1
|
Sultana A, Geethakumari AM, Islam Z, Kolatkar PR, Biswas KH. BRET-based biosensors for SARS-CoV-2 oligonucleotide detection. Front Bioeng Biotechnol 2024; 12:1353479. [PMID: 38887615 PMCID: PMC11181354 DOI: 10.3389/fbioe.2024.1353479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 05/09/2024] [Indexed: 06/20/2024] Open
Abstract
The need for the early detection of emerging pathogenic viruses and their newer variants has driven the urgent demand for developing point-of-care diagnostic tools. Although nucleic acid-based methods such as reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and loop-mediated isothermal amplification (LAMP) have been developed, a more facile and robust platform is still required. To address this need, as a proof-of-principle study, we engineered a prototype-the versatile, sensitive, rapid, and cost-effective bioluminescence resonance energy transfer (BRET)-based biosensor for oligonucleotide detection (BioOD). Specifically, we designed BioODs against the SARS-CoV-2 parental (Wuhan strain) and B.1.617.2 Delta variant through the conjugation of specific, fluorescently modified molecular beacons (sensor module) through a complementary oligonucleotide handle DNA functionalized with the NanoLuc (NLuc) luciferase protein such that the dissolution of the molecular beacon loop upon the binding of the viral oligonucleotide will result in a decrease in BRET efficiency and, thus, a change in the bioluminescence spectra. Following the assembly of the BioODs, we determined their kinetics response, affinity for variant-specific oligonucleotides, and specificity, and found them to be rapid and highly specific. Furthermore, the decrease in BRET efficiency of the BioODs in the presence of viral oligonucleotides can be detected as a change in color in cell phone camera images. We envisage that the BioODs developed here will find application in detecting viral infections with variant specificity in a point-of-care-testing format, thus aiding in large-scale viral infection surveillance.
Collapse
Affiliation(s)
- Asfia Sultana
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
| | - Anupriya M. Geethakumari
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
| | - Zeyaul Islam
- Diabetes Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
| | - Prasanna R. Kolatkar
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
- Diabetes Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
| | - Kabir H. Biswas
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
| |
Collapse
|
2
|
Morey K, Thomas-Fenderson T, Watson A, Sebesta J, Peebles C, Gentry-Weeks C. Toehold switch plus signal amplification enables rapid detection. Biotechnol J 2023; 18:e2200607. [PMID: 37641181 PMCID: PMC10840733 DOI: 10.1002/biot.202200607] [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: 12/02/2022] [Revised: 08/04/2023] [Accepted: 08/14/2023] [Indexed: 08/31/2023]
Abstract
Recent world events have led to an increased interest in developing rapid and inexpensive clinical diagnostic platforms for viral detection. Here, the development of a cell-free toehold switch-based biosensor, which does not require upstream amplification of target RNA, is described for the detection of RNA viruses. Toehold switches were designed to avoid interfering secondary structure in the viral RNA binding region, mutational hotspots, and cross-reacting sequences of other coronaviruses. Using these design criteria, toehold switches were targeted to a low mutation region of the SARS-CoV-2 genome nonstructural protein 2 (nsp2). The designs were tested in a cell-free system using trigger RNA based on the viral genome and a highly sensitive fluorescent reporter gene, mNeonGreen. The detection sensitivity of our best toehold design, CSU 08, was in the low picomolar range of target (trigger) RNA. To increase the sensitivity of our cell-free biosensor to a clinically relevant level, we developed a modular downstream amplification system that utilizes toehold switch activation of tobacco etch virus (TEV) protease expression. The TEV protease cleaves a quenched fluorescent reporter, both increasing the signal fold change between control and sample and increasing the sensitivity to a clinically relevant low femtomolar range for target RNA detection.
