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Ma YH, Liu Y, Li T, Xu ZQ, Chai JJ, Liu A, Ma QH, Gao LJ, Li MC. An experimental study on the visual identification of Fritillaria ussuriensis based on LAMP and nucleic acid colloidal gold technique. Anal Biochem 2024; 687:115430. [PMID: 38147947 DOI: 10.1016/j.ab.2023.115430] [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: 11/26/2023] [Revised: 12/11/2023] [Accepted: 12/13/2023] [Indexed: 12/28/2023]
Abstract
Fritillaria ussuriensis Maxim is one of the traditional Chinese valuable herbs, which is the dried bulb of Fritillaria, a plant of the lily family. The identification of authenticity about F. ussuriensis is still technically challenging. In this study, visual identification was performed by ring-mediated isothermal amplification and nucleic acid colloidal gold techniques. Firstly, multiple sequence comparative analysis was performed by DNAMAN to find the differential sites of F. ussuriensis and its mixed pseudo-products, and the specific identification primers of F. ussuriensis were designed. Genomic DNA was extracted by the modified CTAB method, and the reaction system and reaction conditions were optimized to construct LAMP for the visual detection of F. ussuriensis, meanwhile, the genuine product was cloned and the extracted plasmid was sequenced. The specificity and sensitivity were detected, and also verified by nucleic acid colloidal gold method, and 20 commercially available samples were tested. The extracted DNA met the requirements of the experiment, and the genuine F. ussuriensis PCR product titrated on a test strip showed two bands on the T and C lines, while the counterfeit and negative control showed only one band on the C line, which matched the LAMP results. The specificity was 100 %, and the sensitivity of LAMP assay was up to 0.01 ng μL-1, while that of colloidal gold assay was 0.1 ng μL-1, thus the LAMP assay had high sensitivity. 14 out of 20 commercially available samples of F. ussuriensis were qualified, and 6 were unqualified, and the results of the two methods of identification were consistent. In this study, the combined detection method of LAMP and colloidal gold for nucleic acid was established to be specific, rapid, precise and visualized, which can provide a new technical idea for the detection of F. ussuriensis.
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Affiliation(s)
- Yu-He Ma
- School of Medical Technology, Beihua University, Jilin, 132013, China
| | - Yue Liu
- School of Medical Technology, Beihua University, Jilin, 132013, China
| | - Tao Li
- School of Medical Technology, Beihua University, Jilin, 132013, China
| | - Zi-Qiang Xu
- School of Medical Technology, Beihua University, Jilin, 132013, China
| | - Jin-Jun Chai
- School of Medical Technology, Beihua University, Jilin, 132013, China
| | - Ang Liu
- School of Medical Technology, Beihua University, Jilin, 132013, China
| | - Qiu-He Ma
- School of Medical Technology, Beihua University, Jilin, 132013, China
| | - Li-Jun Gao
- School of Medical Technology, Beihua University, Jilin, 132013, China.
| | - Ming-Cheng Li
- School of Medical Technology, Beihua University, Jilin, 132013, China; Innovation Center for Detection on DNA Fingerprint of Traditional Chinese Medicine, Jilin, 132013, China
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2
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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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3
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Wang Y, Wang C, Zhou Z, Si J, Li S, Zeng Y, Deng Y, Chen Z. Advances in Simple, Rapid, and Contamination-Free Instantaneous Nucleic Acid Devices for Pathogen Detection. BIOSENSORS 2023; 13:732. [PMID: 37504131 PMCID: PMC10377012 DOI: 10.3390/bios13070732] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 07/05/2023] [Accepted: 07/12/2023] [Indexed: 07/29/2023]
Abstract
Pathogenic pathogens invade the human body through various pathways, causing damage to host cells, tissues, and their functions, ultimately leading to the development of diseases and posing a threat to human health. The rapid and accurate detection of pathogenic pathogens in humans is crucial and pressing. Nucleic acid detection offers advantages such as higher sensitivity, accuracy, and specificity compared to antibody and antigen detection methods. However, conventional nucleic acid testing is time-consuming, labor-intensive, and requires sophisticated equipment and specialized medical personnel. Therefore, this review focuses on advanced nucleic acid testing systems that aim to address the issues of testing time, portability, degree of automation, and cross-contamination. These systems include extraction-free rapid nucleic acid testing, fully automated extraction, amplification, and detection, as well as fully enclosed testing and commercial nucleic acid testing equipment. Additionally, the biochemical methods used for extraction, amplification, and detection in nucleic acid testing are briefly described. We hope that this review will inspire further research and the development of more suitable extraction-free reagents and fully automated testing devices for rapid, point-of-care diagnostics.
