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Islam S, Parves MR, Islam MJ, Ali MA, Efaz FM, Hossain MS, Ullah MO, Halim MA. Structural and functional effects of the L84S mutant in the SARS-COV-2 ORF8 dimer based on microsecond molecular dynamics study. J Biomol Struct Dyn 2024; 42:5770-5787. [PMID: 37403295 DOI: 10.1080/07391102.2023.2228919] [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: 01/10/2023] [Accepted: 06/17/2023] [Indexed: 07/06/2023]
Abstract
The L84S mutation has been observed frequently in the ORF8 protein of SARS-CoV-2, which is an accessory protein involved in various important functions such as virus propagation, pathogenesis, and evading the immune response. However, the specific effects of this mutation on the dimeric structure of ORF8 and its impacts on interactions with host components and immune responses are not well understood. In this study, we performed one microsecond molecular dynamics (MD) simulation and analyzed the dimeric behavior of the L84S and L84A mutants in comparison to the native protein. The MD simulations revealed that both mutations caused changes in the conformation of the ORF8 dimer, influenced protein folding mechanisms, and affected the overall structural stability. In particular, the 73YIDI76 motif has found to be significantly affected by the L84S mutation, leading to structural flexibility in the region connecting the C-terminal β4 and β5 strands. This flexibility might be responsible for virus immune modulation. The free energy landscape (FEL) and principle component analysis (PCA) have also supported our investigation. Overall, the L84S and L84A mutations affect the ORF8 dimeric interfaces by reducing the frequency of protein-protein interacting residues (Arg52, Lys53, Arg98, Ile104, Arg115, Val117, Asp119, Phe120, and Ile121) in the ORF8 dimer. Our findings provide detail insights for further research in designing structure-based therapeutics against the SARS-CoV-2.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shafiqul Islam
- Division of Infectious disease and Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - Md Rimon Parves
- Division of Infectious disease and Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - Md Jahirul Islam
- Division of Infectious disease and Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - Md Ackas Ali
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA, USA
| | - Faiyaz Md Efaz
- Division of Infectious disease and Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - Md Shahadat Hossain
- Division of Infectious disease and Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - M Obayed Ullah
- Division of Infectious disease and Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - Mohammad A Halim
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA, USA
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2
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Shao HH, Yin RX. Pathogenic mechanisms of cardiovascular damage in COVID-19. Mol Med 2024; 30:92. [PMID: 38898389 PMCID: PMC11186295 DOI: 10.1186/s10020-024-00855-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 06/07/2024] [Indexed: 06/21/2024] Open
Abstract
BACKGROUND COVID-19 is a new infectious disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS CoV-2). Since the outbreak in December 2019, it has caused an unprecedented world pandemic, leading to a global human health crisis. Although SARS CoV-2 mainly affects the lungs, causing interstitial pneumonia and severe acute respiratory distress syndrome, a number of patients often have extensive clinical manifestations, such as gastrointestinal symptoms, cardiovascular damage and renal dysfunction. PURPOSE This review article discusses the pathogenic mechanisms of cardiovascular damage in COVID-19 patients and provides some useful suggestions for future clinical diagnosis, treatment and prevention. METHODS An English-language literature search was conducted in PubMed and Web of Science databases up to 12th April, 2024 for the terms "COVID-19", "SARS CoV-2", "cardiovascular damage", "myocardial injury", "myocarditis", "hypertension", "arrhythmia", "heart failure" and "coronary heart disease", especially update articles in 2023 and 2024. Salient medical literatures regarding the cardiovascular damage of COVID-19 were selected, extracted and synthesized. RESULTS The most common cardiovascular damage was myocarditis and pericarditis, hypertension, arrhythmia, myocardial injury and heart failure, coronary heart disease, stress cardiomyopathy, ischemic stroke, blood coagulation abnormalities, and dyslipidemia. Two important pathogenic mechanisms of the cardiovascular damage may be direct viral cytotoxicity as well as indirect hyperimmune responses of the body to SARS CoV-2 infection. CONCLUSIONS Cardiovascular damage in COVID-19 patients is common and portends a worse prognosis. Although the underlying pathophysiological mechanisms of cardiovascular damage related to COVID-19 are not completely clear, two important pathogenic mechanisms of cardiovascular damage may be the direct damage of the SARSCoV-2 infection and the indirect hyperimmune responses.
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Affiliation(s)
- Hong-Hua Shao
- Department of Infectious Diseases, HIV/AIDS Clinical Treatment Center of Guangxi (Nanning), The Fourth People's Hospital of Nanning, No. 1 Erli, Changgang Road, Nanning, Guangxi, 530023, People's Republic of China
| | - Rui-Xing Yin
- Department of Infectious Diseases, HIV/AIDS Clinical Treatment Center of Guangxi (Nanning), The Fourth People's Hospital of Nanning, No. 1 Erli, Changgang Road, Nanning, Guangxi, 530023, People's Republic of China.
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University, 6 Shuangyong Road, Nanning, Guangxi, 530021, People's Republic of China.
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3
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Suleman M, Murshed A, Imran K, Khan A, Ali Z, Albekairi NA, Wei DQ, Yassine HM, Crovella S. Abrogation of ORF8-IRF3 binding interface with Carbon nanotube derivatives to rescue the host immune system against SARS-CoV-2 by using molecular screening and simulation approaches. BMC Chem 2024; 18:99. [PMID: 38734638 PMCID: PMC11088783 DOI: 10.1186/s13065-024-01185-4] [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: 01/13/2024] [Accepted: 04/11/2024] [Indexed: 05/13/2024] Open
Abstract
The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has led to over six million deaths worldwide. In human immune system, the type 1 interferon (IFN) pathway plays a crucial role in fighting viral infections. However, the ORF8 protein of the virus evade the immune system by interacting with IRF3, hindering its nuclear translocation and consequently downregulate the type I IFN signaling pathway. To block the binding of ORF8-IRF3 and inhibit viral pathogenesis a quick discovery of an inhibitor molecule is needed. Therefore, in the present study, the interface between the ORF8 and IRF3 was targeted on a high-affinity carbon nanotube by using computational tools. After analysis of 62 carbon nanotubes by multiple docking with the induced fit model, the top five compounds with high docking scores of - 7.94 kcal/mol, - 7.92 kcal/mol, - 7.28 kcal/mol, - 7.19 kcal/mol and - 7.09 kcal/mol (top hit1-5) were found to have inhibitory activity against the ORF8-IRF3 complex. Molecular dynamics analysis of the complexes revealed the high compactness of residues, stable binding, and strong hydrogen binding network among the ORF8-nanotubes complexes. Moreover, the total binding free energy for top hit1-5 was calculated to be - 43.21 ± 0.90 kcal/mol, - 41.17 ± 0.99 kcal/mol, - 48.85 ± 0.62 kcal/mol, - 43.49 ± 0.77 kcal/mol, and - 31.18 ± 0.78 kcal/mol respectively. These results strongly suggest that the identified top five nanotubes (hit1-5) possess significant potential for advancing and exploring innovative drug therapies. This underscores their suitability for subsequent in vivo and in vitro experiments, marking them as promising candidates worthy of further investigation.
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Affiliation(s)
- Muhammad Suleman
- Laboratory of Animal Research Center (LARC), Qatar University, Doha, Qatar
- Center for Biotechnology and Microbiology, University of Swat, Swat, Pakistan
| | - Abduh Murshed
- Department of Intensive Care Unit, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524000, China
| | - Kashif Imran
- Services Institute of Medical Sciences, Lahore, Pakistan
| | - Abbas Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
- School of Medical and Life Sciences, Sunway University, 47500, Sunway City, Malaysia
| | - Zafar Ali
- Center for Biotechnology and Microbiology, University of Swat, Swat, Pakistan
| | - Norah A Albekairi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Post Box 2455, 11451, Riyadh, Saudi Arabia
| | - Dong-Qing Wei
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Hadi M Yassine
- Biomedical Research Center, Qatar University, 2713, Doha, Qatar.
- College of Health Sciences-QU Health, Qatar University, 2713, Doha, Qatar.
| | - Sergio Crovella
- Laboratory of Animal Research Center (LARC), Qatar University, Doha, Qatar.
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4
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Cheng LD, Li P, Lin YC, Hu HX, Zhang Y, Li HF, Huang J, Tan L, Ma N, Xia DY. Monoclonal neutralizing antibodies against SARS-COV-2 S protein. Am J Transl Res 2024; 16:681-689. [PMID: 38463597 PMCID: PMC10918147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 10/17/2023] [Indexed: 03/12/2024]
Abstract
Novel coronavirus pneumonia, also known as coronavirus disease 2019 (COVID-19), is caused by sub-severe acute respiratory syndrome type 2 coronavirus (SARS-CoV-2) infection. The spike (S) protein of SARS-CoV-2 binds to angiotensin-converting enzyme 2 (ACE2) receptors widely expressed on the surface of human cells leading to life-threatening respiratory infections. A serious hazard to human health is posed by the lack of particular treatment medications for this virus infection. We advocate the creation of high-affinity antibodies using the receptor binding domain (RBD) of S protein as a specific antigenic epitope to develop a drug that can precisely target therapy COVID-19 because SARS-CoV-2 infection of the host cells is dependent on S protein binding to ACE2. Finally, we obtained high-affinity antibodies 14F4HL and 14E3HL that have high affinity with RBD and well-drug-forming properties, suitable for further humanization studies. Thus, monoclonal antibodies that neutralize the S protein were identified in our study, which may provide new insights for the development of COVID-19 therapeutic drugs.
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Affiliation(s)
- Lin-Dong Cheng
- Graduate School, Hebei North UniversityZhangjiakou 075000, Hebei, China
| | - Ping Li
- Graduate School, Wannan Medical CollegeWuhu 241000, Anhui, China
| | - Yan-Chen Lin
- Graduate School, Hebei North UniversityZhangjiakou 075000, Hebei, China
| | - Hui-Xiu Hu
- Graduate School, Hebei North UniversityZhangjiakou 075000, Hebei, China
| | - Ying Zhang
- Graduate School, Hebei North UniversityZhangjiakou 075000, Hebei, China
| | - Hou-Feng Li
- Graduate School, Hebei North UniversityZhangjiakou 075000, Hebei, China
| | - Jing Huang
- Graduate School, Wannan Medical CollegeWuhu 241000, Anhui, China
| | - Li Tan
- Department of Anesthesiology, Chongqing University Cancer HospitalChongqing 400030, China
| | - Ning Ma
- Department of Clinical Laboratory, 905th Hospital of PLAShanghai 200052, China
| | - Deng-Yun Xia
- Department of Anesthesiology, The First Affiliated Hospital of Hebei North UniversityZhangjiakou 075000, Hebei, China
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5
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Móvio MI, de Almeida GWC, Martines IDGL, Barros de Lima G, Sasaki SD, Kihara AH, Poole E, Nevels M, Carlan da Silva MC. SARS-CoV-2 ORF8 as a Modulator of Cytokine Induction: Evidence and Search for Molecular Mechanisms. Viruses 2024; 16:161. [PMID: 38275971 PMCID: PMC10819295 DOI: 10.3390/v16010161] [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: 11/28/2023] [Revised: 01/11/2024] [Accepted: 01/14/2024] [Indexed: 01/27/2024] Open
Abstract
Severe cases of SARS-CoV-2 infection are characterized by an immune response that leads to the overproduction of pro-inflammatory cytokines, resulting in lung damage, cardiovascular symptoms, hematologic symptoms, acute kidney injury and multiple organ failure that can lead to death. This remarkable increase in cytokines and other inflammatory molecules is primarily caused by viral proteins, and particular interest has been given to ORF8, a unique accessory protein specific to SARS-CoV-2. Despite plenty of research, the precise mechanisms by which ORF8 induces proinflammatory cytokines are not clear. Our investigations demonstrated that ORF8 augments production of IL-6 induced by Poly(I:C) in human embryonic kidney (HEK)-293 and monocyte-derived dendritic cells (mono-DCs). We discuss our findings and the multifaceted roles of ORF8 as a modulator of cytokine response, focusing on type I interferon and IL-6, a key component of the immune response to SARS-CoV-2. In addition, we explore the hypothesis that ORF8 may act through pattern recognition receptors of dsRNA such as TLRs.
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Affiliation(s)
- Marília Inês Móvio
- Laboratório de Neurogenética, Universidade Federal do ABC (UFABC), São Bernardo do Campo, São Paulo 09606-070, Brazil; (M.I.M.)
| | - Giovana Waner Carneiro de Almeida
- Centro de Ciências Naturais e Humanas (CCNH), Universidade Federal do UFABC (UFABC), São Bernardo do Campo, São Paulo 09606-070, Brazil; (G.W.C.d.A.); (G.B.d.L.); (S.D.S.)
| | - Isabella das Graças Lopes Martines
- Centro de Ciências Naturais e Humanas (CCNH), Universidade Federal do UFABC (UFABC), São Bernardo do Campo, São Paulo 09606-070, Brazil; (G.W.C.d.A.); (G.B.d.L.); (S.D.S.)
| | - Gilmara Barros de Lima
- Centro de Ciências Naturais e Humanas (CCNH), Universidade Federal do UFABC (UFABC), São Bernardo do Campo, São Paulo 09606-070, Brazil; (G.W.C.d.A.); (G.B.d.L.); (S.D.S.)
| | - Sergio Daishi Sasaki
- Centro de Ciências Naturais e Humanas (CCNH), Universidade Federal do UFABC (UFABC), São Bernardo do Campo, São Paulo 09606-070, Brazil; (G.W.C.d.A.); (G.B.d.L.); (S.D.S.)
| | - Alexandre Hiroaki Kihara
- Laboratório de Neurogenética, Universidade Federal do ABC (UFABC), São Bernardo do Campo, São Paulo 09606-070, Brazil; (M.I.M.)
| | - Emma Poole
- Division of Virology, Department of Pathology, Cambridge University, Level 5, Addenbrooke’s Hospital, Hills Road, Cambridge CB2 0QQ, UK
| | - Michael Nevels
- School of Biology, University of St Andrews, St Andrews KY16 9ST, UK;
| | - Maria Cristina Carlan da Silva
- Centro de Ciências Naturais e Humanas (CCNH), Universidade Federal do UFABC (UFABC), São Bernardo do Campo, São Paulo 09606-070, Brazil; (G.W.C.d.A.); (G.B.d.L.); (S.D.S.)
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6
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Rabaan AA, Alenazy MF, Alshehri AA, Alshahrani MA, Al-Subaie MF, Alrasheed HA, Al Kaabi NA, Thakur N, Bouafia NA, Alissa M, Alsulaiman AM, AlBaadani AM, Alhani HM, Alhaddad AH, Alfouzan WA, Ali BMA, Al-Abdulali KH, Khamis F, Bayahya A, Al Fares MA, Sharma M, Dhawan M. An updated review on pathogenic coronaviruses (CoVs) amid the emergence of SARS-CoV-2 variants: A look into the repercussions and possible solutions. J Infect Public Health 2023; 16:1870-1883. [PMID: 37839310 DOI: 10.1016/j.jiph.2023.09.004] [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: 05/04/2023] [Revised: 09/04/2023] [Accepted: 09/06/2023] [Indexed: 10/17/2023] Open
Abstract
SARS-CoV-2, responsible for COVID-19, shares 79% and 50% of its identity with SARS-CoV-1 and MERS-CoV, respectively. It uses the same main cell attachment and entry receptor as SARS-CoV-1, which is the ACE-2 receptor. However, key residues in the receptor-binding domain of its S-protein seem to give it a stronger affinity for the receptor and a better ability to hide from the host immune system. Like SARS-CoV-1 and MERS-CoV, cytokine storms in critically ill COVID-19 patients cause ARDS, neurological pathology, multiorgan failure, and increased death. Though many issues remain, the global research effort and lessons from SARS-CoV-1 and MERS-CoV are hopeful. The emergence of novel SARS-CoV-2 variants and subvariants raised serious concerns among the scientific community amid the emergence of other viral diseases like monkeypox and Marburg virus, which are major concerns for healthcare settings worldwide. Hence, an updated review on the comparative analysis of various coronaviruses (CoVs) has been developed, which highlights the evolution of CoVs and their repercussions.
