM Core Facility, Yale School of Medicine, New Haven, CT
| | - Lin Wang
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT
- Department of Emergency Medicine, Shengjing Hospital of China Medical University, Shenyang, China
| | - Ying Cai
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT
| | - Xuefei Tian
- Department of Medicine; Yale School of Medicine, New Haven, CT
| | - Shuta Ishibe
- Department of Medicine; Yale School of Medicine, New Haven, CT
| | - Min-Jong Kang
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT
| | - Susan Compton
- Comparative Medicine Molecular and Serological Diagnostics; Yale School of Medicine, New Haven, CT
| | - Craig B Wilen
- Department of Pediatrics (Critical Care Medicine), Yale School of Medicine, New Haven, CT
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT
| | - Charles S Dela Cruz
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT;
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT; and
- Veterans Affairs Medical Center, West Haven, CT
| | - Lokesh Sharma
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT;
| |
Collapse
|
22
|
Wang S, Wu D, Xiong H, Wang J, Tang Z, Chen Z, Wang Y, Zhang Y, Ying D, Lin X, Liu C, Guo S, Tian W, Lin Y, Zhang X, Yuan Q, Yu H, Zhang T, Zheng Z, Xia N. Potential of conserved antigenic sites in development of universal SARS-like coronavirus vaccines. Front Immunol 2022; 13:952650. [PMID: 36203593 PMCID: PMC9530325 DOI: 10.3389/fimmu.2022.952650] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 09/05/2022] [Indexed: 11/13/2022] Open
Abstract
Given pandemic risks of zoonotic SARS-CoV-2 variants and other SARS-like coronaviruses in the future, it is valuable to perform studies on conserved antigenic sites to design universal SARS-like coronavirus vaccines. By using antibodies obtained from convalescent COVID-19 patients, we succeeded in functional comparison of conserved antigenic sites at multiple aspects with each other, and even with SARS-CoV-2 unique antigenic sites, which promotes the cognition of process of humoral immune response to the conserved antigenic sites. The conserved antigenic sites between SARS-CoV-2 and SARS-CoV can effectively induce affinity maturation of cross-binding antibodies, finally resulting in broadly neutralizing antibodies against multiple variants of concern, which provides an important basis for universal vaccine design, however they are subdominant, putatively due to their lower accessibility relative to SARS-CoV-2 unique antigenic sites. Furthermore, we preliminarily design RBDs to improve the immunogenicity of these conserved antigenic sites. Our study focusing on conserved antigenic sites provides insights for promoting the development of universal SARS-like coronavirus vaccines, thereby enhancing our pandemic preparedness.
Collapse
Affiliation(s)
- Siling Wang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, China
| | - Dinghui Wu
- Department of Pulmonary Medicine, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Hualong Xiong
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, China
| | - Juan Wang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, China
| | - Zimin Tang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, China
| | - Zihao Chen
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, China
| | - Yizhen Wang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, China
| | - Yali Zhang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, China
| | - Dong Ying
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, China
| | - Xue Lin
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, China
| | - Chang Liu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, China
| | - Shaoqi Guo
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, China
| | - Weikun Tian
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, China
| | - Yajie Lin
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, China
| | - Xiaoping Zhang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, China
| | - Quan Yuan
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, China
| | - Hai Yu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, China
| | - Tianying Zhang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, China
- *Correspondence: Tianying Zhang, ; Zizheng Zheng, ; Ningshao Xia,
| | - Zizheng Zheng
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, China
- *Correspondence: Tianying Zhang, ; Zizheng Zheng, ; Ningshao Xia,
| | - Ningshao Xia
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, China
- *Correspondence: Tianying Zhang, ; Zizheng Zheng, ; Ningshao Xia,
| |
Collapse
|
23
|
Houssein M, Al Hossainy AEA, Al Soussi J, El Batch J, El-Samadi L, El Imam S, Fakih R, Dakdouk H, Khalil M. Insights into COVID-19 vaccines development: Translation from benchside to bedside. HEALTH SCIENCES REVIEW (OXFORD, ENGLAND) 2022; 4:100040. [PMID: 35856085 PMCID: PMC9271228 DOI: 10.1016/j.hsr.2022.100040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 07/09/2022] [Indexed: 11/24/2022]
Abstract
Over the past decades, the rapid pace of vaccine development saved 37 million lives, mostly children. The ongoing corona virus disease (COVID-19) pandemic caused the death of more than 4 million worldwide. During 2020, to encounter the pandemic, scientists developed more than 300 vaccines projects against SARS-CoV (severe acute respiratory syndrome coronavirus 2). In 2021, the results emerging from the clinical trials led to the approval and rollout of few vaccines in different countries. To date, at least one dose of a COVID-19 vaccine has been received by more than 3.81 billion people worldwide, equal to about 49.7 percent of the world population. This review was written to the aim of providing a snapshot of COVID-19 disease, highlighting the well-known vaccines, and, finally understanding the effect of mix and match vaccines from different types.
Collapse
Affiliation(s)
- Marwa Houssein
- Department of Biological Sciences, Faculty of Science, Beirut Arab University, Beirut, Lebanon
- Department of General Sciences and English Language, College of Applied Sciences, Al Maarefa University, Riyadh, Saudi Arabia
| | - Aya El Asir Al Hossainy
- Department of Biological Sciences, Faculty of Science, Beirut Arab University, Beirut, Lebanon
| | - Jana Al Soussi
- Department of Biological Sciences, Faculty of Science, Beirut Arab University, Beirut, Lebanon
| | - Jana El Batch
- Department of Biological Sciences, Faculty of Science, Beirut Arab University, Beirut, Lebanon
| | - Lana El-Samadi
- Department of Biological Sciences, Faculty of Science, Beirut Arab University, Beirut, Lebanon
| | - Sherine El Imam
- Department of Biological Sciences, Faculty of Science, Beirut Arab University, Beirut, Lebanon
| | - Rawan Fakih
- Department of Biological Sciences, Faculty of Science, Beirut Arab University, Beirut, Lebanon
| | - Hoda Dakdouk
- Department of Biological Sciences, Faculty of Science, Beirut Arab University, Beirut, Lebanon
| | - Mahmoud Khalil
- Department of Biological Sciences, Faculty of Science, Beirut Arab University, Beirut, Lebanon
- Molecular Biology Unit, Zoology Department, Faculty of Science, Alexandria University, Alexandria, Egypt
| |
Collapse
|
24
|
Lessons from SARS-CoV, MERS-CoV, and SARS-CoV-2 Infections: What We Know So Far. CANADIAN JOURNAL OF INFECTIOUS DISEASES AND MEDICAL MICROBIOLOGY 2022; 2022:1156273. [PMID: 35992513 PMCID: PMC9391183 DOI: 10.1155/2022/1156273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 07/19/2022] [Indexed: 01/08/2023]
Abstract
Within past decades, human infections with emerging and reemerging zoonotic viral pathogens have raised the eminent public health concern. Since November 2002, three highly pathogenic and major deadly human coronaviruses of the βετα-genera (β-hCoVs), namely, severe acute respiratory distress syndrome-coronavirus (SARS-CoV), middle east respiratory syndrome-coronavirus (MERS-CoV), and SARS-CoV-2, have been globally emerged and culminated in the occurrence of SARS epidemic, MERS outbreak, and coronavirus disease 19 (COVID-19) pandemic, respectively. The global emergence and spread of these three major deadly β-hCoVs have extremely dreadful impacts on human health and become an economic burden. Unfortunately, clear specific and highly efficient medical countermeasures for these three β-hCoVs and their underlying fatal illnesses remain under development. Although they belong to the same family and share many features and convergent evolution, these three deadly β-hCoVs have some important and obvious differences. By utilizing their lessons and gaining a deeper understanding of these β-hCoVs, we can identify areas of improvement and provide preparedness plans for fighting and controlling the future reemerging human infections that might arise from them or from other potential pathogenic hCoVs. Therefore, this review summarizes the state-of-the-art information and compares the similarities and dissimilarities between SARS-CoV, MERS-CoV, and SARS-CoV-2, in terms of their evolution trait, genome organization, host cell entry mechanisms, tissue infectivity tropisms, transmission routes and contagiousness, and the clinical characteristics, laboratory features, and immunological abnormalities of their related illnesses. It also provides an overview of the emerging SARS-CoV-2 variants. Additionally, it discusses the challenges of the most proposed treatment options for SARS-CoV-2 infections.
Collapse
|
25
|
Chauhan M, Bhardwaj VK, Kumar A, Kumar V, Kumar P, Enayathullah MG, Thomas J, George J, Kumar BK, Purohit R, Kumar A, Kumar S. Theaflavin 3-gallate inhibits the main protease (M pro) of SARS-CoV-2 and reduces its count in vitro. Sci Rep 2022; 12:13146. [PMID: 35908093 PMCID: PMC9338964 DOI: 10.1038/s41598-022-17558-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 07/27/2022] [Indexed: 12/26/2022] Open
Abstract
The main protease (Mpro) of SARS-CoV-2 has been recognized as an attractive drug target because of its central role in viral replication. Our previous preliminary molecular docking studies showed that theaflavin 3-gallate (a natural bioactive molecule derived from theaflavin and found in high abundance in black tea) exhibited better docking scores than repurposed drugs (Atazanavir, Darunavir, Lopinavir). In this study, conventional and steered MD-simulations analyses revealed stronger interactions of theaflavin 3-gallate with the active site residues of Mpro than theaflavin and a standard molecule GC373 (a known inhibitor of Mpro and novel broad-spectrum anti-viral agent). Theaflavin 3-gallate inhibited Mpro protein of SARS-CoV-2 with an IC50 value of 18.48 ± 1.29 μM. Treatment of SARS-CoV-2 (Indian/a3i clade/2020 isolate) with 200 μM of theaflavin 3-gallate in vitro using Vero cells and quantifying viral transcripts demonstrated reduction of viral count by 75% (viral particles reduced from Log106.7 to Log106.1). Overall, our findings suggest that theaflavin 3-gallate effectively targets the Mpro thus limiting the replication of the SARS-CoV-2 virus in vitro.
