1
|
Park KS, Choi A, Park TI, Pack SP. Fluorometric and Colorimetric Method for SARS-CoV-2 Detection Using Designed Aptamer Display Particles. BIOSENSORS 2024; 14:113. [PMID: 38534220 DOI: 10.3390/bios14030113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 02/16/2024] [Accepted: 02/17/2024] [Indexed: 03/28/2024]
Abstract
SARS-CoV-2, the virus responsible for the COVID-19 pandemic, has spurred the urgent need for practical diagnostics with high sensitivity and selectivity. Although advanced diagnostic tools have emerged to efficiently control pandemics, they still have costly limitations owing to their reliance on antibodies or enzymes and require high-tech equipment. Therefore, there is still a need to develop rapid and low-cost diagnostics with high sensitivity and selectivity. In this study, we generated aptamer display particles (AdP), enabling easy fabrication of a SARS-CoV-2 detection matrix through particle PCR, and applied it to diagnosis using fluorometric and colorimetric assays. We designed two AdPs, C1-AdP and C4-AdP, displayed with SpS1-C1 and SpS1-C4 aptamers, respectively, and showed their high binding ability against SARS-CoV-2 spike protein with a concentration-dependent fluorescence increase. This enabled detection even at low concentrations (0.5 nM). To validate its use as a diagnostic tool for SARS-CoV-2, we designed a sandwich-type assay using two AdPs and high-quality aptamers targeting SARS-CoV-2 pseudoviruses. The fluorometric assay achieved a detection limit of 3.9 × 103 pseudoviruses/mL. The colorimetric assay using an amplification approach exhibited higher sensitivity, with a detection limit of 1 × 101 pseudoviruses/mL, and a broad range of over four orders of magnitude was observed.
Collapse
Affiliation(s)
- Ki Sung Park
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
| | - Anna Choi
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
| | - Tae-In Park
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
| | - Seung Pil Pack
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
| |
Collapse
|
2
|
Dsouza N, C SK. Predicting the changes in neutralizing antibody interaction with G protein derived from Bangladesh isolates of Nipah virus: molecular dynamics based approach. J Biomol Struct Dyn 2023:1-11. [PMID: 37643003 DOI: 10.1080/07391102.2023.2252084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 08/18/2023] [Indexed: 08/31/2023]
Abstract
The infectious Nipah virus (NiV) is categorized into NiV-M (Malaysia) and NiV-B (Bangladesh) groups based on its genome comparison, pathogenicity, and mortality rate. The development of therapeutic molecules has used NiV-M-derived data in multiple studies than NiV-B. In continuation with this, the protein level investigation is also less explored to understand the interaction with therapeutic neutralizing antibodies for NiV-B. So, this study focuses on understanding the impact of NiV-B-specific mutations on the interaction of therapeutic neutralizing antibodies with the G protein. The population-based comparative analysis of NiV-B G protein sequences with NiV-M sequence identified twenty-six mutations. These predominantly polar mutations were then used to model the mutant protein (G_MT). In a comparative study, the G protein G_MT and reference protein G_WT (Malaysian origin) were subjected to a protein docking with neutralizing human monoclonal antibody HENV26. The binding affinity and the free binding energy of the glycoprotein in complex with G-WT and G_MT were calculated using PRODIGY and MM/PBSA tools respectively. Based on the PRODIGY report, G-WT showed stronger binding (-13.8 kcal/mol) compared to that of the G_MT (-9.0 kcal/mol) with the HENV26 antibody. The stability of the complexes was evaluated using MM/PBSA which showed higher binding energy with HENV26 for G_WT (-75.11 kcal/mol) in contrast to G_MT (-41.66 kcal/mol). The results indicate that the mutant G protein has a reduced ability to bind to neutralizing antibodies, resulting in a decreased effectiveness against strains carrying these mutations.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Norine Dsouza