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Affiliation(s)
- Ali A Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia; College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; Department of Public Health and Nutrition, The University of Haripur, Haripur 22610, Pakistan.
| | - Maha Fahad Alenazy
- Department of Physiology, College of Medicine, King Khalid university hospital, King Saud University, Riyadh 4545, Saudi Arabia
| | - Ahmad A Alshehri
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia
| | - Mohammed Abdulrahman Alshahrani
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia
| | - Maha F Al-Subaie
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; Research Center, Dr. Sulaiman Alhabib Medical Group, Riyadh 13328, Saudi Arabia; Department of Infectious Diseases, Dr. Sulaiman Alhabib Medical Group, Riyadh 13328, Saudi Arabia
| | - Hayam A Alrasheed
- Department of pharmacy Practice, College of Pharmacy, Princess Nourah Bint Abdulrahman University, Riyadh 11671, Saudi Arabia; Pharmacy Department, King Abdullah Bin Abdulaziz University Hospital, Riyadh 11671, Saudi Arabia
| | - Nawal A Al Kaabi
- Sheikh Khalifa Medical City, Abu Dhabi Health Services Company (SEHA), Abu Dhabi, 51900, United Arab Emirates; College of Medicine and Health Science, Khalifa University, Abu Dhabi 127788, United Arab Emirates
| | - Nanamika Thakur
- University Institute of Biotechnology, Department of Biotechnology, Chandigarh University, Mohali 140413, India
| | - Nabiha A Bouafia
- Infection prevention and control centre of Excellence, Prince Sultan Medical Military City, Riyadh 12233, Saudi Arabia
| | - Mohammed Alissa
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | | | - Abeer M AlBaadani
- Internal Medicine Department, Infectious Disease Division, London health science Center, London, Ontario N6G0X2, Canada
| | - Hatem M Alhani
- Department of Pediatric Infectious Disease, Maternity and Children Hospital, Dammam 31176, Saudi Arabia; Department of Infection Control, Maternity and Children Hospital, Dammam 31176, Saudi Arabia; Preventive Medicine and Infection Prevention and Control Department, Directorate of Ministry of Health, Dammam 32245, Saudi Arabia
| | - Ali H Alhaddad
- Assistant Agency for Hospital Affairs, Ministry of Health, Riyadh 12382, Saudi Arabia
| | - Wadha A Alfouzan
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat 13110, Kuwait; Microbiology Unit, Department of Laboratories, Farwania Hospital, Farwania 85000, Kuwait
| | - Batool Mohammed Abu Ali
- Infectious disease section, Department of internal medicine, King Fahad Hospital Hofuf, Hofuf 36365, Saudi Arabia
| | - Khadija H Al-Abdulali
- Nursing Department, Home health care, Qatif Health Network, Qatif 31911, Saudi Arabia
| | - Faryal Khamis
- Infection Diseases unit, Department of Internal Medicine, Royal Hospital, Muscat 1331, Oman
| | - Ali Bayahya
- Microbiology Department, Alqunfudah General Hospital, Alqunfudah 28813, Saudi Arabia
| | - Mona A Al Fares
- Department of Internal Medicine, King Abdulaziz University Hospital, Jeddah 21589, Saudi Arabia.
| | - Manish Sharma
- University Institute of Biotechnology, Department of Biotechnology, Chandigarh University, Mohali 140413, India
| | - Manish Dhawan
- Department of Microbiology, Punjab Agricultural University, Ludhiana 141004, India; Trafford College, Altrincham, Manchester WA14 5PQ, UK.
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7
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Lu Y, Ye Z, Liu X, Zhou L, Ding X, Hou Y. Role of SARS‑CoV‑2 nucleocapsid protein in affecting immune cells and insights on its molecular mechanisms. Exp Ther Med 2023; 26:504. [PMID: 37822585 PMCID: PMC10562965 DOI: 10.3892/etm.2023.12203] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 08/07/2023] [Indexed: 10/13/2023] Open
Abstract
The present study aimed to explore the immune regulatory function of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid (N) protein and related mechanisms. In a series of protein activity experiments, SARS-CoV-2 N protein promoted proliferation of three immune cell lines: mouse Raw264.7, human Jurkat and human Raji in a dose-dependent manner. A total of 10 µg/ml N protein could significantly change cell cycle progression of the aforementioned three immune cell lines and could promote quick entry of Raw264.7 cells into G2/M phase from S phase to achieve rapid growth. Additionally, the N protein could also stimulate Raw264.7 cells to secrete a number of proinflammatory factors such as TNF-α, IL-6 and IL-10. RNA sequencing analysis indicated that the N protein changed the expression of certain genes involved in immune-related functions and four important signaling pathways, including JAK-STAT, TNF, NF-κB and MAPK signaling pathways, which suggested that the N protein may not only regulate the expression of genes involved in the process of resisting viral infection in macrophages of the immune system, but also change cellular signal processing.
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Affiliation(s)
- Yan Lu
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Sciences, China West Normal University, Nanchong, Sichuan 637009, P.R. China
| | - Ziyu Ye
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Sciences, China West Normal University, Nanchong, Sichuan 637009, P.R. China
| | - Xinlan Liu
- Key Laboratory of Nanchong City of Ecological Environment Protection and Pollution Prevention in Jialing River Basin, College of Environmental Science and Engineering, China West Normal University, Nanchong, Sichuan 637009, P.R. China
| | - Liqian Zhou
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Sciences, China West Normal University, Nanchong, Sichuan 637009, P.R. China
| | - Xiang Ding
- Key Laboratory of Nanchong City of Ecological Environment Protection and Pollution Prevention in Jialing River Basin, College of Environmental Science and Engineering, China West Normal University, Nanchong, Sichuan 637009, P.R. China
| | - Yiling Hou
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Sciences, China West Normal University, Nanchong, Sichuan 637009, P.R. China
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8
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Hussain MA, Hassan MM, Bashir BA, Gamar TA, Gasmalbari E, Mohamed AO, Osman W, Sherif AE, Elgaml A, Alhaddad AA, Ghazawi KF, Miski SF, Ainousah BE, Andijani YS, Ibrahim SRM, Mohamed GA, Ashour A. Potential Therapeutic Target and Vaccines for SARS-CoV-2. Pathogens 2023; 12:926. [PMID: 37513773 PMCID: PMC10386482 DOI: 10.3390/pathogens12070926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/06/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023] Open
Abstract
The coronavirus has become the most interesting virus for scientists because of the recently emerging deadly SARS-CoV-2. This study aimed to understand the behavior of SARS-CoV-2 through the comparative genomic analysis with the closest one among the seven species of coronavirus that infect humans. The genomes of coronavirus species that infect humans were retrieved from NCBI, and then subjected to comparative genomic analysis using different bioinformatics tools. The study revealed that SARS-CoV-2 is the most similar to SARS-CoV among the coronavirus species. The core genes were shared by the two genomes, but there were some genes, found in one of them but not in both, such as ORF8, which is found in SARS-CoV-2. The ORF8 protein of SARS-CoV-2 could be considered as a good therapeutic target for stopping viral transmission, as it was predicted to be a transmembrane protein, which is responsible for interspecies transmission. This is supported by the molecular interaction of ORF8 with both the ORF7 protein, which contains a transmembrane domain that is essential to retaining the protein in the Golgi compartment, and the S protein, which facilitates the entry of the coronavirus into host cells. ORF1ab, ORF1a, ORF8, and S proteins of SARS-CoV-2 could be immunogenic and capable of evoking an immune response, which means that these four proteins could be considered a potential vaccine source. Overall, SARS-CoV-2 is most related to SARS-CoV. ORF8 could be considered a potential therapeutic target for stopping viral transmission, and ORF1ab, ORF1a, ORF8, and the S proteins of SARS-CoV-2 could be utilized as a potential vaccine source.
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Affiliation(s)
- Mohamed A Hussain
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, International University of Africa, Khartoum 11111, Sudan
| | - Mohamed M Hassan
- Department of Hematology, Faculty of Medical Laboratory Science, National University, Khartoum 11111, Sudan
| | - Bashir Abdrhman Bashir
- Department of Hematology, Faculty of Medical Laboratory Sciences, Port Sudan Ahlia College, Port Sudan 33312, Sudan
| | - Tarig A Gamar
- Department of Medical Parasitology, Faculty of Medical Laboratory Sciences, University of Sciences and Technology, Khartoum North 13311, Sudan
| | - Elmuaiz Gasmalbari
- Faculty of Medicine, Omdurman Islamic University, Al Khartoum 14415, Sudan
| | - Ahmed Osman Mohamed
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, International University of Africa, Khartoum 11111, Sudan
| | - Wadah Osman
- Department of Pharmacognosy, Faculty of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
- Department of Pharmacognosy, Faculty of Pharmacy, University of Khartoum, Al-Qasr Ave, Khartoum 11111, Sudan
| | - Asmaa E Sherif
- Department of Pharmacognosy, Faculty of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
- Department of Pharmacognosy, Faculty of Pharmacy, Mansoura University, Mansoura 35511, Egypt
| | - Abdelaziz Elgaml
- Microbiology and Immunology Department, Faculty of Pharmacy, Mansoura University, Mansoura 35511, Egypt
- Microbiology and Immunology Department, Faculty of Pharmacy, Horus University, New Damietta 34517, Egypt
| | - Aisha A Alhaddad
- Department of Pharmacology and Toxicology, College of Pharmacy, Taibah University, Al-Madinah Al-Munawwarah 30078, Saudi Arabia
| | - Kholoud F Ghazawi
- Clinical Pharmacy Department, College of Pharmacy, Umm Al-Qura University, Makkah 24382, Saudi Arabia
| | - Samar F Miski
- Department of Pharmacology and Toxicology, College of Pharmacy, Taibah University, Al-Madinah Al-Munawwarah 30078, Saudi Arabia
| | - Bayan E Ainousah
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Yusra Saleh Andijani
- Department of Pharmacology and Toxicology, College of Pharmacy, Taibah University, Al-Madinah Al-Munawwarah 30078, Saudi Arabia
| | - Sabrin R M Ibrahim
- Preparatory Year Program, Department of Chemistry, Batterjee Medical College, Jeddah 21442, Saudi Arabia
- Department of Pharmacognosy, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt
| | - Gamal A Mohamed
- Department of Natural Products and Alternative Medicine, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Ahmed Ashour
- Department of Pharmacognosy, Faculty of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
- Department of Pharmacognosy, Faculty of Pharmacy, Mansoura University, Mansoura 35511, Egypt
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9
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Wu X, Manske MK, Ruan GJ, Witter TL, Nowakowski KE, Abeykoon JP, Tang X, Yu Y, Gwin KA, Wu A, Taupin V, Bhardwaj V, Paludo J, Dasari S, Dong H, Ansell SM, Badley AD, Schellenberg MJ, Witzig TE. Secreted ORF8 induces monocytic pro-inflammatory cytokines through NLRP3 pathways in patients with severe COVID-19. iScience 2023; 26:106929. [PMID: 37260746 PMCID: PMC10193824 DOI: 10.1016/j.isci.2023.106929] [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: 09/26/2022] [Revised: 04/06/2023] [Accepted: 05/16/2023] [Indexed: 06/02/2023] Open
Abstract
Despite extensive research, the specific factor associated with SARS-CoV-2 infection that mediates the life-threatening inflammatory cytokine response in patients with severe COVID-19 remains unidentified. Herein we demonstrate that the virus-encoded Open Reading Frame 8 (ORF8) protein is abundantly secreted as a glycoprotein in vitro and in symptomatic patients with COVID-19. ORF8 specifically binds to the NOD-like receptor family pyrin domain-containing 3 (NLRP3) in CD14+ monocytes to induce inflammasomal cytokine/chemokine responses including IL1β, IL8, and CCL2. Levels of ORF8 protein in the blood correlate with severity and disease-specific mortality in patients with acute SARS-CoV-2 infection. Furthermore, the ORF8-induced inflammasome response was readily inhibited by the NLRP3 inhibitor MCC950 in vitro. Our study identifies a dominant cause of pathogenesis, its underlying mechanism, and a potential new treatment strategy for severe COVID-19.
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Affiliation(s)
- Xiaosheng Wu
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Michelle K Manske
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Gordon J Ruan
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Taylor L Witter
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Kevin E Nowakowski
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Jithma P Abeykoon
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Xinyi Tang
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Yue Yu
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905, USA
| | - Kimberly A Gwin
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Annie Wu
- Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
| | - Vanessa Taupin
- Electron Microscopy Core, University of California San Diego, La Jolla, CA, USA
| | - Vaishali Bhardwaj
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Jonas Paludo
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Surendra Dasari
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905, USA
| | - Haidong Dong
- Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
| | - Stephen M Ansell
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Andrew D Badley
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | | | - Thomas E Witzig
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
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10
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Archana VP, Armaković SJ, Armaković S, Celik I, Bhagyasree J, Dinesh Babu K, Rudrapal M, Divya IS, Pillai RR. Exploring the structural, photophysical and optoelectronic properties of a diaryl heptanoid curcumin derivative and identification as a SARS-CoV-2 inhibitor. J Mol Struct 2023; 1281:135110. [PMID: 36785704 PMCID: PMC9910092 DOI: 10.1016/j.molstruc.2023.135110] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 02/03/2023] [Accepted: 02/05/2023] [Indexed: 02/11/2023]
Abstract
Developing modifiable natural products those having antiviral activities against SARS-CoV-2 is a key research area which is popular in current scenario of COVID pandemic. A diaryl heptanoid curcumin and its derivatives are already presenting promising candidates for anti-viral drug development. We have synthesized single crystals of a dimethylamino derivative of natural curcumin and structural characterization was done by single crystal XRD analysis. Using steady-state absorption and emission spectra and guided by complimentary ab initio calculations, we unraveled the solvent effects on the photophysical properties of the dimethyl amino curcumin derivative. Chemical reactivity of the compound has investigated using frontier molecular orbitals and molecular electrostatic potential surface. High stability of the curcumin derivative in water environment has evaluated by Radial Distributions Functions (RDF) calculated via Molecular Dynamics (MD) simulations. The inhibitory activity of the title compound was evaluated by in silico methods and the stability of the protein-ligand complexes were studied using Molecular Dynamics simulations and MM-PBSA analysis. With this detailed study, we hope to motivate scientific community to develop new curcumin derivatives against SARS-CoV-2 virus.
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Affiliation(s)
- Vikaraman P. Archana
- Department of Polymer Chemistry, Government College, Attingal, University of Kerala, Thiruvananthapuram, Kerala, India,Department of Chemistry, Government College for Women, University of Kerala, Vazhuthacaud, Thiruvananthapuram, Kerala, India
| | - Sanja J. Armaković
- University of Novi Sad, Faculty of Sciences, Department of Chemistry, Biochemistry and Environmental Protection, Trg D. Obradovića 3, 21000 Novi Sad, Serbia,Association for the International Development of Academic and Scientific Collaboration (AIDASCO), Novi Sad, Serbia
| | - Stevan Armaković
- University of Novi Sad, Faculty of Sciences, Department of Physics, Trg D. Obradovića 4, 21000 Novi Sad, Serbia,Association for the International Development of Academic and Scientific Collaboration (AIDASCO), Novi Sad, Serbia
| | - Ismail Celik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Erciyes University, Kayseri 38280, Turkey
| | - J.B. Bhagyasree
- Department of Polymer Chemistry, Government College, Attingal, University of Kerala, Thiruvananthapuram, Kerala, India
| | - K.V. Dinesh Babu
- Department of Chemistry, Government College for Women, University of Kerala, Vazhuthacaud, Thiruvananthapuram, Kerala, India
| | - Mithun Rudrapal
- Department of Pharmaceutical Sciences, School of Biotechnology & Pharmaceutical Sciences, Vignan's Foundation for Science, Technology and Research (Deemed to be University), Vadlamudi, Guntur-522213, India
| | - Indira S. Divya
- Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, India
| | - Renjith Raveendran Pillai
- Department of Physics, University College, University of Kerala, Thiruvananthapuram, Kerala, India,Association for the International Development of Academic and Scientific Collaboration (AIDASCO), Novi Sad, Serbia,Corresponding author
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11
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Moriyama M, Lucas C, Monteiro V, Iwasaki A. Enhanced inhibition of MHC-I expression by SARS-CoV-2 Omicron subvariants. Proc Natl Acad Sci U S A 2023; 120:e2221652120. [PMID: 37036977 PMCID: PMC10120007 DOI: 10.1073/pnas.2221652120] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/09/2023] [Indexed: 04/12/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) possess mutations that confer resistance to neutralizing antibodies within the Spike protein and are associated with breakthrough infection and reinfection. By contrast, less is known about the escape from CD8+ T cell-mediated immunity by VOC. Here, we demonstrated that all SARS-CoV-2 VOCs possess the ability to suppress major histocompatibility complex class I (MHC-I) expression. We identified several viral genes that contribute to the suppression of MHC I expression. Notably, MHC-I upregulation was strongly inhibited after SARS-CoV-2 but not influenza virus infection in vivo. While earlier VOCs possess similar capacity as the ancestral strain to suppress MHC-I, the Omicron subvariants exhibited a greater ability to suppress surface MHC-I expression. We identified a common mutation in the E protein of Omicron that further suppressed MHC-I expression. Collectively, our data suggest that in addition to escaping from neutralizing antibodies, the success of Omicron subvariants to cause breakthrough infection and reinfection may in part be due to its optimized evasion from T cell recognition.