Collapse
Affiliation(s)
- Mahima Chauhan
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India.,Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, 201002, India
| | - Vijay Kumar Bhardwaj
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India.,Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, 201002, India.,Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
| | - Asheesh Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India.,Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, 201002, India
| | - Vinod Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
| | - Pawan Kumar
- Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, 201002, India.,Chemical Technology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
| | - M Ghalib Enayathullah
- CSIR-Center for Cellular and Molecular Biology, Annexe-II, Medical Biotechnology Complex, Uppal Road, Hyderabad, Telangana, 500007, India
| | - Jessie Thomas
- CSIR-Center for Cellular and Molecular Biology, Annexe-II, Medical Biotechnology Complex, Uppal Road, Hyderabad, Telangana, 500007, India
| | - Joel George
- CSIR-Center for Cellular and Molecular Biology, Annexe-II, Medical Biotechnology Complex, Uppal Road, Hyderabad, Telangana, 500007, India
| | - Bokara Kiran Kumar
- CSIR-Center for Cellular and Molecular Biology, Annexe-II, Medical Biotechnology Complex, Uppal Road, Hyderabad, Telangana, 500007, India.
| | - Rituraj Purohit
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India. .,Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, 201002, India. .,Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India.
| | - Arun Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India. .,Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, 201002, India.
| | - Sanjay Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
| |
Collapse
|
26
|
Rigo MM, Fasoulis R, Conev A, Hall-Swan S, Antunes DA, Kavraki LE. SARS-Arena: Sequence and Structure-Guided Selection of Conserved Peptides from SARS-related Coronaviruses for Novel Vaccine Development. Front Immunol 2022; 13:931155. [PMID: 35903104 PMCID: PMC9315150 DOI: 10.3389/fimmu.2022.931155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/10/2022] [Indexed: 02/01/2023] Open
Abstract
The pandemic caused by the SARS-CoV-2 virus, the agent responsible for the COVID-19 disease, has affected millions of people worldwide. There is constant search for new therapies to either prevent or mitigate the disease. Fortunately, we have observed the successful development of multiple vaccines. Most of them are focused on one viral envelope protein, the spike protein. However, such focused approaches may contribute for the rise of new variants, fueled by the constant selection pressure on envelope proteins, and the widespread dispersion of coronaviruses in nature. Therefore, it is important to examine other proteins, preferentially those that are less susceptible to selection pressure, such as the nucleocapsid (N) protein. Even though the N protein is less accessible to humoral response, peptides from its conserved regions can be presented by class I Human Leukocyte Antigen (HLA) molecules, eliciting an immune response mediated by T-cells. Given the increased number of protein sequences deposited in biological databases daily and the N protein conservation among viral strains, computational methods can be leveraged to discover potential new targets for SARS-CoV-2 and SARS-CoV-related viruses. Here we developed SARS-Arena, a user-friendly computational pipeline that can be used by practitioners of different levels of expertise for novel vaccine development. SARS-Arena combines sequence-based methods and structure-based analyses to (i) perform multiple sequence alignment (MSA) of SARS-CoV-related N protein sequences, (ii) recover candidate peptides of different lengths from conserved protein regions, and (iii) model the 3D structure of the conserved peptides in the context of different HLAs. We present two main Jupyter Notebook workflows that can help in the identification of new T-cell targets against SARS-CoV viruses. In fact, in a cross-reactive case study, our workflows identified a conserved N protein peptide (SPRWYFYYL) recognized by CD8+ T-cells in the context of HLA-B7+. SARS-Arena is available at https://github.com/KavrakiLab/SARS-Arena.
Collapse
Affiliation(s)
| | - Romanos Fasoulis
- Kavraki Lab, Department of Computer Science, Rice University, Houston, TX, United States
| | - Anja Conev
- Kavraki Lab, Department of Computer Science, Rice University, Houston, TX, United States
| | - Sarah Hall-Swan
- Kavraki Lab, Department of Computer Science, Rice University, Houston, TX, United States
| | - Dinler Amaral Antunes
- Antunes Lab, Center for Nuclear Receptors and Cell Signaling, Department of Biology and Biochemistry, University of Houston, Houston, TX, United States,*Correspondence: Lydia E. Kavraki, ; Dinler Amaral Antunes,
| | - Lydia E. Kavraki
- Kavraki Lab, Department of Computer Science, Rice University, Houston, TX, United States,*Correspondence: Lydia E. Kavraki, ; Dinler Amaral Antunes,
| |
Collapse
|
27
|
Stenglein MD. The Case for Studying New Viruses of New Hosts. Annu Rev Virol 2022; 9:157-172. [PMID: 35671564 DOI: 10.1146/annurev-virology-100220-112915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Virology has largely focused on viruses that are pathogenic to humans or to the other species that we care most about. There is no doubt that this has been a worthwhile investment. But many transformative advances have been made through the in-depth study of relatively obscure viruses that do not appear on lists of prioritized pathogens. In this review, I highlight the benefits that can accrue from the study of viruses and hosts off the beaten track. I take stock of viral sequence diversity across host taxa as an estimate of the bias that exists in our understanding of host-virus interactions. I describe the gains that have been made through the metagenomic discovery of thousands of new viruses in previously unsampled hosts as well as the limitations of metagenomic surveys. I conclude by suggesting that the study of viruses that naturally infect existing and emerging model organisms represents an opportunity to push virology forward in useful and hard to predict ways.Expected final online publication date for the Annual Review of Virology, Volume 9 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Mark D Stenglein
- Center for Vector-Borne Infectious Diseases, Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA;
| |
Collapse
|
28
|
Souza PF, Mesquita FP, Amaral JL, Landim PG, Lima KR, Costa MB, Farias IR, Belém MO, Pinto YO, Moreira HH, Magalhaes IC, Castelo-Branco DS, Montenegro RC, de Andrade CR. The spike glycoprotein of SARS-CoV-2: A review of how mutations of spike glycoproteins have driven the emergence of variants with high transmissibility and immune escape. Int J Biol Macromol 2022; 208:105-125. [PMID: 35300999 PMCID: PMC8920968 DOI: 10.1016/j.ijbiomac.2022.03.058] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 03/08/2022] [Accepted: 03/10/2022] [Indexed: 12/23/2022]
Abstract
Late in 2019, SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2) emerged, causing an unknown type of pneumonia today called coronaviruses disease 2019 (COVID-19). COVID-19 is still an ongoing global outbreak that has claimed and threatened many lives worldwide. Along with the fastest vaccine developed in history to fight SARS-CoV-2 came a critical problem, SARS-CoV-2. These new variants are a result of the accumulation of mutations in the sequence and structure of spike (S) glycoprotein, which is by far the most critical protein for SARS-CoV-2 to recognize cells and escape the immune system, in addition to playing a role in SARS-CoV-2 infection, pathogenicity, transmission, and evolution. In this review, we discuss mutation of S protein and how these mutations have led to new variants that are usually more transmissible and can thus mitigate the immunity produced by vaccination. Here, analysis of S protein sequences and structures from variants point out the mutations among them, how they emerge, and the behavior of S protein from each variant. This review brings details in an understandable way about how the variants of SARS-CoV-2 are a result of mutations in S protein, making them more transmissible and even more aggressive than their relatives.
Collapse
Affiliation(s)
- Pedro F.N. Souza
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Brazil,Drug research and Development Center, Department of Medicine, Federal University of Ceará, Brazil,Corresponding author at: Drug research and Development Center, Department of Physiology and Pharmacology, Federal University of Ceará, Brazil, Rua Coronel Nunes de Melo 100, Caixa 60430-275 Fortaleza, CE, Brazil
| | - Felipe P. Mesquita
- Drug research and Development Center, Department of Medicine, Federal University of Ceará, Brazil
| | - Jackson L. Amaral
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Brazil
| | - Patrícia G.C. Landim
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Brazil
| | - Karollyny R.P. Lima
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Brazil
| | - Marília B. Costa
- Drug research and Development Center, Department of Medicine, Federal University of Ceará, Brazil
| | - Izabelle R. Farias
- Drug research and Development Center, Department of Medicine, Federal University of Ceará, Brazil
| | - Mônica O. Belém
- Laboratory of Translational Research, Christus University Center, Fortaleza, Ceará 60192, Brazil
| | - Yago O. Pinto
- Medical Education Institution-Idomed, Canindé, Ceará, Brazil
| | | | | | - Débora S.C.M. Castelo-Branco
- Department of Pathology and Legal Medicine, Postgraduate Program in Medical Microbiology, Group of Applied Medical Microbiology, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Raquel C. Montenegro
- Drug research and Development Center, Department of Medicine, Federal University of Ceará, Brazil
| | - Claudia R. de Andrade
- Laboratory of Translational Research, Christus University Center, Fortaleza, Ceará 60192, Brazil
| |
Collapse
|
29
|
Ng TI, Correia I, Seagal J, DeGoey DA, Schrimpf MR, Hardee DJ, Noey EL, Kati WM. Antiviral Drug Discovery for the Treatment of COVID-19 Infections. Viruses 2022; 14:961. [PMID: 35632703 PMCID: PMC9143071 DOI: 10.3390/v14050961] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 02/04/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a recently emerged human coronavirus. COVID-19 vaccines have proven to be successful in protecting the vaccinated from infection, reducing the severity of disease, and deterring the transmission of infection. However, COVID-19 vaccination faces many challenges, such as the decline in vaccine-induced immunity over time, and the decrease in potency against some SARS-CoV-2 variants including the recently emerged Omicron variant, resulting in breakthrough infections. The challenges that COVID-19 vaccination is facing highlight the importance of the discovery of antivirals to serve as another means to tackle the pandemic. To date, neutralizing antibodies that block viral entry by targeting the viral spike protein make up the largest class of antivirals that has received US FDA emergency use authorization (EUA) for COVID-19 treatment. In addition to the spike protein, other key targets for the discovery of direct-acting antivirals include viral enzymes that are essential for SARS-CoV-2 replication, such as RNA-dependent RNA polymerase and proteases, as judged by US FDA approval for remdesivir, and EUA for Paxlovid (nirmatrelvir + ritonavir) for treating COVID-19 infections. This review presents an overview of the current status and future direction of antiviral drug discovery for treating SARS-CoV-2 infections, covering important antiviral targets such as the viral spike protein, non-structural protein (nsp) 3 papain-like protease, nsp5 main protease, and the nsp12/nsp7/nsp8 RNA-dependent RNA polymerase complex.
