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Hlekelele L, Setshedi K, Mandiwana V, Kalombo L, Lemmer Y, Chauke V, Maity A. Carboxy-PEG-thiol functionalized gold nanoparticle conjugates for the detection of SARS-CoV-2: Detection tools and analytical method development. J Virol Methods 2024; 330:115028. [PMID: 39236987 DOI: 10.1016/j.jviromet.2024.115028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2024] [Accepted: 08/30/2024] [Indexed: 09/07/2024]
Abstract
Addressing the need for accessible SARS-CoV-2 testing, carboxy-PEG 12-thiol functionalized gold nanoparticles conjugates were developed for rapid point-of-care (POC) detection against SARS-CoV-2 spike protein, pseudo-SARS-CoV-2, and authentic Beta SARS-CoV-2 virus particles. These conjugates leverage gold nanoparticles (AuNPs) as signal transducers, cross-linked to either angiotensin-converting enzyme 2 (ACE2) or SARS-CoV-2 spike protein receptor-binding domain (RBD) antibodies as bioreceptors and showed a distinct color shift from pink to blue. To assess their POC feasibility, the conjugates were integrated into facemasks and breathalyzers, wherein aerosolized SARS-CoV-2 antigens were successfully detected, producing a color change within 10 and 30 minutes for the breathalyzer and facemask prototypes, respectively. Furthermore, we explored quantitative analysis using varying concentrations of SARS-CoV-2 spike protein. Both conjugates demonstrated a linear relationship between blue color intensity and virus concentration, with linear ranges of 0.08-0.6 ng/mL and 0.04-0.5 ng/mL, respectively. Low limits of detection and quantification were also achieved. They exhibited specificity, responding solely to SARS-CoV-2 even in complex matrices containing diverse proteins, including the SARS-CoV-1 spike protein. Precision tests yielded coefficient of variations below 2 %, showcasing their remarkable reproducibility. This work presents a promising approach for rapid, sensitive, and specific POC detection of SARS-CoV-2 paving the way for improved pandemic response and management.
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Affiliation(s)
- Lerato Hlekelele
- Centre for Nanostructures and Advanced Materials, DSI-CSIR Nanotechnology Innovation Centre, Council for Scientific and Industrial Research, Pretoria 0001, South Africa.
| | - Katlego Setshedi
- Centre for Nanostructures and Advanced Materials, DSI-CSIR Nanotechnology Innovation Centre, Council for Scientific and Industrial Research, Pretoria 0001, South Africa
| | - Vusani Mandiwana
- Centre for Nanostructures and Advanced Materials, DSI-CSIR Nanotechnology Innovation Centre, Council for Scientific and Industrial Research, Pretoria 0001, South Africa
| | - Lonji Kalombo
- Centre for Nanostructures and Advanced Materials, DSI-CSIR Nanotechnology Innovation Centre, Council for Scientific and Industrial Research, Pretoria 0001, South Africa
| | - Yolandy Lemmer
- Next Generation Health, Council for Scientific and Industrial Research, Pretoria 0001, South Africa
| | - Vongani Chauke
- Centre for Nanostructures and Advanced Materials, DSI-CSIR Nanotechnology Innovation Centre, Council for Scientific and Industrial Research, Pretoria 0001, South Africa
| | - Arjun Maity
- Centre for Nanostructures and Advanced Materials, DSI-CSIR Nanotechnology Innovation Centre, Council for Scientific and Industrial Research, Pretoria 0001, South Africa; Department of Chemical Engineering, Faculty of Engineering, Built Environment and Information Technology, University of Pretoria, Pretoria, South Africa.
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Zhu B, Lin H, Huang JS, Zhang W. Semi-Covariance Coefficient Analysis of Spike Proteins from SARS-CoV-2 and Its Variants Omicron, BA.5, EG.5, and JN.1 for Viral Infectivity, Virulence and Immune Escape. Viruses 2024; 16:1192. [PMID: 39205166 PMCID: PMC11360586 DOI: 10.3390/v16081192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 07/21/2024] [Accepted: 07/24/2024] [Indexed: 09/04/2024] Open
Abstract
Semi-covariance has attracted significant attention in recent years and is increasingly employed to elucidate statistical phenomena exhibiting fluctuations, such as the similarity or difference in charge patterns of spike proteins among coronaviruses. In this study, by examining values above and below the average/mean based on the positive and negative charge patterns of amino acid residues in the spike proteins of SARS-CoV-2 and its current circulating variants, the proposed methods offer profound insights into the nonlinear evolving trends in those viral spike proteins. Our study indicates that the charge span value can predict the infectivity of the virus and the charge density can estimate the virulence of the virus, and both predicated infectivity and virulence appear to be associated with the capability of viral immune escape. This semi-covariance coefficient analysis may be used not only to predict the infectivity, virulence and capability of immune escape for coronaviruses but also to analyze the functionality of other viral proteins. This study improves our understanding of the trend of viral evolution in terms of viral infectivity, virulence or the capability of immune escape, which remains further validated by more future studies and statistical data.
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Affiliation(s)
- Botao Zhu
- Department of Electrical and Computer engineering, Western University, London, ON N6A 5B9, Canada;
| | - Huancheng Lin
- School of Information Technology, Carleton University, Ottawa, ON K1S 5B6, Canada;
| | - Jun Steed Huang
- School of Information Technology, Carleton University, Ottawa, ON K1S 5B6, Canada;
| | - Wandong Zhang
- Human Health Therapeutics Research Centre, National Research Council of Canada, 1200 Montreal Road, Building M54, Ottawa, ON K1A 0R6, Canada
- Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
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3
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Tian Y, Yu T, Wang J, Zhang H, Jian Y, Li X, Wang G, Wang G, Hu Y, Lu C, Zhou J, Ma L, Liao M. Genetic characterization of the first Deltacoronavirus from wild birds around Qinghai Lake. Front Microbiol 2024; 15:1423367. [PMID: 38933020 PMCID: PMC11199898 DOI: 10.3389/fmicb.2024.1423367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 05/15/2024] [Indexed: 06/28/2024] Open
Abstract
Deltacoronavirus, widely distributed among pigs and wild birds, pose a significant risk of cross-species transmission, including potential human epidemics. Metagenomic analysis of bird samples from Qinghai Lake, China in 2021 reported the presence of Deltacoronavirus. A specific gene fragment of Deltacoronavirus was detected in fecal samples from wild birds at a positive rate of 5.94% (6/101). Next-generation sequencing (NGS) identified a novel Deltacoronavirus strain, which was closely related to isolates from the United Arab Emirates (2018), China (2022), and Poland (2023). Subsequently the strain was named A/black-headed gull/Qinghai/2021(BHG-QH-2021) upon confirmation of the Cytochrome b gene of black-headed gull in the sample. All available genome sequences of avian Deltacoronavirus, including the newly identified BHG-QH-2021 and 5 representative strains of porcine Deltacoronavirus (PDCoV), were classified according to ICTV criteria. In contrast to Coronavirus HKU15, which infects both mammals and birds and shows the possibility of cross-species transmission from bird to mammal host, our analysis revealed that BHG-QH-2021 is classified as Putative species 4. Putative species 4 has been reported to infect 5 species of birds but not mammals, suggesting that cross-species transmission of Putative species 4 is more prevalent among birds. Recombination analysis traced BHG-QH-2021 origin to dut148cor1 and MW01_1o strains, with MW01_1o contributing the S gene. Surprisingly, SwissModle prediction showed that the optimal template for receptor-binding domain (RBD) of BHG-QH-2021 is derived from the human coronavirus 229E, a member of the Alphacoronavirus, rather than the anticipated RBD structure of PDCoV of Deltacoronavirus. Further molecular docking analysis revealed that substituting the loop 1-2 segments of HCoV-229E significantly enhanced the binding capability of BHG-QH-2021 with human Aminopeptidase N (hAPN), surpassing its native receptor-binding domain (RBD). Most importantly, this finding was further confirmed by co-immunoprecipitation experiment that loop 1-2 segments of HCoV-229E enable BHG-QH-2021 RBD binding to hAPN, indicating that the loop 1-2 segment of the RBD in Putative species 4 is a probable key determinant for the virus ability to spill over into humans. Our results summarize the phylogenetic relationships among known Deltacoronavirus, reveal an independent putative avian Deltacoronavirus species with inter-continental and inter-species transmission potential, and underscore the importance of continuous surveillance of wildlife Deltacoronavirus.
