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Sahani SK, Jakhad A. Incidence rate drive the multiple wave in the COVID-19 pandemic. MethodsX 2023; 11:102317. [PMID: 37637293 PMCID: PMC10457448 DOI: 10.1016/j.mex.2023.102317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 08/03/2023] [Indexed: 08/29/2023] Open
Abstract
The last three years have been the most challenging for humanity due to the COVID-19 pandemic. The novel viral infection has eventually been able to infect most of the human population. It is now considered to be in the endemic stage, meaning it will remain in our world throughout our lifetime. There will be an intermittent outbreak of the COVID infection from time to time. Therefore, it is necessary to formulate a robust Mathematical model to study the dynamics of disease to have a control mechanism in place. In this article, we suggest a modified MSEIR model to explain the dynamics of COVID-19 infection. We assume that a susceptible person contracting the coronavirus develops a transient immunity to the illness. Further, infectives comprise asymptomatic, symptomatic, hospitalized and quarantined individuals. We assume that the incidence rate is of standard type, and susceptible can only become infective if they come in contact with either asymptomatic or symptomatic individuals. This basic and simple model effectively models the various waves every country has seen during the Pandemic. The simple analysis shows that the model could suggest various waves in future if we carefully select the incidence rate for the infection. In summary, we have discussed the following major points in this article. •We have analysed for local behavior infection-free equilibrium solution. Further, a thorough numerical exploration with various parameter settings has been performed to obtain the different cases of infection dynamics of the coronavirus epidemic.•We have found some interesting scenarios which explain the emergence of multiple waves observed in many countries.
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Affiliation(s)
- Saroj Kumar Sahani
- Faculty of Mathematics and Computer Science, Department of Mathematics, South Asian University Akbar Bhawan, Chankyapuri, New Delhi, Delhi 110021, India
| | - Anjali Jakhad
- Faculty of Mathematics and Computer Science, Department of Mathematics, South Asian University Akbar Bhawan, Chankyapuri, New Delhi, Delhi 110021, India
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de Vries M, Ciabattoni GO, Rodriguez-Rodriguez BA, Crosse KM, Papandrea D, Samanovic MI, Dimartino D, Marier C, Mulligan MJ, Heguy A, Desvignes L, Duerr R, Dittmann M. Generation of quality-controlled SARS-CoV-2 variant stocks. Nat Protoc 2023; 18:3821-3855. [PMID: 37833423 DOI: 10.1038/s41596-023-00897-6] [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: 01/17/2023] [Accepted: 07/28/2023] [Indexed: 10/15/2023]
Abstract
One of the main challenges in the fight against coronavirus disease 2019 (COVID-19) stems from the ongoing evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) into multiple variants. To address this hurdle, research groups around the world have independently developed protocols to isolate these variants from clinical samples. These isolates are then used in translational and basic research-for example, in vaccine development, drug screening or characterizing SARS-CoV-2 biology and pathogenesis. However, over the course of the COVID-19 pandemic, we have learned that the introduction of artefacts during both in vitro isolation and subsequent propagation to virus stocks can lessen the validity and reproducibility of data. We propose a rigorous pipeline for the generation of high-quality SARS-CoV-2 variant clonal isolates that minimizes the acquisition of mutations and introduces stringent controls to detect them. Overall, the process includes eight stages: (i) cell maintenance, (ii) isolation of SARS-CoV-2 from clinical specimens, (iii) determination of infectious virus titers by plaque assay, (iv) clonal isolation by plaque purification, (v) whole-virus-genome deep-sequencing, (vi and vii) amplification of selected virus clones to master and working stocks and (viii) sucrose purification. This comprehensive protocol will enable researchers to generate reliable SARS-CoV-2 variant inoculates for in vitro and in vivo experimentation and will facilitate comparisons and collaborative work. Quality-controlled working stocks for most applications can be generated from acquired biorepository virus within 1 month. An additional 5-8 d are required when virus is isolated from clinical swab material, and another 6-7 d is needed for sucrose-purifying the stocks.
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Affiliation(s)
- Maren de Vries
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
| | - Grace O Ciabattoni
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
| | | | - Keaton M Crosse
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
| | - Dominick Papandrea
- High Containment Laboratories-Office of Science and Research, NYU Langone Health, New York, NY, USA
| | - Marie I Samanovic
- Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
- NYU Langone Vaccine Center, NYU Grossman School of Medicine, New York, NY, USA
| | - Dacia Dimartino
- Genome Technology Center, Office of Science and Research, NYU Langone Health, New York, NY, USA
| | - Christian Marier
- Genome Technology Center, Office of Science and Research, NYU Langone Health, New York, NY, USA
| | - Mark J Mulligan
- Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
- NYU Langone Vaccine Center, NYU Grossman School of Medicine, New York, NY, USA
| | - Adriana Heguy
- Genome Technology Center, Office of Science and Research, NYU Langone Health, New York, NY, USA
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
| | - Ludovic Desvignes
- High Containment Laboratories-Office of Science and Research, NYU Langone Health, New York, NY, USA
- Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
| | - Ralf Duerr
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
- Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
- NYU Langone Vaccine Center, NYU Grossman School of Medicine, New York, NY, USA
| | - Meike Dittmann
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA.
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Giordani S, Marassi V, Zattoni A, Roda B, Reschiglian P. Liposomes characterization for market approval as pharmaceutical products: Analytical methods, guidelines and standardized protocols. J Pharm Biomed Anal 2023; 236:115751. [PMID: 37778202 DOI: 10.1016/j.jpba.2023.115751] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 09/13/2023] [Accepted: 09/24/2023] [Indexed: 10/03/2023]
Abstract
Liposomes are nano-sized lipid-based vesicles widely studied for their drug delivery capabilities. Compared to standard carries they exhibit better properties such as improved site-targeting and drug release, protection of drugs from degradation and clearance, and lower toxic side effects. At present, scientific literature is rich of studies regarding liposomes-based systems, while 14 types of liposomal products have been authorized to the market by EMA and FDA and many others have been approved by national agencies. Although the interest in nanodevices and nanomedicine has steadily increased in the last two decades the development of documentation regulating and standardizing all the phases of their development and quality control still suffers from major inadequacy due to the intrinsic complexity of nano-systems characterization. Many generic documents (Type 1) discussing guidelines for the study of nano-systems (lipidic and not) have been proposed while there is a lack of robust and standardized methods (Type 2 documents). As a result, a widespread of different techniques, approaches and methodologies are being used, generating results of variable quality and hard to compare with each other. Additionally, such documents are often subject to updates and rewriting further complicating the topic. Within this context the aim of this work is focused on bridging the gap in liposome characterization: the most recent standardized methodologies suitable for liposomes characterization are here reported (with the corresponding Type 2 documents) and revised in a short and pragmatical way focused on providing the reader with a practical background of the state of the art. In particular, this paper will put the accent on the methodologies developed to evaluate the main critical quality attributes (CQAs) necessary for liposomes market approval.
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Affiliation(s)
- Stefano Giordani
- Department of Chemistry "Giacomo Ciamician", University of Bologna, 40126 Bologna, Italy
| | - Valentina Marassi
- Department of Chemistry "Giacomo Ciamician", University of Bologna, 40126 Bologna, Italy; byFlow srl, 40129 Bologna, Italy.
| | - Andrea Zattoni
- Department of Chemistry "Giacomo Ciamician", University of Bologna, 40126 Bologna, Italy; byFlow srl, 40129 Bologna, Italy
| | - Barbara Roda
- Department of Chemistry "Giacomo Ciamician", University of Bologna, 40126 Bologna, Italy; byFlow srl, 40129 Bologna, Italy.
| | - Pierluigi Reschiglian
- Department of Chemistry "Giacomo Ciamician", University of Bologna, 40126 Bologna, Italy; byFlow srl, 40129 Bologna, Italy
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Ashraf J, Bukhari SARS, Kanji A, Iqbal T, Yameen M, Nisar MI, Khan W, Hasan Z. Substitution spectra of SARS-CoV-2 genome from Pakistan reveals insights into the evolution of variants across the pandemic. Sci Rep 2023; 13:20955. [PMID: 38017265 PMCID: PMC10684861 DOI: 10.1038/s41598-023-48272-5] [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: 07/09/2023] [Accepted: 11/24/2023] [Indexed: 11/30/2023] Open
Abstract
Changing morbidity and mortality due to COVID-19 across the pandemic has been linked with factors such as the emergence of SARS-CoV-2 variants and vaccination. Mutations in the Spike glycoprotein enhanced viral transmission and virulence. We investigated whether SARS-CoV-2 mutation rates and entropy were associated COVID-19 in Pakistan, before and after the introduction of vaccinations. We analyzed 1,705 SARS-CoV-2 genomes using the Augur phylogenetic pipeline. Substitution rates and entropy across the genome, and in the Spike glycoprotein were compared between 2020, 2021 and 2022 (as periods A, B and C). Mortality was greatest in B whilst cases were highest during C. In period A, G clades were predominant, and substitution rate was 5.25 × 10-4 per site per year. In B, Delta variants dominated, and substitution rates increased to 9.74 × 10-4. In C, Omicron variants led to substitution rates of 5.02 × 10-4. Genome-wide entropy was the highest during B particularly, at Spike E484K and K417N. During C, genome-wide mutations increased whilst entropy was reduced. Enhanced SARS-CoV-2 genome substitution rates were associated with a period when more virulent SARS-CoV-2 variants were prevalent. Reduced substitution rates and stabilization of genome entropy was subsequently evident when vaccinations were introduced. Whole genome entropy analysis can help predict virus evolution to guide public health interventions.
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Affiliation(s)
- Javaria Ashraf
- Department of Pathology and Laboratory Medicine, Aga Khan University, Stadium Road, P.O. Box 3500, Karachi, 74800, Pakistan
| | - Sayed Ali Raza Shah Bukhari
- Department of Pathology and Laboratory Medicine, Aga Khan University, Stadium Road, P.O. Box 3500, Karachi, 74800, Pakistan
| | - Akbar Kanji
- Department of Pathology and Laboratory Medicine, Aga Khan University, Stadium Road, P.O. Box 3500, Karachi, 74800, Pakistan
| | - Tulaib Iqbal
- Department of Pathology and Laboratory Medicine, Aga Khan University, Stadium Road, P.O. Box 3500, Karachi, 74800, Pakistan
| | - Maliha Yameen
- Department of Pathology and Laboratory Medicine, Aga Khan University, Stadium Road, P.O. Box 3500, Karachi, 74800, Pakistan
| | - Muhammad Imran Nisar
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
- Department of Pediatrics and Child Health, CITRIC Center for Bioinformatics and Computational Biology, Aga Khan University, Karachi, Pakistan
| | - Waqasuddin Khan
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
- Department of Pediatrics and Child Health, CITRIC Center for Bioinformatics and Computational Biology, Aga Khan University, Karachi, Pakistan
| | - Zahra Hasan
- Department of Pathology and Laboratory Medicine, Aga Khan University, Stadium Road, P.O. Box 3500, Karachi, 74800, Pakistan.
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De-Simone SG, Napoleão-Pêgo P, Lechuga GC, Carvalho JPRS, Monteiro ME, Morel CM, Provance DW. Mapping IgA Epitope and Cross-Reactivity between Severe Acute Respiratory Syndrome-Associated Coronavirus 2 and DENV. Vaccines (Basel) 2023; 11:1749. [PMID: 38140154 PMCID: PMC10747746 DOI: 10.3390/vaccines11121749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/12/2023] [Accepted: 11/16/2023] [Indexed: 12/24/2023] Open
Abstract
BACKGROUND The newly introduced COVID-19 vaccines have reduced disease severity and hospitalizations. However, they do not significantly prevent infection or transmission. In the same context, measuring IgM and IgG antibody levels is important, but it does not provide information about the status of the mucosal immune response. This article describes a comprehensive mapping of IgA epitopes of the S protein, its cross-reactivity, and the development of an ELISA-peptide assay. METHODS IgA epitope mapping was conducted using SPOT synthesis and sera from RT-qPCR COVID-19-positive patients. Specific and cross-reacting epitopes were identified, and an evolutionary analysis from the early Wuhan strain to the Omicron variant was performed using bioinformatics tools and a microarray of peptides. The selected epitopes were chemically synthesized and evaluated using ELISA-IgA. RESULTS A total of 40 IgA epitopes were identified with 23 in S1 and 17 in the S2 subunit. Among these, at least 23 epitopes showed cross-reactivity with DENV and other organisms and 24 showed cross-reactivity with other associated coronaviruses. Three MAP4 polypeptides were validated by ELISA, demonstrating a sensitivity of 90-99.96% and a specificity of 100%. Among the six IgA-RBD epitopes, only the SC/18 epitope of the Omicron variants (BA.2 and BA.2.12.1) presented a single IgA epitope. CONCLUSIONS This research unveiled the IgA epitome of the S protein and identified many epitopes that exhibit cross-reactivity with DENV and other coronaviruses. The S protein of variants from Wuhan to Omicron retains many conserved IgA epitopes except for one epitope (#SCov/18). The cross-reactivity with DENV suggests limitations in using the whole S protein or the S1/S2/RBD segment for IgA serological diagnostic tests for COVID-19. The expression of these identified specific epitopes as diagnostic biomarkers could facilitate monitoring mucosal immunity to COVID-19, potentially leading to more accurate diagnoses and alternative mucosal vaccines.
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Affiliation(s)
- Salvatore G. De-Simone
- Center for Technological Development in Health (CDTS)/National Institute of Science and Technology for Innovation in Neglected Population Diseases (INCT-IDPN), Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, RJ, Brazil; (P.N.-P.); (G.C.L.); (J.P.R.S.C.); (M.E.M.); (C.M.M.); (D.W.P.J.)
- Epidemiology and Molecular Systematics Laboratory (LEMS), Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, RJ, Brazil
- Program of Post-Graduation on Science and Biotechnology, Department of Molecular and Cellular Biology, Biology Institute, Federal Fluminense University, Niterói 22040-036, RJ, Brazil
- Program of Post-Graduation on Parasitic Biology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, RJ, Brazil
| | - Paloma Napoleão-Pêgo
- Center for Technological Development in Health (CDTS)/National Institute of Science and Technology for Innovation in Neglected Population Diseases (INCT-IDPN), Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, RJ, Brazil; (P.N.-P.); (G.C.L.); (J.P.R.S.C.); (M.E.M.); (C.M.M.); (D.W.P.J.)
- Epidemiology and Molecular Systematics Laboratory (LEMS), Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, RJ, Brazil
| | - Guilherme C. Lechuga
- Center for Technological Development in Health (CDTS)/National Institute of Science and Technology for Innovation in Neglected Population Diseases (INCT-IDPN), Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, RJ, Brazil; (P.N.-P.); (G.C.L.); (J.P.R.S.C.); (M.E.M.); (C.M.M.); (D.W.P.J.)
- Epidemiology and Molecular Systematics Laboratory (LEMS), Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, RJ, Brazil
| | - João P. R. S. Carvalho
- Center for Technological Development in Health (CDTS)/National Institute of Science and Technology for Innovation in Neglected Population Diseases (INCT-IDPN), Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, RJ, Brazil; (P.N.-P.); (G.C.L.); (J.P.R.S.C.); (M.E.M.); (C.M.M.); (D.W.P.J.)
- Program of Post-Graduation on Science and Biotechnology, Department of Molecular and Cellular Biology, Biology Institute, Federal Fluminense University, Niterói 22040-036, RJ, Brazil
| | - Maria E. Monteiro
- Center for Technological Development in Health (CDTS)/National Institute of Science and Technology for Innovation in Neglected Population Diseases (INCT-IDPN), Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, RJ, Brazil; (P.N.-P.); (G.C.L.); (J.P.R.S.C.); (M.E.M.); (C.M.M.); (D.W.P.J.)
- Program of Post-Graduation on Parasitic Biology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, RJ, Brazil
| | - Carlos M. Morel
- Center for Technological Development in Health (CDTS)/National Institute of Science and Technology for Innovation in Neglected Population Diseases (INCT-IDPN), Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, RJ, Brazil; (P.N.-P.); (G.C.L.); (J.P.R.S.C.); (M.E.M.); (C.M.M.); (D.W.P.J.)
| | - David W. Provance
- Center for Technological Development in Health (CDTS)/National Institute of Science and Technology for Innovation in Neglected Population Diseases (INCT-IDPN), Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, RJ, Brazil; (P.N.-P.); (G.C.L.); (J.P.R.S.C.); (M.E.M.); (C.M.M.); (D.W.P.J.)