Collapse
Affiliation(s)
- Teresa I. Ng
- Virology Drug Discovery, AbbVie Inc., North Chicago, IL 60064, USA;
| | - Ivan Correia
- Department of Cell and Protein Sciences, Drug Discovery Science and Technology, AbbVie Inc., Worcester, MA 01605, USA;
| | - Jane Seagal
- Department of Biologics Discovery, Drug Discovery Science and Technology, AbbVie Inc., Worcester, MA 01605, USA;
| | - David A. DeGoey
- Department of Centralized Medicinal Chemistry, Drug Discovery Science and Technology, AbbVie Inc., North Chicago, IL 60064, USA; (D.A.D.); (M.R.S.); (D.J.H.)
| | - Michael R. Schrimpf
- Department of Centralized Medicinal Chemistry, Drug Discovery Science and Technology, AbbVie Inc., North Chicago, IL 60064, USA; (D.A.D.); (M.R.S.); (D.J.H.)
| | - David J. Hardee
- Department of Centralized Medicinal Chemistry, Drug Discovery Science and Technology, AbbVie Inc., North Chicago, IL 60064, USA; (D.A.D.); (M.R.S.); (D.J.H.)
| | - Elizabeth L. Noey
- Department of Structural Biology, Drug Discovery Science and Technology, AbbVie Inc., North Chicago, IL 60064, USA;
| | - Warren M. Kati
- Virology Drug Discovery, AbbVie Inc., North Chicago, IL 60064, USA;
| |
Collapse
|
30
|
Khan T, Khan A, Ansari JK, Najmi MH, Wei DQ, Muhammad K, Waheed Y. Potential Immunogenic Activity of Computationally Designed mRNA- and Peptide-Based Prophylactic Vaccines against MERS, SARS-CoV, and SARS-CoV-2: A Reverse Vaccinology Approach. Molecules 2022; 27:molecules27072375. [PMID: 35408772 PMCID: PMC9000378 DOI: 10.3390/molecules27072375] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/26/2022] [Accepted: 03/28/2022] [Indexed: 02/07/2023] Open
Abstract
The continued emergence of human coronaviruses (hCoVs) in the last few decades has posed an alarming situation and requires advanced cross-protective strategies against these pandemic viruses. Among these, Middle East Respiratory Syndrome coronavirus (MERS-CoV), Severe Acute Respiratory Syndrome coronavirus (SARS-CoV), and Severe Acute Respiratory Syndrome coronavirus-2 (SARS-CoV-2) have been highly associated with lethality in humans. Despite the challenges posed by these viruses, it is imperative to develop effective antiviral therapeutics and vaccines for these human-infecting viruses. The proteomic similarity between the receptor-binding domains (RBDs) among the three viral species offers a potential target for advanced cross-protective vaccine designs. In this study, putative immunogenic epitopes including Cytotoxic T Lymphocytes (CTLs), Helper T Lymphocytes (HTLs), and Beta-cells (B-cells) were predicted for each RBD-containing region of the three highly pathogenic hCoVs. This was followed by the structural organization of peptide- and mRNA-based prophylactic vaccine designs. The validated 3D structures of these epitope-based vaccine designs were subjected to molecular docking with human TLR4. Furthermore, the CTL and HTL epitopes were processed for binding with respective human Lymphocytes Antigens (HLAs). In silico cloning designs were obtained for the prophylactic vaccine designs and may be useful in further experimental designs. Additionally, the epitope-based vaccine designs were evaluated for immunogenic activity through immune simulation. Further studies may clarify the safety and efficacy of these prophylactic vaccine designs through experimental testing against these human-pathogenic coronaviruses.
Collapse
Affiliation(s)
- Taimoor Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (T.K.); (A.K.); (D.-Q.W.)
| | - Abbas Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (T.K.); (A.K.); (D.-Q.W.)
| | - Jawad Khaliq Ansari
- Foundation University Medical College, Foundation University Islamabad, Islamabad 46000, Pakistan; (J.K.A.); (M.H.N.)
| | - Muzammil Hasan Najmi
- Foundation University Medical College, Foundation University Islamabad, Islamabad 46000, Pakistan; (J.K.A.); (M.H.N.)
| | - Dong-Qing Wei
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (T.K.); (A.K.); (D.-Q.W.)
- Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nashan District, Shenzhen 518055, China
- State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Khalid Muhammad
- Department of Biology, College of Sciences, United Arab Emirates University, Al Ain 15551, United Arab Emirates
- Correspondence: (K.M.); (Y.W.)
| | - Yasir Waheed
- Foundation University Medical College, Foundation University Islamabad, Islamabad 46000, Pakistan; (J.K.A.); (M.H.N.)
- Correspondence: (K.M.); (Y.W.)
| |
Collapse
|
31
|
Siripanthong B, Asatryan B, Hanff TC, Chatha SR, Khanji MY, Ricci F, Muser D, Ferrari VA, Nazarian S, Santangeli P, Deo R, Cooper LT, Mohiddin SA, Chahal CAA. The Pathogenesis and Long-Term Consequences of COVID-19 Cardiac Injury. JACC Basic Transl Sci 2022; 7:294-308. [PMID: 35165665 PMCID: PMC8828362 DOI: 10.1016/j.jacbts.2021.10.011] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 10/18/2021] [Accepted: 10/20/2021] [Indexed: 12/14/2022]
Abstract
COVID-19 myocardial injury results from immune and hypercoagulability responses. Long-term cardiac consequences of COVID-19 include structural and functional changes. Myocarditis after COVID-19 vaccination is uncommon (highest risk in teenage males). Larger population-based studies are necessary to validate these early results.
The mechanisms of coronavirus disease-2019 (COVID-19)–related myocardial injury comprise both direct viral invasion and indirect (hypercoagulability and immune-mediated) cellular injuries. Some patients with COVID-19 cardiac involvement have poor clinical outcomes, with preliminary data suggesting long-term structural and functional changes. These include persistent myocardial fibrosis, edema, and intraventricular thrombi with embolic events, while functionally, the left ventricle is enlarged, with a reduced ejection fraction and new-onset arrhythmias reported in a number of patients. Myocarditis post-COVID-19 vaccination is rare but more common among young male patients. Larger studies, including prospective data from biobanks, will be useful in expanding these early findings and determining their validity.
Collapse
Affiliation(s)
| | - Babken Asatryan
- Department of Cardiology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | | | - Salman R Chatha
- Barts Heart Centre, St Bartholomew's Hospital, Barts Health NHS Trust, London, United Kingdom.,University Hospital of North Midlands NHS Trust, Stoke-on-Trent, United Kingdom
| | - Mohammed Y Khanji
- Barts Heart Centre, St Bartholomew's Hospital, Barts Health NHS Trust, London, United Kingdom.,Newham University Hospital, Barts Health NHS Trust, London, United Kingdom.,NIHR Barts Biomedical Research Centre, William Harvey Research Institute, Queen Mary University of London, London, United Kingdom
| | - Fabrizio Ricci
- Department of Neuroscience, Imaging and Clinical Sciences, "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy.,Casa di Cura Villa Serena, Città Sant'Angelo, Pescara, Italy.,Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Daniele Muser
- Dipartimento Cardiotoracico, U.O.C. di Cardiologia, Presidio Ospedaliero Universitario "Santa Maria Della Misericordia," Udine, Italy
| | - Victor A Ferrari
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Penn Cardiovascular Institute, Philadelphia, Pennsylvania, USA
| | - Saman Nazarian
- Electrophysiology Section, Division of Cardiovascular Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Pasquale Santangeli
- Electrophysiology Section, Division of Cardiovascular Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Rajat Deo
- Electrophysiology Section, Division of Cardiovascular Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Saidi A Mohiddin
- Barts Heart Centre, St Bartholomew's Hospital, Barts Health NHS Trust, London, United Kingdom.,NIHR Barts Biomedical Research Centre, William Harvey Research Institute, Queen Mary University of London, London, United Kingdom
| | - C Anwar A Chahal
- Barts Heart Centre, St Bartholomew's Hospital, Barts Health NHS Trust, London, United Kingdom.,Electrophysiology Section, Division of Cardiovascular Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota, USA.,WellSpan Center for Inherited Cardiovascular Diseases, WellSpan Health, Lancaster, Pennsylvania, USA
| |
Collapse
|
32
|
Known Cellular and Receptor Interactions of Animal and Human Coronaviruses: A Review. Viruses 2022; 14:v14020351. [PMID: 35215937 PMCID: PMC8878323 DOI: 10.3390/v14020351] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/03/2022] [Accepted: 02/05/2022] [Indexed: 12/12/2022] Open
Abstract
This article aims to review all currently known interactions between animal and human coronaviruses and their cellular receptors. Over the past 20 years, three novel coronaviruses have emerged that have caused severe disease in humans, including SARS-CoV-2 (severe acute respiratory syndrome virus 2); therefore, a deeper understanding of coronavirus host-cell interactions is essential. Receptor-binding is the first stage in coronavirus entry prior to replication and can be altered by minor changes within the spike protein-the coronavirus surface glycoprotein responsible for the recognition of cell-surface receptors. The recognition of receptors by coronaviruses is also a major determinant in infection, tropism, and pathogenesis and acts as a key target for host-immune surveillance and other potential intervention strategies. We aim to highlight the need for a continued in-depth understanding of this subject area following on from the SARS-CoV-2 pandemic, with the possibility for more zoonotic transmission events. We also acknowledge the need for more targeted research towards glycan-coronavirus interactions as zoonotic spillover events from animals to humans, following an alteration in glycan-binding capability, have been well-documented for other viruses such as Influenza A.
