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Jiang Y, Cheng X, Gao M, Yu Y, Dou X, Shen H, Tang M, Zhou S, Peng D. Two mutations on S2 subunit were critical for Vero cell tropism expansion of infectious bronchitis virus HV80. Vet Microbiol 2024; 294:110134. [PMID: 38820725 DOI: 10.1016/j.vetmic.2024.110134] [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: 03/05/2024] [Revised: 05/23/2024] [Accepted: 05/27/2024] [Indexed: 06/02/2024]
Abstract
Infectious bronchitis virus (IBV) restricts cell tropism. Except for the Beaudette strain, other IBVs cannot infect mammalian cell lines. The limited cell tropism of other IBVs has hindered IBV vaccine development and research on the mechanisms of IBV infection. A novel Vero cell-adapted strain, HV80, has been previously reported. In this study, we constructed recombinants expressing the chimeric S glycoprotein, S1 or S2 subunit of strain H120 and demonstrated that mutations on S2 subunit are associated with the strain HV80 Vero cell adaptation. R687P or P687R substitution recombinants were constructed with the genome backbone of strains HV80 or H120. We found that the RRRR690/S motif at the S2' cleavage site is crucial to the Vero cell adaptation of strain HV80. Another six amino acid substitutions in the S2 subunit of the recombinants showed that the Q855H mutation induced syncytium formation. A transient transfection assay demonstrated the S glycoprotein with the PRRR690/S motif at the S2' cleavage site induced low-level cell-cell fusion, while H855Q substitution hindered cell-cell fusion and blocked cleavage event with S20 product. This study provides a basis for the construction of IBV recombinants capable of replicating in Vero cells, thus contributing to the advancement in the development of genetically engineered cell-based IBV vaccines.
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Affiliation(s)
- Yi Jiang
- College of Veterinary Medicine, Yangzhou University, 225009, China; Jiangsu Institute of Poultry Sciences, Yangzhou 225125, China
| | - Xu Cheng
- Jiangsu Institute of Poultry Sciences, Yangzhou 225125, China
| | - Mingyan Gao
- Jiangsu Institute of Poultry Sciences, Yangzhou 225125, China
| | - Yan Yu
- Jiangsu Institute of Poultry Sciences, Yangzhou 225125, China
| | - Xinhong Dou
- Jiangsu Institute of Poultry Sciences, Yangzhou 225125, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Haiyu Shen
- Jiangsu Institute of Poultry Sciences, Yangzhou 225125, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Mengjun Tang
- Jiangsu Institute of Poultry Sciences, Yangzhou 225125, China
| | - Sheng Zhou
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266109, China.
| | - Daxin Peng
- College of Veterinary Medicine, Yangzhou University, 225009, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China.
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2
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Aleem MT, Munir F, Shakoor A, Gao F. mRNA vaccines against infectious diseases and future direction. Int Immunopharmacol 2024; 135:112320. [PMID: 38788451 DOI: 10.1016/j.intimp.2024.112320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 04/28/2024] [Accepted: 05/19/2024] [Indexed: 05/26/2024]
Abstract
Vaccines are used for the control of infectious diseases of animals. Over other types of vaccinations like live attenuated or killed vaccines, mRNA-based vaccines have significant advantages. As only a small portion of the pathogen's genetic material is employed and the dose rate of mRNA-based vaccines is low, there is the least possibility that the pathogen will reverse itself. A carrier or vehicle that shields mRNA-based vaccines from the host's cellular RNases is necessary for their delivery. mRNA vaccines have been shown to be effective and to induce both a cell-mediated immune response and a humoral immune response in clinical trials against various infectious diseases (viral and parasitic) affecting the animals, including rabies, foot and mouth disease, toxoplasmosis, Zikavirus, leishmaniasis, and COVID-19. The current review aims to highlight the use of mRNA-based vaccines both in viral and parasitic diseases of animals.
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Affiliation(s)
- Muhammad Tahir Aleem
- Department of Pharmacology, Shantou University Medical College, Shantou 515041, China; Center for Gene Regulation in Health and Disease, Department of Biological, Geological, and Environmental Sciences, College of Sciences and Health Professions, Clevaland State University, Clevaland, OH 44115, USA.
| | - Furqan Munir
- Department of Parasitology, Faculty of Veterinary Science, University of Agriculture, Faisalabad 38040, Pakistan
| | - Amna Shakoor
- Department of Anatomy, Faculty of Veterinary Science, University of Agriculture, Faisalabad 38040, Pakistan
| | - Fenfei Gao
- Department of Pharmacology, Shantou University Medical College, Shantou 515041, China.
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Wu G, Li Q, Dai J, Mao G, Ma Y. Design and Application of Biosafe Coronavirus Engineering Systems without Virulence. Viruses 2024; 16:659. [PMID: 38793541 PMCID: PMC11126016 DOI: 10.3390/v16050659] [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: 03/29/2024] [Revised: 04/15/2024] [Accepted: 04/18/2024] [Indexed: 05/26/2024] Open
Abstract
In the last twenty years, three deadly zoonotic coronaviruses (CoVs)-namely, severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and SARS-CoV-2-have emerged. They are considered highly pathogenic for humans, particularly SARS-CoV-2, which caused the 2019 CoV disease pandemic (COVID-19), endangering the lives and health of people globally and causing unpredictable economic losses. Experiments on wild-type viruses require biosafety level 3 or 4 laboratories (BSL-3 or BSL-4), which significantly hinders basic virological research. Therefore, the development of various biosafe CoV systems without virulence is urgently needed to meet the requirements of different research fields, such as antiviral and vaccine evaluation. This review aimed to comprehensively summarize the biosafety of CoV engineering systems. These systems combine virological foundations with synthetic genomics techniques, enabling the development of efficient tools for attenuated or non-virulent vaccines, the screening of antiviral drugs, and the investigation of the pathogenic mechanisms of novel microorganisms.
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Affiliation(s)
- Guoqiang Wu
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; (G.W.); (Q.L.); (J.D.)
- School of Pharmacy, Faculty of Medicine, Macau University of Science and Technology, Macau SAR 999078, China
| | - Qiaoyu Li
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; (G.W.); (Q.L.); (J.D.)
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Junbiao Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; (G.W.); (Q.L.); (J.D.)
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Guobin Mao
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; (G.W.); (Q.L.); (J.D.)
| | - Yingxin Ma
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; (G.W.); (Q.L.); (J.D.)
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4
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Xu J, Abdulsalam Khaleel R, Zaidan HK, Faisal Mutee A, Fahmi Fawy K, Gehlot A, Abbas AH, Arias Gonzáles JL, Amin AH, Ruiz-Balvin MC, Imannezhad S, Bahrami A, Akhavan-Sigari R. Discovery of common molecular signatures and drug repurposing for COVID-19/Asthma comorbidity: ACE2 and multi-partite networks. Cell Cycle 2024:1-30. [PMID: 38640424 DOI: 10.1080/15384101.2024.2340859] [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: 06/27/2023] [Accepted: 04/04/2024] [Indexed: 04/21/2024] Open
Abstract
Angiotensin-converting enzyme 2 (ACE2) is identified as the functional receptor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the ongoing global coronavirus disease-2019 (COVID-19) pandemic. This study aimed to elucidate potential therapeutic avenues by scrutinizing approved drugs through the identification of the genetic signature associated with SARS-CoV-2 infection in individuals with asthma. This exploration was conducted through an integrated analysis, encompassing interaction networks between the ACE2 receptor and common host (co-host) factors implicated in COVID-19/asthma comorbidity. The comprehensive analysis involved the identification of common differentially expressed genes (cDEGs) and hub-cDEGs, functional annotations, interaction networks, gene set variation analysis (GSVA), gene set enrichment analysis (GSEA), and module construction. Interaction networks were used to identify overlapping disease modules and potential drug targets. Computational biology and molecular docking analyzes were utilized to discern functional drug modules. Subsequently, the impact of the identified drugs on the expression of hub-cDEGs was experimentally validated using a mouse model. A total of 153 cDEGs or co-host factors associated with ACE2 were identified in the COVID-19 and asthma comorbidity. Among these, seven significant cDEGs and proteins - namely, HRAS, IFNG, JUN, CDH1, TLR4, ICAM1, and SCD-were recognized as pivotal host factors linked to ACE2. Regulatory network analysis of hub-cDEGs revealed eight top-ranked transcription factors (TFs) proteins and nine microRNAs as key regulatory factors operating at the transcriptional and post-transcriptional levels, respectively. Molecular docking simulations led to the proposal of 10 top-ranked repurposable drug molecules (Rapamycin, Ivermectin, Everolimus, Quercetin, Estradiol, Entrectinib, Nilotinib, Conivaptan, Radotinib, and Venetoclax) as potential treatment options for COVID-19 in individuals with comorbid asthma. Validation analysis demonstrated that Rapamycin effectively inhibited ICAM1 expression in the HDM-stimulated mice group (p < 0.01). This study unveils the common pathogenesis and genetic signature underlying asthma and SARS-CoV-2 infection, delineated by the interaction networks of ACE2-related host factors. These findings provide valuable insights for the design and discovery of drugs aimed at more effective therapeutics within the context of lung disease comorbidities.
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Affiliation(s)
- Jiajun Xu
- College of Veterinary & Life Sciences, the University of Glasgow, Glasgow, UK
| | | | | | | | - Khaled Fahmi Fawy
- Department of Chemistry, Faculty of Science, King Khalid University, Abha, Saudi Arabia
| | - Anita Gehlot
- Uttaranchal Institute of Technology, Uttaranchal University, Dehradun, India
| | | | - José Luis Arias Gonzáles
- Department of Social Sciences, Faculty of Social Studies, University of British Columbia, Vancouver, Canada
| | - Ali H Amin
- Zoology Department, Faculty of Science, Mansoura University, Mansoura, Egypt
| | | | - Shima Imannezhad
- Department of Pediatrics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Abolfazl Bahrami
- Biomedical Center for Systems Biology Science Munich, Ludwig-Maximilians-University, Munich, Germany
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Reza Akhavan-Sigari
- Department of Neurosurgery, University Medical Center Tuebingen, Tuebingen, Germany
- Department of Health Care Management and Clinical Research, Collegium Humanum, Warsaw, Poland
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Schatz C, Knabl L, Lee HK, Seeboeck R, von Laer D, Lafon E, Borena W, Mangge H, Prüller F, Qerimi A, Wilflingseder D, Posch W, Haybaeck J. Machine Learning to Identify Critical Biomarker Profiles in New SARS-CoV-2 Variants. Microorganisms 2024; 12:798. [PMID: 38674742 PMCID: PMC11052335 DOI: 10.3390/microorganisms12040798] [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: 02/02/2024] [Revised: 03/31/2024] [Accepted: 04/03/2024] [Indexed: 04/28/2024] Open
Abstract
The global dissemination of SARS-CoV-2 resulted in the emergence of several variants, including Alpha, Alpha + E484K, Beta, and Omicron. Our research integrated the study of eukaryotic translation factors and fundamental components in general protein synthesis with the analysis of SARS-CoV-2 variants and vaccination status. Utilizing statistical methods, we successfully differentiated between variants in infected individuals and, to a lesser extent, between vaccinated and non-vaccinated infected individuals, relying on the expression profiles of translation factors. Additionally, our investigation identified common causal relationships among the translation factors, shedding light on the interplay between SARS-CoV-2 variants and the host's translation machinery.
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Affiliation(s)
- Christoph Schatz
- Tyrolpath Obrist Brunhuber GmbH, 6311 Zams, Austria (L.K.)
- Institute of Pathology, Neuropathology and Molecular Pathology, Medical University of Innsbruck, Muellerstrasse 44, 6020 Innsbruck, Austria;
| | - Ludwig Knabl
- Tyrolpath Obrist Brunhuber GmbH, 6311 Zams, Austria (L.K.)
| | - Hye Kyung Lee
- Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA;
| | - Rita Seeboeck
- Department Life Sciences, IMC University of Applied Sciences Krems, 3500 Krems, Austria;
- Clinical Institute of Pathology, University Hospital St. Poelten, Karl Landsteiner University of Health Science, 3100 St. Poelten, Austria
| | - Dorothee von Laer
- Institute of Virology, Medical University of Innsbruck, Peter-Mayr-Strasse 4b, 6020 Innsbruck, Austria (W.B.)
| | - Eliott Lafon
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Schöpfstrasse 41, 6020 Innsbruck, Austria (D.W.); (W.P.)
| | - Wegene Borena
- Institute of Virology, Medical University of Innsbruck, Peter-Mayr-Strasse 4b, 6020 Innsbruck, Austria (W.B.)
| | - Harald Mangge
- Clinical Institute for Medical and Chemical Laboratory Diagnosis (CIMCL), Medical University of Graz, Auenbruggerplatz 15, 8036 Graz, Austria
| | - Florian Prüller
- Clinical Institute for Medical and Chemical Laboratory Diagnosis (CIMCL), Medical University of Graz, Auenbruggerplatz 15, 8036 Graz, Austria
| | - Adelina Qerimi
- Institute of Pathology, Neuropathology and Molecular Pathology, Medical University of Innsbruck, Muellerstrasse 44, 6020 Innsbruck, Austria;
| | - Doris Wilflingseder
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Schöpfstrasse 41, 6020 Innsbruck, Austria (D.W.); (W.P.)
- Department of Pathobiology, Infectiology, Veterinary University of Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - Wilfried Posch
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Schöpfstrasse 41, 6020 Innsbruck, Austria (D.W.); (W.P.)
| | - Johannes Haybaeck
- Department of Pathology, Saint Vincent Hospital Zams, 6511 Zams, Austria
- Diagnostic and Research Center for Molecular BioMedicine, Institute of Pathology, Medical University of Graz, 8010 Graz, Austria
- Department of Pathology, Laborteam, 9403 Goldach, Switzerland
- Department of Pathology, University Medical Centre Maribor, 2000 Maribor, Slovenia
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6
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Guo J, Lai Y, Yang Z, Song W, Zhou J, Li Z, Su W, Xiao S, Fang L. Coinfection and Nonrandom Recombination Drive the Evolution of Swine Enteric Coronaviruses. Emerg Microbes Infect 2024:2332653. [PMID: 38517703 DOI: 10.1080/22221751.2024.2332653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2024]
Abstract
Coinfection with multiple viruses is a common phenomenon in clinical settings and is a crucial driver of viral evolution. Although numerous studies have demonstrated viral recombination arising from coinfections of different strains of a specific species, the role of coinfections of different species or genera during viral evolution is rarely investigated. Here, we analyzed coinfections of and recombination events between four different swine enteric coronaviruses that infect the jejunum and ileum in pigs, including porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), and swine acute diarrhea syndrome coronavirus (SADS-CoV), and a deltacoronavirus, porcine deltacoronavirus (PDCoV). Various coinfection patterns were observed in 4,468 fecal and intestinal tissue samples collected from pigs in a 4-year survey. PEDV/PDCoV was the most frequent coinfection. However, recombination analyses have only detected events involving PEDV/TGEV and SADS-CoV/TGEV, indicating that inter-species recombination among coronaviruses is most likely to occur within the same genus. We also analyzed recombination events within the newly identified genus Deltacoronavirus and found that sparrows have played a unique host role in the recombination history of the deltacoronaviruses. The emerging virus PDCoV, which can infect humans, has a different recombination history. In summary, our study demonstrates that swine enteric coronaviruses are a valuable model for investigating the relationship between viral coinfection and recombination, which provide new insights into both inter- and intraspecies recombination events among swine enteric coronaviruses, and extend our understanding of the relationship between coronavirus coinfection and recombination.