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Affiliation(s)
- Yue Wang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Chengming Wang
- Department of Cardiovascular Medicine, The Affiliated Zhuzhou Hospital Xiangya Medical College, Central South University, Zhuzhou 412000, China
| | - Zepeng Zhou
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Jiajia Si
- 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
| | - Yezhan Zeng
- School of Electrical and Information Engineering, 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
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4
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The Future of Point-of-Care Nucleic Acid Amplification Diagnostics after COVID-19: Time to Walk the Walk. Int J Mol Sci 2022; 23:ijms232214110. [PMID: 36430586 PMCID: PMC9693045 DOI: 10.3390/ijms232214110] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/09/2022] [Accepted: 11/09/2022] [Indexed: 11/18/2022] Open
Abstract
Since the onset of the COVID-19 pandemic, over 610 million cases have been diagnosed and it has caused over 6.5 million deaths worldwide. The crisis has forced the scientific community to develop tools for disease control and management at a pace never seen before. The control of the pandemic heavily relies in the use of fast and accurate diagnostics, that allow testing at a large scale. The gold standard diagnosis of viral infections is the RT-qPCR. Although it provides consistent and reliable results, it is hampered by its limited throughput and technical requirements. Here, we discuss the main approaches to rapid and point-of-care diagnostics based on RT-qPCR and isothermal amplification diagnostics. We describe the main COVID-19 molecular diagnostic tests approved for self-testing at home or for point-of-care testing and compare the available options. We define the influence of specimen selection and processing, the clinical validation, result readout improvement strategies, the combination with CRISPR-based detection and the diagnostic challenge posed by SARS-CoV-2 variants for different isothermal amplification techniques, with a particular focus on LAMP and recombinase polymerase amplification (RPA). Finally, we try to shed light on the effect the improvement in molecular diagnostics during the COVID-19 pandemic could have in the future of other infectious diseases.
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Yalley AK, Ahiatrogah S, Kafintu-Kwashie AA, Amegatcher G, Prah D, Botwe AK, Adusei-Poku MA, Obodai E, Nii-Trebi NI. A Systematic Review on Suitability of Molecular Techniques for Diagnosis and Research into Infectious Diseases of Concern in Resource-Limited Settings. Curr Issues Mol Biol 2022; 44:4367-4385. [PMID: 36286015 PMCID: PMC9601131 DOI: 10.3390/cimb44100300] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/15/2022] [Accepted: 09/16/2022] [Indexed: 11/16/2022] Open
Abstract
Infectious diseases significantly impact the health status of developing countries. Historically, infectious diseases of the tropics especially have received insufficient attention in worldwide public health initiatives, resulting in poor preventive and treatment options. Many molecular tests for human infections have been established since the 1980s, when polymerase chain reaction (PCR) testing was introduced. In spite of the substantial innovative advancements in PCR technology, which currently has found wide application in most viral pathogens of global concern, the development and application of molecular diagnostics, particularly in resource-limited settings, poses potential constraints. This review accessed data from sources including PubMed, Google Scholar, the Web of Knowledge, as well as reports from the World Health Organization’s Annual Meeting on infectious diseases and examined these for current molecular approaches used to identify, monitor, or investigate some neglected tropical infectious diseases. This review noted some growth efforts in the development of molecular techniques for diagnosis of pathogens that appear to be common in resource limited settings and identified gaps in the availability and applicability of most of these molecular diagnostics, which need to be addressed if the One Health goal is to be achieved.