Collapse
|
33
|
Bastard P, Zhang Q, Zhang SY, Jouanguy E, Casanova JL. Type I interferons and SARS-CoV-2: from cells to organisms. Curr Opin Immunol 2022; 74:172-182. [PMID: 35149239 PMCID: PMC8786610 DOI: 10.1016/j.coi.2022.01.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 01/12/2022] [Accepted: 01/15/2022] [Indexed: 02/06/2023]
Abstract
Type I interferons (IFNs) have broad and potent antiviral activity. We review the interplay between type I IFNs and SARS-CoV-2. Human cells infected with SARS-CoV-2 in vitro produce low levels of type I IFNs, and SARS-CoV-2 proteins can inhibit various steps in type I IFN production and response. Exogenous type I IFNs inhibit viral growth in vitro. In various animal species infected in vivo, type I IFN deficiencies underlie higher viral loads and more severe disease than in control animals. The early administration of exogenous type I IFNs improves infection control. In humans, inborn errors of, and auto-antibodies against type I IFNs underlie life-threatening COVID-19 pneumonia. Overall, type I IFNs are essential for host defense against SARS-CoV-2 in individual cells and whole organisms.
Collapse
Affiliation(s)
- Paul Bastard
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France; University of Paris, Imagine Institute, Paris, France; St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA; Department of Pediatrics, Necker Hospital for Sick Children, AP-HP, Paris, France.
| | - Qian Zhang
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France; University of Paris, Imagine Institute, Paris, France; St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Shen-Ying Zhang
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France; University of Paris, Imagine Institute, Paris, France; St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Emmanuelle Jouanguy
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France; University of Paris, Imagine Institute, Paris, France; St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France; University of Paris, Imagine Institute, Paris, France; St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA; Department of Pediatrics, Necker Hospital for Sick Children, AP-HP, Paris, France; Howard Hughes Medical Institute, New York, NY, USA.
| |
Collapse
|
34
|
Identifying Inhibitors of −1 Programmed Ribosomal Frameshifting in a Broad Spectrum of Coronaviruses. Viruses 2022; 14:v14020177. [PMID: 35215770 PMCID: PMC8876150 DOI: 10.3390/v14020177] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/30/2021] [Accepted: 01/10/2022] [Indexed: 02/06/2023] Open
Abstract
Recurrent outbreaks of novel zoonotic coronavirus (CoV) diseases in recent years have highlighted the importance of developing therapeutics with broad-spectrum activity against CoVs. Because all CoVs use −1 programmed ribosomal frameshifting (−1 PRF) to control expression of key viral proteins, the frameshift signal in viral mRNA that stimulates −1 PRF provides a promising potential target for such therapeutics. To test the viability of this strategy, we explored whether small-molecule inhibitors of −1 PRF in SARS-CoV-2 also inhibited −1 PRF in a range of bat CoVs—the most likely source of future zoonoses. Six inhibitors identified in new and previous screens against SARS-CoV-2 were evaluated against the frameshift signals from a panel of representative bat CoVs as well as MERS-CoV. Some drugs had strong activity against subsets of these CoV-derived frameshift signals, while having limited to no effect on −1 PRF caused by frameshift signals from other viruses used as negative controls. Notably, the serine protease inhibitor nafamostat suppressed −1 PRF significantly for multiple CoV-derived frameshift signals. These results suggest it is possible to find small-molecule ligands that inhibit −1 PRF specifically in a broad spectrum of CoVs, establishing frameshift signals as a viable target for developing pan-coronaviral therapeutics.
Collapse
|
35
|
Lee SR, Roh JY, Ryu J, Shin HJ, Hong EJ. Activation of TCA cycle restrains virus-metabolic hijacking and viral replication in mouse hepatitis virus-infected cells. Cell Biosci 2022; 12:7. [PMID: 35042550 PMCID: PMC8764321 DOI: 10.1186/s13578-021-00740-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 12/24/2021] [Indexed: 12/28/2022] Open
Abstract
Abstract
Background
One of coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has caused coronavirus disease 2019 (COVID-19) pandemic and threatened worldwide. However, therapy for COVID-19 has rarely been proven to possess specific efficacy. As the virus relies on host metabolism for its survival, several studies have reported metabolic intervention by SARS-CoV-2.
Results
We investigated the coronavirus-metabolic hijacking using mouse hepatitis virus (MHV) as a surrogate for SARS-CoV-2. Based on the altered host metabolism by MHV infection, an increase of glycolysis with low mitochondrial metabolism, we tried to investigate possible therapeutic molecules which increase the TCA cycle. Endogenous metabolites and metabolic regulators were introduced to restrain viral replication by metabolic intervention. We observed that cells deprived of cellular energy nutrition with low glycolysis strongly suppress viral replication. Furthermore, viral replication was also significantly suppressed by electron transport chain inhibitors which exhaust cellular energy. Apart from glycolysis and ETC, pyruvate supplement suppressed viral replication by the TCA cycle induction. As the non-glucose metabolite, fatty acids supplement decreased viral replication via the TCA cycle. Additionally, as a highly possible therapeutic metabolite, nicotinamide riboside (NR) supplement, which activates the TCA cycle by supplying NAD+, substantially suppressed viral replication.
Conclusions
This study suggests that metabolite-mediated TCA cycle activation suppresses replication of coronavirus and suggests that NR might play a role as a novel therapeutic metabolite for coronavirus.
Collapse
|
36
|
Svobodova M, Skouridou V, Jauset-Rubio M, Viéitez I, Fernández-Villar A, Cabrera Alvargonzalez JJ, Poveda E, Bofill CB, Sans T, Bashammakh A, Alyoubi AO, O’Sullivan CK. Aptamer Sandwich Assay for the Detection of SARS-CoV-2 Spike Protein Antigen. ACS OMEGA 2021; 6:35657-35666. [PMID: 34957366 PMCID: PMC8691202 DOI: 10.1021/acsomega.1c05521] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 11/25/2021] [Indexed: 05/10/2023]
Abstract
The novel severe acute respiratory syndrome coronavirus (SARS-CoV-2) emerged at the end of 2019, resulting in the ongoing COVID-19 pandemic. The high transmissibility of the virus and the substantial number of asymptomatic individuals have led to an exponential rise in infections worldwide, urgently requiring global containment strategies. Reverse transcription-polymerase chain reaction is the gold standard for the detection of SARS-CoV-2 infections. Antigen tests, targeting the spike (S) or nucleocapsid (N) viral proteins, are considered as complementary tools. Despite their shortcomings in terms of sensitivity and specificity, antigen tests could be deployed for the detection of potentially contagious individuals with high viral loads. In this work, we sought to develop a sandwich aptamer-based assay for the detection of the S protein of SARS-CoV-2. A detailed study on the binding properties of aptamers to the receptor-binding domain of the S protein in search of aptamer pairs forming a sandwich is presented. Screening of aptamer pairs and optimization of assay conditions led to the development of a laboratory-based sandwich assay able to detect 21 ng/mL (270 pM) of the protein with negligible cross-reactivity with the other known human coronaviruses. The detection of 375 pg of the protein in viral transport medium demonstrates the compatibility of the assay with clinical specimens. Finally, successful detection of the S antigen in nasopharyngeal swab samples collected from suspected patients further establishes the suitability of the assay for screening purposes as a complementary tool to assist in the control of the pandemic.