- School of Biotechnology and Bioinformatics, D.Y. Patil Deemed to be University, CBD Belapur, Navi Mumbai, India
- Department of Biotechnology, St. Xavier's College, Mumbai, India
| | - Selvaa Kumar C
- School of Biotechnology and Bioinformatics, D.Y. Patil Deemed to be University, CBD Belapur, Navi Mumbai, India
| |
Collapse
|
3
|
Park KS, Choi A, Kim HJ, Park I, Eom MS, Yeo SG, Son RG, Park TI, Lee G, Soh HT, Hong Y, Pack SP. Ultra-sensitive label-free SERS biosensor with high-throughput screened DNA aptamer for universal detection of SARS-CoV-2 variants from clinical samples. Biosens Bioelectron 2023; 228:115202. [PMID: 36940632 PMCID: PMC9993738 DOI: 10.1016/j.bios.2023.115202] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 02/28/2023] [Accepted: 03/04/2023] [Indexed: 03/21/2023]
Abstract
COVID-19, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has caused an ongoing global pandemic with economic and social disruption. Moreover, the virus has persistently and rapidly evolved into novel lineages with mutations. The most effective strategy to control the pandemic is suppressing virus spread through early detection of infections. Therefore, developing a rapid, accurate, easy-to-use diagnostic platform against SARS-CoV-2 variants of concern remains necessary. Here, we developed an ultra-sensitive label-free surface-enhanced Raman scattering-based aptasensor as a countermeasure for the universal detection of SARS-CoV-2 variants of concern. In this aptasensor platform, we discovered two DNA aptamers that enable binding to SARS-CoV-2 spike protein via the Particle Display, a high-throughput screening approach. These showed high affinity that exhibited dissociation constants of 1.47 ± 0.30 nM and 1.81 ± 0.39 nM. We designed a combination with the aptamers and silver nanoforest for developing an ultra-sensitive SERS platform and achieved an attomolar (10-18 M) level detection limit with a recombinant trimeric spike protein. Furthermore, using the intrinsic properties of the aptamer signal, we demonstrated a label-free aptasensor approach, enabling use without the Raman tag. Finally, our label-free SERS-combined aptasensor succeeded in detecting SARS-CoV-2 with excellent accuracy, even in clinical samples with variants of concern, including the wild-type, delta, and omicron variants.
Collapse
Affiliation(s)
- Ki Sung Park
- Department of Biotechnology and Bioinformatics, Korea University, Sejong, 30019, Republic of Korea
| | - Anna Choi
- Department of Biotechnology and Bioinformatics, Korea University, Sejong, 30019, Republic of Korea
| | - Hyun Jung Kim
- Department of Biotechnology and Bioinformatics, Korea University, Sejong, 30019, Republic of Korea; Department of Medical Device, Korea Institute of Machinery and Materials (KIMM), Daegu, 42994, Republic of Korea
| | - Insu Park
- Department of Biotechnology and Bioinformatics, Korea University, Sejong, 30019, Republic of Korea; Department of Biomedical Engineering, Konyang University, Daejeon, 35365, Republic of Korea
| | - Mi-Suk Eom
- Division of Infectious Diseases, Sejong Institute of Health & Environment, Sejong, 30015, Republic of Korea
| | - Sang-Gu Yeo
- Division of Infectious Diseases, Sejong Institute of Health & Environment, Sejong, 30015, Republic of Korea
| | - Ryeo Gang Son
- 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
| | - Gyudo Lee
- Department of Biotechnology and Bioinformatics, Korea University, Sejong, 30019, Republic of Korea
| | - Hyongsok Tom Soh
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA; Department of Radiology, Stanford University, Stanford, CA, 94305, USA
| | - Yoochan Hong
- Department of Medical Device, Korea Institute of Machinery and Materials (KIMM), Daegu, 42994, Republic of Korea.
| | - Seung Pil Pack
- Department of Biotechnology and Bioinformatics, Korea University, Sejong, 30019, Republic of Korea.
| |
Collapse
|
4
|
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.