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Affiliation(s)
- Akua K. Yalley
- Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, University of Ghana, Accra P.O. Box KB 143, Ghana
| | - Selasie Ahiatrogah
- Department of Obstetrics and Gynaecology, College of Medicine, Pan African University of Life and Earth Sciences Institute, University of Ibadan, Ibadan P.O. Box 22133, Nigeria
| | - Anna A. Kafintu-Kwashie
- Department of Medical Microbiology, University of Ghana Medical School, Accra GA-221-1570, Ghana
| | - Gloria Amegatcher
- Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, University of Ghana, Accra P.O. Box KB 143, Ghana
| | - Diana Prah
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra P.O. Box LG 54, Ghana
| | - Akua K. Botwe
- Molecular Biology Unit, Kintampo Health Research Centre, Ghana Health Service, Kintampo P.O. Box 200, Ghana
| | - Mildred A. Adusei-Poku
- Department of Medical Microbiology, University of Ghana Medical School, Accra GA-221-1570, Ghana
| | - Evangeline Obodai
- Department of Virology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra P.O. Box LG 581, Ghana
| | - Nicholas I. Nii-Trebi
- Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, University of Ghana, Accra P.O. Box KB 143, Ghana
- Correspondence: ; Tel.: +233-54-827-6424
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6
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Wei Z, Wang X, Feng H, Ji F, Bai D, Dong X, Huang W. Isothermal nucleic acid amplification technology for rapid detection of virus. Crit Rev Biotechnol 2022; 43:415-432. [PMID: 35156471 DOI: 10.1080/07388551.2022.2030295] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
While the research field and industrial market of in vitro diagnosis (IVD) thrived during and post the COVID-19 pandemic, the development of isothermal nucleic acid amplification test (INAAT) based rapid diagnosis was engendered in a global wised large measure as a problem-solving exercise. This review systematically analyzed the recent advances of INAAT strategies with practical case for the real-world scenario virus detection applications. With the qualities that make INAAT systems useful for making diagnosis relevant decisions, the key performance indicators and the cost-effectiveness of enzyme-assisted methods and enzyme-free methods were compared. The modularity of nucleic acid amplification reactions that can lead to thresholding signal amplifications using INAAT reagents and their methodology design were examined, alongside the potential application with rapid test platform/device integration. Given that clinical practitioners are, by and large, unaware of many the isothermal nucleic acid test advances. This review could bridge the arcane research field of different INAAT systems and signal output modalities with end-users in clinic when choosing suitable test kits and/or methods for rapid virus detection.
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Affiliation(s)
- Zhenting Wei
- Frontiers Science Center for Flexible Electronics (FSCFE), Institute of Flexible Electronics (IFE), MIIT Key Laboratory of Flexible Electronics (KLoFE), Xi'an Key Laboratory of Special Medicine and Health Engineering, Northwestern Polytechnical University, Xi'an, China
- North Sichuan Medical College, Nanchong, China
| | - Xiaowen Wang
- Frontiers Science Center for Flexible Electronics (FSCFE), Institute of Flexible Electronics (IFE), MIIT Key Laboratory of Flexible Electronics (KLoFE), Xi'an Key Laboratory of Special Medicine and Health Engineering, Northwestern Polytechnical University, Xi'an, China
- North Sichuan Medical College, Nanchong, China
| | - Huhu Feng
- Frontiers Science Center for Flexible Electronics (FSCFE), Institute of Flexible Electronics (IFE), MIIT Key Laboratory of Flexible Electronics (KLoFE), Xi'an Key Laboratory of Special Medicine and Health Engineering, Northwestern Polytechnical University, Xi'an, China
| | - Fanpu Ji
- Department of Infectious Diseases, The 2nd Hospital of Xi'an Jiaotong University, Nanchong, China
- National and Local Joint Engineering Research Center of Biodiagnosis and Biotherapy, The 2nd Hospital of Xi'an Jiaotong University, Nanchong, China
- Division of Gastroenterology and Hepatology, Stanford University Medical Center, Nanchong, China
| | - Dan Bai
- Frontiers Science Center for Flexible Electronics (FSCFE), Institute of Flexible Electronics (IFE), MIIT Key Laboratory of Flexible Electronics (KLoFE), Xi'an Key Laboratory of Special Medicine and Health Engineering, Northwestern Polytechnical University, Xi'an, China
- Research and Development Institute of Northwestern Polytechnical University in Shenzhen, Northwestern Polytechnical University, Nanchong, China
| | - Xiaoping Dong
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Nanchong, China
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Nanchong, China
| | - Wei Huang
- Frontiers Science Center for Flexible Electronics (FSCFE), Institute of Flexible Electronics (IFE), MIIT Key Laboratory of Flexible Electronics (KLoFE), Xi'an Key Laboratory of Special Medicine and Health Engineering, Northwestern Polytechnical University, Xi'an, China
- Research and Development Institute of Northwestern Polytechnical University in Shenzhen, Northwestern Polytechnical University, Nanchong, China
- Institute of Advanced Materials (IAM), Nanjing Tech University, Nanchong, China
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7
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Diagnostic Techniques for COVID-19: A Mini-review of Early Diagnostic Methods. JOURNAL OF ANALYSIS AND TESTING 2021; 5:314-326. [PMID: 34631199 PMCID: PMC8488931 DOI: 10.1007/s41664-021-00198-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 08/25/2021] [Indexed: 12/26/2022]
Abstract
The outbreak of severe pneumonia at the end of 2019 was proved to be caused by the SARS-CoV-2 virus spreading out the world. And COVID-19 spread rapidly through a terrible transmission way by human-to-human, which led to many suspected cases waiting to be diagnosed and huge daily samples needed to be tested by an effective and rapid detection method. With an increasing number of COVID-19 infections, medical pressure is severe. Therefore, more efficient and accurate diagnosis methods were keen urgently established. In this review, we summarized several methods that can rapidly and sensitively identify COVID-19; some of them are widely used as the diagnostic techniques for SARS-CoV-2 in various countries, some diagnostic technologies refer to SARS (Severe Acute Respiratory Syndrome) or/and MERS (Middle East Respiratory Syndrome) detection, which may provide potential diagnosis ideas.