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Affiliation(s)
- Jiahui Guo
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University. Wuhan, Hubei, 430070, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, China
| | - Yinan Lai
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University. Wuhan, Hubei, 430070, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, China
| | - Zhixiang Yang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University. Wuhan, Hubei, 430070, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, China
| | - Wenbo Song
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University. Wuhan, Hubei, 430070, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, China
| | - Junwei Zhou
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University. Wuhan, Hubei, 430070, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, China
| | - Zhuang Li
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University. Wuhan, Hubei, 430070, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, China
| | - Wen Su
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University. Wuhan, Hubei, 430070, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University. Wuhan, Hubei, 430070, China
| | - Shaobo Xiao
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University. Wuhan, Hubei, 430070, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, China
| | - Liurong Fang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University. Wuhan, Hubei, 430070, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, China
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Huecksteadt TP, Myers EJ, Aamodt SE, Trivedi S, Warren KJ. An Evaluation of Type 1 Interferon Related Genes in Male and Female-Matched, SARS-CoV-2 Infected Individuals Early in the COVID-19 Pandemic. Viruses 2024; 16:472. [PMID: 38543837 PMCID: PMC10975322 DOI: 10.3390/v16030472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 03/08/2024] [Accepted: 03/16/2024] [Indexed: 05/23/2024] Open
Abstract
SARS-CoV-2 infection has claimed just over 1.1 million lives in the US since 2020. Globally, the SARS-CoV-2 respiratory infection spread to 771 million people and caused mortality in 6.9 million individuals to date. Much of the early literature showed that SARS-CoV-2 immunity was defective in the early stages of the pandemic, leading to heightened and, sometimes, chronic inflammatory responses in the lungs. This lung-associated 'cytokine storm' or 'cytokine release syndrome' led to the need for oxygen supplementation, respiratory distress syndrome, and mechanical ventilation in a relatively high number of people. In this study, we evaluated circulating PBMC from non-hospitalized, male and female, COVID-19+ individuals over the course of infection, from the day of diagnosis (day 0) to one-week post diagnosis (day 7), and finally 4 weeks after diagnosis (day 28). In our early studies, we included hospitalized and critically care patient PBMC; however, most of these individuals were lymphopenic, which limited our assessments of their immune integrity. We chose a panel of 30 interferon-stimulated genes (ISG) to evaluate by PCR and completed flow analysis for immune populations present in those PBMC. Lastly, we assessed immune activation by stimulating PBMC with common TLR ligands. We identified changes in innate cells, primarily the innate lymphoid cells (ILC, NK cells) and adaptive immune cells (CD4+ and CD8+ T cells) over this time course of infection. We found that the TLR-7 agonist, Resiquimod, and the TLR-4 ligand, LPS, induced significantly better IFNα and IFNγ responses in the later phase (day 28) of SARS-CoV-2 infection in those non-hospitalized COVID-19+ individuals as compared to early infection (day 0 and day 7). We concluded that TLR-7 and TLR-4 agonists may be effective adjuvants in COVID-19 vaccines for mounting immunity that is long-lasting against SARS-CoV-2 infection.
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Affiliation(s)
- Tom P. Huecksteadt
- Salt Lake City VA Medical Center, Salt Lake City, UT 84148, USA; (T.P.H.); (E.J.M.); (S.E.A.); (S.T.)
| | - Elizabeth J. Myers
- Salt Lake City VA Medical Center, Salt Lake City, UT 84148, USA; (T.P.H.); (E.J.M.); (S.E.A.); (S.T.)
- Department of Neurology, University of Utah, Salt Lake City, UT 84132, USA
| | - Samuel E. Aamodt
- Salt Lake City VA Medical Center, Salt Lake City, UT 84148, USA; (T.P.H.); (E.J.M.); (S.E.A.); (S.T.)
- Department of Internal Medicine, Pulmonary Division, University of Utah Health Science Center, Salt Lake City, UT 84132, USA
| | - Shubhanshi Trivedi
- Salt Lake City VA Medical Center, Salt Lake City, UT 84148, USA; (T.P.H.); (E.J.M.); (S.E.A.); (S.T.)
- Department of Internal Medicine, Pulmonary Division, University of Utah Health Science Center, Salt Lake City, UT 84132, USA
- Division of Infectious Diseases, University of Utah, Salt Lake City, UT 84132, USA
| | - Kristi J. Warren
- Salt Lake City VA Medical Center, Salt Lake City, UT 84148, USA; (T.P.H.); (E.J.M.); (S.E.A.); (S.T.)
- Department of Internal Medicine, Pulmonary Division, University of Utah Health Science Center, Salt Lake City, UT 84132, USA
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8
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Zhao Z, Zhang Y, Luo B. The role of pyroptosis in viral infection. Arch Virol 2024; 169:69. [PMID: 38456965 DOI: 10.1007/s00705-024-05978-9] [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: 09/07/2023] [Accepted: 12/17/2023] [Indexed: 03/09/2024]
Abstract
Pyroptosis, also known as inflammatory necrosis, is a form of programmed cell death, which is an important natural immune response. Pyroptosis plays a major role in combating pathogenic infections. The mechanism of pyroptosis is distinct from other forms of cell death and is characterized by its dependence on inflammatory caspases (mainly caspases 1, 4, 5, and 11). Activation of NOD-like receptor thermal protein domain associated protein 3 (NLRP3) inflammatory vesicles is involved in caspase-1 activation and cleavage, which in turn triggers cleavage and multimerization of multiple gasdermin family members, including gasdermin-D (GSDMD). This further leads to cell perforation and cellular distension, causing cell membrane rupture, resulting in a massive efflux of cell contents, which triggers inflammatory reactions. In recent years, detailed study of viral diseases, has demonstrated that pyroptosis is closely associated with the development of viral diseases. This article focuses on the mechanism of pyroptosis and the connection between pyroptosis and viral infection.
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Affiliation(s)
- Zhen Zhao
- Department of Pathogenic Biology, School of Basic Medicine, Qingdao University, Qingdao, 266071, China
| | - Yan Zhang
- Department of Pathogenic Biology, School of Basic Medicine, Qingdao University, Qingdao, 266071, China.
- Department of Clinical Laboratory, Zibo Central Hospital, Zibo, 255036, China.
| | - Bing Luo
- Department of Pathogenic Biology, School of Basic Medicine, Qingdao University, Qingdao, 266071, China.
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9
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Nie J, Yang H, Liu X, Deng W, Fu B. Identification and validation of shared gene signature of kidney renal clear cell carcinoma and COVID-19. PeerJ 2024; 12:e16927. [PMID: 38464749 PMCID: PMC10921934 DOI: 10.7717/peerj.16927] [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: 08/30/2023] [Accepted: 01/22/2024] [Indexed: 03/12/2024] Open
Abstract
Background COVID-19 is a severe infectious disease caused by the SARS-CoV-2 virus, and previous studies have shown that patients with kidney renal clear cell carcinoma (KIRC) are more susceptible to SARS-CoV-2 infection than the general population. Nevertheless, their co-pathogenesis remains incompletely elucidated. Methods We obtained shared genes between these two diseases based on public datasets, constructed a prognostic risk model consisting of hub genes, and validated the accuracy of the model using internal and external validation sets. We further analyzed the immune landscape of the prognostic risk model, investigated the biological functions of the hub genes, and detected their expression in renal cell carcinoma cells using qPCR. Finally, we searched the candidate drugs associated with hub gene-related targets from DSigDB and CellMiner databases. Results We obtained 156 shared genes between KIRC and COVID-19 and constructed a prognostic risk model consisting of four hub genes. Both shared genes and hub genes were highly enriched in immune-related functions and pathways. Hub genes were significantly overexpressed in COVID-19 and KIRC. ROC curves, nomograms, etc., showed the reliability and robustness of the risk model, which was validated in both internal and external datasets. Moreover, patients in the high-risk group showed a higher proportion of immune cells, higher expression of immune checkpoint genes, and more active immune-related functions. Finally, we identified promising drugs for COVID-19 and KIRC, such as etoposide, fulvestrant, and topotecan. Conclusion This study identified and validated four shared genes for KIRC and COVID-19. These genes are associated with immune functions and may serve as potential prognostic biomarkers for KIRC. The shared pathways and genes may provide new insights for further mechanistic research and treatment of comorbidities.
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Affiliation(s)
- Jianqiang Nie
- First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Hailang Yang
- First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xiaoqiang Liu
- First Affiliated Hospital of Nanchang University, Nanchang, China
- Jiangxi Institute of Urology, Nanchang, China
| | - Wen Deng
- First Affiliated Hospital of Nanchang University, Nanchang, China
- Jiangxi Institute of Urology, Nanchang, China
| | - Bin Fu
- First Affiliated Hospital of Nanchang University, Nanchang, China
- Jiangxi Institute of Urology, Nanchang, China
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10
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Kumari M, Gupta V, Kumar N, Arun RK. Microfluidics-Based Nanobiosensors for Healthcare Monitoring. Mol Biotechnol 2024; 66:378-401. [PMID: 37166577 PMCID: PMC10173227 DOI: 10.1007/s12033-023-00760-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 04/22/2023] [Indexed: 05/12/2023]
Abstract
Efficient healthcare management demands prompt decision-making based on fast diagnostics tools, astute data analysis, and informatics analysis. The rapid detection of analytes at the point of care is ensured using microfluidics in synergy with nanotechnology and biotechnology. The nanobiosensors use nanotechnology for testing, rapid disease diagnosis, monitoring, and management. In essence, nanobiosensors detect biomolecules through bioreceptors by modulating the physicochemical signals generating an optical and electrical signal as an outcome of the binding of a biomolecule with the help of a transducer. The nanobiosensors are sensitive and selective and play a significant role in the early identification of diseases. This article reviews the detection method used with the microfluidics platform for nanobiosensors and illustrates the benefits of combining microfluidics and nanobiosensing techniques by various examples. The fundamental aspects, and their application are discussed to illustrate the advancement in the development of microfluidics-based nanobiosensors and the current trends of these nano-sized sensors for point-of-care diagnosis of various diseases and their function in healthcare monitoring.
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Affiliation(s)
- Monika Kumari
- Department of Chemical Engineering, Indian Institute of Technology, NH-44, Jagti, PO Nagrota, Jammu, Jammu & Kashmir, 181221, India
| | - Verruchi Gupta
- School of Biotechnology, Shri Mata Vaishno Devi University, Kakryal, Katra, Jammu & Kashmir, 182320, India
| | - Natish Kumar
- Department of Chemical Engineering, Indian Institute of Technology, NH-44, Jagti, PO Nagrota, Jammu, Jammu & Kashmir, 181221, India
| | - Ravi Kumar Arun
- Department of Chemical Engineering, Indian Institute of Technology, NH-44, Jagti, PO Nagrota, Jammu, Jammu & Kashmir, 181221, India.
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11
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Deng M, Zhang C, Yan W, Chen L, He B, Li Y. Development of Fluorescence-Based Assays for Key Viral Proteins in the SARS-CoV-2 Infection Process and Lifecycle. Int J Mol Sci 2024; 25:2850. [PMID: 38474097 DOI: 10.3390/ijms25052850] [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: 01/09/2024] [Revised: 02/09/2024] [Accepted: 02/25/2024] [Indexed: 03/14/2024] Open
Abstract
Since the appearance of SARS-CoV-2 in 2019, the ensuing COVID-19 (Corona Virus Disease 2019) pandemic has posed a significant threat to the global public health system, human health, life, and economic well-being. Researchers worldwide have devoted considerable efforts to curb its spread and development. The latest studies have identified five viral proteins, spike protein (Spike), viral main protease (3CLpro), papain-like protease (PLpro), RNA-dependent RNA polymerase (RdRp), and viral helicase (Helicase), which play crucial roles in the invasion of SARS-CoV-2 into the human body and its lifecycle. The development of novel anti-SARS-CoV-2 drugs targeting these five viral proteins holds immense promise. Therefore, the development of efficient, high-throughput screening methodologies specifically designed for these viral proteins is of utmost importance. Currently, a plethora of screening techniques exists, with fluorescence-based assays emerging as predominant contenders. In this review, we elucidate the foundational principles and methodologies underpinning fluorescence-based screening approaches directed at these pivotal viral targets, hoping to guide researchers in the judicious selection and refinement of screening strategies, thereby facilitating the discovery and development of lead compounds for anti-SARS-CoV-2 pharmaceuticals.
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Affiliation(s)
- Mingzhenlong Deng
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, Guizhou Medical University, Guiyang 550004, China
| | - Chuang Zhang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, Guizhou Medical University, Guiyang 550004, China
| | - Wanli Yan
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, Guizhou Medical University, Guiyang 550004, China
| | - Lei Chen
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, Guizhou Medical University, Guiyang 550004, China
| | - Bin He
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, Guizhou Medical University, Guiyang 550004, China
| | - Yan Li
- School of Basic Medical Science, Guizhou Medical University, Guiyang 550004, China
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12
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Wang W, Wang B, Li Q, Tian R, Lu X, Peng Y, Sun J, Bai J, Gao Z, Sun X. Ultrasensitive Detection Strategy of Norovirus Based on a Dual Enhancement Strategy: CRISPR-Responsive Self-Assembled SNA and Isothermal Amplification. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:4415-4425. [PMID: 38355417 DOI: 10.1021/acs.jafc.4c00557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
Spherical nucleic acids (SNAs) have been used to construct various nanobiosensors with gold nanoparticles (AuNPs) as nuclei. The SNAs play a critical role in biosensing due to their various physical and chemical properties, programmability, and specificity recognition ability. In this study, CRISPR-responsive self-assembled spherical nucleic acid (CRISPR-rsSNA) detection probes were constructed by conjugating fluorescein-labeled probes to the surface of AuNPs to improve the sensing performance. Also, the mechanism of ssDNA and the role of different fluorescent groups in the self-assembly process of CRISPR-rsSNA were explored. Then, CRISPR-rsSNA and reverse transcription-recombinase polymerase amplification (RT-RPA) were combined to develop an ultrasensitive fluorescence-detection strategy for norovirus. In the presence of the virus, the target RNA sequence of the virus was transformed and amplified by RT-RPA. The resulting dsDNA activated the trans-cleavage activity of CRISPR cas12a, resulting in disintegrating the outer nucleic acid structure of the CRISPR-rsSNA at a diffusible rate, which released reporter molecules. Norovirus was quantitated by fluorescence detection. This strategy facilitated the detection of the norovirus at the attomolar level. An RT-RPA kit for norovirus detected would be developed based on this method. The proposed method would be used for the detection of different viruses just by changing the target RNA and crRNA of the CRISPR cas12a system which provided a foundation for high-throughput detection of various substances.