Collapse
Affiliation(s)
- Marketa Svobodova
- INTERFIBIO
Research Group, Departament d’Enginyeria Química, Universitat Rovira i Virgili, Avinguda Països Catalans
26, Tarragona 43007, Spain
| | - Vasso Skouridou
- INTERFIBIO
Research Group, Departament d’Enginyeria Química, Universitat Rovira i Virgili, Avinguda Països Catalans
26, Tarragona 43007, Spain
| | - Miriam Jauset-Rubio
- INTERFIBIO
Research Group, Departament d’Enginyeria Química, Universitat Rovira i Virgili, Avinguda Països Catalans
26, Tarragona 43007, Spain
| | - Irene Viéitez
- Rare
Diseases & Pediatric Medicine Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-Uvigo, Vigo 36213, Spain
| | - Alberto Fernández-Villar
- Pneumology
Service, Galicia Sur Health Research Institute
(IIS Galicia Sur), SERGAS-Uvigo, Vigo 36213, Spain
| | | | - Eva Poveda
- Group
of Virology and Pathogenesis, Galicia Sur
Health Research Institute (IIS Galicia Sur)-Complexo Hospitalario
Universitario de Vigo, SERGAS-UVigo, Vigo 36213, Spain
| | - Clara Benavent Bofill
- Laboratori
Clinic ICS Camp de Tarragona, Hospital Universitari
de Tarragona Joan XXIII, Avda. Dr. Mallafré Guasch, 4, Tarragona 43007, Spain
| | - Teresa Sans
- Laboratori
Clinic ICS Camp de Tarragona, Hospital Universitari
de Tarragona Joan XXIII, Avda. Dr. Mallafré Guasch, 4, Tarragona 43007, Spain
| | - Abdulaziz Bashammakh
- Department
of Chemistry, Faculty of Science, King Abdulaziz
University, Jeddah 80215, Kingdom of Saudi Arabia
| | - Abdulrahman O. Alyoubi
- Department
of Chemistry, Faculty of Science, King Abdulaziz
University, Jeddah 80215, Kingdom of Saudi Arabia
| | - Ciara K. O’Sullivan
- INTERFIBIO
Research Group, Departament d’Enginyeria Química, Universitat Rovira i Virgili, Avinguda Països Catalans
26, Tarragona 43007, Spain
- Institució
Catalana de Recerca i Estudis Avancats (ICREA), Passeig Lluís Companys 23, Barcelona 08010, Spain
| |
Collapse
|
37
|
Khan M, Yoo SJ, Clijsters M, Backaert W, Vanstapel A, Speleman K, Lietaer C, Choi S, Hether TD, Marcelis L, Nam A, Pan L, Reeves JW, Van Bulck P, Zhou H, Bourgeois M, Debaveye Y, De Munter P, Gunst J, Jorissen M, Lagrou K, Lorent N, Neyrinck A, Peetermans M, Thal DR, Vandenbriele C, Wauters J, Mombaerts P, Van Gerven L. Visualizing in deceased COVID-19 patients how SARS-CoV-2 attacks the respiratory and olfactory mucosae but spares the olfactory bulb. Cell 2021; 184:5932-5949.e15. [PMID: 34798069 PMCID: PMC8564600 DOI: 10.1016/j.cell.2021.10.027] [Citation(s) in RCA: 224] [Impact Index Per Article: 74.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/01/2021] [Accepted: 10/25/2021] [Indexed: 12/28/2022]
Abstract
Anosmia, the loss of smell, is a common and often the sole symptom of COVID-19. The onset of the sequence of pathobiological events leading to olfactory dysfunction remains obscure. Here, we have developed a postmortem bedside surgical procedure to harvest endoscopically samples of respiratory and olfactory mucosae and whole olfactory bulbs. Our cohort of 85 cases included COVID-19 patients who died a few days after infection with SARS-CoV-2, enabling us to catch the virus while it was still replicating. We found that sustentacular cells are the major target cell type in the olfactory mucosa. We failed to find evidence for infection of olfactory sensory neurons, and the parenchyma of the olfactory bulb is spared as well. Thus, SARS-CoV-2 does not appear to be a neurotropic virus. We postulate that transient insufficient support from sustentacular cells triggers transient olfactory dysfunction in COVID-19. Olfactory sensory neurons would become affected without getting infected.
Collapse
Affiliation(s)
- Mona Khan
- Max Planck Research Unit for Neurogenetics, Frankfurt, Germany
| | - Seung-Jun Yoo
- Max Planck Research Unit for Neurogenetics, Frankfurt, Germany
| | - Marnick Clijsters
- Department of Neurosciences, Experimental Otorhinolaryngology, Rhinology Research, KU Leuven, Leuven, Belgium
| | - Wout Backaert
- Department of Otorhinolaryngology, Head and Neck Surgery, University Hospitals Leuven, Leuven, Belgium; Department of Microbiology, Immunology and Transplantation, Allergy and Clinical Immunology Research Unit, KU Leuven, Leuven, Belgium
| | - Arno Vanstapel
- Department of Pathology, University Hospitals Leuven, Leuven, Belgium
| | - Kato Speleman
- Department of Otorhinolaryngology, Head and Neck Surgery, AZ Sint-Jan Brugge-Oostende AV, Bruges, Belgium
| | - Charlotte Lietaer
- Department of Otorhinolaryngology, Head and Neck Surgery, AZ Sint-Jan Brugge-Oostende AV, Bruges, Belgium
| | - Sumin Choi
- Max Planck Research Unit for Neurogenetics, Frankfurt, Germany
| | | | - Lukas Marcelis
- Department of Pathology, University Hospitals Leuven, Leuven, Belgium
| | - Andrew Nam
- NanoString Technologies Inc., Seattle, WA, USA
| | - Liuliu Pan
- NanoString Technologies Inc., Seattle, WA, USA
| | | | - Pauline Van Bulck
- Department of Otorhinolaryngology, Head and Neck Surgery, University Hospitals Leuven, Leuven, Belgium
| | - Hai Zhou
- Max Planck Research Unit for Neurogenetics, Frankfurt, Germany
| | - Marc Bourgeois
- Department of Anesthesiology and Intensive Care Medicine, AZ Sint-Jan Brugge-Oostende AV, Bruges, Belgium
| | - Yves Debaveye
- Intensive Care Medicine, University Hospitals Leuven, Leuven, Belgium; Department of Cellular and Molecular Medicine, Laboratory of Intensive Care Medicine, KU Leuven, Leuven, Belgium
| | - Paul De Munter
- Department of General Internal Medicine, University Hospitals Leuven, Leuven, Belgium; Department of Microbiology, Immunology and Transplantation, Laboratory for Clinical Infectious and Inflammatory Disorders, KU Leuven, Leuven, Belgium
| | - Jan Gunst
- Intensive Care Medicine, University Hospitals Leuven, Leuven, Belgium; Department of Cellular and Molecular Medicine, Laboratory of Intensive Care Medicine, KU Leuven, Leuven, Belgium
| | - Mark Jorissen
- Department of Neurosciences, Experimental Otorhinolaryngology, Rhinology Research, KU Leuven, Leuven, Belgium; Department of Otorhinolaryngology, Head and Neck Surgery, University Hospitals Leuven, Leuven, Belgium
| | - Katrien Lagrou
- Department of Laboratory Medicine and National Reference Centre for Respiratory Pathogens, University Hospitals Leuven, Leuven, Belgium; Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical Bacteriology and Mycology, KU Leuven, Leuven, Belgium
| | - Natalie Lorent
- Department of Respiratory Diseases, University Hospitals Leuven, Leuven, Belgium
| | - Arne Neyrinck
- Department of Anesthesia, University Hospitals Leuven, Leuven, Belgium; Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium
| | - Marijke Peetermans
- Department of General Internal Medicine, University Hospitals Leuven, Leuven, Belgium; Department of Microbiology, Immunology and Transplantation, Laboratory for Clinical Infectious and Inflammatory Disorders, KU Leuven, Leuven, Belgium
| | - Dietmar Rudolf Thal
- Department of Pathology, University Hospitals Leuven, Leuven, Belgium; Department of Imaging and Pathology, Laboratory of Neuropathology and Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - Christophe Vandenbriele
- Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium; Department of Cardiovascular Diseases, University Hospitals Leuven, Leuven, Belgium
| | - Joost Wauters
- Department of General Internal Medicine, University Hospitals Leuven, Leuven, Belgium; Department of Microbiology, Immunology and Transplantation, Laboratory for Clinical Infectious and Inflammatory Disorders, KU Leuven, Leuven, Belgium
| | - Peter Mombaerts
- Max Planck Research Unit for Neurogenetics, Frankfurt, Germany.
| | - Laura Van Gerven
- Department of Neurosciences, Experimental Otorhinolaryngology, Rhinology Research, KU Leuven, Leuven, Belgium; Department of Otorhinolaryngology, Head and Neck Surgery, University Hospitals Leuven, Leuven, Belgium; Department of Microbiology, Immunology and Transplantation, Allergy and Clinical Immunology Research Unit, KU Leuven, Leuven, Belgium.
| |
Collapse
|
38
|
Tayara H, Abdelbaky I, To Chong K. Recent omics-based computational methods for COVID-19 drug discovery and repurposing. Brief Bioinform 2021; 22:6355836. [PMID: 34423353 DOI: 10.1093/bib/bbab339] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 07/09/2021] [Indexed: 12/22/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is the main reason for the increasing number of deaths worldwide. Although strict quarantine measures were followed in many countries, the disease situation is still intractable. Thus, it is needed to utilize all possible means to confront this pandemic. Therefore, researchers are in a race against the time to produce potential treatments to cure or reduce the increasing infections of COVID-19. Computational methods are widely proving rapid successes in biological related problems, including diagnosis and treatment of diseases. Many efforts in recent months utilized Artificial Intelligence (AI) techniques in the context of fighting the spread of COVID-19. Providing periodic reviews and discussions of recent efforts saves the time of researchers and helps to link their endeavors for a faster and efficient confrontation of the pandemic. In this review, we discuss the recent promising studies that used Omics-based data and utilized AI algorithms and other computational tools to achieve this goal. We review the established datasets and the developed methods that were basically directed to new or repurposed drugs, vaccinations and diagnosis. The tools and methods varied depending on the level of details in the available information such as structures, sequences or metabolic data.
