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Yang X, Zeng X, Huang J, Yang L, Mao S, Chen X, Wang Y, Wei X, Li S. Loop-mediated isothermal amplification linked a nanoparticles-based biosensor for detecting Epstein-Barr virus. Appl Microbiol Biotechnol 2024; 108:91. [PMID: 38212962 PMCID: PMC10784390 DOI: 10.1007/s00253-023-12948-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 11/24/2023] [Accepted: 12/01/2023] [Indexed: 01/13/2024]
Abstract
Epstein-Barr virus (EBV) is a ubiquitous gamma herpesvirus that maintains a lifelong latent association with B lymphocytes. Here, a rapid and reliable diagnosis platform for detecting EBV infection, employing loop-mediated isothermal amplification (LAMP) combined with a gold nanoparticles-based lateral flow biosensors (AuNPs-LFB) (termed LAMP Amplification Mediated AuNPs-LFB Detection, LAMAD), was developed in the current study. A set of specific LAMP primers targeting the Epstein-Barr nuclear antigen (EBNA) leader protein (EBNA-LP) gene was designed and synthesized. Subsequently, these templates extracted from various pathogens and whole blood samples were used to optimize and evaluate the EBV-LAMAD assay. As a result, the limit of detection (LoD) of the EBV-LAMAD assay was 45 copies/reaction. The EBV-LAMAD assay can detect all representative EBV pathogens used in the study, and of note, no cross-reactions were observed with other non-EBV organisms. Moreover, the whole workflow of the EBV-LAMAD assay can be completed within 70 min, including rapid EBV template preparation, EBV-LAMP amplification, and AuNPs-LFB-mediated detection. Taken together, the EBV-LAMAD assay targeting the EBNA-LP gene is a rapid, simplified, sensitive, reliable, and easy-to-use detection protocol that can be used as a competitive potential diagnostic/screening tool for EBV infection in clinical settings, especially in basic laboratories in resource-limited regions. KEY POINTS: • A novel, simplified, and easy-to-use AuNPs-LFB biosensor was designed and prepared. • LAMP combined with an AuNPs-LFB targeting the novel EBNA-LP gene was established. • EBV-LAMAD is a rapid, sensitive, and reliable detection protocol for EBV infection.
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Affiliation(s)
- Xinggui Yang
- Guizhou Provincial Center for Disease Control and Prevention, Guiyang, 550004, Guizhou, People's Republic of China
| | - Xiaoyan Zeng
- The Second Affiliated Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, 550003, Guizhou, People's Republic of China
| | - Junfei Huang
- Guizhou Provincial Center for Disease Control and Prevention, Guiyang, 550004, Guizhou, People's Republic of China
| | - Ludi Yang
- Tongren People's Hospital, Tongren, 554399, Guizhou, People's Republic of China
| | - Sha Mao
- Guizhou Provincial Center for Disease Control and Prevention, Guiyang, 550004, Guizhou, People's Republic of China
| | - Xu Chen
- The Second Affiliated Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, 550003, Guizhou, People's Republic of China
| | - Yu Wang
- Department of Clinical Laboratory, The First People's Hospital of Guiyang, Guiyang, 550002, Guizhou, People's Republic of China
| | - Xiaoyu Wei
- Guizhou Provincial Center for Disease Control and Prevention, Guiyang, 550004, Guizhou, People's Republic of China
| | - Shijun Li
- Guizhou Provincial Center for Disease Control and Prevention, Guiyang, 550004, Guizhou, People's Republic of China.
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Cerdeira Ferreira LM, Lima D, Marcolino-Junior LH, Bergamini MF, Kuss S, Campanhã Vicentini F. Cutting-edge biorecognition strategies to boost the detection performance of COVID-19 electrochemical biosensors: A review. Bioelectrochemistry 2024; 157:108632. [PMID: 38181592 DOI: 10.1016/j.bioelechem.2023.108632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 12/16/2023] [Accepted: 12/19/2023] [Indexed: 01/07/2024]
Abstract
Electrochemical biosensors are known for their high sensitivity, selectivity, and low cost. Recently, they have gained significant attention and became particularly important as promising tools for the detection of COVID-19 biomarkers, since they offer a rapid and accurate means of diagnosis. Biorecognition strategies are a crucial component of electrochemical biosensors and determine their specificity and sensitivity based on the interaction of biological molecules, such as antibodies, enzymes, and DNA, with target analytes (e.g., viral particles, proteins and genetic material) to create a measurable signal. Different biorecognition strategies have been developed to enhance the performance of electrochemical biosensors, including direct, competitive, and sandwich binding, alongside nucleic acid hybridization mechanisms and gene editing systems. In this review article, we present the different strategies used in electrochemical biosensors to target SARS-CoV-2 and other COVID-19 biomarkers, as well as explore the advantages and disadvantages of each strategy and highlight recent progress in this field. Additionally, we discuss the challenges associated with developing electrochemical biosensors for clinical COVID-19 diagnosis and their widespread commercialization.
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Affiliation(s)
- Luís Marcos Cerdeira Ferreira
- Center of Nature Sciences, Federal University of São Carlos, Rod. Lauri Simões de Barros km 12, 18290-000, Buri, SP, Brazil; Laboratory of Electrochemical Sensors (LabSensE) Department of Chemistry, Federal University of Paraná, 81.531-980, Curitiba, PR, Brazil
| | - Dhésmon Lima
- Laboratory for Bioanalytics and Electrochemical Sensing (LBES), Department of Chemistry, University of Manitoba, 144 Dysart Road, Winnipeg, MB, R3T 2N2, Canada.
| | - Luiz Humberto Marcolino-Junior
- Laboratory of Electrochemical Sensors (LabSensE) Department of Chemistry, Federal University of Paraná, 81.531-980, Curitiba, PR, Brazil
| | - Marcio Fernando Bergamini
- Laboratory of Electrochemical Sensors (LabSensE) Department of Chemistry, Federal University of Paraná, 81.531-980, Curitiba, PR, Brazil
| | - Sabine Kuss
- Laboratory for Bioanalytics and Electrochemical Sensing (LBES), Department of Chemistry, University of Manitoba, 144 Dysart Road, Winnipeg, MB, R3T 2N2, Canada
| | - Fernando Campanhã Vicentini
- Center of Nature Sciences, Federal University of São Carlos, Rod. Lauri Simões de Barros km 12, 18290-000, Buri, SP, Brazil.
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Silva SJRD, Magalhães JJFD, Matthews Q, Divarzak ALL, Mendes RPG, Santos BNR, Cabral DGDA, Silva JBD, Kohl A, Pardee K, Pena L. Development and field validation of a reverse transcription loop-mediated isothermal amplification assay (RT-LAMP) for the rapid detection of chikungunya virus in patient and mosquito samples. Clin Microbiol Infect 2024; 30:810-815. [PMID: 38460820 DOI: 10.1016/j.cmi.2024.03.004] [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: 09/03/2023] [Revised: 03/02/2024] [Accepted: 03/04/2024] [Indexed: 03/11/2024]
Abstract
OBJECTIVES We aimed to develop a reverse transcription loop-mediated isothermal amplification (RT-LAMP) platform for the rapid detection of chikungunya virus (CHIKV) in both patient and mosquito samples from Brazil. METHODS We optimized an RT-LAMP assay and then evaluated the specificity and sensitivity using visual detection. In comparison with the RT-qPCR reference method, we validated the utility of this assay as a molecular diagnostic test in a reference laboratory for arbovirus diagnostics using 100 serum samples collected from suspected CHIKV cases. RESULTS Our RT-LAMP assay specifically detected CHIKV without cross-reactivity against other arboviruses. The limit of detection of our RT-LAMP was estimated in -1.18 PFU (confidence interval [CI] ranging from -2.08 to 0.45), resulting in a similar analytical sensitivity when directly compared with the reference standard RT-qPCR assay. Then, we demonstrate the ability of our RT-LAMP assay to detect the virus in different human specimens (serum, urine, and saliva), and crude lysate of Aedes aegypti mosquitoes in as little as 20-30 minutes and without a separate RNA isolation step. Lastly, we showed that our RT-LAMP assay could be lyophilized and reactivated by adding water, indicating potential for room-temperature storage. Our RT-LAMP had a clinical sensitivity of 100% (95% CI, 90.97-100.00%), clinical specificity of 96.72% (95% CI, 88.65-99.60%), and overall accuracy of 98.00% (95% CI, 92.96-99.76%). DISCUSSION Taken together, these findings indicate that the RT-LAMP assay reported here solves important practical drawbacks to the deployment of molecular diagnostics in the field and can be used to improve testing capacity, particularly in low- and middle-income countries.
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Affiliation(s)
- Severino Jefferson Ribeiro da Silva
- Laboratory of Virology and Experimental Therapy (Lavite), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), Recife, Pernambuco, Brazil; Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada.
| | - Jurandy Júnior Ferraz de Magalhães
- Laboratory of Virology and Experimental Therapy (Lavite), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), Recife, Pernambuco, Brazil; Department of Virology, Pernambuco State Central Laboratory (LACEN/PE), Recife, Pernambuco, Brazil; University of Pernambuco (UPE), Serra Talhada Campus, Serra Talhada, Pernambuco, Brazil; Public Health Laboratory of the XI Regional Health, Pernambuco, Brazil
| | - Quinn Matthews
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
| | | | - Renata Pessôa Germano Mendes
- Laboratory of Virology and Experimental Therapy (Lavite), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), Recife, Pernambuco, Brazil
| | - Bárbara Nazly Rodrigues Santos
- Laboratory of Virology and Experimental Therapy (Lavite), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), Recife, Pernambuco, Brazil
| | | | | | - Alain Kohl
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK; Department of Vector Biology and Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Keith Pardee
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada; Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, ON, Canada
| | - Lindomar Pena
- Laboratory of Virology and Experimental Therapy (Lavite), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), Recife, Pernambuco, Brazil.
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Liu Y, Cui X, Lu R, Yang D, Ai Y, Cheow LF. Digital Sort-Enabled Counting Allows Absolute Electrical Quantification of Target Nucleic Acid. ACS Sens 2024; 9:2695-2702. [PMID: 38747895 DOI: 10.1021/acssensors.4c00750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Quantitative nucleic acid amplification tests are of great importance for diagnostics, but current approaches require complex and costly optical setups that limit their nonlaboratory applications. Herein we describe the implementation of a microfluidics platform that can perform binary DNA-amplification-activated droplet sorting. The digital sort-enabled counting (DISCO) platform enables label-free absolute quantification of the nucleic acid. This is achieved by provoking a pH change in droplets through a loop-mediated isothermal amplification (LAMP) reaction, followed by using sorting by interfacial tension (SIFT) to direct positive and negative droplets to different outlets. With the use of on-chip electrodes at both outlets, we demonstrate that the digital electrical counting of target DNA and RNA can be realized. DISCO is a promising approach for realizing sensitive nucleic acid quantification in point-of-care settings.
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Affiliation(s)
- Yi Liu
- Department of Biomedical Engineering and Institute for Health Innovation and Technology, National University of Singapore, Singapore 119077, Singapore
| | - Xu Cui
- Department of Biomedical Engineering and Institute for Health Innovation and Technology, National University of Singapore, Singapore 119077, Singapore
| | - Ri Lu
- Department of Biomedical Engineering and Institute for Health Innovation and Technology, National University of Singapore, Singapore 119077, Singapore
| | - Dahou Yang
- Critical Analytics for Manufacturing Personalized Medicine, Singapore MIT Alliance for Research and Technology, Singapore 138602, Singapore
| | - Ye Ai
- Critical Analytics for Manufacturing Personalized Medicine, Singapore MIT Alliance for Research and Technology, Singapore 138602, Singapore
- Pillar of Engineering Product Development, Singapore University of Technology and Design, Singapore 387372, Singapore
| | - Lih Feng Cheow
- Department of Biomedical Engineering and Institute for Health Innovation and Technology, National University of Singapore, Singapore 119077, Singapore
- Critical Analytics for Manufacturing Personalized Medicine, Singapore MIT Alliance for Research and Technology, Singapore 138602, Singapore
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Almulla N, Soltane R, Alasiri A, Kamal Allayeh A, Alqadi T, Alshehri F, Hamad Alrokban A, Zaghlool SS, Zayan AZ, Abdalla KF, Sayed AM. Advancements in SARS-CoV-2 detection: Navigating the molecular landscape and diagnostic technologies. Heliyon 2024; 10:e29909. [PMID: 38707469 PMCID: PMC11068538 DOI: 10.1016/j.heliyon.2024.e29909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 05/07/2024] Open
Abstract
According to information from the World Health Organization, the world has experienced about 430 million cases of COVID-19, a world-wide health crisis caused by the SARS-CoV-2 virus. This outbreak, originating from China in 2019, has led to nearly 6 million deaths worldwide. As the number of confirmed infections continues to rise, the need for cutting-edge techniques that can detect SARS-CoV-2 infections early and accurately has become more critical. To address this, the Federal Drug Administration (FDA) has issued emergency use authorizations (EUAs) for a wide range of diagnostic tools. These include tests based on detecting nucleic acids and antigen-antibody reactions. The quantitative real-time reverse transcription PCR (qRT-PCR) assay stands out as the gold standard for early virus detection. However, despite its accuracy, qRT-PCR has limitations, such as complex testing protocols and a risk of false negatives, which drive the continuous improvement in nucleic acid and serological testing approaches. The emergence of highly contagious variants of the coronavirus, such as Alpha (B.1.1.7), Delta (B.1.617.2), and Omicron (B.1.1.529), has increased the need for tests that can specifically identify these mutations. This article explores both nucleic acid-based and antigen-antibody serological assays, assessing the performance of recently approved FDA tests and those documented in scientific research, especially in identifying new coronavirus strains.
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Affiliation(s)
- Nuha Almulla
- Department of Biology, Adham University College, Umm Al-Qura University, Makkah, 21955, Saudi Arabia
| | - Raya Soltane
- Department of Biology, Adham University College, Umm Al-Qura University, Makkah, 21955, Saudi Arabia
| | - Ahlam Alasiri
- Department of Biology, Adham University College, Umm Al-Qura University, Makkah, 21955, Saudi Arabia
| | - Abdou Kamal Allayeh
- Virology Lab 176, Environment and Climate Change Institute, National Research Centre, Giza, 12622, Egypt
| | - Taha Alqadi
- Department of Biology, Adham University College, Umm Al-Qura University, Makkah, 21955, Saudi Arabia
| | - Fatma Alshehri
- Department of Biology, College of Sciences, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh, 11671, Saudi Arabia
| | - Ahlam Hamad Alrokban
- Department of Biology, College of Sciences, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh, 11671, Saudi Arabia
| | - Sameh S. Zaghlool
- Department of Pharmacology and Toxicology, College of Pharmacy, Almaaqal University, 61014, Al-Maaqal, Basra, Iraq
| | - Abdallah Z. Zayan
- Department of Pharmaceutics, Collage of Pharmacy, Almaaqal University, 61014, Basrah, Iraq
| | - Karam F. Abdalla
- Department of Pharmaceutics, Collage of Pharmacy, Almaaqal University, 61014, Basrah, Iraq
| | - Ahmed M. Sayed
- Department of Pharmacognosy, Collage of Pharmacy, Almaaqal University, 61014, Basrah, Iraq
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Yu S, Lei X, Qu C. MicroRNA Sensors Based on CRISPR/Cas12a Technologies: Evolution From Indirect to Direct Detection. Crit Rev Anal Chem 2024:1-17. [PMID: 38489095 DOI: 10.1080/10408347.2024.2329229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2024]
Abstract
MicroRNA (miRNA) has emerged as a promising biomarker for disease diagnosis and a potential therapeutic targets for drug development. The detection of miRNA can serve as a noninvasive tool in diseases diagnosis and predicting diseases prognosis. CRISPR/Cas12a system has great potential in nucleic acid detection due to its high sensitivity and specificity, which has been developed to be a versatile tool for nucleic acid-based detection of targets in various fields. However, conversion from RNA to DNA with or without amplification operation is necessary for miRNA detection based on CRISPR/Cas12a system, because dsDNA containing PAM sequence or ssDNA is traditionally considered as the activator of Cas12a. Until recently, direct detection of miRNA by CRISPR/Cas12a system has been reported. In this review, we provide an overview of the evolution of biosensors based on CRISPR/Cas12a for miRNA detection from indirect to direct, which would be beneficial to the development of CRISPR/Cas12a-based sensors with better performance for direct detection of miRNA.