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Affiliation(s)
- Weiya Wang
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi 214122, Jiangsu, P. R. China
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, P.R. of China
| | - Botao Wang
- School of Instrument Science and Optoelectronics Engineering, Beihang University, Beijing 100191, China
| | - Qiaofeng Li
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi 214122, Jiangsu, P. R. China
| | - Run Tian
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi 214122, Jiangsu, P. R. China
| | - Xin Lu
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi 214122, Jiangsu, P. R. China
| | - Yuan Peng
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, P.R. of China
| | - Jiadi Sun
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi 214122, Jiangsu, P. R. China
| | - Jialei Bai
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, P.R. of China
| | - Zhixian Gao
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, P.R. of China
| | - Xiulan Sun
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi 214122, Jiangsu, P. R. China
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13
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Li Z, Chen Y, Li L, Xue M, Feng L. Different Infectivity of Swine Enteric Coronaviruses in Cells of Various Species. Pathogens 2024; 13:174. [PMID: 38392912 PMCID: PMC10891669 DOI: 10.3390/pathogens13020174] [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: 12/19/2023] [Revised: 01/31/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
Swine enteric coronaviruses (SECoVs), including porcine deltacoronavirus (PDCoV), transmissible gastroenteritis virus (TGEV), porcine epidemic diarrhea virus (PEDV), and swine acute diarrhea syndrome coronavirus (SADS-CoV), have caused high mortality in piglets and, therefore, pose serious threats to the pork industry. Coronaviruses exhibit a trend of interspecies transmission, and understanding the host range of SECoVs is crucial for improving our ability to predict and control future epidemics. Here, the replication of PDCoV, TGEV, and PEDV in cells from different host species was compared by measuring viral genomic RNA transcription and protein synthesis. We demonstrated that PDCoV had a higher efficiency in infecting human lung adenocarcinoma cells (A549), Madin-Darby bovine kidney cells (MDBK), Madin-Darby canine kidney cells (MDCK), and chicken embryonic fibroblast cells (DF-1) than PEDV and TGEV. Moreover, trypsin can enhance the infectivity of PDCoV to MDCK cells that are nonsusceptible to TGEV. Additionally, structural analyses of the receptor ectodomain indicate that PDCoV S1 engages Aminopeptidase N (APN) via domain II, which is highly conserved among animal species of different vertebrates. Our findings provide a basis for understanding the interspecies transmission potential of these three porcine coronaviruses.
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Affiliation(s)
| | | | | | - Mei Xue
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Li Feng
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
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14
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Chavda VP, Ghali ENHK, Balar PC, Chauhan SC, Tiwari N, Shukla S, Athalye M, Patravale V, Apostolopoulos V, Yallapu MM. Protein subunit vaccines: Promising frontiers against COVID-19. J Control Release 2024; 366:761-782. [PMID: 38219913 DOI: 10.1016/j.jconrel.2024.01.017] [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: 06/07/2023] [Revised: 01/07/2024] [Accepted: 01/09/2024] [Indexed: 01/16/2024]
Abstract
The emergence of COVID-19 has posed an unprecedented global health crisis, challenging the healthcare systems worldwide. Amidst the rapid development of several vaccine formulations, protein subunit vaccines have emerged as a promising approach. This article provides an in-depth evaluation of the role of protein subunit vaccines in the management of COVID-19. Leveraging viral protein fragments, particularly the spike protein from SARS-CoV-2, these vaccines elicit a targeted immune response without the risk of inducing disease. Notably, the robust safety profile of protein subunit vaccines makes them a compelling candidate in the management of COVID-19. Various innovative approaches, including reverse vaccinology, virus like particles, and recombinant modifications are incorporated to develop protein subunit vaccines. In addition, the utilization of advanced manufacturing techniques facilitates large-scale production, ensuring widespread distribution. Despite these advancements, challenges persist, such as the requirement for cold-chain storage and the necessity for booster doses. This article evaluates the formulation and applications of protein subunit vaccines, providing a comprehensive overview of their clinical development and approvals in the context of COVID-19. By addressing the current status and challenges, this review aims to contribute to the ongoing discourse on optimizing protein subunit vaccines for effective pandemic control.
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Affiliation(s)
- Vivek P Chavda
- Department of Pharmaceutics and Pharmaceutical Technology, L. M. College of Pharmacy, Ahmedabad 380009, Gujarat, India.
| | - Eswara Naga Hanuma Kumar Ghali
- Department of Immunology and Microbiology, School of Medicine, The University of Texas Rio Grande Valley, McAllen, TX 78504, USA; South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA.
| | - Pankti C Balar
- Pharmacy Section, L. M. College of Pharmacy, Ahmedabad 380009, Gujarat, India
| | - Subhash C Chauhan
- Department of Immunology and Microbiology, School of Medicine, The University of Texas Rio Grande Valley, McAllen, TX 78504, USA; South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA.
| | - Nikita Tiwari
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Mumbai 400019, India
| | - Somanshi Shukla
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Mumbai 400019, India
| | - Mansi Athalye
- Department of Pharmaceutics and Pharmaceutical Technology, L. M. College of Pharmacy, Ahmedabad 380009, Gujarat, India
| | - Vandana Patravale
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Mumbai 400019, India
| | - Vasso Apostolopoulos
- Institute for Health and Sport, Immunology and Translational Research, Victoria University, Melbourne, VIC 3030, Australia; Immunology Program, Australian Institute for Musculoskeletal Science (AIMSS), Melbourne, VIC 3021, Australia.
| | - Murali M Yallapu
- Department of Immunology and Microbiology, School of Medicine, The University of Texas Rio Grande Valley, McAllen, TX 78504, USA; South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA.
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15
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Liu C, Huang W, He X, Feng Z, Chen Q. Research Advances on Swine Acute Diarrhea Syndrome Coronavirus. Animals (Basel) 2024; 14:448. [PMID: 38338091 PMCID: PMC10854734 DOI: 10.3390/ani14030448] [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: 12/13/2023] [Revised: 01/23/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Swine acute diarrhea syndrome coronavirus (SADS-CoV) is a virulent pathogen that causes acute diarrhea in piglets. The virus was first discovered in Guangdong Province, China, in 2017 and has since emerged in Jiangxi, Fujian, and Guangxi Provinces. The outbreak exhibited a localized and sporadic pattern, with no discernable temporal continuity. The virus can infect human progenitor cells and demonstrates considerable potential for cross-species transmission, representing a potential risk for zoonotic transmission. Therefore, continuous surveillance of and comprehensive research on SADS-CoV are imperative. This review provides an overview of the temporal and evolutionary features of SADS-CoV outbreaks, focusing on the structural characteristics of the virus, which serve as the basis for discussing its potential for interspecies transmission. Additionally, the review summarizes virus-host interactions, including the effects on host cells, as well as apoptotic and autophagic behaviors, and discusses prevention and treatment modalities for this viral infection.
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Affiliation(s)
- Chuancheng Liu
- College of Life Science, Fujian Normal University, Fuzhou 350117, China; (C.L.); (W.H.); (X.H.)
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, Fujian Normal University, Fuzhou 350117, China
| | - Weili Huang
- College of Life Science, Fujian Normal University, Fuzhou 350117, China; (C.L.); (W.H.); (X.H.)
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, Fujian Normal University, Fuzhou 350117, China
| | - Xinyan He
- College of Life Science, Fujian Normal University, Fuzhou 350117, China; (C.L.); (W.H.); (X.H.)
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, Fujian Normal University, Fuzhou 350117, China
| | - Zhihua Feng
- College of Life Science, Fujian Normal University, Fuzhou 350117, China; (C.L.); (W.H.); (X.H.)
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, Fujian Normal University, Fuzhou 350117, China
| | - Qi Chen
- College of Life Science, Fujian Normal University, Fuzhou 350117, China; (C.L.); (W.H.); (X.H.)
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, Fujian Normal University, Fuzhou 350117, China
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16
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Vu Thi H, Tran LT, Nguyen HQ, Chu DT. RNA therapeutics for respiratory diseases. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 203:257-271. [PMID: 38360002 DOI: 10.1016/bs.pmbts.2023.12.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
It has become increasingly common to utilize RNA treatment to treat respiratory illnesses. Experimental research on both people and animals has advanced quickly since the turn of the twenty-first century in an effort to discover a treatment for respiratory ailments that could not be accomplished with earlier techniques, specifically in treating prevalent respiratory diseases such as lung cancer, chronic obstructive pulmonary disease (COPD), respiratory infections caused by viruses, and asthma. This chapter has provided a comprehensive overview of the scientific evidence in applying RNA therapy to treat respiratory diseases. The chapter describes the development of this therapy for respiratory diseases. At the same time, the types of RNA therapy for respiratory diseases have been highlighted. In addition, the mechanism of this therapy for respiratory diseases has also been covered. These insights are indispensable if this therapy is to be developed widely.
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Affiliation(s)
- Hue Vu Thi
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam; Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Vietnam
| | - Linh Thao Tran
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam
| | - Huy Quang Nguyen
- LMI DRISA, Department of Life Sciences, University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Dinh-Toi Chu
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam; Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Vietnam.
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17
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Bartak M, Bąska P, Chodkowski M, Tymińska B, Bańbura MW, Cymerys J. Neurons cytoskeletal architecture remodeling during the replication cycle of mouse coronavirus MHV-JHM: a morphological in vitro study. BMC Vet Res 2024; 20:18. [PMID: 38195523 PMCID: PMC10775625 DOI: 10.1186/s12917-023-03813-y] [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] [Accepted: 11/10/2023] [Indexed: 01/11/2024] Open
Abstract
Nowadays, the population is still struggling with a post-COVID19 syndrome known as long COVID, including a broad spectrum of neurological problems. There is an urgent need for a better understanding and exploration of the mechanisms of coronavirus neurotropism. For this purpose, the neurotropic strain of mouse hepatitis virus (MHV-JHM) originating from the beta-coronavirus genus, the same as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been used. The role of the cytoskeleton during virus replication in neurons in vitro was determined to understand the mechanisms of MHV-JHM neuroinfection. We have described for the first time the changes of actin filaments during MHV-JHM infection. We also observed productive replication of MHV-JHM in neurons during 168 h p.i. and syncytial cytopathic effect. We discovered that the MHV-JHM strain modulated neuronal cytoskeleton during infection, which were manifested by: (i) condensation of actin filaments in the cortical layer of the cytoplasm, (ii) formation of microtubule cisternae structures containing viral antigen targeting viral replication site (iii) formation of tunneling nanotubes used by MHV-JHM for intercellular transport. Additionally, we demonstrated that the use of cytoskeletal inhibitors have reduced virus replication in neurons, especially noscapine and nocodazole, the microtubule shortening factors.
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Affiliation(s)
- Michalina Bartak
- Division of Microbiology, Department of Preclinical Sciences, Institute of Veterinary Medicine, Warsaw University of Life Sciences, Ciszewskiego 8 St., Warsaw, 02-786, Poland.
| | - Piotr Bąska
- Division of Pharmacology and Toxicology, Department of Preclinical Sciences, Institute of Veterinary Medicine, Warsaw University of Life Sciences-SGGW, Ciszewskiego 8 St., Warsaw, 02-786, Poland
| | - Marcin Chodkowski
- Laboratory of Nanobiology and Biomaterials, Military Institute of Hygiene and Epidemiology, Kozielska 4 St., Warsaw, 01-063, Poland
| | - Beata Tymińska
- Division of Microbiology, Department of Preclinical Sciences, Institute of Veterinary Medicine, Warsaw University of Life Sciences, Ciszewskiego 8 St., Warsaw, 02-786, Poland
| | - Marcin W Bańbura
- Division of Microbiology, Department of Preclinical Sciences, Institute of Veterinary Medicine, Warsaw University of Life Sciences, Ciszewskiego 8 St., Warsaw, 02-786, Poland
| | - Joanna Cymerys
- Division of Microbiology, Department of Preclinical Sciences, Institute of Veterinary Medicine, Warsaw University of Life Sciences, Ciszewskiego 8 St., Warsaw, 02-786, Poland.
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18
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Khalil AM, Martinez-Sobrido L, Mostafa A. Zoonosis and zooanthroponosis of emerging respiratory viruses. Front Cell Infect Microbiol 2024; 13:1232772. [PMID: 38249300 PMCID: PMC10796657 DOI: 10.3389/fcimb.2023.1232772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 12/11/2023] [Indexed: 01/23/2024] Open
Abstract
Lung infections in Influenza-Like Illness (ILI) are triggered by a variety of respiratory viruses. All human pandemics have been caused by the members of two major virus families, namely Orthomyxoviridae (influenza A viruses (IAVs); subtypes H1N1, H2N2, and H3N2) and Coronaviridae (severe acute respiratory syndrome coronavirus 2, SARS-CoV-2). These viruses acquired some adaptive changes in a known intermediate host including domestic birds (IAVs) or unknown intermediate host (SARS-CoV-2) following transmission from their natural reservoirs (e.g. migratory birds or bats, respectively). Verily, these acquired adaptive substitutions facilitated crossing species barriers by these viruses to infect humans in a phenomenon that is known as zoonosis. Besides, these adaptive substitutions aided the variant strain to transmit horizontally to other contact non-human animal species including pets and wild animals (zooanthroponosis). Herein we discuss the main zoonotic and reverse-zoonosis events that occurred during the last two pandemics of influenza A/H1N1 and SARS-CoV-2. We also highlight the impact of interspecies transmission of these pandemic viruses on virus evolution and possible prophylactic and therapeutic interventions. Based on information available and presented in this review article, it is important to close monitoring viral zoonosis and viral reverse zoonosis of pandemic strains within a One-Health and One-World approach to mitigate their unforeseen risks, such as virus evolution and resistance to limited prophylactic and therapeutic interventions.
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Affiliation(s)
- Ahmed Magdy Khalil
- Disease Intervention & Prevention and Host Pathogen Interactions Programs, Texas Biomedical Research Institute, San Antonio, TX, United States
- Department of Zoonotic Diseases, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Luis Martinez-Sobrido
- Disease Intervention & Prevention and Host Pathogen Interactions Programs, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Ahmed Mostafa
- Disease Intervention & Prevention and Host Pathogen Interactions Programs, Texas Biomedical Research Institute, San Antonio, TX, United States
- Center of Scientific Excellence for Influenza Viruses, Water Pollution Research Department, Environment and Climate Change Research Institute, National Research Centre, Giza, Egypt
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19
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Ramachandran AK, Das S, Shenoy GG, Mudgal J, Joseph A. Relation between Apolipoprotein E in Alzheimer's Disease and SARS-CoV-2 and their Treatment Strategy: A Review. CNS & NEUROLOGICAL DISORDERS DRUG TARGETS 2024; 23:9-20. [PMID: 36573058 DOI: 10.2174/1871527322666221226145141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 10/27/2022] [Accepted: 11/01/2022] [Indexed: 12/28/2022]
Abstract
COVID-19, which primarily affects the pulmonary system, turned out to be a global pandemic, whereas the effects on other systems are still unknown. SARS-CoV-2, binds to angiotensinconverting enzyme 2 (ACE2) receptors in the lungs, causing pneumonia-like symptoms. The same ACE receptors are also present in organs other than the lungs. Therefore, there is a need to study the impact of coronavirus on other human body organs. Recently, UK Biobank reports on the genetic risk factor of the virus attack. A double mutation in the apolipoprotein E (APOE4) allele has shown a significant role in COVID-19. The same APOE4 mutation has already been proven to hold a key role in developing early-onset Alzheimer's disease (EOAD). Despite this data, Alzheimer's disease is believed to be a comorbidity of COVID-19. Previous virus attacks on the same viral family, Coronaviridae, produced neurological effects like neurodegeneration, neuronal inflammation, and other central nervous system-related dysfunctions. Since the long-term implications of COVID-19 are unknown, more research into the impact of the virus on the central nervous system is needed. Both COVID-19 and AD share a common genetic factor, so that AD patients may have a greater risk of SARS-CoV-2. Here, in this review, we have briefly discussed the role of APOE4 in the pathogenesis of AD and SARS-CoV-2, along with their treatment strategy, current scenario, and possible future directions.