Collapse
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.
| |
Collapse
|
5
|
Castro-Fuentes CA, Reyes-Montes MDR, Frías-De-León MG, Valencia-Ledezma OE, Acosta-Altamirano G, Duarte-Escalante E. Aspergillus-SARS-CoV-2 Coinfection: What Is Known? Pathogens 2022; 11:1227. [PMID: 36364979 PMCID: PMC9694759 DOI: 10.3390/pathogens11111227] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/17/2022] [Accepted: 10/21/2022] [Indexed: 07/30/2023] Open
Abstract
COVID-19-associated pulmonary aspergillosis (CAPA) has had a high incidence. In addition, it has been associated with prolonged hospital stays, as well as several predisposing risk factors, such as fungal factors (nosocomial organism, the size of the conidia, and the ability of the Aspergillus spp. of colonizing the respiratory tract), environmental factors (remodeling in hospitals, use of air conditioning and negative pressure in intensive care units), comorbidities, and immunosuppressive therapies. In addition to these factors, SARS-CoV-2 per se is associated with significant dysfunction of the patient's immune system, involving both innate and acquired immunity, with reduced CD4+ and CD8+ T cell counts and cytokine storm. Therefore, this review aims to identify the factors influencing the fungus so that coinfection with SARS-CoV-2 can occur. In addition, we analyze the predisposing factors in the fungus, host, and the immune response alteration due to the pathogenicity of SARS-CoV-2 that causes the development of CAPA.
Collapse
Affiliation(s)
- Carlos Alberto Castro-Fuentes
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Ciudad Universitaria, Coyoacán, Mexico City 04510, Mexico
| | - María del Rocío Reyes-Montes
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Ciudad Universitaria, Coyoacán, Mexico City 04510, Mexico
| | - María Guadalupe Frías-De-León
- Hospital Regional de Alta Especialidad de Ixtapaluca, Carretera Federal México-Puebla Km. 34.5, Pueblo de Zoquiapan, Ixtapaluca 56530, Mexico
| | - Omar E. Valencia-Ledezma
- Hospital Regional de Alta Especialidad de Ixtapaluca, Carretera Federal México-Puebla Km. 34.5, Pueblo de Zoquiapan, Ixtapaluca 56530, Mexico
| | - Gustavo Acosta-Altamirano
- Hospital Regional de Alta Especialidad de Ixtapaluca, Carretera Federal México-Puebla Km. 34.5, Pueblo de Zoquiapan, Ixtapaluca 56530, Mexico
| | - Esperanza Duarte-Escalante
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Ciudad Universitaria, Coyoacán, Mexico City 04510, Mexico
| |
Collapse
|
6
|
Antiviral effects of azithromycin: A narrative review. Biomed Pharmacother 2022; 147:112682. [PMID: 35131658 PMCID: PMC8813546 DOI: 10.1016/j.biopha.2022.112682] [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: 11/30/2021] [Revised: 01/26/2022] [Accepted: 01/31/2022] [Indexed: 12/20/2022] Open
Abstract
Viral infections have a great impact on human health. The urgent need to find a cure against different viruses led us to investigations in a vast range of drugs. Azithromycin (AZT), classified as a macrolide, showed various effects on different known viruses such as severe acute respiratory syndrome coronavirus (SARS-CoV), Zika, Ebola, Enterovirus (EVs) and Rhinoviruses (RVs), and Influenza A previously; namely, these viruses, which caused global concerns, are considered as targets for AZT different actions. Due to AZT background in the treatment of known viral infections mentioned above (which is described in this study), in the early stages of COVID-19 (a new zoonotic disease caused by a novel coronavirus called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)) development, AZT drew attention to itself due to its antiviral and immunomodulatory effects as a valuable candidate for COVID-19 treatment. AZT usage instructions for treating different viral infections have always been under observation, and COVID-19 is no exception. There are still debates about the use of AZT in COVID-19 treatment. However, eventually, novel researches convinced WHO to announce the discontinuation of AZT use (alone or in combination with hydroxychloroquine) in treating SARS-CoV-2 infection. This research aims to study the structure of all of the viruses mentioned above and the molecular and clinical effects of AZT against the virus.