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Affiliation(s)
- Songcheng Yu
- College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Xueying Lei
- College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Chenling Qu
- School of Food and Strategic Reserves, Henan University of Technology, Zhengzhou, China
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El-Daly MM. Advances and Challenges in SARS-CoV-2 Detection: A Review of Molecular and Serological Technologies. Diagnostics (Basel) 2024; 14:519. [PMID: 38472991 DOI: 10.3390/diagnostics14050519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/20/2024] [Accepted: 02/24/2024] [Indexed: 03/14/2024] Open
Abstract
The urgent need for accurate COVID-19 diagnostics has led to the development of various SARS-CoV-2 detection technologies. Real-time reverse transcriptase polymerase chain reaction (RT-qPCR) remains a reliable viral gene detection technique, while other molecular methods, including nucleic acid amplification techniques (NAATs) and isothermal amplification techniques, provide diverse and effective approaches. Serological assays, detecting antibodies in response to viral infection, are crucial for disease surveillance. Saliva-based immunoassays show promise for surveillance purposes. The efficiency of SARS-CoV-2 antibody detection varies, with IgM indicating recent exposure and IgG offering prolonged detectability. Various rapid tests, including lateral-flow immunoassays, present opportunities for quick diagnosis, but their clinical significance requires validation through further studies. Challenges include variations in specificity and sensitivity among testing platforms and evolving assay sensitivities over time. SARS-CoV-2 antigens, particularly the N and S proteins, play a crucial role in diagnostic methods. Innovative approaches, such as nanozyme-based assays and specific nucleotide aptamers, offer enhanced sensitivity and flexibility. In conclusion, ongoing advancements in SARS-CoV-2 detection methods contribute to the global effort in combating the COVID-19 pandemic.
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Affiliation(s)
- Mai M El-Daly
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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Shi Y, Zhou Q, Dong S, Zhao Q, Wu X, Yang P, Zeng X, Yang X, Tan Y, Luo X, Xiao Z, Chen X. Rapid, visual, label-based biosensor platform for identification of hepatitis C virus in clinical applications. BMC Microbiol 2024; 24:68. [PMID: 38413863 PMCID: PMC10900634 DOI: 10.1186/s12866-024-03220-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 02/09/2024] [Indexed: 02/29/2024] Open
Abstract
OBJECTIVES In the current study, for the first time, we reported a novel HCV molecular diagnostic approach termed reverse transcription loop-mediated isothermal amplification integrated with a gold nanoparticles-based lateral flow biosensor (RT-LAMP-AuNPs-LFB), which we developed for rapid, sensitive, specific, simple, and visual identification of HCV. METHODS A set of LAMP primer was designed according to 5'untranslated region (5'UTR) gene from the major HCV genotypes 1b, 2a, 3b, 6a, and 3a, which are prevalent in China. The HCV-RT-LAMP-AuNPs-LFB assay conditions, including HCV-RT-LAMP reaction temperature and time were optimized. The sensitivity, specificity, and selectivity of our assay were evaluated in the current study. The feasibility of HCV-RT-LAMP-AuNPs-LFB was confirmed through clinical serum samples from patients with suspected HCV infections. RESULTS An unique set of HCV-RT-LAMP primers were successfully designed targeting on the 5'UTR gene. The optimal detection process, including crude nucleic acid extraction (approximately 5 min), RT-LAMP reaction (67℃, 30 min), and visual interpretation of AuNPs-LFB results (~ 2 min), could be performed within 40 min without specific instruments. The limit of detection was determined to be 20 copies per test. The HCV-RT-LAMP-AuNPs-LFB assay exhibited high specificity and anti-interference. CONCLUSIONS These preliminary results confirmed that the HCV-RT-LAMP-AuNPs-LFB assay is a sensitive, specific, rapid, visual, and cost-saving assay for identification of HCV. This diagnostic approach has great potential value for point-of-care (POC) diagnostic of HCV, especially in resource-challenged regions.
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Affiliation(s)
- Yuanfang Shi
- The Second Clinical Medical College, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, 550003, People's Republic of China
- Central Laboratory of the Second Affiliated Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, 550003, People's Republic of China
| | - Qingxue Zhou
- Clinical Laboratory, Hangzhou Women's Hospital, Hangzhou, Zhejiang, 310008, People's Republic of China
| | - Shilei Dong
- Department of Clinical Laboratory, Zhejiang Hospital, Hangzhou, Zhejiang, 310013, People's Republic of China
| | - Qi Zhao
- Department of gastroenterology, the Second Affiliated Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, 550003, People's Republic of China
| | - Xue Wu
- Department of Scientific Research, the Second Affiliated Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, 550003, People's Republic of China
| | - Peng Yang
- Clinical Laboratory, the Second Affiliated Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, 550003, People's Republic of China
| | - Xiaoyan Zeng
- Central Laboratory of the Second Affiliated Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, 550003, People's Republic of China
| | - Xinggui Yang
- Experiment Center, Guizhou Provincial Centre for Disease Control and Prevention, Guiyang, Guizhou, 550004, People's Republic of China
| | - Yan Tan
- Clinical Laboratory, Guizhou Provincial Center for Clinical Laboratory, Guiyang, Guizhou, 550002, People's Republic of China
| | - Xinhua Luo
- Department of Infectious Disease, Guizhou Provincial People's Hospital, Guiyang, Guizhou, 550002, People's Republic of China
| | - Zhenghua Xiao
- The Second Clinical Medical College, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, 550003, People's Republic of China.
- Department of gastroenterology, the Second Affiliated Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, 550003, People's Republic of China.
| | - Xu Chen
- The Second Clinical Medical College, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, 550003, People's Republic of China.
- Central Laboratory of the Second Affiliated Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, 550003, People's Republic of China.
- Department of Scientific Research, the Second Affiliated Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, 550003, People's Republic of China.
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Layne TR, Scott A, Cunha LL, Turiello R, Landers JP. Three-Dimensional-Printed Instrument for Isothermal Nucleic Acid Amplification with Real-Time Colorimetric Imaging. MICROMACHINES 2024; 15:271. [PMID: 38398999 PMCID: PMC10892149 DOI: 10.3390/mi15020271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 01/30/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024]
Abstract
Isothermal amplification methods have become popular in research due to the simplicity of the technology needed to run the reactions. Specifically, loop-mediated isothermal amplification (LAMP) has been widely used for various applications since first reported in 2000. LAMP reactions are commonly monitored with the use of colorimetry. Although color changes associated with positive amplification are apparent to the naked eye, this detection method is subjective due to inherent differences in visual perception from person to person. The objectivity of the colorimetric detection method may be improved by programmed image capture over time with simultaneous heating. As such, the development of a novel, one-step, automated, and integrated analysis system capable of performing these tasks in parallel is detailed herein. The device is adaptable to multiple colorimetric dyes, cost-effective, 3D-printed for single-temperature convective heating, and features an easy-to-use LabVIEW software program developed for automated image analysis. The device was optimized and subsequently validated using four messenger-RNA targets and mock forensic samples. The performance of our device was determined to be comparable to that of a conventional thermal cycler and smartphone image analysis, respectively. Moreover, the outlined system is capable of objective colorimetric analysis, with exceptional throughput of up to 96 samples at once.
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Affiliation(s)
- Tiffany R. Layne
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA; (T.R.L.); (R.T.); (J.P.L.)
| | - Anchi Scott
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA; (T.R.L.); (R.T.); (J.P.L.)
| | - Larissa L. Cunha
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA; (T.R.L.); (R.T.); (J.P.L.)
| | - Rachelle Turiello
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA; (T.R.L.); (R.T.); (J.P.L.)
| | - James P. Landers
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA; (T.R.L.); (R.T.); (J.P.L.)
- Department of Mechanical and Aerospace Engineering, University of Virginia, Charlottesville, VA 22903, USA
- Department of Pathology, University of Virginia, Charlottesville, VA 22908, USA
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10
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Ngoc LTN, Lee YC. Current Trends in RNA Virus Detection via Nucleic Acid Isothermal Amplification-Based Platforms. BIOSENSORS 2024; 14:97. [PMID: 38392016 PMCID: PMC10886876 DOI: 10.3390/bios14020097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 02/07/2024] [Accepted: 02/09/2024] [Indexed: 02/24/2024]
Abstract
Ribonucleic acid (RNA) viruses are one of the major classes of pathogens that cause human diseases. The conventional method to detect RNA viruses is real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR), but it has some limitations. It is expensive and time-consuming, with infrastructure and trained personnel requirements. Its high throughput requires sophisticated automation and large-scale infrastructure. Isothermal amplification methods have been explored as an alternative to address these challenges. These methods are rapid, user-friendly, low-cost, can be performed in less specialized settings, and are highly accurate for detecting RNA viruses. Microfluidic technology provides an ideal platform for performing virus diagnostic tests, including sample preparation, immunoassays, and nucleic acid-based assays. Among these techniques, nucleic acid isothermal amplification methods have been widely integrated with microfluidic platforms for RNA virus detection owing to their simplicity, sensitivity, selectivity, and short analysis time. This review summarizes some common isothermal amplification methods for RNA viruses. It also describes commercialized devices and kits that use isothermal amplification techniques for SARS-CoV-2 detection. Furthermore, the most recent applications of isothermal amplification-based microfluidic platforms for RNA virus detection are discussed in this article.
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Affiliation(s)
- Le Thi Nhu Ngoc
- Department of Nano Science and Technology Convergence, Gachon University, 1342 Seongnam-Daero, Sujeong-gu, Seongnam-si 13120, Gyeonggi-do, Republic of Korea
| | - Young-Chul Lee
- Department of BioNano Technology, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 13120, Gyeonggi-do, Republic of Korea
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11
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Nawab M, Riaz SK, Ismail E, Ahamed A, Tariq A, Malik MFA, Qusty NF, Bantun F, Slama P, Umair M, Haque S, Bonilla-Aldana DK, Rodriguez-Morales AJ. Integrated approach for detection of SARS-CoV-2 and its variant by utilizing LAMP and ARMS-PCR. Ann Clin Microbiol Antimicrob 2024; 23:11. [PMID: 38303011 PMCID: PMC10836012 DOI: 10.1186/s12941-023-00665-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 12/26/2023] [Indexed: 02/03/2024] Open
Abstract
Global impact of COVID-19 pandemic has heightened the urgency for efficient virus detection and identification of variants such as the Q57H mutation. Early and efficient detection of SARS-CoV-2 among densely populated developing countries is paramount objective. Although RT-PCR assays offer accuracy, however, dependence on expansive kits and availability of allied health resources pose an immense challenge for developing countries. In the current study, RT-LAMP based detection of SARS-Cov-2 with subsequent confirmation of Q57H variant through ARMS-PCR was performed. Among the 212 collected samples, 134 yielded positive results, while 78 tested negative using RT-LAMP. Oropharyngeal swabs of suspected individuals were collected and processed for viral RNA isolation. Isolated viral RNA was processed further by using either commercially available WarmStart Master Mix or our in house developed LAMP master mix separately. Subsequently, the end results of each specimen were evaluated by colorimetry. For LAMP assays, primers targeting three genes (ORF1ab, N and S) were designed using PrimerExplorer software. Interestingly, pooling of these three genes in single reaction tube increased sensitivity (95.5%) and specificity (93.5%) of LAMP assay. SARS-CoV-2 positive specimens were screened further for Q57H mutation using ARMS-PCR. Based on amplicon size variation, later confirmed by sequencing, our data showed 18.5% samples positive for Q57H mutation. Hence, these findings strongly advocate use of RT-LAMP-based assay for SARS-CoV-2 screening within suspected general population. Furthermore, ARMS-PCR also provides an efficient mean to detect prevalent mutations against SARS-Cov-2.
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Affiliation(s)
- Maryam Nawab
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Syeda Kiran Riaz
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
- Department of Molecular Biology, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan
| | - Eiman Ismail
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Alfar Ahamed
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Aaysha Tariq
- Molecular Diagnostic Unit, Clinical Pathology Department, PAEC General Hospital, Islamabad, Pakistan
| | | | - Naeem F Qusty
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, PO Box 7607, Makkah, Al Abdeyah, Saudi Arabia
| | - Farkad Bantun
- Department of Microbiology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Petr Slama
- Laboratory of Animal Immunology and Biotechnology, Department of Animal Morphology, Physiology and Genetics, Faculty of AgriSciences, Mendel University in Brno, Brno, 61300, Czech Republic
| | - Massab Umair
- Department of Virology, National Institute of Health (NIH), Islamabad, Pakistan
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Health Sciences, Jazan University, Jazan, 45142, Saudi Arabia
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, 1102 2801, Lebanon
- Centre of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman, 13306, United Arab Emirates
| | | | - Alfonso J Rodriguez-Morales
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, 1102 2801, Lebanon
- Master Program on Clinical Epidemiology and Biostatistics, Faculty of Health Sciences, Universidad Científica del Sur, Lima, 15046, Peru
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12
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Wongchai T, Chuenchom N, Klayut W, Phetsuksiri B, Bhakdeenuan P, Bunchoo S, Srisungngam S, Rudeeaneksin J. Clinical Performance of the Reverse Transcription-Loop-Mediated Isothermal Amplification Assay for the Diagnosis of COVID-19 in a Thai Community Hospital at the Thailand-Myanmar Border. Cureus 2024; 16:e54447. [PMID: 38510857 PMCID: PMC10954319 DOI: 10.7759/cureus.54447] [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] [Accepted: 02/09/2024] [Indexed: 03/22/2024] Open
Abstract
INTRODUCTION Coronavirus disease 2019 (COVID-19) continues to be a global health threat and is a public health issue in Thailand and other countries. The extensive cross-border between Thailand and Myanmar is considered to be at a potentially high risk for COVID-19 distribution in this region. In this instance, simple and cost-effective tests for rapid and early detection of COVID-19 would be useful for effective patient management and control of the disease. METHODS This study was conducted at Mae Sot Hospital on the border of Thailand-Myanmar to evaluate the diagnostic performance of a simple colorimetric reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay developed recently for the rapid detection of SARS-CoV-2. Nasopharyngeal specimens were routinely collected and processed through automated nucleic acid extraction followed by real-time reverse transcription-polymerase chain reaction (rRT-PCR) using the Molaccu® COVID-19 Detection Kit. The RT-LAMP assay was further performed on remnant RNA samples, and the visual results were compared to those of rRT-PCR as a reference. RESULTS Of the 727 samples tested, the RT-LAMP assay could detect 322 out of 374 samples positive for SARS-CoV-2 by rRT-PCR with 100% (n = 353/353) negative agreement. The comparative analysis demonstrated the overall accuracy, sensitivity, specificity, positive predictive value, and negative predictive value of the RT-LAMP at 92.85% (n = 675/727, 95% CI: 90.73-94.61), 86.10% (n = 322/374, 95% CI: 82.17-89.44), 100% (n = 353/353, 95% CI: 98.96-100), 100% (n = 322/322, 95% CI: 98.86-100), and 87.16% (n = 353/405, 95% CI: 84.06-89.73), respectively. CONCLUSION This RT-LAMP assay showed good diagnostic performance in the hospital setting. It can increase laboratory capacity for rapid SARS-CoV-2 testing and has the potential for use as an alternative or a backup assay at the point of need, especially where alternatives are unavailable for any reason, such as a decline in COVID-19 cases.
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Affiliation(s)
- Thanee Wongchai
- Infectious Diseases, Mae Sot Hospital, Ministry of Public Health, Tak, THA
| | | | - Wiphat Klayut
- Infectious Diseases, National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, THA
| | - Benjawan Phetsuksiri
- Infectious Diseases, National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, THA
| | - Payu Bhakdeenuan
- Infectious Diseases, National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, THA
| | - Supranee Bunchoo
- Infectious Diseases, National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, THA
| | - Sopa Srisungngam
- Infectious Diseases, National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, THA
| | - Janisara Rudeeaneksin
- Infectious Diseases, National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, THA
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13
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Sen S, Bhowmik P, Tiwari S, Peleg Y, Bandyopadhyay B. Versatility of reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) from diagnosis of early pathological infection to mutation detection in organisms. Mol Biol Rep 2024; 51:211. [PMID: 38270670 DOI: 10.1007/s11033-023-09110-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 12/05/2023] [Indexed: 01/26/2024]
Abstract
Loop-mediated isothermal amplification (LAMP) is a rapid, state-of-the-art DNA amplification technology, used primarily for the quick diagnosis and early identification of microbial infection, caused by pathogens such as virus, bacteria and malaria. A target DNA can be amplified within 30 min using the LAMP reaction, taking place at a steady temperature. The LAMP method uses four or six primers to bind eight regions of a target DNA and has a very high specificity. The devices used for conducting LAMP are usually simple since the LAMP method is an isothermal process. When LAMP is coupled with Reverse Transcription (RT), it allows direct detection of RNA in a sample. This greatly enhances the efficiency of diagnosis of RNA viruses in a sample. Recently, the rampant spread of COVID-19 demanded such a rapid, simple, and cost-effective Point of Care Test (PoCT) for the accurate diagnosis of this pandemic. Loop-mediated isothermal amplification (LAMP) assays are not only used for the detection of microbial pathogens, but there are various other applications such as detection of genetic mutations in food and various organisms. In this review, various implementations of RT-LAMP techniques would be discussed.