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Affiliation(s)
- Anu Kunnath Ramachandran
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Subham Das
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
- Manipal McGill Centre for Infectious Diseases, Prasanna School of Public Health, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Gurupur Gautham Shenoy
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Jayesh Mudgal
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Alex Joseph
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
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20
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Arumugam M, Shanmugavel B, Sellppan M, Pavadai P. In silico evaluation of some commercially available terpenoids as spike glycoprotein of SARS-CoV-2 - inhibitors using molecular dynamic approach. J Biomol Struct Dyn 2024; 42:1072-1078. [PMID: 37139540 DOI: 10.1080/07391102.2023.2201848] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 03/28/2023] [Indexed: 05/05/2023]
Abstract
Coronavirus, an extremely contagious infections disease had a harmful effect on the world's population. It is a family of enveloped, single-stranded, positive-strand RNA viruses of Nidovirales order belongs to coroviridae family. At present, worldwide several lakhs of deaths and several billions of infections have been reported. Hence, the focus of the present study was to assess the SARS-CoV-2 enzyme inhibitory potential of certain commercially available terpenoids using Lamarckian genetic algorithm as a working principle and molecular dynamic studies was also performed. AutoDock 4.2 software was used to perform the computational docking calculations of terpenoids against SARS-CoV-2 enzyme. The terpenoids such as, Andrographolide, Betulonic acid, Erythrodiol, Friedelin, Mimuscopic acid, Moronic acid, and Retinol were selected based on the drug likeness properties. Remdesivir a well-known anti-viral drug was selected as the standard drug. Molecular dynamic simulation studies were carried using Desmond module of Schrodinger Suite. In the current study we observed that, Friedelin was exhibited excellent SARS-CoV-2 enzyme inhibitory potential than the standard drug and other selected terpenoids. Friedelin and the standard Remdesivir was undergone the molecular dynamic studies and Friedelin showed a good number of hydrogen bonds over the simulation time of 100 ns. Based on the in silico computational evaluation, it can be concluded that Friedelin could be worthwhile terpenoid against SARS-CoV-2 spike protein. A further study on Friedelin is required to develop a potential chemical entity against the management of COVID disease.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Madeswaran Arumugam
- Department of Pharmacology, Karpagam College of Pharmacy, Affiliated to The Tamil Nadu Dr. M.G.R. Medical University, Coimbatore, Tamil Nadu, India
| | - Brahmasundari Shanmugavel
- Department of Pharmacology, Sri Ramakrishna Institute of Paramedical Sciences, Affiliated to The Tamil Nadu Dr. M.G.R. Medical University, Coimbatore, Tamil Nadu, India
| | - Mohan Sellppan
- Karpagam College of Pharmacy, Affiliated to The Tamil Nadu Dr. M.G.R. Medical University, Coimbatore, Tamil Nadu, India
| | - Parasuraman Pavadai
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, Bengaluru, Karnataka, India
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Zhang S, Cao Y, Xu C, Wang G, Huang Y, Bao W, Zhang S. Integrated metabolomics and transcriptomics analyses reveal metabolic responses to TGEV infection in porcine intestinal epithelial cells. J Gen Virol 2023; 104. [PMID: 38116760 DOI: 10.1099/jgv.0.001942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023] Open
Abstract
Transmissible gastroenteritis virus (TGEV) is a coronavirus that infects piglets with severe diarrhoea, vomiting, dehydration, and even death, causing huge economic losses to the pig industry. The underlying pathogenesis of TGEV infection and the effects of TGEV infection on host metabolites remain poorly understood. To investigate the critical metabolites and regulatory factors during TGEV infection in intestinal porcine epithelial cells (IPEC-J2), we performed metabolomic and transcriptomic analyses of TGEV-infected IPEC-J2 cells by LC/MS and RNA-seq techniques. A total of 87 differential metabolites and 489 differentially expressed genes were detected. A series of metabolites and candidate genes from glutathione metabolism and AMPK signalling pathway were examined through combined analysis of metabolome and transcriptome. We found glutathione peroxidase 3 (GPX3) is markedly reduced after TGEV infection, and a significant negative correlation between AMPK signalling pathway and TGEV infection. Exogenous addition of the AMPK activator COH-SR4 significantly downregulates stearoyl coenzyme A (SCD1) mRNA and inhibits TGEV replication; while exogenous GSK-690693 significantly promotes TGEV infection by inhibiting AMPK signalling pathway. In summary, our study provides insights into the key metabolites and regulators for TGEV infection from the metabolome and transcriptome perspective, which will offer promising antiviral metabolic and molecular targets and enrich the understanding of the existence of a similar mechanism in the host.
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Affiliation(s)
- Shuoshuo Zhang
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, PR China
| | - Yanan Cao
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, PR China
| | - Chao Xu
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, PR China
| | - Guangzheng Wang
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, PR China
| | - Yanjie Huang
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, PR China
| | - Wenbin Bao
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, PR China
- Joint International Research Laboratory of Agriculture and Agri-product Safety, Yangzhou University, Yangzhou 225009, PR China
| | - Shuai Zhang
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, PR China
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22
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Marc MS, Rosca D, Bratosin F, Fira-Mladinescu O, Oancea C, Pescaru CC, Velescu D, Wellmann N, Motofelea AC, Ciuca IM, Saracin K, Manolescu D. The Effect of Comorbidities and Complications on COVID-19 Mortality: A Detailed Retrospective Study in Western Romania. J Pers Med 2023; 13:1552. [PMID: 38003867 PMCID: PMC10672588 DOI: 10.3390/jpm13111552] [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: 09/25/2023] [Revised: 10/24/2023] [Accepted: 10/27/2023] [Indexed: 11/26/2023] Open
Abstract
COVID-19 continues to impact global health systems even after being declared over, with some patients exhibiting severe complications linked to pre-existing conditions. This study aimed to investigate the association between comorbidities, complications, and survival outcomes among COVID-19 survivors in Western Romania. Our hypothesis posited that comorbidities and complications significantly influence survival rates. We conducted a retrospective analysis of 1948 COVID-19 survivors admitted from January to December 2021, with 192 selected for detailed analysis based on inclusion and exclusion criteria. The severity of COVID-19 was classified according to WHO guidelines, and conditions like hypertension and obesity were defined using criteria from the European Society of Hypertension (ESH), the European Society of Cardiology (ESC), and WHO, respectively. Among the 192 patients, 33 had mild, 62 had moderate, and 97 had severe COVID-19. The median age across the severity groups was 63.2 years. Patients undergoing tracheostomy had a mortality rate of 83.3% versus 22.2% for non-tracheostomy patients (p < 0.001) and presented with significantly higher lung injury, hospitalization duration, and complications. Remarkably, tracheostomized patients were 17.50 times more likely to succumb to the disease (95% CI 4.39-116.91, p < 0.001). Furthermore, pneumothorax increased the mortality risk significantly (OR 22.11, 95% CI 5.72-146.03, p < 0.001). Intriguingly, certain conditions like grade I hypertension and grade II obesity showed a protective effect against mortality, whereas type 2 diabetes mellitus increased mortality risk (univariate OR 2.89, p = 0.001). The presence of certain comorbidities and complications significantly impacts the survival rates of COVID-19 patients in Western Romania. Notably, tracheostomy, pneumothorax, and T2DM were associated with increased mortality. This study underscores the importance of personalized patient care and provides insights for healthcare policymakers in Western Romania to improve clinical management strategies.
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Affiliation(s)
- Monica Steluta Marc
- Center for Research and Innovation in Precision Medicine of Respiratory Diseases, “Victor Babes” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square 2, 300041 Timisoara, Romania; (M.S.M.); (O.F.-M.); (C.O.); (C.C.P.); (D.V.); (D.M.)
- Department of Infectious Diseases, Discipline of Pulmonology, “Victor Babes” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square 2, 300041 Timisoara, Romania
| | - Daniela Rosca
- Doctoral School, “Victor Babes” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square 2, 300041 Timisoara, Romania; (F.B.); (N.W.)
| | - Felix Bratosin
- Doctoral School, “Victor Babes” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square 2, 300041 Timisoara, Romania; (F.B.); (N.W.)
- Discipline of Infectious Diseases, “Victor Babes” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square 2, 300041 Timisoara, Romania
| | - Ovidiu Fira-Mladinescu
- Center for Research and Innovation in Precision Medicine of Respiratory Diseases, “Victor Babes” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square 2, 300041 Timisoara, Romania; (M.S.M.); (O.F.-M.); (C.O.); (C.C.P.); (D.V.); (D.M.)
- Department of Infectious Diseases, Discipline of Pulmonology, “Victor Babes” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square 2, 300041 Timisoara, Romania
| | - Cristian Oancea
- Center for Research and Innovation in Precision Medicine of Respiratory Diseases, “Victor Babes” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square 2, 300041 Timisoara, Romania; (M.S.M.); (O.F.-M.); (C.O.); (C.C.P.); (D.V.); (D.M.)
- Department of Infectious Diseases, Discipline of Pulmonology, “Victor Babes” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square 2, 300041 Timisoara, Romania
| | - Camelia Corina Pescaru
- Center for Research and Innovation in Precision Medicine of Respiratory Diseases, “Victor Babes” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square 2, 300041 Timisoara, Romania; (M.S.M.); (O.F.-M.); (C.O.); (C.C.P.); (D.V.); (D.M.)
- Department of Infectious Diseases, Discipline of Pulmonology, “Victor Babes” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square 2, 300041 Timisoara, Romania
| | - Diana Velescu
- Center for Research and Innovation in Precision Medicine of Respiratory Diseases, “Victor Babes” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square 2, 300041 Timisoara, Romania; (M.S.M.); (O.F.-M.); (C.O.); (C.C.P.); (D.V.); (D.M.)
- Department of Infectious Diseases, Discipline of Pulmonology, “Victor Babes” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square 2, 300041 Timisoara, Romania
| | - Norbert Wellmann
- Doctoral School, “Victor Babes” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square 2, 300041 Timisoara, Romania; (F.B.); (N.W.)
| | - Alexandru Catalin Motofelea
- Department of Internal Medicine, “Victor Babes” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square 2, 300041 Timisoara, Romania;
| | - Ioana Mihaiela Ciuca
- Department of Pediatrics, “Victor Babes” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square 2, 300041 Timisoara, Romania;
- Pediatric Pulmonology Unit, Clinical County Hospital, Evliya Celebi 1-3, 300226 Timisoara, Romania
| | - Karina Saracin
- Emergency County Hospital Craiova, Strada Tabaci 1, 200642 Craiova, Romania;
| | - Diana Manolescu
- Center for Research and Innovation in Precision Medicine of Respiratory Diseases, “Victor Babes” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square 2, 300041 Timisoara, Romania; (M.S.M.); (O.F.-M.); (C.O.); (C.C.P.); (D.V.); (D.M.)
- Department of Radiology, “Victor Babes” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square 2, 300041 Timisoara, Romania
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23
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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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24
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Wang W, Zhou L, Ge X, Han J, Guo X, Zhang Y, Yang H. Analysis of codon usage patterns of porcine enteric alphacoronavirus and its host adaptability. Virology 2023; 587:109879. [PMID: 37677987 DOI: 10.1016/j.virol.2023.109879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/20/2023] [Accepted: 08/31/2023] [Indexed: 09/09/2023]
Abstract
Porcine enteric alphacoronavirus (PEAV) is a newly emerging swine enteropathogen that poses a threat to the swine industry. To understand the PEAV genome evolution, we performed a comprehensive analysis of the codon usage patterns in fifty-nine PEAV strains currently available. Phylogenetic analysis showed that PEAV can be divided into six lineages. Effective number of codons analysis demonstrated that the PEAV genome exhibits a low codon usage bias (CUB). Nucleotide composition analysis indicated that the PEAV genome has the most abundant nucleotide U content, with GC content (39.37% ± 0.08%) much lower than AU content (60.63% ± 0.08%). Neutrality and effective number of codons plot analyses suggested that natural selection rather than mutation pressure dominates the CUB of PEAV. Host adaptation analysis revealed that PEAV fits the codon usage pattern of non-human primates, humans and mice better than that of pigs. Our data enriches information on PEAV evolution, host adaptability, and cross-species transmission.
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Affiliation(s)
- Wenlong Wang
- National Key Laboratory of Veterinary Public Health and Safety, Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Lei Zhou
- National Key Laboratory of Veterinary Public Health and Safety, Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Xinna Ge
- National Key Laboratory of Veterinary Public Health and Safety, Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Jun Han
- National Key Laboratory of Veterinary Public Health and Safety, Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Xin Guo
- National Key Laboratory of Veterinary Public Health and Safety, Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Yongning Zhang
- National Key Laboratory of Veterinary Public Health and Safety, Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, People's Republic of China.
| | - Hanchun Yang
- National Key Laboratory of Veterinary Public Health and Safety, Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, People's Republic of China
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25
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Tayal S, Bhatnagar S. Role of molecular mimicry in the SARS-CoV-2-human interactome for pathogenesis of cardiovascular diseases: An update to ImitateDB. Comput Biol Chem 2023; 106:107919. [PMID: 37463554 DOI: 10.1016/j.compbiolchem.2023.107919] [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: 01/15/2023] [Revised: 06/13/2023] [Accepted: 07/06/2023] [Indexed: 07/20/2023]
Abstract
Mimicry of host proteins is a strategy employed by pathogens to hijack host functions. Domain and motif mimicry was explored in the experimental and predicted SARS-CoV-2-human interactome. The host first interactor proteins were also added to capture the continuum of the interactions. The domains and motifs of the proteins were annotated using NCBI CD Search and ScanProsite, respectively. Host and pathogen proteins with a common host interactor and similar domain/motif constitute a mimicry pair indicating global structural similarity (domain mimicry pair; DMP) or local sequence similarity (motif mimicry pair; MMP). 593 DMPs and 7,02,472 MMPs were determined. AAA, DEXDc and Macro domains were frequent among DMPs whereas glycosylation, myristoylation and RGD motifs were abundant among MMP. The proteins involved in mimicry were visualised as a SARS-CoV-2 mimicry interaction network. The host proteins were enriched in multiple CVD pathways indicating the role of mimicry in COVID-19 associated CVDs. Bridging nodes were identified as potential drug targets. Approved antihypertensive and anti-inflammatory drugs are proposed for repurposing against COVID-19 associated CVDs. The SARS-CoV-2 mimicry data has been updated in ImitateDB (http://imitatedb.sblab-nsit.net/SARSCoV2Mimicry). Determination of key mechanisms, proteins, pathways, drug targets and repurposing candidates is critical for developing therapeutics for SARS CoV-2 associated CVDs.
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Affiliation(s)
- Sonali Tayal
- Computational and Structural Biology Laboratory, Department of Biological Sciences and Engineering, Netaji Subhas University of Technology, Dwarka, New Delhi 110078, India
| | - Sonika Bhatnagar
- Computational and Structural Biology Laboratory, Department of Biological Sciences and Engineering, Netaji Subhas University of Technology, Dwarka, New Delhi 110078, India.