Collapse
Affiliation(s)
- Hilal Tayara
- School of international Engineering and Science, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Ibrahim Abdelbaky
- Artificial Intelligence Department, Faculty of Computers and Artificial Intelligence, Benha University, Banha 13518, Egypt
| | - Kil To Chong
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju, Jeollabukdo 54896, Republic of Korea.,Advances Electronics and Information Research Center, Jeonbuk National University, Jeonju 54896, Republic of Korea
| |
Collapse
|
39
|
Konstantinidis TG, Iliadi V, Martinis G, Panopoulou M. The Usefulness of Rare Blood Group Systems in the Risk Determination for Severe COVID-19. PATHOPHYSIOLOGY 2021; 28:496-500. [PMID: 35366247 PMCID: PMC8830445 DOI: 10.3390/pathophysiology28040032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 10/29/2021] [Accepted: 11/02/2021] [Indexed: 12/11/2022] Open
Abstract
The newly identified human coronavirus was named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), based on a detailed analysis of clinical manifestation. It was reported that blood type O individuals were less likely to become infected by SARS-CoV, while blood type A individuals have an increased risk of severe illness. The Forssman antigen, or Forssman glycolipid synthase (FS), was first described in 1911 by John Frederick Forssman. Blood type A/B glycosyltransferases (AT/BTs) and Forssman glycolipid synthase (FS) are encoded by the evolutionarily related ABO (A/B alleles) and GBGT1 genes. In this article, based on published studies about the pathogenesis of the COVID-19, we hypothesize the possible relationship between the COVID-19 infection and rare blood type systems, such as the Forssman antigen system.
Collapse
Affiliation(s)
- Theocharis G. Konstantinidis
- Blood Transfusion Center, University General Hospital of Alexandroupolis Dragana Campus, 68100 Alexandroupolis, Greece;
- Laboratory of Microbiology, Democritus University of Thrace, University General Hospital of Alexandroupolis Dragana Campus, 68100 Alexandroupolis, Greece;
| | - Valeria Iliadi
- Izhevsk State Medical Academy, Kommunarov Street 281, 426034 Izhevsk, Russia;
| | - Georges Martinis
- Blood Transfusion Center, University General Hospital of Alexandroupolis Dragana Campus, 68100 Alexandroupolis, Greece;
| | - Maria Panopoulou
- Laboratory of Microbiology, Democritus University of Thrace, University General Hospital of Alexandroupolis Dragana Campus, 68100 Alexandroupolis, Greece;
| |
Collapse
|
40
|
Roe K. Proposed classifications of immunogenomic editing by cancers and pathogens. INFECTION GENETICS AND EVOLUTION 2021; 96:105126. [PMID: 34715386 DOI: 10.1016/j.meegid.2021.105126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 10/14/2021] [Accepted: 10/23/2021] [Indexed: 10/20/2022]
Abstract
Several evolutionary mechanisms exist between a lethal disease agent, such as a cancer or a pathogen, and the immune system of a surviving subpopulation of hosts. Immunogenomic editing is herein defined as the evolution of a lethal disease agent genome or the surviving carrier or host subpopulation immune system genomes. One type of immunogenomic editing called immunoediting has already been identified for cancer genomes. The effects of two other types of immunogenomic editing have been observed for pathogens and humans. However, these types of editing are only a few types of a much broader immunogenomic editing process, and some of the other types of immunogenomic editing have not been explicitly recognized. Immunogenomic editing can include seven types, and several types of immunogenomic editing have applications including analysis of subpopulation responses to cancers and pathogens. Applications would also include facilitating analysis of substantial subpopulation vulnerability differences to lethal pathogen epidemics. The need for quicker analysis of the actual transmission chains and the immunogenomic mechanisms for the faster spread of dangerously virulent pathogens can be expected to increase, since modern transportation technology can spread new pathogens very rapidly around the world.
Collapse
Affiliation(s)
- Kevin Roe
- San Jose, CA, United States of America.
| |
Collapse
|
41
|
Kirby EN, Shue B, Thomas PQ, Beard MR. CRISPR Tackles Emerging Viral Pathogens. Viruses 2021; 13:2157. [PMID: 34834963 PMCID: PMC8624524 DOI: 10.3390/v13112157] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/16/2021] [Accepted: 10/19/2021] [Indexed: 12/17/2022] Open
Abstract
Understanding the dynamic relationship between viral pathogens and cellular host factors is critical to furthering our knowledge of viral replication, disease mechanisms and development of anti-viral therapeutics. CRISPR genome editing technology has enhanced this understanding, by allowing identification of pro-viral and anti-viral cellular host factors for a wide range of viruses, most recently the cause of the COVID-19 pandemic, SARS-CoV-2. This review will discuss how CRISPR knockout and CRISPR activation genome-wide screening methods are a robust tool to investigate the viral life cycle and how other class 2 CRISPR systems are being repurposed for diagnostics.
Collapse
Affiliation(s)
- Emily N. Kirby
- Research Centre for Infectious Diseases, Department of Molecular and Biomedical Sciences, School of Biological Sciences, The University of Adelaide, Adelaide 5005, Australia; (E.N.K.); (B.S.)
| | - Byron Shue
- Research Centre for Infectious Diseases, Department of Molecular and Biomedical Sciences, School of Biological Sciences, The University of Adelaide, Adelaide 5005, Australia; (E.N.K.); (B.S.)
| | - Paul Q. Thomas
- Adelaide Medical School, The University of Adelaide, Adelaide 5000, Australia;
- Robinson Research Institute, The University of Adelaide, Adelaide 5006, Australia
- Genome Editing Program, South Australian Health & Medical Research Institute, North Terrace, Adelaide 5000, Australia
| | - Michael R. Beard
- Research Centre for Infectious Diseases, Department of Molecular and Biomedical Sciences, School of Biological Sciences, The University of Adelaide, Adelaide 5005, Australia; (E.N.K.); (B.S.)
| |
Collapse
|
42
|
Saadi F, Pal D, Sarma JD. Spike Glycoprotein Is Central to Coronavirus Pathogenesis-Parallel Between m-CoV and SARS-CoV-2. Ann Neurosci 2021; 28:201-218. [PMID: 35341224 PMCID: PMC8948335 DOI: 10.1177/09727531211023755] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 03/24/2021] [Indexed: 01/04/2023] Open
Abstract
Coronaviruses (CoVs) are single-stranded, polyadenylated, enveloped RNA of positive polarity with a unique potential to alter host tropism. This has been exceptionally demonstrated by the emergence of deadly virus outbreaks of the past: Severe Acute Respiratory Syndrome (SARS-CoV) in 2003 and Middle East Respiratory Syndrome (MERS-CoV) in 2012. The 2019 outbreak by the new cross-species transmission of SARS-CoV-2 has put the world on alert. CoV infection is triggered by receptor recognition, membrane fusion, and successive viral entry mediated by the surface Spike (S) glycoprotein. S protein is one of the major antigenic determinants and the target for neutralizing antibodies. It is a valuable target in antiviral therapies because of its central role in cell-cell fusion, viral antigen spread, and host immune responses leading to immunopathogenesis. The receptor-binding domain of S protein has received greater attention as it initiates host attachment and contains major antigenic determinants. However, investigating the therapeutic potential of fusion peptide as a part of the fusion core complex assembled by the heptad repeats 1 and 2 (HR1 and HR2) is also warranted. Along with receptor attachment and entry, fusion mechanisms should also be explored for designing inhibitors as a therapeutic intervention. In this article, we review the S protein function and its role in mediating membrane fusion, spread, tropism, and its associated pathogenesis with notable therapeutic strategies focusing on results obtained from studies on a murine β-Coronavirus (m-CoV) and its associated disease process.
Collapse
Affiliation(s)
- Fareeha Saadi
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Kolkata, West Bengal, India
| | - Debnath Pal
- Department of Computational and Data Sciences, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Jayasri Das Sarma
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Kolkata, West Bengal, India
- Department of Ophthalmology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| |
Collapse
|
43
|
Sengupta S, Bhattacharyya D, Kasle G, Karmakar S, Sahu O, Ganguly A, Addya S, Das Sarma J. Potential Immunomodulatory Properties of Biologically Active Components of Spices Against SARS-CoV-2 and Pan β-Coronaviruses. Front Cell Infect Microbiol 2021; 11:729622. [PMID: 34513735 PMCID: PMC8431827 DOI: 10.3389/fcimb.2021.729622] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 08/11/2021] [Indexed: 12/15/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-induced COVID-19 has emerged as a defining global health crisis in current times. Data from the World Health Organization shows demographic variations in COVID-19 severity and lethality. Diet may play a significant role in providing beneficial host cell factors contributing to immunity against deadly SARS-CoV-2 pathogenesis. Spices are essential components of the diet that possess anti-inflammatory, antioxidant, and antiviral properties. Hyperinflammation, an aberrant systemic inflammation associated with pneumonia, acute respiratory failure, and multiorgan dysfunction, is a major clinical outcome in COVID-19. Knowing the beneficial properties of spices, we hypothesize that spice-derived bioactive components can modulate host immune responses to provide protective immunity in COVID-19. This study emphasizes that biologically active components of spices might alleviate the sustained pro-inflammatory condition by inhibiting the activity of tumor necrosis factor-alpha (TNF-α), interleukins (IL6, IL8), and chemokine (CCL2) known to be elevated in COVID-19. Spices may potentially prevent the tissue damage induced by oxidative stress and pro-inflammatory mediators during SARS-CoV-2 infection. The current study also highlights the effects of spices on the antioxidant pathways mediated by Nrf2 (nuclear factor erythroid 2-related factor 2) and Hmox1 (heme oxygenase 1) to restore oxidative homeostasis and protect from aberrant tissue damage. Taken together, the anti-inflammatory and antioxidant activities of bioactive components of spices may hold a promise to target the cellular pathways for developing antivirals against SARS-CoV-2 and pan β-coronaviruses.