- Epidemiology and Molecular Systematics Laboratory (LEMS), Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, RJ, Brazil
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Gabbianelli R, Shahar E, de Simone G, Rucci C, Bordoni L, Feliziani G, Zhao F, Ferrati M, Maggi F, Spinozzi E, Mahajna J. Plant-Derived Epi-Nutraceuticals as Potential Broad-Spectrum Anti-Viral Agents. Nutrients 2023; 15:4719. [PMID: 38004113 PMCID: PMC10675658 DOI: 10.3390/nu15224719] [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: 10/17/2023] [Revised: 10/29/2023] [Accepted: 10/31/2023] [Indexed: 11/26/2023] Open
Abstract
Although the COVID-19 pandemic appears to be diminishing, the emergence of SARS-CoV-2 variants represents a threat to humans due to their inherent transmissibility, immunological evasion, virulence, and invulnerability to existing therapies. The COVID-19 pandemic affected more than 500 million people and caused over 6 million deaths. Vaccines are essential, but in circumstances in which vaccination is not accessible or in individuals with compromised immune systems, drugs can provide additional protection. Targeting host signaling pathways is recommended due to their genomic stability and resistance barriers. Moreover, targeting host factors allows us to develop compounds that are effective against different viral variants as well as against newly emerging virus strains. In recent years, the globe has experienced climate change, which may contribute to the emergence and spread of infectious diseases through a variety of factors. Warmer temperatures and changing precipitation patterns can increase the geographic range of disease-carrying vectors, increasing the risk of diseases spreading to new areas. Climate change may also affect vector behavior, leading to a longer breeding season and more breeding sites for disease vectors. Climate change may also disrupt ecosystems, bringing humans closer to wildlife that transmits zoonotic diseases. All the above factors may accelerate the emergence of new viral epidemics. Plant-derived products, which have been used in traditional medicine for treating pathological conditions, offer structurally novel therapeutic compounds, including those with anti-viral activity. In addition, plant-derived bioactive substances might serve as the ideal basis for developing sustainable/efficient/cost-effective anti-viral alternatives. Interest in herbal antiviral products has increased. More than 50% of approved drugs originate from herbal sources. Plant-derived compounds offer diverse structures and bioactive molecules that are candidates for new drug development. Combining these therapies with conventional drugs could improve patient outcomes. Epigenetics modifications in the genome can affect gene expression without altering DNA sequences. Host cells can use epigenetic gene regulation as a mechanism to silence incoming viral DNA molecules, while viruses recruit cellular epitranscriptomic (covalent modifications of RNAs) modifiers to increase the translational efficiency and transcript stability of viral transcripts to enhance viral gene expression and replication. Moreover, viruses manipulate host cells' epigenetic machinery to ensure productive viral infections. Environmental factors, such as natural products, may influence epigenetic modifications. In this review, we explore the potential of plant-derived substances as epigenetic modifiers for broad-spectrum anti-viral activity, reviewing their modulation processes and anti-viral effects on DNA and RNA viruses, as well as addressing future research objectives in this rapidly emerging field.
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Affiliation(s)
- Rosita Gabbianelli
- Unit of Molecular Biology and Nutrigenomics, University of Camerino, Via Madonna delle Carceri, 62032 Camerino, Italy; (R.G.); (G.d.S.); (L.B.); (G.F.); (F.Z.)
| | - Ehud Shahar
- Department of Nutrition and Natural Products, Migal—Galilee Research Institute, Kiryat Shmona 11016, Israel;
- Department of Biotechnology, Tel-Hai College, Kiryat Shmona 1220800, Israel
| | - Gaia de Simone
- Unit of Molecular Biology and Nutrigenomics, University of Camerino, Via Madonna delle Carceri, 62032 Camerino, Italy; (R.G.); (G.d.S.); (L.B.); (G.F.); (F.Z.)
| | - Chiara Rucci
- Unit of Molecular Biology and Nutrigenomics, University of Camerino, Via Madonna delle Carceri, 62032 Camerino, Italy; (R.G.); (G.d.S.); (L.B.); (G.F.); (F.Z.)
| | - Laura Bordoni
- Unit of Molecular Biology and Nutrigenomics, University of Camerino, Via Madonna delle Carceri, 62032 Camerino, Italy; (R.G.); (G.d.S.); (L.B.); (G.F.); (F.Z.)
| | - Giulia Feliziani
- Unit of Molecular Biology and Nutrigenomics, University of Camerino, Via Madonna delle Carceri, 62032 Camerino, Italy; (R.G.); (G.d.S.); (L.B.); (G.F.); (F.Z.)
| | - Fanrui Zhao
- Unit of Molecular Biology and Nutrigenomics, University of Camerino, Via Madonna delle Carceri, 62032 Camerino, Italy; (R.G.); (G.d.S.); (L.B.); (G.F.); (F.Z.)
| | - Marta Ferrati
- Chemistry Interdisciplinary Project (ChIP) Research Centre, School of Pharmacy, University of Camerino, Via Madonna delle Carceri, 62032 Camerino, Italy; (M.F.); (F.M.); (E.S.)
| | - Filippo Maggi
- Chemistry Interdisciplinary Project (ChIP) Research Centre, School of Pharmacy, University of Camerino, Via Madonna delle Carceri, 62032 Camerino, Italy; (M.F.); (F.M.); (E.S.)
| | - Eleonora Spinozzi
- Chemistry Interdisciplinary Project (ChIP) Research Centre, School of Pharmacy, University of Camerino, Via Madonna delle Carceri, 62032 Camerino, Italy; (M.F.); (F.M.); (E.S.)
| | - Jamal Mahajna
- Department of Nutrition and Natural Products, Migal—Galilee Research Institute, Kiryat Shmona 11016, Israel;
- Department of Biotechnology, Tel-Hai College, Kiryat Shmona 1220800, Israel
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Mandal N, Mitra R, Pramanick B. C-MEMS-derived glassy carbon electrochemical biosensors for rapid detection of SARS-CoV-2 spike protein. MICROSYSTEMS & NANOENGINEERING 2023; 9:137. [PMID: 37937185 PMCID: PMC10625972 DOI: 10.1038/s41378-023-00601-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 11/09/2023]
Abstract
According to a World Health Organization (WHO) report, the world has experienced more than 766 million cases of positive SARS-CoV-2 infection and more than 6.9 million deaths due to COVID through May 2023. The WHO declared a pandemic due to the rapid spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, and the fight against this pandemic is not over yet. Important reasons for virus spread include the lack of detection kits, appropriate detection techniques, delay in detection, asymptomatic cases and failure in mass screening. In the last 3 years, several researchers and medical companies have introduced successful test kits to detect the infection of symptomatic patients in real time, which was necessary to monitor the spread. However, it is also important to have information on asymptomatic cases, which can be obtained by antibody testing for the SARS-CoV-2 virus. In this work, we developed a simple, advantageous immobilization procedure for rapidly detecting the SARS-CoV-2 spike protein. Carbon-MEMS-derived glassy carbon (GC) is used as the sensor electrode, and the detection is based on covalently linking the SARS-CoV-2 antibody to the GC surface. Glutaraldehyde was used as a cross-linker between the antibody and glassy carbon electrode (GCE). The binding was investigated using Fourier transform infrared spectroscopy (FTIR) characterization and cyclic voltammetric (CV) analysis. Electrochemical impedance spectroscopy (EIS) was utilized to measure the change in total impedance before and after incubation of the SARS-CoV-2 antibody with various concentrations of SARS-CoV-2 spike protein. The developed sensor can sense 1 fg/ml to 1 µg/ml SARS-CoV-2 spike protein. This detection is label-free, and the chances of false positives are minimal. The calculated LOD was ~31 copies of viral RNA/mL. The coefficient of variation (CV) number is calculated from EIS data at 100 Hz, which is found to be 0.398%. The developed sensor may be used for mass screening because it is cost-effective. A schematic representation of the SARS-CoV-2 spike protein sensing using surface functionalized glassy carbon electrode.
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Affiliation(s)
- Naresh Mandal
- School of Electrical Sciences, Indian Institute of Technology Goa, 403401 Ponda, Goa India
| | - Raja Mitra
- School of Chemical and Materials Sciences, Indian Institute of Technology Goa, 403401 Ponda, Goa India
| | - Bidhan Pramanick
- School of Electrical Sciences, Indian Institute of Technology Goa, 403401 Ponda, Goa India
- Centre of Excellence in Particulates Colloids and Interfaces, Indian Institute of Technology Goa, 403401 Ponda, Goa India
- School of Interdisciplinary Life Sciences, Indian Institute of Technology Goa, 403401 Ponda, Goa India
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Habeebur‐Rahman SP, Noni V, Khan FAA, Tan C. Detection of novel coronaviruses from dusky fruit bat (Penthetor lucasi) in Sarawak, Malaysian Borneo. Vet Med Sci 2023; 9:2634-2641. [PMID: 37658663 PMCID: PMC10650259 DOI: 10.1002/vms3.1251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 08/01/2023] [Accepted: 08/18/2023] [Indexed: 09/03/2023] Open
Abstract
BACKGROUND Sarawak has one of the highest diversity of fruit bats species (family Pteropodidae) in Malaysia, with 19 species described. Most coronavirus (CoV) studies have mainly focused on insectivorous bats, resulting in a lack of information on CoVs present in frugivorous bats. In addition, bat CoV surveillance activities are lacking in Malaysia. OBJECTIVES Our study focuses on determining the presence of bat CoVs in dusky fruit bat (Penthetor lucasi). METHODS Guano samples belonging to P. lucasi were collected from Wind Cave Nature Reserve. The samples were screened for the presence of CoVs using validated hemi-nested consensus RNA-dependent RNA polymerase consensus primers. RESULTS The bat CoV positivity rate was 38.5% (n = 15/39), with the viruses belonging to two subgenera: Alphacoronavirus (α-CoV) and Betacoronavirus (β-CoV). Phylogenetic analysis revealed that CoVs from 14 samples of P. lucasi belong to the genus α-CoV and may represent previously described genetic lineages in insectivorous bats in Wind Cave. However, only one sample of P. lucasi was detected with β-CoV which is closely related to subgenus Nobecovirus, which is commonly seen in frugivorous bats. CONCLUSIONS This study provides the first available data on CoVs circulating in P. lucasi.
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Affiliation(s)
- Sultana Parvin Habeebur‐Rahman
- Center for Tropical and Emerging DiseasesFaculty of Medicine and Health SciencesUniversiti Malaysia SarawakKota SamarahanSarawakMalaysia
| | - Vaenessa Noni
- Center for Tropical and Emerging DiseasesFaculty of Medicine and Health SciencesUniversiti Malaysia SarawakKota SamarahanSarawakMalaysia
| | - Faisal Ali Anwarali Khan
- Faculty of Resource Science and TechnologyUniversiti Malaysia SarawakKota SamarahanSarawakMalaysia
| | - Cheng‐Siang Tan
- Center for Tropical and Emerging DiseasesFaculty of Medicine and Health SciencesUniversiti Malaysia SarawakKota SamarahanSarawakMalaysia
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Alhadrami HA, El-Din ASGS, Hassan HM, Sayed AM, Alhadrami AH, Rateb ME, Naguib DM. Development and Evaluation of a Self-Nanoemulsifying Drug Delivery System for Sinapic Acid with Improved Antiviral Efficacy against SARS-CoV-2. Pharmaceutics 2023; 15:2531. [PMID: 38004511 PMCID: PMC10674535 DOI: 10.3390/pharmaceutics15112531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/05/2023] [Accepted: 10/20/2023] [Indexed: 11/26/2023] Open
Abstract
This study aimed to develop a self-nanoemulsifying drug delivery system (SNE) for sinapic acid (SA) to improve its solubility and antiviral activity. Optimal components for the SA-SNE formulation were selected, including Labrafil as the oil, Cremophor EL as the surfactant, and Transcutol as the co-surfactant. The formulation was optimized using surface response design, and the optimized SA-SNE formulation exhibited a small globule size of 83.6 nm, high solubility up to 127.1 ± 3.3, and a 100% transmittance. In vitro release studies demonstrated rapid and high SA release from the formulation. Pharmacokinetic analysis showed improved bioavailability by 2.43 times, and the optimized SA-SNE formulation exhibited potent antiviral activity against SARS-CoV-2. The developed SA-SNE formulation can enhance SA's therapeutic efficacy by improving its solubility, bioavailability, and antiviral activity. Further in silico, modeling, and Gaussian accelerated molecular dynamics (GaMD)-based studies revealed that SA could interact with and inhibit the viral main protease (Mpro). This research contributes to developing effective drug delivery systems for poorly soluble drugs like SA, opening new possibilities for their application via nebulization in SARS-CoV-2 therapy.
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Affiliation(s)
- Hani A Alhadrami
- Faculty of Applied Medical Sciences, Department of Medical Laboratory Technology, King Abdulaziz University, P.O. Box 80402, Jeddah 21589, Saudi Arabia
- King Fahd Medical Research Centre, King Abdulaziz University, P.O. Box 80402, Jeddah 21589, Saudi Arabia
- Molecular Diagnostics Laboratory, King Abdulaziz University Hospital, P.O. Box 80402, Jeddah 21589, Saudi Arabia
| | - Ahmed S G Srag El-Din
- Department of Pharmaceutics, Faculty of Pharmacy, Delta University for Science & Technology, Gamasa City 35712, Egypt
| | - Hossam M Hassan
- Department of Pharmacognosy, Faculty of Pharmacy, Nahda University, Beni-Suef 62513, Egypt
- Department of Pharmacognosy, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62514, Egypt
| | - Ahmed M Sayed
- Department of Pharmacognosy, Faculty of Pharmacy, Nahda University, Beni-Suef 62513, Egypt
| | - Albaraa H Alhadrami
- School of Computing, Engineering & Physical Sciences, University of the West of Scotland, Paisley PA1 2BE, UK
| | - Mostafa E Rateb
- School of Computing, Engineering & Physical Sciences, University of the West of Scotland, Paisley PA1 2BE, UK
| | - Demiana M Naguib
- Department of Pharmaceutics, Faculty of Pharmacy, Nahda University (NUB), Beni-Suef 62513, Egypt
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Jiang X, Liu J, Xi Y, Zhang Q, Wang Y, Zhao M, Lu X, Wu H, Shan T, Ni B, Zhang W, Ma X. Virome of high-altitude canine digestive tract and genetic characterization of novel viruses potentially threatening human health. mSphere 2023; 8:e0034523. [PMID: 37724888 PMCID: PMC10597464 DOI: 10.1128/msphere.00345-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 07/25/2023] [Indexed: 09/21/2023] Open
Abstract
The majority of currently emerging infectious illnesses are zoonotic infections, which have caused serious public health and economic implications. The development of viral metagenomics has helped us to explore unknown viruses. We collected 1,970 canine feces from Yushu and Guoluo in the plateau region of China for this study to do a metagenomics analysis of the viral community of the canine digestive tract. Our analysis identified 203 novel viruses, classified into 11 known families and 2 unclassified groups. These viruses include the hepatitis E virus, first identified in dogs, and the astrovirus, coronavirus, polyomavirus, and others. The relationship between the newly identified canine viruses and known viruses was investigated through the use of phylogenetic analysis. Furthermore, we demonstrated the cross-species transmission of viruses and predicted new viruses that may cause diseases in both humans and animals, providing technical support for the prevention and control of diseases caused by environmental pollution viruses. IMPORTANCE Most emerging infectious diseases are due to zoonotic disease agents. Because of their effects on the security of human or animal life, agriculture production, and food safety, zoonotic illnesses and livestock diseases are of worldwide significance. Because dogs are closely related to humans and domestic animals, they serve as one of the important links in the transmission of zoonotic and livestock diseases. Canines can contaminate the environment in which humans live such as water and soil through secretions, potentially altering the human gut microbiota or causing diseases. Our study enriched the viral community in the digestive tract microbiome of dogs and found types of viruses that threaten human health, providing technical support for the prevention and control of early warning of diseases caused by environmental contaminant viruses.