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26
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Liu Y, Chen D, Wang Y, Li X, Qiu Y, Zheng M, Song Y, Li G, Song C, Liu T, Zhang Y, Guo JT, Lin H, Zhao X. Characterization of CCoV-HuPn-2018 spike protein-mediated viral entry. J Virol 2023; 97:e0060123. [PMID: 37676001 PMCID: PMC10537617 DOI: 10.1128/jvi.00601-23] [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: 04/23/2023] [Accepted: 07/25/2023] [Indexed: 09/08/2023] Open
Abstract
Canine coronavirus-human pneumonia-2018 (CCoV-HuPn-2018) was recently isolated from a child with pneumonia. This novel human pathogen resulted from cross-species transmission of a canine coronavirus. It has been known that CCoV-HuPn-2018 uses aminopeptidase N (APN) from canines, felines, and porcines, but not humans, as functional receptors for cell entry. The molecular mechanism of cell entry in CCoV-HuPn-2018 remains poorly understood. In this study, we demonstrated that among the nine APN orthologs tested, the APN of the Mexican free-tailed bat could also efficiently support CCoV-HuPn-2018 spike (S) protein-mediated entry, raising the possibility that bats may also be an alternative host epidemiologically important for the transmission of this virus. The glycosylation at residue N747 of canine APN is critical for its receptor activity. The gain of glycosylation at the corresponding residues in human and rabbit APNs converted them to functional receptors for CCoV-HuPn-2018. Interestingly, the CCoV-HuPn-2018 spike protein pseudotyped virus infected multiple human cancer cell lines in a human APN-independent manner, whereas sialic acid appeared to facilitate the entry of the pseudotyped virus into human cancer cells. Moreover, while host cell surface proteases trypsin and TMPRSS2 did not promote the entry of CCoV-HuPn-2018, endosomal proteases cathepsin L and B are required for the entry of CCoV-HuPn-2018 in a pH-dependent manner. IFITMs and LY6E are host restriction factors for the CCoV-HuPn-2018 entry. Our results thus suggest that CCoV-HuPn-2018 has not yet evolved to be an efficient human pathogen. Collectively, this study helps us understand the cell tropism, receptor usage, cross-species transmission, natural reservoir, and pathogenesis of this potential human coronavirus. IMPORTANCE Viral entry is driven by the interaction between the viral spike protein and its specific cellular receptor, which determines cell tropism and host range and is the major constraint to interspecies transmission of coronaviruses. Aminopeptidase N (APN; also called CD13) is a cellular receptor for HCoV-229E, the newly discovered canine coronavirus-human pneumonia-2018 (CCoV-HuPn-2018), and many other animal alphacoronaviruses. We examined the receptor activity of nine APN orthologs and found that CCoV-HuPn-2018 utilizes APN from a broad range of animal species, including bats but not humans, to enter host cells. To our surprise, we found that CCoV-HuPn-2018 spike protein pseudotyped viral particles successfully infected multiple human hepatoma-derived cell lines and a lung cancer cell line, which is independent of the expression of human APN. Our findings thus provide mechanistic insight into the natural hosts and interspecies transmission of CCoV-HuPn-2018-like coronaviruses.
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Affiliation(s)
- Yongmei Liu
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- Beijing Institute of Infectious Diseases, Beijing, China
- National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing, China
| | - Danying Chen
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- Beijing Institute of Infectious Diseases, Beijing, China
- National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing, China
| | - Yuanyuan Wang
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- Peking University Ditan Teaching Hospital, Beijing, China
| | - Xinglin Li
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- Beijing Institute of Infectious Diseases, Beijing, China
- National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing, China
| | - Yaruo Qiu
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- Peking University Ditan Teaching Hospital, Beijing, China
| | - Mei Zheng
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing, China
| | - Yanjun Song
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- Beijing Institute of Infectious Diseases, Beijing, China
- National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing, China
| | - Guoli Li
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- Beijing Institute of Infectious Diseases, Beijing, China
- National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing, China
| | - Chuan Song
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- Beijing Institute of Infectious Diseases, Beijing, China
- National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing, China
| | - Tingting Liu
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- Beijing Institute of Infectious Diseases, Beijing, China
- National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing, China
| | - Yuanyuan Zhang
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- Beijing Institute of Infectious Diseases, Beijing, China
- National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing, China
| | - Ju-Tao Guo
- Baruch S. Blumberg Institute, Hepatitis B Foundation, Doylestown, Pennsylvania, USA
| | - Hanxin Lin
- Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
- Molecular Genetics Laboratory, Alberta Precision Laboratories, Edmonton, Alberta, Canada
| | - Xuesen Zhao
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- Beijing Institute of Infectious Diseases, Beijing, China
- National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing, China
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27
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Dave B, Shah KC, Chorawala MR, Shah N, Patel P, Patel S, Shah P. Molnupiravir: an antiviral drug against COVID-19. Arch Virol 2023; 168:252. [PMID: 37710056 DOI: 10.1007/s00705-023-05881-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 05/28/2023] [Indexed: 09/16/2023]
Abstract
SARS-CoV-2, the virus responsible for COVID-19, has caused numerous deaths worldwide and poses significant challenges. Researchers have recently studied a new antiviral drug called molnupiravir for treating COVID-19. This review examines the causes and immunopathogenesis of COVID-19, as well as the role of molnupiravir in its treatment. Molnupiravir is a prodrug of β-D-N4-hydroxyctytidine (NHC) and has demonstrated activity against various viruses, including MERS-CoV, SARS-CoV, SARS-CoV-2, and influenza virus. The active form of molnupiravir, NHC triphosphate, acts as a nucleoside analog that disrupts viral replication by causing mutations in the viral RNA, thereby inhibiting viral growth. This review summarizes the results of multiple clinical trials that have evaluated the effectiveness of molnupiravir against SARS-CoV-2 and its variants. Animal studies have also shown that molnupiravir significantly reduces the viral load and prevents transmission to other animals. Overall, molnupiravir has demonstrated strong efficacy and reasonable safety, reducing hospitalization rates by nearly 50% among COVID-19-positive individuals at risk of complications. Patients in clinical settings have tolerated molnupiravir well and experienced positive outcomes, such as clearance of viral RNA, decreased viral load, and reduced hospitalization rates. Additionally, compared to a placebo, molnupiravir has been associated with lower mortality rates. Therefore, molnupiravir can be a beneficial drug to treat patients suffering from SARS-CoV-2, and further studies can provide more information about its safety and efficacy.
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Affiliation(s)
- Bhavarth Dave
- Department of Pharmacology and Pharmacy Practice, L. M. College of Pharmacy, Opp. Gujarat University, Navrangpura, Ahmedabad, Gujarat, 380 009, India
| | - Kashvi C Shah
- Department of Pharmacology and Pharmacy Practice, L. M. College of Pharmacy, Opp. Gujarat University, Navrangpura, Ahmedabad, Gujarat, 380 009, India
| | - Mehul R Chorawala
- Department of Pharmacology and Pharmacy Practice, L. M. College of Pharmacy, Opp. Gujarat University, Navrangpura, Ahmedabad, Gujarat, 380 009, India.
| | - Nirav Shah
- Department of Pharmaceutics, SAL Institute of Pharmacy, Sola, Ahmedabad, Gujarat, 380015, India
| | - Pranjal Patel
- Department of Pharmaceutics, SAL Institute of Pharmacy, Sola, Ahmedabad, Gujarat, 380015, India
| | - Suzan Patel
- Department of Pharmaceutics, SAL Institute of Pharmacy, Sola, Ahmedabad, Gujarat, 380015, India
| | - Palak Shah
- Department of Pharmacology and Pharmacy Practice, K. B. Institute of Pharmaceutical Education and Research, Gh-6, Sector-23, Gandhinagar, Gujarat, 382023, India
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Al-Momani H, Mashal S, Al Balawi D, Almasri M, Al-Shudifat AE, Khasawneh AI, Pearson J, Ward C. A prospective study of extraesophageal reflux and potential microaspiration in patients hospitalized with COVID-19 in Jordan. BMC Pulm Med 2023; 23:341. [PMID: 37697259 PMCID: PMC10496175 DOI: 10.1186/s12890-023-02638-7] [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: 03/17/2023] [Accepted: 09/07/2023] [Indexed: 09/13/2023] Open
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lung infection has represented a global challenge. Intriguingly, it has been shown that the alveolar lung epithelium expresses little Angiotensin Converting Enzyme receptor protein (ACE2), the entry receptor for SARS-CoV-2. Upper airway establishment of infection and translocation to the lung is well documented but other anatomical niches may be relevant to potentially serious lung infection. ACE2 is heavily expressed in the gastrointestinal tract and gastrointestinal symptoms support a clinical diagnosis of Coronavirus disease 2019 (COVID-19). This suggests a research question and the need to gather patient data exploring potential aerodigestive links in SARS-CoV-2 tranlocation and infection which may be relevant in the peripheral lung. This recognizes anatomical proximity and concepts of bi-directional movement between the Gastrointestinal and lung systems in normal physiology and disease. We have therefore explored the potential for gastro oesophageal reflux disease (GORD) micro aspiration and aeorodigestive pathophysiology in a novel prospective investigation of patients hospitalized with COVID-19. METHODS This is a prospective descriptive cohort study of 210 patients who were hospitalized with a confirmed diagnosis of COVID-19. The cohort was divided into three groups of patients based on symptom severity and radiological results. The Reflux Symptom Index (RSI) was used to evaluate the presence and severity of GOR. An RSI greater than 13 is considered to be abnormal. Patients' saliva samples were tested using enzyme-linked immunosorbent assay (ELISA) to determine the level of salivary pepsin among the cohort of patients. RESULTS A total of 210 patients with COVID-19 were enrolled in the study with 55.2% (116/210) classified as mildly ill, 31.9% (67/210) moderately ill and 12.9% (27/210) as severely ill. 34% (72/210) of the patients had an RSI score of over 13 and a median salivary pepsin value of 54 ± 29 ng/ml which suggested an incidence of extraesophageal reflux (EOR) in around a third of patients. The presence of respiratory comorbid conditions, an RSI score of over 13 and a salivary pepsin level of > 76ng/ml increased the risk of developing a more severe COVID-19 infection. CONCLUSION The study showed a high prevalence of EOR among the study cohort and provide the first prospective evidence suggesting the potential for aerodigestive pathophysiology including microaspiration in COVID-19 disease. We believe that the results of our study support the need for more extensive research.
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Affiliation(s)
- Hafez Al-Momani
- Department of Microbiology, Pathology and Forensic medicine, Faculty of Medicine, The Hashemite University, Zarqa, 13133, Jordan.
| | - Safaa Mashal
- Department of Microbiology, Pathology and Forensic medicine, Faculty of Medicine, The Hashemite University, Zarqa, 13133, Jordan
| | - Dua'a Al Balawi
- Faculty of Applied Medical Sciences, The Hashemite University, Zarqa, 13133, Jordan
| | - Muna Almasri
- Faculty of Applied Medical Sciences, The Hashemite University, Zarqa, 13133, Jordan
| | - Abdel-Ellah Al-Shudifat
- Department of Internal and family Medicine, Faculty of Medicine, The Hashemite University, Zarqa, 13133, Jordan
| | - Ashraf I Khasawneh
- Department of Microbiology, Pathology and Forensic medicine, Faculty of Medicine, The Hashemite University, Zarqa, 13133, Jordan
| | - Jeffrey Pearson
- Translational and clinical research and Biosciences institutes, Newcastle University Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Christopher Ward
- Translational and clinical research and Biosciences institutes, Newcastle University Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
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Misra G, Manzoor A, Chopra M, Upadhyay A, Katiyar A, Bhushan B, Anvikar A. Genomic epidemiology of SARS-CoV-2 from Uttar Pradesh, India. Sci Rep 2023; 13:14847. [PMID: 37684328 PMCID: PMC10491582 DOI: 10.1038/s41598-023-42065-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 09/05/2023] [Indexed: 09/10/2023] Open
Abstract
The various strains and mutations of SARS-CoV-2 have been tracked using several forms of genomic classification systems. The present study reports high-throughput sequencing and analysis of 99 SARS-CoV-2 specimens from Western Uttar Pradesh using sequences obtained from the GISAID database, followed by phylogeny and clade classification. Phylogenetic analysis revealed that Omicron lineages BA-2-like (55.55%) followed by Delta lineage-B.1.617.2 (45.5%) were predominantly circulating in this area Signature substitution at positions S: N501Y, S: D614G, S: T478K, S: K417N, S: E484A, S: P681H, and S: S477N were commonly detected in the Omicron variant-BA-2-like, however S: D614G, S: L452R, S: P681R and S: D950N were confined to Delta variant-B.1.617.2. We have also identified three escape variants in the S gene at codon position 19 (T19I/R), 484 (E484A/Q), and 681 (P681R/H) during the fourth and fifth waves in India. Based on the phylogenetic diversification studies and similar changes in other lineages, our analysis revealed indications of convergent evolution as the virus adjusts to the shifting immunological profile of its human host. To the best of our knowledge, this study is an approach to comprehensively map the circulating SARS-CoV-2 strains from Western Uttar Pradesh using an integrated approach of whole genome sequencing and phylogenetic analysis. These findings will be extremely valuable in developing a structured approach toward pandemic preparedness and evidence-based intervention plans in the future.
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Affiliation(s)
- Gauri Misra
- Molecular Diagnostics and COVID-19 Kit Testing Laboratory, National Institute of Biologicals (Ministry of Health and Family Welfare), A-32, Sector-62, Institutional Area, Noida, UP, 201309, India.
| | - Ashrat Manzoor
- Molecular Diagnostics and COVID-19 Kit Testing Laboratory, National Institute of Biologicals (Ministry of Health and Family Welfare), A-32, Sector-62, Institutional Area, Noida, UP, 201309, India
| | - Meenu Chopra
- National Dairy Research Institute, Karnal, Haryana, India
| | - Archana Upadhyay
- Molecular Diagnostics and COVID-19 Kit Testing Laboratory, National Institute of Biologicals (Ministry of Health and Family Welfare), A-32, Sector-62, Institutional Area, Noida, UP, 201309, India
| | - Amit Katiyar
- Bioinformatics Facility, Centralized Core Research Facility, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Brij Bhushan
- Molecular Diagnostics and COVID-19 Kit Testing Laboratory, National Institute of Biologicals (Ministry of Health and Family Welfare), A-32, Sector-62, Institutional Area, Noida, UP, 201309, India
| | - Anup Anvikar
- Molecular Diagnostics and COVID-19 Kit Testing Laboratory, National Institute of Biologicals (Ministry of Health and Family Welfare), A-32, Sector-62, Institutional Area, Noida, UP, 201309, India
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George U, George O, Oguzie J, Osasona O, Motayo B, Kamani J, Eromon P, Folarin O, Happi A, Komolafe I, Happi C. Genomic characterization of Alphacoronavirus from Mops condylurus bats in Nigeria. Virus Res 2023; 334:199174. [PMID: 37467933 PMCID: PMC10392604 DOI: 10.1016/j.virusres.2023.199174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/12/2023] [Accepted: 07/15/2023] [Indexed: 07/21/2023]
Abstract
Coronaviruses (CoVs) are responsible for sporadic, epidemic and pandemic respiratory diseases worldwide. Bats have been identified as the reservoir for CoVs. To increase the number of complete coronavirus genomes in Africa and to comprehend the molecular epidemiology of bat Alphacoronaviruses (AlphaCoVs), we used deep metagenomics shotgun sequencing to obtain three (3) near-complete genomes of AlphaCoVs from Mops condylurus (Angolan free-tailed) bat in Nigeria. Phylogenetic and pairwise identity analysis of open reading frame 1ab (ORF1ab), spike (S), envelope (E), membrane (M) and nucleocapsid (N) genes of AlphaCoV in this study to previously described AlphaCoVs subgenera showed that the Nigerian AlphaCoVs may be members of potentially unique AlphaCoV subgenera circulating exclusively in bats in the Molossidae bat family. Recombination events were detected, suggesting the evolution of AlphaCoVs within the Molossidae family. The pairwise identity of the S gene in this study and previously published S gene sequences of other AlphaCoVs indicate that the Nigerian strains may have a genetically unique spike protein that is distantly related to other AlphaCoVs. Variations involving non-polar to polar amino acid substitution in both the Heptad Repeat (HR) regions 1 and 2 were observed. Further monitoring of bats to understand the host receptor use requirements of CoVs and interspecies CoV transmission in Africa is necessary to identify and prevent the potential danger that bat CoVs pose to public health.