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Affiliation(s)
- Miyu Moriyama
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT06520
| | - Carolina Lucas
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT06520
| | | | | | - Akiko Iwasaki
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT06520
- Department of Molecular Cellular and Developmental Biology, Yale University, New HavenCT06520
- HHMI, Chevy Chase, MD20815
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12
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A triple-target reverse transcription loop-mediated isothermal amplification (RT-LAMP) for rapid and accurate detection of SARS-CoV-2 virus. Anal Chim Acta 2023; 1255:341146. [PMID: 37032059 PMCID: PMC10039734 DOI: 10.1016/j.aca.2023.341146] [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: 01/24/2023] [Revised: 03/22/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023]
Abstract
The spreading of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) across the world has impacted people's health and lives worldwide in recent years. Rapid and accurate diagnosis is crucial for curbing the pandemic of coronavirus disease 2019 (COVID-19). Reverse transcription loop-mediated isothermal amplification (RT-LAMP) has great potential for SARS-CoV-2 detection but fails to completely replace conventional PCR due to the high false-positive rate (FPR). We proposed a triple-target RT-LAMP method for dual-signal, sensitive, and simultaneous detection of conserved genes of SARS-CoV-2. Multiple LAMP primer sets were designed for N, E, and M genes and their amplification efficacy were screened. Then, using artificial plasmids and RNA, the optimal primer set for each gene was examined on specificity, sensitivity, and detection range. The RT-LAMP initiated by these primer sets exhibited better specificity and sensitivity than that of RT-qPCR, and the triple-target RT-LAMP could determine different variants of SARS-CoV-2. By testing 78 artificial RNA samples, the total FPR of triple-target RT-LAMP was eliminated compared with that of mono-target RT-LAMP. The triple-target RT-LAMP method precisely identified throat swab specimens through colorimetry and fluorescent signals within 60 min, and the limit of detection (LOD) was as low as 187 copies/reaction. In the future, the triple-target RT-LAMP can be applied to in-field and on-site diagnosis of symptomatic and asymptomatic virus carriers.
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13
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Kandwal S, Fayne D. Genetic conservation across SARS-CoV-2 non-structural proteins - Insights into possible targets for treatment of future viral outbreaks. Virology 2023; 581:97-115. [PMID: 36940641 PMCID: PMC9999249 DOI: 10.1016/j.virol.2023.02.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 02/10/2023] [Accepted: 02/20/2023] [Indexed: 03/12/2023]
Abstract
The majority of SARS-CoV-2 therapeutic development work has focussed on targeting the spike protein, viral polymerase and proteases. As the pandemic progressed, many studies reported that these proteins are prone to high levels of mutation and can become drug resistant. Thus, it is necessary to not only target other viral proteins such as the non-structural proteins (NSPs) but to also target the most conserved residues of these proteins. In order to understand the level of conservation among these viruses, in this review, we have focussed on the conservation across RNA viruses, conservation across the coronaviruses and then narrowed our focus to conservation of NSPs across coronaviruses. We have also discussed the various treatment options for SARS-CoV-2 infection. A synergistic melding of bioinformatics, computer-aided drug-design and in vitro/vivo studies can feed into better understanding of the virus and therefore help in the development of small molecule inhibitors against the viral proteins.
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Affiliation(s)
- Shubhangi Kandwal
- Molecular Design Group, School of Biochemistry & Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Pearse Street, Dublin, 2, Ireland
| | - Darren Fayne
- Molecular Design Group, School of Biochemistry & Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Pearse Street, Dublin, 2, Ireland.
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14
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Atwah B, Iqbal MS, Kabrah S, Kabrah A, Alghamdi S, Tabassum A, Baghdadi MA, Alzahrani H. Susceptibility of Diabetic Patients to COVID-19 Infections: Clinico-Hematological and Complications Analysis. Vaccines (Basel) 2023; 11:vaccines11030561. [PMID: 36992148 DOI: 10.3390/vaccines11030561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/26/2023] [Accepted: 02/27/2023] [Indexed: 03/05/2023] Open
Abstract
Background: Coronavirus disease 2019 has become a global health threat resulting in a catastrophic spread and more than 3.8 million deaths worldwide. It has been suggested that there is a negative influence of diabetes mellites (DM), which is a complex chronic disease, on COVID-19 severe outcomes. Other factors in diabetic patients may also contribute to COVID-19 disease outcomes, such as older age, obesity, hyperglycaemia, hypertension, and other chronic conditions. Methods: A cohort study was conducted on the demographics, clinical information, and laboratory findings of the hospitalised COVID-19 with DM and non-DM patients were obtained from the medical records in King Faisal Specialist Hospital and Research Centre, Saudi Arabia. Results: Among the study population, 108 patients had DM, and 433 were non-DM patients. Patients with DM were more likely to present symptoms such as fever (50.48%), anorexia (19.51%), dry cough (47.96%), shortness of breath (35.29%), chest pain (16.49%), and other symptoms. There was a significant decrease in the mean of haematological and biochemical parameters, such as haemoglobin, calcium, and alkaline phosphate in people with diabetes compared to non-diabetics and a considerable increase in other parameters, such as glucose, potassium, and cardiac troponin. Conclusions: According to the findings of this study, patients who have diabetes have a greater risk of developing more severe symptoms associated with COVID-19 disease. This could result in more patients being admitted to the intensive care unit as well as higher mortality rates.
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Affiliation(s)
- Banan Atwah
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Mohammad Shahid Iqbal
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Saeed Kabrah
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Ahmed Kabrah
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Saad Alghamdi
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Aisha Tabassum
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Mohammed A Baghdadi
- Research Center, King Faisal Specialist Hospital and Research Centre (KFSH&RC), Jeddah 23431, Saudi Arabia
| | - Hissah Alzahrani
- Mathematical Sciences Department, Faculty of Applied Sciences, Umm Al-Qura University, Makkah 21955, Saudi Arabia
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15
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Wei X, Li M, Pei X, Liu Z, Zhang J. Assessing the effectiveness of the intervention measures of COVID-19 in China based on dynamical method. Infect Dis Model 2023; 8:159-171. [PMID: 36624814 PMCID: PMC9812467 DOI: 10.1016/j.idm.2022.12.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/29/2022] [Accepted: 12/29/2022] [Indexed: 01/06/2023] Open
Abstract
Normalized interventions were implemented in different cities in China to contain the outbreak of COVID-19 before December 2022. However, the differences in the intensity and timeliness of the implementations lead to differences in final size of the infections. Taking the outbreak of COVID-19 in three representative cities Xi'an, Zhengzhou and Yuzhou in January 2022, as examples, we develop a compartmental model to describe the spread of novel coronavirus and implementation of interventions to assess concretely the effectiveness of Chinese interventions and explore their impact on epidemic patterns. After applying reported human confirmed cases to verify the rationality of the model, we apply the model to speculate transmission trend and length of concealed period at the initial spread phase of the epidemic (they are estimated as 10.5, 7.8, 8.2 days, respectively), to estimate the range of basic reproduction number (2.9, 0.7, 1.6), and to define two indexes (transmission rate v t and controlled rate v c ) to evaluate the overall effect of the interventions. It is shown that for Zhengzhou, v c is always more than v t with regular interventions, and Xi'an take 8 days to achieve v c > v t twice as long as Yuzhou, which can interpret the fact that the epidemic situation in Xi'an was more severe. By carrying out parameter values, it is concluded that in the early stage, strengthening the precision of close contact tracking and frequency of large-scale nucleic acid testing of non-quarantined population are the most effective on controlling the outbreaks and reducing final size. And, if the close contact tracking strategy is sufficiently implemented, at the late stage large-scale nucleic acid testing of non-quarantined population is not essential.
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Affiliation(s)
- Xiaomeng Wei
- Complex Systems Research Center, Shanxi University, 030006, Shanxi, China,Shanxi Key Laboratory of Mathematical Techniques and Big Data Analysis on Disease Control and Prevention, 030006, Shanxi, China,School of Mathematical Sciences, Shanxi University, 030006, Shanxi, China
| | - Mingtao Li
- College of Mathematics, Taiyuan University of Technology, 030024, Shanxi, China
| | - Xin Pei
- College of Mathematics, Taiyuan University of Technology, 030024, Shanxi, China
| | - Zhiping Liu
- School of Data Science and Technology, North University of China, 030051, Shanxi, China
| | - Juan Zhang
- Complex Systems Research Center, Shanxi University, 030006, Shanxi, China,Shanxi Key Laboratory of Mathematical Techniques and Big Data Analysis on Disease Control and Prevention, 030006, Shanxi, China,Corresponding author. Complex Systems Research Center, Shanxi University, 030006, Shanxi, China
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16
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Abenavoli L, Aquila I, Sacco MA, Procopio AC, Cinaglia P, Zanza C, Longhitano Y, Arena V, Fagoonee S, Ricci P, Luzza F. Liver injury associated with high value of D-dimer plasmatic level in COVID-19 patients. Minerva Gastroenterol (Torino) 2023; 69:141-148. [PMID: 35470356 DOI: 10.23736/s2724-5985.22.03189-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
BACKGROUND The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), causal agent of the coronavirus disease (COVID-19), has infected millions of people worldwide. Currently, the scientific community debates on the direct viral responsibility of liver damage or whether the observed changes are secondary manifestations of systemic inflammation triggered by COVID-19. The hepatic involvement is associated with worse clinical outcomes and higher risk of COVID-19 related morbidity and mortality. Furthermore, SARS-CoV-2 infection may predispose patients to thrombotic disease due to excessive inflammation, platelet activation, and endothelial dysfunction. METHODS In this paper, we reported a cross-sectional analysis of five patients affected by a severe form of COVID-19, who died between April 11 and May 1, 2020. Each patient has been subjected to a medico-legal autopsy in which both gross and histological liver changes were evaluated, as well as the correlation with the related coagulation profile. RESULTS In three cases of our cohort, the thromboembolism was recognized as cause of death. Furthermore, a significant statistical difference between D-dimer values at hospital admission and death among enrolled patients (P=0.033), was evaluated. No patient has recorded a pre-existing liver disease. CONCLUSIONS Our results support the evidence that hepatic damage in subjects with severe form of COVID-19 is related to the changes in coagulative and fibrinolytic pathways. Hence, the evaluation of D-dimer blood levels may be useful in clinical practice to predict the involvement of the liver and the prognosis of these patients. This data highlights the fundamental role of coagulation balance in subjects with advanced form of COVID-19.
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Affiliation(s)
- Ludovico Abenavoli
- Department of Health Sciences, Magna Grecia University, Catanzaro, Italy -
| | - Isabella Aquila
- Department of Surgical and Medical Sciences, Magna Grecia University, Catanzaro, Italy
| | - Matteo A Sacco
- Department of Surgical and Medical Sciences, Magna Grecia University, Catanzaro, Italy
| | - Anna C Procopio
- Department of Health Sciences, Magna Grecia University, Catanzaro, Italy
| | - Pietro Cinaglia
- Department of Health Sciences, Magna Grecia University, Catanzaro, Italy
| | - Christian Zanza
- Department of Emergency, Anesthesia and Critical Care, Foundation "Ospedale Alba-Bra", Michele and Pietro Ferrero Hospital, Verduno, Cuneo, Italy
| | - Yaroslava Longhitano
- Department of Emergency Medicine, Section of Anesthesia and Critical Care, St Giacomo Hospital, Novi Ligure, Alessandria, Italy
| | - Vincenzo Arena
- Department of Woman and Child Health and Public Health, IRCCS A. Gemelli University Polyclinic Foundation, Rome, Italy
| | - Sharmila Fagoonee
- Institute of Biostructure and Bioimaging, National Research Council, Molecular Biotechnology Center, Turin, Italy
| | - Pietrantonio Ricci
- Department of Surgical and Medical Sciences, Magna Grecia University, Catanzaro, Italy
| | - Francesco Luzza
- Department of Health Sciences, Magna Grecia University, Catanzaro, Italy
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17
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Câmara AB, Bonfante J, da Penha MG, Cassini STA, de Pinho Keller R. Detecting SARS-CoV-2 in sludge samples: A systematic review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 859:160012. [PMID: 36368397 PMCID: PMC9643039 DOI: 10.1016/j.scitotenv.2022.160012] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 11/02/2022] [Accepted: 11/03/2022] [Indexed: 06/16/2023]
Abstract
AIMS This paper aims to review the main sludge concentration methods used for SARS-CoV-2 detection in sewage sludge samples, discussing the main methods and sample volume related to increased viral load. In addition, we aim to evaluate the countries associated with increased positivity rates for SARS-CoV-2 in sludge samples. METHODS This systematic methodology was registered in PROSPERO and followed the PRISMA guidelines. The search was carried out in the SciELO, PubMed/MEDLINE, Lilacs, and Google Scholar databases in January-March 2022. Quantitative studies with conclusive results were included in this review. Concentration methods (polyethylene glycol (PEG), PEG + NaCl, gravity thickening, skimmed milk flocculation, ultrafiltration, filtration using charged filters, primary sedimentation, and anaerobic digestion), as well as detection methods (RTqPCR and reverse transcription droplet digital PCR assay) were evaluated in this review. The SPSS v23 software program was used for statistical analysis. RESULTS PEG (with or without NaCl addition) and gravity thickening were the most used sludge concentration methods to detect SARS-CoV-2. The main method associated with increased viral load (>2,02 × 10^4 copies/mL) was PEG + NaCl (p < 0.05, Mann-Whitney test). The average positivity rate for SARS-CoV-2 in sludge samples was 61 %, and a correlation was found between the sludge volume and the viral load (ro 0.559, p = 0.03, Spearman correlation). CONCLUSION The sludge volume may influence the SARS-CoV-2 load since the virus can adhere to solid particles in these samples. Other factors may be associated with SARS-CoV-2 load, including the methods used; especially PEG + NaCl may result in a high viral load detected in sludge, and may provide a suitable pH for SARS-CoV-2 recovery.