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Affiliation(s)
- Ye Tian
- Key Laboratory of Animal Virology, Ministry of Agriculture and Rural Affairs, Zhejiang University, Hangzhou, China
| | - Tianqi Yu
- Key Laboratory of Animal Virology, Ministry of Agriculture and Rural Affairs, Zhejiang University, Hangzhou, China
| | - Jun Wang
- Animal Husbandry and Veterinary Workstation of the Third Division, Xinjiang Production and Construction Corps, Tumushuke, China
| | - Haoxiang Zhang
- Key Laboratory of Animal Virology, Ministry of Agriculture and Rural Affairs, Zhejiang University, Hangzhou, China
| | - Yingna Jian
- Qinghai Provincial Key Laboratory of Pathogen Diagnosis for Animal Disease and Green Technical Research for Prevention and Control, Qinghai Academy of Animal Sciences and Veterinary Medicine, Qinghai University, Xining, Qinghai, China
| | - Xiuping Li
- Qinghai Provincial Key Laboratory of Pathogen Diagnosis for Animal Disease and Green Technical Research for Prevention and Control, Qinghai Academy of Animal Sciences and Veterinary Medicine, Qinghai University, Xining, Qinghai, China
| | - Geping Wang
- Qinghai Provincial Key Laboratory of Pathogen Diagnosis for Animal Disease and Green Technical Research for Prevention and Control, Qinghai Academy of Animal Sciences and Veterinary Medicine, Qinghai University, Xining, Qinghai, China
| | - Guanghua Wang
- Qinghai Provincial Key Laboratory of Pathogen Diagnosis for Animal Disease and Green Technical Research for Prevention and Control, Qinghai Academy of Animal Sciences and Veterinary Medicine, Qinghai University, Xining, Qinghai, China
| | - Yong Hu
- Qinghai Provincial Key Laboratory of Pathogen Diagnosis for Animal Disease and Green Technical Research for Prevention and Control, Qinghai Academy of Animal Sciences and Veterinary Medicine, Qinghai University, Xining, Qinghai, China
| | - Chenhe Lu
- Key Laboratory of Animal Virology, Ministry of Agriculture and Rural Affairs, Zhejiang University, Hangzhou, China
| | - Jiyong Zhou
- Key Laboratory of Animal Virology, Ministry of Agriculture and Rural Affairs, Zhejiang University, Hangzhou, China
| | - Liqing Ma
- Qinghai Provincial Key Laboratory of Pathogen Diagnosis for Animal Disease and Green Technical Research for Prevention and Control, Qinghai Academy of Animal Sciences and Veterinary Medicine, Qinghai University, Xining, Qinghai, China
| | - Min Liao
- Key Laboratory of Animal Virology, Ministry of Agriculture and Rural Affairs, Zhejiang University, Hangzhou, China
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Ahn YM, Maddumage JC, Grant EJ, Chatzileontiadou DS, Perera WG, Baker BM, Szeto C, Gras S. The impact of SARS-CoV-2 spike mutation on peptide presentation is HLA allomorph-specific. Curr Res Struct Biol 2024; 7:100148. [PMID: 38742159 PMCID: PMC11089313 DOI: 10.1016/j.crstbi.2024.100148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 04/11/2024] [Accepted: 04/28/2024] [Indexed: 05/16/2024] Open
Abstract
CD8+ T cells are crucial for viral elimination and recovery from viral infection. Nonetheless, the current understanding of the T cell response to SARS-CoV-2 at the antigen level remains limited. The Spike protein is an external structural protein that is prone to mutations, threatening the efficacy of current vaccines. Therefore, we have characterised the immune response towards the immunogenic Spike-derived peptide (S976-984, VLNDILSRL), restricted to the HLA-A*02:01 molecule, which is mutated in both Alpha (S982A) and Omicron BA.1 (L981F) variants of concern. We determined that the mutation in the Alpha variant (S982A) impacted both the stability and conformation of the peptide, bound to HLA-A*02:01, in comparison to the original S976-984. We identified a longer and overlapping immunogenic peptide (S975-984, SVLNDILSRL) that could be presented by HLA-A*02:01, HLA-A*11:01 and HLA-B*13:01 allomorphs. We showed that S975-specific CD8+ T cells were weakly cross-reactive to the mutant peptides despite their similar conformations when presented by HLA-A*11:01. Altogether, our results show that the impact of SARS-CoV-2 mutations on peptide presentation is HLA allomorph-specific, and that post vaccination there are T cells able to react and cross-react towards the variant of concern peptides.