Collapse
|
7
|
Fass E, Zizelski Valenci G, Rubinstein M, Freidlin PJ, Rosencwaig S, Kutikov I, Werner R, Ben-Tovim N, Bucris E, Erster O, Zuckerman NS, Mor O, Mendelson E, Dveyrin Z, Rorman E, Nissan I. HiSpike Method for High-Throughput Cost Effective Sequencing of the SARS-CoV-2 Spike Gene. Front Med (Lausanne) 2022; 8:798130. [PMID: 35087848 PMCID: PMC8787038 DOI: 10.3389/fmed.2021.798130] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 12/13/2021] [Indexed: 11/15/2022] Open
Abstract
The changing nature of the SARS-CoV-2 pandemic poses unprecedented challenges to the world's health systems. Emerging spike gene variants jeopardize global efforts to produce immunity and reduce morbidity and mortality. These challenges require effective real-time genomic surveillance solutions that the medical community can quickly adopt. The SARS-CoV-2 spike protein mediates host receptor recognition and entry into the cell and is susceptible to generation of variants with increased transmissibility and pathogenicity. The spike protein is the primary target of neutralizing antibodies in COVID-19 patients and the most common antigen for induction of effective vaccine immunity. Tight monitoring of spike protein gene variants is key to mitigating COVID-19 spread and generation of vaccine escape mutants. Currently, SARS-CoV-2 sequencing methods are labor intensive and expensive. When sequence demands are high sequencing resources are quickly exhausted. Consequently, most SARS-CoV-2 strains are sequenced in only a few developed countries and rarely in developing regions. This poses the risk that undetected, dangerous variants will emerge. In this work, we present HiSpike, a method for high-throughput cost effective targeted next generation sequencing of the spike gene. This simple three-step method can be completed in < 30 h, can sequence 10-fold more samples compared to conventional methods and at a fraction of their cost. HiSpike has been validated in Israel, and has identified multiple spike variants from real-time field samples including Alpha, Beta, Delta and the emerging Omicron variants. HiSpike provides affordable sequencing options to help laboratories conserve resources for widespread high-throughput, near real-time monitoring of spike gene variants.
Collapse
Affiliation(s)
- Ephraim Fass
- National Public Health Laboratory, Public Health Services, Ministry of Health, Tel Aviv, Israel
| | - Gal Zizelski Valenci
- National Public Health Laboratory, Public Health Services, Ministry of Health, Tel Aviv, Israel
| | - Mor Rubinstein
- National Public Health Laboratory, Public Health Services, Ministry of Health, Tel Aviv, Israel
| | - Paul J. Freidlin
- National Public Health Laboratory, Public Health Services, Ministry of Health, Tel Aviv, Israel
| | - Shira Rosencwaig
- National Public Health Laboratory, Public Health Services, Ministry of Health, Tel Aviv, Israel
| | - Inna Kutikov
- National Public Health Laboratory, Public Health Services, Ministry of Health, Tel Aviv, Israel
| | - Robert Werner
- National Public Health Laboratory, Public Health Services, Ministry of Health, Tel Aviv, Israel
| | - Nofar Ben-Tovim
- National Public Health Laboratory, Public Health Services, Ministry of Health, Tel Aviv, Israel
| | - Efrat Bucris
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Oran Erster
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Neta S. Zuckerman
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Orna Mor
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
- School of Public Health, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ella Mendelson
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
- School of Public Health, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Zeev Dveyrin
- National Public Health Laboratory, Public Health Services, Ministry of Health, Tel Aviv, Israel
| | - Efrat Rorman
- National Public Health Laboratory, Public Health Services, Ministry of Health, Tel Aviv, Israel
| | - Israel Nissan
- National Public Health Laboratory, Public Health Services, Ministry of Health, Tel Aviv, Israel
| |
Collapse
|