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Affiliation(s)
- Xiaojie Jiang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Jia Liu
- Qinghai Institute of Endemic Disease Prevention and Control, Xining, Qinghai, China
| | - Yuan Xi
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Qing Zhang
- Qinghai Institute of Endemic Disease Prevention and Control, Xining, Qinghai, China
| | - Yongshun Wang
- Qinghai Institute of Endemic Disease Prevention and Control, Xining, Qinghai, China
| | - Min Zhao
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Xiang Lu
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Haisheng Wu
- Qinghai Institute of Endemic Disease Prevention and Control, Xining, Qinghai, China
| | - Tongling Shan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Bin Ni
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Wen Zhang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Xiao Ma
- Qinghai Institute of Endemic Disease Prevention and Control, Xining, Qinghai, China
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Singh M, Pushpakumar S, Zheng Y, Smolenkova I, Akinterinwa OE, Luulay B, Tyagi SC. Novel mechanism of the COVID-19 associated coagulopathy (CAC) and vascular thromboembolism. NPJ VIRUSES 2023; 1:3. [PMID: 38077924 PMCID: PMC10710223 DOI: 10.1038/s44298-023-00003-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 09/20/2023] [Indexed: 01/31/2024]
Abstract
Previous studies from our laboratory revealed that SARS-CoV-2 spike protein (SP) administration to a genetically engineered model expressing the human angiotensin-converting enzyme 2; ACE2 receptor (i.e., hACE2 humanized mouse) mimicked the coronavirus disease-19 (COVID-19) pathology. In humans the cause of high morbidity, and mortality is due to 'cytokine-storm' led thromboembolism; however, the exact mechanisms of COVID-19 associated coagulopathy (CAC) have yet to be discovered. Current knowledge suggests that CAC is distinct from the standard coagulopathy, in that the intrinsic and extrinsic thrombin-dependent coagulation factors, and the pathway(s) that are common to coagulopathy, are not recruited by SARS-CoV-2. Findings from patients revealed that there is little change in their partial thromboplastin, or the prothrombin time coupled with a significant decline in platelets. Further, there appears to be an endothelial dysfunction during COVID-19 suggesting an interaction of the endothelia with immune cells including neutrophils. There are also reports that inflammatory NGAL is elevated during COVID-19. Furthermore, the levels of NPT are also increased indicating an increase in inflammatory M1 macrophage iNOS which sequesters BH4; an essential enzyme co-factor that acts as a potent antioxidant thus causing damage to endothelia. SARS-CoV-2 entry into the host cells is facilitated by a co-operative action between TMPRSS2 and the main ACE2 receptor. Interestingly, after infection ADAMTS13; a von Willebrand factor; VWF cleaving enzyme is found to be decreased. Based on these facts, we hypothesize that vascular thromboembolism is associated with serine and metalloproteinase, and in that context, we opine that inhibition of iNOS might help mitigate COVID-19 harmful effects. To test this hypothesis, we administered SP to the hACE2 mice that were subsequently treated with amino guanidine (AG; a potent inhibitor of glycoxidation, lipoxidation and oxidative vicious cycles). Our results revealed increase in TMPRSS2, and NGAL by SP but treatment with AG mitigated their levels. Similarly, levels of MMP-2, and -9 were increased; however, AG treatment normalized these levels. Our findings suggest that occurrence of CAC is influenced by TMPRSS2, ADAMTS13, NGAL and MMP- 2, and -9 factors, and an intervention with iNOS blocker helped mitigate the CAC condition in experimental settings.
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Affiliation(s)
- Mahavir Singh
- Department of Physiology, University of Louisville School of Medicine, Louisville, KY 40202, USA
- These authors contributed equally: Mahavir Singh, Sathnur Pushpakumar
| | - Sathnur Pushpakumar
- Department of Physiology, University of Louisville School of Medicine, Louisville, KY 40202, USA
- These authors contributed equally: Mahavir Singh, Sathnur Pushpakumar
| | - Yuting Zheng
- Department of Physiology, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Irina Smolenkova
- Department of Physiology, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Oluwaseun E. Akinterinwa
- Department of Physiology, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Bana Luulay
- Department of Physiology, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Suresh C. Tyagi
- Department of Physiology, University of Louisville School of Medicine, Louisville, KY 40202, USA
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Shamim S, Akhtar M, Gul S. Novel designed analogues of quercetin against SARS-CoV2:an in-silico pharmacokinetic evaluation, molecular modeling, MD simulations based study. J Biomol Struct Dyn 2023:1-19. [PMID: 37798928 DOI: 10.1080/07391102.2023.2265469] [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: 10/25/2022] [Accepted: 09/24/2023] [Indexed: 10/07/2023]
Abstract
Here we present the design of the series of quercetin analogues and their molecular docking study involving the binding of quercetin and its analogues with SARS-CoV2 3CLpro. The scientific literature shows that quercetin compound has been successfully used against SARS-CoV by inhibiting the replication of virus in respiratory epithelial cell through the inhibition of the SARS-CoV main protease (3CLpro.) It was suggested that the modification at position 3 in quercetin structure may produce potent compounds against SARS-CoV2. A series of quercetin analogues were designed and screened for physicochemical and pharmacokinetics parameters. The activities of selected compounds against SARS-CoV2 were screened by molecular modelling and evaluated that analogues, Q5, Q6 and Q13 have the best docking scores (-8.01 to -8.17 kcal/mol) and also better than quercetin, α-ketoamide and current available inhibitors of the same target. The structure-activity relationship (SAR) study revealed that the introduction of the amino group in a designed molecule was highly promising for increasing the inhibitory activity against SARS-CoV2 3CL pro. Moreover, to check the stability and orientation of selected compounds inside the binding pocket, the molecular dynamic simulations were performed for 100 ns. Results revealed that the designed analogues Q1, Q6 and Q13 having lowest binding energies (-8.0, -8.17 and -8.06 kcal/mol respectively) as well as better physicochemical properties, pharmacokinetics, and toxicity profile show their potential to synthesize and develop as the therapeutic agents against corona virus.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sumbul Shamim
- Department of Pharmacology, Faculty of Pharmaceutical Sciences, Dow College of Pharmacy, Dow University of Health Sciences, Karachi, Pakistan
| | - Mahwish Akhtar
- Department of Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences, Dow College of Pharmacy, Dow University of Health Sciences, Karachi, Pakistan
| | - Somia Gul
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Jinnah University for Women, Karachi, Pakistan
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Aguida B, Chabi MM, Baouz S, Mould R, Bell JD, Pooam M, André S, Archambault D, Ahmad M, Jourdan N. Near-Infrared Light Exposure Triggers ROS to Downregulate Inflammatory Cytokines Induced by SARS-CoV-2 Spike Protein in Human Cell Culture. Antioxidants (Basel) 2023; 12:1824. [PMID: 37891903 PMCID: PMC10604116 DOI: 10.3390/antiox12101824] [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: 07/31/2023] [Revised: 09/13/2023] [Accepted: 09/28/2023] [Indexed: 10/29/2023] Open
Abstract
The leading cause of mortality from SARS-CoV-2 is an exaggerated host immune response, triggering cytokine storms, multiple organ failure and death. Current drug- and vaccine-based therapies are of limited efficacy against novel viral variants. Infrared therapy is a non-invasive and safe method that has proven effective against inflammatory conditions for over 100 years. However, its mechanism of action is poorly understood and has not received widespread acceptance. We herein investigate whether near-infrared (NIR) light exposure in human primary alveolar and macrophage cells could downregulate inflammatory cytokines triggered by the SARS-CoV-2 spike (S) protein or lipopolysaccharide (LPS), and via what underlying mechanism. Our results showed a dramatic reduction in pro-inflammatory cytokines within days of NIR light treatment, while anti-inflammatory cytokines were upregulated. Mechanistically, NIR light stimulated mitochondrial metabolism, induced transient bursts in reactive oxygen species (ROS) and activated antioxidant gene transcription. These, in turn, downregulated ROS and inflammatory cytokines. A causal relationship was shown between the induction of cellular ROS by NIR light exposure and the downregulation of inflammatory cytokines triggered by SARS-CoV-2 S. If confirmed by clinical trials, this method would provide an immediate defense against novel SARS-CoV-2 variants and other inflammatory infectious diseases.
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Affiliation(s)
- Blanche Aguida
- UMR8256, CNRS, IBPS, Sorbonne University, 75005 Paris, France; (B.A.)
| | | | - Soria Baouz
- UMR8256, CNRS, IBPS, Sorbonne University, 75005 Paris, France; (B.A.)
| | - Rhys Mould
- Research Centre for Optimal Health, University of Westminster, London W1W 6UW, UK (J.D.B.)
| | - Jimmy D. Bell
- Research Centre for Optimal Health, University of Westminster, London W1W 6UW, UK (J.D.B.)
| | - Marootpong Pooam
- Department of Biology, Faculty of Science, Naresuan University, Phitsanulok 65000, Thailand;
| | - Sebastien André
- Nutrition and Obesities: Systemic Approaches, NutriOmics, Research Unit, Sorbonne University, INSERM, 75013 Paris, France
| | - Dominique Archambault
- Laboratoire CHArt, University of Paris 8-Vincennes-Saint-Denis, 93526 Saint-Denis, France
| | - Margaret Ahmad
- UMR8256, CNRS, IBPS, Sorbonne University, 75005 Paris, France; (B.A.)
- Department of Biology, Xavier University, 3800 Victory Parkway, Cincinnati, OH 45207, USA
| | - Nathalie Jourdan
- UMR8256, CNRS, IBPS, Sorbonne University, 75005 Paris, France; (B.A.)
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Sharma G, Kumar N, Sharma CS, Mishra SS. In silico guided screening of active components of C. lanceolata as 3-chymotrypsin-like protease inhibitors of novel coronavirus. 3 Biotech 2023; 13:324. [PMID: 37663751 PMCID: PMC10471561 DOI: 10.1007/s13205-023-03745-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 08/14/2023] [Indexed: 09/05/2023] Open
Abstract
Despite the intense worldwide efforts towards the identification of potential anti-CoV therapeutics, no antiviral drugs have yet been discovered. Numerous vaccines are now approved for use, but they all serve as preventative measures. To effectively treat viral infections, it is crucial to find new antiviral drugs that are derived from natural sources. Various compounds with potential activity against 3 chymotrypsin-like protease (3CLpro) were reported and some are validated by bioassay studies. Therefore, we performed the computational screening of phytoconstituents of Codonopsis lanceolata to search for potential antiviral hit candidates. The curated compounds of the plant C. lanceolata were collected and downloaded from the literature. The binding affinity of the curated datasets was predicted for the target 3CLpro. Stigmasterol exhibits the highest docking score for the 3CLpro target. In addition, molecular dynamics (MD) simulations were conducted for the validation of docking results using root mean square deviation and root mean square fluctuation plots. The MD results indicated that the docked complex was stable and retained hydrogen bonding and non-bonding interactions. Furthermore, the calculation of pharmacokinetic parameters and Lipinski's rule of five suggest that C. lanceolata has the potential for drug-likeness. In order to develop new medicines for this debilitating disease, we will focus on the primary virus-based and host-based targets that can direct medicinal chemists to identify novel treatments to produce new drugs for it. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03745-2.
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Affiliation(s)
- Ganesh Sharma
- Department of Pharmaceutical Chemistry, Bhupal Nobles’ College of Pharmacy, Bhupal Nobles’ University, Udaipur, 313002 India
| | - Neeraj Kumar
- Department of Pharmaceutical Chemistry, Bhupal Nobles’ College of Pharmacy, Bhupal Nobles’ University, Udaipur, 313002 India
| | - Chandra Shekhar Sharma
- Department of Pharmaceutical Chemistry, Bhupal Nobles’ College of Pharmacy, Bhupal Nobles’ University, Udaipur, 313002 India
| | - Shashank Shekher Mishra
- Faculty of Pharmacy, School of Pharmaceutical and Populations Health Informatics, DIT University, Dehradun, 248009 India
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Xia CS, Zhan M, Liu Y, Yue ZH, Song Y, Zhang F, Wang H. SARS-CoV-2 antibody response in SARS survivors with and without the COVID-19 vaccine. Int J Antimicrob Agents 2023; 62:106947. [PMID: 37544384 DOI: 10.1016/j.ijantimicag.2023.106947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 07/12/2023] [Accepted: 08/01/2023] [Indexed: 08/08/2023]
Abstract
OBJECTIVES Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to spread worldwide. However, it remains unknown whether individuals with prior SARS-CoV-1 infection are protected from SARS-CoV-2 infection. This study assessed protective antibody levels in SARS survivors with and without the COVID-19 vaccine. METHODS We recruited 17 SARS survivors infected with SARS-CoV-1 in 2003, including 8 not vaccinated with the COVID-19 vaccine and 9 vaccinated with two doses of inactivated whole-virion COVID-19 vaccine (Sinopharm). In addition, 105 healthy adult volunteers without SARS-CoV-1 and SARS-CoV-2 infections were used as controls. The relative concentrations of three protective antibodies including anti-SARS-CoV-2 spike IgG (nCoV S-IgG), anti-SARS-CoV-2 spike receptor-binding domain IgG (nCoV RBD-IgG), and anti-SARS-CoV-2 neutralizing antibodies (nCoV NAbs) were measured to evaluate humoral immunity. RESULTS We found that the positive rates of these antibodies in unvaccinated SARS survivors were 37.5%, 37.5%, and 62.5%, respectively. In contrast, the corresponding positive rates were all 0% in controls before vaccination. In controls, the levels of protective antibodies reached a peak ca. 28 days after the second dose of vaccine and then started to decline. Surprisingly, the levels of these antibodies were maintained at very high levels even 166 days after the second dose of vaccine in SARS survivors. CONCLUSION Our study suggests that there are protective antibodies cross-reacting with SARS-CoV-2 in recovered SARS patients and that SARS survivors can generate a much stronger antibody response induced by the COVID-19 vaccine than can controls. These initial findings show the feasibility of developing novel pan-sarbecovirus vaccines.
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Affiliation(s)
- Chang-Sheng Xia
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Minghua Zhan
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Yudong Liu
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China; The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Zhi-Hong Yue
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Ying Song
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Feifei Zhang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Hui Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China.
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Sharma D, Joshi M, Apparsundaram S, Goyal RK, Patel B, Dhobi M. Solanum nigrum L. in COVID-19 and post-COVID complications: a propitious candidate. Mol Cell Biochem 2023; 478:2221-2240. [PMID: 36689040 PMCID: PMC9868520 DOI: 10.1007/s11010-022-04654-3] [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: 07/22/2022] [Accepted: 12/30/2022] [Indexed: 01/24/2023]
Abstract
COVID-19 is caused by severe acute respiratory syndrome coronavirus-2, SARS-CoV-2. COVID-19 has changed the world scenario and caused mortality around the globe. Patients who recovered from COVID-19 have shown neurological, psychological, renal, cardiovascular, pulmonary, and hematological complications. In some patients, complications lasted more than 6 months. However, significantly less attention has been given to post-COVID complications. Currently available drugs are used to tackle the complications, but new interventions must address the problem. Phytochemicals from natural sources have been evaluated in recent times to cure or alleviate COVID-19 symptoms. An edible plant, Solanum nigrum, could be therapeutic in treating COVID-19 as the AYUSH ministry of India prescribes it during the pandemic. S. nigrum demonstrates anti-inflammatory, immunomodulatory, and antiviral action to treat the SARS-CoV-2 infection and its post-complications. Different parts of the plant represent a reduction in proinflammatory cytokines and prevent multi-organ failure by protecting various organs (liver, kidney, heart, neuro, and lung). The review proposes the possible role of the plant S. nigrum in managing the symptoms of COVID-19 and its post-COVID complications based on in silico docking and pharmacological studies. Further systematic and experimental studies are required to validate our hypothesis.
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Affiliation(s)
- Divya Sharma
- Delhi Pharmaceutical Sciences and Research University, 110017, New Delhi, India
| | - Mit Joshi
- Institute of Pharmacy, Nirma University, 382481, Ahmedabad, Gujarat, India
| | - Subbu Apparsundaram
- Delhi Pharmaceutical Sciences and Research University, 110017, New Delhi, India
| | - Ramesh K Goyal
- Delhi Pharmaceutical Sciences and Research University, 110017, New Delhi, India
| | - Bhoomika Patel
- National Forensic Sciences University, Sector-9, Gandhinagar-382007, Gujarat, India.
| | - Mahaveer Dhobi
- Delhi Pharmaceutical Sciences and Research University, 110017, New Delhi, India.
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Lin HF, Liu MQ, Jiang RD, Gong QC, Su J, Guo ZS, Chen Y, Jia JK, Dong TY, Zhu Y, Li A, Shen XR, Wang Y, Li B, Xie TT, Yang XL, Hu B, Shi ZL. Characterization of a mouse-adapted strain of bat severe acute respiratory syndrome-related coronavirus. J Virol 2023; 97:e0079023. [PMID: 37607058 PMCID: PMC10537601 DOI: 10.1128/jvi.00790-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 06/18/2023] [Indexed: 08/24/2023] Open
Abstract
Bats carry genetically diverse severe acute respiratory syndrome-related coronaviruses (SARSr-CoVs). Some of them utilize human angiotensin-converting enzyme 2 (hACE2) as a receptor and cannot efficiently replicate in wild-type mice. Our previous study demonstrated that the bat SARSr-CoV rRsSHC014S induces respiratory infection and lung damage in hACE2 transgenic mice but not wild-type mice. In this study, we generated a mouse-adapted strain of rRsSHC014S, which we named SMA1901, by serial passaging of wild-type virus in BALB/c mice. SMA1901 showed increased infectivity in mouse lungs and induced interstitial lung pneumonia in both young and aged mice after intranasal inoculation. Genome sequencing revealed mutations in not only the spike protein but the whole genome, which may be responsible for the enhanced pathogenicity of SMA1901 in wild-type BALB/c mice. SMA1901 induced age-related mortality similar to that observed in SARS and COVID-19. Drug testing using antibodies and antiviral molecules indicated that this mouse-adapted virus strain can be used to test prophylactic and therapeutic drug candidates against SARSr-CoVs. IMPORTANCE The genetic diversity of SARSr-CoVs in wildlife and their potential risk of cross-species infection highlights the importance of developing a powerful animal model to evaluate the antibodies and antiviral drugs. We acquired the mouse-adapted strain of a bat-origin coronavirus named SMA1901 by natural serial passaging of rRsSHC014S in BALB/c mice. The SMA1901 infection caused interstitial pneumonia and inflammatory immune responses in both young and aged BALB/c mice after intranasal inoculation. Our model exhibited age-related mortality similar to SARS and COVID-19. Therefore, our model will be of high value for investigating the pathogenesis of bat SARSr-CoVs and could serve as a prospective test platform for prophylactic and therapeutic candidates.