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Affiliation(s)
- Uwem George
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State, Nigeria; Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
| | | | - Judith Oguzie
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State, Nigeria; Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
| | - Oluwadamilola Osasona
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State, Nigeria; Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
| | - Babatunde Motayo
- Department of Medical Microbiology, Federal Medical Centre, Abeokuta, Nigeria
| | - Joshua Kamani
- Parasitology Division National Veterinary Research Institute NVRI PMB 01, Vom, Plateau state Nigeria
| | - Philomena Eromon
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State, Nigeria
| | - Onikepe Folarin
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State, Nigeria; Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
| | - Anise Happi
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State, Nigeria
| | - Isaac Komolafe
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
| | - Christian Happi
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State, Nigeria; Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria.
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Annamalai A, Karuppaiya V, Ezhumalai D, Cheruparambath P, Balakrishnan K, Venkatesan A. Nano-based techniques: A revolutionary approach to prevent covid-19 and enhancing human awareness. J Drug Deliv Sci Technol 2023; 86:104567. [PMID: 37313114 PMCID: PMC10183109 DOI: 10.1016/j.jddst.2023.104567] [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: 01/25/2023] [Revised: 04/22/2023] [Accepted: 05/13/2023] [Indexed: 06/15/2023]
Abstract
In every century of history, there are many new diseases emerged, which are not even cured by many developed countries. Today, despite of scientific development, new deadly pandemic diseases are caused by microorganisms. Hygiene is considered to be one of the best methods of avoiding such communicable diseases, especially viral diseases. Illness caused by SARS-CoV-2 was termed COVID-19 by the WHO, the acronym derived from "coronavirus disease 2019. The globe is living in the worst epidemic era, with the highest infection and mortality rate owing to COVID-19 reaching 6.89% (data up to March 2023). In recent years, nano biotechnology has become a promising and visible field of nanotechnology. Interestingly, nanotechnology is being used to cure many ailments and it has revolutionized many aspects of our lives. Several COVID-19 diagnostic approaches based on nanomaterial have been developed. The various metal NPs, it is highly anticipated that could be viable and economical alternatives for treating drug resistant in many deadly pandemic diseases in near future. This review focuses on an overview of nanotechnology's increasing involvement in the diagnosis, prevention, and therapy of COVID-19, also this review provides readers with an awareness and knowledge of importance of hygiene.
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Affiliation(s)
- Asaikkutti Annamalai
- Marine Biotechnology Laboratory, Department of Biotechnology, School of Life Sciences, Pondicherry University, Pondicherry, 605 014, Puducherry, India
| | - Vimala Karuppaiya
- Cancer Nanomedicine Laboratory, Department of Zoology, School of Life Sciences, Periyar University, Salem, 636 011, Tamil Nadu, India
| | - Dhineshkumar Ezhumalai
- Dr. Krishnamoorthi Foundation for Advanced Scientific Research, Vellore, 632 001, Tamil Nadu, India
- Manushyaa Blossom Private Limited, Chennai, 600 102, Tamil Nadu, India
| | | | - Kaviarasu Balakrishnan
- Dr. Krishnamoorthi Foundation for Advanced Scientific Research, Vellore, 632 001, Tamil Nadu, India
- Manushyaa Blossom Private Limited, Chennai, 600 102, Tamil Nadu, India
| | - Arul Venkatesan
- Marine Biotechnology Laboratory, Department of Biotechnology, School of Life Sciences, Pondicherry University, Pondicherry, 605 014, Puducherry, India
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Rawal G, Yim-im W, Aljets E, Halbur PG, Zhang J, Opriessnig T. Porcine Respiratory Coronavirus (PRCV): Isolation and Characterization of a Variant PRCV from USA Pigs. Pathogens 2023; 12:1097. [PMID: 37764905 PMCID: PMC10536027 DOI: 10.3390/pathogens12091097] [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: 07/04/2023] [Revised: 08/23/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023] Open
Abstract
Porcine respiratory coronavirus (PRCV), a mutant of the transmissible gastroenteritis virus (TGEV), was first reported in Belgium in 1984. PRCV typically replicates and induces mild lesions in the respiratory tract, distinct from the enteric tropism of TGEV. In the past 30 years, PRCV has rarely been studied, and most cited information is on traditional isolates obtained during the 1980s and 1990s. Little is known about the genetic makeup and pathogenicity of recent PRCV isolates. The objective of this study was to obtain a contemporary PRCV isolate from US pigs for genetic characterization. In total, 1245 lung homogenate samples from pigs in various US states were tested via real-time PCR targeting PRCV and TGEV RNA. Overall, PRCV RNA was detected in five samples, and a single isolate (ISU20-92330) was successfully cultured and sequenced for its full-length genome. The isolate clustered with a new group of variant TGEVs and differed in various genomic regions compared to traditional PRCV isolates. Pathogens, such as PRCV, commonly circulate in pig herds without causing major disease. There may be value in tracking genomic changes and regularly updating the diagnostic methods for such viruses to be better prepared for the emergence of variants in ecology and pathogenicity.
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Affiliation(s)
- Gaurav Rawal
- Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, IA 50011, USA; (G.R.); (W.Y.-i.); (E.A.); (P.G.H.)
| | - Wannarat Yim-im
- Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, IA 50011, USA; (G.R.); (W.Y.-i.); (E.A.); (P.G.H.)
| | - Ethan Aljets
- Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, IA 50011, USA; (G.R.); (W.Y.-i.); (E.A.); (P.G.H.)
| | - Patrick G. Halbur
- Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, IA 50011, USA; (G.R.); (W.Y.-i.); (E.A.); (P.G.H.)
| | - Jianqiang Zhang
- Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, IA 50011, USA; (G.R.); (W.Y.-i.); (E.A.); (P.G.H.)
| | - Tanja Opriessnig
- Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, IA 50011, USA; (G.R.); (W.Y.-i.); (E.A.); (P.G.H.)
- Vaccines and Diagnostics Department, Moredun Research Institute, Penicuik EH26 0PZ, UK
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Salukhe I, Choi R, Van Voorhis W, Barrett L, Hyde J. Regulation of coronavirus nsp15 cleavage specificity by RNA structure. PLoS One 2023; 18:e0290675. [PMID: 37616296 PMCID: PMC10449227 DOI: 10.1371/journal.pone.0290675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 08/13/2023] [Indexed: 08/26/2023] Open
Abstract
SARS-CoV-2, the etiologic agent of the COVID-19 pandemic, has had an enduring impact on global public health. However, SARS-CoV-2 is only one of multiple pathogenic human coronaviruses (CoVs) to have emerged since the turn of the century. CoVs encode for several nonstructural proteins (nsps) that are essential for viral replication and pathogenesis. Among them is nsp15, a uridine-specific viral endonuclease that is important in evading the host immune response and promoting viral replication. Despite the established endonuclease function of nsp15, little is known about other determinants of its cleavage specificity. In this study we investigate the role of RNA secondary structure in SARS-CoV-2 nsp15 endonuclease activity. Using a series of in vitro endonuclease assays, we observed that thermodynamically stable RNA structures were protected from nsp15 cleavage relative to RNAs lacking stable structure. We leveraged the s2m RNA from the SARS-CoV-1 3'UTR as a model for our structural studies as it adopts a well-defined structure with several uridines, two of which are unpaired and thus highly probable targets for nsp15 cleavage. We found that SARS-CoV-2 nsp15 specifically cleaves s2m at the unpaired uridine within the GNRNA pentaloop of the RNA. Further investigation revealed that the position of uridine within the pentaloop also impacted nsp15 cleavage efficiency suggesting that positioning within the pentaloop is necessary for optimal presentation of the scissile uridine and alignment within the nsp15 catalytic pocket. Our findings indicate that RNA secondary structure is an important determinant of nsp15 cleavage and provides insight into the molecular mechanisms of RNA recognition by nsp15.
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Affiliation(s)
- Indraneel Salukhe
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA, United States of America
| | - Ryan Choi
- Division of Allergy and Infectious Diseases, Department of Medicine, Center for Emerging and Reemerging Infectious Diseases (CERID), University of Washington School of Medicine, Seattle, WA, United States of America
| | - Wesley Van Voorhis
- Division of Allergy and Infectious Diseases, Department of Medicine, Center for Emerging and Reemerging Infectious Diseases (CERID), University of Washington School of Medicine, Seattle, WA, United States of America
| | - Lynn Barrett
- Division of Allergy and Infectious Diseases, Department of Medicine, Center for Emerging and Reemerging Infectious Diseases (CERID), University of Washington School of Medicine, Seattle, WA, United States of America
| | - Jennifer Hyde
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA, United States of America
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He WT, Li D, Baele G, Zhao J, Jiang Z, Ji X, Veit M, Suchard MA, Holmes EC, Lemey P, Boni MF, Su S. Newly identified lineages of porcine hemagglutinating encephalomyelitis virus exhibit respiratory phenotype. Virus Evol 2023; 9:vead051. [PMID: 37711483 PMCID: PMC10499004 DOI: 10.1093/ve/vead051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 05/18/2023] [Accepted: 08/13/2023] [Indexed: 09/16/2023] Open
Abstract
Swine pathogens have a long history of zoonotic transmission to humans, occasionally leading to sustained outbreaks or pandemics. Through a retrospective epidemiological study of swine populations in China, we describe novel lineages of porcine hemagglutinating encephalomyelitis virus (PHEV) complex coronaviruses (CoVs) that cause exclusively respiratory symptoms with no signs of the neurological symptoms typically associated with classical PHEV infection. Through large-scale epidemiological surveillance, we show that these novel lineages have circulated in at least eight provinces in southeastern China. Phylogenetic and recombination analyses of twenty-four genomes identified two major viral lineages causing respiratory symptoms with extensive recombination within them, between them, and between classical PHEV and the novel respiratory variant PHEV (rvPHEV) lineages. Divergence times among the sampled lineages in the PHEV virus complex date back to 1886-1958 (mean estimate 1928), with the two major rvPHEV lineages separating approximately 20 years later. Many rvPHEV viruses show amino acid substitutions at the carbohydrate-binding site of hemagglutinin esterase (HE) and/or have lost the cysteine required for HE dimerization. This resembles the early adaptation of human CoVs, where HE lost its hemagglutination ability to adapt to growth in the human respiratory tract. Our study represents the first report of the evolutionary history of rvPHEV circulating in swine and highlights the importance of characterizing CoV diversity and recombination in swine to identify pathogens with outbreak potential that could threaten swine farming.
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Affiliation(s)
- Wan-Ting He
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, Leuven 3000, Belgium
| | - Dongyan Li
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, Leuven 3000, Belgium
| | - Jin Zhao
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhiwen Jiang
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiang Ji
- Department of Mathematics, School of Science & Engineering, Tulane University, New Orleans, LA 70118, USA
| | - Michael Veit
- Institute for Virology, Center for Infection Medicine, Veterinary Faculty, Free University Berlin, Berlin 14163, Germany
| | - Marc A Suchard
- Department of Biostatistics, Fielding School of Public Health, and Departments of Biomathematics and Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, Leuven 3000, Belgium
| | | | - Shuo Su
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
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David D, Asiku J, Storm N, Lapin K, Berkowitz A, Kovtunenko A, Edery N, King R, Sol A. Identification, Isolation, and Molecular Characterization of Betacoronavirus in Oryx leucoryx. Microbiol Spectr 2023; 11:e0484822. [PMID: 37428095 PMCID: PMC10433975 DOI: 10.1128/spectrum.04848-22] [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: 11/27/2022] [Accepted: 06/08/2023] [Indexed: 07/11/2023] Open
Abstract
Coronaviruses (CoVs) are enveloped viruses with a large RNA genome (26 to 32 kb) and are classified into four genera: Alphacoronavirus, Betacoronavirus, Gammacoronavirus, and Deltacoronavirus. CoV infections cause respiratory, enteric, and neurologic disorders in mammalian and avian species. In 2019, Oryx leucoryx animals suffered from severe hemorrhagic diarrhea and high morbidity rates. Upon initial diagnosis, we found that the infected animals were positive for coronavirus by pancoronavirus reverse transcriptase RT-PCR. Next, we detected the presence of CoV particles in these samples by electron microscopy and immunohistochemistry. CoV was isolated and propagated on the HRT-18G cell line, and its full genome was sequenced. Full-genome characterization and amino acid comparisons of this viral agent demonstrated that this virus is an evolutionarily distinct Betacoronavirus belonging to the subgenus Embecovirus and the Betacoronavirus 1 species. Furthermore, we found that it is most similar to the subspecies dromedary camel coronavirus HKU23 by phylogenetic analysis. Here, we present the first report of isolation and characterization of Betacoronavirus associated with enteric disease in Oryx leucoryx. IMPORTANCE CoVs cause enteric and respiratory infections in humans and animal hosts. The ability of CoVs to cross interspecies barriers is well recognized, as emphasized by the ongoing pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The identification of novel CoV strains and surveillance of CoVs in both humans and animals are relevant and important to global health. In this study, we isolated and characterized a newly identified Betacoronavirus that causes enteric disease in a wild animal, Oryx leucoryx (the Arabian oryx). This work is the first report describing CoV infection in Oryx leucoryx and provides insights into its origin.
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Affiliation(s)
- Dan David
- Kimron Veterinary Institute, Beit Dagan, Israel
| | - Jimmy Asiku
- Kimron Veterinary Institute, Beit Dagan, Israel
- The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Nick Storm
- Kimron Veterinary Institute, Beit Dagan, Israel
| | - Katya Lapin
- Kimron Veterinary Institute, Beit Dagan, Israel
| | | | | | - Nir Edery
- Kimron Veterinary Institute, Beit Dagan, Israel
| | - Roni King
- Israel Nature and Parks Authority, Jerusalem, Israel
| | - Asaf Sol
- Kimron Veterinary Institute, Beit Dagan, Israel
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36
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Mondol SM, Hasib M, Limon MBH, Alam ASMRU. Insights into Omicron's Low Fusogenicity through In Silico Molecular Studies on Spike-Furin Interactions. Bioinform Biol Insights 2023; 17:11779322231189371. [PMID: 37529484 PMCID: PMC10387760 DOI: 10.1177/11779322231189371] [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: 03/17/2023] [Accepted: 07/03/2023] [Indexed: 08/03/2023] Open
Abstract
The Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant and its subvariants have a unique set of mutations. Two of those mutations (N679 K and P681 H) reside close to the S1 /S2 furin cleavage site (FCS; 685-686). When these mutations reside together, they exert less-efficient membrane fusion than wild type and most other variants of concern such as the Delta variant. Here, we in silico targeted these mutations to find out which of the amino acids and interactions change plays the key role in fusion. To comprehend the epistatic effect of N679 K and P681 H mutations on the spike protein, we in silico constructed three types of spike protein sequences by changing the respective amino acids on 679 and 681 positions (P681 H, N679 K, K679 N-H681 P variants). We then analyzed the binding affinity of furin and spike (Furin-Wild, Furin-Omicron, Furin-P681 H, Furin-N679 K, and Furin-K679 N/H681 P) complexes. Omicron and P681 H variants showed a similar higher binding energy trend compared to the wild type and N679 K. The variation in hydrogen, hydrophobic, and salt bridge bonds between spike protein and furin provided an explanation for the observed low fusogenicity of Omicron. The fate of the epistasis in furin binding and possible cleavage depends on the efficient interaction between FCS in spike and furin catalytic triad, and in addition, the loss of the hydrogen bond between Arg 681 (spike) and Asn 295 (furin) along with inhibitor-like ineffective higher affinity plays an important role in the enzymatic activity.