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Affiliation(s)
- Srishti Sen
- School of Bioscience, Engineering and Technology, VIT Bhopal University, Bhopal, Madhya Pradesh, India
| | - Priyanka Bhowmik
- Department of Biological Sciences, School of Life Science and Biotechnology, Adamas University, Kolkata, India
| | - Shubhangi Tiwari
- School of Bioscience, Engineering and Technology, VIT Bhopal University, Bhopal, Madhya Pradesh, India
| | - Yoav Peleg
- Structural Proteomics Unit (SPU), Life Sciences Core Facilities (LSCF), Weizmann Institute of Science, Rehovot, Israel
| | - Boudhayan Bandyopadhyay
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, India.
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14
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Rioboó-Legaspi P, González-López A, Beltrán-Sánchez JF, Cima-Cabal MD, García-Suárez MM, Sánchez AJG, Fernández-Otero T, Haro JG, Costa-Rama E, Fernández-Abedul MT. Phenol red as electrochemical indicator for highly sensitive quantification of SARS-CoV-2 by loop-mediated isothermal amplification detection. Talanta 2024; 266:124963. [PMID: 37517341 DOI: 10.1016/j.talanta.2023.124963] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 07/14/2023] [Accepted: 07/16/2023] [Indexed: 08/01/2023]
Abstract
The current COVID-19 pandemic has made patent the need for rapid and cost-effective diagnostic tests, crucial for future infectious outbreaks. Loop-mediated isothermal amplification (LAMP) is a promising and decentralized alternative to qPCR. In this work we have developed a sensitive, fast, and simple innovative methodology for quantification of SARS-CoV-2 RNA copies, combining reverse-transcription LAMP with electrochemical detection. This is based on the oxidation of phenol red (PR), a visual and electroactive LAMP indicator, which oxidation peak potential (Ep) changes with the progress of the LAMP reaction. Using that Ep shift as analytical signal, a calibration curve was obtained for fragment N1 copies of SARS-CoV2 (which provided better results than N or S fragments), with a potential shift of 16.2 mV per order of magnitude, and a practical limit of detection of 21 copies·μL-1. Moreover, the precision of Ep is excellent (RSD < 2%): 557 ± 5 mV for negative and 602 ± 7 mV for positive (2148 N fragment RNA copies·µL-1·-1) LAMP controls. This methodology has been applied to the analysis of nasopharyngeal swab samples, resulting in total concordance with clinical RT-qPCR results. Advances towards fully decentralization have been achieved by designing and fabricating a small portable heater for isothermal procedures, obtaining comparable results to those from a commercial benchtop thermal cycler.
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Affiliation(s)
- P Rioboó-Legaspi
- Departamento de Química Física y Analítica, Facultad de Química, Universidad de Oviedo, Spain
| | - A González-López
- Departamento de Química Física y Analítica, Facultad de Química, Universidad de Oviedo, Spain
| | - J F Beltrán-Sánchez
- Departamento de Tecnologías de la Información y las Comunicaciones, Universidad Politécnica de Cartagena, Murcia, Spain
| | - M D Cima-Cabal
- Escuela Superior de Ingeniería y Tecnología, Universidad Internacional de La Rioja, Spain.
| | - M M García-Suárez
- Escuela Superior de Ingeniería y Tecnología, Universidad Internacional de La Rioja, Spain
| | - A J García Sánchez
- Departamento de Tecnologías de la Información y las Comunicaciones, Universidad Politécnica de Cartagena, Murcia, Spain
| | - T Fernández-Otero
- Departamento de Tecnologías de la Información y las Comunicaciones, Universidad Politécnica de Cartagena, Murcia, Spain
| | - J García Haro
- Departamento de Tecnologías de la Información y las Comunicaciones, Universidad Politécnica de Cartagena, Murcia, Spain
| | - E Costa-Rama
- Departamento de Química Física y Analítica, Facultad de Química, Universidad de Oviedo, Spain
| | - M T Fernández-Abedul
- Departamento de Química Física y Analítica, Facultad de Química, Universidad de Oviedo, Spain.
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15
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Kobayashi T, Tsuyuguchi K, Shimatani Y, Matsuda Y, Kagawa T, Takimoto T, Takeuchi N, Arai T, Inoue Y. Utility of a loop-mediated isothermal amplification detection kit to diagnose chronic pulmonary aspergillosis. J Infect Chemother 2024; 30:7-11. [PMID: 37660734 DOI: 10.1016/j.jiac.2023.08.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 08/27/2023] [Accepted: 08/30/2023] [Indexed: 09/05/2023]
Abstract
BACKGROUND Diagnosing chronic pulmonary aspergillosis (CPA) is still challenging, and infection with Aspergillus spp. must be detected early. The aim of this study was to evaluate, for the first time, the usefulness of a new loop-mediated isothermal amplification (LAMP) test kit in diagnosing CPA. METHODS This cross-sectional study was performed at the National Hospital Organization Kinki-Chuo Chest Medical Center. We prospectively enrolled patients with and without CPA. The primary outcomes of this study were the sensitivity and specificity of LAMP for the diagnosis of CPA. RESULTS In total, 34 patients with CPA and 21 without CPA (the control group) were enrolled between October 2019 and December 2021. Among the 34 patients with CPA, cultures were positive for CPA in 16 and negative for 18. The majority of fungi isolated in sputum were A. fumigatus in 15 specimens; Aspergillus flavus was isolated in 1) LAMP demonstrated 55.9% sensitivity (95% confidence interval [CI] 37.9-72.8) and 100.0% specificity (95% CI 77.2-100.0). CONCLUSION LAMP is an acceptable tool for diagnosing CPA, and its application in clinical practice necessitates more studies.
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Affiliation(s)
- Takehiko Kobayashi
- Clinical Research Center, National Hospital Organization, Kinki-Chuo Chest Medical Center, Sakai City, Osaka, Japan
| | - Kazunari Tsuyuguchi
- Clinical Research Center, National Hospital Organization, Kinki-Chuo Chest Medical Center, Sakai City, Osaka, Japan; Department of Internal Medicine, National Hospital Organization, Kinki-Chuo Chest Medical Center, Sakai City, Osaka, Japan.
| | - Yasuaki Shimatani
- Department of Clinical Microbiology, National Hospital Organization, Kinki-Chuo Chest Medical Center, Sakai City, Osaka, Japan
| | - Yoshinobu Matsuda
- Clinical Research Center, National Hospital Organization, Kinki-Chuo Chest Medical Center, Sakai City, Osaka, Japan; Department of Internal Medicine, National Hospital Organization, Kinki-Chuo Chest Medical Center, Sakai City, Osaka, Japan
| | - Tomoko Kagawa
- Department of Internal Medicine, National Hospital Organization, Kinki-Chuo Chest Medical Center, Sakai City, Osaka, Japan
| | - Takayuki Takimoto
- Department of Internal Medicine, National Hospital Organization, Kinki-Chuo Chest Medical Center, Sakai City, Osaka, Japan
| | - Naoko Takeuchi
- Department of Internal Medicine, National Hospital Organization, Kinki-Chuo Chest Medical Center, Sakai City, Osaka, Japan
| | - Toru Arai
- Clinical Research Center, National Hospital Organization, Kinki-Chuo Chest Medical Center, Sakai City, Osaka, Japan
| | - Yoshikazu Inoue
- Clinical Research Center, National Hospital Organization, Kinki-Chuo Chest Medical Center, Sakai City, Osaka, Japan
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16
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Biswas SK, Bairagi A, Nag S, Bandopadhyay A, Banerjee I, Mondal A, Chakraborty S. Nucleic acid based point-of-care diagnostic technology for infectious disease detection using machine learning empowered smartphone-interfaced quantitative colorimetry. Int J Biol Macromol 2023; 253:127137. [PMID: 37776929 DOI: 10.1016/j.ijbiomac.2023.127137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 09/26/2023] [Accepted: 09/27/2023] [Indexed: 10/02/2023]
Abstract
We report a nucleic acid-based point of care testing technology for infectious disease detection at resource limited settings by integrating a low-cost portable device with machine learning-empowered quantitative colorimetric analytics that can be interfaced via a smartphone application. We substantiate our proposition by demonstrating the efficacy of this technology in detecting COVID-19 infection from human swab samples, using the RT-LAMP protocol. Comparison with gold standard results from real-time PCR evidences high sensitivity and specificity, ensuring simplicity, portability, and user-friendliness of the technology at the same time. Colorimetric analytics of the reaction output without necessitating the opening of the reaction microchambers enables execution of the complete test workflow without any laboratory control that may otherwise be required stringently for safeguarding against carryover contamination. Seamless sample-to-answer workflow and machine learning-based readout further assures minimal human intervention for the test readout, thus eliminating inevitable inaccuracies stemming from erroneous execution of the test as well as subjectivity in interpreting the outcome. Our results further indicate the possibilities of upgrading the technology to predict the pathogenic load on the infected patients akin to the cyclic threshold value of the real-time PCR, when calibrated with reference to a wide range of 'training' data for the machine learner, thereby putting forward the same as viable alternative to the resource-intensive PCR tests that cannot be made readily accessible at underserved community settings.
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Affiliation(s)
- Sujay K Biswas
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Ankan Bairagi
- Department of Mechanical Engineering, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Sudip Nag
- Department of Mechanical Engineering, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Aditya Bandopadhyay
- Department of Mechanical Engineering, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Indranath Banerjee
- B.C. Roy Technology Hospital, Indian Institute of Technology Kharagpur, 721302, India
| | - Arindam Mondal
- School of Bioscience, Indian Institute of Technology Kharagpur, 721302, India
| | - Suman Chakraborty
- Department of Mechanical Engineering, Indian Institute of Technology Kharagpur, Kharagpur 721302, India.
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17
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Salazar-Ardiles C, Asserella-Rebollo L, Cornejo C, Arias D, Vasquez-Muñoz M, Toledo C, Andrade DC. Molecular diagnostic approaches for SARS-CoV-2 detection and pathophysiological consequences. Mol Biol Rep 2023; 50:10367-10382. [PMID: 37817022 DOI: 10.1007/s11033-023-08844-0] [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: 07/06/2023] [Accepted: 09/25/2023] [Indexed: 10/12/2023]
Abstract
SARS-CoV-2, a novel coronavirus within the Coronaviridae family, is the causative agent behind the respiratory ailment referred to as COVID-19. Operating on a global scale, COVID-19 has led to a substantial number of fatalities, exerting profound effects on both public health and the global economy. The most frequently reported symptoms encompass fever, cough, muscle or body aches, loss of taste or smell, headaches, and fatigue. Furthermore, a subset of individuals may manifest more severe symptoms, including those consistent with viral pneumonitis, which can be so profound as to result in fatalities. Consequently, this situation has spurred the rapid advancement of disease diagnostic technologies worldwide. Predominantly employed in diagnosing COVID-19, the real-time quantitative reverse transcription PCR has been the foremost diagnostic method, effectively detecting SARS-CoV-2 viral RNA. As the pandemic has evolved, antigen and serological tests have emerged as valuable diagnostic tools. Antigen tests pinpoint specific viral proteins of SARS-CoV-2, offering swift results, while serological tests identify the presence of antibodies in blood samples. Additionally, there have been notable strides in sample collection methods, notably with the introduction of saliva-based tests, presenting a non-invasive substitute to nasopharyngeal swabs. Given the ongoing mutations in SARS-CoV-2, there has been a continuous need for genomic surveillance, encompassing full genome sequencing and the identification of new variants through Illumina technology and, more recently, nanopore metagenomic sequencing (SMTN). Consequently, while diagnostic testing methods for COVID-19 have experienced remarkable progress, no test is flawless, and there exist limitations with each technique, including sensitivity, specificity, sample collection, and the minimum viral load necessary for accurate detection. These aspects are comprehensively addressed within this current review.
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Affiliation(s)
- Camila Salazar-Ardiles
- Exercise Applied Physiology Laboratory, Centro de Investigación en Fisiología y Medicina de Altura (FIMEDALT), Biomedical Department, Faculty of Health Sciences, Universidad de Antofagasta, Av. Universidad de Antofagasta #02800, Antofagasta, Chile
| | | | - Carlos Cornejo
- Exercise Applied Physiology Laboratory, Centro de Investigación en Fisiología y Medicina de Altura (FIMEDALT), Biomedical Department, Faculty of Health Sciences, Universidad de Antofagasta, Av. Universidad de Antofagasta #02800, Antofagasta, Chile
| | - Dayana Arias
- Exercise Applied Physiology Laboratory, Centro de Investigación en Fisiología y Medicina de Altura (FIMEDALT), Biomedical Department, Faculty of Health Sciences, Universidad de Antofagasta, Av. Universidad de Antofagasta #02800, Antofagasta, Chile
| | - Manuel Vasquez-Muñoz
- Dirección de Docencia de Especialidades Médicas, Dirección de Postgrado, Facultad de Medicina y Ciencias de la Salud, Universidad Mayor, Santiago, Chile
| | - Camilo Toledo
- Laboratory of Cardiorespiratory and Sleep Physiology, Institute of Physiology, Faculty of Medicine, Universidad Austral de Chile, Valdivia, Chile
| | - David C Andrade
- Exercise Applied Physiology Laboratory, Centro de Investigación en Fisiología y Medicina de Altura (FIMEDALT), Biomedical Department, Faculty of Health Sciences, Universidad de Antofagasta, Av. Universidad de Antofagasta #02800, Antofagasta, Chile.
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18
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Yigci D, Atçeken N, Yetisen AK, Tasoglu S. Loop-Mediated Isothermal Amplification-Integrated CRISPR Methods for Infectious Disease Diagnosis at Point of Care. ACS OMEGA 2023; 8:43357-43373. [PMID: 38027359 PMCID: PMC10666231 DOI: 10.1021/acsomega.3c04422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 09/26/2023] [Indexed: 12/01/2023]
Abstract
Infectious diseases continue to pose an imminent threat to global public health, leading to high numbers of deaths every year and disproportionately impacting developing countries where access to healthcare is limited. Biological, environmental, and social phenomena, including climate change, globalization, increased population density, and social inequity, contribute to the emergence of novel communicable diseases. Rapid and accurate diagnoses of infectious diseases are essential to preventing the transmission of infectious diseases. Although some commonly used diagnostic technologies provide highly sensitive and specific measurements, limitations including the requirement for complex equipment/infrastructure and refrigeration, the need for trained personnel, long sample processing times, and high cost remain unresolved. To ensure global access to affordable diagnostic methods, loop-mediated isothermal amplification (LAMP) integrated clustered regularly interspaced short palindromic repeat (CRISPR) based pathogen detection has emerged as a promising technology. Here, LAMP-integrated CRISPR-based nucleic acid detection methods are discussed in point-of-care (PoC) pathogen detection platforms, and current limitations and future directions are also identified.
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Affiliation(s)
- Defne Yigci
- School
of Medicine, Koç University, Istanbul 34450, Turkey
| | - Nazente Atçeken
- Koç
University Translational Medicine Research Center (KUTTAM), Koç University, Istanbul 34450, Turkey
| | - Ali K. Yetisen
- Department
of Chemical Engineering, Imperial College
London, London SW7 2AZ, U.K.
| | - Savas Tasoglu
- Koç
University Translational Medicine Research Center (KUTTAM), Koç University, Istanbul 34450, Turkey
- Boğaziçi
Institute of Biomedical Engineering, Boğaziçi
University, Istanbul 34684, Turkey
- Koç
University Arçelik Research Center for Creative Industries
(KUAR), Koç University, Istanbul 34450, Turkey
- Physical
Intelligence Department, Max Planck Institute
for Intelligent Systems, Stuttgart 70569, Germany
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19
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Park H, Kim DR, Shin A, Jeong E, Son S, Ahn JH, Ahn SY, Choi SJ, Oh SY, Chang YS, Kim YJ, Kang M. Loop-mediated isothermal amplification assay for screening congenital cytomegalovirus infection in newborns. Appl Microbiol Biotechnol 2023; 107:6789-6798. [PMID: 37725139 PMCID: PMC10589182 DOI: 10.1007/s00253-023-12771-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 08/17/2023] [Accepted: 09/02/2023] [Indexed: 09/21/2023]
Abstract
Congenital cytomegalovirus (CMV) infection is a common cause of sensorineural hearing loss and neurodevelopmental impairment in newborns. However, congenital CMV infection cannot be diagnosed using samples collected more than 3 weeks after birth because testing after this time cannot distinguish between congenital infection and postnatal infection. Herein, we developed a robust loop-mediated isothermal amplification (LAMP) assay for the large-scale screening of newborns for congenital CMV infection. In contrast to conventional quantitative polymerase chain reaction (qPCR), which detects CMV within a dynamic range of 1.0 × 106 to 1.0 × 102 copies/μL, our quantitative LAMP assay (qLAMP) detects CMV within a dynamic range of 1.1 × 108 to 1.1 × 103 copies/μL. Moreover, the turnaround time for obtaining results following DNA extraction is 90 min in qPCR but only 15 min in qLamp. The colorimetric LAMP assay can also detect CMV down to 1.1 × 103 copies/μL within 30 min, irrespective of the type of heat source. Our LAMP assay can be utilized in central laboratories as an alternative to conventional qPCR for quantitative CMV detection, or for point-of-care testing in low-resource environments, such as developing countries, via colorimetric naked-eye detection. KEY POINTS: • LAMP assay enables large-scale screening of newborns for congenital CMV infection. • LAMP allows colorimetric or quantitative detection of congenital CMV infection. • LAMP assay can be used as a point-of-care testing tool in low-resource environments.