Collapse
Affiliation(s)
- Kevin Morey
- Chemical and Biological Engineering Department, Colorado State University, Fort Collins, Colorado, USA
| | - Tyler Thomas-Fenderson
- Microbiology, Immunology, and Pathology Department, Colorado State University, Fort Collins, Colorado, USA
| | - Al Watson
- Chemical and Biological Engineering Department, Colorado State University, Fort Collins, Colorado, USA
| | - Jacob Sebesta
- Chemical and Biological Engineering Department, Colorado State University, Fort Collins, Colorado, USA
| | - Christie Peebles
- Chemical and Biological Engineering Department, Colorado State University, Fort Collins, Colorado, USA
| | - Claudia Gentry-Weeks
- Microbiology, Immunology, and Pathology Department, Colorado State University, Fort Collins, Colorado, USA
| |
Collapse
|
3
|
Khera HK, Mishra R. Nucleic Acid Based Testing (NABing): A Game Changer Technology for Public Health. Mol Biotechnol 2023:10.1007/s12033-023-00870-4. [PMID: 37695473 DOI: 10.1007/s12033-023-00870-4] [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: 04/28/2023] [Accepted: 08/21/2023] [Indexed: 09/12/2023]
Abstract
Timely and accurate detection of the causal agent of a disease is crucial to restrict suffering and save lives. Mere symptoms are often not enough to detect the root cause of the disease. Better diagnostics applied for screening at a population level and sensitive detection assays remain the crucial component of disease surveillance which may include clinical, plant, and environmental samples, including wastewater. The recent advances in genome sequencing, nucleic acid amplification, and detection methods have revolutionized nucleic acid-based testing (NABing) and screening assays. A typical NABing assay consists of three modules: isolation of the nucleic acid from the collected sample, identification of the target sequence, and final reading the target with the help of a signal, which may be in the form of color, fluorescence, etc. Here, we review current NABing assays covering the different aspects of all three modules. We also describe the frequently used target amplification or signal amplification procedures along with the variety of applications of this fast-evolving technology and challenges in implementation of NABing in the context of disease management especially in low-resource settings.
Collapse
Affiliation(s)
- Harvinder Kour Khera
- Tata Institute for Genetics and Society, New inStem Building NCBS Campus, GKVK Post, Bellary Road, Bengaluru, 560065, India.
| | - Rakesh Mishra
- Tata Institute for Genetics and Society, New inStem Building NCBS Campus, GKVK Post, Bellary Road, Bengaluru, 560065, India.
- CSIR-Centre for Cellular and Molecular Biology, Uppal Rd, IICT Colony, Habsiguda, Hyderabad, Telangana, 500007, India.
| |
Collapse
|
4
|
Hussein HA, Hanora A, Solyman SM, Hassan RYA. Designing and fabrication of electrochemical nano-biosensor for the fast detection of SARS-CoV-2-RNA. Sci Rep 2023; 13:5139. [PMID: 36991070 PMCID: PMC10054215 DOI: 10.1038/s41598-023-32168-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 03/23/2023] [Indexed: 03/31/2023] Open
Abstract
SARS-CoV-2 caused a global panic among populations. Rapid diagnostic procedures for the virus are crucial for disease control. Thus, the designed signature probe from a highly conserved region of the virus was chemically immobilized onto the nanostructured-AuNPs/WO3-screen printed electrodes. Different concentrations of the matched oligonucleotides were spiked to test the specificity of the hybridization affinity whereas the electrochemical impedance spectroscopy was used for tracking the electrochemical performance. After a full assay optimization, limits of detection and quantification were calculated based on linear regression and were valued at 298 and 994 fM, respectively. Further, the high performance of the fabricated RNA-sensor chips was confirmed after testing the interference status in the presence of the mismatched oligos in one nucleotide and completely one. Worthy to mention that the single-stranded matched oligos can be hybridized to the immobilized probe in 5 min at room temperature. The designed disposable sensor chips are capable of detecting the virus genome directly. Therefore, the chips are a rapid tool for SARS-CoV-2 detection.