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Haque MFU, Bukhari SS, Ejaz R, Zaman FU, Sreejith KR, Rashid N, Umer M, Shahzad N. A novel RdRp-based colorimetric RT-LAMP assay for rapid and sensitive detection of SARS-CoV-2 in clinical and sewage samples from Pakistan. Virus Res 2021; 302:198484. [PMID: 34146608 PMCID: PMC8214975 DOI: 10.1016/j.virusres.2021.198484] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/29/2021] [Accepted: 06/07/2021] [Indexed: 01/08/2023]
Abstract
Novel corona virus SARS-CoV-2, causing coronavirus disease 2019 (COVID-19), has become a global health challenge particularly for developing countries like Pakistan where overcrowded cities, inadequate sanitation, little health awareness and poor socioeconomic conditions exist. The SARS-CoV-2 has been known to spread primarily through direct contact and respiratory droplets. However, detection of SARS-CoV-2 in stool and sewage have raised the possibility of fecal-oral mode of transmission. Currently, quantitative reverse-transcriptase PCR (qRT-PCR) is the only method being used for SARS-CoV-2 detection, which requires expensive instrumentation, dedicated laboratory setup, highly skilled staff, and several hours to report results. Considering the high transmissibility and rapid spread, a robust, sensitive, specific and cheaper assay for rapid SARS-CoV-2 detection is highly needed. Herein, we report a novel colorimetric RT-LAMP assay for naked-eye detection of SARS-COV-2 in clinical as well as sewage samples. Our SARS-CoV-2 RdRp-based LAMP assay could successfully detect the virus RNA in 26/28 (93%) of RT-PCR positive COVID-19 clinical samples with 100% specificity (n = 7) within 20 min. We also tested the effect of various additives on the performance of LAMP assay and found that addition of 1 mg/ml bovine serum albumin (BSA) could increase the sensitivity of assay up to 101 copies of target sequence. Moreover, we also successfully applied this assay to detect SARS-CoV-2 in sewage waters collected from those areas of Lahore, a city of Punjab province of Pakistan, declared as virus hotspots by local government. Our optimized LAMP assay could provide a sensitive first tier strategy for SARS-CoV-2 screening and can potentially help diagnostic laboratories in better handling of high sample turnout during pandemic situation. By providing rapid naked-eye SARS-CoV-2 detection in sewage samples, this assay may support pandemic readiness and emergency response to any possible virus outbreaks in future.
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Affiliation(s)
| | | | - Rabia Ejaz
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Faheem Uz Zaman
- School of Life Sciences, Forman Christian College University, Lahore, Pakistan
| | | | - Naeem Rashid
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Muhammad Umer
- Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan Australia.
| | - Naveed Shahzad
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan.