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Affiliation(s)
- Hyeonseek Park
- Biomedical Engineering Research Center, Smart Healthcare Research Institute, Samsung Medical Center, Seoul, Republic of Korea
- Department of Medical Device Management and Research, Samsung Advanced Institute for Health Science & Technology, Sungkyunkwan University, Seoul, Republic of Korea
| | - Doo Ri Kim
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Areum Shin
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Eunjung Jeong
- Biomedical Engineering Research Center, Smart Healthcare Research Institute, Samsung Medical Center, Seoul, Republic of Korea
- Department of Medical Device Management and Research, Samsung Advanced Institute for Health Science & Technology, Sungkyunkwan University, Seoul, Republic of Korea
| | - Sohee Son
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Jin-Hyun Ahn
- Department of Microbiology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - So Yoon Ahn
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Suk-Joo Choi
- Department of Gynecology and Obstetrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Soo-Young Oh
- Department of Gynecology and Obstetrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Yun Sil Chang
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Yae-Jean Kim
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.
- Samsung Advanced Institute for Health Science & Technology, Sungkyunkwan University, Seoul, Republic of Korea.
| | - Minhee Kang
- Biomedical Engineering Research Center, Smart Healthcare Research Institute, Samsung Medical Center, Seoul, Republic of Korea.
- Department of Medical Device Management and Research, Samsung Advanced Institute for Health Science & Technology, Sungkyunkwan University, Seoul, Republic of Korea.
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20
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Taslimi Y, Habibzadeh S, Goyonlo VM, Akbarzadeh A, Azarpour Z, Gharibzadeh S, Shokouhy M, Persson J, Harandi AM, Mizbani A, Rafati S. Tape-disc-loop-mediated isothermal amplification (TD-LAMP) method as noninvasive approach for diagnosis of cutaneous leishmaniasis caused by L. tropica. Heliyon 2023; 9:e21397. [PMID: 38027876 PMCID: PMC10643283 DOI: 10.1016/j.heliyon.2023.e21397] [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: 06/08/2023] [Revised: 10/17/2023] [Accepted: 10/20/2023] [Indexed: 12/01/2023] Open
Abstract
Cutaneous leishmaniasis (CL) is a parasitic disease caused by the bite of infectious female sand flies with high socioeconomic burdens. There is currently no non-invasive, point-of-care, diagnostic method with high sensitivity and specificity available for CL. We herein report the development of a non-invasive tape disc (TD) sampling method combined with a loop-mediated isothermal amplification (LAMP) assay using primer sets targeting kinetoplast DNA (kDNA) of Leishmania tropica (L. tropica) with a colorimetric readout for species-specific diagnosis of CL. We tested our Tape-Disc (TD)-LAMP method on a panel of skin samples collected by TD from 35 confirmed L. tropica patients, 35 healthy individuals and 35 patients with non-L. tropica infections. The detection limit of the TD-LAMP assay was determined as 1 fg (fg), and the assay sensitivity and specificity of 97 % and 100 % for L. tropica infection, respectively. This non-invasive, sensitive and rapid diagnostic method warrants further exploration of its use for differential diagnosis of CL in disease endemic settings.
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Affiliation(s)
- Yasaman Taslimi
- Department of Immunotherapy and Leishmania Vaccine Research, Pasteur Institute of Iran, Tehran, Iran
| | - Sima Habibzadeh
- Department of Immunotherapy and Leishmania Vaccine Research, Pasteur Institute of Iran, Tehran, Iran
| | | | - Amin Akbarzadeh
- Cutaneous Leishmaniasis Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Zahra Azarpour
- Cutaneous Leishmaniasis Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Safoora Gharibzadeh
- Department of Epidemiology and Biostatistics, Pasteur Institute of Iran, Tehran, Iran
| | - Mehrdad Shokouhy
- Department of Immunotherapy and Leishmania Vaccine Research, Pasteur Institute of Iran, Tehran, Iran
| | - Josefine Persson
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Sweden
| | - Ali M. Harandi
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Sweden
- Vaccine Evaluation Center, BC Children's Hospital Research Institute, The University of British Columbia, Vancouver, Canada
| | | | - Sima Rafati
- Department of Immunotherapy and Leishmania Vaccine Research, Pasteur Institute of Iran, Tehran, Iran
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21
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Lim JW, Vu TTH, Le VP, Yeom M, Song D, Jeong DG, Park SK. Advanced Strategies for Developing Vaccines and Diagnostic Tools for African Swine Fever. Viruses 2023; 15:2169. [PMID: 38005846 PMCID: PMC10674204 DOI: 10.3390/v15112169] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 11/26/2023] Open
Abstract
African swine fever (ASF) is one of the most lethal infectious diseases affecting domestic pigs and wild boars of all ages. Over a span of 100 years, ASF has continued to spread over continents and adversely affects the global pig industry. To date, no vaccine or treatment has been approved. The complex genome structure and diverse variants facilitate the immune evasion of the ASF virus (ASFV). Recently, advanced technologies have been used to design various potential vaccine candidates and effective diagnostic tools. This review updates vaccine platforms that are currently being used worldwide, with a focus on genetically modified live attenuated vaccines, including an understanding of their potential efficacy and limitations of safety and stability. Furthermore, advanced ASFV detection technologies are presented that discuss and incorporate the challenges that remain to be addressed for conventional detection methods. We also highlight a nano-bio-based system that enhances sensitivity and specificity. A combination of prophylactic vaccines and point-of-care diagnostics can help effectively control the spread of ASFV.
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Affiliation(s)
- Jong-Woo Lim
- Department of Veterinary Medicine Virology Laboratory, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea; (J.-W.L.); (M.Y.); (D.S.)
| | - Thi Thu Hang Vu
- College of Pharmacy, Korea University, Sejong 30019, Republic of Korea;
| | - Van Phan Le
- Department of Veterinary Microbiology and Infectious Diseases, Faculty of Veterinary Medicine, Vietnam National University of Agriculture, Hanoi 131000, Vietnam;
| | - Minjoo Yeom
- Department of Veterinary Medicine Virology Laboratory, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea; (J.-W.L.); (M.Y.); (D.S.)
| | - Daesub Song
- Department of Veterinary Medicine Virology Laboratory, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea; (J.-W.L.); (M.Y.); (D.S.)
| | - Dae Gwin Jeong
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
- Bio-Analytical Science Division, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Song-Kyu Park
- College of Pharmacy, Korea University, Sejong 30019, Republic of Korea;
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22
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Rivas-Macho A, Eletxigerra U, Diez-Ahedo R, Barros Á, Merino S, Goñi-de-Cerio F, Olabarria G. Development of an Electrochemical Sensor for SARS-CoV-2 Detection Based on Loop-Mediated Isothermal Amplification. BIOSENSORS 2023; 13:924. [PMID: 37887117 PMCID: PMC10605850 DOI: 10.3390/bios13100924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 10/28/2023]
Abstract
The pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused more than 6 million deaths all over the world, demonstrating the need for a simple, fast and cost-effective point-of-care (POC) test for the detection of the virus. In this work, we developed an electrochemical sensor for SARS-CoV-2 virus detection on clinical samples based on loop-mediated isothermal amplification (LAMP). With the development of this novel sensor, the time of each measurement is significantly reduced by avoiding the DNA extraction step and replacing it with inactivation of the sample by heating it at 95 °C for 10 min. To make the reaction compatible with the sample pre-treatment, an RNase inhibitor was added directly to the premix. The LAMP product was measured in a novel, easy-to-use manufactured sensor containing a custom-made screen-printed carbon electrode. Electrochemical detection was performed with a portable potentiostat, and methylene blue was used as the redox-transducing molecule. The developed sensor achieved a limit of detection of 62 viral copies and was 100% specific for the detection of the SARS-CoV-2 virus. The performance of the electrochemical sensor was validated with nasopharyngeal samples, obtaining a sensibility and specificity of 100% compared to the gold standard RT-PCR method.
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Affiliation(s)
- Ane Rivas-Macho
- Gaiker, GAIKER Technology Centre, Basque Research and Technology Alliance, 48170 Zamudio, Spain
- Molecular Biology and Biomedicine PhD Program, University of the Basque Country UPV/EHU, 48940 Leioa, Spain
| | - Unai Eletxigerra
- Surface Chemistry and Nanotechnologies Unit, Tekniker, 20600 Eibar, Spain
| | - Ruth Diez-Ahedo
- Surface Chemistry and Nanotechnologies Unit, Tekniker, 20600 Eibar, Spain
| | - Ángela Barros
- Surface Chemistry and Nanotechnologies Unit, Tekniker, 20600 Eibar, Spain
| | - Santos Merino
- Surface Chemistry and Nanotechnologies Unit, Tekniker, 20600 Eibar, Spain
- Electricity and Electronics Department, University of the Basque Country UPV/EHU, 48940 Leioa, Spain
| | - Felipe Goñi-de-Cerio
- Gaiker, GAIKER Technology Centre, Basque Research and Technology Alliance, 48170 Zamudio, Spain
| | - Garbiñe Olabarria
- Gaiker, GAIKER Technology Centre, Basque Research and Technology Alliance, 48170 Zamudio, Spain
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23
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Rocchi A, Sariyer IK, Berger JR. Revisiting JC virus and progressive multifocal leukoencephalopathy. J Neurovirol 2023; 29:524-537. [PMID: 37659983 DOI: 10.1007/s13365-023-01164-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 07/10/2023] [Accepted: 07/27/2023] [Indexed: 09/04/2023]
Abstract
Since its definition 65 years ago, progressive multifocal leukoencephalopathy (PML) has continued to devastate a growing population of immunosuppressed patients despite major advances in our understanding of the causative JC virus (JCV). Unless contained by the immune system, JCV lyses host oligodendrocytes collateral to its life cycle, leading to demyelination, neurodegeneration, and death. Novel treatments have stagnated in the absence of an animal model while current antiviral agents fail to address the now ubiquitous polyomavirus. In this review, we highlight the established pathogenesis by which JCV infection progresses to PML, highlighting major challenges that must be overcome to eliminate the underlying virus and, therefore, the debilitating disease.
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Affiliation(s)
- Angela Rocchi
- Department of Microbiology, Immunology and Inflammation, Center for Neurovirology and Gene Editing, Temple University Lewis Katz School of Medicine, Philadelphia, PA, 19140, USA
| | - Ilker K Sariyer
- Department of Microbiology, Immunology and Inflammation, Center for Neurovirology and Gene Editing, Temple University Lewis Katz School of Medicine, Philadelphia, PA, 19140, USA.
| | - Joseph R Berger
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, 3400 Convention Avenue, Philadelphia, PA, 19104, USA.
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24
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Nguyen T, Vinayaka AC, Huynh VN, Linh QT, Andreasen SZ, Golabi M, Bang DD, Møller JK, Wolff A. PATHPOD - A loop-mediated isothermal amplification (LAMP)-based point-of-care system for rapid clinical detection of SARS-CoV-2 in hospitals in Denmark. SENSORS AND ACTUATORS. B, CHEMICAL 2023; 392:134085. [PMID: 37304211 PMCID: PMC10245468 DOI: 10.1016/j.snb.2023.134085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 05/19/2023] [Accepted: 06/03/2023] [Indexed: 06/13/2023]
Abstract
Sensitive and rapid detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been a vital goal in the ongoing COVID-19 pandemic. We present in this comprehensive work, for the first time, detailed fabrication and clinical validation of a point of care (PoC) device for rapid, onsite detection of SARS-CoV-2 using a real-time reverse-transcription loop-mediated isothermal amplification (RT-LAMP) reaction on a polymer cartridge. The PoC system, namely PATHPOD, consisting of a standalone device (weight less than 1.2 kg) and a cartridge, can perform the detection of 10 different samples and two controls in less than 50 min, which is much more rapid than the golden standard real-time reverse-transcription Polymerase Chain Reaction (RT-PCR), typically taking 16-48 h. The novel total internal reflection (TIR) scheme and the reactions inside the cartridge in the PoC device allow monitoring of the diagnostic results in real-time and onsite. The analytical sensitivity and specificity of the PoC test are comparable with the current RT-PCR, with a limit of detection (LOD) down to 30-50 viral genome copies. The robustness of the PATHPOD PoC system has been confirmed by analyzing 398 clinical samples initially examined in two hospitals in Denmark. The clinical sensitivity and specificity of these tests are discussed.
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Affiliation(s)
- Trieu Nguyen
- BioLabChip Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Aaydha Chidambara Vinayaka
- Laboratory of Applied Micro and Nanotechnology (LAMINATE), Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Van Ngoc Huynh
- BioLabChip Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Quyen Than Linh
- BioLabChip Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Sune Zoëga Andreasen
- BioLabChip Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Mohsen Golabi
- Laboratory of Applied Micro and Nanotechnology (LAMINATE), Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Dang Duong Bang
- Laboratory of Applied Micro and Nanotechnology (LAMINATE), Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Jens Kjølseth Møller
- Department of Clinical Microbiology, University Hospital of Southern Denmark, Vejle Hospital, Beriderbakken 4, DK-7100 Vejle, Denmark
| | - Anders Wolff
- BioLabChip Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
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25
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Poirier AC, Riaño Moreno RD, Takaindisa L, Carpenter J, Mehat JW, Haddon A, Rohaim MA, Williams C, Burkhart P, Conlon C, Wilson M, McClumpha M, Stedman A, Cordoni G, Branavan M, Tharmakulasingam M, Chaudhry NS, Locker N, Fernando A, Balachandran W, Bullen M, Collins N, Rimer D, Horton DL, Munir M, La Ragione RM. VIDIIA Hunter diagnostic platform: a low-cost, smartphone connected, artificial intelligence-assisted COVID-19 rapid diagnostics approved for medical use in the UK. Front Mol Biosci 2023; 10:1144001. [PMID: 37842636 PMCID: PMC10572354 DOI: 10.3389/fmolb.2023.1144001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 09/12/2023] [Indexed: 10/17/2023] Open
Abstract
Introduction: Accurate and rapid diagnostics paired with effective tracking and tracing systems are key to halting the spread of infectious diseases, limiting the emergence of new variants and to monitor vaccine efficacy. The current gold standard test (RT-qPCR) for COVID-19 is highly accurate and sensitive, but is time-consuming, and requires expensive specialised, lab-based equipment. Methods: Herein, we report on the development of a SARS-CoV-2 (COVID-19) rapid and inexpensive diagnostic platform that relies on a reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay and a portable smart diagnostic device. Automated image acquisition and an Artificial Intelligence (AI) deep learning model embedded in the Virus Hunter 6 (VH6) device allow to remove any subjectivity in the interpretation of results. The VH6 device is also linked to a smartphone companion application that registers patients for swab collection and manages the entire process, thus ensuring tests are traced and data securely stored. Results: Our designed AI-implemented diagnostic platform recognises the nucleocapsid protein gene of SARS-CoV-2 with high analytical sensitivity and specificity. A total of 752 NHS patient samples, 367 confirmed positives for coronavirus disease (COVID-19) and 385 negatives, were used for the development and validation of the test and the AI-assisted platform. The smart diagnostic platform was then used to test 150 positive clinical samples covering a dynamic range of clinically meaningful viral loads and 250 negative samples. When compared to RT-qPCR, our AI-assisted diagnostics platform was shown to be reliable, highly specific (100%) and sensitive (98-100% depending on viral load) with a limit of detection of 1.4 copies of RNA per µL in 30 min. Using this data, our CE-IVD and MHRA approved test and associated diagnostic platform has been approved for medical use in the United Kingdom under the UK Health Security Agency's Medical Devices (Coronavirus Test Device Approvals, CTDA) Regulations 2022. Laboratory and in-silico data presented here also indicates that the VIDIIA diagnostic platform is able to detect the main variants of concern in the United Kingdom (September 2023). Discussion: This system could provide an efficient, time and cost-effective platform to diagnose SARS-CoV-2 and other infectious diseases in resource-limited settings.