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Affiliation(s)
- You Min Ahn
- Infection & Immunity Program, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Bundoora, Victoria, Australia
- Department of Biochemistry and Chemistry, School of Agriculture, Biomedicine and Agriculture (SABE), La Trobe University, Bundoora, Victoria, Australia
| | - Janesha C. Maddumage
- Infection & Immunity Program, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Bundoora, Victoria, Australia
- Department of Biochemistry and Chemistry, School of Agriculture, Biomedicine and Agriculture (SABE), La Trobe University, Bundoora, Victoria, Australia
| | - Emma J. Grant
- Infection & Immunity Program, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Bundoora, Victoria, Australia
- Department of Biochemistry and Chemistry, School of Agriculture, Biomedicine and Agriculture (SABE), La Trobe University, Bundoora, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Demetra S.M. Chatzileontiadou
- Infection & Immunity Program, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Bundoora, Victoria, Australia
- Department of Biochemistry and Chemistry, School of Agriculture, Biomedicine and Agriculture (SABE), La Trobe University, Bundoora, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - W.W.J. Gihan Perera
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA
| | - Brian M. Baker
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA
| | - Christopher Szeto
- Infection & Immunity Program, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Bundoora, Victoria, Australia
- Department of Biochemistry and Chemistry, School of Agriculture, Biomedicine and Agriculture (SABE), La Trobe University, Bundoora, Victoria, Australia
- Australian Synchrotron, ANSTO, Clayton, Victoria, Australia
| | - Stephanie Gras
- Infection & Immunity Program, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Bundoora, Victoria, Australia
- Department of Biochemistry and Chemistry, School of Agriculture, Biomedicine and Agriculture (SABE), La Trobe University, Bundoora, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
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Park KS, Park TI, Lee JE, Hwang SY, Choi A, Pack SP. Aptamers and Nanobodies as New Bioprobes for SARS-CoV-2 Diagnostic and Therapeutic System Applications. BIOSENSORS 2024; 14:146. [PMID: 38534253 DOI: 10.3390/bios14030146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/10/2024] [Accepted: 03/12/2024] [Indexed: 03/28/2024]
Abstract
The global challenges posed by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic have underscored the critical importance of innovative and efficient control systems for addressing future pandemics. The most effective way to control the pandemic is to rapidly suppress the spread of the virus through early detection using a rapid, accurate, and easy-to-use diagnostic platform. In biosensors that use bioprobes, the binding affinity of molecular recognition elements (MREs) is the primary factor determining the dynamic range of the sensing platform. Furthermore, the sensitivity relies mainly on bioprobe quality with sufficient functionality. This comprehensive review investigates aptamers and nanobodies recently developed as advanced MREs for SARS-CoV-2 diagnostic and therapeutic applications. These bioprobes might be integrated into organic bioelectronic materials and devices, with promising enhanced sensitivity and specificity. This review offers valuable insights into advancing biosensing technologies for infectious disease diagnosis and treatment using aptamers and nanobodies as new bioprobes.
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Affiliation(s)
- Ki Sung Park
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
| | - Tae-In Park
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
| | - Jae Eon Lee
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
| | - Seo-Yeong Hwang
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
| | - Anna Choi
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
| | - Seung Pil Pack
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
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Shuaib F, Odusolu Y, Okposen BB, Osibogun O, Akanmu S, Mohammed A, Yahya S, Akande T, Aliyu A, Ifeadike C, Akande A, Aigbokhaode A, Adebiyi A, Tobin-West C, Olatunya OS, Aguwa E, Danjuma G, Dika J, Nwosu A, Olubodun T, Oladunjoye A, Giwa O, Osibogun A. Coronavirus Disease 2019 Vaccination Coverage and Seropositivity amongst Nigerians 18 Years Old and Above. Niger Postgrad Med J 2024; 31:8-13. [PMID: 38321792 DOI: 10.4103/npmj.npmj_299_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 12/30/2023] [Indexed: 02/08/2024]
Abstract
BACKGROUND This was a cross-sectional community-based survey to study the prevalence of serum antibodies against the severe acute respiratory syndrome coronavirus 1 (SARS-COV-1) and determine possible source of antibodies as to whether from vaccination or from natural infection as well as attempt to compare antibody levels in response to the different four types of vaccines administered in Nigeria. METHODS A cross-sectional community-based study of the prevalence of serum antibodies against all four vaccine types used in Nigeria amongst a representative sample of people aged 18 years and above in the six geopolitical zones of the country using a multistage sampling technique covering 12 states of the country with two states being randomly selected from each geopolitical zone. High-throughput Roche electrochemiluminescence immunoassay system (Elecsys Anti-SARS-COV-1 Cobas) was used for qualitative and quantitative detection of antibodies to SARS-COV-1 in human plasma. RESULTS There was no statistically significant difference between the proportions with seropositivity for both the vaccinated and the unvaccinated (P = 0.95). The nucleocapsid antibody (anti-Nc) titres were similar in both the vaccinated and the unvaccinated, whereas the Spike protein antibody (anti-S) titres were significantly higher amongst the vaccinated than amongst the unvaccinated. Antibody levels in subjects who received different vaccines were compared to provide information for policy. CONCLUSION While only 45.9% of the subjects were reported to have been vaccinated, 98.7% of the subjects had had contact with the SARS-COV-1 as evidenced by the presence of nucleocapsid (NC) antibodies in their plasma. The 1.3% who had not been exposed to the virus, had spike protein antibodies which most likely resulted from vaccination in the absence of NC antibodies. Successive vaccination and booster doses either through heterogeneous or homologous vaccines increased antibody titres, and this stimulation of immune memory may offer greater protection against coronavirus disease 2019.
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Affiliation(s)
- Faisal Shuaib
- National Primary Health Care Development Agency, Lagos, Nigeria
| | - Yetunde Odusolu
- Department of Community Health and Primary Care, Lagos University Teaching Hospital, Lagos, Nigeria
| | | | | | - Sulaimon Akanmu
- Department of Haematology and Blood Transfusion, College of Medicine University of Lagos, Zaria, Nigeria
| | | | - Shuaib Yahya
- Department of Community Health, University of Maiduguri, Maiduguri, Nigeria
| | - Tanimola Akande
- Department of Epidemiology and Community Health, University of Ilorin, Ilorin, Nigeria
| | - Alhaji Aliyu
- Department of Community Health, Ahmadu Bello University, Zaria, Nigeria
| | - Chigozie Ifeadike
- Department of Community Medicine, Nnamdi Azikiwe University Teaching Hospital, Nnewi, Nigeria
| | - Aderonke Akande
- Primary Health Care Board, Federal Capital Territory Administration, Abuja, Nigeria
| | | | - Akin Adebiyi
- Department of Epidemiology, College of Medicine University of Ibadan, Ibadan, Nigeria
| | - Charles Tobin-West
- Department of Community Health, University of Port Harcourt Teaching Hospital, Port Harcourt, Nigeria
| | | | - Emmanuel Aguwa
- Department of Community Health University of Nigeria Teaching Hospital, Enugu, Nigeria
| | | | - Joseph Dika
- Modibbo Adama University Teaching Hospital, Yola, Nigeria
| | - Augustina Nwosu
- Department of Haematology and Blood Transfusion, College of Medicine University of Lagos, Zaria, Nigeria
| | - Tope Olubodun
- Department of Community Medicine and Primary Care, Federal Medical Center, Abeokuta, Nigeria
| | - Adebimpe Oladunjoye
- Primary Health Care Department, Badagry West Local Government Area, Lagos State, Nigeria
| | - Opeyemi Giwa
- Department of Community Health and Primary Care, Lagos University Teaching Hospital, Lagos, Nigeria
| | - Akin Osibogun
- Department of Community Health and Primary Care, Lagos University Teaching Hospital, Lagos, Nigeria
- Department of Community Health, Lagos University Teaching Hospital, Lagos, Nigeria
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7
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Le K, Kannappan S, Kim T, Lee JH, Lee HR, Kim KK. Structural understanding of SARS-CoV-2 virus entry to host cells. Front Mol Biosci 2023; 10:1288686. [PMID: 38033388 PMCID: PMC10683510 DOI: 10.3389/fmolb.2023.1288686] [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: 09/04/2023] [Accepted: 10/16/2023] [Indexed: 12/02/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a major global health concern associated with millions of fatalities worldwide. Mutant variants of the virus have further exacerbated COVID-19 mortality and infection rates, emphasizing the urgent need for effective preventive strategies. Understanding the viral infection mechanism is crucial for developing therapeutics and vaccines. The entry of SARS-CoV-2 into host cells is a key step in the infection pathway and has been targeted for drug development. Despite numerous reviews of COVID-19 and the virus, there is a lack of comprehensive reviews focusing on the structural aspects of viral entry. In this review, we analyze structural changes in Spike proteins during the entry process, dividing the entry process into prebinding, receptor binding, proteolytic cleavage, and membrane fusion steps. By understanding the atomic-scale details of viral entry, we can better target the entry step for intervention strategies. We also examine the impacts of mutations in Spike proteins, including the Omicron variant, on viral entry. Structural information provides insights into the effects of mutations and can guide the development of therapeutics and vaccines. Finally, we discuss available structure-based approaches for the development of therapeutics and vaccines. Overall, this review provides a detailed analysis of the structural aspects of SARS-CoV-2 viral entry, highlighting its significance in the development of therapeutics and vaccines against COVID-19. Therefore, our review emphasizes the importance of structural information in combating SARS-CoV-2 infection.