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9
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Andryukov BG, Besednova NN, Kuznetsova TA, Fedyanina LN. Laboratory-Based Resources for COVID-19 Diagnostics: Traditional Tools and Novel Technologies. A Perspective of Personalized Medicine. J Pers Med 2021; 11:jpm11010042. [PMID: 33451039 PMCID: PMC7828525 DOI: 10.3390/jpm11010042] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 01/09/2021] [Accepted: 01/12/2021] [Indexed: 01/08/2023] Open
Abstract
The coronavirus infection 2019 (COVID-19) pandemic, caused by the highly contagious SARS-CoV-2 virus, has provoked a global healthcare and economic crisis. The control over the spread of the disease requires an efficient and scalable laboratory-based strategy for testing the population based on multiple platforms to provide rapid and accurate diagnosis. With the onset of the pandemic, the reverse transcription polymerase chain reaction (RT-PCR) method has become a standard diagnostic tool, which has received wide clinical use. In large-scale and repeated examinations, these tests can identify infected patients with COVID-19, with their accuracy, however, dependent on many factors, while the entire process takes up to 6–8 h. Here we also describe a number of serological systems for detecting antibodies against SARS-CoV-2. These are used to assess the level of population immunity in various categories of people, as well as for retrospective diagnosis of asymptomatic and mild COVID-19 in patients. However, the widespread use of traditional diagnostic tools in the context of the rapid spread of COVID-19 is hampered by a number of limitations. Therefore, the sharp increase in the number of patients with COVID-19 necessitates creation of new rapid, inexpensive, sensitive, and specific tests. In this regard, we focus on new laboratory technologies such as loop mediated isothermal amplification (LAMP) and lateral flow immunoassay (LFIA), which have proven to work well in the COVID-19 diagnostics and can become a worthy alternative to traditional laboratory-based diagnostics resources. To cope with the COVID-19 pandemic, the healthcare system requires a combination of various types of laboratory diagnostic testing techniques, whodse sensitivity and specificity increases with the progress in the SARS-CoV-2 research. The testing strategy should be designed in such a way to provide, depending on the timing of examination and the severity of the infection in patients, large-scale and repeated examinations based on the principle: screening–monitoring–control. The search and development of new methods for rapid diagnostics of COVID-19 in laboratory, based on new analytical platforms, is still a highly important and urgent healthcare issue. In the final part of the review, special emphasis is made on the relevance of the concept of personalized medicine to combat the COVID-19 pandemic in the light of the recent studies carried out to identify the causes of variation in individual susceptibility to SARS-CoV-2 and increase the efficiency and cost-effectiveness of treatment.
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Affiliation(s)
- Boris G. Andryukov
- G.P. Somov Institute of Epidemiology and Microbiology, Russian Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, 690087 Vladivostok, Russia; (N.N.B.); (T.A.K.)
- School of Biomedicine, Far Eastern Federal University (FEFU), 690091 Vladivostok, Russia;
- Correspondence: ; Tel.: +7-4232-304-647
| | - Natalya N. Besednova
- G.P. Somov Institute of Epidemiology and Microbiology, Russian Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, 690087 Vladivostok, Russia; (N.N.B.); (T.A.K.)
| | - Tatyana A. Kuznetsova
- G.P. Somov Institute of Epidemiology and Microbiology, Russian Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, 690087 Vladivostok, Russia; (N.N.B.); (T.A.K.)
| | - Ludmila N. Fedyanina
- School of Biomedicine, Far Eastern Federal University (FEFU), 690091 Vladivostok, Russia;
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10
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Li N, Wang P, Wang X, Geng C, Chen J, Gong Y. Molecular diagnosis of COVID-19: Current situation and trend in China (Review). Exp Ther Med 2020; 20:13. [PMID: 32934678 PMCID: PMC7471877 DOI: 10.3892/etm.2020.9142] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 07/29/2020] [Indexed: 12/13/2022] Open
Abstract
COVID-19 is caused by a novel coronavirus (2019-nCoV or SARS-CoV-2) and has become a global public health emergency. Rapid and accurate molecular diagnostic technologies are crucial for the screening, isolation, treatment, prevention and control of COVID-19. Currently, nucleic acid detection-based techniques and rapid diagnostic tests that detect antigens or antibodies specific to 2019-nCoV infections are the primary diagnostic tools. China National Medical Products Administration has opened a special channel for approval of new pharmaceuticals owing to urgent clinical needs, with 18 nucleic acid detection kits, 11 protein detection kits and 1 sequencing-related equipment and supporting software having been approved until April 23, 2020. The current review summarizes the application situation, advantages, disadvantages and associated technology improvement trends of molecular diagnostics for COVID-19 in China, identifies knowledge gaps and indicates future priorities for research in this field. The most effective way to prevent and control COVID-19 is early detection, diagnosis, isolation and treatment. In the clinical application of molecular diagnosis technology, it is necessary to combine pathogenic microbiology, immunology and other associated detection technologies, advocate the combination of multiple technologies, determine how they complement each other, enhance practicability and improve the ability of rapid and accurate diagnosis and differential diagnosis of COVID-19.