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Affiliation(s)
- Aurore C. Poirier
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, University of Surrey, Guildford, United Kingdom
| | | | - Leona Takaindisa
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, University of Surrey, Guildford, United Kingdom
| | - Jessie Carpenter
- VIDIIA Ltd., Surrey Technology Centre, Guildford, United Kingdom
| | - Jai W. Mehat
- Department of Microbial Sciences, School of Biosciences, University of Surrey, Guildford, United Kingdom
| | - Abi Haddon
- Berkshire and Surrey Pathology Services, Molecular Diagnostics, Royal Surrey County Hospital, Guildford, United Kingdom
| | - Mohammed A. Rohaim
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, The Lancaster University, Lancaster, United Kingdom
| | - Craig Williams
- The Royal Lancaster Infirmary, University Hospitals of Morecambe Bay NHS Foundation Trust, Kendal, United Kingdom
| | - Peter Burkhart
- The Royal Lancaster Infirmary, University Hospitals of Morecambe Bay NHS Foundation Trust, Kendal, United Kingdom
| | - Chris Conlon
- GB Electronics (UK) Ltd, Worthing, United Kingdom
| | | | | | - Anna Stedman
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, University of Surrey, Guildford, United Kingdom
| | - Guido Cordoni
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, University of Surrey, Guildford, United Kingdom
| | - Manoharanehru Branavan
- College of Engineering, Design and Physical Sciences, Brunel University London, Uxbridge, United Kingdom
| | | | - Nouman S. Chaudhry
- Centre for Vision, Speech and Signal Processing, University of Surrey, Guildford, United Kingdom
| | - Nicolas Locker
- Department of Microbial Sciences, School of Biosciences, University of Surrey, Guildford, United Kingdom
| | - Anil Fernando
- Centre for Vision, Speech and Signal Processing, University of Surrey, Guildford, United Kingdom
| | - Wamadeva Balachandran
- College of Engineering, Design and Physical Sciences, Brunel University London, Uxbridge, United Kingdom
| | - Mark Bullen
- GB Electronics (UK) Ltd, Worthing, United Kingdom
| | - Nadine Collins
- Berkshire and Surrey Pathology Services, Molecular Diagnostics, Royal Surrey County Hospital, Guildford, United Kingdom
| | - David Rimer
- VIDIIA Ltd., Surrey Technology Centre, Guildford, United Kingdom
| | - Daniel L. Horton
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, University of Surrey, Guildford, United Kingdom
| | - Muhammad Munir
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, The Lancaster University, Lancaster, United Kingdom
| | - Roberto M. La Ragione
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, University of Surrey, Guildford, United Kingdom
- Department of Microbial Sciences, School of Biosciences, University of Surrey, Guildford, United Kingdom
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26
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Jiang L, Lan X, Ren L, Jin Z, Shan X, Yang M, Chang L. Single-molecule RNA capture-assisted droplet digital loop-mediated isothermal amplification for ultrasensitive and rapid detection of infectious pathogens. MICROSYSTEMS & NANOENGINEERING 2023; 9:118. [PMID: 37767528 PMCID: PMC10519972 DOI: 10.1038/s41378-023-00576-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/27/2023] [Accepted: 06/16/2023] [Indexed: 09/29/2023]
Abstract
To minimize and control the transmission of infectious diseases, a sensitive, accurate, rapid, and robust assay strategy for application on-site screening is critical. Here, we report single-molecule RNA capture-assisted digital RT-LAMP (SCADL) for point-of-care testing of infectious diseases. Target RNA was captured and enriched by specific capture probes and oligonucleotide probes conjugated to magnetic beads, replacing laborious RNA extraction. Droplet generation, amplification, and the recording of results are all integrated on a microfluidic chip. In assaying commercial standard samples, quantitative results precisely corresponded to the actual concentration of samples. This method provides a limit of detection of 10 copies mL-1 for the N gene within 1 h, greatly reducing the need for skilled personnel and precision instruments. The ultrasensitivity, specificity, portability, rapidity and user-friendliness make SCADL a competitive candidate for the on-site screening of infectious diseases.
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Affiliation(s)
- Liying Jiang
- School of Electrical and Information Engineering, Zhengzhou University of Light Industry, 450002 Zhengzhou, China
- Academy for Quantum Science and Technology, Zhengzhou University of Light Industry, 450002 Zhengzhou, China
| | - Xianghao Lan
- School of Electrical and Information Engineering, Zhengzhou University of Light Industry, 450002 Zhengzhou, China
| | - Linjiao Ren
- School of Electrical and Information Engineering, Zhengzhou University of Light Industry, 450002 Zhengzhou, China
| | - Zhiyuan Jin
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, 100191 Beijing, China
| | - Xuchen Shan
- School of Physics, Beihang University, 100191 Beijing, China
| | - Mingzhu Yang
- Beijing Research Institute of Mechanical Equipment, 100143 Beijing, China
| | - Lingqian Chang
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, 100191 Beijing, China
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27
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Hongjaisee S, Kham-Kjing N, Musikul P, Daengkaokhew W, Kongson N, Guntala R, Jaiyapan N, Kline E, Panpradist N, Ngo-Giang-Huong N, Khamduang W. A Single-Tube Colorimetric Loop-Mediated Isothermal Amplification for Rapid Detection of SARS-CoV-2 RNA. Diagnostics (Basel) 2023; 13:3040. [PMID: 37835783 PMCID: PMC10572433 DOI: 10.3390/diagnostics13193040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/21/2023] [Accepted: 09/23/2023] [Indexed: 10/15/2023] Open
Abstract
Since SARS-CoV-2 is a highly transmissible virus, a rapid and accurate diagnostic method is necessary to prevent virus spread. We aimed to develop and evaluate a new rapid colorimetric reverse transcription loop--mediated isothermal amplification (RT-LAMP) assay for SARS-CoV-2 detection in a single closed tube. Nasopharyngeal and throat swabs collected from at-risk individuals testing for SARS-CoV-2 were used to assess the sensitivity and specificity of a new RT-LAMP assay against a commercial qRT-PCR assay. Total RNA extracts were submitted to the RT-LAMP reaction under optimal conditions and amplified at 65 °C for 30 min using three sets of specific primers targeting the nucleocapsid gene. The reaction was detected using two different indicator dyes, hydroxynaphthol blue (HNB) and cresol red. A total of 82 samples were used for detection with HNB and 94 samples with cresol red, and results were compared with the qRT-PCR assay. The sensitivity of the RT-LAMP-based HNB assay was 92.1% and the specificity was 93.2%. The sensitivity of the RT-LAMP-based cresol red assay was 80.3%, and the specificity was 97%. This colorimetric feature makes this assay highly accessible, low-cost, and user-friendly, which can be deployed for massive scale-up and rapid diagnosis of SARS-CoV-2 infection, particularly in low-resource settings.
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Affiliation(s)
- Sayamon Hongjaisee
- Research Institute for Health Sciences, Chiang Mai University, Chiang Mai 50200, Thailand;
- LUCENT International Collaboration, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; (N.K.-K.); (N.P.); (N.N.-G.-H.)
| | - Nang Kham-Kjing
- LUCENT International Collaboration, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; (N.K.-K.); (N.P.); (N.N.-G.-H.)
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; (P.M.); (W.D.); (N.K.); (N.J.)
| | - Piyagorn Musikul
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; (P.M.); (W.D.); (N.K.); (N.J.)
| | - Wannaporn Daengkaokhew
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; (P.M.); (W.D.); (N.K.); (N.J.)
| | - Nuntita Kongson
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; (P.M.); (W.D.); (N.K.); (N.J.)
| | | | - Nitipoom Jaiyapan
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; (P.M.); (W.D.); (N.K.); (N.J.)
| | - Enos Kline
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA;
| | - Nuttada Panpradist
- LUCENT International Collaboration, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; (N.K.-K.); (N.P.); (N.N.-G.-H.)
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA;
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
| | - Nicole Ngo-Giang-Huong
- LUCENT International Collaboration, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; (N.K.-K.); (N.P.); (N.N.-G.-H.)
- Maladies Infectieuses et Vecteurs: Écologie, Génétique, Évolution et Contrôle (MIVEGEC), Agropolis University Montpellier, Centre National de la Recherche Scientifique (CNRS), Institut de Recherche Pour le Développement (IRD), 34394 Montpellier, France
- International Joint Laboratory PRESTO, Chiang Mai 50200, Thailand
| | - Woottichai Khamduang
- LUCENT International Collaboration, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; (N.K.-K.); (N.P.); (N.N.-G.-H.)
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; (P.M.); (W.D.); (N.K.); (N.J.)
- International Joint Laboratory PRESTO, Chiang Mai 50200, Thailand
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28
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Werbajh S, Larocca L, Carrillo C, Stolowicz F, Ogas L, Pallotto S, Cassará S, Mammana L, Zapiola I, Bouzas MB, Vojnov AA. Colorimetric RT-LAMP Detection of Multiple SARS-CoV-2 Variants and Lineages of Concern Direct from Nasopharyngeal Swab Samples without RNA Isolation. Viruses 2023; 15:1910. [PMID: 37766315 PMCID: PMC10537693 DOI: 10.3390/v15091910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/31/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Since, during the Coronavirus disease 19 (COVID-19) pandemic, a large part of the human population has become infected, a rapid and simple diagnostic method has been necessary to detect its causative agent, the Severe Acute Respiratory Syndrome-related Coronavirus-2 (SARS-CoV-2), and control its spread. Thus, in the present study, we developed a colorimetric reverse transcription-loop-mediated isothermal amplification (RT-LAMP) kit that allows the detection of SARS-CoV-2 from nasopharyngeal swab samples without the need for RNA extraction. The kit utilizes three sets of LAMP primers targeting two regions of ORF1ab and one region in the E gene. The results are based on the colorimetric change of hydroxynaphthol blue, which allows visual interpretation without needing an expensive instrument. The kit demonstrated sensitivity to detect between 50 and 100 copies of the viral genome per reaction. The kit was authorized by the National Administration of Drugs, Food and Technology (ANMAT) of Argentina after validation using samples previously analyzed by the gold standard RT-qPCR. The results showed a sensitivity of 90.6% and specificity of 100%, consistent with conventional RT-qPCR. In silico analysis confirmed the recognition of SARS-CoV-2 variants of concern (B.1.1.7, B.1.351, P.1, B.1.617.2, B.1.427, and B.1.429), and lineages of the Omicron variant (B.1.1.529) with 100% homology. This rapid, simple, and sensitive RT-LAMP method paves the way for a large screening strategy to be carried out at locations lacking sophisticated instrumental and trained staff, as it particularly happens in regional hospitals and medical centers from rural areas.
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Affiliation(s)
- Santiago Werbajh
- Instituto de Ciencia y Tecnología Dr. César Milstein, Fundación Pablo Cassará, CONICET. Saladillo 2468, Buenos Aires C1440FFX, Argentina (C.C.); (S.C.)
| | - Luciana Larocca
- Instituto de Ciencia y Tecnología Dr. César Milstein, Fundación Pablo Cassará, CONICET. Saladillo 2468, Buenos Aires C1440FFX, Argentina (C.C.); (S.C.)
| | - Carolina Carrillo
- Instituto de Ciencia y Tecnología Dr. César Milstein, Fundación Pablo Cassará, CONICET. Saladillo 2468, Buenos Aires C1440FFX, Argentina (C.C.); (S.C.)
| | - Fabiana Stolowicz
- Instituto de Ciencia y Tecnología Dr. César Milstein, Fundación Pablo Cassará, CONICET. Saladillo 2468, Buenos Aires C1440FFX, Argentina (C.C.); (S.C.)
| | - Lorena Ogas
- Instituto de Ciencia y Tecnología Dr. César Milstein, Fundación Pablo Cassará, CONICET. Saladillo 2468, Buenos Aires C1440FFX, Argentina (C.C.); (S.C.)
| | - Sergio Pallotto
- Laboratorio Pablo Cassará S.R.L. Saladillo 2452, Buenos Aires C1440FFX, Argentina
| | - Solange Cassará
- Instituto de Ciencia y Tecnología Dr. César Milstein, Fundación Pablo Cassará, CONICET. Saladillo 2468, Buenos Aires C1440FFX, Argentina (C.C.); (S.C.)
| | - Liliana Mammana
- Sección Virología, Hospital de Enfermedades Infecciosas Francisco Javier Muñiz Uspallata 2272, Buenos Aires C1282AEN, Argentina (I.Z.); (M.B.B.)
| | - Inés Zapiola
- Sección Virología, Hospital de Enfermedades Infecciosas Francisco Javier Muñiz Uspallata 2272, Buenos Aires C1282AEN, Argentina (I.Z.); (M.B.B.)
| | - María Belén Bouzas
- Sección Virología, Hospital de Enfermedades Infecciosas Francisco Javier Muñiz Uspallata 2272, Buenos Aires C1282AEN, Argentina (I.Z.); (M.B.B.)
| | - Adrian A. Vojnov
- Instituto de Ciencia y Tecnología Dr. César Milstein, Fundación Pablo Cassará, CONICET. Saladillo 2468, Buenos Aires C1440FFX, Argentina (C.C.); (S.C.)
- Facultad de Medicina-Universidad del Salvador, Av. Córdoba 1601, Buenos Aires C1055AAG, Argentina
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Kubo T, Kanao E, Ishida K, Minami S, Tanigawa T, Mizuta R, Sasaki Y, Otsuka K, Kobayashi T. Efficient Selective Adsorption of SARS-CoV-2 via the Recognition of Spike Proteins Using an Affinity Spongy Monolith. Anal Chem 2023; 95:13185-13190. [PMID: 37610704 DOI: 10.1021/acs.analchem.3c02097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Since the outbreak of COVID-19, SARS-CoV-2, the infection has been spreading to date. The rate of false-negative result on a polymerase chain reaction (PCR) test considered the gold standard is roughly 20%. Therefore, its accuracy poses a question as well as needs improvement in the test. This study reports fabrication of a substrate of an anti-spike protein (AS)-immobilized porous material having selective adsorption toward a spike protein protruding from the surface of SARS-CoV-2. We have employed an organic polymer substrate called spongy monolith (SPM). The SPM has through-pores of about 10 μm and is adequate for flowing liquid containing virus particles. It also involves an epoxy group on the surface, enabling arbitrary proteins such as antibodies to immobilize. When antibodies of the spike protein toward receptor binding domain were immobilized, selective adsorption of the spike protein was observed. At the same time, when mixed analytes of spike proteins, lysozymes and amylases, were flowed into an AS-SPM, selective adsorption toward the spike proteins was observed. Then, SARS-CoV-2 was flowed into the BSA-SPM or AS-SPM, amounts of SARS-CoV-2 adsorption toward the AS-SPM were much larger compared to the ones toward the BSA-SPM. Furthermore, rotavirus was not adsorbed to the AS-SPM at all. These results show that the AS-SPM recognizes selectively the spike proteins of SARS-CoV-2 and may be possible applications for the purification and concentration of SARS-CoV-2.
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Affiliation(s)
- Takuya Kubo
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Eisuke Kanao
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
- National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Ibaraki 567-0085, Japan
| | - Koki Ishida
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Shohei Minami
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Tetsuya Tanigawa
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Ryosuke Mizuta
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-Ko, Kyoto 615-8510, Japan
| | - Yoshihiro Sasaki
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-Ko, Kyoto 615-8510, Japan
| | - Koji Otsuka
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Takeshi Kobayashi
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
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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: 2] [Impact Index Per Article: 2.0] [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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31
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Fu Q, Pang X, Su Z, Yang Y, Liu Y, Zhang Z, Fu Y, Wang J, Zhou J. Rapid On-Site Detection of SARS-CoV-2 Using RT-LAMP Assay with a Portable Low-Cost Device. BIOSENSORS 2023; 13:724. [PMID: 37504122 PMCID: PMC10377351 DOI: 10.3390/bios13070724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/03/2023] [Accepted: 07/09/2023] [Indexed: 07/29/2023]
Abstract
Emerging infectious diseases pose a serious threat to human health and affect social stability. In recent years, the epidemic situation of emerging infectious diseases is very serious; among these infectious diseases, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has affected many countries and regions in a short time. The prevention and treatment of these diseases require rapid on-site detection methods. However, the common detection method, RT-PCR, requires expensive instruments, complex operations, and professional operators. Here, we developed a portable low-cost assay for rapid on-site detection of viral nucleic acid using reverse transcription-loop-mediated isothermal amplification (RT-LAMP). The SARS-CoV-2 RNA can be successfully amplified within 15 min in a thermos, and the detection result is read rapidly in a portable low-cost device with a sensitivity of 100 copies/µL. The portable low-cost device consists of a black box, a laser or LED and a filter, costing only a few cents. The rapid on-site detection method can provide strong support for the control of biological threats such as infectious diseases. It is also an emergency detection method for low-resource settings, relieving the huge pressure on health care.