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Affiliation(s)
- Kim Le
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Institute of Antibacterial Resistance Research and Therapeutics, Sungkyunkwan University, Suwon, Republic of Korea
| | - Shrute Kannappan
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Institute of Antibacterial Resistance Research and Therapeutics, Sungkyunkwan University, Suwon, Republic of Korea
- Research Center for Advanced Materials Technology Core Research Institute, Suwon, Republic of Korea
| | - Truc Kim
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Institute of Antibacterial Resistance Research and Therapeutics, Sungkyunkwan University, Suwon, Republic of Korea
| | - Jung Heon Lee
- Research Center for Advanced Materials Technology Core Research Institute, Suwon, Republic of Korea
- School of Advanced Materials and Science Engineering, Sungkyunkwan University, Suwon, Republic of Korea
| | - Hye-Ra Lee
- Department of Biotechnology and Bioinformatics, College of Science and Technology, Korea University, Sejong, Republic of Korea
| | - Kyeong Kyu Kim
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Institute of Antibacterial Resistance Research and Therapeutics, Sungkyunkwan University, Suwon, Republic of Korea
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8
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Zheng P, Zhou C, Ding Y, Liu B, Lu L, Zhu F, Duan S. Nanopore sequencing technology and its applications. MedComm (Beijing) 2023; 4:e316. [PMID: 37441463 PMCID: PMC10333861 DOI: 10.1002/mco2.316] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 05/29/2023] [Accepted: 05/31/2023] [Indexed: 07/15/2023] Open
Abstract
Since the development of Sanger sequencing in 1977, sequencing technology has played a pivotal role in molecular biology research by enabling the interpretation of biological genetic codes. Today, nanopore sequencing is one of the leading third-generation sequencing technologies. With its long reads, portability, and low cost, nanopore sequencing is widely used in various scientific fields including epidemic prevention and control, disease diagnosis, and animal and plant breeding. Despite initial concerns about high error rates, continuous innovation in sequencing platforms and algorithm analysis technology has effectively addressed its accuracy. During the coronavirus disease (COVID-19) pandemic, nanopore sequencing played a critical role in detecting the severe acute respiratory syndrome coronavirus-2 virus genome and containing the pandemic. However, a lack of understanding of this technology may limit its popularization and application. Nanopore sequencing is poised to become the mainstream choice for preventing and controlling COVID-19 and future epidemics while creating value in other fields such as oncology and botany. This work introduces the contributions of nanopore sequencing during the COVID-19 pandemic to promote public understanding and its use in emerging outbreaks worldwide. We discuss its application in microbial detection, cancer genomes, and plant genomes and summarize strategies to improve its accuracy.
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Affiliation(s)
- Peijie Zheng
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Chuntao Zhou
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Yuemin Ding
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
- Institute of Translational Medicine, School of MedicineZhejiang University City CollegeHangzhouChina
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of MedicineZhejiang University City CollegeHangzhouChina
| | - Bin Liu
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Liuyi Lu
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Feng Zhu
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Shiwei Duan
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
- Institute of Translational Medicine, School of MedicineZhejiang University City CollegeHangzhouChina
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of MedicineZhejiang University City CollegeHangzhouChina
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9
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de Andrade-Lima ALM, Lins MM, Borborema MDCD, Matos APR, de Oliveira KMM, Gonçalves Mello MJ. The Infection Profile and Survival of Children and Adolescents With COVID-19 Undergoing Cancer Treatment: A Cohort Study. Pediatr Infect Dis J 2023; 42:614-619. [PMID: 37053592 PMCID: PMC10289072 DOI: 10.1097/inf.0000000000003928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/12/2023] [Indexed: 04/15/2023]
Abstract
OBJECTIVE The objective of this study was to evaluate the clinical evolution of coronavirus disease 2019 (COVID-19) in children and adolescents with cancer. METHODS Cohort involving patients undergoing cancer treatment, 19 years old and under, with the diagnosis of COVID-19 by real-time polymerase chain reaction, in a reference hospital, between March 2020 and November 2021. Data were collected from medical records and interviews with patients and/or guardians. The primary outcomes studied were severe/critical COVID-19 presentation, deaths from any cause and overall survival. The Cox proportional hazards multivariate regression analysis was performed to determine the risk of death. RESULTS Sixty-two participants were included, most (67.7%) were male, with a median age of 6.8 years. Severe/critical forms of COVID-19, observed in 24.2%, seemed to indicate that the pediatric population undergoing cancer treatment has a higher morbidity rate than the general pediatric population (8-9.2%). During follow-up (4.5-18 months), 20 patients (32.3%) completed their cancer treatment and 18 died (29%)-6 during hospitalization and 12 after discharge. In total 61.1% of deaths occurred within 63 days of a detectable real-time polymerase chain reaction. Patients with a higher risk of death presented with severe/critical COVID-19 [adjusted hazard risk (aHR): 8.51; 95% confidence interval (CI): 2.91-24.80; P < 0.00] solid tumors (aHR: 3.99; 95% CI: 1.43-11.12; P = 0.008) and diarrhea as a symptom of COVID-19 (aHR: 3.9; 95% CI: 1.23-12.73; P = 0.021). CONCLUSIONS These findings support the impact that severe acute respiratory syndrome-associated coronavirus 2 infection has on the population of children and adolescents with cancer, not only regarding immediate severity but also in their survival rate. Further studies evaluating long-term outcomes of COVID-19 in children and adolescents with cancer should be encouraged.