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Affiliation(s)
- Hao-Feng Lin
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mei-Qin Liu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ren-Di Jiang
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Qian-Chun Gong
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Jia Su
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zi-Shuo Guo
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ying Chen
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jing-Kun Jia
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tian-Yi Dong
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yan Zhu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Ang Li
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xu-Rui Shen
- Guangzhou Laboratory, Guangzhou International Bio Island, Guangzhou, Guangdong, China
| | - Yi Wang
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Bei Li
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Ting-Ting Xie
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xing-Lou Yang
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Ben Hu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Zheng-Li Shi
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
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Shafiq N, Mehroze A, Sarwar W, Arshad U, Parveen S, Rashid M, Farooq A, Rafiq N, Wondmie GF, Bin Jardan YA, Brogi S, Bourhia M. Exploration of phenolic acid derivatives as inhibitors of SARS-CoV-2 main protease and receptor binding domain: potential candidates for anti-SARS-CoV-2 therapy. Front Chem 2023; 11:1251529. [PMID: 37822772 PMCID: PMC10562575 DOI: 10.3389/fchem.2023.1251529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 09/06/2023] [Indexed: 10/13/2023] Open
Abstract
Severe acute respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) is the etiological virus of Coronavirus Disease 2019 (COVID-19) which has been a public health concern due to its high morbidity and high mortality. Hence, the search for drugs that incapacitate the virus via inhibition of vital proteins in its life cycle is ongoing due to the paucity of drugs in clinical use against the virus. Consequently, this study was aimed at evaluating the potentials of natural phenolics against the Main protease (Mpro) and the receptor binding domain (RBD) using molecular modeling techniques including molecular docking, molecular dynamics (MD) simulation, and density functional theory (DFT) calculations. To this end, thirty-five naturally occurring phenolics were identified and subjected to molecular docking simulation against the proteins. The results showed the compounds including rosmarinic acid, cynarine, and chlorogenic acid among many others possessed high binding affinities for both proteins as evident from their docking scores, with some possessing lower docking scores compared to the standard compound (Remdesivir). Further subjection of the hit compounds to drug-likeness, pharmacokinetics, and toxicity profiling revealed chlorogenic acid, rosmarinic acid, and chicoric acid as the compounds with desirable profiles and toxicity properties, while the study of their electronic properties via density functional theory calculations revealed rosmarinic acid as the most reactive and least stable among the sets of lead compounds that were identified in the study. Molecular dynamics simulation of the complexes formed after docking revealed the stability of the complexes. Ultimately, further experimental procedures are needed to validate the findings of this study.
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Affiliation(s)
- Nusrat Shafiq
- Synthetic and Natural Products Discovery (SNPD) Laboratory, Department of Chemistry, Government College Women University Faisalabad, Faisalabad, Pakistan
| | - Aiman Mehroze
- Synthetic and Natural Products Discovery (SNPD) Laboratory, Department of Chemistry, Government College Women University Faisalabad, Faisalabad, Pakistan
| | - Warda Sarwar
- Synthetic and Natural Products Discovery (SNPD) Laboratory, Department of Chemistry, Government College Women University Faisalabad, Faisalabad, Pakistan
| | - Uzma Arshad
- Synthetic and Natural Products Discovery (SNPD) Laboratory, Department of Chemistry, Government College Women University Faisalabad, Faisalabad, Pakistan
| | - Shagufta Parveen
- Synthetic and Natural Products Discovery (SNPD) Laboratory, Department of Chemistry, Government College Women University Faisalabad, Faisalabad, Pakistan
| | - Maryam Rashid
- Synthetic and Natural Products Discovery (SNPD) Laboratory, Department of Chemistry, Government College Women University Faisalabad, Faisalabad, Pakistan
| | - Ariba Farooq
- Department of Chemistry, University of Lahore, Lahore, Pakistan
| | - Naila Rafiq
- Department of Biochemistry, Government College Women University Faisalabad, Faisalabad, Pakistan
| | | | - Yousef A. Bin Jardan
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Simone Brogi
- Department of Pharmacy, Pisa University, Pisa, Italy
| | - Mohammed Bourhia
- Department of Chemistry and Biochemistry, Faculty of Medicine and Pharmacy, Ibn Zohr University, Laayoune, Morocco
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69
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Ali H, Naseem A, Siddiqui ZI. SARS-CoV-2 Syncytium under the Radar: Molecular Insights of the Spike-Induced Syncytia and Potential Strategies to Limit SARS-CoV-2 Replication. J Clin Med 2023; 12:6079. [PMID: 37763019 PMCID: PMC10531702 DOI: 10.3390/jcm12186079] [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: 08/04/2023] [Revised: 09/14/2023] [Accepted: 09/17/2023] [Indexed: 09/29/2023] Open
Abstract
SARS-CoV-2 infection induces non-physiological syncytia when its spike fusogenic protein on the surface of the host cells interacts with the ACE2 receptor on adjacent cells. Spike-induced syncytia are beneficial for virus replication, transmission, and immune evasion, and contribute to the progression of COVID-19. In this review, we highlight the properties of viral fusion proteins, mainly the SARS-CoV-2 spike, and the involvement of the host factors in the fusion process. We also highlight the possible use of anti-fusogenic factors as an antiviral for the development of therapeutics against newly emerging SARS-CoV-2 variants and how the fusogenic property of the spike could be exploited for biomedical applications.
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Affiliation(s)
- Hashim Ali
- Department of Pathology, University of Cambridge, Addenbrookes Hospital, Cambridge CB2 0QQ, UK
| | - Asma Naseem
- Infection, Immunity and Inflammation Research and Teaching Department, Great Ormond Street Institute of Child Health, University College London, London WC1N 1DZ, UK
| | - Zaheenul Islam Siddiqui
- Diabetes and Obesity Research Center, NYU Grossman Long Island School of Medicine, New York, NY 11501, USA
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70
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Lee J, Zepeda SK, Park YJ, Taylor AL, Quispe J, Stewart C, Leaf EM, Treichel C, Corti D, King NP, Starr TN, Veesler D. Broad receptor tropism and immunogenicity of a clade 3 sarbecovirus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.12.557371. [PMID: 37745523 PMCID: PMC10515872 DOI: 10.1101/2023.09.12.557371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Although Rhinolophus bats harbor diverse clade 3 sarbecoviruses, the structural determinants of receptor tropism along with the antigenicity of their spike (S) glycoproteins remain uncharacterized. Here, we show that the African Rinolophus bat clade 3 sarbecovirus PRD-0038 S has a broad ACE2 usage and that RBD mutations further expand receptor promiscuity and enable human ACE2 utilization. We determined a cryoEM structure of the PRD-0038 RBD bound to R. alcyone ACE2, explaining receptor tropism and highlighting differences with SARS-CoV-1 and SARS-CoV-2. Characterization of PRD-0038 S using cryoEM and monoclonal antibody reactivity revealed its distinct antigenicity relative to SARS-CoV-2 and identified PRD-0038 cross-neutralizing antibodies for pandemic preparedness. PRD-0038 S vaccination elicited greater titers of antibodies cross-reacting with vaccine-mismatched clade 2 and clade 1a sarbecoviruses compared to SARS-CoV-2 S due to broader antigenic targeting, motivating the inclusion of clade 3 antigens in next-generation vaccines for enhanced resilience to viral evolution.
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Affiliation(s)
- Jimin Lee
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Samantha K. Zepeda
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Ashley L. Taylor
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Joel Quispe
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Cameron Stewart
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Elizabeth M. Leaf
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Catherine Treichel
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Neil P. King
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Tyler N. Starr
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
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71
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Gonzaga A, Andreu E, Hernández-Blasco LM, Meseguer R, Al-Akioui-Sanz K, Soria-Juan B, Sanjuan-Gimenez JC, Ferreras C, Tejedo JR, Lopez-Lluch G, Goterris R, Maciá L, Sempere-Ortells JM, Hmadcha A, Borobia A, Vicario JL, Bonora A, Aguilar-Gallardo C, Poveda JL, Arbona C, Alenda C, Tarín F, Marco FM, Merino E, Jaime F, Ferreres J, Figueira JC, Cañada-Illana C, Querol S, Guerreiro M, Eguizabal C, Martín-Quirós A, Robles-Marhuenda Á, Pérez-Martínez A, Solano C, Soria B. Rationale for combined therapies in severe-to-critical COVID-19 patients. Front Immunol 2023; 14:1232472. [PMID: 37767093 PMCID: PMC10520558 DOI: 10.3389/fimmu.2023.1232472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/22/2023] [Indexed: 09/29/2023] Open
Abstract
An unprecedented global social and economic impact as well as a significant number of fatalities have been brought on by the coronavirus disease 2019 (COVID-19), produced by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Acute SARS-CoV-2 infection can, in certain situations, cause immunological abnormalities, leading to an anomalous innate and adaptive immune response. While most patients only experience mild symptoms and recover without the need for mechanical ventilation, a substantial percentage of those who are affected develop severe respiratory illness, which can be fatal. The absence of effective therapies when disease progresses to a very severe condition coupled with the incomplete understanding of COVID-19's pathogenesis triggers the need to develop innovative therapeutic approaches for patients at high risk of mortality. As a result, we investigate the potential contribution of promising combinatorial cell therapy to prevent death in critical patients.
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Affiliation(s)
- Aitor Gonzaga
- Alicante Institute for Health and Biomedical Research (ISABIAL), Alicante, Spain
- Institute of Bioengineering, Miguel Hernández University, Elche, Spain
| | - Etelvina Andreu
- Alicante Institute for Health and Biomedical Research (ISABIAL), Alicante, Spain
- Applied Physics Department, Miguel Hernández University, Elche, Spain
| | | | - Rut Meseguer
- Alicante Institute for Health and Biomedical Research (ISABIAL), Alicante, Spain
- Clinic University Hospital, Fundación para la Investigación del Hospital Clínico de la Comunidad Valenciana (INCLIVA) Health Research Institute, Valencia, Spain
| | - Karima Al-Akioui-Sanz
- Alicante Institute for Health and Biomedical Research (ISABIAL), Alicante, Spain
- Hospital La Paz Institute for Health Research, IdiPAZ, University Hospital La Paz, Madrid, Spain
| | - Bárbara Soria-Juan
- Réseau Hospitalier Neuchâtelois, Hôpital Pourtalès, Neuchâtel, Switzerland
| | | | - Cristina Ferreras
- Hospital La Paz Institute for Health Research, IdiPAZ, University Hospital La Paz, Madrid, Spain
| | - Juan R. Tejedo
- Department of Molecular Biology and Biochemical Engineering, University Pablo de Olavide, Seville, Spain
- Biomedical Research Network for Diabetes and Related Metabolic Diseases-Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM) of the Carlos III Health Institute (ISCIII), Madrid, Spain
| | - Guillermo Lopez-Lluch
- University Pablo de Olavide, Centro Andaluz de Biología del Desarrollo - Consejo Superior de Investigaciones Científicas (CABD-CSIC), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Sevilla, Spain
| | - Rosa Goterris
- Clinic University Hospital, Fundación para la Investigación del Hospital Clínico de la Comunidad Valenciana (INCLIVA) Health Research Institute, Valencia, Spain
| | - Loreto Maciá
- Nursing Department, University of Alicante, Alicante, Spain
| | - Jose M. Sempere-Ortells
- Alicante Institute for Health and Biomedical Research (ISABIAL), Alicante, Spain
- Biotechnology Department, University of Alicante, Alicante, Spain
| | - Abdelkrim Hmadcha
- Department of Molecular Biology and Biochemical Engineering, University Pablo de Olavide, Seville, Spain
- Biosanitary Research Institute (IIB-VIU), Valencian International University (VIU), Valencia, Spain
| | - Alberto Borobia
- Clinical Pharmacology Department, La Paz University Hospital, School of Medicine, Universidad Autónoma de Madrid, IdiPAz, Madrid, Spain
| | - Jose L. Vicario
- Transfusion Center of the Autonomous Community of Madrid, Madrid, Spain
| | - Ana Bonora
- Health Research Institute Hospital La Fe, Valencia, Spain
| | | | - Jose L. Poveda
- Health Research Institute Hospital La Fe, Valencia, Spain
| | - Cristina Arbona
- Valencian Community Blood Transfusion Center, Valencia, Spain
| | - Cristina Alenda
- Alicante Institute for Health and Biomedical Research (ISABIAL), Alicante, Spain
| | - Fabian Tarín
- Alicante Institute for Health and Biomedical Research (ISABIAL), Alicante, Spain
| | - Francisco M. Marco
- Alicante Institute for Health and Biomedical Research (ISABIAL), Alicante, Spain
- Immunology Department, Dr. Balmis General University Hospital, Alicante, Spain
| | - Esperanza Merino
- Alicante Institute for Health and Biomedical Research (ISABIAL), Alicante, Spain
- Department of Clinical Medicine, Miguel Hernández University, Elche, Spain
- Infectious Diseases Unit, Dr. Balmis General University Hospital, Alicante, Spain
| | - Francisco Jaime
- Alicante Institute for Health and Biomedical Research (ISABIAL), Alicante, Spain
| | - José Ferreres
- Intensive Care Service, Hospital Clinico Universitario, Fundación para la Investigación del Hospital Clínico de la Comunidad Valenciana (INCLIVA), Valencia, Spain
| | | | | | | | - Manuel Guerreiro
- Department of Hematology, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Cristina Eguizabal
- Research Unit, Basque Center for Blood Transfusion and Human Tissues, Galdakao, Spain
- Cell Therapy, Stem Cells and Tissues Group, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | | | | | - Antonio Pérez-Martínez
- Hospital La Paz Institute for Health Research, IdiPAZ, University Hospital La Paz, Madrid, Spain
- Department of Pediatrics, Faculty of Medicine, Universidad Autónoma de Madrid, Madrid, Spain
| | - Carlos Solano
- Hematology Service, Hospital Clínico Universitario, Fundación para la Investigación del Hospital Clínico de la Comunidad Valenciana (INCLIVA), Valencia, Spain
| | - Bernat Soria
- Alicante Institute for Health and Biomedical Research (ISABIAL), Alicante, Spain
- Institute of Bioengineering, Miguel Hernández University, Elche, Spain
- Biomedical Research Network for Diabetes and Related Metabolic Diseases-Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM) of the Carlos III Health Institute (ISCIII), Madrid, Spain
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72
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Lin C, Jiang H, Li W, Zeng P, Zhou X, Zhang J, Li J. Structural basis for the inhibition of coronaviral main proteases by ensitrelvir. Structure 2023; 31:1016-1024.e3. [PMID: 37421945 DOI: 10.1016/j.str.2023.06.010] [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: 02/07/2023] [Revised: 03/31/2023] [Accepted: 06/13/2023] [Indexed: 07/10/2023]
Abstract
Main protease (Mpro) is a highly conserved cysteine protease that plays a vital role in the replication of coronaviruses, making it an attractive pan-coronaviral therapeutic target. Ensitrelvir (S-217622), developed by Shionogi, is the first orally active non-covalent, non-peptidic SARS-CoV-2 Mpro inhibitor, which also displays antiviral efficacy against other human coronaviruses as well as SARS-CoV-2 variants of concern (VOCs) and variants of interest (VOIs). Here, we report the crystal structures of the main proteases from SARS-CoV-2, SARS-CoV-2 VOC/VOIs, SARS-CoV, MERS-CoV, and HCoV-NL63 bound to the inhibitor S-217622. A detailed analysis of these structures illuminates key structural determinants essential for inhibition and elucidates the binding modes of the main proteases from different coronaviruses. Given the importance of the main protease for the treatment of coronaviral infection, structural insights obtained from this study could accelerate the design of novel antivirals with broad-spectrum efficacy against different human coronaviruses.
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Affiliation(s)
- Cheng Lin
- College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou 341000, China
| | - Haihai Jiang
- School of Basic Medical Sciences, Nanchang University, Nanchang 330031, China
| | - Wenwen Li
- Shenzhen Crystalo Biopharmaceutical Co., Ltd., Shenzhen 518118, China; Jiangxi Jmerry Biopharmaceutical Co., Ltd., Ganzhou 341000, China
| | - Pei Zeng
- Jiangxi Jmerry Biopharmaceutical Co., Ltd., Ganzhou 341000, China
| | - Xuelan Zhou
- Jiangxi Jmerry Biopharmaceutical Co., Ltd., Ganzhou 341000, China
| | - Jin Zhang
- School of Basic Medical Sciences, Nanchang University, Nanchang 330031, China.
| | - Jian Li
- College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou 341000, China.