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Affiliation(s)
- Alice Barros Câmara
- Sanitation Laboratory, Department of Environmental Engineering, Universidade Federal do Espírito Santo, Ave. Fernando Ferrari, 515, Goiabeiras, 29075051 Vitória, ES, Brazil.
| | - Júlia Bonfante
- Sanitation Laboratory, Department of Environmental Engineering, Universidade Federal do Espírito Santo, Ave. Fernando Ferrari, 515, Goiabeiras, 29075051 Vitória, ES, Brazil
| | - Marília Gueler da Penha
- Sanitation Laboratory, Department of Environmental Engineering, Universidade Federal do Espírito Santo, Ave. Fernando Ferrari, 515, Goiabeiras, 29075051 Vitória, ES, Brazil
| | - Sérvio Túlio Alves Cassini
- Sanitation Laboratory, Department of Environmental Engineering, Universidade Federal do Espírito Santo, Ave. Fernando Ferrari, 515, Goiabeiras, 29075051 Vitória, ES, Brazil
| | - Regina de Pinho Keller
- Sanitation Laboratory, Department of Environmental Engineering, Universidade Federal do Espírito Santo, Ave. Fernando Ferrari, 515, Goiabeiras, 29075051 Vitória, ES, Brazil
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18
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Umitaibatin R, Harisna AH, Jauhar MM, Syaifie PH, Arda AG, Nugroho DW, Ramadhan D, Mardliyati E, Shalannanda W, Anshori I. Immunoinformatics Study: Multi-Epitope Based Vaccine Design from SARS-CoV-2 Spike Glycoprotein. Vaccines (Basel) 2023; 11:vaccines11020399. [PMID: 36851275 PMCID: PMC9964839 DOI: 10.3390/vaccines11020399] [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: 12/09/2022] [Revised: 02/04/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023] Open
Abstract
The coronavirus disease 2019 outbreak has become a huge challenge in the human sector for the past two years. The coronavirus is capable of mutating at a higher rate than other viruses. Thus, an approach for creating an effective vaccine is still needed to induce antibodies against multiple variants with lower side effects. Currently, there is a lack of research on designing a multiepitope of the COVID-19 spike protein for the Indonesian population with comprehensive immunoinformatic analysis. Therefore, this study aimed to design a multiepitope-based vaccine for the Indonesian population using an immunoinformatic approach. This study was conducted using the SARS-CoV-2 spike glycoprotein sequences from Indonesia that were retrieved from the GISAID database. Three SARS-CoV-2 sequences, with IDs of EIJK-61453, UGM0002, and B.1.1.7 were selected. The CD8+ cytotoxic T-cell lymphocyte (CTL) epitope, CD4+ helper T lymphocyte (HTL) epitope, B-cell epitope, and IFN-γ production were predicted. After modeling the vaccines, molecular docking, molecular dynamics, in silico immune simulations, and plasmid vector design were performed. The designed vaccine is antigenic, non-allergenic, non-toxic, capable of inducing IFN-γ with a population reach of 86.29% in Indonesia, and has good stability during molecular dynamics and immune simulation. Hence, this vaccine model is recommended to be investigated for further study.
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Affiliation(s)
- Ramadhita Umitaibatin
- Lab-on-Chip Group, Department of Biomedical Engineering, School of Electrical Engineering and Informatics, Bandung Institute of Technology, Bandung 40132, Indonesia
| | - Azza Hanif Harisna
- Nano Center Indonesia, Jl. Raya Puspiptek, South Tangerang 15314, Indonesia
| | | | - Putri Hawa Syaifie
- Nano Center Indonesia, Jl. Raya Puspiptek, South Tangerang 15314, Indonesia
| | | | - Dwi Wahyu Nugroho
- Nano Center Indonesia, Jl. Raya Puspiptek, South Tangerang 15314, Indonesia
| | - Donny Ramadhan
- Research Center for Pharmaceutical Ingredients and Traditional Medicine, National Research and Innovation Agency (BRIN), Cibinong 16911, Indonesia
| | - Etik Mardliyati
- Research Center for Vaccine and Drug, National Research and Innovation Agency (BRIN), Cibinong 16911, Indonesia
| | - Wervyan Shalannanda
- Department of Telecommunication Engineering, School of Electrical Engineering and Informatics, Bandung Institute of Technology, Bandung 40132, Indonesia
| | - Isa Anshori
- Lab-on-Chip Group, Department of Biomedical Engineering, School of Electrical Engineering and Informatics, Bandung Institute of Technology, Bandung 40132, Indonesia
- Correspondence:
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Diessner EM, Takahashi GR, Cross TJ, Martin RW, Butts CT. Mutation Effects on Structure and Dynamics: Adaptive Evolution of the SARS-CoV-2 Main Protease. Biochemistry 2023; 62:747-758. [PMID: 36656653 PMCID: PMC9888416 DOI: 10.1021/acs.biochem.2c00479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 12/29/2022] [Indexed: 01/20/2023]
Abstract
The main protease of SARS-CoV-2 (Mpro) plays a critical role in viral replication; although it is relatively conserved, Mpro has nevertheless evolved over the course of the COVID-19 pandemic. Here, we examine phenotypic changes in clinically observed variants of Mpro, relative to the originally reported wild-type enzyme. Using atomistic molecular dynamics simulations, we examine effects of mutation on protein structure and dynamics. In addition to basic structural properties such as variation in surface area and torsion angles, we use protein structure networks and active site networks to evaluate functionally relevant characters related to global cohesion and active site constraint. Substitution analysis shows a continuing trend toward more hydrophobic residues that are dependent on the location of the residue in primary, secondary, tertiary, and quaternary structures. Phylogenetic analysis provides additional evidence for the impact of selective pressure on mutation of Mpro. Overall, these analyses suggest evolutionary adaptation of Mpro toward more hydrophobicity and a less-constrained active site in response to the selective pressures of a novel host environment.
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Affiliation(s)
- Elizabeth M Diessner
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Gemma R Takahashi
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Thomas J Cross
- Department of Chemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Rachel W Martin
- Departments of Chemistry and Molecular Biology & Biochemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Carter T Butts
- Departments of Sociology, Statistics, Computer Science, and EECS, University of California, Irvine, Irvine, California 92697, United States
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20
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Vengesai A, Naicker T, Midzi H, Kasambala M, Muleya V, Chipako I, Choto E, Moyo P, Mduluza T. Peptide microarray analysis of in-silico predicted B-cell epitopes in SARS-CoV-2 sero-positive healthcare workers in Bulawayo, Zimbabwe. Acta Trop 2023; 238:106781. [PMID: 36460093 PMCID: PMC9705268 DOI: 10.1016/j.actatropica.2022.106781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 10/31/2022] [Accepted: 11/27/2022] [Indexed: 11/30/2022]
Abstract
Immunogenic peptides that mimic linear B-cell epitopes coupled with immunoassay validation may improve serological tests for emerging diseases. This study reports a general approach for profiling linear B-cell epitopes derived from SARS-CoV-2 using an in-silico method and peptide microarray immunoassay, using healthcare workers' SARS-CoV-2 sero-positive sera. SARS-CoV-2 was tested using rapid chromatographic immunoassays and real-time reverse-transcriptase polymerase chain reaction. Immunogenic peptides mimicking linear B-cell epitopes were predicted in-silico using ABCpred. Peptides with the lowest sequence identity with human protein and proteins from other human pathogens were selected using the NCBI Protein BLAST. IgG and IgM antibodies against the SARS-CoV-2 spike protein, membrane glycoprotein and nucleocapsid derived peptides were measured in sera using peptide microarray immunoassay. Fifty-three healthcare workers included in the study were RT-PCR negative for SARS-CoV-2. Using rapid chromatographic immunoassays, 10 were SARS-CoV-2 IgM sero-positive and 7 were SARS-CoV-2 IgG sero-positive. From a total of 10 SARS-CoV-2 peptides contained on the microarray, 3 (QTH34388.1-1-14, QTN64908.1-135-148, and QLL35955.1-22-35) showed reactivity against IgG. Three peptides (QSM17284.1-76-89, QTN64908.1-135-148 and QPK73947.1-8-21) also showed reactivity against IgM. Based on the results we predicted one peptide (QSM17284.1-76-89) that had an acceptable diagnostic performance. Peptide QSM17284.1-76-89 was able to detect IgM antibodies against SARS-CoV-2 with area under the curve (AUC) 0.781 when compared to commercial antibody tests. In conclusion in silico peptide prediction and peptide microarray technology may provide a platform for the development of serological tests for emerging infectious diseases such as COVID-19. However, we recommend using at least three in-silico peptide prediction tools to improve the sensitivity and specificity of B-cell epitope prediction, to predict peptides with excellent diagnostic performances.
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Affiliation(s)
- Arthur Vengesai
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Midlands State University, Senga Road, Gweru, Zimbabwe.
| | - Thajasvarie Naicker
- Discipline of Optics and Imaging, Doris Duke Medical Research Institute, University of KwaZulu-Natal, College of Health Sciences Durban, ZA, South Africa
| | - Herald Midzi
- Department of Biotechnology and Biochemistry, Faculty of Science, University of Zimbabwe, Harare, Zimbabwe
| | - Maritha Kasambala
- Department of Biological Sciences and Ecology, Faculty of Science, University of Zimbabwe, Harare, Zimbabwe
| | - Victor Muleya
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Midlands State University, Senga Road, Gweru, Zimbabwe
| | - Isaac Chipako
- Aravas Pharmaceuticals Pvt LTD, Prospect Industrial Area, Harare, Zimbabwe
| | - Emilia Choto
- Immunology Department, Simon Mazorodze School of Medical and Health Sciences, Great Zimbabwe University, Masvingo, Zimbabwe
| | - Praise Moyo
- Department of Applied Biosciences and Biotechnology, Faculty of Science and Technology, Midlands State University, Senga Road, Gweru, Zimbabwe
| | - Takafira Mduluza
- Department of Biotechnology and Biochemistry, Faculty of Science, University of Zimbabwe, Harare, Zimbabwe
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21
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Deletions across the SARS-CoV-2 Genome: Molecular Mechanisms and Putative Functional Consequences of Deletions in Accessory Genes. Microorganisms 2023; 11:microorganisms11010229. [PMID: 36677521 PMCID: PMC9862619 DOI: 10.3390/microorganisms11010229] [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: 12/21/2022] [Revised: 01/13/2023] [Accepted: 01/13/2023] [Indexed: 01/18/2023] Open
Abstract
The analysis of deletions may reveal evolutionary trends and provide new insight into the surprising variability and rapidly spreading capability that SARS-CoV-2 has shown since its emergence. To understand the factors governing genomic stability, it is important to define the molecular mechanisms of deletions in the viral genome. In this work, we performed a statistical analysis of deletions. Specifically, we analyzed correlations between deletions in the SARS-CoV-2 genome and repetitive elements and documented a significant association of deletions with runs of identical (poly-) nucleotides and direct repeats. Our analyses of deletions in the accessory genes of SARS-CoV-2 suggested that there may be a hypervariability in ORF7A and ORF8 that is not associated with repetitive elements. Such recurrent search in a "sequence space" of accessory genes (that might be driven by natural selection) did not yet cause increased viability of the SARS-CoV-2 variants. However, deletions in the accessory genes may ultimately produce new variants that are more successful compared to the viral strains with the conventional architecture of the SARS-CoV-2 accessory genes.
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22
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2019-nCoV effects, transmission and preventive measures: an overview. ZEITSCHRIFT FUR GESUNDHEITSWISSENSCHAFTEN = JOURNAL OF PUBLIC HEALTH 2023; 31:27-35. [PMID: 33432288 PMCID: PMC7787937 DOI: 10.1007/s10389-020-01435-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 11/20/2020] [Indexed: 02/08/2023]
Abstract
Aim COVID-19 has led to a global crisis not only in the health sector but also in the economic, social and education sectors, as well as the lives of common man. This paper reviews the origin, characteristics and transmission of the SARS-CoV-2 Virus and the preventive measures adopted by the world's nations to curb the effects of the pandemic. Subjects and methods The temporal and spatial profile of the COVID-19 spread is highly dynamic and is progressively changing at a rapid pace. This article is an attempt to mitigate the pandemic threat by sharing the review outcome from an extensive literature survey on recent articles on COVID-19 and its impact. Results Statistical analysis presented by the World Health Organization and other health organizations explicitly indicates that optimized support and care extended to infected persons is the key to therapy, and the clinical effectiveness of alternative techniques is still under study. Though there have been announcements on the discovery of drugs for the virus, the authenticity of these reports are yet to be verified. Conclusion Based on the review, it can be inferred that it is important to boost one's immune system and to stay healthy by developing healthy habits of food intake, sleep, exercise, personal hygiene and so on. Practicing social distancing with a self-motivated attitude will help to control the virus to a large extent. The current situation also demands a great sense of responsibility of people towards society by protecting oneself from the virus in order to protect the society one lives in.
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Abulsoud AI, El-Husseiny HM, El-Husseiny AA, El-Mahdy HA, Ismail A, Elkhawaga SY, Khidr EG, Fathi D, Mady EA, Najda A, Algahtani M, Theyab A, Alsharif KF, Albrakati A, Bayram R, Abdel-Daim MM, Doghish AS. Mutations in SARS-CoV-2: Insights on structure, variants, vaccines, and biomedical interventions. Biomed Pharmacother 2023; 157:113977. [PMID: 36370519 PMCID: PMC9637516 DOI: 10.1016/j.biopha.2022.113977] [Citation(s) in RCA: 67] [Impact Index Per Article: 67.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 10/29/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022] Open
Abstract
COVID-19 is a worldwide pandemic caused by SARS-coronavirus-2 (SARS-CoV-2). Less than a year after the emergence of the Covid-19 pandemic, many vaccines have arrived on the market with innovative technologies in the field of vaccinology. Based on the use of messenger RNA (mRNA) encoding the Spike SARS-Cov-2 protein or on the use of recombinant adenovirus vectors enabling the gene encoding the Spike protein to be introduced into our cells, these strategies make it possible to envisage the vaccination in a new light with tools that are more scalable than the vaccine strategies used so far. Faced with the appearance of new variants, which will gradually take precedence over the strain at the origin of the pandemic, these new strategies will allow a much faster update of vaccines to fight against these new variants, some of which may escape neutralization by vaccine antibodies. However, only a vaccination policy based on rapid and massive vaccination of the population but requiring a supply of sufficient doses could make it possible to combat the emergence of these variants. Indeed, the greater the number of infected individuals, the faster the virus multiplies, with an increased risk of the emergence of variants in these RNA viruses. This review will discuss SARS-CoV-2 pathophysiology and evolution approaches in altered transmission platforms and emphasize the different mutations and how they influence the virus characteristics. Also, this article summarizes the common vaccines and the implication of the mutations and genetic variety of SARS-CoV-2 on the COVID-19 biomedical arbitrations.
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Affiliation(s)
- Ahmed I Abulsoud
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt; Department of Biochemistry and Biotechnology, Faculty of Pharmacy, Heliopolis University, Cairo 11785, Egypt
| | - Hussein M El-Husseiny
- Laboratory of Veterinary Surgery, Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai Cho, Fuchu-shi, Tokyo 183-8509, Japan; Department of Surgery, Anesthesiology, and Radiology, Faculty of Veterinary Medicine, Benha University, Moshtohor, Toukh, Elqaliobiya 13736, Egypt.
| | - Ahmed A El-Husseiny
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt; Department of Biochemistry, Faculty of Pharmacy, Egyptian Russian University, Badr City 11829, Cairo, Egypt
| | - Hesham A El-Mahdy
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt
| | - Ahmed Ismail
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt
| | - Samy Y Elkhawaga
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt
| | - Emad Gamil Khidr
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt
| | - Doaa Fathi
- Department of Biochemistry and Biotechnology, Faculty of Pharmacy, Heliopolis University, Cairo 11785, Egypt
| | - Eman A Mady
- Laboratory of Veterinary Physiology, Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai Cho, Fuchu-shi, Tokyo 183-8509, Japan; Department of Animal Hygiene, Behavior and Management, Faculty of Veterinary Medicine, Benha University, Moshtohor, Toukh, Elqaliobiya 13736, Egypt
| | - Agnieszka Najda
- Department of Vegetable Crops and Medicinal Plants University of Life Sciences, Lublin 50A Doświadczalna Street, 20-280, Lublin, Poland.
| | - Mohammad Algahtani
- Department of Laboratory & Blood Bank, Security Forces Hospital, P.O. Box 14799, Mecca 21955, Saudi Arabia
| | - Abdulrahman Theyab
- Department of Laboratory & Blood Bank, Security Forces Hospital, P.O. Box 14799, Mecca 21955, Saudi Arabia; College of Medicine, Al-Faisal University, P.O. Box 50927, Riyadh 11533, Saudi Arabia
| | - Khalaf F Alsharif
- Department of Clinical Laboratory sciences, College of Applied medical sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Ashraf Albrakati
- Department of Human Anatomy, College of Medicine, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Roula Bayram
- Department of Pharmaceutical Sciences, Pharmacy Program, Batterjee Medical College, P.O. Box 6231, Jeddah 21442, Saudi Arabia
| | - Mohamed M Abdel-Daim
- Department of Pharmaceutical Sciences, Pharmacy Program, Batterjee Medical College, P.O. Box 6231, Jeddah 21442, Saudi Arabia; Pharmacology Department, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt
| | - Ahmed S Doghish
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt.