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Affiliation(s)
| | - Mecneide Mendes Lins
- Departamento de Oncologia Pediátrica, Instituto de Medicina Integral Prof. Fernando Figueira (IMIP), Recife, PE, Brazil
| | - Maria do Céu Diniz Borborema
- Departamento de Oncologia Pediátrica, Instituto de Medicina Integral Prof. Fernando Figueira (IMIP), Recife, PE, Brazil
| | - Ana Paula Rodrigues Matos
- Departamento de Oncologia Pediátrica, Instituto de Medicina Integral Prof. Fernando Figueira (IMIP), Recife, PE, Brazil
| | | | - Maria Júlia Gonçalves Mello
- Departamento de pós-graduação strictu sensu, Instituto de Medicina Integral Prof. Fernando Figueira (IMIP), docente e pesquisadora da pós-graduação do IMIP, Recife, PE, Brazil
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10
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Zhou S, Lv P, Li M, Chen Z, Xin H, Reilly S, Zhang X. SARS-CoV-2 E protein: Pathogenesis and potential therapeutic development. Biomed Pharmacother 2023; 159:114242. [PMID: 36652729 PMCID: PMC9832061 DOI: 10.1016/j.biopha.2023.114242] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 01/09/2023] [Accepted: 01/09/2023] [Indexed: 01/13/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a devastating global pandemic, which has seriously affected human health worldwide. The discovery of therapeutic agents is extremely urgent, and the viral structural proteins are particularly important as potential drug targets. SARS-CoV-2 envelope (E) protein is one of the main structural proteins of the virus, which is involved in multiple processes of the virus life cycle and is directly related to pathogenesis process. In this review, we present the amino acid sequence of the E protein and compare it with other two human coronaviruses. We then explored the role of E protein in the viral life cycle and discussed the pathogenic mechanisms that E protein may be involved in. Next, we summarize the potential drugs against E protein discovered in the current studies. Finally, we described the possible effects of E protein mutation on virus and host. This established a knowledge system of E protein to date, aiming to provide theoretical insights for mitigating the current COVID-19 pandemic and potential future coronavirus outbreaks.
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Affiliation(s)
- Shilin Zhou
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai, China.
| | - Panpan Lv
- Clinical Laboratory, Minhang Hospital, Fudan University, Shanghai, China.
| | - Mingxue Li
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai, China.
| | - Zihui Chen
- School of Basic Medical Sciences, Fudan University, Shanghai, China.
| | - Hong Xin
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai, China.
| | - Svetlana Reilly
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK.
| | - Xuemei Zhang
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai, China.
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11
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Gao X, Xia Y, Liu X, Xu Y, Lu P, dong Z, Liu J, Liang G. A perspective on SARS-CoV-2 virus-like particles vaccines. Int Immunopharmacol 2023; 115:109650. [PMID: 36649673 PMCID: PMC9832101 DOI: 10.1016/j.intimp.2022.109650] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 12/18/2022] [Accepted: 12/25/2022] [Indexed: 01/13/2023]
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) first appeared in Wuhan, China, in December 2019. The 2019 coronavirus disease (COVID-19) pandemic, caused by SARS-CoV-2, has spread to almost all corners of the world at an alarming rate. Vaccination is important for the prevention and control of the COVID-19 pandemic. Efforts are underway worldwide to develop an effective vaccine against COVID-19 using both traditional and innovative vaccine strategies. Compared to other vaccine platforms, SARS-CoV-2 virus-like particles (VLPs )vaccines, as a new vaccine platform, have unique advantages: they have artificial nanostructures similar to natural SARS-CoV-2, which can stimulate good cellular and humoral immune responses in the organism; they have no viral nucleic acids, have good safety and thermal stability, and can be mass-produced and stored; their surfaces can be processed and modified, such as the adjuvant addition, etc.; they can be considered as an ideal platform for COVID-19 vaccine development. This review aims to shed light on the current knowledge and progress of VLPs vaccines against COVID-19, especially those undergoing clinical trials.
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Affiliation(s)
- Xiaoyang Gao
- Henan Provincial Engineering Center for Tumor Molecular Medicine, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China,School of Basic Medical Sciences, Henan University of Science & Technology, Luoyang 471023, China
| | - Yeting Xia
- Henan Provincial Engineering Center for Tumor Molecular Medicine, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China
| | - Xiaofang Liu
- The First People's Hospital of Nanyang Affiliated to Henan University, Nanyang 473000, China
| | - Yinlan Xu
- School of Public Health, Xinxiang Medical University, Xinxiang, Henan Province 453003, China
| | - Pengyang Lu
- Henan Provincial Engineering Center for Tumor Molecular Medicine, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China
| | - Zhipeng dong
- Henan Provincial Engineering Center for Tumor Molecular Medicine, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China
| | - Jing Liu
- Henan Provincial Engineering Center for Tumor Molecular Medicine, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China.
| | - Gaofeng Liang
- School of Basic Medical Sciences, Henan University of Science & Technology, Luoyang 471023, China.
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12
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Ayón-Núñez DA, Cervantes-Torres J, Cabello-Gutiérrez C, Rosales-Mendoza S, Rios-Valencia D, Huerta L, Bobes RJ, Carrero JC, Segura-Velázquez R, Fierro NA, Hernández M, Zúñiga-Ramos J, Gamba G, Cárdenas G, Frías-Jiménez E, Herrera LA, Fragoso G, Sciutto E, Suárez-Güemes F, Laclette JP. An RBD-Based Diagnostic Method Useful for the Surveillance of Protective Immunity against SARS-CoV-2 in the Population. Diagnostics (Basel) 2022; 12:diagnostics12071629. [PMID: 35885534 PMCID: PMC9324632 DOI: 10.3390/diagnostics12071629] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/24/2022] [Accepted: 04/30/2022] [Indexed: 12/17/2022] Open
Abstract
After more than two years, the COVID-19 pandemic is still ongoing and evolving all over the world; human herd immunity against SARS-CoV-2 increases either by infection or by unprecedented mass vaccination. A substantial change in population immunity is expected to contribute to the control of transmission. It is essential to monitor the extension and duration of the population’s immunity to support the decisions of health authorities in each region and country, directed to chart the progressive return to normality. For this purpose, the availability of simple and cheap methods to monitor the levels of relevant antibodies in the population is a widespread necessity. Here, we describe the development of an RBD-based ELISA for the detection of specific antibodies in large numbers of samples. The recombinant expression of an RBD-poly-His fragment was carried out using either bacterial or eukaryotic cells in in vitro culture. After affinity chromatography purification, the performance of both recombinant products was compared by ELISA in similar trials. Our results showed that eukaryotic RBD increased the sensitivity of the assay. Interestingly, our results also support a correlation of the eukaryotic RBD-based ELISA with other assays aimed to test for neutralizing antibodies, which suggests that it provides an indication of protective immunity against SARS-CoV-2.