Collapse
Affiliation(s)
- Sourodip Sengupta
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata (IISER-K), Mohanpur, India
| | - Debina Bhattacharyya
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata (IISER-K), Mohanpur, India
| | - Grishma Kasle
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata (IISER-K), Mohanpur, India
| | - Souvik Karmakar
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata (IISER-K), Mohanpur, India
| | - Omkar Sahu
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata (IISER-K), Mohanpur, India
| | - Anirban Ganguly
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata (IISER-K), Mohanpur, India
| | - Sankar Addya
- Kimmel Cancer Centre, Thomas Jefferson University, Philadelphia, PA, United States
| | - Jayasri Das Sarma
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata (IISER-K), Mohanpur, India
| |
Collapse
|
44
|
Mohapatra RK, Dhama K, Mishra S, Sarangi AK, Kandi V, Tiwari R, Pintilie L. The microbiota-related coinfections in COVID-19 patients: a real challenge. BENI-SUEF UNIVERSITY JOURNAL OF BASIC AND APPLIED SCIENCES 2021; 10:47. [PMID: 34458380 PMCID: PMC8380112 DOI: 10.1186/s43088-021-00134-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 07/29/2021] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of ongoing global pandemic of coronavirus disease 2019 (COVID-19), has infected millions of people around the world, especially the elderly and immunocompromised individuals. The infection transmission rate is considered more rapid than other deadly pandemics and severe epidemics encountered earlier, such as Ebola, Zika, Influenza, Marburg, SARS, and MERS. The public health situation therefore is really at a challenging crossroads. MAIN BODY The internal and external and resident microbiota community is crucial in human health and is essential for immune responses. This community tends to be altered due to pathogenic infections which would lead to severity of the disease as it progresses. Few of these resident microflora become negatively active during infectious diseases leading to coinfection, especially the opportunistic pathogens. Once such a condition sets in, it is difficult to diagnose, treat, and manage COVID-19 in a patient. CONCLUSION This review highlights the various reported possible coinfections that arise in COVID-19 patients vis-à-vis other serious pathological conditions. The local immunity in lungs, nasal passages, oral cavity, and salivary glands are involved with different aspects of COVID-19 transmission and pathology. Also, the role of adaptive immune system is discussed at the site of infection to control the infection along with the proinflammatory cytokine therapy.
Collapse
Affiliation(s)
- Ranjan K. Mohapatra
- Department of Chemistry, Government College of Engineering, Keonjhar, Odisha 758002 India
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243122 India
| | - Snehasish Mishra
- School of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024 India
| | - Ashish K. Sarangi
- Department of Chemistry, School of Applied Sciences, Centurion University of Technology and Management, Odisha, India
| | - Venkataramana Kandi
- Department of Microbiology, Prathima Institute of Medical Sciences, Karimnagar, Telangana India
| | - Ruchi Tiwari
- Department of Veterinary Microbiology and Immunology, College of Veterinary Sciences, Uttar Pradesh Pandit Deen Dayal Upadhyaya Pashu Chikitsa Vigyan Vishwavidyalaya Evam Go Anusandhan Sansthan (DUVASU), Mathura, 281001 India
| | - Lucia Pintilie
- Department of Synthesis of Bioactive Substances and Pharmaceutical Technologies, National Institute for Chemical and Pharmaceutical Research and Development, Bucharest, Romania
| |
Collapse
|
45
|
Specificity and Mechanism of Coronavirus, Rotavirus, and Mammalian Two-Histidine Phosphoesterases That Antagonize Antiviral Innate Immunity. mBio 2021; 12:e0178121. [PMID: 34372695 PMCID: PMC8406329 DOI: 10.1128/mbio.01781-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The 2′,5′-oligoadenylate (2-5A)-dependent endoribonuclease, RNase L, is a principal mediator of the interferon (IFN) antiviral response. Therefore, the regulation of cellular levels of 2-5A is a key point of control in antiviral innate immunity. Cellular 2-5A levels are determined by IFN-inducible 2′,5′-oligoadenylate synthetases (OASs) and by enzymes that degrade 2-5A. Importantly, many coronaviruses (CoVs) and rotaviruses encode 2-5A-degrading enzymes, thereby antagonizing RNase L and its antiviral effects. A-kinase-anchoring protein 7 (AKAP7), a mammalian counterpart, could possibly limit tissue damage from excessive or prolonged RNase L activation during viral infections or from self-double-stranded RNAs that activate OAS. We show that these enzymes, members of the two-histidine phosphoesterase (2H-PE) superfamily, constitute a subfamily referred here as 2′,5′-PEs. 2′,5′-PEs from the mouse CoV mouse hepatitis virus (MHV) (NS2), Middle East respiratory syndrome coronavirus (MERS-CoV) (NS4b), group A rotavirus (VP3), and mouse (AKAP7) were investigated for their evolutionary relationships and activities. While there was no activity against 3′,5′-oligoribonucleotides, they all cleaved 2′,5′-oligoadenylates efficiently but with variable activity against other 2′,5′-oligonucleotides. The 2′,5′-PEs are shown to be metal ion-independent enzymes that cleave trimer 2-5A (2′,5′-p3A3) producing mono- or diadenylates with 2′,3′-cyclic phosphate termini. Our results suggest that the elimination of 2-5A might be the sole function of viral 2′,5′-PEs, thereby promoting viral escape from innate immunity by preventing or limiting the activation of RNase L.
Collapse
|
46
|
Xydakis MS, Albers MW, Holbrook EH, Lyon DM, Shih RY, Frasnelli JA, Pagenstecher A, Kupke A, Enquist LW, Perlman S. Post-viral effects of COVID-19 in the olfactory system and their implications. Lancet Neurol 2021; 20:753-761. [PMID: 34339626 PMCID: PMC8324113 DOI: 10.1016/s1474-4422(21)00182-4] [Citation(s) in RCA: 110] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 05/17/2021] [Accepted: 06/02/2021] [Indexed: 12/16/2022]
Abstract
BACKGROUND The mechanisms by which any upper respiratory virus, including SARS-CoV-2, impairs chemosensory function are not known. COVID-19 is frequently associated with olfactory dysfunction after viral infection, which provides a research opportunity to evaluate the natural course of this neurological finding. Clinical trials and prospective and histological studies of new-onset post-viral olfactory dysfunction have been limited by small sample sizes and a paucity of advanced neuroimaging data and neuropathological samples. Although data from neuropathological specimens are now available, neuroimaging of the olfactory system during the acute phase of infection is still rare due to infection control concerns and critical illness and represents a substantial gap in knowledge. RECENT DEVELOPMENTS The active replication of SARS-CoV-2 within the brain parenchyma (ie, in neurons and glia) has not been proven. Nevertheless, post-viral olfactory dysfunction can be viewed as a focal neurological deficit in patients with COVID-19. Evidence is also sparse for a direct causal relation between SARS-CoV-2 infection and abnormal brain findings at autopsy, and for trans-synaptic spread of the virus from the olfactory epithelium to the olfactory bulb. Taken together, clinical, radiological, histological, ultrastructural, and molecular data implicate inflammation, with or without infection, in either the olfactory epithelium, the olfactory bulb, or both. This inflammation leads to persistent olfactory deficits in a subset of people who have recovered from COVID-19. Neuroimaging has revealed localised inflammation in intracranial olfactory structures. To date, histopathological, ultrastructural, and molecular evidence does not suggest that SARS-CoV-2 is an obligate neuropathogen. WHERE NEXT?: The prevalence of CNS and olfactory bulb pathosis in patients with COVID-19 is not known. We postulate that, in people who have recovered from COVID-19, a chronic, recrudescent, or permanent olfactory deficit could be prognostic for an increased likelihood of neurological sequelae or neurodegenerative disorders in the long term. An inflammatory stimulus from the nasal olfactory epithelium to the olfactory bulbs and connected brain regions might accelerate pathological processes and symptomatic progression of neurodegenerative disease. Persistent olfactory impairment with or without perceptual distortions (ie, parosmias or phantosmias) after SARS-CoV-2 infection could, therefore, serve as a marker to identify people with an increased long-term risk of neurological disease.