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Affiliation(s)
- Quanying Fu
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Xueyuan Pang
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Zhenning Su
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Yuxiao Yang
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Yiren Liu
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Ziyue Zhang
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Yuqiu Fu
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Jiasi Wang
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Jianhua Zhou
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Sun Yat-sen University, Guangzhou 510275, China
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Iijima T, Sakai J, Kanamori D, Ando S, Nomura T, Tisi L, Kilgore PE, Percy N, Kohase H, Hayakawa S, Maesaki S, Hoshino T, Seki M. A New Method to Detect Variants of SARS-CoV-2 Using Reverse Transcription Loop-Mediated Isothermal Amplification Combined with a Bioluminescent Assay in Real Time (RT-LAMP-BART). Int J Mol Sci 2023; 24:10698. [PMID: 37445876 DOI: 10.3390/ijms241310698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/22/2023] [Accepted: 06/22/2023] [Indexed: 07/15/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), of which there are several variants. The three major variants (Alpha, Delta, and Omicron) carry the N501Y, L452R, and Q493R/Q498R mutations, respectively, in the S gene. Control of COVID-19 requires rapid and reliable detection of not only SARS-CoV-2 but also its variants. We previously developed a reverse transcription loop-mediated isothermal amplification assay combined with a bioluminescent assay in real time (RT-LAMP-BART) to detect the L452R mutation in the SARS-CoV-2 spike protein. In this study, we established LAMP primers and peptide nucleic acid probes to detect N501Y and Q493R/Q498R. The LAMP primer sets and PNA probes were designed for the N501Y and Q493R/Q498R mutations on the S gene of SARS-CoV-2. The specificities of RT-LAMP-BART assays were evaluated using five viral and four bacterial reference strains. The sensitivities of RT-LAMP-BART assays were evaluated using synthetic RNAs that included the target sequences, together with RNA-spiked clinical nasopharyngeal and salivary specimens. The results were compared with those of conventional real-time reverse transcription-polymerase chain reaction (RT-PCR) methods. The method correctly identified N501Y and Q493R/Q498R. Within 30 min, the RT-LAMP-BART assays detected up to 100-200 copies of the target genes; conventional real-time RT-PCR required 130 min and detected up to 500-3000 copies. Surprisingly, the real-time RT-PCR for N501Y did not detect the BA.1 and BA.2 variants (Omicron) that exhibited the N501Y mutation. The novel RT-LAMP-BART assay is highly specific and more sensitive than conventional real-time RT-PCR. The new assay is simple, inexpensive, and rapid; thus, it can be useful in efforts to identify SARS-CoV-2 variants of concern.
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Affiliation(s)
- Takahiro Iijima
- Division of Pediatric Dentistry, Department of Human Development and Fostering, Meikai University School of Dentistry, Sakado 350-0283, Japan
| | - Jun Sakai
- Department of Infectious Disease and Infection Control, Saitama Medical University, Moroyama 350-8550, Japan
| | - Dai Kanamori
- Division of Pediatric Dentistry, Department of Human Development and Fostering, Meikai University School of Dentistry, Sakado 350-0283, Japan
| | - Shinnosuke Ando
- Division of Dental Anesthesiology, Department of Diagnostic and Therapeutic Sciences, Meikai University School of Dentistry, Sakado 350-0248, Japan
| | - Tsutomu Nomura
- Division of Otolaryngology, Department of Comprehensive Medical Sciences, Meikai University School of Dentistry, Sakado 350-0248, Japan
| | | | - Paul E Kilgore
- Department of Pharmacy Practice, Eugene Applebaum College of Pharmacy & Health Sciences, Wayne State University, Detroit, MI 48201, USA
| | | | - Hikaru Kohase
- Division of Dental Anesthesiology, Department of Diagnostic and Therapeutic Sciences, Meikai University School of Dentistry, Sakado 350-0248, Japan
| | - Satoshi Hayakawa
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo 113-8602, Japan
| | - Shigefumi Maesaki
- Department of Infectious Disease and Infection Control, Saitama Medical University, Moroyama 350-8550, Japan
| | - Tomonori Hoshino
- Division of Pediatric Dentistry, Department of Human Development and Fostering, Meikai University School of Dentistry, Sakado 350-0283, Japan
| | - Mitsuko Seki
- Division of Pediatric Dentistry, Department of Human Development and Fostering, Meikai University School of Dentistry, Sakado 350-0283, Japan
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo 113-8602, Japan
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Ciannella S, González-Fernández C, Gomez-Pastora J. Recent progress on wastewater-based epidemiology for COVID-19 surveillance: A systematic review of analytical procedures and epidemiological modeling. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 878:162953. [PMID: 36948304 PMCID: PMC10028212 DOI: 10.1016/j.scitotenv.2023.162953] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/13/2023] [Accepted: 03/15/2023] [Indexed: 05/13/2023]
Abstract
On March 11, 2020, the World Health Organization declared the coronavirus disease 2019 (COVID-19), whose causative agent is the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), a pandemic. This virus is predominantly transmitted via respiratory droplets and shed via sputum, saliva, urine, and stool. Wastewater-based epidemiology (WBE) has been able to monitor the circulation of viral pathogens in the population. This tool demands both in-lab and computational work to be meaningful for, among other purposes, the prediction of outbreaks. In this context, we present a systematic review that organizes and discusses laboratory procedures for SARS-CoV-2 RNA quantification from a wastewater matrix, along with modeling techniques applied to the development of WBE for COVID-19 surveillance. The goal of this review is to present the current panorama of WBE operational aspects as well as to identify current challenges related to it. Our review was conducted in a reproducible manner by following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines for systematic reviews. We identified a lack of standardization in wastewater analytical procedures. Regardless, the reverse transcription-quantitative polymerase chain reaction (RT-qPCR) approach was the most reported technique employed to detect and quantify viral RNA in wastewater samples. As a more convenient sample matrix, we suggest the solid portion of wastewater to be considered in future investigations due to its higher viral load compared to the liquid fraction. Regarding the epidemiological modeling, the data-driven approach was consistently used for the prediction of variables associated with outbreaks. Future efforts should also be directed toward the development of rapid, more economical, portable, and accurate detection devices.
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Affiliation(s)
- Stefano Ciannella
- Department of Chemical Engineering, Texas Tech University, Lubbock 79409, TX, USA.
| | - Cristina González-Fernández
- Department of Chemical Engineering, Texas Tech University, Lubbock 79409, TX, USA; Departamento de Ingenierías Química y Biomolecular, Universidad de Cantabria, Avda. Los Castros, s/n, 39005 Santander, Spain.
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Silva SJRD, Kohl A, Pena L, Pardee K. Clinical and laboratory diagnosis of monkeypox (mpox): Current status and future directions. iScience 2023; 26:106759. [PMID: 37206155 PMCID: PMC10183700 DOI: 10.1016/j.isci.2023.106759] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023] Open
Abstract
The emergence and rapid spread of the monkeypox virus (MPXV) to non-endemic countries has brought this once obscure pathogen to the forefront of global public health. Given the range of conditions that cause similar skin lesions, and because the clinical manifestation may often be atypical in the current mpox outbreak, it can be challenging to diagnose patients based on clinical signs and symptoms. With this perspective in mind, laboratory-based diagnosis assumes a critical role for the clinical management, along with the implementation of countermeasures. Here, we review the clinical features reported in mpox patients, the available laboratory tests for mpox diagnosis, and discuss the principles, advances, advantages, and drawbacks of each assay. We also highlight the diagnostic platforms with the potential to guide ongoing clinical response, particularly those that increase diagnostic capacity in low- and middle-income countries. With the outlook of this evolving research area, we hope to provide a resource to the community and inspire more research and the development of diagnostic alternatives with applications to this and future public health crises.
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Affiliation(s)
| | - Alain Kohl
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Lindomar Pena
- Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
| | - Keith Pardee
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto ON M5S 3M2, Canada
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto ON M5S 3G8, Canada
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35
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Tang YN, Jiang D, Wang X, Liu Y, Wei D. Recent progress on rapid diagnosis of COVID-19 by point-of-care testing platforms. CHINESE CHEM LETT 2023:108688. [PMID: 37362324 PMCID: PMC10266891 DOI: 10.1016/j.cclet.2023.108688] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 05/25/2023] [Accepted: 06/12/2023] [Indexed: 06/28/2023]
Abstract
The outbreak of COVID-19 has drawn great attention around the world. SARS-CoV-2 is a highly infectious virus with occult transmission by many mutations and a long incubation period. In particular, the emergence of asymptomatic infections has made the epidemic even more severe. Therefore, early diagnosis and timely management of suspected cases are essential measures to control the spread of the virus. Developing simple, portable, and accurate diagnostic techniques for SARS-CoV-2 is the key to epidemic prevention. The advantages of point-of-care testing technology make it play an increasingly important role in viral detection and screening. This review summarizes the point-of-care testing platforms developed by nucleic acid detection, immunological detection, and nanomaterial-based biosensors detection. Furthermore, this paper provides a prospect for designing future highly accurate, cheap, and convenient SARS-CoV-2 diagnostic technology.
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Affiliation(s)
- Ya-Nan Tang
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200433, China
- Institute of Molecular Materials and Devices, Fudan University, Shanghai 200433, China
| | - Dingding Jiang
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200433, China
- Institute of Molecular Materials and Devices, Fudan University, Shanghai 200433, China
| | - Xuejun Wang
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200433, China
- Institute of Molecular Materials and Devices, Fudan University, Shanghai 200433, China
| | - Yunqi Liu
- Institute of Molecular Materials and Devices, Fudan University, Shanghai 200433, China
| | - Dacheng Wei
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200433, China
- Institute of Molecular Materials and Devices, Fudan University, Shanghai 200433, China
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36
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Dong T, Wang M, Liu J, Ma P, Pang S, Liu W, Liu A. Diagnostics and analysis of SARS-CoV-2: current status, recent advances, challenges and perspectives. Chem Sci 2023; 14:6149-6206. [PMID: 37325147 PMCID: PMC10266450 DOI: 10.1039/d2sc06665c] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 05/03/2023] [Indexed: 06/17/2023] Open
Abstract
The disastrous spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has induced severe public healthcare issues and weakened the global economy significantly. Although SARS-CoV-2 infection is not as fatal as the initial outbreak, many infected victims suffer from long COVID. Therefore, rapid and large-scale testing is critical in managing patients and alleviating its transmission. Herein, we review the recent advances in techniques to detect SARS-CoV-2. The sensing principles are detailed together with their application domains and analytical performances. In addition, the advantages and limits of each method are discussed and analyzed. Besides molecular diagnostics and antigen and antibody tests, we also review neutralizing antibodies and emerging SARS-CoV-2 variants. Further, the characteristics of the mutational locations in the different variants with epidemiological features are summarized. Finally, the challenges and possible strategies are prospected to develop new assays to meet different diagnostic needs. Thus, this comprehensive and systematic review of SARS-CoV-2 detection technologies may provide insightful guidance and direction for developing tools for the diagnosis and analysis of SARS-CoV-2 to support public healthcare and effective long-term pandemic management and control.
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Affiliation(s)
- Tao Dong
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
- School of Pharmacy, Medical College, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Mingyang Wang
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Junchong Liu
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Pengxin Ma
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Shuang Pang
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Wanjian Liu
- Qingdao Hightop Biotech Co., Ltd 369 Hedong Road, Hi-tech Industrial Development Zone Qingdao 266112 China
| | - Aihua Liu
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
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Kallem P, Hegab H, Alsafar H, Hasan SW, Banat F. SARS-CoV-2 detection and inactivation in water and wastewater: Review on analytical methods, limitations and future research recommendations. Emerg Microbes Infect 2023:2222850. [PMID: 37279167 DOI: 10.1080/22221751.2023.2222850] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been detected in wastewater. Wastewater-based epidemiology (WBE) is a practical and cost-effective tool for the assessment and controlling of pandemics and probably for examining SARS-CoV-2 presence. Implementation of WBE during the outbreaks is not without limitations. Temperature, suspended solids, pH, and disinfectants affect the stability of viruses in wastewater. Due to these limitations, instruments and techniques have been utilized to detect SARS-CoV-2. SARS-CoV-2 has been detected in sewage using various concentration methods and computer-aided analyzes. RT-qPCR, ddRT-PCR, multiplex PCR, RT-LAMP, and electrochemical immunosensors have been employed to detect low levels of viral contamination. Inactivation of SARS-CoV-2 is a crucial preventive measure against coronavirus disease 2019 (COVID-19). To better assess the role of wastewater as a transmission route, detection, and quantification methods need to be refined. In this paper, the latest improvements in quantification, detection, and inactivation of SARS-CoV-2 in wastewater are explained. Finally, limitations and future research recommendations are thoroughly described.
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Affiliation(s)
- Parashuram Kallem
- Center for Membranes and Advanced Water Technology (CMAT), Khalifa University of Science and Technology, PO Box 127788, Abu Dhabi, United Arab Emirates
- Department of Chemical Engineering, Khalifa University of Science and Technology, PO Box 127788, Abu Dhabi, United Arab Emirates
- Environmental Health and Safety Program, College of Health Sciences, Abu Dhabi University, Abu Dhabi P.O. Box 59911, United Arab Emirates
| | - Hanaa Hegab
- Center for Membranes and Advanced Water Technology (CMAT), Khalifa University of Science and Technology, PO Box 127788, Abu Dhabi, United Arab Emirates
- Department of Chemical Engineering, Khalifa University of Science and Technology, PO Box 127788, Abu Dhabi, United Arab Emirates
| | - Habiba Alsafar
- Center for Biotechnology (BTC), Khalifa University of Science and Technology, PO Box 127788, Abu Dhabi, United Arab Emirates
- Department of Biomedical Engineering, College of Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Emirates Bio-research center, Ministry of interior, Abu Dhabi, United Arab Emirates
| | - Shadi W Hasan
- Center for Membranes and Advanced Water Technology (CMAT), Khalifa University of Science and Technology, PO Box 127788, Abu Dhabi, United Arab Emirates
- Department of Chemical Engineering, Khalifa University of Science and Technology, PO Box 127788, Abu Dhabi, United Arab Emirates
| | - Fawzi Banat
- Center for Membranes and Advanced Water Technology (CMAT), Khalifa University of Science and Technology, PO Box 127788, Abu Dhabi, United Arab Emirates
- Department of Chemical Engineering, Khalifa University of Science and Technology, PO Box 127788, Abu Dhabi, United Arab Emirates
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Barboza VDS, Domingues WB, de Souza TT, Collares TV, Seixas FK, Pacheco BS, Sousa FSS, Oliveira TL, de Lima M, de Pereira CMP, Spilki FR, Giongo JL, Vaucher RDA. Reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay as a rapid molecular diagnostic tool for COVID-19 in healthcare workers. JOURNAL OF CLINICAL VIROLOGY PLUS 2023; 3:100134. [PMID: 36742065 PMCID: PMC9891106 DOI: 10.1016/j.jcvp.2023.100134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 10/19/2022] [Accepted: 01/06/2023] [Indexed: 01/28/2023] Open
Abstract
In December 2019, the Chinese Center for Disease Control (CDC of China) reported an outbreak of pneumonia in the city of Wuhan (Hubei province, China) that haunted the world, resulting in a global pandemic. This outbreak was caused by a betacoronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Several of these cases have been observed in healthcare professionals working in hospitals and providing care on the pandemic's frontline. In the present study, nasopharyngeal swab samples of healthcare workers were used to assess the performance of the reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay and subsequently compared with the real-time reverse-transcription quantitative PCR (RT-qPCR) method. Thus, in this study, we validated a method for detecting SARS-CoV-2 based on RT-LAMP that can be used to diagnose these workers. The methodology used was based on analyzing the sensitivity, specificity, evaluation of the detection limit, and cross-reaction with other respiratory viruses. The agreement was estimated using a dispersion diagram designed using the Bland-Altman method. A total of 100 clinical specimens of nasopharyngeal swabs were collected from symptomatic and asymptomatic healthcare workers in Pelotas, Brazil, during the SARS-CoV-2 outbreak. RT-LAMP assay, it was possible to detect SARS-CoV-2 in 96.7% of the healthcare professionals tested using the E gene and N gene primers approximately and 100% for the gene of human β-actin. The observed agreement was considered excellent for the primer set of the E and N genes (k = 0.957 and k = 0.896), respectively. The sensitivity of the RT-LAMP assay was positive for the primer set of the E gene, detected to approximately 2 copies per reaction. For the primer set of the N gene, the assay was possible to verify an LoD of approximately 253 copies per reaction. After executing the RT-LAMP assay, no positive reactions were observed for any of the virus respiratory tested. Therefore, we conclude that RT-LAMP is effective for rapid molecular diagnosis during the COVID-19 outbreak period in healthcare professionals.