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Affiliation(s)
- Dolores Adriana Ayón-Núñez
- School of Veterinary Medicine and Zootechnics, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México 04510, Mexico; (D.A.A.-N.); (R.S.-V.)
| | - Jacquelynne Cervantes-Torres
- Biomedical Research Institute, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México 04510, Mexico; (J.C.-T.); (D.R.-V.); (L.H.); (R.J.B.); (J.C.C.); (N.A.F.); (M.H.); (G.G.); (G.F.); (E.S.)
| | - Carlos Cabello-Gutiérrez
- Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Calzada de Tlalpan 4502, Belisario Domínguez Secc. 16, Tlalpan, Ciudad de México 14080, Mexico; (C.C.-G.); (J.Z.-R.)
| | - Sergio Rosales-Mendoza
- Laboratorio de Biofarmacéuticos Recombinantes, Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, Av. Dr. Manuel Nava 6, San Luis Potosí 78210, Mexico;
| | - Diana Rios-Valencia
- Biomedical Research Institute, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México 04510, Mexico; (J.C.-T.); (D.R.-V.); (L.H.); (R.J.B.); (J.C.C.); (N.A.F.); (M.H.); (G.G.); (G.F.); (E.S.)
| | - Leonor Huerta
- Biomedical Research Institute, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México 04510, Mexico; (J.C.-T.); (D.R.-V.); (L.H.); (R.J.B.); (J.C.C.); (N.A.F.); (M.H.); (G.G.); (G.F.); (E.S.)
| | - Raúl J. Bobes
- Biomedical Research Institute, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México 04510, Mexico; (J.C.-T.); (D.R.-V.); (L.H.); (R.J.B.); (J.C.C.); (N.A.F.); (M.H.); (G.G.); (G.F.); (E.S.)
| | - Julio César Carrero
- Biomedical Research Institute, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México 04510, Mexico; (J.C.-T.); (D.R.-V.); (L.H.); (R.J.B.); (J.C.C.); (N.A.F.); (M.H.); (G.G.); (G.F.); (E.S.)
| | - René Segura-Velázquez
- School of Veterinary Medicine and Zootechnics, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México 04510, Mexico; (D.A.A.-N.); (R.S.-V.)
| | - Nora Alma Fierro
- Biomedical Research Institute, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México 04510, Mexico; (J.C.-T.); (D.R.-V.); (L.H.); (R.J.B.); (J.C.C.); (N.A.F.); (M.H.); (G.G.); (G.F.); (E.S.)
| | - Marisela Hernández
- Biomedical Research Institute, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México 04510, Mexico; (J.C.-T.); (D.R.-V.); (L.H.); (R.J.B.); (J.C.C.); (N.A.F.); (M.H.); (G.G.); (G.F.); (E.S.)
| | - Joaquín Zúñiga-Ramos
- Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Calzada de Tlalpan 4502, Belisario Domínguez Secc. 16, Tlalpan, Ciudad de México 14080, Mexico; (C.C.-G.); (J.Z.-R.)
| | - Gerardo Gamba
- Biomedical Research Institute, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México 04510, Mexico; (J.C.-T.); (D.R.-V.); (L.H.); (R.J.B.); (J.C.C.); (N.A.F.); (M.H.); (G.G.); (G.F.); (E.S.)
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Vasco de Quiroga 15, Belisario Domínguez Secc. 16, Tlalpan, Ciudad de México 14080, Mexico
| | - Graciela Cárdenas
- Instituto Nacional de Neurología y Neurocirugía, Av. Insurgentes Sur 3877, Tlalpan, Ciudad de México 14269, Mexico;
| | - Emmanuel Frías-Jiménez
- Instituto Nacional de Medicina Genómica, Periférico Sur 4809, Ciudad de México 14610, Mexico; (E.F.-J.); (L.A.H.)
| | - Luis Alonso Herrera
- Instituto Nacional de Medicina Genómica, Periférico Sur 4809, Ciudad de México 14610, Mexico; (E.F.-J.); (L.A.H.)
| | - Gladis Fragoso
- Biomedical Research Institute, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México 04510, Mexico; (J.C.-T.); (D.R.-V.); (L.H.); (R.J.B.); (J.C.C.); (N.A.F.); (M.H.); (G.G.); (G.F.); (E.S.)
| | - Edda Sciutto
- Biomedical Research Institute, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México 04510, Mexico; (J.C.-T.); (D.R.-V.); (L.H.); (R.J.B.); (J.C.C.); (N.A.F.); (M.H.); (G.G.); (G.F.); (E.S.)
| | - Francisco Suárez-Güemes
- School of Veterinary Medicine and Zootechnics, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México 04510, Mexico; (D.A.A.-N.); (R.S.-V.)
- Correspondence: (F.S.-G.); (J.P.L.); Tel.: +52(55)-5622-3153 (J.P.L.)
| | - Juan Pedro Laclette
- Biomedical Research Institute, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México 04510, Mexico; (J.C.-T.); (D.R.-V.); (L.H.); (R.J.B.); (J.C.C.); (N.A.F.); (M.H.); (G.G.); (G.F.); (E.S.)
- Correspondence: (F.S.-G.); (J.P.L.); Tel.: +52(55)-5622-3153 (J.P.L.)
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13
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Lima Neto JX, Vieira DS, de Andrade J, Fulco UL. Exploring the Spike-hACE 2 Residue-Residue Interaction in Human Coronaviruses SARS-CoV-2, SARS-CoV, and HCoV-NL63. J Chem Inf Model 2022; 62:2857-2868. [PMID: 35617018 PMCID: PMC9159508 DOI: 10.1021/acs.jcim.1c01544] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Indexed: 12/20/2022]
Abstract
Coronaviruses (CoVs) have been responsible for three major outbreaks since the beginning of the 21st century, and the emergence of the recent COVID-19 pandemic has resulted in considerable efforts to design new therapies against coronaviruses. Thus, it is crucial to understand the structural features of their major proteins related to the virus-host interaction. Several studies have shown that from the seven known CoV human pathogens, three of them use the human Angiotensin-Converting Enzyme 2 (hACE-2) to mediate their host's cell entry: SARS-CoV-2, SARS-CoV, and HCoV-NL63. Therefore, we employed quantum biochemistry techniques within the density function theory (DFT) framework and the molecular fragmentation with conjugate caps (MFCC) approach to analyze the interactions between the hACE-2 and the spike protein-RBD of the three CoVs in order to map the hot-spot residues that form the recognition surface for these complexes and define the similarities and differences in the interaction scenario. The total interaction energy evaluated showed a good agreement with the experimental binding affinity order: SARS-2 > SARS > NL63. A detailed investigation revealed the energetically most relevant regions of hACE-2 and the spike protein for each complex, as well as the key residue-residue interactions. Our results provide valuable information to deeply understand the structural behavior and binding site characteristics that could help to develop antiviral therapeutics that inhibit protein-protein interactions between CoVs S protein and hACE-2.