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Moriyama M, Lucas C, Monteiro VS, Iwasaki A. SARS-CoV-2 Omicron subvariants evolved to promote further escape from MHC-I recognition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.05.04.490614. [PMID: 35547852 PMCID: PMC9094094 DOI: 10.1101/2022.05.04.490614] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
SARS-CoV-2 variants of concern (VOCs) possess mutations that confer resistance to neutralizing antibodies within the Spike protein and are associated with breakthrough infection and reinfection. By contrast, less is known about the escape from CD8+ T cell-mediated immunity by VOC. Here, we demonstrated that all SARS-CoV-2 VOCs possess the ability to suppress MHC I expression. We identified several viral genes that contribute to the suppression of MHC I expression. Notably, MHC-I upregulation was strongly inhibited after SARS-CoV-2 infection in vivo. While earlier VOCs possess similar capacity as the ancestral strain to suppress MHC I, Omicron subvariants exhibit a greater ability to suppress surface MHC-I expressions. Collectively, our data suggest that, in addition to escape from neutralizing antibodies, the success of Omicron subvariants to cause breakthrough infection and reinfection may in part be due to its optimized evasion from T cell recognition.
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25
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Bello M, Hasan MK. Elucidation of the inhibitory activity of plant-derived SARS-CoV inhibitors and their potential as SARS-CoV-2 inhibitors. J Biomol Struct Dyn 2022; 40:9992-10004. [PMID: 34121618 DOI: 10.1080/07391102.2021.1938234] [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: 01/08/2023]
Abstract
Several drugs are now being tested as possible therapies due to the necessity of treating SARS-CoV-2 infection. Although approved vaccines bring much hope, a vaccination program covering the entire global population will take a very long time, making the development of effective antiviral drugs an effective solution for the immediate treatment of this dangerous infection. Previous studies found that three natural compounds, namely, tannic acid, 3-isotheaflavin-3-gallate and theaflavin-3,3-digallate, are effective proteinase (3CLpro) inhibitors of SARS-CoV (IC50 <10 µM). Based on this information and due to the high sequence identity between SARS-CoV and SARS-CoV-2 3CLpro, these three compounds could be candidate inhibitors of SARS-CoV-2 3CLpro. This paper explores the structural and energetic features that guided the molecular recognition of these three compounds for dimeric SARS-CoV-2 and SARS-CoV 3CLpro, the functional state of this enzyme, using docking and MD simulations with the molecular mechanics-generalized-born surface area (MMGBSA) approach. Energetic analysis demonstrated that the three compounds reached good affinities in both systems in the following order: tannic acid > 3-isotheaflavin-3-gallate > theaflavin-3,3-digallate. This tendency is in line with that experimentally reported between these ligands and SARS-CoV 3CLpro. Therefore, tannic acid may have clinical usefulness against COVID-19 by acting as a potent inhibitor of SARS-CoV-2 3CLpro.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Martiniano Bello
- Laboratorio de Modelado Molecular, Bioinformática y Diseño de Fármacos de la Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City, México
| | - Md Kamrul Hasan
- Department of Biochemistry and Molecular Biology, Tejgaon College, National University, Gazipur, Bangladesh
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Lobato TB, Gennari-Felipe M, Pauferro JRB, Correa IS, Santos BF, Dias BB, de Oliveira Borges JC, dos Santos CS, de Sousa Santos ES, de Araújo MJL, Ferreira LA, Pereira SA, Serdan TDA, Levada-Pires AC, Hatanaka E, Borges L, Cury-Boaventura MF, Vinolo MAR, Pithon-Curi TC, Masi LN, Curi R, Hirabara SM, Gorjão R. Leukocyte metabolism in obese type 2 diabetic individuals associated with COVID-19 severity. Front Microbiol 2022; 13:1037469. [PMID: 36406408 PMCID: PMC9670542 DOI: 10.3389/fmicb.2022.1037469] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 10/12/2022] [Indexed: 03/27/2024] Open
Abstract
Recent studies show that the metabolic characteristics of different leukocytes, such as, lymphocytes, neutrophils, and macrophages, undergo changes both in the face of infection with SARS-CoV-2 and in obesity and type 2 diabetes mellitus (DM2) condition. Thus, the objective of this review is to establish a correlation between the metabolic changes caused in leukocytes in DM2 and obesity that may favor a worse prognosis during SARS-Cov-2 infection. Chronic inflammation and hyperglycemia, specific and usual characteristics of obesity and DM2, contributes for the SARS-CoV-2 replication and metabolic disturbances in different leukocytes, favoring the proinflammatory response of these cells. Thus, obesity and DM2 are important risk factors for pro-inflammatory response and metabolic dysregulation that can favor the occurrence of the cytokine storm, implicated in the severity and high mortality risk of the COVID-19 in these patients.
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Affiliation(s)
- Tiago Bertola Lobato
- Programa de Pós-graduação Interdisciplinar em Ciências da Saúde, Universidade Cruzeiro do Sul, São Paulo, São Paulo, Brasil
| | - Matheus Gennari-Felipe
- Programa de Pós-graduação Interdisciplinar em Ciências da Saúde, Universidade Cruzeiro do Sul, São Paulo, São Paulo, Brasil
| | | | - Ilana Souza Correa
- Programa de Pós-graduação Interdisciplinar em Ciências da Saúde, Universidade Cruzeiro do Sul, São Paulo, São Paulo, Brasil
| | - Beatriz Ferreira Santos
- Programa de Pós-graduação Interdisciplinar em Ciências da Saúde, Universidade Cruzeiro do Sul, São Paulo, São Paulo, Brasil
| | - Beatriz Belmiro Dias
- Programa de Pós-graduação Interdisciplinar em Ciências da Saúde, Universidade Cruzeiro do Sul, São Paulo, São Paulo, Brasil
| | - João Carlos de Oliveira Borges
- Programa de Pós-graduação Interdisciplinar em Ciências da Saúde, Universidade Cruzeiro do Sul, São Paulo, São Paulo, Brasil
| | - Camila Soares dos Santos
- Programa de Pós-graduação Interdisciplinar em Ciências da Saúde, Universidade Cruzeiro do Sul, São Paulo, São Paulo, Brasil
| | | | - Maria Janaína Leite de Araújo
- Programa de Pós-graduação Interdisciplinar em Ciências da Saúde, Universidade Cruzeiro do Sul, São Paulo, São Paulo, Brasil
| | - Liliane Araújo Ferreira
- Programa de Pós-graduação Interdisciplinar em Ciências da Saúde, Universidade Cruzeiro do Sul, São Paulo, São Paulo, Brasil
| | - Sara Araujo Pereira
- Programa de Pós-graduação Interdisciplinar em Ciências da Saúde, Universidade Cruzeiro do Sul, São Paulo, São Paulo, Brasil
| | | | - Adriana Cristina Levada-Pires
- Programa de Pós-graduação Interdisciplinar em Ciências da Saúde, Universidade Cruzeiro do Sul, São Paulo, São Paulo, Brasil
| | - Elaine Hatanaka
- Programa de Pós-graduação Interdisciplinar em Ciências da Saúde, Universidade Cruzeiro do Sul, São Paulo, São Paulo, Brasil
| | - Leandro Borges
- Programa de Pós-graduação Interdisciplinar em Ciências da Saúde, Universidade Cruzeiro do Sul, São Paulo, São Paulo, Brasil
| | - Maria Fernanda Cury-Boaventura
- Programa de Pós-graduação Interdisciplinar em Ciências da Saúde, Universidade Cruzeiro do Sul, São Paulo, São Paulo, Brasil
| | - Marco Aurélio Ramirez Vinolo
- Laboratory of Immunoinflammation, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Tania Cristina Pithon-Curi
- Programa de Pós-graduação Interdisciplinar em Ciências da Saúde, Universidade Cruzeiro do Sul, São Paulo, São Paulo, Brasil
| | - Laureane Nunes Masi
- Programa de Pós-graduação Interdisciplinar em Ciências da Saúde, Universidade Cruzeiro do Sul, São Paulo, São Paulo, Brasil
| | - Rui Curi
- Programa de Pós-graduação Interdisciplinar em Ciências da Saúde, Universidade Cruzeiro do Sul, São Paulo, São Paulo, Brasil
- Immunobiological Production Section, Bioindustrial Center, Butantan Institute, São Paulo, Brazil
| | - Sandro Massao Hirabara
- Programa de Pós-graduação Interdisciplinar em Ciências da Saúde, Universidade Cruzeiro do Sul, São Paulo, São Paulo, Brasil
| | - Renata Gorjão
- Programa de Pós-graduação Interdisciplinar em Ciências da Saúde, Universidade Cruzeiro do Sul, São Paulo, São Paulo, Brasil
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Vinjamuri S, Li L, Bouvier M. SARS-CoV-2 ORF8: One protein, seemingly one structure, and many functions. Front Immunol 2022; 13:1035559. [PMID: 36353628 PMCID: PMC9637571 DOI: 10.3389/fimmu.2022.1035559] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/10/2022] [Indexed: 07/30/2023] Open
Abstract
SARS-CoV-2 is the virus responsible for the COVID-19 pandemic. The genome of SARS-CoV-2 encodes nine accessory proteins that are involved in host-pathogen interaction. ORF8 is unique among these accessory proteins. SARS-CoV-2 ORF8 shares a surprisingly low amino acid sequence similarity with SARS-COV ORF8 (30%), and it is presumed to have originated from bat. Studies have shown that ORF8 exerts multiple different functions that interfere with host immune responses, including the downregulation of MHC class I molecules. These functions may represent strategies of host immune evasion. The x-ray crystal structure of ORF8 revealed an immunoglobulin-like domain with several distinguishing features. To date, there are numerous unanswered questions about SARS-CoV-2 ORF8 protein and its structure-function relationship that we discuss in this mini-review. A better understanding of how ORF8 interacts with components of the immune system is needed for elucidating COVID-19 pathogenesis and to develop new avenues for the treatment of the disease.
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Affiliation(s)
| | | | - Marlene Bouvier
- Department of Microbiology and Immunology, University of Illinois at Chicago, College of Medicine, Chicago, IL, United States
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28
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Zhang Y, Wang X, Niu C, Wang D, Shen Q, Gao Y, Zhou H, Zhang Y, Zhang Y, Dong L. Evaluation of factors contributing to variability of qualitative and quantitative proficiency testing for SARS-CoV-2 nucleic acid detection. BIOSAFETY AND HEALTH 2022; 4:321-329. [PMID: 36091480 PMCID: PMC9450473 DOI: 10.1016/j.bsheal.2022.08.004] [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: 05/10/2022] [Revised: 08/24/2022] [Accepted: 08/31/2022] [Indexed: 11/29/2022] Open
Abstract
The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to unprecedented social and economic disruption. Many nucleic acid testing (NAT) laboratories in China have been established to control the epidemic better. This proficiency testing (PT) aims to evaluate the participants' performance in qualitative and quantitative SARS-CoV-2 NAT and to explore the factors that contribute to differences in detection capabilities. Two different concentrations of RNA samples (A, B) were used for quantitative PT. Pseudovirus samples D, E (different concentrations) and negative sample (F) were used for qualitative PT. 50 data sets were reported for qualitative PT, of which 74.00% were entirely correct for all samples. Forty-two laboratories participated in the quantitative PT. 37 submitted all gene results, of which only 56.76% were satisfactory. For qualitative detection, it is suggested that laboratories should strengthen personnel training, select qualified detection kits, and reduce cross-contamination to improve detection accuracy. For quantitative detection, the results of the reverse transcription digital PCR (RT-dPCR) method were more comparable and reliable than those of reverse transcription quantitative PCR (RT-qPCR). The copy number concentration of ORF1ab and N in samples A and B scattered in 85, 223, 50, and 106 folds, respectively. The differences in the quantitative result of RT-qPCR was mainly caused by the non-standard use of reference materials and the lack of personnel operating skills. Comparing the satisfaction of participants participating in both quantitative and qualitative proficiency testing, 95.65% of the laboratories with satisfactory quantitative results also judged the qualitative results correctly, while 85.71% of the laboratories with unsatisfactory quantitative results were also unsatisfied with their qualitative judgments. Therefore, the quantitative ability is the basis of qualitative judgment. Overall, participants from hospitals reported more satisfactory results than those from enterprises and universities. Therefore, surveillance, daily qualitiy control and standardized operating procedures should be strengthened to improve the capability of SARS-CoV-2 NAT.
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Affiliation(s)
| | - Xia Wang
- National Institute of Metrology, Beijing 100029, China
| | - Chunyan Niu
- National Institute of Metrology, Beijing 100029, China
| | - Di Wang
- National Institute of Metrology, Beijing 100029, China
| | - Qingfei Shen
- National Institute of Metrology, Beijing 100029, China
| | - Yunhua Gao
- National Institute of Metrology, Beijing 100029, China
| | - Haiwei Zhou
- Division II of In Vitro Diagnostics for Infectious Diseases, Institute for In Vitro Diagnostics Control, National Institutes for Food and Drug Control, Beijing 100050, China
| | - Yujing Zhang
- National Institute of Metrology, Beijing 100029, China
| | - Yan Zhang
- National Institute of Metrology, Beijing 100029, China
| | - Lianhua Dong
- National Institute of Metrology, Beijing 100029, China,Corresponding author: Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, China
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Latini A, Vancheri C, Amati F, Morini E, Grelli S, Claudia M, Vita P, Colona VL, Murdocca M, Andreoni M, Malagnino V, Raponi M, Cocciadiferro D, Novelli A, Borgiani P, Novelli G. Expression analysis of miRNA hsa-let7b-5p in naso-oropharyngeal swabs of COVID-19 patients supports its role in regulating ACE2 and DPP4 receptors. J Cell Mol Med 2022; 26:4940-4948. [PMID: 36073344 PMCID: PMC9538662 DOI: 10.1111/jcmm.17492] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 06/13/2022] [Accepted: 06/30/2022] [Indexed: 11/28/2022] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is the novel coronavirus responsible for worldwide coronavirus disease (COVID-19). We previously observed that Angiotensin-converting enzyme 2 (ACE2) and Dipeptidyl peptidase-4 (DPP4) are significantly overexpressed in naso-oropharyngeal swabs (NPS) of COVID-19 patients, suggesting their putative functional role in the disease progression. ACE2 and DPP4 overexpression in COVID-19 patients may be associated to epigenetic mechanism, such as miRNA differential expression. We investigated if hsa-let7b-5p, reported to target both ACE2 and DPP4 transcripts, could be involved in the regulation of these genes. We verified that the inhibition and overexpression of hsa-let7b-5p matched to a modulation of both ACE2 and DPP4 levels. Then, we observed a statistically significant downregulation (FC = -1.5; p < 0.05) of hsa-let7b-5p in the same COVID-19 and control samples of our previous study. This is the first study that shows hsa-let7b-5p low expression in naso-oropharyngeal swabs of COVID-19 patients and demonstrates a functional role of this miR in regulating ACE2 and DPP4 levels. These data suggest the involvement of hsa-let7b-5p in the regulation of genes necessary for SARS-CoV-2 infections and its putative role as a therapeutic target for COVID-19.