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Affiliation(s)
- Victor dos Santos Barboza
- Laboratório de Pesquisa em Bioquímica e Biologia Molecular de Micro-organismos, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - William Borges Domingues
- Laboratório de Genômica Estrutural, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Thobias Toniolo de Souza
- Laboratório de Pesquisa em Bioquímica e Biologia Molecular de Micro-organismos, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Tiago Veiras Collares
- Laboratório de Biotecnologia do Câncer, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Fabiana Kommling Seixas
- Laboratório de Biotecnologia do Câncer, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Bruna Silveira Pacheco
- Laboratório de Biotecnologia do Câncer, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Fernanda Severo Sabedra Sousa
- Laboratório de Biotecnologia do Câncer, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Thaís Larré Oliveira
- Laboratório de Vacinologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Marcelo de Lima
- Laboratório de Virologia e Imunologia, Faculdade de Veterinária, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | | | - Fernando Rosado Spilki
- Laboratório de Microbiologia Molecular, Universidade FEEVALE, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Janice Luehring Giongo
- Laboratório de Pesquisa em Bioquímica e Biologia Molecular de Micro-organismos, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Rodrigo de Almeida Vaucher
- Laboratório de Pesquisa em Bioquímica e Biologia Molecular de Micro-organismos, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil,Corresponding author
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Simon DS, Yew CW, Kumar VS. Multiplexed Reverse Transcription Loop-Mediated Isothermal Amplification Coupled with a Nucleic Acid-Based Lateral Flow Dipstick as a Rapid Diagnostic Method to Detect SARS-CoV-2. Microorganisms 2023; 11:1233. [PMID: 37317207 PMCID: PMC10223058 DOI: 10.3390/microorganisms11051233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 04/30/2023] [Accepted: 05/03/2023] [Indexed: 06/16/2023] Open
Abstract
Due to the high reproduction rate of COVID-19, it is important to identify and isolate infected patients at the early stages of infection. The limitations of current diagnostic methods are speed, cost, and accuracy. Furthermore, new viral variants have emerged with higher rates of infectivity and mortality, many with mutations at various primer binding sites, which may evade detection via conventional PCR kits. Therefore, a rapid method that is sensitive, specific, and cost-effective is needed for a point-of-care molecular test. Accordingly, we developed a rapid molecular SARS-CoV-2 detection kit with high specificity and sensitivity, RT-PCR, taking advantage of the loop-mediated isothermal amplification (LAMP) technique. Four sets of six primers were designed based on conserved regions of the SARS-CoV-2 genome: two outer, two inner and two loop primers. Using the optimized protocol, SARS-CoV-2 genes were detected as quickly as 10 min but were most sensitive at 30 min, detecting as little as 100 copies of template DNA. We then coupled the RT-LAMP with a lateral flow dipstick (LFD) for multiplex detection. The LFD could detect two genic amplifications on a single strip, making it suitable for multiplexed detection. The development of a multiplexed RT-LAMP-LFD reaction on crude VTM samples would be suitable for the point-of-care diagnosis of COVID-19 in diagnostic laboratories as well as in private homes.
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Affiliation(s)
| | | | - Vijay Subbiah Kumar
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu 88400, Malaysia; (D.S.S.); (C.-W.Y.)
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Bumbrah GS, Jain S, Singh S, Fatima Z, Hameed S. Diagnostic Efficacy of LAMP Assay for Human Fungal Pathogens: a Systematic Review and Meta-analysis. CURRENT FUNGAL INFECTION REPORTS 2023; 17:1-11. [PMID: 37360855 PMCID: PMC10150145 DOI: 10.1007/s12281-023-00466-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/24/2023] [Indexed: 06/28/2023]
Abstract
Purpose Human fungal infections particularly caused by Candida and Aspergillus have emerged as major public health burden. Long turnaround time and poor sensitivity of the conventional diagnostics are the major impediments for faster diagnosis of human fungal pathogens. Recent Findings To overcome these issues, molecular-based diagnostics have been developed. They offer enhanced sensitivity but require sophisticated infrastructure, skilled manpower, and remained expensive. In that context, loop-mediated isothermal amplification (LAMP) assay represents a promising alternative that facilitates visual read outs. However, to eradicate fungal infections, all forms of fungi must be accurately detected. Thus, a need for alternative testing methodologies is imperative that should be rapid, accurate and facilitate widespread adoption. Therefore, the aim of the present study is to conduct a meta-analysis to assess the diagnostic efficiency of LAMP in the detection of a panel of human fungal pathogens following PRISMA guidelines using scientific databases viz. PubMed, Google Scholar, Science Direct, Scopus, BioRxiv, and MedRxiv. Summary From various studies reported on the diagnosis of fungi, only 9 articles were identified as eligible to meet the criteria of LAMP based diagnosis. Through this meta-analysis, it was found that most of the studies were conducted in China and Japan with sputum and blood as the most common specimens to be used for LAMP assay. The collected data underlined that ITS gene and fluorescence-based detections ranked as the most used target and method. The pooled sensitivity values of meta-analysis ranged between 0.71 and 1.0 and forest plot and SROC (summary receiver operating characteristic) curve revealed a pooled specificity values between 0.13 and 1.0 with the confidence interval of 95%, respectively. The accuracy and precision rates of eligible studies mostly varied between 70 to 100% and 68 to 100%, respectively. A quality assessment based on QUADAS-2 (Quality Assessment of Diagnostic Accuracy Studies) of bias and applicability was conducted which depicted low risk of bias and applicability concerns. Together, LAMP technology could be considered as a feasible alternative to current diagnostics considering high fungal burden for rapid testing in low resource regions.
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Affiliation(s)
- Gurvinder Singh Bumbrah
- Department of Forensic Sciences, Amity School of Applied Sciences, Amity University Haryana, Gurugram, 122413 Manesar India
| | - Sarika Jain
- Department of Mathematics, Amity School of Applied Sciences, Amity University Haryana, Gurugram, 122413 Manesar India
| | - Shweta Singh
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram, 122413 Manesar India
| | - Zeeshan Fatima
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram, 122413 Manesar India
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Bisha, Bisha, 61922 Saudi Arabia
| | - Saif Hameed
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram, 122413 Manesar India
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Salahandish R, Hyun JE, Haghayegh F, Tabrizi HO, Moossavi S, Khetani S, Ayala-Charca G, Berenger BM, Niu YD, Ghafar-Zadeh E, Nezhad AS. CoVSense: Ultrasensitive Nucleocapsid Antigen Immunosensor for Rapid Clinical Detection of Wildtype and Variant SARS-CoV-2. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2206615. [PMID: 36995043 DOI: 10.1002/advs.202206615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 01/31/2023] [Indexed: 05/27/2023]
Abstract
The widespread accessibility of commercial/clinically-viable electrochemical diagnostic systems for rapid quantification of viral proteins demands translational/preclinical investigations. Here, Covid-Sense (CoVSense) antigen testing platform; an all-in-one electrochemical nano-immunosensor for sample-to-result, self-validated, and accurate quantification of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid (N)-proteins in clinical examinations is developed. The platform's sensing strips benefit from a highly-sensitive, nanostructured surface, created through the incorporation of carboxyl-functionalized graphene nanosheets, and poly(3,4-ethylenedioxythiophene) polystyrene sulfonate (PEDOT:PSS) conductive polymers, enhancing the overall conductivity of the system. The nanoengineered surface chemistry allows for compatible direct assembly of bioreceptor molecules. CoVSense offers an inexpensive (<$2 kit) and fast/digital response (<10 min), measured using a customized hand-held reader (<$25), enabling data-driven outbreak management. The sensor shows 95% clinical sensitivity and 100% specificity (Ct<25), and overall sensitivity of 91% for combined symptomatic/asymptomatic cohort with wildtype SARS-CoV-2 or B.1.1.7 variant (N = 105, nasal/throat samples). The sensor correlates the N-protein levels to viral load, detecting high Ct values of ≈35, with no sample preparation steps, while outperforming the commercial rapid antigen tests. The current translational technology fills the gap in the workflow of rapid, point-of-care, and accurate diagnosis of COVID-19.
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Affiliation(s)
- Razieh Salahandish
- BioMEMS and Bioinspired Microfluidic Laboratory, Department of Biomedical Engineering, University of Calgary, Calgary, AB, T2N 1N4, Canada
- Department of Mechanical and Manufacturing Engineering, University of Calgary, Calgary, AB, T2N 1N4, Canada
- Laboratory of Advanced Biotechnologies for Health Assessments (LAB-HA), Department of Electrical Engineering and Computer Science, Lassonde School of Engineering, York University, Toronto, M3J 1P3, Canada
| | - Jae Eun Hyun
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Fatemeh Haghayegh
- BioMEMS and Bioinspired Microfluidic Laboratory, Department of Biomedical Engineering, University of Calgary, Calgary, AB, T2N 1N4, Canada
- Department of Mechanical and Manufacturing Engineering, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Hamed Osouli Tabrizi
- Biologically Inspired Sensors and Actuators (BioSA), Department of Electrical Engineering and Computer Science, Lassonde School of Engineering, York University, Toronto, M3J 1P3, Canada
| | - Shirin Moossavi
- BioMEMS and Bioinspired Microfluidic Laboratory, Department of Biomedical Engineering, University of Calgary, Calgary, AB, T2N 1N4, Canada
- Department of Physiology and Pharmacology, University of Calgary, Calgary, AB, T2N 1N4, Canada
- International Microbiome Centre, Cumming School of Medicine, Health Sciences Centre, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Sultan Khetani
- BioMEMS and Bioinspired Microfluidic Laboratory, Department of Biomedical Engineering, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Giancarlo Ayala-Charca
- Biologically Inspired Sensors and Actuators (BioSA), Department of Electrical Engineering and Computer Science, Lassonde School of Engineering, York University, Toronto, M3J 1P3, Canada
| | - Byron M Berenger
- Alberta Public Health Laboratory, Alberta Precision Laboratories, 3330 Hospital Drive, Calgary, AB, T2N 4W4, Canada
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Yan Dong Niu
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Ebrahim Ghafar-Zadeh
- Biologically Inspired Sensors and Actuators (BioSA), Department of Electrical Engineering and Computer Science, Lassonde School of Engineering, York University, Toronto, M3J 1P3, Canada
| | - Amir Sanati Nezhad
- BioMEMS and Bioinspired Microfluidic Laboratory, Department of Biomedical Engineering, University of Calgary, Calgary, AB, T2N 1N4, Canada
- Department of Mechanical and Manufacturing Engineering, University of Calgary, Calgary, AB, T2N 1N4, Canada
- Biomedical Engineering Graduate Program, University of Calgary, Calgary, AB, T2N 1N4, Canada
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GhaderiShekhiAbadi P, Irani M, Noorisepehr M, Maleki A. Magnetic biosensors for identification of SARS-CoV-2, Influenza, HIV, and Ebola viruses: a review. NANOTECHNOLOGY 2023; 34:272001. [PMID: 36996779 DOI: 10.1088/1361-6528/acc8da] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 03/29/2023] [Indexed: 06/19/2023]
Abstract
Infectious diseases such as novel coronavirus (SARS-CoV-2), Influenza, HIV, Ebola, etc kill many people around the world every year (SARS-CoV-2 in 2019, Ebola in 2013, HIV in 1980, Influenza in 1918). For example, SARS-CoV-2 has plagued higher than 317 000 000 people around the world from December 2019 to January 13, 2022. Some infectious diseases do not yet have not a proper vaccine, drug, therapeutic, and/or detection method, which makes rapid identification and definitive treatments the main challenges. Different device techniques have been used to detect infectious diseases. However, in recent years, magnetic materials have emerged as active sensors/biosensors for detecting viral, bacterial, and plasmids agents. In this review, the recent applications of magnetic materials in biosensors for infectious viruses detection have been discussed. Also, this work addresses the future trends and perspectives of magnetic biosensors.
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Affiliation(s)
| | - Mohammad Irani
- Department of Pharmaceutics, Faculty of Pharmacy, Alborz University of Medical Sciences, Karaj, Iran
| | - Mohammad Noorisepehr
- Environmental Health Engineering Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Ali Maleki
- Catalysts and Organic Synthesis Research Laboratory, Department of Chemistry, Iran University of Science and Technology, Tehran 16846-13114, Iran
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Thwala LN, Ndlovu SC, Mpofu KT, Lugongolo MY, Mthunzi-Kufa P. Nanotechnology-Based Diagnostics for Diseases Prevalent in Developing Countries: Current Advances in Point-of-Care Tests. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:1247. [PMID: 37049340 PMCID: PMC10096522 DOI: 10.3390/nano13071247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 03/24/2023] [Accepted: 03/27/2023] [Indexed: 06/19/2023]
Abstract
The introduction of point-of-care testing (POCT) has revolutionized medical testing by allowing for simple tests to be conducted near the patient's care point, rather than being confined to a medical laboratory. This has been especially beneficial for developing countries with limited infrastructure, where testing often involves sending specimens off-site and waiting for hours or days for results. However, the development of POCT devices has been challenging, with simplicity, accuracy, and cost-effectiveness being key factors in making these tests feasible. Nanotechnology has played a crucial role in achieving this goal, by not only making the tests possible but also masking their complexity. In this article, recent developments in POCT devices that benefit from nanotechnology are discussed. Microfluidics and lab-on-a-chip technologies are highlighted as major drivers of point-of-care testing, particularly in infectious disease diagnosis. These technologies enable various bioassays to be used at the point of care. The article also addresses the challenges faced by these technological advances and interesting future trends. The benefits of point-of-care testing are significant, especially in developing countries where medical care is shifting towards prevention, early detection, and managing chronic conditions. Infectious disease tests at the point of care in low-income countries can lead to prompt treatment, preventing infections from spreading.
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Affiliation(s)
- Lungile Nomcebo Thwala
- National Laser Centre, Council for Scientific and Industrial Research, P.O. Box 395, Pretoria 0001, South Africa
| | - Sphumelele Colin Ndlovu
- National Laser Centre, Council for Scientific and Industrial Research, P.O. Box 395, Pretoria 0001, South Africa
| | - Kelvin Tafadzwa Mpofu
- National Laser Centre, Council for Scientific and Industrial Research, P.O. Box 395, Pretoria 0001, South Africa
| | - Masixole Yvonne Lugongolo
- National Laser Centre, Council for Scientific and Industrial Research, P.O. Box 395, Pretoria 0001, South Africa
| | - Patience Mthunzi-Kufa
- National Laser Centre, Council for Scientific and Industrial Research, P.O. Box 395, Pretoria 0001, South Africa
- College of Agriculture, Engineering and Science, School of Chemistry and Physics, University of Kwa-Zulu Natal, University Road, Westville, Durban 3630, South Africa
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Alhamid G, Tombuloglu H, Al-Suhaimi E. Development of loop-mediated isothermal amplification (LAMP) assays using five primers reduces the false-positive rate in COVID-19 diagnosis. Sci Rep 2023; 13:5066. [PMID: 36977756 PMCID: PMC10044074 DOI: 10.1038/s41598-023-31760-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
The reverse-transcription loop-mediated isothermal amplification (RT-LAMP) is a cheaper and faster testing alternative for detecting SARS-CoV-2. However, a high false-positive rate due to misamplification is one of the major limitations. To overcome misamplifications, we developed colorimetric and fluorometric RT-LAMP assays using five LAMP primers, instead of six. The gold-standard RT-PCR technique verified the assays' performance. Compared to other primer sets with six primers (N, S, and RdRp), the E-ID1 primer set, including five primers, performed superbly on both colorimetric and fluorometric assays. The sensitivity of colorimetric and fluorometric assays was 89.5% and 92.2%, respectively, with a limit of detection of 20 copies/µL. The colorimetric RT-LAMP had a specificity of 97.2% and an accuracy of 94.5%, while the fluorometric RT-LAMP obtained 99% and 96.7%, respectively. No misamplification was evident even after 120 min, which is crucial for the success of this technique. These findings are important to support the use of RT-LAMP in the healthcare systems in fighting COVID-19.
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Affiliation(s)
- Galyah Alhamid
- Master Program of Biotechnology, Institute for Research and Medical Consultations, Imam Abdulrahman Bin Faisal University, Dammam, 31441, Saudi Arabia
- Department of Genetics Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, 31441, Saudi Arabia
| | - Huseyin Tombuloglu
- Department of Genetics Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, 31441, Saudi Arabia.
| | - Ebtesam Al-Suhaimi
- Biology Department, College of Science and Institute of Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, 31441, Saudi Arabia
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Zhang X, Chen Y, Pan Y, Ma X, Hu G, Li S, Deng Y, Chen Z, Chen H, Wu Y, Jiang Z, Li Z. Research progress of severe acute respiratory syndrome coronavirus 2 on aerosol collection and detection. CHINESE CHEM LETT 2023:108378. [PMID: 37362323 PMCID: PMC10039702 DOI: 10.1016/j.cclet.2023.108378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 03/02/2023] [Accepted: 03/22/2023] [Indexed: 06/28/2023]
Abstract
The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in late 2019 has negatively affected people's lives and productivity. Because the mode of transmission of SARS-CoV-2 is of great concern, this review discusses the sources of virus aerosols and possible transmission routes. First, we discuss virus aerosol collection methods, including natural sedimentation, solid impact, liquid impact, centrifugal, cyclone and electrostatic adsorption methods. Then, we review common virus aerosol detection methods, including virus culture, metabolic detection, nucleic acid-based detection and immunology-based detection methods. Finally, possible solutions for the detection of SARS-CoV-2 aerosols are introduced. Point-of-care testing has long been a focus of attention. In the near future, the development of an instrument that integrates sampling and output results will enable the real-time, automatic monitoring of patients.