Collapse
Affiliation(s)
- Heba A Hussein
- Virology Department, Animal Health Research Institute (AHRI), Agricultural Research Center (ARC), Giza, 12619, Egypt.
| | - Amro Hanora
- Department of Microbiology and Immunology, College of Pharmacy, Suez Canal University, Ismailia, Egypt
| | - Samar M Solyman
- Department of Microbiology and Immunology, College of Pharmacy, Suez Canal University, Ismailia, Egypt
| | - Rabeay Y A Hassan
- Biosensors Research Laboratory, Zewail City of Science and Technology, 6Th October City, Giza, 12578, Egypt.
| |
Collapse
|
5
|
Progress and Challenges of Point-of-Need Photonic Biosensors for the Diagnosis of COVID-19 Infections and Immunity. BIOSENSORS 2022; 12:bios12090678. [PMID: 36140063 PMCID: PMC9496547 DOI: 10.3390/bios12090678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/13/2022] [Accepted: 08/16/2022] [Indexed: 11/25/2022]
Abstract
The new coronavirus disease, COVID-19, caused by SARS-CoV-2, continues to affect the world and after more than two years of the pandemic, approximately half a billion people are reported to have been infected. Due to its high contagiousness, our life has changed dramatically, with consequences that remain to be seen. To prevent the transmission of the virus, it is crucial to diagnose COVID-19 accurately, such that the infected cases can be rapidly identified and managed. Currently, the gold standard of testing is polymerase chain reaction (PCR), which provides the highest accuracy. However, the reliance on centralized rapid testing modalities throughout the COVID-19 pandemic has made access to timely diagnosis inconsistent and inefficient. Recent advancements in photonic biosensors with respect to cost-effectiveness, analytical performance, and portability have shown the potential for such platforms to enable the delivery of preventative and diagnostic care beyond clinics and into point-of-need (PON) settings. Herein, we review photonic technologies that have become commercially relevant throughout the COVID-19 pandemic, as well as emerging research in the field of photonic biosensors, shedding light on prospective technologies for responding to future health outbreaks. Therefore, in this article, we provide a review of recent progress and challenges of photonic biosensors that are developed for the testing of COVID-19, consisting of their working fundamentals and implementation for COVID-19 testing in practice with emphasis on the challenges that are faced in different development stages towards commercialization. In addition, we also present the characteristics of a biosensor both from technical and clinical perspectives. We present an estimate of the impact of testing on disease burden (in terms of Disability-Adjusted Life Years (DALYs), Quality Adjusted Life Years (QALYs), and Quality-Adjusted Life Days (QALDs)) and how improvements in cost can lower the economic impact and lead to reduced or averted DALYs. While COVID19 is the main focus of these technologies, similar concepts and approaches can be used and developed for future outbreaks of other infectious diseases.
Collapse
|
6
|
Engineering Toehold-Mediated Switches for Native RNA Detection and Regulation in Bacteria. J Mol Biol 2022; 434:167689. [PMID: 35717997 DOI: 10.1016/j.jmb.2022.167689] [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: 03/11/2022] [Revised: 05/19/2022] [Accepted: 06/09/2022] [Indexed: 01/24/2023]
Abstract
RNA switches are versatile tools in synthetic biology for sensing and regulation applications. The discoveries of RNA-mediated translational and transcriptional control have facilitated the development of complexde novodesigns of RNA switches. Specifically, RNA toehold-mediated switches, in which binding to the toehold sensing domain controls the transition between switch states via strand displacement, have been extensively adapted for coupling systems responses to specifictrans-RNA inputs. This review highlights some of the challenges associated with applying these switches for native RNA detectionin vivo, including transferability between organisms. The applicability and design considerations of toehold-mediated switches are discussed by highlighting twelve recently developed switch designs. This review finishes with future perspectives to address current gaps in the field, particularly regarding the power of structural prediction algorithms for improved in vivo functionality of RNA switches.