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Affiliation(s)
- Andrea Latini
- Department of Biomedicine and Prevention, Genetics Unit, University of Rome "Tor Vergata", Rome, Italy
| | - Chiara Vancheri
- Department of Biomedicine and Prevention, Genetics Unit, University of Rome "Tor Vergata", Rome, Italy
| | - Francesca Amati
- Department of Biomedicine and Prevention, Genetics Unit, University of Rome "Tor Vergata", Rome, Italy
| | - Elena Morini
- Department of Biomedicine and Prevention, Genetics Unit, University of Rome "Tor Vergata", Rome, Italy
| | - Sandro Grelli
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Matteucci Claudia
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Petrone Vita
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
| | | | - Michela Murdocca
- Department of Biomedicine and Prevention, Genetics Unit, University of Rome "Tor Vergata", Rome, Italy
| | - Massimo Andreoni
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Vincenzo Malagnino
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
| | | | | | | | - Paola Borgiani
- Department of Biomedicine and Prevention, Genetics Unit, University of Rome "Tor Vergata", Rome, Italy
| | - Giuseppe Novelli
- Department of Biomedicine and Prevention, Genetics Unit, University of Rome "Tor Vergata", Rome, Italy.,Bambino Gesù Pediatric Hospital, IRCCS, Rome, Italy.,Neuromed IRCCS Institute, Pozzilli, Italy.,School of Medicine, Reno University of Nevada, Reno, Nevada, USA
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Ortuso F, Mercatelli D, Guzzi PH, Giorgi FM. Structural genetics of circulating variants affecting the SARS-CoV-2 spike/human ACE2 complex. J Biomol Struct Dyn 2022; 40:6545-6555. [PMID: 33583326 PMCID: PMC7885719 DOI: 10.1080/07391102.2021.1886175] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 02/01/2021] [Indexed: 01/08/2023]
Abstract
SARS-CoV-2 entry in human cells is mediated by the interaction between the viral Spike protein and the human ACE2 receptor. This mechanism evolved from the ancestor bat coronavirus and is currently one of the main targets for antiviral strategies. However, there currently exist several Spike protein variants in the SARS-CoV-2 population as the result of mutations, and it is unclear if these variants may exert a specific effect on the affinity with ACE2 which, in turn, is also characterized by multiple alleles in the human population. In the current study, the GBPM analysis, originally developed for highlighting host-guest interaction features, has been applied to define the key amino acids responsible for the Spike/ACE2 molecular recognition, using four different crystallographic structures. Then, we intersected these structural results with the current mutational status, based on more than 295,000 sequenced cases, in the SARS-CoV-2 population. We identified several Spike mutations interacting with ACE2 and mutated in at least 20 distinct patients: S477N, N439K, N501Y, Y453F, E484K, K417N, S477I and G476S. Among these, mutation N501Y in particular is one of the events characterizing SARS-CoV-2 lineage B.1.1.7, which has recently risen in frequency in Europe. We also identified five ACE2 rare variants that may affect interaction with Spike and susceptibility to infection: S19P, E37K, M82I, E329G and G352V.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Francesco Ortuso
- Department of Health Sciences, University “Magna Graecia” of Catanzaro, Catanzaro, Italy
- Net4Science srl, c/o University “Magna Graecia” of Catanzaro, Catanzaro, Italy
| | - Daniele Mercatelli
- Department of Surgical and Medical Sciences, University “Magna Graecia” of Catanzaro, Catanzaro, Italy
| | - Pietro Hiram Guzzi
- Department of Surgical and Medical Sciences, University “Magna Graecia” of Catanzaro, Catanzaro, Italy
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31
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Morenikeji OB, Adegbaju MS, Okoh OS, Babalola AE, Grytsay A, Braimah OA, Akinyemi MO, Thomas BN. Deciphering inhibitory mechanism of coronavirus replication through host miRNAs-RNA-dependent RNA polymerase interactome. Front Genet 2022; 13:973252. [PMID: 36092931 PMCID: PMC9459146 DOI: 10.3389/fgene.2022.973252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 07/28/2022] [Indexed: 11/13/2022] Open
Abstract
Despite what we know so far, Covid-19, caused by SARS-CoV-2 virus, remains a pandemic that still require urgent healthcare intervention. The frequent mutations of the SARS-CoV-2 virus has rendered disease control with vaccines and antiviral drugs quite challenging, with newer variants surfacing constantly. There is therefore the need for newer, effective and efficacious drugs against coronaviruses. Considering the central role of RNA dependent, RNA polymerase (RdRp) as an enzyme necessary for the virus life cycle and its conservation among coronaviruses, we investigated potential host miRNAs that can be employed as broad-range antiviral drugs averse to coronaviruses, with particular emphasis on BCoV, MERS-CoV, SARS-CoV and SARS-CoV-2. miRNAs are small molecules capable of binding mRNA and regulate expression at transcriptional or translational levels. Our hypothesis is that host miRNAs have the potential of blocking coronavirus replication through miRNA-RdRp mRNA interaction. To investigate this, we retrieved the open reading frame (ORF1ab) nucleotide sequences and used them to interrogate miRNA databases for miRNAs that can bind them. We employed various bioinformatics tools to predict and identify the most effective host miRNAs. In all, we found 27 miRNAs that target RdRp mRNA sequence of multiple coronaviruses, of which three - hsa-miR-1283, hsa-miR-579-3p, and hsa-miR-664b-3p target BCoV, SARS-CoV and SARS-CoV-2. Additionally, hsa-miR-374a-5p has three bovine miRNA homologs viz bta-miR-374a, bta-miR-374b, and bta-miR-374c. Inhibiting the expression of RdRp enzyme via non-coding RNA is novel and of great therapeutic importance in the control of coronavirus replication, and could serve as a broad-spectrum antiviral, with hsa-miR-1283, hsa-miR-579-3p, and hsa-miR-664b-3p as highly promising.
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Affiliation(s)
- Olanrewaju B. Morenikeji
- Division of Biological and Health Sciences, University of Pittsburgh at Bradford, Bradford, PA, United States
- *Correspondence: Olanrewaju B. Morenikeji,
| | - Muyiwa S. Adegbaju
- Institute for Plant Biotechnology, Stellenbosch University, Stellenbosch, South Africa
| | - Olayinka S. Okoh
- Department of Chemical Sciences, Anchor University, Lagos, Nigeria
| | | | - Anastasia Grytsay
- Division of Biological and Health Sciences, University of Pittsburgh at Bradford, Bradford, PA, United States
| | - Olubumi A. Braimah
- Division of Biological and Health Sciences, University of Pittsburgh at Bradford, Bradford, PA, United States
| | - Mabel O. Akinyemi
- Department of Biological Sciences, Fairleigh Dickinson University, Madison, NJ, United States
| | - Bolaji N. Thomas
- Department of Biomedical Sciences, Rochester Institute of Technology, Rochester, NY, United States
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32
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Rashid F, Xie Z, Suleman M, Shah A, Khan S, Luo S. Roles and functions of SARS-CoV-2 proteins in host immune evasion. Front Immunol 2022; 13:940756. [PMID: 36003396 PMCID: PMC9394213 DOI: 10.3389/fimmu.2022.940756] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 07/07/2022] [Indexed: 12/27/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evades the host immune system through a variety of regulatory mechanisms. The genome of SARS-CoV-2 encodes 16 non-structural proteins (NSPs), four structural proteins, and nine accessory proteins that play indispensable roles to suppress the production and signaling of type I and III interferons (IFNs). In this review, we discussed the functions and the underlying mechanisms of different proteins of SARS-CoV-2 that evade the host immune system by suppressing the IFN-β production and TANK-binding kinase 1 (TBK1)/interferon regulatory factor 3 (IRF3)/signal transducer and activator of transcription (STAT)1 and STAT2 phosphorylation. We also described different viral proteins inhibiting the nuclear translocation of IRF3, nuclear factor-κB (NF-κB), and STATs. To date, the following proteins of SARS-CoV-2 including NSP1, NSP6, NSP8, NSP12, NSP13, NSP14, NSP15, open reading frame (ORF)3a, ORF6, ORF8, ORF9b, ORF10, and Membrane (M) protein have been well studied. However, the detailed mechanisms of immune evasion by NSP5, ORF3b, ORF9c, and Nucleocapsid (N) proteins are not well elucidated. Additionally, we also elaborated the perspectives of SARS-CoV-2 proteins.
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Affiliation(s)
- Farooq Rashid
- Division of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
| | - Zhixun Xie
- Department of Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
- Guangxi Key Laboratory of Veterinary Biotechnology, Nanning, China
- *Correspondence: Zhixun Xie,
| | - Muhammad Suleman
- Center for Biotechnology and Microbiology, University of Swat, Swat, Pakistan
| | - Abdullah Shah
- Department of Biotechnology, Shaheed Benazir Bhutto University, Sheringal, Pakistan
| | - Suliman Khan
- Department of Medical Lab Technology, The University of Haripur, Haripur, Pakistan
| | - Sisi Luo
- Department of Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
- Guangxi Key Laboratory of Veterinary Biotechnology, Nanning, China
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Niraula A, Baral N, Lamsal M, Bataju M, Thapa S. Potential role of biochemical markers in the prognosis of COVID-19 patients. SAGE Open Med 2022; 10:20503121221108613. [PMID: 35832258 PMCID: PMC9272200 DOI: 10.1177/20503121221108613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 06/01/2022] [Indexed: 01/08/2023] Open
Abstract
The global pandemic due to coronavirus disease 2019 (COVID-19) has posed an overall threat to modern medicine. The course of the disease is uncertain with varying forms of presentation that cannot be managed solely with clinical skills and vigor. Since its inception, laboratory medicine forms a backbone for the proper diagnosis, treatment, monitoring, and prediction of the severity of the disease. Clinical biochemistry, an integral component of laboratory medicine, has been an unsung hero in the disease prognosis and severity assessment in COVID-19. This review attempts to highlight the biomarkers which have shown a significant role and can be used in the identification, stratification, and prediction of disease severity in COVID-19 patients. It also highlights the basis of the use of these biomarkers in the disease course and their implications.
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Affiliation(s)
- Apeksha Niraula
- Department of Clinical Biochemistry, Institute of Medicine, Tribhuvan University Teaching Hospital, Maharajgunj, Nepal
| | - Nirmal Baral
- Department of Biochemistry, B.P. Koirala Institute of Health Sciences, Dharan, Nepal
| | - Madhab Lamsal
- Department of Biochemistry, B.P. Koirala Institute of Health Sciences, Dharan, Nepal
| | - Mahima Bataju
- Department of Biochemistry, KIST Medical College and Teaching Hospital, Lalitpur, Nepal
| | - Saroj Thapa
- Department of Biochemistry, Kathmandu University School of Medical Sciences, Dhulikhel, Nepal
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34
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Webb WR, Thapa G, Tirnoveanu A, Kallu S, Loo Jin Yi C, Shah N, Macari J, Mitchell S, Fagg GJ, Jeremiah RN, Theminimulle S, Vuono R, Mylona A. Single vs replicate Real-Time PCR SARS-CoV-2 testing: Lessons learned for effective pandemic management. PLoS One 2022; 17:e0269883. [PMID: 35834476 PMCID: PMC9282535 DOI: 10.1371/journal.pone.0269883] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 05/29/2022] [Indexed: 12/26/2022] Open
Abstract
Coronavirus Disease 19 (COVID-19) caused by the SARS-CoV-2 virus remains a global pandemic having a serious impact on national economies and healthcare infrastructure. Accurate infection detection protocols are key to policy guidance and decision making. In this pilot study, we compared single versus replicate PCR testing for effective and accurate SARS-CoV-2 infection detection. One-Step Real-Time RT-PCR was employed for the detection of SARS-CoV-2 RNA isolated from individual nasopharyngeal swabs. A total of 10,014 swabs, sampled from the general public (hospital admissions, A&E, elective surgeries, cancer patients, care home residents and healthcare staff), were tested using standard replicate testing. Our analysis demonstrates that approximately 19% of SARS-CoV-2 infected individuals would have been reported as false negative if single sample Real-Time PCR testing was used. Therefore, two replicate tests can substantially decrease the risk of false negative reporting and reduce hospital and community infection rates. As the number of variants of concern increases, we believe that replicate testing is an essential consideration for effective SARS-CoV-2 infection detection and prevention of further outbreaks. A strategic approach limiting the number of missed infections is crucial in controlling the rise of new SARS-CoV-2 variants as well as the management of future pandemics.
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Affiliation(s)
- William R. Webb
- Faculty of Medicine, Institute of Medical Sciences, Health and Social Care, Canterbury Christ Church University, Canterbury, United Kingdom
| | - Gauri Thapa
- Faculty of Medicine, Institute of Medical Sciences, Health and Social Care, Canterbury Christ Church University, Canterbury, United Kingdom
| | - Alice Tirnoveanu
- Faculty of Natural and Applied Sciences, School of Psychology and Life Sciences, Canterbury Christ Church University, Canterbury, United Kingdom
| | - Sabrina Kallu
- North Kent Pathology Service, Microbiology, Darent Valley Hospital, Dartford and Gravesham NHS Foundation Trust, Dartford, England
| | - Charlene Loo Jin Yi
- North Kent Pathology Service, Microbiology, Darent Valley Hospital, Dartford and Gravesham NHS Foundation Trust, Dartford, England
| | - Nirali Shah
- North Kent Pathology Service, Microbiology, Darent Valley Hospital, Dartford and Gravesham NHS Foundation Trust, Dartford, England
| | - Joseph Macari
- North Kent Pathology Service, Microbiology, Darent Valley Hospital, Dartford and Gravesham NHS Foundation Trust, Dartford, England
| | - Sadie Mitchell
- North Kent Pathology Service, Microbiology, Darent Valley Hospital, Dartford and Gravesham NHS Foundation Trust, Dartford, England
| | - Graham J. Fagg
- North Kent Pathology Service, Microbiology, Darent Valley Hospital, Dartford and Gravesham NHS Foundation Trust, Dartford, England
| | - Rachael N. Jeremiah
- North Kent Pathology Service, Microbiology, Darent Valley Hospital, Dartford and Gravesham NHS Foundation Trust, Dartford, England
| | - Sandiya Theminimulle
- North Kent Pathology Service, Microbiology, Darent Valley Hospital, Dartford and Gravesham NHS Foundation Trust, Dartford, England
| | - Romina Vuono
- Medway School of Pharmacy, University of Kent, Canterbury, England
- * E-mail: (AM); (RV)
| | - Athina Mylona
- Faculty of Medicine, Institute of Medical Sciences, Health and Social Care, Canterbury Christ Church University, Canterbury, United Kingdom
- Faculty of Natural and Applied Sciences, School of Psychology and Life Sciences, Canterbury Christ Church University, Canterbury, United Kingdom
- * E-mail: (AM); (RV)
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Asif M, Amir M, Hussain A, Achakzai NM, Natesan Pushparaj P, Rasool M. Role of tyrosine kinase inhibitor in chronic myeloid leukemia patients with SARS-CoV-2 infection: A narrative Review. Medicine (Baltimore) 2022; 101:e29660. [PMID: 35777011 PMCID: PMC9239670 DOI: 10.1097/md.0000000000029660] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Severe acute respiratory syndrome (SARS) caused by a novel coronavirus-2 (CoV-2), also known as COVID-19, has spread rapidly worldwide since it is recognized as a public health emergency and has now been declared a pandemic on March 11, 2020, by the World Health Organization. The genome of SARS-CoV-2 comprises a single-stranded positive-sense RNA approximately 27 to 30 kb in size. The virus is transmitted through droplets from humans to humans. Infection with the SARS virus varies from asymptomatic to lethal, such as fever, cough, sore throat, and headache, but in severe cases, pneumonia and acute respiratory distress syndrome. Recently, no specific and effective treatment has been recommended for patients infected with the SARS virus. However, several options can be investigated to control SARS-CoV-2 infection, including monoclonal antibodies, interferons, therapeutic vaccines, and molecular-based targeted drugs. In the current review, we focus on tyrosine kinase inhibitor management and their protective role in SARS-CoV-2 patients with chronic myelogenous leukemia.
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Affiliation(s)
- Muhammad Asif
- Department of Biotechnology, BUITEMS, Quetta, Pakistan
- Office of Research Innovation and Commercialization, BUITEMS, Quetta, Pakistan
| | - Muhammad Amir
- Department of Biotechnology, BUITEMS, Quetta, Pakistan
| | - Abrar Hussain
- Department of Biotechnology, BUITEMS, Quetta, Pakistan
| | - Niaz M. Achakzai
- Department of Molecular Biology, City Medical Complex, Kabul, Afghanistan
- Department of Molecular Biology, DNA section, Legal Medicine Directorate, Ministry of Public Health, Kabul, Afghanistan
- *Correspondence: Niaz M. Achakzai, Senior forensic DNA specialist, Department of Molecular Biology, DNA section, Legal Medicine Directorate, Ministry of Public Health, Kabul, Afghanistan (e-mail: ),
| | - Peter Natesan Pushparaj
- Center of Excellence in Genomic Medicine Research, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mahmood Rasool
- Center of Excellence in Genomic Medicine Research, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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36
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Mortezaei Z, Mohammadian A, Tavallaei M. Variations of SARS-CoV-2 in the Iranian population and candidate putative drug-like compounds to inhibit the mutated proteins. Heliyon 2022; 8:e09910. [PMID: 35847618 PMCID: PMC9271419 DOI: 10.1016/j.heliyon.2022.e09910] [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: 09/30/2021] [Revised: 04/16/2022] [Accepted: 07/04/2022] [Indexed: 11/30/2022] Open
Abstract
The first cases of the novel coronavirus, SARS-CoV-2, were detected in December 2019 in Wuhan, China. Nucleotide substitutions and mutations in the SARS-CoV-2 sequence can result in the evolution of the virus and its rapid spread across the world. Therefore, understanding genetic variants of SARS-CoV-2 and targeting the conserved elements responsible for viral replication have great benefits for detecting its infection sources and diagnosing and treating COVID-19. In this study, we used the SARS-CoV-2 sequence isolated from a 59-year-old man in Ardabil, Iran, in April 2020 and sequenced using Oxford Nanopore technology. A meta-analysis comparing the sequence under study with other sequences from Iran indicated long nucleotide insertions/deletions (indels) that code for NSP15, the NSP14-NSP10 complex, open reading frame ORF9b, and ORF1ab polyproteins. In addition, replicating the NSP8 protein in the study sequence is another topic that can affect viral replication. Then using the DNA structure of NSP8, NSP15, NSP14-NSP10 complex, and ORF1ab as a genetic target can help find drug-like compounds for COVID-19. Potential drug-like compounds reported in this study for their mechanism of action and interactions with SARS-CoV-2 genes using drug repurposing are resveratrol, erythromycin, chloramphenicol, indomethacin, ciclesonide, and PDE4 inhibitor. Ciclesonide appears to show the best results when docked with chosen viral proteins. Therefore, different proteins isolated from nucleotide mutations in the virus sequence can indicate distinct inducers for antibodies and are important in vaccine design.