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Affiliation(s)
| | - Md Hasib
- Department of Biochemistry and Biotechnology, University of Barishal, Barishal, Bangladesh
| | | | - A S M Rubayet Ul Alam
- Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh
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Manuja A, Kumar B, Chhabra D, Brar B, Thachamvally R, Pal Y, Prasad M. Synergistic Effect of Zinc-Chitosan Nanoparticles and Hydroxychloroquine to Inhibit Buffalo Coronavirus. Polymers (Basel) 2023; 15:2949. [PMID: 37447594 DOI: 10.3390/polym15132949] [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: 02/25/2023] [Revised: 04/29/2023] [Accepted: 05/06/2023] [Indexed: 07/15/2023] Open
Abstract
Zinc ions can hinder the synthesis of proteins required for accomplishing several stages of the viral life cycle. The intracellular zinc concentration can be increased by using zinc ionophores which transport zinc ions into the cells and hinder viral replication. (Hydroxy)chloroquine is an example of a zinc ionophore, but both zinc and (hydroxy)chloroquine can be toxic to the host organism. The nanocarriers may serve as camouflage to evade the adverse effects of drugs, chemicals, and nanoparticles on the host. We formulated ZnO nanoparticles with flower-like morphology (ZnONFs). It was further decorated with chitosan along with hydroxychloroquine (as a zinc ionophore) (CHCZnO NPs). We have chosen the cationic polymer chitosan since it is biocompatible, biodegradable and binds easily with the cells, and enhances the transport of drugs across cell membranes. The formulation was investigated for size, shape, surface charge, and interaction of chemicals used. We evaluated the formulations for cytotoxicity, and biocompatibility in embryonated chicks and their efficacy against bovine coronavirus (BCoV) isolated from a buffalo calf, and pneumo-enteric coronaviruses isolated from a buffalo calf with promising results in comparison to ZnONFs/hydroxychloroquine alone. Furthermore, we elucidate the mechanism underlying the lysosomotropic effect of various formulations on Vero cells infected with the buffalo coronavirus.
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Affiliation(s)
- Anju Manuja
- ICAR-National Research Centre on Equines, Hisar 125001, India
| | - Balvinder Kumar
- ICAR-National Research Centre on Equines, Hisar 125001, India
| | - Dharvi Chhabra
- ICAR-National Research Centre on Equines, Hisar 125001, India
| | - Basanti Brar
- Lala Lajpat Rainiversity of Veterinary & Animal Sciences, Hisar 125004, India
| | | | - Yash Pal
- ICAR-National Research Centre on Equines, Hisar 125001, India
| | - Minakshi Prasad
- ICAR-National Research Centre on Equines, Hisar 125001, India
- Lala Lajpat Rainiversity of Veterinary & Animal Sciences, Hisar 125004, India
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Mulgaonkar N, Wang H, Zhang J, Roundy CM, Tang W, Chaki SP, Pauvolid-Corrêa A, Hamer GL, Fernando S. Montelukast and Telmisartan as Inhibitors of SARS-CoV-2 Omicron Variant. Pharmaceutics 2023; 15:1891. [PMID: 37514075 PMCID: PMC10385313 DOI: 10.3390/pharmaceutics15071891] [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] [Revised: 06/29/2023] [Accepted: 06/30/2023] [Indexed: 07/30/2023] Open
Abstract
Earlier studies with montelukast (M) and telmisartan (T) have revealed their potential antiviral properties against SARS-CoV-2 wild-type (WT) but have not assessed their efficacy against emerging Variants of Concern (VOCs) such as Omicron. Our research fills this gap by investigating these drugs' impact on VOCs, a topic that current scientific literature has largely overlooked. We employed computational methodologies, including molecular mechanics and machine learning tools, to identify drugs that could potentially disrupt the SARS-CoV-2 spike RBD-ACE2 protein interaction. This led to the identification of two FDA-approved small molecule drugs, M and T, conventionally used for treating asthma and hypertension, respectively. Our study presents an additional potential use for these drugs as antivirals. Our results show that both M and T can inhibit not only the WT SARS-CoV-2 but also, in the case of M, the Omicron variant, without reaching cytotoxic concentrations. This novel finding fills an existing gap in the literature and introduces the possibility of repurposing these drugs for SARS-CoV-2 VOCs, an essential step in responding to the evolving global pandemic.
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Affiliation(s)
- Nirmitee Mulgaonkar
- Biological and Agricultural Engineering Department, Texas A&M University, College Station, TX 77843, USA
| | - Haoqi Wang
- Biological and Agricultural Engineering Department, Texas A&M University, College Station, TX 77843, USA
| | - Junrui Zhang
- Biological and Agricultural Engineering Department, Texas A&M University, College Station, TX 77843, USA
| | | | - Wendy Tang
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
| | - Sankar Prasad Chaki
- Texas A&M Global Health Research Complex, Division of Research, Texas A&M University, College Station, TX 77843, USA
| | - Alex Pauvolid-Corrêa
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
| | - Gabriel L Hamer
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
| | - Sandun Fernando
- Biological and Agricultural Engineering Department, Texas A&M University, College Station, TX 77843, USA
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Senthilazhagan K, Sakthimani S, Kallanja D, Venkataraman S. SARS-CoV-2: analysis of the effects of mutations in non-structural proteins. Arch Virol 2023; 168:186. [PMID: 37344726 DOI: 10.1007/s00705-023-05818-2] [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: 03/06/2023] [Accepted: 05/10/2023] [Indexed: 06/23/2023]
Abstract
A worldwide pandemic that started in China in late 2019 was caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a single-stranded RNA virus belonging to the family Coronaviridae. Due to its structural variability and mutability, this virus continues to evolve and pose a major health threat around the world. Its characteristics, such as transmissibility, antigenicity, and resistance to drugs and vaccines, are continually altered through mutations. Examining mutational hotspots and their structural repercussions can thus aid in the development of more-effective vaccinations and treatment plans. In this study, we used full genome sequences of SARS-CoV-2 variants to predict structural changes in viral proteins. These sequences were obtained from the Global Initiative on Sharing Avian Influenza Data (GISAID), and a set of significant mutations were identified in each of the non-structural proteins (NSP1-16) and structural proteins, including the envelope, nucleocapsid, membrane, and spike proteins. The mutations were characterized as stabilizing or destabilizing based on their effect on protein dynamics and stability, and their impact on structure and function was evaluated. Among all of the proteins, NSP6 stands out as especially variable. The results of this study augment our understanding of how mutational events influence virus pathogenicity and evolution.
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Affiliation(s)
- Kavya Senthilazhagan
- Department of Biotechnology, Anna University, 600025, Guindy, Chennai, Tamil Nādu, India
| | - Seshagiri Sakthimani
- Department of Biotechnology, Anna University, 600025, Guindy, Chennai, Tamil Nādu, India
| | - Deepthi Kallanja
- Department of Biotechnology, Anna University, 600025, Guindy, Chennai, Tamil Nādu, India
| | - Sangita Venkataraman
- Department of Biotechnology, Anna University, 600025, Guindy, Chennai, Tamil Nādu, India.
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40
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Al-Momani H, Aolymat I, Almasri M, Mahmoud SA, Mashal S. Prevalence of gastro-intestinal symptoms among COVID-19 patients and the association with disease clinical outcomes. Future Sci OA 2023; 9:FSO858. [PMID: 37180610 PMCID: PMC10167716 DOI: 10.2144/fsoa-2023-0040] [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: 03/03/2023] [Accepted: 04/11/2023] [Indexed: 05/16/2023] Open
Abstract
Aim This study examined the various manifestations of COVID-19 in people's gastro-intestinal system and how gastro-intestinal involvement relates to the progression and outcome of the disease. Methodology A questionnaire survey was used to collect data from 561 COVID-19 patients between February 6 and 6 April 2022. Laboratory data and clinical outcomes were obtained from the patients' medical records. Results 39.9% of patients presented gastro-intestinal symptoms, mainly loss of appetite, nausea, vomiting and diarrhea. Gastro-intestinal symptoms were not linked to poorer outcomes such as mortality, ICU admission or length of hospital stays. Conclusion gastro-intestinal symptoms were common among patients and may manifest with respiratory symptoms. We recommended clinicians to watch out for gastro-intestinal symptoms as related to COVID-19 infection.
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Affiliation(s)
- Hafez Al-Momani
- Department of Microbiology, Pathology & Forensic medicine, Faculty of Medicine, The Hashemite University, PO box 330127, Zarqa 13133, Jordan
| | - Iman Aolymat
- Department of Anatomy, Physiology & Biochemistry, Faculty of Medicine, The Hashemite University, PO box 330127, Zarqa 13133, Jordan
| | - Muna Almasri
- Department of Microbiology, Pathology & Forensic medicine, Faculty of Medicine, The Hashemite University, PO box 330127, Zarqa 13133, Jordan
| | - Sameer Alhaj Mahmoud
- Department of basic medical science, Faculty of Medicine, Al-Balqa’ Applied University, As-Salt, Jordan
| | - Safaa Mashal
- Department of Microbiology, Pathology & Forensic medicine, Faculty of Medicine, The Hashemite University, PO box 330127, Zarqa 13133, Jordan
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41
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Chen C, Liang J, Hu H, Li X, Wang L, Wang Z. Research progress in methods for detecting neutralizing antibodies against SARS-CoV-2. Anal Biochem 2023:115199. [PMID: 37257735 DOI: 10.1016/j.ab.2023.115199] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/13/2023] [Accepted: 05/27/2023] [Indexed: 06/02/2023]
Abstract
The emergence of SARS-CoV-2 has seriously affected the lives of people worldwide. Clarifying the attenuation rule of SARS-CoV-2 neutralizing antibody (NAb) in vivo is the key to prevent reinfection and recurrence of virus. Currently, the commonly used methods for detecting NAb include virus neutralization tests, pseudovirus neutralization assays, lateral flow immunochromatography and enzyme-linked immunosorbent assays. The detection of NAb not only can be used to evaluate the level of immunity after vaccination or infection but also can provide important theoretical support for virus reinfection, recurrence and vaccine iteration. In this research, the related technologies of SARS-CoV-2 NAb detection were reviewed, aiming to provide better research ideas for SARS-CoV-2 epidemic prevention and control.
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Affiliation(s)
- Chunxia Chen
- Joint National Laboratory for Antibody Drug Engineering, Clinical Laboratory of the First Affiliated Hospital, Henan University, Kaifeng, 475004, China
| | - Jiahui Liang
- Joint National Laboratory for Antibody Drug Engineering, Clinical Laboratory of the First Affiliated Hospital, Henan University, Kaifeng, 475004, China
| | - Hangzhan Hu
- Joint National Laboratory for Antibody Drug Engineering, Clinical Laboratory of the First Affiliated Hospital, Henan University, Kaifeng, 475004, China; Heze Municipal Hospital, Heze, 274000, China
| | - Xiaoquan Li
- Heze Municipal Hospital, Heze, 274000, China
| | - Li Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Henan University, Kaifeng, 475004, China.
| | - Zhizeng Wang
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing, 400044, China; Joint National Laboratory for Antibody Drug Engineering, Clinical Laboratory of the First Affiliated Hospital, Henan University, Kaifeng, 475004, China.
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42
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Baroni C, Potito J, Perticone ME, Orausclio P, Luna CM. How Does Long-COVID Impact Prognosis and the Long-Term Sequelae? Viruses 2023; 15:v15051173. [PMID: 37243259 DOI: 10.3390/v15051173] [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: 04/13/2023] [Revised: 05/01/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
CONTEXT We reviewed what has been studied and published during the last 3 years about the consequences, mainly respiratory, cardiac, digestive, and neurological/psychiatric (organic and functional), in patients with COVID-19 of prolonged course. OBJECTIVE To conduct a narrative review synthesizing current clinical evidence of abnormalities of signs, symptoms, and complementary studies in COVID-19 patients who presented a prolonged and complicated course. METHODS A review of the literature focused on the involvement of the main organic functions mentioned, based almost exclusively on the systematic search of publications written in English available on PubMed/MEDLINE. RESULTS Long-term respiratory, cardiac, digestive, and neurological/psychiatric dysfunction are present in a significant number of patients. Lung involvement is the most common; cardiovascular involvement may happen with or without symptoms or clinical abnormalities; gastrointestinal compromise includes the loss of appetite, nausea, gastroesophageal reflux, diarrhea, etc.; and neurological/psychiatric compromise can produce a wide variety of signs and symptoms, either organic or functional. Vaccination is not associated with the emergence of long-COVID, but it may happen in vaccinated people. CONCLUSIONS The severity of illness increases the risk of long-COVID. Pulmonary sequelae, cardiomyopathy, the detection of ribonucleic acid in the gastrointestinal tract, and headaches and cognitive impairment may become refractory in severely ill COVID-19 patients.
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Affiliation(s)
- Carolina Baroni
- Department of Medicine, Pulmonary Diseases Division, Hospital de Clínicas, University of Buenos Aires, Buenos Aires C1120 AAF, Argentina
| | - Jorge Potito
- Department of Medicine, Pulmonary Diseases Division, Hospital de Clínicas, University of Buenos Aires, Buenos Aires C1120 AAF, Argentina
| | - María Eugenia Perticone
- Department of Medicine, Pulmonary Diseases Division, Hospital de Clínicas, University of Buenos Aires, Buenos Aires C1120 AAF, Argentina
| | - Paola Orausclio
- Department of Radiology, Centro Rossi, Buenos Aires C1035 ABC, Argentina
| | - Carlos Marcelo Luna
- Department of Medicine, Pulmonary Diseases Division, Hospital de Clínicas, University of Buenos Aires, Buenos Aires C1120 AAF, Argentina
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43
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Hafsi T, Baba S. Exploring the Process of Policy Overreaction: The COVID-19 Lockdown Decisions. JOURNAL OF MANAGEMENT INQUIRY 2023; 32:152-173. [PMID: 36814993 PMCID: PMC9936179 DOI: 10.1177/10564926221082494] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Policy overreaction is a common phenomenon, especially in complex and emergency situations where politicians are led to make decisions fast. In these emergency decisions, emotions run generally high and cognitive processes are often impaired. The conditions of policy overreaction are in place as emotions overwhelm decision makers' rational processes. Drawing on the response patterns of three countries to the COVID-19 pandemic, we develop a process model of policy overreaction which describes the effects of negative emotions and institutional isomorphism on policy decision-making. Our model highlights four critical stages: negative emotions buildup, propagation of fear, isomorphic decision-making, and leading to an intractable crisis. This article shows precisely how the cascading effect of negative emotions, particularly fear, is contagious and spreads to generate crowd effects, which bend considerably policy makers' ability to make rational decisions. Our theory provides a better understanding of the process by which policy overreaction takes place.
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Affiliation(s)
- Taieb Hafsi
- Holder of the Strategy and Society Chair, HEC Montréal
| | - Sofiane Baba
- Université de Sherbrooke,Sofiane Baba, Université de Sherbrooke.