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73
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Lee JD, Menasche BL, Mavrikaki M, Uyemura MM, Hong SM, Kozlova N, Wei J, Alfajaro MM, Filler RB, Müller A, Saxena T, Posey RR, Cheung P, Muranen T, Heng YJ, Paulo JA, Wilen CB, Slack FJ. Differences in syncytia formation by SARS-CoV-2 variants modify host chromatin accessibility and cellular senescence via TP53. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.31.555625. [PMID: 37693555 PMCID: PMC10491142 DOI: 10.1101/2023.08.31.555625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
COVID-19 remains a significant public health threat due to the ability of SARS-CoV-2 variants to evade the immune system and cause breakthrough infections. Although pathogenic coronaviruses such as SARS-CoV-2 and MERS-CoV lead to severe respiratory infections, how these viruses affect the chromatin proteomic composition upon infection remains largely uncharacterized. Here we used our recently developed integrative DNA And Protein Tagging (iDAPT) methodology to identify changes in host chromatin accessibility states and chromatin proteomic composition upon infection with pathogenic coronaviruses. SARS-CoV-2 infection induces TP53 stabilization on chromatin, which contributes to its host cytopathic effect. We mapped this TP53 stabilization to the SARS-CoV-2 spike and its propensity to form syncytia, a consequence of cell-cell fusion. Differences in SARS-CoV-2 spike variant-induced syncytia formation modify chromatin accessibility, cellular senescence, and inflammatory cytokine release via TP53. Our findings suggest that differences in syncytia formation alter senescence-associated inflammation, which varies among SARS-CoV-2 variants.
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74
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Aravind Kumar N, Aradhana S, Harleen, Vishnuraj MR. SARS-CoV-2 in digital era: Diagnostic techniques and importance of nucleic acid quantification with digital PCRs. Rev Med Virol 2023; 33:e2471. [PMID: 37529971 DOI: 10.1002/rmv.2471] [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: 04/19/2023] [Revised: 07/04/2023] [Accepted: 07/12/2023] [Indexed: 08/03/2023]
Abstract
Studies related to clinical diagnosis and research of SARS-CoV-2 are important in the current pandemic era. Although molecular biology has emphasised the importance of qualitative analysis, quantitative analysis with nucleic acids in relation to SARS-CoV-2 needs to be clearly emphasised, which can provide perspective for viral dynamic studies of SARS-CoV-2. In this regard, the requirement and utilization of digital PCR in COVID-19 research has substantially increased during the pandemic, necessitating the aggregation of its cardinal applications and future scopes. Hence, this meta-review comprehensively addresses and emphasises the importance of nucleic acid quantification of SARS-CoV-2 RNA with digital PCR (dPCR). Various quantitative techniques of clinical significance like immunological, proteomic and nucleic acid-based diagnosis and quantification, have been comparatively discussed. Furthermore, the core part of the article focusses on the working principle and advantages of digital PCR, along with its applications in COVID-19 research. Several important applications like viral load quantitation, environmental surveillance and assay validation have been extensively investigated and discussed. Certain key future scopes of clinical importance, like mortality prediction, viral/variant-symbiosis, and antiviral studies were also identified, suggesting several possible digital PCR applications in COVID-19 research.
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Affiliation(s)
- N Aravind Kumar
- Meat Species Identification Laboratory, ICAR - National Meat Research Institute, Hyderabad, Telangana, India
| | - S Aradhana
- Department of Biotechnology, School of Bio Sciences & Technology (SBST), Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Harleen
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana, India
| | - M R Vishnuraj
- Meat Species Identification Laboratory, ICAR - National Meat Research Institute, Hyderabad, Telangana, India
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75
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AlSamhori JF, Alshrouf MA, AlSamhori ARF, Alshadeedi FM, Madi AS, Alzoubi O. Implications of the COVID-19 pandemic on athletes, sports events, and mass gathering events: Review and recommendations. SPORTS MEDICINE AND HEALTH SCIENCE 2023; 5:165-173. [PMID: 37753427 PMCID: PMC10518794 DOI: 10.1016/j.smhs.2023.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 07/02/2023] [Accepted: 07/24/2023] [Indexed: 09/28/2023] Open
Abstract
Since the coronavirus disease 19 (COVID-19), which caused several respiratory diseases, was formally declared a global pandemic by the World Health Organization (WHO) on March 11, 2020, it affected the lifestyle and health of athletes, both directly through cardiorespiratory and other health related effects, and indirectly as the pandemic has forced the suspension, postponement, or cancellation of most professional sporting events around the world. In this review, we explore the journey of athletes throughout the pandemic and during their return to their competitive routine. We also highlight potential pitfalls during the process and summarize the recommendations for the optimal return to sport participation. We further discuss the impact of the pandemic on the psychology of athletes, the variance between the team and individual athletes, and their ability to cope with the changes. Moreover, we specifically reviewed the pandemic impact on younger professional athletes in terms of mental and fitness health. Finally, we shaded light on the various impacts of mass gathering events and recommendations for managing upcoming events.
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Affiliation(s)
| | - Mohammad Ali Alshrouf
- Medical Internship, Jordan University Hospital, The University of Jordan, Amman, 11942, Jordan
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76
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Li X, Zhu S, Zhang X, Ren Y, He J, Zhou J, Yin L, Wang G, Zhong T, Wang L, Xiao Y, Zhu C, Yin C, Yu X. Advances in the application of recombinase-aided amplification combined with CRISPR-Cas technology in quick detection of pathogenic microbes. Front Bioeng Biotechnol 2023; 11:1215466. [PMID: 37720320 PMCID: PMC10502170 DOI: 10.3389/fbioe.2023.1215466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 08/15/2023] [Indexed: 09/19/2023] Open
Abstract
The rapid diagnosis of pathogenic infections plays a vital role in disease prevention, control, and public health safety. Recombinase-aided amplification (RAA) is an innovative isothermal nucleic acid amplification technology capable of fast DNA or RNA amplification at low temperatures. RAA offers advantages such as simplicity, speed, precision, energy efficiency, and convenient operation. This technology relies on four essential components: recombinase, single-stranded DNA-binding protein (SSB), DNA polymerase, and deoxyribonucleoside triphosphates, which collectively replace the laborious thermal cycling process of traditional polymerase chain reaction (PCR). In recent years, the CRISPR-Cas (clustered regularly interspaced short palindromic repeats-associated proteins) system, a groundbreaking genome engineering tool, has garnered widespread attention across biotechnology, agriculture, and medicine. Increasingly, researchers have integrated the recombinase polymerase amplification system (or RAA system) with CRISPR technology, enabling more convenient and intuitive determination of detection results. This integration has significantly expanded the application of RAA in pathogen detection. The step-by-step operation of these two systems has been successfully employed for molecular diagnosis of pathogenic microbes, while the single-tube one-step method holds promise for efficient pathogen detection. This paper provides a comprehensive review of RAA combined with CRISPR-Cas and its applications in pathogen detection, aiming to serve as a valuable reference for further research in related fields.
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Affiliation(s)
- Xiaoping Li
- Faculty of Medicine, Macau University of Science and Technology, Avenida Wai Long Taipa, Macau, 999078, China
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, Zhejiang Province, 310015, China
| | - Shuying Zhu
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, Zhejiang Province, 310015, China
| | - Xinling Zhang
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, Zhejiang Province, 310015, China
| | - Yanli Ren
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310003, China
| | - Jing He
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, Zhejiang Province, 310015, China
| | - Jiawei Zhou
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, Zhejiang Province, 310015, China
| | - Liliang Yin
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, Zhejiang Province, 310015, China
| | - Gang Wang
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, Zhejiang Province, 310015, China
| | - Tian Zhong
- Faculty of Medicine, Macau University of Science and Technology, Avenida Wai Long Taipa, Macau, 999078, China
| | - Ling Wang
- Faculty of Medicine, Macau University of Science and Technology, Avenida Wai Long Taipa, Macau, 999078, China
| | - Ying Xiao
- Faculty of Medicine, Macau University of Science and Technology, Avenida Wai Long Taipa, Macau, 999078, China
- Guangdong-Hong Kong-Macau Joint Laboratory for Contaminants Exposure and Health, Guangzhou, Guangdong Province, 510006, China
| | - Chunying Zhu
- Clinical Psychology Department, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, Zhejiang Province, 310005, China
| | - Chengliang Yin
- Faculty of Medicine, Macau University of Science and Technology, Avenida Wai Long Taipa, Macau, 999078, China
| | - Xi Yu
- Faculty of Medicine, Macau University of Science and Technology, Avenida Wai Long Taipa, Macau, 999078, China
- Guangdong-Hong Kong-Macau Joint Laboratory for Contaminants Exposure and Health, Guangzhou, Guangdong Province, 510006, China
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77
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Santosh KC, GhoshRoy D, Nakarmi S. A Systematic Review on Deep Structured Learning for COVID-19 Screening Using Chest CT from 2020 to 2022. Healthcare (Basel) 2023; 11:2388. [PMID: 37685422 PMCID: PMC10486542 DOI: 10.3390/healthcare11172388] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 08/16/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023] Open
Abstract
The emergence of the COVID-19 pandemic in Wuhan in 2019 led to the discovery of a novel coronavirus. The World Health Organization (WHO) designated it as a global pandemic on 11 March 2020 due to its rapid and widespread transmission. Its impact has had profound implications, particularly in the realm of public health. Extensive scientific endeavors have been directed towards devising effective treatment strategies and vaccines. Within the healthcare and medical imaging domain, the application of artificial intelligence (AI) has brought significant advantages. This study delves into peer-reviewed research articles spanning the years 2020 to 2022, focusing on AI-driven methodologies for the analysis and screening of COVID-19 through chest CT scan data. We assess the efficacy of deep learning algorithms in facilitating decision making processes. Our exploration encompasses various facets, including data collection, systematic contributions, emerging techniques, and encountered challenges. However, the comparison of outcomes between 2020 and 2022 proves intricate due to shifts in dataset magnitudes over time. The initiatives aimed at developing AI-powered tools for the detection, localization, and segmentation of COVID-19 cases are primarily centered on educational and training contexts. We deliberate on their merits and constraints, particularly in the context of necessitating cross-population train/test models. Our analysis encompassed a review of 231 research publications, bolstered by a meta-analysis employing search keywords (COVID-19 OR Coronavirus) AND chest CT AND (deep learning OR artificial intelligence OR medical imaging) on both the PubMed Central Repository and Web of Science platforms.
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Affiliation(s)
- KC Santosh
- 2AI: Applied Artificial Intelligence Research Lab, Vermillion, SD 57069, USA
| | - Debasmita GhoshRoy
- School of Automation, Banasthali Vidyapith, Tonk 304022, Rajasthan, India;
| | - Suprim Nakarmi
- Department of Computer Science, University of South Dakota, Vermillion, SD 57069, USA;
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78
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Su X, Huang Z, Xu W, Wang Q, Xing L, Lu L, Jiang S, Xia S. IgG Fc-Binding Peptide-Conjugated Pan-CoV Fusion Inhibitor Exhibits Extended In Vivo Half-Life and Synergistic Antiviral Effect When Combined with Neutralizing Antibodies. Biomolecules 2023; 13:1283. [PMID: 37759683 PMCID: PMC10526447 DOI: 10.3390/biom13091283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 08/13/2023] [Accepted: 08/16/2023] [Indexed: 09/29/2023] Open
Abstract
The peptide-based pan-coronavirus fusion inhibitor EK1 is in phase III clinical trials, and it has, thus far, shown good clinical application prospects against SARS-CoV-2 and its variants. To further improve its in vivo long-acting property, we herein developed an Fc-binding strategy by conjugating EK1 with human immunoglobulin G Fc-binding peptide (IBP), which can exploit the long half-life advantage of IgG in vivo. The newly engineered peptide IBP-EK1 showed potent and broad-spectrum inhibitory activity against SARS-CoV-2 and its variants, including various Omicron sublineages and other human coronaviruses (HCoVs) with low cytotoxicity. In mouse models, IBP-EK1 possessed potent prophylactic and therapeutic efficacy against lethal HCoV-OC43 challenge, and it showed good safety profile and low immunogenicity. More importantly, IBP-EK1 exhibited a significantly extended in vivo half-life in rhesus monkeys of up to 37.7 h, which is about 20-fold longer than that reported for EK1. Strikingly, IBP-EK1 displayed strong in vitro or ex vivo synergistic anti-HCoV effect when combined with monoclonal neutralizing antibodies, including REGN10933 or S309, suggesting that IBP-conjugated EK1 can be further developed as a long-acting, broad-spectrum anti-HCoV agent, either alone or in combination with neutralizing antibodies, to combat the current COVID-19 pandemic or future outbreaks caused by emerging and re-emerging highly pathogenic HCoVs.
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Affiliation(s)
| | | | | | | | | | | | - Shibo Jiang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Fudan University, Shanghai 200032, China; (X.S.); (Z.H.); (W.X.); (Q.W.); (L.X.); (L.L.)
| | - Shuai Xia
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Fudan University, Shanghai 200032, China; (X.S.); (Z.H.); (W.X.); (Q.W.); (L.X.); (L.L.)
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79
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Brian Chia CS, Pheng Lim S. A Patent Review on SARS Coronavirus Papain-Like Protease (PL pro ) Inhibitors. ChemMedChem 2023; 18:e202300216. [PMID: 37248169 DOI: 10.1002/cmdc.202300216] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/29/2023] [Accepted: 05/29/2023] [Indexed: 05/31/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic is an unprecedented global health emergency causing more than 6.6 million fatalities by 31 December 2022. So far, only three antiviral drugs have been granted emergency use authorisation or approved by the FDA. The SARS-CoV-2 papain-like protease (PLpro ) is deemed an attractive drug target as it plays an essential role in viral polyprotein processing and pathogenesis although no inhibitors have yet been approved. This patent review discusses coronavirus PLpro inhibitors reported in patents published between 1 January 2003 to 2 March 2023, giving an overview on the inhibitors that have generated commercial interest, especially amongst drug companies.
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Affiliation(s)
- C S Brian Chia
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, Chromos #08-01, Singapore, 138670, Singapore
| | - Siew Pheng Lim
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, Chromos #08-01, Singapore, 138670, Singapore
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80
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Song W, Fang Z, Ma F, Li J, Huang Z, Zhang Y, Li J, Chen K. The role of SARS-CoV-2 N protein in diagnosis and vaccination in the context of emerging variants: present status and prospects. Front Microbiol 2023; 14:1217567. [PMID: 37675423 PMCID: PMC10478715 DOI: 10.3389/fmicb.2023.1217567] [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: 05/15/2023] [Accepted: 07/31/2023] [Indexed: 09/08/2023] Open
Abstract
Despite many countries rapidly revising their strategies to prevent contagions, the number of people infected with Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to surge. The emergent variants that can evade the immune response significantly affect the effectiveness of mainstream vaccines and diagnostic products based on the original spike protein. Therefore, it is essential to focus on the highly conserved nature of the nucleocapsid protein as a potential target in the field of vaccines and diagnostics. In this regard, our review initially discusses the structure, function, and mechanism of action of N protein. Based on this discussion, we summarize the relevant research on the in-depth development and application of diagnostic methods and vaccines based on N protein, such as serology and nucleic acid detection. Such valuable information can aid in designing more efficient diagnostic and vaccine tools that could help end the SARS-CoV-2 pandemic.
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Affiliation(s)
- Wanchen Song
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, China
| | - Zhongbiao Fang
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Feike Ma
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Jiaxuan Li
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Zhiwei Huang
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Yanjun Zhang
- Key Laboratory of Public Health Detection and Etiological Research of Zhejiang Province, Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Jianhua Li
- Key Laboratory of Public Health Detection and Etiological Research of Zhejiang Province, Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Keda Chen
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
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81
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Yu J, Im H, Lee G. Unwinding mechanism of SARS-CoV helicase (nsp13) in the presence of Ca 2+, elucidated by biochemical and single-molecular studies. Biochem Biophys Res Commun 2023; 668:35-41. [PMID: 37235917 PMCID: PMC10193821 DOI: 10.1016/j.bbrc.2023.05.062] [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: 05/07/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023]
Abstract
The recent outbreak of COVID-19 has created a serious health crisis with fatFal infectious viral diseases, such as Severe Acute Respiratory Syndrome (SARS). The nsp13, a helicase of coronaviruses is an essential element for viral replication that unwinds secondary structures of DNA and RNA, and is thus considered a major therapeutic target for treatment. The replication of coronaviruses and other retroviruses occurs in the cytoplasm of infected cells, in association with viral replication organelles, called virus-induced cytosolic double-membrane vesicles (DMVs). In addition, an increase in cytosolic Ca2+ concentration accelerates viral replication. However, the molecular mechanism of nsp13 in the presence of Ca2+ is not well understood. In this study, we applied biochemical methods and single-molecule techniques to demonstrate how nsp13 achieves its unwinding activity while performing ATP hydrolysis in the presence of Ca2+. Our study found that nsp13 could efficiently unwind double stranded (ds) DNA under physiological concentration of Ca2+ of cytosolic DMVs. These findings provide new insights into the properties of nsp13 in the range of calcium in cytosolic DMVs.