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Affiliation(s)
- Zahra Mortezaei
- Human Genetic Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Ali Mohammadian
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mahmood Tavallaei
- Human Genetic Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
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Martínez-Murcia A, García-Sirera A, Navarro A, Pérez L. Current RT-qPCR to detect SARS-CoV-2 may give positive results for related coronaviruses. Arch Microbiol 2022; 204:415. [PMID: 35737122 PMCID: PMC9223264 DOI: 10.1007/s00203-022-03029-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 05/27/2022] [Accepted: 06/01/2022] [Indexed: 12/12/2022]
Abstract
Some weeks after the first CoVID-19 outbreak, the World Health Organization published some real-time PCR (qPCR) protocols developed by different health reference centers. These qPCR designs are being used worldwide to detect SARS-CoV-2 in the population, to monitor the prevalence of the virus during the pandemic. Moreover, some of these protocols to detect SARS-CoV-2 have widely been applied to environmental samples for epidemiological surveillance purposes. In the present work, the specificity of these currently used RT-qPCR designs was validated in vitro using SARS-CoV-2 and highly related coronaviral genomic sequences and compared to performance of the commercially available GPS™ CoVID-19 dtec-RT-qPCR Test. Assays performed with SARS-CoV-2-related genomes showed positive amplification when using some of these qPCR methods, indicating they may give SARS-CoV-2 false positives. This finding may be particularly relevant for SARS-CoV-2 monitoring of environmental samples, where an unknown pool of phylogenetically close-related viruses may exist.
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Affiliation(s)
- Antonio Martínez-Murcia
- Department of Microbiology, University Miguel Hernández, 03312, Orihuela, Alicante, Spain.
- Genetic PCR Solutions™, 03206, Elche, Alicante, Spain.
| | | | - Aaron Navarro
- Genetic PCR Solutions™, 03206, Elche, Alicante, Spain
| | - Laura Pérez
- Genetic PCR Solutions™, 03206, Elche, Alicante, Spain
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The impact of the suppression of highly connected protein interactions on the corona virus infection. Sci Rep 2022; 12:9188. [PMID: 35654986 PMCID: PMC9160517 DOI: 10.1038/s41598-022-13373-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 05/09/2022] [Indexed: 11/28/2022] Open
Abstract
Several highly effective Covid-19 vaccines are in emergency use, although more-infectious coronavirus strains, could delay the end of the pandemic even further. Because of this, it is highly desirable to develop fast antiviral drug treatments to accelerate the lasting immunity against the virus. From a theoretical perspective, computational approaches are useful tools for antiviral drug development based on the data analysis of gene expression, chemical structure, molecular pathway, and protein interaction mapping. This work studies the structural stability of virus–host interactome networks based on the graphical representation of virus–host protein interactions as vertices or nodes connected by commonly shared proteins. These graphical network visualization methods are analogous to those use in the design of artificial neural networks in neuromorphic computing. In standard protein-node-based network representation, virus–host interaction merges with virus–protein and host–protein networks, introducing redundant links associated with the internal virus and host networks. On the contrary, our approach provides a direct geometrical representation of viral infection structure and allows the effective and fast detection of the structural robustness of the virus–host network through proteins removal. This method was validated by applying it to H1N1 and HIV viruses, in which we were able to pinpoint the changes in the Interactome Network produced by known vaccines. The application of this method to the SARS-CoV-2 virus–host protein interactome implies that nonstructural proteins nsp4, nsp12, nsp16, the nuclear pore membrane glycoprotein NUP210, and ubiquitin specific peptidase USP54 play a crucial role in the viral infection, and their removal may provide an efficient therapy. This method may be extended to any new mutations or other viruses for which the Interactome Network is experimentally determined. Since time is of the essence, because of the impact of more-infectious strains on controlling the spread of the virus, this method may be a useful tool for novel antiviral therapies.
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39
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Febrianti RA, Narulita E. In-silico analysis of recombinant protein vaccines based on the spike protein of Indonesian SARS-CoV-2 through a reverse vaccinology approach. J Taibah Univ Med Sci 2022; 17:467-478. [PMID: 35250426 PMCID: PMC8881762 DOI: 10.1016/j.jtumed.2022.02.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 01/04/2022] [Accepted: 02/09/2022] [Indexed: 01/23/2023] Open
Abstract
Objectives This study aimed to produce a recombinant protein vaccine candidate based on an epitope of spike protein from Indonesian SARS-CoV-2 to provide immunogenicity and protection against future infection. Methods A reverse vaccinology approach was used to identify potential vaccine candidates by screening the pathogen's genome through computational analyses. Results Epitope vaccine candidates with the amino acid sequence of FKNHTSPDV were selected. This peptide is hydrophilic, does not induce autoimmune and allergic reactions, is antigenic, is classified as a stable protein, and is predicted to be present in the cell membrane. The selected epitope sequences were inserted into the plasmid vector pcDNA3.1(+) N-GST (thrombin). Inclusion of additional features of the gene encoding glutathione-S transferase, which can increase antigen expression and solubility, and the genes encoding NSP 1-4 proteins, which are essential in replication, added value to the produced recombinant protein. Conclusion Recombinant protein vaccine candidates with the FKNHTSPDV epitope have parameters sufficient for production on a laboratory scale for further testing.
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Affiliation(s)
- Riska A. Febrianti
- Department of Biotechnology, Postgraduate Program, University of Jember, Indonesia
| | - Erlia Narulita
- Department of Biotechnology, Postgraduate Program, University of Jember, Indonesia
- Department of Biology Education, University of Jember, Indonesia
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Chou JM, Tsai JL, Hung JN, Chen IH, Chen ST, Tsai MH. The ORF8 Protein of SARS-CoV-2 Modulates the Spike Protein and Its Implications in Viral Transmission. Front Microbiol 2022; 13:883597. [PMID: 35663899 PMCID: PMC9161165 DOI: 10.3389/fmicb.2022.883597] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/01/2022] [Indexed: 01/09/2023] Open
Abstract
COVID-19 is currently global pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Accompanying the rapid spread of the error-prone RNA-based genome, several dominant SARS-CoV-2 variants have been genetically identified. The mutations in the spike protein, which are essential for receptor binding and fusion, have been intensively investigated for their contributions to viral transmission. Nevertheless, the importance of other viral proteins and their mutations in SARS-CoV-2 lifecycle and transmission remains fairly understood. Here, we report the strong potency of an accessory protein ORF8 in modulating the level and processing of the spike protein. The expression of ORF8 protein does not affect propagation but expression of spike protein, which may lead to pseudovirions with less spike protein on the surface, therefore less infection potential. At the protein level, ORF8 expression led to downregulation and insufficient S1/S2 cleavage of the spike protein in a dose-dependent manner. ORF8 exhibits a strong interaction with the spike protein mainly at S1 domains and mediates its degradation through multiple pathways. The dominant clinical isolated ORF8 variants with the reduced protein stability exhibited the increased capacity of viral transmission without compromising their inhibitory effects on HLA-A2. Although the increase in spike protein level and Spike pseudovirus production observed by using highly transmissible clinical spike variants, there was no significant compromise in ORF8-mediated downregulation. Because ORF8 is important for immune surveillance and might be required for viral fitness in vivo, the alteration of the spike protein might be an optional strategy used by SARS-CoV-2 to promote viral transmission by escaping the inhibitory effects of ORF8. Therefore, our report emphasized the importance of ORF8 in SARS-CoV-2 spike protein production, maturation, and possible evolution.
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Affiliation(s)
- Jen-Mei Chou
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
| | - Jo-Ling Tsai
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
| | - Jo-Ning Hung
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
| | - I-Hua Chen
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
- College of Medicine, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Szu-Ting Chen
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- Research Center for Epidemic Prevention, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Ming-Han Tsai
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
- Research Center for Epidemic Prevention, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- *Correspondence: Ming-Han Tsai,
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M.D OC, Solomon BA, Tauseef A, Haroon H, R. E. E. AG, K.C. SM. EMERGENCE OF NEW STRAINS OF SARS-COV-2: AFRICA'S FATE AND ITS PREPAREDNESS AGAINST COVID-19 INFECTION WAVES. Afr J Infect Dis 2022; 16:1-12. [PMID: 35582064 PMCID: PMC9097310 DOI: 10.21010/ajid.v16i2.1] [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: 07/24/2021] [Revised: 11/13/2021] [Accepted: 11/17/2021] [Indexed: 11/29/2022] Open
Abstract
Background Severe acute respiratory syndrome coronavirus-2(SARS-CoV-2) has infected over 100million individuals worldwide with diverse impacts on nations. The rising cases of new strains and resultant infection waves create an urgent need to assess the readiness of countries especially in Africa to mitigate the impact on community transmission. This paper delivers a brief synopsis of the novel SARS-CoV-2, emerging cases of new variants reported worldwide, and implications for genetic surveillance of disease transmission in low- and middle-income countries (LMICs) especially Africa. Materials and Methods Literature search used keywords like SARS-CoV-2; COVID-19 epidemiology; pandemic waves; corona outbreak, clinical syndromes, treatments, prevention and control. Cross-sectional and observational studies published on COVID-19 from 2019 till date of study provided main information sources. Databases such as Web of Science, Embase, PubMed and Google Scholar were utilised. Main findings Over 220 countries have documented COVID-19 cases with varied severity till date. Before the spikes in resurgence, a highly virulent mutated (>90% fatality rate) novel strain of COVID-19 had been documented. There is very little data to ascertain the impact of the COVID-19 infection waves in LMICs. Discussion LMICs especially African countries still grapple with significant challenges like inefficient surveillance mechanisms, inadequate vaccination coverage, inadequate enforcement of environmental health strategies, poor health systems etc. Hence, Africa's fate remains dicey in the face of the dynamic evolution of the SARS-CoV-2 and other identified challenges. Conclusion The adoption of a multidisciplinary approach to mitigate the impact of emergence of mutant SARS-CoV-2 variants and resurgence of infection spike is recommended.
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Affiliation(s)
- Ohia Chinenyenwa M.D
- Department of Environmental Health Sciences, Faculty of Public Health, College of Medicine, University of Ibadan, Nigeria
| | - Bakarey Adeleye Solomon
- Institute for Advanced Medical Research and Training (IAMRAT), College of Medicine, University of Ibadan, Nigeria
| | - Ahmad Tauseef
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing 210096, China
| | - Haroon Haroon
- College of Life Sciences, Northwest University, No. 229, North Taibai Road, Xian, Shaanxi Province, 710069, China
| | - Ana Godson R. E. E.
- Department of Environmental Health Sciences, Faculty of Public Health, College of Medicine, University of Ibadan, Nigeria
| | - Sridhar Mynepalli K.C.
- Department of Environmental Health Sciences, Faculty of Public Health, College of Medicine, University of Ibadan, Nigeria
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Frequently Used Allopathic and Traditional Medicine for COVID-19 Treatment and Feasibility of Their Integration. Chin J Integr Med 2022; 28:1040-1047. [PMID: 35507298 PMCID: PMC9065245 DOI: 10.1007/s11655-021-3512-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/28/2021] [Indexed: 02/06/2023]
Abstract
To date, no satisfactory treatment for COVID-19 is available. This review reported few recent updates regarding the drugs (allopathy/traditional medicines) used for the treatment of COVID-19 concerning clinical studies. Content of the article spotlight the contribution of allopathic and Ayurvedic drugs to the scientific basis for utilization as a potential therapy against COVID-19 infection and provide new insights on the integration of allopathy and traditional medicine. It advocated the combination of these two systems of treatment will ascertain their integrations, and there would be a good possibility and scope for developing a model of integration in the management of COVID-19. Provided discussion may help researchers, physicians, and healthcare policymakers to encourage for effective and integrated use of allopathic and Ayurvedic medicines to control the COVID-19 pandemic more effectively.
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Zhang Q, Guo HL, Wang J, Zhang Y, Deng PJ, Li FF. Structural Genomic Analysis of SARS-CoV-2 and Other Coronaviruses. Front Genet 2022; 13:801902. [PMID: 35464844 PMCID: PMC9024071 DOI: 10.3389/fgene.2022.801902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 03/01/2022] [Indexed: 11/15/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the causative agent of the coronavirus disease 2019 (COVID-19) pandemic. In this study, we conducted a comparative analysis of the structural genes of SARS-CoV-2 and other CoVs. We found that the sequence of the E gene was the most evolutionarily conserved across 200 SARS-CoV-2 isolates. The E gene and M gene sequences of SARS-CoV-2 and NC014470 CoV were closely related and fell within the same branch of a phylogenetic tree. The absolute diversity of E gene and M gene sequences of SARS-CoV-2 isolates was similar to that of common CoVs (C-CoVs) infecting other organisms. The absolute diversity of the M gene sequence of the KJ481931 CoV that can infect humans was similar to that of SARS-CoV-2 and C-CoVs infecting other organisms. The M gene sequence of KJ481931 CoV (infecting humans), SARS-CoV-2 and NC014470 CoV (infecting other organisms) were closely related, falling within the same branch of a phylogenetic tree. Patterns of variation and evolutionary characteristics of the N gene and S gene were very similar. These data may be of value for understanding the origins and intermediate hosts of SARS-CoV-2.