Collapse
|
7
|
Kia V, Tafti A, Paryan M, Mohammadi-Yeganeh S. Evaluation of real-time NASBA assay for the detection of SARS-CoV-2 compared with real-time PCR. Ir J Med Sci 2022; 192:723-729. [PMID: 35668337 PMCID: PMC9170118 DOI: 10.1007/s11845-022-03046-2] [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: 03/12/2022] [Accepted: 06/02/2022] [Indexed: 01/08/2023]
Abstract
Purpose
In January 2020, the COVID-19 pandemic started and has severely affected all countries around the world. The clinical symptoms alone are not sufficient for a proper diagnosis. Thus, molecular tests are required. Various institutes and researchers developed real-time PCR-based methods for the detection of the virus. However, the method needs expensive equipment. In the present study, we developed a real-time NASBA assay for the detection of SARS-CoV-2. Methods Primers and molecular beacon probes for RdRp and N genes were designed. In silico analysis showed that primers and the probes were specific for SARS-CoV-2. The standard samples with known copy numbers of the virus were tested using the NASBA assay and an FDA-approved real-time PCR kit. A series of standard samples were prepared and tested. Clinical sensitivity, precision analysis, and clinical assessment of the assay were performed. Results The limit of detection of the assay was 200 copies/mL. The clinical sensitivity of the assay was 97.64%. The intra-assay and inter-assay for both N and RdRp genes were less than 5% and 10%, respectively. Clinical assessment of the assay showed that the positive agreement rate and negative agreement rate of the assays were determined to be 97.64% and 100%, respectively. Conclusions The results of the present study show that the developed real-time NASBA is a sensitive and specific method for the detection of SARS-CoV-2 and is comparable with real-time PCR. NASBA is an isothermal signal amplification method, and if stand-alone fluorescent readers are available, the real-time NASBA can be used without the need for expensive thermocyclers. In addition compared to other isothermal methods like LAMP, the primer design is straightforward. Thus, real-time NASBA could be a suitable method for inexpensive SARS-CoV-2 detection. Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1007/s11845-022-03046-2.
Collapse
Affiliation(s)
- Vahid Kia
- Department of Medical Biotechnology, School of Medicine, Shahroud University of Medical Sciences, Shahroud, Iran
| | - Ali Tafti
- Department of Medical Biotechnology, Faculty of Medicine, Arak University of Medical Science, Arak, Iran
| | - Mahdi Paryan
- Department of Research and Development, Production and Research Complex, Pasteur Institute of Iran, Tehran, Iran.
| | - Samira Mohammadi-Yeganeh
- Medical Nanotechnology and Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran. .,Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| |
Collapse
|
8
|
Update on the Development of Toehold Switch-Based Approach for Molecular Diagnostic Tests of COVID-19. J Nucleic Acids 2022; 2022:7130061. [PMID: 35586794 PMCID: PMC9110250 DOI: 10.1155/2022/7130061] [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: 02/18/2022] [Accepted: 04/22/2022] [Indexed: 11/18/2022] Open
Abstract
A high volume of diagnostic tests is needed during the coronavirus disease 2019 (COVID-19) pandemic to obtain representative results. These results can help to design and implement effective policies to prevent the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Diagnosis using current gold standard methods, i.e., real-time quantitative PCR (RT-qPCR), is challenging, especially in areas with limited trained personnel and health-related infrastructure. The toehold switch-based diagnostic system is a promising alternative method for detecting SARS-CoV-2 that has advantages such as inexpensive cost per testing, rapid, and highly sensitive and specific analysis. Moreover, the system can be applied to paper-based platforms, simplifying the distribution and utilization in low-resource settings. This review provides insight into the development of toehold switch-based diagnostic devices as the most recent methods for detecting SARS-CoV-2.