Collapse
Affiliation(s)
- Michael S Xydakis
- Human Performance Wing, Air Force Research Lab, US Department of Defense, Wright-Patterson Air Force Base, Dayton, OH, USA.
| | - Mark W Albers
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Eric H Holbrook
- Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Dina M Lyon
- Human Performance Wing, Air Force Research Lab, US Department of Defense, Wright-Patterson Air Force Base, Dayton, OH, USA
| | - Robert Y Shih
- Division of Neuroradiology, Walter Reed National Military Medical Center, US Department of Defense, Bethesda, MD, USA
| | - Johannes A Frasnelli
- Department of Anatomy, Université du Québec à Trois-Rivières, Trois-Rivières, QC, Canada
| | - Axel Pagenstecher
- Department of Neuropathology, Philipps University of Marburg, Marburg, Germany
| | - Alexandra Kupke
- Marburg Virology Institute, Philipps University of Marburg, Marburg, Germany
| | - Lynn W Enquist
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | - Stanley Perlman
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, USA
| |
Collapse
|
47
|
Chu L, Huang F, Zhang M, Huang B, Wang Y. Current status of traditional Chinese medicine for the treatment of COVID-19 in China. Chin Med 2021; 16:63. [PMID: 34315521 PMCID: PMC8314260 DOI: 10.1186/s13020-021-00461-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 06/26/2021] [Indexed: 01/08/2023] Open
Abstract
An ongoing outbreak of severe respiratory illness and pneumonia caused by the severe acute respiratory coronavirus 2 (SARS-CoV-2) commenced in December 2019, and the disease was named as coronavirus disease 2019 (COVID-19). Soon after, scientists identified the characteristics of SARS-CoV-2, including its genome sequence and protein structure. The clinical manifestations of COVID-19 have now been established; and nucleic acid amplification is used for the direct determination of the virus, whereas immunoassays can determine the antibodies against SARS-CoV-2. Clinical trials of several antiviral drugs are ongoing. However, there is still no specific drugs to treat COVID-19. Traditional Chinese medicine (TCM) was used in the treatment of COVID-19 during the early stages of the outbreak in China. Some ancient TCM prescriptions, which were efficacious in the treatment of severe acute respiratory syndrome (SARS) in 2002-03 and the influenza pandemic (H1N1) of 2009, have been improved by experienced TCM practitioners for the treatment of COVID-19 based on their clinical symptoms. These developed new prescriptions include Lianhua Qingwen capsules/granules, Jinhua Qinggan granules and XueBiJing injection, among others. In this review, we have summarized the presenting features of SARS-CoV-2, the clinical characteristics of COVID-19, and the progress in the treatment of COVID-19 using TCMs.
Collapse
Affiliation(s)
- Liang Chu
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No.1095 Jie Fang Avenue, Wuhan, 430030, Hubei, China.
| | - Fang Huang
- Department of Pathology, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, 310014, Zhejiang, China
| | - Mengdan Zhang
- College of Life and Medicine Sciences, Zhejiang Sci-Tech University, No. 928, 2nd Street, Xiasha Higher Education Park, Hangzhou, 310018, Zhejiang, China
| | - Biao Huang
- College of Life and Medicine Sciences, Zhejiang Sci-Tech University, No. 928, 2nd Street, Xiasha Higher Education Park, Hangzhou, 310018, Zhejiang, China
| | - Yigang Wang
- College of Life and Medicine Sciences, Zhejiang Sci-Tech University, No. 928, 2nd Street, Xiasha Higher Education Park, Hangzhou, 310018, Zhejiang, China.
| |
Collapse
|
48
|
Abstract
The OC43 coronavirus is a human pathogen that usually causes only the common cold. One of its key enzymes, similar to other coronaviruses, is the 2'-O-RNA methyltransferase (MTase), which is essential for viral RNA stability and expression. Here, we report the crystal structure of the 2'-O-RNA MTase in a complex with the pan-methyltransferase inhibitor sinefungin solved at 2.2-Å resolution. The structure reveals an overall fold consistent with the fold observed in other coronaviral MTases. The major differences are in the conformation of the C terminus of the nsp16 subunit and an additional helix in the N terminus of the nsp10 subunits. The structural analysis also revealed very high conservation of the S-adenosyl methionine (SAM) binding pocket, suggesting that the SAM pocket is a suitable spot for the design of antivirals effective against all human coronaviruses. IMPORTANCE Some coronaviruses are dangerous pathogens, while some cause only common colds. The reasons are not understood, although the spike proteins probably play an important role. However, to understand the coronaviral biology in sufficient detail, we need to compare the key enzymes from different coronaviruses. We solved the crystal structure of 2'-O-RNA methyltransferase of the OC43 coronavirus, a virus that usually causes mild colds. The structure revealed some differences in the overall fold but also revealed that the SAM binding site is conserved, suggesting that development of antivirals against multiple coronaviruses is feasible.
Collapse
|
49
|
Cho E, Rosa M, Anjum R, Mehmood S, Soban M, Mujtaba M, Bux K, Moin ST, Tanweer M, Dantu S, Pandini A, Yin J, Ma H, Ramanathan A, Islam B, Mey ASJ, Bhowmik D, Haider S. Dynamic Profiling of β-Coronavirus 3CL M pro Protease Ligand-Binding Sites. J Chem Inf Model 2021; 61:3058-3073. [PMID: 34124899 PMCID: PMC8230960 DOI: 10.1021/acs.jcim.1c00449] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Indexed: 01/11/2023]
Abstract
β-coronavirus (CoVs) alone has been responsible for three major global outbreaks in the 21st century. The current crisis has led to an urgent requirement to develop therapeutics. Even though a number of vaccines are available, alternative strategies targeting essential viral components are required as a backup against the emergence of lethal viral variants. One such target is the main protease (Mpro) that plays an indispensable role in viral replication. The availability of over 270 Mpro X-ray structures in complex with inhibitors provides unique insights into ligand-protein interactions. Herein, we provide a comprehensive comparison of all nonredundant ligand-binding sites available for SARS-CoV2, SARS-CoV, and MERS-CoV Mpro. Extensive adaptive sampling has been used to investigate structural conservation of ligand-binding sites using Markov state models (MSMs) and compare conformational dynamics employing convolutional variational auto-encoder-based deep learning. Our results indicate that not all ligand-binding sites are dynamically conserved despite high sequence and structural conservation across β-CoV homologs. This highlights the complexity in targeting all three Mpro enzymes with a single pan inhibitor.
Collapse
Affiliation(s)
- Eunice Cho
- UCL
School of Pharmacy, London WC1N 1AX, U.K.
| | | | - Ruhi Anjum
- Department
of Biochemistry, Aligarh Muslim University, Aligarh, Uttar Pradesh 202002, India
| | - Saman Mehmood
- Department
of Zoology, Aligarh Muslim University, Aligarh, Uttar Pradesh 202002, India
| | - Mariya Soban
- Department
of Biochemistry, Aligarh Muslim University, Aligarh, Uttar Pradesh 202002, India
| | - Moniza Mujtaba
- Herricks
High School, New Hyde
Park, New York 11040 United States
| | - Khair Bux
- Third
World Center for Science and Technology, H.E.J. Research Institute
of Chemistry, International Centre of Chemical and Biological Sciences, University of Karachi, Karachi 75270 Pakistan
| | - Syed T. Moin
- Third
World Center for Science and Technology, H.E.J. Research Institute
of Chemistry, International Centre of Chemical and Biological Sciences, University of Karachi, Karachi 75270 Pakistan
| | | | - Sarath Dantu
- Department
of Computer Science, Brunel University, Uxbridge UB8 3PH, U.K.
| | - Alessandro Pandini
- Department
of Computer Science, Brunel University, Uxbridge UB8 3PH, U.K.
| | - Junqi Yin
- Center
for Computational Sciences, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Heng Ma
- Data
Science and Learning Division, Argonne National
Laboratory, Lemont, Illinois 60439, United States
| | - Arvind Ramanathan
- Data
Science and Learning Division, Argonne National
Laboratory, Lemont, Illinois 60439, United States
- Consortium
for Advanced Science and Engineering, University
of Chicago, Chicago, Illinois 60637, United
States
| | - Barira Islam
- Department
of Bioscience, University of Huddersfield, Huddersfield HD1 3DH, U.K.
| | - Antonia S. J.
S. Mey
- EaStCHEM
School of Chemistry, University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, U.K.
| | - Debsindhu Bhowmik
- Computer
Sciences and Engineering Division, Oak Ridge
National Laboratory, Oak Ridge, Tennessee 37830, United States
| | | |
Collapse
|
50
|
Nagaraja S, Jain D, Kesavardhana S. Inflammasome regulation in driving COVID-19 severity in humans and immune tolerance in bats. J Leukoc Biol 2021; 111:497-508. [PMID: 34057760 PMCID: PMC8242921 DOI: 10.1002/jlb.4covhr0221-093rr] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Coronaviruses (CoVs) are RNA viruses that cause human respiratory infections. Zoonotic transmission of the SARS‐CoV‐2 virus caused the recent COVID‐19 pandemic, which led to over 2 million deaths worldwide. Elevated inflammatory responses and cytotoxicity in the lungs are associated with COVID‐19 severity in SARS‐CoV‐2‐infected individuals. Bats, which host pathogenic CoVs, operate dampened inflammatory responses and show tolerance to these viruses with mild clinical symptoms. Delineating the mechanisms governing these host‐specific inflammatory responses is essential to understand host–virus interactions determining the outcome of pathogenic CoV infections. Here, we describe the essential role of inflammasome activation in determining COVID‐19 severity in humans and innate immune tolerance in bats that host several pathogenic CoVs. We further discuss mechanisms leading to inflammasome activation in human SARS‐CoV‐2 infection and how bats are molecularly adapted to suppress these inflammasome responses. We also report an analysis of functionally important residues of inflammasome components that provide new clues of bat strategies to suppress inflammasome signaling and innate immune responses. As spillover of bat viruses may cause the emergence of new human disease outbreaks, the inflammasome regulation in bats and humans likely provides specific strategies to combat the pathogenic CoV infections.
Collapse
Affiliation(s)
- Sahana Nagaraja
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Disha Jain
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Sannula Kesavardhana
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| |
Collapse
|