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Affiliation(s)
- Qiong Zhang
- School of Pharmaceutical Sciences, Hubei University of Medicine, Shiyan, China
- Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Hubei University of Medicine, Shiyan, China
- Hubei Biomedical Detection Sharing Platform in Water Source Area of South to North Water Diversion Project, Hubei University of Medicine, Shiyan, China
| | - Huai-Lan Guo
- Hubei Biomedical Detection Sharing Platform in Water Source Area of South to North Water Diversion Project, Hubei University of Medicine, Shiyan, China
- School of Public Health, Hubei University of Medicine, Shiyan, China
| | - Jing Wang
- Hubei Biomedical Detection Sharing Platform in Water Source Area of South to North Water Diversion Project, Hubei University of Medicine, Shiyan, China
- School of Public Health, Hubei University of Medicine, Shiyan, China
| | - Yao Zhang
- Hubei Biomedical Detection Sharing Platform in Water Source Area of South to North Water Diversion Project, Hubei University of Medicine, Shiyan, China
- School of Public Health, Hubei University of Medicine, Shiyan, China
| | - Ping-Ji Deng
- Hubei Biomedical Detection Sharing Platform in Water Source Area of South to North Water Diversion Project, Hubei University of Medicine, Shiyan, China
- School of Public Health, Hubei University of Medicine, Shiyan, China
- *Correspondence: Fei-Feng Li, ; Ping-Ji Deng,
| | - Fei-Feng Li
- Hubei Biomedical Detection Sharing Platform in Water Source Area of South to North Water Diversion Project, Hubei University of Medicine, Shiyan, China
- School of Public Health, Hubei University of Medicine, Shiyan, China
- *Correspondence: Fei-Feng Li, ; Ping-Ji Deng,
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Sharma P, Joshi T, Mathpal S, Joshi T, Pundir H, Chandra S, Tamta S. Identification of natural inhibitors against Mpro of SARS-CoV-2 by molecular docking, molecular dynamics simulation, and MM/PBSA methods. J Biomol Struct Dyn 2022; 40:2757-2768. [PMID: 33143552 PMCID: PMC7651194 DOI: 10.1080/07391102.2020.1842806] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 10/22/2020] [Indexed: 10/26/2022]
Abstract
The recent outbreak of SARS-CoV-2 disease, also known as COVID-19, has emerged as a pandemic. The unavailability of specific therapeutic drugs and vaccines urgently demands sincere efforts for drug discovery against COVID-19. The main protease (Mpro) of SARS-CoV-2 is a critical drug target as it plays an essential role in virus replication. Therefore for the identification of potential inhibitors of SARS-CoV-2 Mpro, we applied a structure-based virtual screening approach followed by molecular dynamics (MD) study. A library of 686 phytochemicals was subjected to virtual screening which resulted in 28 phytochemicals based on binding energy. These phytochemicals were further subjected to drug-likeness and toxicity analysis, which resulted in seven drug-like hits. Out of seven, five phytochemicals viz., Mpro-Dehydrtectol (-10.3 kcal/mol), Epsilon-viniferin (-8.6 kcal/mol), Peimisine (-8.6 kcal/mol), Gmelanone (-8.4 kcal/mol), and Isocolumbin (-8.4 kcal/mol) were non-toxic. Consequently, these phytochemicals are subjected to MD, post MD analysis, and MM/PBSA calculations. The results of 100 ns MD simulation, RMSF, SASA, Rg, and MM/PBSA show that Epsilon-viniferin (-29.240 kJ/mol), Mpro-Peimisine (-43.031 kJ/mol) and Gmelanone (-13.093 kJ/mol) form a stable complex with Mpro and could be used as potential inhibitors of SARS-CoV-2 Mpro. However, further investigation of these inhibitors against Mpro receptor of COVID-19 is needed to validate their candidacy for clinical trials. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Priyanka Sharma
- Department of Botany, D.S.B Campus, Kumaun University, Nainital, Uttarakhand, India
| | - Tushar Joshi
- Department of Biotechnology, Bhimtal Campus, Kumaun University Uttarakhand, Bhimtal, Uttarakhand, India
| | - Shalini Mathpal
- Department of Biotechnology, Bhimtal Campus, Kumaun University Uttarakhand, Bhimtal, Uttarakhand, India
| | - Tanuja Joshi
- Department of Botany, Kumaun University, S.S.J Campus, Almora, Uttarakhand, India
| | - Hemlata Pundir
- Department of Biotechnology, Bhimtal Campus, Kumaun University Uttarakhand, Bhimtal, Uttarakhand, India
| | - Subhash Chandra
- Department of Botany, Kumaun University, S.S.J Campus, Almora, Uttarakhand, India
| | - Sushma Tamta
- Department of Botany, D.S.B Campus, Kumaun University, Nainital, Uttarakhand, India
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45
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Fast Phylogeny of SARS-CoV-2 by Compression. ENTROPY 2022; 24:e24040439. [PMID: 35455102 PMCID: PMC9030035 DOI: 10.3390/e24040439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 12/10/2022]
Abstract
The compression method to assess similarity, in the sense of having a small normalized compression distance (NCD), was developed based on algorithmic information theory to quantify the similarity in files ranging from words and languages to genomes and music pieces. It has been validated on objects from different domains always using essentially the same software. We analyze the whole-genome phylogeny and taxonomy of the SARS-CoV-2 virus, which is responsible for causing the COVID-19 disease, using the alignment-free compression method to assess similarity. We compare the SARS-CoV-2 virus with a database of over 6500 viruses. The results suggest that the SARS-CoV-2 virus is closest in that database to the RaTG13 virus and rather close to the bat SARS-like coronaviruses bat-SL-CoVZXC21 and bat-SL-CoVZC45. Over 6500 viruses are identified (given by their registration code) with larger NCDs. The NCDs are compared with the NCDs between the mtDNA of familiar species. We address the question of whether pangolins are involved in the SARS-CoV-2 virus. The compression method is simpler and possibly faster than any other whole-genome method, which makes it the ideal tool to explore phylogeny. Here, we use it for the complex case of determining this similarity between the COVID-19 virus, SARS-CoV-2 and many other viruses. The resulting phylogeny and taxonomy closely resemble earlier results from by alignment-based methods and a machine-learning method, providing the most compelling evidence to date for the compression method, showing that one can achieve equivalent results both simply and quickly.
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Gumba H, Opiyo M, Musyoki J, Mutunga M, Ngetsa C, Mwarumba S, Mosobo M, Njuguna S, Kai O, Lambisia AW, Kimani D, Cheruiyot R, Kiyuka P, Lewa C, Gicheru E, Tendwa M, Said Mohammed K, Osoti V, Makale J, Tawa B, Odundo C, Cheruiyot W, Nyamu W, Gumbi W, Mwacharo J, Nyamako L, Otieno E, Amadi D, Ouma N, Karia B, Thoya J, Karani A, Mugo D, Gichuki BM, Riako D, Mutua S, Gitonga JN, Ominde K, Wanjiku P, Mutiso A, Mwanzu A, Sein Y, Bartilol B, Mwangi S, Omuoyo DO, Morobe JM, de Laurent ZR, Mitsanze F, Mwakubia A, Rono M, Nyaguara A, Tsofa B, Bejon P, Agoti CN, Ochola-Oyier LI. Maintaining laboratory quality assurance and safety in a pandemic: Experiences from the KEMRI-Wellcome Trust Research Programme laboratory’s COVID-19 response. Wellcome Open Res 2022. [DOI: 10.12688/wellcomeopenres.16704.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Laboratory diagnosis plays a critical role in the containment of a pandemic. Strong laboratory quality management systems (QMS) are essential for laboratory diagnostic services. However, low laboratory capacities in resource-limited countries has made the maintenance of laboratory quality assurance, especially during a pandemic, a daunting task. In this paper, we describe our experience of how we went about providing diagnostic testing services for SARS-CoV-2 through laboratory reorganization, redefining of the laboratory workflow, and training and development of COVID-19 documented procedures, all while maintaining the quality assurance processes during the COVID-19 pandemic at the Kenya Medical Research Institute (KEMRI) Wellcome Trust Research Programme (KWTRP) laboratory. The KWTRP laboratory managed to respond to the COVID-19 outbreak in Kenya by providing diagnostic testing for the coastal region of the country, while maintaining its research standard quality assurance processes. A COVID-19 team comprising of seven sub-teams with assigned specific responsibilities and an organizational chart with established reporting lines were developed. Additionally, a total of four training sessions were conducted for county Rapid Response Teams (RRTs) and laboratory personnel. A total of 11 documented procedures were developed to support the COVID-19 testing processes, with three for the pre-analytical phases, seven for the analytical phase, and one for the post-analytical phase. With the workflow re-organization, the development of appropriate standard operating procedures, and training, research laboratories can effectively respond to pandemic outbreaks while maintaining research standard QMS procedures.
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Secondary structural ensembles of the SARS-CoV-2 RNA genome in infected cells. Nat Commun 2022; 13:1128. [PMID: 35236847 PMCID: PMC8891300 DOI: 10.1038/s41467-022-28603-2] [Citation(s) in RCA: 66] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 01/20/2022] [Indexed: 12/25/2022] Open
Abstract
SARS-CoV-2 is a betacoronavirus with a single-stranded, positive-sense, 30-kilobase RNA genome responsible for the ongoing COVID-19 pandemic. Although population average structure models of the genome were recently reported, there is little experimental data on native structural ensembles, and most structures lack functional characterization. Here we report secondary structure heterogeneity of the entire SARS-CoV-2 genome in two lines of infected cells at single nucleotide resolution. Our results reveal alternative RNA conformations across the genome and at the critical frameshifting stimulation element (FSE) that are drastically different from prevailing population average models. Importantly, we find that this structural ensemble promotes frameshifting rates much higher than the canonical minimal FSE and similar to ribosome profiling studies. Our results highlight the value of studying RNA in its full length and cellular context. The genomic structures detailed here lay groundwork for coronavirus RNA biology and will guide the design of SARS-CoV-2 RNA-based therapeutics. Lan et al. report RNA structure ensembles across the entire SARSCoV-2 genome in infected human cells at single nucleotide resolution. They find alternative RNA conformations critical for promoting near-native frameshifting rates in ORF1ab.
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48
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Rout RK, Hassan SS, Sheikh S, Umer S, Sahoo KS, Gandomi AH. Feature-extraction and analysis based on spatial distribution of amino acids for SARS-CoV-2 Protein sequences. Comput Biol Med 2022; 141:105024. [PMID: 34815067 PMCID: PMC8577876 DOI: 10.1016/j.compbiomed.2021.105024] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 10/15/2021] [Accepted: 11/04/2021] [Indexed: 12/28/2022]
Abstract
BACKGROUND AND OBJECTIVE The world is currently facing a global emergency due to COVID-19, which requires immediate strategies to strengthen healthcare facilities and prevent further deaths. To achieve effective remedies and solutions, research on different aspects, including the genomic and proteomic level characterizations of SARS-CoV-2, are critical. In this work, the spatial representation/composition and distribution frequency of 20 amino acids across the primary protein sequences of SARS-CoV-2 were examined according to different parameters. METHOD To identify the spatial distribution of amino acids over the primary protein sequences of SARS-CoV-2, the Hurst exponent and Shannon entropy were applied as parameters to fetch the autocorrelation and amount of information over the spatial representations. The frequency distribution of each amino acid over the protein sequences was also evaluated. In the case of a one-dimensional sequence, the Hurst exponent (HE) was utilized due to its linear relationship with the fractal dimension (D), i.e. D+HE=2, to characterize fractality. Moreover, binary Shannon entropy was considered to measure the uncertainty in a binary sequence then further applied to calculate amino acid conservation in the primary protein sequences. RESULTS AND CONCLUSION Fourteen (14) SARS-CoV protein sequences were evaluated and compared with 105 SARS-CoV-2 proteins. The simulation results demonstrate the differences in the collected information about the amino acid spatial distribution in the SARS-CoV-2 and SARS-CoV proteins, enabling researchers to distinguish between the two types of CoV. The spatial arrangement of amino acids also reveals similarities and dissimilarities among the important structural proteins, E, M, N and S, which is pivotal to establish an evolutionary tree with other CoV strains.
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Affiliation(s)
- Ranjeet Kumar Rout
- Department of Computer Science & Engineering, National Institute of Technology Srinagar, Hazratbal, Jammu and Kashmir, India.
| | - Sk Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, Paschim Medinipur, 721140, India.
| | - Sabha Sheikh
- Department of Computer Science & Engineering, National Institute of Technology Srinagar, Hazratbal, Jammu and Kashmir, India.
| | - Saiyed Umer
- Department of Computer Science and Engineering, Aliah University, Kolkata, India.
| | - Kshira Sagar Sahoo
- Department of Computer Science and Engineering, SRM University, Amaravati, AP, 522240, India.
| | - Amir H Gandomi
- Faculty of Engineering and Information Technology, University of Technology Sydney, NSW, Australia.
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49
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Barros FR, Leite DC, Guimarães LJ, Lopes JM, Vasconcelos MW, Ferreira LX, Gonçalves S, Pastre VG, Pereira G, Trentin AB, Gabiatti NC, Kuhn BC, Perseguini JM, Wendt SN, Ghisi NC. Performance of RT-qPCR detection of SARS-CoV-2 in unextracted nasopharyngeal samples using the Seegene Allplex TM 2019-nCoV protocol. J Virol Methods 2022; 300:114429. [PMID: 34919975 PMCID: PMC8668600 DOI: 10.1016/j.jviromet.2021.114429] [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: 10/15/2021] [Revised: 12/10/2021] [Accepted: 12/11/2021] [Indexed: 11/16/2022]
Abstract
The rapid spread of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has led the world to a pandemic. Therefore, rapid, sensitive, and reproducible diagnostic tests are essential to indicate which measures should be taken during pandemics. We retrospectively tested unextracted nasopharyngeal samples from consecutive patients with suspected SARS-CoV-2 infection (n = 334), and compared two different Ct cut-off values for interpretation of results using a modified Allplex protocol. Its performance was evaluated using the USA Centers for Disease Control and Prevention (CDC) as reference. The reduction on Ct cut-off to 35 increased the test NPA from 79.65 to 88.00 %, reducing the number of false positives, from 10.48 to 6.29 %, resulting in an almost perfect agreement between the Allplex and the CDC protocol (Cohen's Kappa coefficient = 0.830 ± 0.032). This study demonstrates that the Seegene Allplex™ 2019-nCoV protocol skipping the viral RNA extraction step using the Ct cut-off of 35 is a rapid and efficient method to detect SARS-CoV-2 in nasopharyngeal samples.
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Affiliation(s)
- Flavia R.O. Barros
- Corresponding authors at: Universidade Tecnológica Federal do Paraná, Estrada para Boa Esperança, Km 4, Dois Vizinhos, PR, 85660-000, Brazil
| | - Deborah C.A. Leite
- Corresponding authors at: Universidade Tecnológica Federal do Paraná, Estrada para Boa Esperança, Km 4, Dois Vizinhos, PR, 85660-000, Brazil
| | | | | | | | | | | | | | | | | | | | | | | | | | - Nédia C. Ghisi
- Corresponding authors at: Universidade Tecnológica Federal do Paraná, Estrada para Boa Esperança, Km 4, Dois Vizinhos, PR, 85660-000, Brazil
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50
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Farhadian S, Heidari-Soureshjani E, Hashemi-Shahraki F, Hasanpour-Dehkordi A, Uversky VN, Shirani M, Shareghi B, Sadeghi M, Pirali E, Hadi-Alijanvand S. Identification of the SARS-CoV-2 surface therapeutic targets and drugs using molecular modeling methods for inhibition the virus entry. J Mol Struct 2022; 1256:132488. [PMID: 35125515 PMCID: PMC8797986 DOI: 10.1016/j.molstruc.2022.132488] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 12/24/2021] [Accepted: 01/24/2022] [Indexed: 01/02/2023]
Abstract
Although COVID-19 emerged as a major concern to public health around the world, no licensed medication has been found as of yet to efficiently stop the virus spread and treat the infection. The SARS-CoV-2 entry into the host cell is driven by the direct interaction of the S1 domain with the ACE-2 receptor followed by conformational changes in the S2 domain, as a result of which fusion peptide is inserted into the target cell membrane, and the fusion process is mediated by the specific interactions between the heptad repeats 1 and 2 (HR1 and HR2) that form the six-helical bundle. Since blocking this interaction between HRs stops virus fusion and prevents its subsequent replication, the HRs inhibitors can be used as anti-COVID drugs. The initial drug selection is based on existing molecular databases to screen for molecules that may have a therapeutic effect on coronavirus. Based on these premises, we chose two approved drugs to investigate their interactions with the HRs (based on docking methods). To this end, molecular dynamics simulations and molecular docking were carried out to investigate the changes in the structure of the SARS-CoV-2 spike protein. Our results revealed, cefpiramide has the highest affinity to S protein, thereby revealing its potential to become an anti-COVID-19 clinical medicine. Therefore, this study offers new ways to re-use existing drugs to combat SARS-CoV-2 infection.
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Affiliation(s)
- Sadegh Farhadian
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P. O. Box.115, Iran.,Central Laboratory, Shahrekord University, Shahrekord, Iran
| | - Ehsan Heidari-Soureshjani
- Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine, Tehran, Iran
| | - Fatemeh Hashemi-Shahraki
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P. O. Box.115, Iran.,Central Laboratory, Shahrekord University, Shahrekord, Iran
| | - Ali Hasanpour-Dehkordi
- Social Determinants of Health Research Center, School of allied medical sciences, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Majid Shirani
- Department of Urology, Shahrekord University of Medical Science, Shahrekord, Iran
| | - Behzad Shareghi
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P. O. Box.115, Iran.,Central Laboratory, Shahrekord University, Shahrekord, Iran
| | - Mehraban Sadeghi
- Department of Environmental Health Engineering Shahrekord University of Medical Science, Shahrekord, Iran
| | - Esmaeil Pirali
- Aquatic Animal Diseases, Department of Fisheries, Faculty of natural Science, Shahrekord University, Iran
| | - Saeid Hadi-Alijanvand
- Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
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