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van Tilburg M, Hilbers PAJ, Markvoort AJ. On the role of membrane embedding, protein rigidity and transmembrane length in lipid membrane fusion. SOFT MATTER 2023; 19:1791-1802. [PMID: 36786821 DOI: 10.1039/d2sm01582j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The fusion of biological membranes is ubiquitous in natural processes like exo- and endocytosis, intracellular trafficking and viral entry. Membrane fusion is also utilized in artificial biomimetic fusion systems, e.g. for drug delivery. Both the natural and the biomimetic fusion systems rely on a wide range of (artificial) proteins mediating the fusion process. Although the exact mechanisms of these proteins differ, clear analogies in their general behavior can be observed in bringing the membranes in close proximity and mediating the fusion reaction. In our study, we use molecular dynamics simulations with coarse grained models, mimicking the general behavior of fusion proteins (spikes), to systematically examine the effects of specific characteristics of these proteins on the fusion process. The protein characteristics considered are (i) the type of membrane embedding, i.e., either transmembrane or not, (ii) the rigidity, and (iii) the transmembrane domain (TMD) length. The results show essential differences in fusion pathway between monotopic and transmembrane spikes, in which transmembrane spikes seem to inhibit the formation of hemifusion diaphragms, leading to a faster fusion development. Furthermore, we observed that an increased rigidity and a decreased TMD length both proved to contribute to a faster fusion development. Finally, we show that a single spike may suffice to successfully induce a fusion reaction, provided that the spike is sufficiently rigid and attractive. Not only does this shed light on biological fusion of membranes, it also provides clear design rules for artificial membrane fusion systems.
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Affiliation(s)
- Marco van Tilburg
- Department of Biomedical Engineering, Computational Biology Group, Eindhoven University of Technology, The Netherlands.
| | - Peter A J Hilbers
- Department of Biomedical Engineering, Computational Biology Group, Eindhoven University of Technology, The Netherlands.
- Institute of Complex Molecular Systems, Eindhoven University of Technology, The Netherlands
| | - Albert J Markvoort
- Department of Biomedical Engineering, Computational Biology Group, Eindhoven University of Technology, The Netherlands.
- Institute of Complex Molecular Systems, Eindhoven University of Technology, The Netherlands
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45
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Cong X, Zhang L, Zhu H, Wu M, Zhu Y, Lian Y, Huang B, Gu Y, Cong F. Preparation of a new monoclonal antibody against nucleocapsid protein of swine acute diarrhea syndrome coronavirus and identification of its linear antigenic epitope. Int J Biol Macromol 2023; 239:124241. [PMID: 36996959 DOI: 10.1016/j.ijbiomac.2023.124241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 03/24/2023] [Accepted: 03/26/2023] [Indexed: 03/31/2023]
Abstract
Swine acute diarrhea syndrome coronavirus (SADS-CoV), which causes severe diarrhea in newborn piglets, was first identified in Southern China in 2017. Since the Nucleocapsid (N) protein in SADS-CoV is highly conserved and plays a key role in virus replication, it is often used as a target protein in scientific research. In this study, the N protein of SADS-CoV was successfully expressed, and a new monoclonal antibody (mAb), 5G12, against the protein was generated successfully. The mAb 5G12 can be used to detect SADS-CoV strains by indirect immunofluorescence assay (IFA) and western blotting. The mAb 5G12 epitope was located to amino acids 11 EQAESRGRK 19 by evaluating the antibody for reactivity with a series of truncated N protein segments. The biological information analysis showed that the antigenic epitope had a high antigenic index and conservation. This study will help further understand the protein structure and function of SADS-CoV and in the establishment of specific SADS-CoV detection methods.
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46
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Yang T, Wang SC, Ye L, Maimaitiyiming Y, Naranmandura H. Targeting viral proteins for restraining SARS-CoV-2: focusing lens on viral proteins beyond spike for discovering new drug targets. Expert Opin Drug Discov 2023; 18:247-268. [PMID: 36723288 DOI: 10.1080/17460441.2023.2175812] [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: 02/02/2023]
Abstract
INTRODUCTION Emergence of highly infectious SARS-CoV-2 variants are reducing protection provided by current vaccines, requiring constant updates in antiviral approaches. The virus encodes four structural and sixteen nonstructural proteins which play important roles in viral genome replication and transcription, virion assembly, release , entry into cells, and compromising host cellular defenses. As alien proteins to host cells, many viral proteins represent potential targets for combating the SARS-CoV-2. AREAS COVERED Based on literature from PubMed and Web of Science databases, the authors summarize the typical characteristics of SARS-CoV-2 from the whole viral particle to the individual viral proteins and their corresponding functions in virus life cycle. The authors also discuss the potential and emerging targeted interventions to curb virus replication and spread in detail to provide unique insights into SARS-CoV-2 infection and countermeasures against it. EXPERT OPINION Our comprehensive analysis highlights the rationale to focus on non-spike viral proteins that are less mutated but have important functions. Examples of this include: structural proteins (e.g. nucleocapsid protein, envelope protein) and extensively-concerned nonstructural proteins (e.g. NSP3, NSP5, NSP12) along with the ones with relatively less attention (e.g. NSP1, NSP10, NSP14 and NSP16), for developing novel drugs to overcome resistance of SARS-CoV-2 variants to preexisting vaccines and antibody-based treatments.
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Affiliation(s)
- Tao Yang
- Department of Hematology of First Affiliated Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Si Chun Wang
- Department of Hematology of First Affiliated Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Linyan Ye
- Department of Hematology of First Affiliated Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yasen Maimaitiyiming
- Department of Hematology of First Affiliated Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Zhejiang Province Key Laboratory of Haematology Oncology Diagnosis and Treatment, Hangzhou, Zhejiang, China.,Department of Neurobiology, NHC and CAMS Key Laboratory of Medical Neurobiology, School of Brain Science and Brain Medicine, and MOE Frontier Science Center for Brain Science and Brain-machine Integration, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Hua Naranmandura
- Department of Hematology of First Affiliated Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Zhejiang Province Key Laboratory of Haematology Oncology Diagnosis and Treatment, Hangzhou, Zhejiang, China.,Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
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47
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Bandyopadhyay SS, Halder AK, Saha S, Chatterjee P, Nasipuri M, Basu S. Assessment of GO-Based Protein Interaction Affinities in the Large-Scale Human–Coronavirus Family Interactome. Vaccines (Basel) 2023; 11:vaccines11030549. [PMID: 36992133 DOI: 10.3390/vaccines11030549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/19/2023] [Accepted: 02/23/2023] [Indexed: 03/03/2023] Open
Abstract
SARS-CoV-2 is a novel coronavirus that replicates itself via interacting with the host proteins. As a result, identifying virus and host protein-protein interactions could help researchers better understand the virus disease transmission behavior and identify possible COVID-19 drugs. The International Committee on Virus Taxonomy has determined that nCoV is genetically 89% compared to the SARS-CoV epidemic in 2003. This paper focuses on assessing the host–pathogen protein interaction affinity of the coronavirus family, having 44 different variants. In light of these considerations, a GO-semantic scoring function is provided based on Gene Ontology (GO) graphs for determining the binding affinity of any two proteins at the organism level. Based on the availability of the GO annotation of the proteins, 11 viral variants, viz., SARS-CoV-2, SARS, MERS, Bat coronavirus HKU3, Bat coronavirus Rp3/2004, Bat coronavirus HKU5, Murine coronavirus, Bovine coronavirus, Rat coronavirus, Bat coronavirus HKU4, Bat coronavirus 133/2005, are considered from 44 viral variants. The fuzzy scoring function of the entire host–pathogen network has been processed with ~180 million potential interactions generated from 19,281 host proteins and around 242 viral proteins. ~4.5 million potential level one host–pathogen interactions are computed based on the estimated interaction affinity threshold. The resulting host–pathogen interactome is also validated with state-of-the-art experimental networks. The study has also been extended further toward the drug-repurposing study by analyzing the FDA-listed COVID drugs.
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Affiliation(s)
- Soumyendu Sekhar Bandyopadhyay
- Department of Computer Science and Engineering, Jadavpur University, Kolkata 700032, India
- Department of Computer Science and Engineering, School of Engineering and Technology, Adamas University, Kolkata 700126, India
| | - Anup Kumar Halder
- Faculty of Mathematics and Information Sciences, Warsaw University of Technology, 00-662 Warsaw, Poland
| | - Sovan Saha
- Department of Computer Science and Engineering (Artificial Intelligence and Machine Learning), Techno Main Salt Lake, Sector V, Kolkata 700091, India
| | - Piyali Chatterjee
- Department of Computer Science and Engineering, Netaji Subhash Engineering College, Kolkata 700152, India
| | - Mita Nasipuri
- Department of Computer Science and Engineering, Jadavpur University, Kolkata 700032, India
| | - Subhadip Basu
- Department of Computer Science and Engineering, Jadavpur University, Kolkata 700032, India
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48
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Intragenomic rearrangements involving 5'-untranslated region segments in SARS-CoV-2, other betacoronaviruses, and alphacoronaviruses. Virol J 2023; 20:36. [PMID: 36829234 PMCID: PMC9957694 DOI: 10.1186/s12985-023-01998-0] [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: 05/08/2022] [Accepted: 02/21/2023] [Indexed: 02/26/2023] Open
Abstract
BACKGROUND Variation of the betacoronavirus SARS-CoV-2 has been the bane of COVID-19 control. Documented variation includes point mutations, deletions, insertions, and recombination among closely or distantly related coronaviruses. Here, we describe yet another aspect of genome variation by beta- and alphacoronaviruses that was first documented in an infectious isolate of the betacoronavirus SARS-CoV-2, obtained from 3 patients in Hong Kong that had a 5'-untranslated region segment at the end of the ORF6 gene that in its new location translated into an ORF6 protein with a predicted modified carboxyl terminus. While comparing the amino acid sequences of translated ORF8 genes in the GenBank database, we found a subsegment of the same 5'-UTR-derived amino acid sequence modifying the distal end of ORF8 of an isolate from the United States and decided to carry out a systematic search. METHODS Using the nucleotide and in the case of SARS-CoV-2 also the translated amino acid sequence in three reading frames of the genomic termini of coronaviruses as query sequences, we searched for 5'-UTR sequences in regions other than the 5'-UTR in SARS-CoV-2 and reference strains of alpha-, beta-, gamma-, and delta-coronaviruses. RESULTS We here report numerous genomic insertions of 5'-untranslated region sequences into coding regions of SARS-CoV-2, other betacoronaviruses, and alphacoronaviruses, but not delta- or gammacoronaviruses. To our knowledge this is the first systematic description of such insertions. In many cases, these insertions would change viral protein sequences and further foster genomic flexibility and viral adaptability through insertion of transcription regulatory sequences in novel positions within the genome. Among human Embecorivus betacoronaviruses, for instance, from 65% to all of the surveyed sequences in publicly available databases contain inserted 5'-UTR sequences. CONCLUSION The intragenomic rearrangements involving 5'-untranslated region sequences described here, which in several cases affect highly conserved genes with a low propensity for recombination, may underlie the generation of variants homotypic with those of concern or interest and with potentially differing pathogenic profiles. Intragenomic rearrangements thus add to our appreciation of how variants of SARS-CoV-2 and other beta- and alphacoronaviruses may arise.
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Konje JC, Al Beloushi M, Ahmed B. Immunisation against COVID-19 in Pregnancy and of Women Planning Pregnancy. Viruses 2023; 15:v15030621. [PMID: 36992330 PMCID: PMC10059008 DOI: 10.3390/v15030621] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 02/15/2023] [Accepted: 02/16/2023] [Indexed: 03/03/2023] Open
Abstract
Following reports of the first human SARS-CoV2 infection in December 2019 from Wuhan Province, China, there was such rapid spread that by March 2021, the World Health Organization (WHO) had declared a pandemic. Over 6.5 million people have died from this infection worldwide, although this is most likely an underestimate. Until vaccines became available, mortality and severe morbidity were costly in terms of life lost as well as the cost of supporting the severely and acutely ill. Vaccination changed the landscape, and following worldwide adoption, life has gradually been returning to normal. The speed of production of the vaccines was unprecedented and undoubtedly ushered in a new era in the science of fighting infections. The developed vaccines were on the already known platforms for vaccine delivery: inactivated virus, virus vector, virus-like particles (VLP) subunit, DNA and mRNA. The mRNA platform was used for the first time to deliver vaccines to humans. An understanding of these platforms and the pros and cons of each are important for clinicians who are often challenged by the recipients on the advantages and risks of these vaccines. These vaccines have so far and reassuringly been shown to be safe in reproduction (with no effect on gametes) and pregnancy (not associated with congenital malformations). However, safety remains paramount and continuing vigilance is critical, especially against rare fatal complications such as vaccine-induced thrombocytopenia and myocarditis. Finally, the waning immunity months after vaccination means repeated immunisation is likely to be ongoing, but just how often and how many such revaccinations should be recommended remains uncertain. Research into other vaccines and alternate delivery methods should continue as this infection is likely to be around for a long time.
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Affiliation(s)
- Justin C. Konje
- Feto-Maternal Centre Al Markhiya, Doha P.O. Box 34181, Qatar
- Obstetrics and Gynecology Department, Weill Cornell Medicine Qatar, Doha P.O. Box 24144, Qatar
- Obstetrics and Gynaecology, Department of Health Sciences, University of Leicester, Leicester LE2 7LX, UK
- Correspondence: ; Tel.: +974-7777-8375
| | - Mariam Al Beloushi
- Women’s Wellness and Research Centre, Hamad Medical Corporation, Doha P.O. Box 3050, Qatar
- Department of Obstetrics and Gynaecology, Qatar University, Doha P.O. Box 2713, Qatar
| | - Badreldeen Ahmed
- Feto-Maternal Centre Al Markhiya, Doha P.O. Box 34181, Qatar
- Obstetrics and Gynecology Department, Weill Cornell Medicine Qatar, Doha P.O. Box 24144, Qatar
- Department of Obstetrics and Gynaecology, Qatar University, Doha P.O. Box 2713, Qatar
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Simões JL, Sobierai LD, Leal IF, Dos Santos MV, Coiado JV, Bagatini MD. Action of the Purinergic and Cholinergic Anti-inflammatory Pathways on Oxidative Stress in Patients with Alzheimer's Disease in the Context of the COVID-19 Pandemic. Neuroscience 2023; 512:110-132. [PMID: 36526078 PMCID: PMC9746135 DOI: 10.1016/j.neuroscience.2022.12.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 12/02/2022] [Accepted: 12/05/2022] [Indexed: 12/15/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiologic agent of the 2019 coronavirus disease (COVID-19), has affected more than 20 million people in Brazil and caused a global health emergency. This virus has the potential to affect various parts of the body and compromise metabolic functions. The virus-mediated neural inflammation of the nervous system is due to a storm of cytokines and oxidative stress, which are the clinical features of Alzheimer's disease (AD). This neurodegenerative disease is aggravated in cases involving SARS-CoV-2 and its inflammatory biomarkers, accelerating accumulation of β-amyloid peptide, hyperphosphorylation of tau protein, and production of reactive oxygen species, which lead to homeostasis imbalance. The cholinergic system, through neurons and the neurotransmitter acetylcholine (ACh), modulates various physiological pathways, such as the response to stress, sleep and wakefulness, sensory information, and the cognitive system. Patients with AD have low concentrations of ACh; hence, therapeutic methods are aimed at adjusting the ACh titers available to the body for maintaining functionality. Herein, we focused on acetylcholinesterase inhibitors, responsible for the degradation of ACh in the synaptic cleft, and muscarinic and nicotinic receptor agonists of the cholinergic system owing to the therapeutic potential of the cholinergic anti-inflammatory pathway in AD associated with SARS-CoV-2 infection.
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Affiliation(s)
- Júlia L.B. Simões
- Medical School, Federal University of Fronteira Sul, Chapecó, SC, Brazil
| | | | - Inayá F. Leal
- Medical School, Federal University of Fronteira Sul, Chapecó, SC, Brazil
| | | | - João Victor Coiado
- Medical School, Federal University of Fronteira Sul, Chapecó, SC, Brazil
| | - Margarete D. Bagatini
- Graduate Program in Biomedical Sciences, Federal University of Fronteira Sul, Chapecó, SC, Brazil,Corresponding author
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