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Affiliation(s)
- José X. Lima Neto
- Departamento de Biofísica e Farmacologia,
Universidade Federal do Rio Grande do Norte, 59072-970
Natal-RN, Brazil
| | - Davi S. Vieira
- Instituto de Química, Universidade
Federal do Rio Grande do Norte, 59072-970 Natal-RN,
Brazil
| | - Jones de Andrade
- Department of Physical Chemistry,
Universidade Federal do Rio Grande do Sul, 91501-970 Porto
Alegre-RS, Brazil
| | - Umberto Laino Fulco
- Departamento de Biofísica e Farmacologia,
Universidade Federal do Rio Grande do Norte, 59072-970
Natal-RN, Brazil
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14
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Dumache R, Enache A, Macasoi I, Dehelean CA, Dumitrascu V, Mihailescu A, Popescu R, Vlad D, Vlad CS, Muresan C. SARS-CoV-2: An Overview of the Genetic Profile and Vaccine Effectiveness of the Five Variants of Concern. Pathogens 2022; 11:pathogens11050516. [PMID: 35631037 PMCID: PMC9144800 DOI: 10.3390/pathogens11050516] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/21/2022] [Accepted: 04/25/2022] [Indexed: 12/13/2022] Open
Abstract
With the onset of the COVID-19 pandemic, enormous efforts have been made to understand the genus SARS-CoV-2. Due to the high rate of global transmission, mutations in the viral genome were inevitable. A full understanding of the viral genome and its possible changes represents one of the crucial aspects of pandemic management. Structural protein S plays an important role in the pathogenicity of SARS-CoV-2, mutations occurring at this level leading to viral forms with increased affinity for ACE2 receptors, higher transmissibility and infectivity, resistance to neutralizing antibodies and immune escape, increasing the risk of infection and disease severity. Thus, five variants of concern are currently being discussed, Alpha, Beta, Gamma, Delta and Omicron. In the present review, a comprehensive summary of the following critical aspects regarding SARS-CoV-2 has been made: (i) the genomic characteristics of SARS-CoV-2; (ii) the pathological mechanism of transmission, penetration into the cell and action on specific receptors; (iii) mutations in the SARS-CoV-2 genome; and (iv) possible implications of mutations in diagnosis, treatment, and vaccination.
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Affiliation(s)
- Raluca Dumache
- Ethics and Human Identification Research Center, Department of Neurosciences, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (R.D.); (A.E.); (A.M.); (C.M.)
| | - Alexandra Enache
- Ethics and Human Identification Research Center, Department of Neurosciences, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (R.D.); (A.E.); (A.M.); (C.M.)
| | - Ioana Macasoi
- Departament of Toxicology and Drug Industry, Faculty of Pharmacy, “Victor Babeş” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square No. 2, 300041 Timişoara, Romania
- Research Center for Pharmaco-Toxicological Evaluations, Faculty of Pharmacy, “Victor Babes” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square No. 2, 300041 Timisoara, Romania
- Correspondence: (I.M.); (C.A.D.)
| | - Cristina Adriana Dehelean
- Departament of Toxicology and Drug Industry, Faculty of Pharmacy, “Victor Babeş” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square No. 2, 300041 Timişoara, Romania
- Research Center for Pharmaco-Toxicological Evaluations, Faculty of Pharmacy, “Victor Babes” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square No. 2, 300041 Timisoara, Romania
- Correspondence: (I.M.); (C.A.D.)
| | - Victor Dumitrascu
- Department of Pharmacology and Biochemistry, Discipline of Pharmacology, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (V.D.); (D.V.); (C.S.V.)
| | - Alexandra Mihailescu
- Ethics and Human Identification Research Center, Department of Neurosciences, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (R.D.); (A.E.); (A.M.); (C.M.)
- Genetics, Genomic Medicine Research Center, Department of Microscopic Morphology, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania
| | - Roxana Popescu
- Department of Microscopic Morphology, Discipline of Molecular and Cell Biology, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania;
| | - Daliborca Vlad
- Department of Pharmacology and Biochemistry, Discipline of Pharmacology, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (V.D.); (D.V.); (C.S.V.)
| | - Cristian Sebastian Vlad
- Department of Pharmacology and Biochemistry, Discipline of Pharmacology, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (V.D.); (D.V.); (C.S.V.)
| | - Camelia Muresan
- Ethics and Human Identification Research Center, Department of Neurosciences, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (R.D.); (A.E.); (A.M.); (C.M.)
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15
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Nugent MA. The Future of the COVID-19 Pandemic: How Good (or Bad) Can the SARS-CoV2 Spike Protein Get? Cells 2022; 11:cells11050855. [PMID: 35269476 PMCID: PMC8909208 DOI: 10.3390/cells11050855] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/22/2022] [Accepted: 02/28/2022] [Indexed: 12/24/2022] Open
Abstract
Severe acute respiratory syndrome virus 2 (SARS-CoV2) has infected an estimated 400 million people world-wide, causing approximately 6 million deaths from severe coronavirus disease 2019 (COVID-19). The SARS-CoV2 Spike protein plays a critical role in viral attachment and entry into host cells. The recent emergence of highly transmissible variants of SARS-CoV2 has been linked to mutations in Spike. This review provides an overview of the structure and function of Spike and describes the factors that impact Spike’s ability to mediate viral infection as well as the potential limits to how good (or bad) Spike protein can become. Proposed here is a framework that considers the processes of Spike-mediated SARS-CoV2 attachment, dissociation, and cell entry where the role of Spike, from the standpoint of the virus, is to maximize cell entry with each viral-cell collision. Key parameters are identified that will be needed to develop models to identify mechanisms that new Spike variants might exploit to enhance viral transmission. In particular, the importance of considering secondary co-receptors for Spike, such as heparan sulfate proteoglycans is discussed. Accurate models of Spike-cell interactions could contribute to the development of new therapies in advance of the emergence of new highly transmissible SARS-CoV2 variants.