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Affiliation(s)
- Jeongmin Yu
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, 61005, South Korea
| | - Hyeryeon Im
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, 61005, South Korea
| | - Gwangrog Lee
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, 61005, South Korea.
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82
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Eriksson C, Gunasekera S, Muhammad T, Zhang M, Laurén I, Mangsbo SM, Lord M, Göransson U. Epitopes Displayed in a Cyclic Peptide Scaffold Bind SARS-COV-2 Antibodies. Chembiochem 2023; 24:e202300103. [PMID: 37021633 DOI: 10.1002/cbic.202300103] [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: 02/07/2023] [Revised: 04/03/2023] [Accepted: 04/05/2023] [Indexed: 04/07/2023]
Abstract
The SARS-CoV-2 virus that causes COVID-19 is a global health issue. The spread of the virus has resulted in seven million deaths to date. The emergence of new viral strains highlights the importance of continuous surveillance of the SARS-CoV-2 virus by using timely and accurate diagnostic tools. Here, we used a stable cyclic peptide scaffolds to present antigenic sequences derived from the spike protein that are reactive to SARS-CoV-2 antibodies. Using peptide sequences from different domains of SARS-CoV-2 spike proteins, we grafted epitopes on the peptide scaffold sunflower trypsin inhibitor 1 (SFTI-1). These scaffold peptides were then used to develop an ELISA to detect SARS-CoV-2 antibodies in serum. We show that displaying epitopes on the scaffold improves reactivity overall. One of the scaffold peptides (S2_1146-1161_c) has reactivity equal to that of commercial assays, and shows diagnostic potential.
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Affiliation(s)
- Camilla Eriksson
- Department of Pharmaceutical Biosciences, Uppsala University Biomedical Centre, Box 591, 75123, Uppsala, Sweden
| | - Sunithi Gunasekera
- Department of Pharmaceutical Biosciences, Uppsala University Biomedical Centre, Box 591, 75123, Uppsala, Sweden
| | - Taj Muhammad
- Department of Pharmaceutical Biosciences, Uppsala University Biomedical Centre, Box 591, 75123, Uppsala, Sweden
| | - Mingshu Zhang
- Department of Pharmaceutical Biosciences, Uppsala University Biomedical Centre, Box 591, 75123, Uppsala, Sweden
| | - Ida Laurén
- Department of Pharmacy, Uppsala University Biomedical Centre, 75123, Uppsala, Sweden
| | - Sara M Mangsbo
- Department of Pharmacy, Uppsala University Biomedical Centre, 75123, Uppsala, Sweden
| | - Martin Lord
- Department of Pharmacy, Uppsala University Biomedical Centre, 75123, Uppsala, Sweden
| | - Ulf Göransson
- Department of Pharmaceutical Biosciences, Uppsala University Biomedical Centre, Box 591, 75123, Uppsala, Sweden
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83
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Nemyatykh OD, Maistrenko MA, Demchenko DD, Narkevich IA, Okovityi SV, Timchenko VN. Principles of Rational COVID-19 Therapy in Pediatrics. J Clin Med 2023; 12:4731. [PMID: 37510846 PMCID: PMC10380754 DOI: 10.3390/jcm12144731] [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: 05/31/2023] [Revised: 07/10/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
The purpose of this review was to conduct a comparative assessment of the concepts of therapy for pediatric patients with COVID-19 in the framework of global clinical practice. A structural analysis of the range of drugs and treatment strategies in the context of etiotropic, pathogenetic, and symptomatic therapy has shown that in the global context and in real clinical practice, the etiotropic-pathogenetic approach based on information about the effectiveness of individual medical technologies prevails today. It has been established that eight international nonproprietary/grouping names are present in international practice as means of etiotropic therapy for pediatric patients with COVID-19, and 18 positions are used for pathogenetic therapy. In terms of frequency of occurrence, the leading positions are occupied by remdesivir and the combination of nirmatrelvir with ritonavir, as well as dexamethasone and tocilizumab. The paper emphasizes the relevance of research in the field of evaluating the effectiveness of individual treatment regimens as well as the analysis of the delayed consequences of pathology suffered in childhood under the conditions of using various approaches to pharmacotherapy.
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Affiliation(s)
- Oksana D. Nemyatykh
- Department of Management and Economics of Pharmacy, Faculty of Pharmacy, Saint-Petersburg State Chemical Pharmaceutical University, Ministry of Health of Russia, Prof. Popova Str., 14 Lit. A, 197376 Saint-Petersburg, Russia
| | - Marina A. Maistrenko
- Department of Management and Economics of Pharmacy, Faculty of Pharmacy, Ryazan State Medical University Named after Academician I.P. Pavlov, Ministry of Health of Russia, Vysokovoltnaya Str., 9, 390026 Ryazan, Russia
| | - Dina D. Demchenko
- Department of Management and Economics of Pharmacy, Faculty of Pharmacy, Saint-Petersburg State Chemical Pharmaceutical University, Ministry of Health of Russia, Prof. Popova Str., 14 Lit. A, 197376 Saint-Petersburg, Russia
| | - Igor A. Narkevich
- Department of Management and Economics of Pharmacy, Faculty of Pharmacy, Saint-Petersburg State Chemical Pharmaceutical University, Ministry of Health of Russia, Prof. Popova Str., 14 Lit. A, 197376 Saint-Petersburg, Russia
| | - Sergey V. Okovityi
- Department of Pharmacology and Clinical Pharmacology, Faculty of Pharmacy, Saint-Petersburg State Chemical Pharmaceutical University, Ministry of Health of Russia, Prof. Popova Str., 14 Lit. A, 197376 Saint-Petersburg, Russia
| | - Vladimir N. Timchenko
- Department of Infectious Diseases in Children Named after Prof. M.G. Danilevich, Faculty of Pediatrics, Saint-Petersburg State Pediatric Medical University, Ministry of Health of Russia, Litovskaya Str., 2, 194100 Saint-Petersburg, Russia
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84
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Devaux CA, Fantini J. ACE2 receptor polymorphism in humans and animals increases the risk of the emergence of SARS-CoV-2 variants during repeated intra- and inter-species host-switching of the virus. Front Microbiol 2023; 14:1199561. [PMID: 37520374 PMCID: PMC10373931 DOI: 10.3389/fmicb.2023.1199561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 06/23/2023] [Indexed: 08/01/2023] Open
Abstract
Like other coronaviruses, SARS-CoV-2 has ability to spread through human-to-human transmission and to circulate from humans to animals and from animals to humans. A high frequency of SARS-CoV-2 mutations has been observed in the viruses isolated from both humans and animals, suggesting a genetic fitness under positive selection in both ecological niches. The most documented positive selection force driving SARS-CoV-2 mutations is the host-specific immune response. However, after electrostatic interactions with lipid rafts, the first contact between the virus and host proteins is the viral spike-cellular receptor binding. Therefore, it is likely that the first level of selection pressure impacting viral fitness relates to the virus's affinity for its receptor, the angiotensin I converting enzyme 2 (ACE2). Although sufficiently conserved in a huge number of species to support binding of the viral spike with enough affinity to initiate fusion, ACE2 is highly polymorphic both among species and within a species. Here, we provide evidence suggesting that when the viral spike-ACE2 receptor interaction is not optimal, due to host-switching, mutations can be selected to improve the affinity of the spike for the ACE2 expressed by the new host. Notably, SARS-CoV-2 is mutation-prone in the spike receptor binding domain (RBD), allowing a better fit for ACE2 orthologs in animals. It is possibly that this may also be true for rare human alleles of ACE2 when the virus is spreading to billions of people. In this study, we present evidence that human subjects expressing the rare E329G allele of ACE2 with higher allele frequencies in European populations exhibit a improved affinity for the SARS-CoV-2 spike N501Y variant of the virus. This may suggest that this viral N501Y variant emerged in the human population after SARS-CoV-2 had infected a human carrying the rare E329G allele of ACE2. In addition, this viral evolution could impact viral replication as well as the ability of the adaptive humoral response to control infection with RBD-specific neutralizing antibodies. In a shifting landscape, this ACE2-driven genetic drift of SARS-CoV-2 which we have named the 'boomerang effect', could complicate the challenge of preventing COVID with a SARS-CoV-2 spike-derived vaccine.
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Affiliation(s)
- Christian A. Devaux
- Laboratory Microbes Evolution Phylogeny and Infection (MEPHI), Aix-Marseille Université, IRD, APHM, MEPHI, IHU–Méditerranée Infection, Marseille, France
- Centre National de la Recherche Scientifique (CNRS-SNC5039), Marseille, France
| | - Jacques Fantini
- INSERM UMR_S1072, Marseille, France, Aix-Marseille Université, Marseille, France
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85
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Sanders S, Jensen Y, Reimer R, Bosse JB. From the beginnings to multidimensional light and electron microscopy of virus morphogenesis. Adv Virus Res 2023; 116:45-88. [PMID: 37524482 DOI: 10.1016/bs.aivir.2023.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Individual functional viral morphogenesis events are often dynamic, short, and infrequent and might be obscured by other pathways and dead-end products. Volumetric live cell imaging has become an essential tool for studying viral morphogenesis events. It allows following entire dynamic processes while providing functional evidence that the imaged process is involved in viral production. Moreover, it allows to capture many individual events and allows quantitative analysis. Finally, the correlation of volumetric live-cell data with volumetric electron microscopy (EM) can provide crucial insights into the ultrastructure and mechanisms of viral morphogenesis events. Here, we provide an overview and discussion of suitable imaging methods for volumetric correlative imaging of viral morphogenesis and frame them in a historical summary of their development.
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Affiliation(s)
- Saskia Sanders
- Department of Virology, Hannover Medical School, Hannover, Germany; Leibniz Institute of Virology (LIV), Hamburg, Germany; Centre for Structural Systems Biology, Hamburg, Germany; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| | - Yannick Jensen
- Department of Virology, Hannover Medical School, Hannover, Germany; Leibniz Institute of Virology (LIV), Hamburg, Germany; Centre for Structural Systems Biology, Hamburg, Germany; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| | | | - Jens B Bosse
- Department of Virology, Hannover Medical School, Hannover, Germany; Leibniz Institute of Virology (LIV), Hamburg, Germany; Centre for Structural Systems Biology, Hamburg, Germany; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany.
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86
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Wang J, Pan YF, Yang LF, Yang WH, Lv K, Luo CM, Wang J, Kuang GP, Wu WC, Gou QY, Xin GY, Li B, Luo HL, Chen S, Shu YL, Guo D, Gao ZH, Liang G, Li J, Chen YQ, Holmes EC, Feng Y, Shi M. Individual bat virome analysis reveals co-infection and spillover among bats and virus zoonotic potential. Nat Commun 2023; 14:4079. [PMID: 37429936 DOI: 10.1038/s41467-023-39835-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 06/26/2023] [Indexed: 07/12/2023] Open
Abstract
Bats are reservoir hosts for many zoonotic viruses. Despite this, relatively little is known about the diversity and abundance of viruses within individual bats, and hence the frequency of virus co-infection and spillover among them. We characterize the mammal-associated viruses in 149 individual bats sampled from Yunnan province, China, using an unbiased meta-transcriptomics approach. This reveals a high frequency of virus co-infection (simultaneous infection of bat individuals by multiple viral species) and spillover among the animals studied, which may in turn facilitate virus recombination and reassortment. Of note, we identify five viral species that are likely to be pathogenic to humans or livestock, based on phylogenetic relatedness to known pathogens or in vitro receptor binding assays. This includes a novel recombinant SARS-like coronavirus that is closely related to both SARS-CoV and SARS-CoV-2. In vitro assays indicate that this recombinant virus can utilize the human ACE2 receptor such that it is likely to be of increased emergence risk. Our study highlights the common occurrence of co-infection and spillover of bat viruses and their implications for virus emergence.
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Affiliation(s)
- Jing Wang
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Yuan-Fei Pan
- Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Li-Fen Yang
- Department of Viral and Rickettsial Disease Control, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute of Endemic Disease Control and Prevention, Dali, Yunnan, China
| | - Wei-Hong Yang
- Department of Viral and Rickettsial Disease Control, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute of Endemic Disease Control and Prevention, Dali, Yunnan, China
| | - Kexin Lv
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Chu-Ming Luo
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Juan Wang
- Department of Viral and Rickettsial Disease Control, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute of Endemic Disease Control and Prevention, Dali, Yunnan, China
| | - Guo-Peng Kuang
- Department of Viral and Rickettsial Disease Control, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute of Endemic Disease Control and Prevention, Dali, Yunnan, China
| | - Wei-Chen Wu
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Qin-Yu Gou
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Gen-Yang Xin
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Bo Li
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, China
| | - Huan-le Luo
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Shoudeng Chen
- Molecular Imaging Center, Central Laboratory, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, Guangdong, China
| | - Yue-Long Shu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Deyin Guo
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou, Guangdong Province, China
| | - Zi-Hou Gao
- Department of Viral and Rickettsial Disease Control, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute of Endemic Disease Control and Prevention, Dali, Yunnan, China
| | - Guodong Liang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jun Li
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - Yao-Qing Chen
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China.
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW, 2006, Australia.
| | - Yun Feng
- Department of Viral and Rickettsial Disease Control, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute of Endemic Disease Control and Prevention, Dali, Yunnan, China.
| | - Mang Shi
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China.
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China.
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87
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Cardoso M, Ragan I, Hartson L, Goodrich RP. Emerging Pathogen Threats in Transfusion Medicine: Improving Safety and Confidence with Pathogen Reduction Technologies. Pathogens 2023; 12:911. [PMID: 37513758 PMCID: PMC10383627 DOI: 10.3390/pathogens12070911] [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: 06/30/2023] [Accepted: 07/02/2023] [Indexed: 07/30/2023] Open
Abstract
Emerging infectious disease threats are becoming more frequent due to various social, political, and geographical pressures, including increased human-animal contact, global trade, transportation, and changing climate conditions. Since blood products for transfusion are derived from donated blood from the general population, emerging agents spread by blood contact or the transfusion of blood products are also a potential risk. Blood transfusions are essential in treating patients with anemia, blood loss, and other medical conditions. However, these lifesaving procedures can contribute to infectious disease transmission, particularly to vulnerable populations. New methods have been implemented on a global basis for the prevention of transfusion transmissions via plasma, platelets, and whole blood products. Implementing proactive pathogen reduction methods may reduce the likelihood of disease transmission via blood transfusions, even for newly emerging agents whose transmissibility and susceptibility are still being evaluated as they emerge. In this review, we consider the Mirasol PRT system for blood safety, which is based on a photochemical method involving riboflavin and UV light. We provide examples of how emerging threats, such as Ebola, SARS-CoV-2, hepatitis E, mpox and other agents, have been evaluated in real time regarding effectiveness of this method in reducing the likelihood of disease transmission via transfusions.
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Affiliation(s)
- Marcia Cardoso
- Terumo BCT, Inc., TERUMO Böood and Cell Technologies, Zaventem, 41 1930 Brussels, Belgium
| | - Izabela Ragan
- Infectious Disease Research Center, Department of Biomedical Science, Colorado State University, Fort Collins, CO 80521, USA
| | - Lindsay Hartson
- Infectious Disease Research Center, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80521, USA
| | - Raymond P Goodrich
- Infectious Disease Research Center, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80521, USA
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88
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Pustake M, Giri P, Ganiyani MA, Mumtaz K, Deshmukh K, Saju M, Nunez JV, Orlova N, Das A. Drawing Parallels between SARS, MERS, and COVID-19: A Comparative Overview of Epidemiology, Pathogenesis, and Pathological Features. Indian J Community Med 2023; 48:518-524. [PMID: 37662119 PMCID: PMC10470569 DOI: 10.4103/ijcm.ijcm_460_22] [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: 05/29/2022] [Accepted: 05/22/2023] [Indexed: 09/05/2023] Open
Abstract
Background Since November 2019, when the novel coronavirus arose in Wuhan City, over 188 million people worldwide have been infected with COVID-19. It is the third coronavirus outbreak in the twenty-first century. Until now, practically all coronavirus epidemics have occurred due to zoonotic spread from an animal or transitional host or through the consumption of their products. Coronaviruses can infect humans and cause severe illness and even death. Material and Methods This review was designed to help us recognize and harmonize the similarities and differences between these three coronaviridae family members. Result Measures aimed at containing the epidemic should be emphasized in this circumstance. Prioritizing and planning these activities require an understanding of the particulars of these three viruses. Given the pandemic's enormous death toll and rapid spread, we should be cognizant of the parallels and differences between these three viruses. Additionally, this pandemic warns us to be cautious against the possibility of a future pandemic. Conclusion We highlight the fundamental characteristics of coronaviruses that are critical for recognizing coronavirus epidemiology, pathogenesis, and pathological features that reveal numerous significant pathological attributes and evolutionary patterns in the viral genome that aid in better understanding and anticipating future epidemics.