Collapse
|
9
|
Dhar BC. Diagnostic assay and technology advancement for detecting SARS-CoV-2 infections causing the COVID-19 pandemic. Anal Bioanal Chem 2022; 414:2903-2934. [PMID: 35211785 PMCID: PMC8872642 DOI: 10.1007/s00216-022-03918-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/01/2022] [Accepted: 01/20/2022] [Indexed: 12/23/2022]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-caused COVID-19 pandemic has transmitted to humans in practically all parts of the world, producing socio-economic turmoil. There is an urgent need for precise, fast, and affordable diagnostic testing to be widely available for detecting SARS-CoV-2 and its mutations in various phases of the disease. Early diagnosis with great precision has been achieved using real-time polymerase chain reaction (RT-PCR) and similar other molecular methods, but theseapproaches are costly and involve rigorous processes that are not easily obtainable. Conversely, immunoassays that detect a small number of antibodies have been employed for quick, low-cost tests, but their efficiency in diagnosing infected people has been restricted. The use of biosensors in the detection of SARS-CoV-2 is vital for the COVID-19 pandemic’s control. This review gives an overview of COVID-19 diagnostic approaches that are currently being developed as well as nanomaterial-based biosensor technologies, to aid future technological advancement and innovation. These approaches can be integrated into point-of-care (POC) devices to quickly identify a large number of infected patients and asymptomatic carriers. The ongoing research endeavors and developments in complementary technologies will play a significant role in curbing the spread of the COVID-19 pandemic and fill the knowledge gaps in current diagnostic accuracy and capacity.
Collapse
Affiliation(s)
- Bidhan C Dhar
- Lineberger Comprehensive Cancer Center, University of North Carolina (UNC), 205 S Columbia St, Chapel Hill, NC, 27514, USA.
| |
Collapse
|
10
|
De Felice M, De Falco M, Zappi D, Antonacci A, Scognamiglio V. Isothermal amplification-assisted diagnostics for COVID-19. Biosens Bioelectron 2022; 205:114101. [PMID: 35202984 PMCID: PMC8849862 DOI: 10.1016/j.bios.2022.114101] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 02/02/2022] [Accepted: 02/14/2022] [Indexed: 12/12/2022]
Abstract
The scenery of molecular diagnostics for infectious diseases is rapidly evolving to respond to the COVID-19 epidemic. The sensitivity and specificity of diagnostics, along with speed and accuracy, are crucial requirements for effective analytical tools to address the disease spreading around the world. Emerging diagnostic devices combine the latest trends in isothermal amplification methods for nucleic acids with state-of-the-art biosensing systems, intending to bypass roadblocks encountered in the last 2 years of the pandemic. Isothermal nucleic acid amplification is a simple procedure that quickly and efficiently accumulates nucleic acid sequences at a constant temperature, without the need for sophisticated equipment. The integration of isothermal amplification into portable biosensing devices confers high sensitivity and improves screening at the point of need in low-resource settings. This review reports the latest trends reached in this field with the latest examples of isothermal amplification-powered biosensors for detecting SARS-CoV-2, with different configurations, as well as their intrinsic advantages and disadvantages.
Collapse
Affiliation(s)
- Mariarita De Felice
- Institute of Bioscience and BioResources, National Research Council, Department of Biology, Agriculture and Food Science, Via P. Castellino 111, 80100, Naples, Italy
| | - Mariarosaria De Falco
- Institute of Bioscience and BioResources, National Research Council, Department of Biology, Agriculture and Food Science, Via P. Castellino 111, 80100, Naples, Italy
| | - Daniele Zappi
- Institute of Crystallography, National Research Council, Department of Chemical Sciences and Materials Technologies, Via Salaria km 29.300, 00015, Monterotondo, Rome, Italy
| | - Amina Antonacci
- Institute of Crystallography, National Research Council, Department of Chemical Sciences and Materials Technologies, Via Salaria km 29.300, 00015, Monterotondo, Rome, Italy
| | - Viviana Scognamiglio
- Institute of Crystallography, National Research Council, Department of Chemical Sciences and Materials Technologies, Via Salaria km 29.300, 00015, Monterotondo, Rome, Italy.
| |
Collapse
|