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Affiliation(s)
- Matthew A Nugent
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, MA 01854, USA
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16
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Bognár Z, Supala E, Yarman A, Zhang X, Bier FF, Scheller FW, Gyurcsányi RE. Peptide epitope-imprinted polymer microarrays for selective protein recognition. Application for SARS-CoV-2 RBD protein. Chem Sci 2022; 13:1263-1269. [PMID: 35222909 PMCID: PMC8809392 DOI: 10.1039/d1sc04502d] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 11/23/2021] [Indexed: 12/18/2022] Open
Abstract
We introduce a practically generic approach for the generation of epitope-imprinted polymer-based microarrays for protein recognition on surface plasmon resonance imaging (SPRi) chips. The SPRi platform allows the subsequent rapid screening of target binding kinetics in a multiplexed and label-free manner. The versatility of such microarrays, both as synthetic and screening platform, is demonstrated through developing highly affine molecularly imprinted polymers (MIPs) for the recognition of the receptor binding domain (RBD) of SARS-CoV-2 spike protein. A characteristic nonapeptide GFNCYFPLQ from the RBD and other control peptides were microspotted onto gold SPRi chips followed by the electrosynthesis of a polyscopoletin nanofilm to generate in one step MIP arrays. A single chip screening of essential synthesis parameters, including the surface density of the template peptide and its sequence led to MIPs with dissociation constants (K D) in the lower nanomolar range for RBD, which exceeds the affinity of RBD for its natural target, angiotensin-convertase 2 enzyme. Remarkably, the same MIPs bound SARS-CoV-2 virus like particles with even higher affinity along with excellent discrimination of influenza A (H3N2) virus. While MIPs prepared with a truncated heptapeptide template GFNCYFP showed only a slightly decreased affinity for RBD, a single mismatch in the amino acid sequence of the template, i.e. the substitution of the central cysteine with a serine, fully suppressed the RBD binding.
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Affiliation(s)
- Zsófia Bognár
- BME "Lendület" Chemical Nanosensors Research Group, Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics Szt. Gellért tér 4 1111 Budapest Hungary
| | - Eszter Supala
- BME "Lendület" Chemical Nanosensors Research Group, Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics Szt. Gellért tér 4 1111 Budapest Hungary
| | - Aysu Yarman
- Institute of Biochemistry and Biology, University of Potsdam Karl-Liebknecht-Str. 24-25 14476 Potsdam OT Golm Germany
| | - Xiaorong Zhang
- Institute of Biochemistry and Biology, University of Potsdam Karl-Liebknecht-Str. 24-25 14476 Potsdam OT Golm Germany
| | - Frank F Bier
- Institute of Biochemistry and Biology, University of Potsdam Karl-Liebknecht-Str. 24-25 14476 Potsdam OT Golm Germany
| | - Frieder W Scheller
- Institute of Biochemistry and Biology, University of Potsdam Karl-Liebknecht-Str. 24-25 14476 Potsdam OT Golm Germany
| | - Róbert E Gyurcsányi
- BME "Lendület" Chemical Nanosensors Research Group, Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics Szt. Gellért tér 4 1111 Budapest Hungary
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17
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Lam AHY, Cai JP, Leung KY, Zhang RR, Liu D, Fan Y, Tam AR, Cheng VCC, To KKW, Yuen KY, Hung IFN, Chan KH. In-House Immunofluorescence Assay for Detection of SARS-CoV-2 Antigens in Cells from Nasopharyngeal Swabs as a Diagnostic Method for COVID-19. Diagnostics (Basel) 2021; 11:diagnostics11122346. [PMID: 34943583 PMCID: PMC8700487 DOI: 10.3390/diagnostics11122346] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/02/2021] [Accepted: 12/10/2021] [Indexed: 12/18/2022] Open
Abstract
Immunofluorescence is a traditional diagnostic method for respiratory viruses, allowing rapid, simple and accurate diagnosis, with specific benefits of direct visualization of antigens-of-interest and quality assessment. This study aims to evaluate the potential of indirect immunofluorescence as an in-house diagnostic method for SARS-CoV-2 antigens from nasopharyngeal swabs (NPS). Three primary antibodies raised from mice were used for immunofluorescence staining, including monoclonal antibody against SARS-CoV nucleocapsid protein, and polyclonal antibodies against SARS-CoV-2 nucleocapsid protein and receptor-binding domain of SARS-CoV-2 spike protein. Smears of cells from NPS of 29 COVID-19 patients and 20 non-infected individuals, and cells from viral culture were stained by the three antibodies. Immunofluorescence microscopy was used to identify respiratory epithelial cells with positive signals. Polyclonal antibody against SARS-CoV-2 N protein had the highest sensitivity and specificity among the three antibodies tested, detecting 17 out of 29 RT-PCR-confirmed COVID-19 cases and demonstrating no cross-reactivity with other tested viruses except SARS-CoV. Detection of virus-infected cells targeting SARS-CoV-2 N protein allow identification of infected individuals, although accuracy is limited by sample quality and number of respiratory epithelial cells. The potential of immunofluorescence as a simple diagnostic method was demonstrated, which could be applied by incorporating antibodies targeting SARS-CoV-2 into multiplex immunofluorescence panels used clinically, such as for respiratory viruses, thus allowing additional routine testing for diagnosis and surveillance of SARS-CoV-2 even after the epidemic has ended with low prevalence of COVID-19.
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Affiliation(s)
- Athene Hoi-Ying Lam
- Department of Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China; (A.H.-Y.L.); (R.-R.Z.); (D.L.); (Y.F.)
| | - Jian-Piao Cai
- Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China; (J.-P.C.); (K.-Y.L.); (K.K.-W.T.); (K.-Y.Y.)
| | - Ka-Yi Leung
- Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China; (J.-P.C.); (K.-Y.L.); (K.K.-W.T.); (K.-Y.Y.)
| | - Ricky-Ruiqi Zhang
- Department of Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China; (A.H.-Y.L.); (R.-R.Z.); (D.L.); (Y.F.)
| | - Danlei Liu
- Department of Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China; (A.H.-Y.L.); (R.-R.Z.); (D.L.); (Y.F.)
| | - Yujing Fan
- Department of Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China; (A.H.-Y.L.); (R.-R.Z.); (D.L.); (Y.F.)
| | | | | | - Kelvin Kai-Wang To
- Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China; (J.-P.C.); (K.-Y.L.); (K.K.-W.T.); (K.-Y.Y.)
- State Key Laboratory for Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China
- Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China
| | - Kwok-Yung Yuen
- Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China; (J.-P.C.); (K.-Y.L.); (K.K.-W.T.); (K.-Y.Y.)
- Department of Microbiology, Queen Mary Hospital, Hospital Authority, Hong Kong, China;
- State Key Laboratory for Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China
- Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China
| | - Ivan Fan-Ngai Hung
- Department of Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China; (A.H.-Y.L.); (R.-R.Z.); (D.L.); (Y.F.)
- Department of Medicine, Queen Mary Hospital, Hong Kong, China;
- State Key Laboratory for Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China
- Correspondence: (I.F.-N.H.); (K.-H.C.)
| | - Kwok-Hung Chan
- Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China; (J.-P.C.); (K.-Y.L.); (K.K.-W.T.); (K.-Y.Y.)
- State Key Laboratory for Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China
- Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China
- Correspondence: (I.F.-N.H.); (K.-H.C.)
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