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Affiliation(s)
- Xinyu Zhang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007, China
| | - Yuting Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007, China
| | - Yueying Pan
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007, China
| | - Xinye Ma
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007, China
| | - Gui Hu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007, China
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007, China
| | - Yan Deng
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007, China
| | - Zhu Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007, China
| | - Hui Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007, China
| | - Yanqi Wu
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, 999078, China
- Shenzhen Lemniscare Med Technol Co. Ltd., Shenzhen, 518000, China
| | - Zhihong Jiang
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, 999078, China
| | - Zhiyang Li
- Department of Clinical Laboratory, the Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, 210008, China
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Alafeef M, Skrodzki D, Moitra P, Gunaseelan N, Pan D. Binding-Induced Folding of DNA Oligonucleotides Targeted to the Nucleocapsid Gene Enables Electrochemical Sensing of SARS-CoV-2. ACS APPLIED BIO MATERIALS 2023; 6:1133-1145. [PMID: 36877613 PMCID: PMC9999945 DOI: 10.1021/acsabm.2c00984] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 02/19/2023] [Indexed: 03/07/2023]
Abstract
In the wake of the COVID-19 pandemic, millions of confirmed cases and deaths have been reported around the world. COVID-19 spread can be slowed and eventually stopped by a rapid test to diagnose positive cases of the disease on the spot. It is still important to test for COVID-19 quickly regardless of the availability of the vaccine. Using the binding-induced folding principle, we developed an electrochemical test for detecting SARS-CoV-2 with no RNA extraction or nucleic acid amplification. The test showed high sensitivity with a limit of detection of 2.5 copies/μL. An electrode mounted with a capture probe and a portable potentiostat are used to conduct the test. To target the N-gene of SARS-CoV-2, a highly specific oligo-capturing probe was used. Based on the binding-induced "folding" principle, the sensor detects binding between the oligo and RNA. When the target is absent, the capture probe tends to form a hairpin as a secondary structure, retaining the redox reporter close to the surface. This can be seen as a large anodic and cathodic peak current. When the target RNA is present, the hairpin structure will open to hybridize with its complementary sequence, causing the redox reporter to pull away from the electrode. Consequently, the anodic/cathodic peak currents are reduced, indicating the presence of the SARS-CoV-2 genetic material. Validation of the test performance was performed using 122 COVID-19 clinical samples (55 positives and 67 negatives) and benchmarked to the gold standard reverse transcription-polymerase chain reaction (RT-PCR) test. As a result of our test, the accuracy, sensitivity, and specificity have been measured at 98.4%, 98.2%, and 98.5%, respectively.
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Affiliation(s)
- Maha Alafeef
- Bioengineering
Department, The University of Illinois at
Urbana-Champaign, Urbana, Illinois 61801, United States
- Departments
of Diagnostic Radiology and Nuclear Medicine and Pediatrics, Center
for Blood Oxygen Transport and Hemostasis, Health Sciences Research
Facility III, University of Maryland School
of Medicine, 670 W Baltimore
Street, Baltimore, Maryland 21201, United States
- Biomedical
Engineering Department, Jordan University
of Science and Technology, Irbid 22110, Jordan
- Department
of Chemical, Biochemical and Environmental Engineering, University of Maryland, Baltimore County, Baltimore, Maryland 21250, United States
- Department
of Nuclear Engineering, Pennsylvania State
University, State
College, Pennsylvania 16801, United States
| | - David Skrodzki
- Department
of Materials Science and Engineering, Pennsylvania
State University, State College, Pennsylvania 16801, United States
| | - Parikshit Moitra
- Department
of Nuclear Engineering, Pennsylvania State
University, State
College, Pennsylvania 16801, United States
| | - Nivetha Gunaseelan
- Biomedical
Engineering Department, Pennsylvania State
University, State College, Pennsylvania 16801, United States
| | - Dipanjan Pan
- Bioengineering
Department, The University of Illinois at
Urbana-Champaign, Urbana, Illinois 61801, United States
- Departments
of Diagnostic Radiology and Nuclear Medicine and Pediatrics, Center
for Blood Oxygen Transport and Hemostasis, Health Sciences Research
Facility III, University of Maryland School
of Medicine, 670 W Baltimore
Street, Baltimore, Maryland 21201, United States
- Department
of Chemical, Biochemical and Environmental Engineering, University of Maryland, Baltimore County, Baltimore, Maryland 21250, United States
- Department
of Nuclear Engineering, Pennsylvania State
University, State
College, Pennsylvania 16801, United States
- Department
of Materials Science and Engineering, Pennsylvania
State University, State College, Pennsylvania 16801, United States
- Biomedical
Engineering Department, Pennsylvania State
University, State College, Pennsylvania 16801, United States
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Tian J, Chen B, Zhang B, Li T, Liang Z, Guo Y, Jiao H, Liang F, Xiang L, Lin F, Ren R, Liu Q. A New Auto-RPA-Fluorescence Detection Platform for SARS-CoV-2. Lab Med 2023; 54:182-189. [PMID: 36200614 PMCID: PMC9619631 DOI: 10.1093/labmed/lmac093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
OBJECTIVE The outbreak of COVID-19 caused by SARS-CoV-2 has led to a serious worldwide pandemic. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR)-based methods were recommended for routine detection of SARS-CoV-2 RNA. Because the reaction time and analytical sensitivity of qRT-PCR limits the diagnosis of SARS-CoV-2, development of a quick process of SARS-CoV-2 detection technology with high analytical sensitivity remains urgent. METHODS We combined isothermal amplification and fluorescence detection technology to develop a new auto-recombinase polymerase amplification (RPA)-fluorescence platform that could be used in the diagnosis of SARS-CoV-2. RESULTS By optimization of primers and probes, the RPA platform could detect SARS-CoV-2 nucleotides within 15 min. The limits of detection and specificity of the auto-RPA-fluorescence platform were 5 copies/µL and 100%, respectively. The accuracy of detection of the auto-RPA-fluorescence platform in the 16 positive samples was 100%. CONCLUSION The RPA platform is a potential technology for the diagnosis of SARS-CoV-2 infection.
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Affiliation(s)
- Jing Tian
- Centers for Disease Control and Prevention, People's Liberation Army Southern Theater Command, Guangzhou, China
| | - Biao Chen
- Laboratory of Medical Mycology, Jining No. 1 People's Hospital, Jining, China
| | - Bin Zhang
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Tantan Li
- Jining Precision Medical Test Center, Jining No. 1 People's Hospital, Jining, China
| | - Zhiqiang Liang
- Medical Laboratory Department, Jining No. 1 People's Hospital, Jining, China
| | - Yujin Guo
- Institute of Clinical Pharmacy & Pharmacology, Jining No. 1 People's Hospital, Jining, China
| | | | - Fenghong Liang
- Laboratory of Medical Mycology, Jining No. 1 People's Hospital, Jining, China
| | - Longquan Xiang
- Department of Pathology, Jining No. 1 People's Hospital, Jining, China
| | - Fanzhong Lin
- Department of Pathology, Jining No. 1 People's Hospital, Jining, China
| | - Ruiwen Ren
- Centers for Disease Control and Prevention, People's Liberation Army Southern Theater Command, Guangzhou, China
| | - Qingbin Liu
- Laboratory of Medical Mycology, Jining No. 1 People's Hospital, Jining, China
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Lizambri D, Giacalone A, Shah PA, Tovani-Palone MR. Reconstruction surgery in head and neck cancer patients amidst the COVID-19 pandemic: Current practice and lessons for the future. World J Clin Cases 2023; 11:1434-1441. [PMID: 36926409 PMCID: PMC10011991 DOI: 10.12998/wjcc.v11.i7.1434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 12/20/2022] [Accepted: 02/13/2023] [Indexed: 03/02/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has imposed a radical change in daily life and work routine. In this context, health systems have suffered important and serious repercussions in all fields. Among the changes brought about by the state of global health emergency, adjustments to guidelines, priorities, structures, professional teams, and epidemiological data stand out. In light of this, the oncological field has witnessed several changes in the approach to cancer, whether due to delay in diagnosis, screening deficit, personnel shortage or the psychological impact that the pandemic has had on cancer patients. This article focuses on the management of oral carcinoma and the surgical approaches that oral and maxillofacial specialists have had at their disposal during the health emergency. In this period, the oral and maxillofacial surgeons have faced many obstacles. The proximity of maxillofacial structures to the airways, the need of elective and punctual procedures in cancerous lesions, the aggressiveness of head and neck tumors, and the need for important healthcare costs to support such delicate surgeries are examples of some of the challenges imposed for this field. One of the possible surgical 'solutions' to the difficulties in managing surgical cases of oral carcinoma during the pandemic is locoregional flaps, which in the pre-COVID-19 era were less used than free flaps. However, during the health emergency, its use has been widely reassessed. This setback may represent a precedent for opening up new reflections. In the course of a long-term pandemic, a reassessment of the validity of different medical and surgical therapeutic approaches should be considered. Finally, given that the pandemic has high-lighted vulnerabilities and shortcomings in a number of ways, including the issues of essential resource shortages, underinvestment in public health services, lack of coordination and versatility among politicians, policymakers and health leaders, resulting in overloaded health systems, rapid case development, and high mortality, a more careful analysis of the changes needed in different health systems to satisfactorily face future emergencies is essential to be carried out. This should be directed especially towards improving the management of health systems, their coordination as well as reviewing related practices, even in the surgical field.
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Affiliation(s)
- Daniele Lizambri
- Department of Advanced Medical and Surgical Sciences, University of Campania Luigi Vanvitelli, Caserta 81100, Italy
| | - Andrea Giacalone
- Department of Industrial Engineering, Technologies for Sports Medicine and Rehabilitation, University of Rome Tor Vergata, Rome 00133, Italy
| | - Pritik A Shah
- Bangalore Medical College and Research Institute, Karnataka 560002, India
| | - Marcos Roberto Tovani-Palone
- Department of Research Analytics, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Chennai 600077, India
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49
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Szobi A, Buranovská K, Vojtaššáková N, Lovíšek D, Özbaşak HÖ, Szeibeczederová S, Kapustian L, Hudáčová Z, Kováčová V, Drobná D, Putaj P, Bírová S, Čirková I, Čarnecký M, Kilián P, Jurkáček P, Čabanová V, Boršová K, Sláviková M, Vaňová V, Klempa B, Čekan P, Paul ED. Vivid COVID-19 LAMP is an ultrasensitive, quadruplexed test using LNA-modified primers and a zinc ion and 5-Br-PAPS colorimetric detection system. Commun Biol 2023; 6:233. [PMID: 36864129 PMCID: PMC9979146 DOI: 10.1038/s42003-023-04612-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 02/20/2023] [Indexed: 03/04/2023] Open
Abstract
Sensitive and rapid point-of-care assays have been crucial in the global response to SARS-CoV-2. Loop-mediated isothermal amplification (LAMP) has emerged as an important diagnostic tool given its simplicity and minimal equipment requirements, although limitations exist regarding sensitivity and the methods used to detect reaction products. We describe the development of Vivid COVID-19 LAMP, which leverages a metallochromic detection system utilizing zinc ions and a zinc sensor, 5-Br-PAPS, to circumvent the limitations of classic detection systems dependent on pH indicators or magnesium chelators. We make important strides in improving RT-LAMP sensitivity by establishing principles for using LNA-modified LAMP primers, multiplexing, and conducting extensive optimizations of reaction parameters. To enable point-of-care testing, we introduce a rapid sample inactivation procedure without RNA extraction that is compatible with self-collected, non-invasive gargle samples. Our quadruplexed assay (targeting E, N, ORF1a, and RdRP) reliably detects 1 RNA copy/µl of sample (=8 copies/reaction) from extracted RNA and 2 RNA copies/µl of sample (=16 copies/reaction) directly from gargle samples, making it one of the most sensitive RT-LAMP tests and even comparable to RT-qPCR. Additionally, we demonstrate a self-contained, mobile version of our assay in a variety of high-throughput field testing scenarios on nearly 9,000 crude gargle samples. Vivid COVID-19 LAMP can be an important asset for the endemic phase of COVID-19 as well as preparing for future pandemics.
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Affiliation(s)
- Adrián Szobi
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Katarína Buranovská
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Nina Vojtaššáková
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Daniel Lovíšek
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Halil Önder Özbaşak
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Sandra Szeibeczederová
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Liudmyla Kapustian
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Zuzana Hudáčová
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
- Stanford University, 730 Escondido Rd., Stanford, CA, 94305, USA
| | - Viera Kováčová
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
- University of Cologne, Institute for Biological Physics, Zülpicher Str. 77, 50937, Köln, Germany
| | - Diana Drobná
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Piotr Putaj
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Stanislava Bírová
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Ivana Čirková
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Martin Čarnecký
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Peter Kilián
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Peter Jurkáček
- AstonITM s.r.o., Račianska 153, 831 54, Bratislava, Slovakia
| | - Viktória Čabanová
- Biomedical Research Center, Slovak Academy of Sciences, Institute of Virology, Dúbravská cesta 9, 845 05, Bratislava, Slovakia
| | - Kristína Boršová
- Biomedical Research Center, Slovak Academy of Sciences, Institute of Virology, Dúbravská cesta 9, 845 05, Bratislava, Slovakia
| | - Monika Sláviková
- Biomedical Research Center, Slovak Academy of Sciences, Institute of Virology, Dúbravská cesta 9, 845 05, Bratislava, Slovakia
| | - Veronika Vaňová
- Biomedical Research Center, Slovak Academy of Sciences, Institute of Virology, Dúbravská cesta 9, 845 05, Bratislava, Slovakia
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University, Ilkovičova 6, 842 15, Bratislava, Slovakia
| | - Boris Klempa
- Biomedical Research Center, Slovak Academy of Sciences, Institute of Virology, Dúbravská cesta 9, 845 05, Bratislava, Slovakia
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University, Ilkovičova 6, 842 15, Bratislava, Slovakia
| | - Pavol Čekan
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia.
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA.
| | - Evan D Paul
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia.
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA.
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50
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Jang YO, Kim NH, Roh Y, Koo B, Lee HJ, Kim JY, Kim SH, Shin Y. Self-directed molecular diagnostics (SdMDx) system for COVID-19 via one-pot processing. SENSORS AND ACTUATORS. B, CHEMICAL 2023; 378:133193. [PMID: 36570722 PMCID: PMC9759472 DOI: 10.1016/j.snb.2022.133193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/03/2022] [Accepted: 12/15/2022] [Indexed: 06/17/2023]
Abstract
Rapid, sensitive, and specific detection of the severe acute respiratory syndrome coronavirus (SARS-CoV)- 2 during early infection is pivotal in controlling the spread and pathological progression of Coronavirus Disease 2019 (COVID-19). Thus, highly accurate, affordable, and scalable point-of-care (POC) diagnostic technologies are necessary. Herein, we developed a rapid and efficient self-directed molecular diagnostic (SdMDx) system for SARS-CoV-2. This system combines the sample preparation step, including virus enrichment and extraction processes, which involve dimethyl suberimidate dihydrochloride and diatomaceous earth functionalized with 3-aminopropyl(diethoxy)methylsilane, and the detection step using loop-mediated isothermal amplification-lateral flow assay (LAMP-LFA). Using the SdMDx system, SARS-CoV-2 could be detected within 47 min by hand without the need for any larger instruments. The SdMDx system enabled detection as low as 0.05 PFU in the culture fluid of SARS-CoV-2-infected VeroE6 cells. We validated the accuracy of the SdMDx system on 38 clinical nasopharyngeal specimens. The clinical utility of the SdMDx system for targeting the S gene of SARS-CoV-2 showed 94.4% sensitivity and 100% specificity. This system is more sensitive than antigen and antibody assays, and it minimizes the use of complicated processes and reduces contamination risks. Accordingly, we demonstrated that the SdMDx system enables a rapid, accurate, simple, efficient, and inexpensive detection of SARS-CoV-2 at home, in emergency facilities, and in low-resource sites as a pre-screening platform and POC testing through self-operation and self-diagnosis.
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Affiliation(s)
- Yoon Ok Jang
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Nam Hun Kim
- INFUSIONTECH, 38 Heungan-daero, 427 beon-gil, Dongan-gu, Anyang-si 14059, Republic of Korea
| | - Yeonjeong Roh
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Bonhan Koo
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Hyo Joo Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Ji Yeun Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Songpa-gu, Seoul 05505, Republic of Korea
| | - Sung-Han Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Songpa-gu, Seoul 05505, Republic of Korea
| | - Yong Shin
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
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