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Affiliation(s)
- Manas Pustake
- Department of Internal Medicine, Grant Govt. Medical College and Sir JJ Group of Hospitals, Mumbai, Maharashtra, India
- Harvard Medical School, Harvard University, Boston, MA, USA
| | - Purushottam Giri
- Department of Community Medicine, IIMSR Medical College, Jalna, Maharashtra, India
| | - Mohammad Arfat Ganiyani
- Department of Internal Medicine, Grant Govt. Medical College and Sir JJ Group of Hospitals, Mumbai, Maharashtra, India
| | - Kahkashan Mumtaz
- Department of Pediatrics, Grant Govt. Medical College and Sir JJ Group of Hospitals, Mumbai, Maharashtra, India
| | - Krishna Deshmukh
- Department of Internal Medicine, Grant Govt. Medical College and Sir JJ Group of Hospitals, Mumbai, Maharashtra, India
| | - Michael Saju
- Department of Community Medicine, Grant Govt. Medical College and Sir JJ Group of Hospitals, Mumbai, Maharashtra, India
| | | | | | - Arghadip Das
- Department of Pathology, Nil Ratan Sircar Medical College and Hospital, Kolkata, West Bengal, India
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89
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Slanina H, Madhugiri R, Wenk K, Reinke T, Schultheiß K, Schultheis J, Karl N, Linne U, Ziebuhr J. Conserved Characteristics of NMPylation Activities of Alpha- and Betacoronavirus NiRAN Domains. J Virol 2023; 97:e0046523. [PMID: 37199624 PMCID: PMC10308930 DOI: 10.1128/jvi.00465-23] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 04/28/2023] [Indexed: 05/19/2023] Open
Abstract
Coronavirus genome replication and expression are mediated by the viral replication-transcription complex (RTC) which is assembled from multiple nonstructural proteins (nsp). Among these, nsp12 represents the central functional subunit. It harbors the RNA-directed RNA polymerase (RdRp) domain and contains, at its N terminus, an additional domain called NiRAN which is widely conserved in coronaviruses and other nidoviruses. In this study, we produced bacterially expressed coronavirus nsp12s to investigate and compare NiRAN-mediated NMPylation activities from representative alpha- and betacoronaviruses. We found that the four coronavirus NiRAN domains characterized to date have a number of conserved properties, including (i) robust nsp9-specific NMPylation activities that appear to operate largely independently of the C-terminal RdRp domain, (ii) nucleotide substrate preference for UTP followed by ATP and other nucleotides, (iii) dependence on divalent metal ions, with Mn2+ being preferred over Mg2+, and (iv) a key role of N-terminal residues (particularly Asn2) of nsp9 for efficient formation of a covalent phosphoramidate bond between NMP and the N-terminal amino group of nsp9. In this context, a mutational analysis confirmed the conservation and critical role of Asn2 across different subfamilies of the family Coronaviridae, as shown by studies using chimeric coronavirus nsp9 variants in which six N-terminal residues were replaced with those from other corona-, pito- and letovirus nsp9 homologs. The combined data of this and previous studies reveal a remarkable degree of conservation among coronavirus NiRAN-mediated NMPylation activities, supporting a key role of this enzymatic activity in viral RNA synthesis and processing. IMPORTANCE There is strong evidence that coronaviruses and other large nidoviruses evolved a number of unique enzymatic activities, including an additional RdRp-associated NiRAN domain, that are conserved in nidoviruses but not in most other RNA viruses. Previous studies of the NiRAN domain mainly focused on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and suggested different functions for this domain, such as NMPylation/RNAylation of nsp9, RNA guanylyltransferase activities involved in canonical and/or unconventional RNA capping pathways, and other functions. To help resolve partly conflicting information on substrate specificities and metal ion requirements reported previously for the SARS-CoV-2 NiRAN NMPylation activity, we extended these earlier studies by characterizing representative alpha- and betacoronavirus NiRAN domains. The study revealed that key features of NiRAN-mediated NMPylation activities, such as protein and nucleotide specificity and metal ion requirements, are very well conserved among genetically divergent coronaviruses, suggesting potential avenues for future antiviral drug development targeting this essential viral enzyme.
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Affiliation(s)
- Heiko Slanina
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany
| | | | - Kai Wenk
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany
| | - Tess Reinke
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany
| | - Karin Schultheiß
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany
| | - Julia Schultheis
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany
| | - Nadja Karl
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany
| | - Uwe Linne
- Mass Spectrometry Facility, Department of Chemistry, Philipps University, Marburg, Germany
| | - John Ziebuhr
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany
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Fukushima A, Manabe Y, Kosaka Y, Akagi S. Sustained exercise load by young adult females while wearing surgical mask raises core body temperature measured with zero-heat-flux thermometer. INTERNATIONAL JOURNAL OF BIOMETEOROLOGY 2023:10.1007/s00484-023-02501-8. [PMID: 37365382 DOI: 10.1007/s00484-023-02501-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 05/25/2023] [Accepted: 05/26/2023] [Indexed: 06/28/2023]
Abstract
When a pandemic such as that caused by the novel coronavirus disease termed COVID-19 emerges, it is recommended to wear a mask when in public situations, with information regarding the impact on thermoregulation essential, especially during exercise or hard physical labor. The present study investigated changes in core body temperature (CBT) while wearing a surgical mask (SM) during exercise (TCBT) using a non-invasive zero-heat-flux (ZHF) thermometer. Nine young adult females performed ergometer exercise for 30 min at 60 W with (mask group) and without (control) a SM under a non-hot condition, shown by wet bulb globe temperature (WBGT) findings. TCBT, mean skin temperature (TMST), heart rate (HR), and humidity in the perioral region of the face (%RH) were determined. Each of those markers showed increased values during exercise, with the increases in TCBT, HR, and %RH, but not TMST, during exercise found to be significantly greater in the mask group. HR reserve (%HRR), derived as load intensity during exercise, was also significantly higher in the mask group. Each subject completed all of the experimental protocols without noting pain or discomfort. These results suggest that wearing a SM while performing mild exercise contributes to increased TCBT associated with increased exercise intensity, expressed as %HRR in a non-heated condition. Furthermore, the ZHF thermometer was shown to be safe and is considered useful for conducting such studies. Additional examinations will be necessary to examine gender and age group differences, as well as the use of different exercise methods and intensity and ambient conditions.
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Affiliation(s)
- Ayako Fukushima
- Graduate School of Contemporary Science, Chugoku Gakuen University, 83 Niwase Kita-Ku, Okayama, 701-0197, Japan
| | - Yoshie Manabe
- Graduate School of Contemporary Science, Chugoku Gakuen University, 83 Niwase Kita-Ku, Okayama, 701-0197, Japan
- Department of Human Nutrition, Faculty of Contemporary Science, Chugoku Gakuen University, Okayama, Japan
| | - Yuri Kosaka
- Department of Human Nutrition, Faculty of Contemporary Science, Chugoku Gakuen University, Okayama, Japan
| | - Shuji Akagi
- Graduate School of Contemporary Science, Chugoku Gakuen University, 83 Niwase Kita-Ku, Okayama, 701-0197, Japan.
- Department of Human Nutrition, Faculty of Contemporary Science, Chugoku Gakuen University, Okayama, Japan.
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91
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Ha CM, Nam Y, Lee S, Park SJ, Lee SH, Kim ES. Impact on Spine Surgery during the First Two Years of COVID-19 Pandemic: A Nationwide Study in South Korea. J Clin Med 2023; 12:4155. [PMID: 37373848 DOI: 10.3390/jcm12124155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/07/2023] [Accepted: 06/17/2023] [Indexed: 06/29/2023] Open
Abstract
Since December 2019, the novel coronavirus (COVID-19) has infected people worldwide. Owing to its rapid spread, elective surgeries, including spine surgery, have been re-scheduled. We analyzed nationwide data to investigate changes in the volume of spine surgery during the first two years of the pandemic. Nationwide data from January 2016 to December 2021 were obtained. We compared the total number of patients who underwent spine surgery and related medical expenses before and during the COVID-19 pandemic. In February and September, the number of patients was significantly smaller compared to January and August, respectively. Despite the pandemic, the proportion of patients undergoing spine surgery for degenerative diseases in 2021 was the highest. In contrast, the proportions of patients undergoing spine surgery for tumors showed a continuous decrease from 2019 to 2021. Although the number of spine surgeries performed at tertiary hospitals was lowest in 2020, it was not significantly smaller than that in 2019.The number of patients who underwent spine surgery in March 2020, during the first outbreak, decreased compared to the previous month, which differed from the trend observed in the pre-COVID-19 period. However, as the pandemic continues, the impact of COVID-19 on spine surgery has become less evident.
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Affiliation(s)
- Chang-Min Ha
- Department of Neurosurgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81, Irwon-ro, Gangnam-gu, Seoul 06351, Republic of Korea
| | - Yunjin Nam
- Department of Orthopedic Surgery, Korea University Guro Hospital, Korea University College of Medicine, 148, Gurodong-ro, Guro-gu, Seoul 08308, Republic of Korea
| | - Sungjoon Lee
- Department of Neurosurgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81, Irwon-ro, Gangnam-gu, Seoul 06351, Republic of Korea
| | - Se-Jun Park
- Department of Orthopedic Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81, Irwon-ro, Gangnam-gu, Seoul 06351, Republic of Korea
| | - Sun-Ho Lee
- Department of Neurosurgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81, Irwon-ro, Gangnam-gu, Seoul 06351, Republic of Korea
| | - Eun-Sang Kim
- Department of Neurosurgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81, Irwon-ro, Gangnam-gu, Seoul 06351, Republic of Korea
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Bukur T, Riesgo-Ferreiro P, Sorn P, Gudimella R, Hausmann J, Rösler T, Löwer M, Schrörs B, Sahin U. CoVigator-A Knowledge Base for Navigating SARS-CoV-2 Genomic Variants. Viruses 2023; 15:1391. [PMID: 37376690 DOI: 10.3390/v15061391] [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: 05/30/2023] [Revised: 06/15/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
BACKGROUND The outbreak of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) resulted in the global COVID-19 pandemic. The urgency for an effective SARS-CoV-2 vaccine has led to the development of the first series of vaccines at unprecedented speed. The discovery of SARS-CoV-2 spike-glycoprotein mutants, however, and consequentially the potential to escape vaccine-induced protection and increased infectivity, demonstrates the persisting importance of monitoring SARS-CoV-2 mutations to enable early detection and tracking of genomic variants of concern. RESULTS We developed the CoVigator tool with three components: (1) a knowledge base that collects new SARS-CoV-2 genomic data, processes it and stores its results; (2) a comprehensive variant calling pipeline; (3) an interactive dashboard highlighting the most relevant findings. The knowledge base routinely downloads and processes virus genome assemblies or raw sequencing data from the COVID-19 Data Portal (C19DP) and the European Nucleotide Archive (ENA), respectively. The results of variant calling are visualized through the dashboard in the form of tables and customizable graphs, making it a versatile tool for tracking SARS-CoV-2 variants. We put a special emphasis on the identification of intrahost mutations and make available to the community what is, to the best of our knowledge, the largest dataset on SARS-CoV-2 intrahost mutations. In the spirit of open data, all CoVigator results are available for download. The CoVigator dashboard is accessible via covigator.tron-mainz.de. CONCLUSIONS With increasing demand worldwide in genome surveillance for tracking the spread of SARS-CoV-2, CoVigator will be a valuable resource of an up-to-date list of mutations, which can be incorporated into global efforts.
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Affiliation(s)
- Thomas Bukur
- TRON-Translational Oncology at the Medical Center of the Johannes Gutenberg-University Mainz Gemeinnützige GmbH, 55131 Mainz, Germany
| | - Pablo Riesgo-Ferreiro
- TRON-Translational Oncology at the Medical Center of the Johannes Gutenberg-University Mainz Gemeinnützige GmbH, 55131 Mainz, Germany
| | - Patrick Sorn
- TRON-Translational Oncology at the Medical Center of the Johannes Gutenberg-University Mainz Gemeinnützige GmbH, 55131 Mainz, Germany
| | - Ranganath Gudimella
- TRON-Translational Oncology at the Medical Center of the Johannes Gutenberg-University Mainz Gemeinnützige GmbH, 55131 Mainz, Germany
| | - Johannes Hausmann
- TRON-Translational Oncology at the Medical Center of the Johannes Gutenberg-University Mainz Gemeinnützige GmbH, 55131 Mainz, Germany
| | - Thomas Rösler
- TRON-Translational Oncology at the Medical Center of the Johannes Gutenberg-University Mainz Gemeinnützige GmbH, 55131 Mainz, Germany
| | - Martin Löwer
- TRON-Translational Oncology at the Medical Center of the Johannes Gutenberg-University Mainz Gemeinnützige GmbH, 55131 Mainz, Germany
| | - Barbara Schrörs
- TRON-Translational Oncology at the Medical Center of the Johannes Gutenberg-University Mainz Gemeinnützige GmbH, 55131 Mainz, Germany
| | - Ugur Sahin
- BioNTech SE, 55131 Mainz, Germany
- Research Center for Immunotherapy (FZI), University Medical Center of the Johannes Gutenberg University Mainz, 55099 Mainz, Germany
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93
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Wells HL, Bonavita CM, Navarrete-Macias I, Vilchez B, Rasmussen AL, Anthony SJ. The coronavirus recombination pathway. Cell Host Microbe 2023; 31:874-889. [PMID: 37321171 PMCID: PMC10265781 DOI: 10.1016/j.chom.2023.05.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/02/2023] [Accepted: 05/04/2023] [Indexed: 06/17/2023]
Abstract
Recombination is thought to be a mechanism that facilitates cross-species transmission in coronaviruses, thus acting as a driver of coronavirus spillover and emergence. Despite its significance, the mechanism of recombination is poorly understood, limiting our potential to estimate the risk of novel recombinant coronaviruses emerging in the future. As a tool for understanding recombination, here, we outline a framework of the recombination pathway for coronaviruses. We review existing literature on coronavirus recombination, including comparisons of naturally observed recombinant genomes as well as in vitro experiments, and place the findings into the recombination pathway framework. We highlight gaps in our understanding of coronavirus recombination illustrated by the framework and outline how further experimental research is critical for disentangling the molecular mechanism of recombination from external environmental pressures. Finally, we describe how an increased understanding of the mechanism of recombination can inform pandemic predictive intelligence, with a retrospective emphasis on SARS-CoV-2.
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Affiliation(s)
- Heather L Wells
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY, USA; Department of Pathology, Microbiology, and Immunology, University of California Davis School of Veterinary Medicine, Davis, CA, USA.
| | - Cassandra M Bonavita
- Department of Pathology, Microbiology, and Immunology, University of California Davis School of Veterinary Medicine, Davis, CA, USA
| | - Isamara Navarrete-Macias
- Department of Pathology, Microbiology, and Immunology, University of California Davis School of Veterinary Medicine, Davis, CA, USA
| | - Blake Vilchez
- Department of Pathology, Microbiology, and Immunology, University of California Davis School of Veterinary Medicine, Davis, CA, USA
| | - Angela L Rasmussen
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada
| | - Simon J Anthony
- Department of Pathology, Microbiology, and Immunology, University of California Davis School of Veterinary Medicine, Davis, CA, USA.
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Samanta PN, Majumdar D, Leszczynski J. Elucidating Atomistic Insight into the Dynamical Responses of the SARS-CoV-2 Main Protease for the Binding of Remdesivir Analogues: Leveraging Molecular Mechanics To Decode the Inhibition Mechanism. J Chem Inf Model 2023; 63:3404-3422. [PMID: 37216421 DOI: 10.1021/acs.jcim.3c00105] [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: 05/24/2023]
Abstract
To combat mischievous coronavirus disease followed by continuous upgrading of therapeutic strategy against the antibody-resistant variants, the molecular mechanistic understanding of protein-drug interactions is a prerequisite in the context of target-specific rational drug development. Herein, we attempt to decipher the structural basis for the inhibition of SARS-CoV-2 main protease (Mpro) through the elemental analysis of potential energy landscape and the associated thermodynamic and kinetic properties of the enzyme-inhibitor complexes using automated molecular docking calculations in conjunction with classical force field-based molecular dynamics (MD) simulations. The crux of the scalable all-atom MD simulations consummated in explicit solvent media is to capture the structural plasticity of the viral enzyme due to the binding of remdesivir analogues and ascertain the subtle interplay of noncovalent interactions in stabilizing specific conformational states of the receptor that controls the biomolecular processes related to the ligand binding and dissociation kinetics. To unravel the critical role of modulation of the ligand scaffold, we place further emphasis on the estimation of binding free energy as well as the energy decomposition analysis by employing the generalized Born and Poisson-Boltzmann models. The estimated binding affinities are found to vary between -25.5 and -61.2 kcal/mol. Furthermore, the augmentation of inhibitory efficacy of the remdesivir analogue crucially stems from the van der Waals interactions with the active site residues of the protease. The polar solvation energy contributes unfavorably to the binding free energy and annihilates the contribution of electrostatic interactions as derived from the molecular mechanical energies.
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Affiliation(s)
- Pabitra Narayan Samanta
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric Sciences, Jackson State University, Jackson, Mississippi 39217, United States
| | - Devashis Majumdar
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric Sciences, Jackson State University, Jackson, Mississippi 39217, United States
| | - Jerzy Leszczynski
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric Sciences, Jackson State University, Jackson, Mississippi 39217, United States
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95
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Perdiguero B, Pérez P, Marcos-Villar L, Albericio G, Astorgano D, Álvarez E, Sin L, Elena Gómez C, García-Arriaza J, Esteban M. Highly attenuated poxvirus-based vaccines against emerging viral diseases. J Mol Biol 2023:168173. [PMID: 37301278 DOI: 10.1016/j.jmb.2023.168173] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 06/04/2023] [Accepted: 06/05/2023] [Indexed: 06/12/2023]
Abstract
Although one member of the poxvirus family, variola virus, has caused one of the most devastating human infections worldwide, smallpox, the knowledge gained over the last 30 years on the molecular, virological and immunological mechanisms of these viruses has allowed the use of members of this family as vectors for the generation of recombinant vaccines against numerous pathogens. In this review, we cover different aspects of the history and biology of poxviruses with emphasis on their application as vaccines, from first- to fourth-generation, against smallpox, monkeypox, emerging viral diseases highlighted by the World Health Organization (COVID-19, Crimean-Congo haemorrhagic fever, Ebola and Marburg virus diseases, Lassa fever, Middle East respiratory syndrome and severe acute respiratory syndrome, Nipah and other henipaviral diseases, Rift Valley fever and Zika), as well as against one of the most concerning prevalent virus, the Human Immunodeficiency Virus, the causative agent of AcquiredImmunodeficiency Syndrome. We discuss the implications in human health of the 2022 monkeypox epidemic affecting many countries, and the rapid prophylactic and therapeutic measures adopted to control virus dissemination within the human population. We also describe the preclinical and clinical evaluation of the Modified Vaccinia virus Ankara and New York vaccinia virus poxviral strains expressing heterologous antigens from the viral diseases listed above. Finally, we report different approaches to improve the immunogenicity and efficacy of poxvirus-based vaccine candidates, such as deletion of immunomodulatory genes, insertion of host-range genes and enhanced transcription of foreign genes through modified viral promoters. Some future prospects are also highlighted.
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Affiliation(s)
- Beatriz Perdiguero
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain.
| | - Patricia Pérez
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain.
| | - Laura Marcos-Villar
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Guillermo Albericio
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - David Astorgano
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Enrique Álvarez
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Laura Sin
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Carmen Elena Gómez
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Juan García-Arriaza
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Mariano Esteban
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain.
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ul Haq Z, Mehmood U, Tariq S, Hanif A, Nawaz H. Role of meteorological parameters with the spread of Covid-19 in Pakistan: application of autoregressive distributed lag approach. INTERNATIONAL JOURNAL OF ENVIRONMENTAL SCIENCE AND TECHNOLOGY : IJEST 2023:1-22. [PMID: 37360555 PMCID: PMC10249560 DOI: 10.1007/s13762-023-04997-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 12/04/2022] [Accepted: 05/08/2023] [Indexed: 06/28/2023]
Abstract
This research focuses on the impacts of different meteorological parameters (temperature, humidity, rainfall, and evapotranspiration) on the transmission of Covid-19 in the administrative regions and provinces of Pakistan, i.e., Azad Jammu and Kashmir, Gilgit Baltistan, Khyber Pakhtunkhwa, Islamabad, Punjab, Sindh, and Balochistan from June 10, 2020, to August 31, 2021. This study analyzes the relation between Covid-19-confirmed cases and the meteorological parameters with the help of the autoregressive distributed lag model. In this research, additional tools (t-statistics, f-statistics, and time series analysis) are used for the motive of examining the linear relationship, the productivity of the model, and for the significant association between dependent and independent variables, lnccc and lnevp, lnhum, lnrain, lntemp, respectively. Values of t-statistics and f-statistics reveal that variables have a connection and individual significance for the model exist. Time series display that the Covid-19 spread increased from June 10, 2020, to August 31, 2021, in Pakistan. Temperature positively influenced the Covid-19-confirmed cases in all provinces of Pakistan in the long run. Evapotranspiration and rainfall influenced positively, while specific humidity influenced negatively on the confirmed Covid-19 cases in Azad Jammu Kashmir, Khyber Pakhtunkhwa, and Punjab. Specific humidity had a positive impact, while evapotranspiration and rainfall had the negative impact on the Covid-19-confirmed cases in Sindh and Balochistan. Evapotranspiration and specific humidity influenced positively, while rainfall influenced the Covid-19-confirmed cases negatively in Gilgit Baltistan. Evapotranspiration influenced positively, while specific humidity and rainfall influenced negatively on the Covid-19-confirmed cases in Islamabad. Supplementary Information The online version contains supplementary material available at 10.1007/s13762-023-04997-4.
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Affiliation(s)
- Z. ul Haq
- Remote Sensing, GIS and Climatic Research Lab, National Center of GIS and Space Applications, Centre for Remote Sensing, University of the Punjab, New-Campus, Lahore, Pakistan
| | - U. Mehmood
- Remote Sensing, GIS and Climatic Research Lab, National Center of GIS and Space Applications, Centre for Remote Sensing, University of the Punjab, New-Campus, Lahore, Pakistan
- Department of political science, University of management and technology, Lahore, Pakistan
| | - S. Tariq
- Remote Sensing, GIS and Climatic Research Lab, National Center of GIS and Space Applications, Centre for Remote Sensing, University of the Punjab, New-Campus, Lahore, Pakistan
- Remote Sensing, GIS and Climatic Research Lab, National Center of GIS and Space Applications, Department of Space Science, University of the Punjab, New-Campus, Lahore, Pakistan
| | - A. Hanif
- Remote Sensing, GIS and Climatic Research Lab, National Center of GIS and Space Applications, Department of Space Science, University of the Punjab, New-Campus, Lahore, Pakistan
| | - H. Nawaz
- Remote Sensing, GIS and Climatic Research Lab, National Center of GIS and Space Applications, Centre for Remote Sensing, University of the Punjab, New-Campus, Lahore, Pakistan
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97
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Gullberg RC, Frydman J. Novel Mode of nanoLuciferase Packaging in SARS-CoV-2 Virions and VLPs Provides Versatile Reporters for Virus Production. Viruses 2023; 15:1335. [PMID: 37376634 DOI: 10.3390/v15061335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 05/31/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023] Open
Abstract
SARS-CoV-2 is a positive-strand RNA virus in the Coronaviridae family that is responsible for morbidity and mortality worldwide. To better understand the molecular pathways leading to SARS-CoV-2 virus assembly, we examined a virus-like particle (VLP) system co-expressing all structural proteins together with an mRNA reporter encoding nanoLuciferase (herein nLuc). Surprisingly, the 19 kDa nLuc protein itself was encapsidated into VLPs, providing a better reporter than nLuc mRNA itself. Strikingly, infecting nLuc-expressing cells with the SARS-CoV-2, NL63 or OC43 coronaviruses yielded virions containing packaged nLuc that served to report viral production. In contrast, infection with the flaviviruses, dengue or Zika, did not lead to nLuc packaging and secretion. A panel of reporter protein variants revealed that the packaging is size-limited and requires cytoplasmic expression, indicating that the large virion of coronaviruses can encaspidate a small cytoplasmic reporter protein. Our findings open the way for powerful new approaches to measure coronavirus particle production, egress and viral entry mechanisms.
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Affiliation(s)
| | - Judith Frydman
- Department of Biology, Stanford University, Stanford, CA 94305, USA
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98
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Kelch MA, Vera-Guapi A, Beder T, Oswald M, Hiemisch A, Beil N, Wajda P, Ciesek S, Erfle H, Toptan T, Koenig R. Machine learning on large scale perturbation screens for SARS-CoV-2 host factors identifies β-catenin/CBP inhibitor PRI-724 as a potent antiviral. Front Microbiol 2023; 14:1193320. [PMID: 37342561 PMCID: PMC10277617 DOI: 10.3389/fmicb.2023.1193320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 05/16/2023] [Indexed: 06/23/2023] Open
Abstract
Expanding antiviral treatment options against SARS-CoV-2 remains crucial as the virus evolves under selection pressure which already led to the emergence of several drug resistant strains. Broad spectrum host-directed antivirals (HDA) are promising therapeutic options, however the robust identification of relevant host factors by CRISPR/Cas9 or RNA interference screens remains challenging due to low consistency in the resulting hits. To address this issue, we employed machine learning, based on experimental data from several knockout screens and a drug screen. We trained classifiers using genes essential for virus life cycle obtained from the knockout screens. The machines based their predictions on features describing cellular localization, protein domains, annotated gene sets from Gene Ontology, gene and protein sequences, and experimental data from proteomics, phospho-proteomics, protein interaction and transcriptomic profiles of SARS-CoV-2 infected cells. The models reached a remarkable performance suggesting patterns of intrinsic data consistency. The predicted HDF were enriched in sets of genes particularly encoding development, morphogenesis, and neural processes. Focusing on development and morphogenesis-associated gene sets, we found β-catenin to be central and selected PRI-724, a canonical β-catenin/CBP disruptor, as a potential HDA. PRI-724 limited infection with SARS-CoV-2 variants, SARS-CoV-1, MERS-CoV and IAV in different cell line models. We detected a concentration-dependent reduction in cytopathic effects, viral RNA replication, and infectious virus production in SARS-CoV-2 and SARS-CoV-1-infected cells. Independent of virus infection, PRI-724 treatment caused cell cycle deregulation which substantiates its potential as a broad spectrum antiviral. Our proposed machine learning concept supports focusing and accelerating the discovery of host dependency factors and identification of potential host-directed antivirals.
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Affiliation(s)
- Maximilian A. Kelch
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt, Germany
| | | | - Thomas Beder
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Marcus Oswald
- Institute for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany
| | - Alicia Hiemisch
- Institute for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany
| | - Nina Beil
- Advanced Biological Screening Facility (ABSF), High-Content Analysis of the Cell (HiCell), BioQuant, Heidelberg University, Heidelberg, Germany
| | - Piotr Wajda
- Advanced Biological Screening Facility (ABSF), High-Content Analysis of the Cell (HiCell), BioQuant, Heidelberg University, Heidelberg, Germany
| | - Sandra Ciesek
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt, Germany
- German Centre for Infection Research (DZIF), External Partner Site Frankfurt, Frankfurt, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Frankfurt, Germany
| | - Holger Erfle
- Advanced Biological Screening Facility (ABSF), High-Content Analysis of the Cell (HiCell), BioQuant, Heidelberg University, Heidelberg, Germany
| | - Tuna Toptan
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt, Germany
| | - Rainer Koenig
- Institute for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany
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99
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Tran HD, Hung TT, Thuy Phuong TH, Tam LT, Tran HG, Le PH. Clinical Features and Treatment Outcomes of COVID-19 Admissions in the Can Tho City Hospital of Tuberculosis and Respiratory Diseases, Vietnam: A Hospital-Based Observational Study. Healthcare (Basel) 2023; 11:healthcare11111632. [PMID: 37297772 DOI: 10.3390/healthcare11111632] [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: 02/21/2023] [Revised: 05/29/2023] [Accepted: 05/30/2023] [Indexed: 06/12/2023] Open
Abstract
BACKGROUND Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, is among the top global health crises. As confirmed by the Vietnam Ministry of Health on 25th January 2023, Vietnam had a cumulative total of more than 11.52 million COVID-19 patients, including 10.61 million recoveries and 43,186 deaths. OBJECTIVES This study aimed to describe the clinical and subclinical characteristics, treatment progress, and outcomes of 310 cases of SARS-CoV-2 infection. METHODS A total of 310 patients with medical records of SARS-CoV-2 were admitted to Can Tho City Hospital of Tuberculosis and Lung Diseases, Can Tho city, Vietnam, between July 2021 and December 2021. Demographic and clinical data, including laboratory examinations, of all the patients were collected and analyzed. RESULTS The median duration of hospital stay was 16.4 ± 5.3 days. There were 243 (78.4%) patients with clinical symptoms of COVID-19 and 67 (21.6%) patients without clinical symptoms. The common symptoms included cough (71.6% of 310 patients), fever (35.4%), shortness of breath (22.6%), sore throat (21.4%), loss of smell/taste (15.6%), and diarrhea (14.4%). Regarding treatment outcomes, 92.3% of the patients were discharged from the hospital, 1.9% of the patients suffered a more severe illness and were transferred to a higher-level hospital, and 5.8% of the patients died. The RT-PCR results were negative in 55.2% of the patients, and 37.1% of the patients had positive RT-PCR results with Ct values of >30 on the discharge/transfer day. Multivariate logistic regression analyses showed that comorbidity and decreased blood pH were statistically significantly related to the treatment outcomes of the patients with COVID-19 (p < 0.05). CONCLUSIONS This study provides useful information (i.e., the clinical characteristics and treatment outcomes) on the COVID-19 pandemic in Vietnam during its biggest outbreak; the information may be used for reference and for making improvements in the handling of future health crises.
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Affiliation(s)
- Hung Do Tran
- Faculty of Nursing and Medical Technology, Can Tho University of Medicine and Pharmacy, 179 Nguyen Van Cu Street, Can Tho City 94000, Vietnam
| | - Tran Thanh Hung
- Faculty of Medicine, Can Tho University of Medicine and Pharmacy, 179 Nguyen Van Cu Street, Can Tho City 94000, Vietnam
| | - Tran Hoang Thuy Phuong
- Can Tho City Hospital of Tuberculosis and Respiratory Diseases, Binh Hoa A Quarter, Phuoc Thoi Ward, O Mon District, Can Tho City 94000, Vietnam
| | - Le Thanh Tam
- Can Tho University of Medicine and Pharmacy Hospital, 179 Nguyen Van Cu Street, Can Tho City 94000, Vietnam
| | - Hung Gia Tran
- Faculty of Medicine, Can Tho University of Medicine and Pharmacy, 179 Nguyen Van Cu Street, Can Tho City 94000, Vietnam
| | - Phuoc Huu Le
- Faculty of Basic Sciences, Can Tho University of Medicine and Pharmacy, 179 Nguyen Van Cu Street, Can Tho City 94000, Vietnam
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100
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Salehi Z, Motlagh Ghoochani BFN, Hasani Nourian Y, Jamalkandi SA, Ghanei M. The controversial effect of smoking and nicotine in SARS-CoV-2 infection. ALLERGY, ASTHMA, AND CLINICAL IMMUNOLOGY : OFFICIAL JOURNAL OF THE CANADIAN SOCIETY OF ALLERGY AND CLINICAL IMMUNOLOGY 2023; 19:49. [PMID: 37264452 DOI: 10.1186/s13223-023-00797-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 04/18/2023] [Indexed: 06/03/2023]
Abstract
The effects of nicotine and cigarette smoke in many diseases, notably COVID-19 infection, are being debated more frequently. The current basic data for COVID-19 is increasing and indicating the higher risk of COVID-19 infections in smokers due to the overexpression of corresponding host receptors to viral entry. However, current multi-national epidemiological reports indicate a lower incidence of COVID-19 disease in smokers. Current data indicates that smokers are more susceptible to some diseases and more protective of some other. Interestingly, nicotine is also reported to play a dual role, being both inflammatory and anti-inflammatory. In the present study, we tried to investigate the effect of pure nicotine on various cells involved in COVID-19 infection. We followed an organ-based systematic approach to decipher the effect of nicotine in damaged organs corresponding to COVID-19 pathogenesis (12 related diseases). Considering that the effects of nicotine and cigarette smoke are different from each other, it is necessary to be careful in generalizing the effects of nicotine and cigarette to each other in the conducted researches. The generalization and the undifferentiation of nicotine from smoke is a significant bias. Moreover, different doses of nicotine stimulate different effects (dose-dependent response). In addition to further assessing the role of nicotine in COVID-19 infection and any other cases, a clever assessment of underlying diseases should also be considered to achieve a guideline for health providers and a personalized approach to treatment.
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Affiliation(s)
- Zahra Salehi
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | | | - Yazdan Hasani Nourian
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Sadegh Azimzadeh Jamalkandi
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran.
| | - Mostafa Ghanei
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran.
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