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Affiliation(s)
- Ning Li
- Institute of Disaster Medicine, Tianjin University, Tianjin 300070, P.R. China
- Tianjin Key Laboratory of Disaster Medicine Technology, Tianjin 300072, P.R. China
| | - Pengtao Wang
- Tianjin Key Laboratory of Disaster Medicine Technology, Tianjin 300072, P.R. China
- General Hospital of Tianjin Medical University, Tianjin 300070, P.R. China
| | - Xinyue Wang
- Institute of Disaster Medicine, Tianjin University, Tianjin 300070, P.R. China
- Tianjin Key Laboratory of Disaster Medicine Technology, Tianjin 300072, P.R. China
| | - Chenhao Geng
- Institute of Disaster Medicine, Tianjin University, Tianjin 300070, P.R. China
- Tianjin Key Laboratory of Disaster Medicine Technology, Tianjin 300072, P.R. China
| | - Jiale Chen
- Institute of Disaster Medicine, Tianjin University, Tianjin 300070, P.R. China
- Tianjin Key Laboratory of Disaster Medicine Technology, Tianjin 300072, P.R. China
| | - Yanhua Gong
- Institute of Disaster Medicine, Tianjin University, Tianjin 300070, P.R. China
- Tianjin Key Laboratory of Disaster Medicine Technology, Tianjin 300072, P.R. China
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11
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Everitt ML, Tillery A, David MG, Singh N, Borison A, White IM. A critical review of point-of-care diagnostic technologies to combat viral pandemics. Anal Chim Acta 2020; 1146:184-199. [PMID: 33461715 PMCID: PMC7548029 DOI: 10.1016/j.aca.2020.10.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 10/03/2020] [Accepted: 10/05/2020] [Indexed: 12/13/2022]
Abstract
The COVID-19 global pandemic of 2019-2020 pointedly revealed the lack of diagnostic solutions that are able to keep pace with the rapid spread of the virus. Despite the promise of decades of lab-on-a-chip research, no commercial products were available to deliver rapid results or enable testing in the field at the onset of the pandemic. In this critical review, we assess the current state of progress on the development of point-of-care technologies for the diagnosis of viral diseases that cause pandemics. While many previous reviews have reported on progress in various lab-on-a-chip technologies, here we address the literature from the perspective of the testing needs of a rapidly expanding pandemic. First, we recommend a set of requirements to heed when designing point-of-care diagnostic technologies to address the testing needs of a pandemic. We then review the current state of assay technologies with a focus on isothermal amplification and lateral-flow immunoassays. Though there is much progress on assay development, we argue that the largest roadblock to deployment exists in sample preparation. We summarize current approaches to automate sample preparation and discuss both the progress and shortcomings of these developments. Finally, we provide our recommendations to the field of specific challenges to address in order to prepare for the next pandemic.
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Affiliation(s)
- Micaela L Everitt
- Fischell Department of Bioengineering, University of Maryland, United States
| | - Alana Tillery
- Fischell Department of Bioengineering, University of Maryland, United States
| | - Martha G David
- Fischell Department of Bioengineering, University of Maryland, United States
| | - Nikita Singh
- Fischell Department of Bioengineering, University of Maryland, United States
| | - Aviva Borison
- Fischell Department of Bioengineering, University of Maryland, United States
| | - Ian M White
- Fischell Department of Bioengineering, University of Maryland, United States.
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12
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Rohaim MA, Clayton E, Sahin I, Vilela J, Khalifa ME, Al-Natour MQ, Bayoumi M, Poirier AC, Branavan M, Tharmakulasingam M, Chaudhry NS, Sodi R, Brown A, Burkhart P, Hacking W, Botham J, Boyce J, Wilkinson H, Williams C, Whittingham-Dowd J, Shaw E, Hodges M, Butler L, Bates MD, La Ragione R, Balachandran W, Fernando A, Munir M. Artificial Intelligence-Assisted Loop Mediated Isothermal Amplification (AI-LAMP) for Rapid Detection of SARS-CoV-2. Viruses 2020; 12:v12090972. [PMID: 32883050 PMCID: PMC7552048 DOI: 10.3390/v12090972] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 08/22/2020] [Accepted: 08/24/2020] [Indexed: 01/13/2023] Open
Abstract
Until vaccines and effective therapeutics become available, the practical solution to transit safely out of the current coronavirus disease 19 (CoVID-19) lockdown may include the implementation of an effective testing, tracing and tracking system. However, this requires a reliable and clinically validated diagnostic platform for the sensitive and specific identification of SARS-CoV-2. Here, we report on the development of a de novo, high-resolution and comparative genomics guided reverse-transcribed loop-mediated isothermal amplification (LAMP) assay. To further enhance the assay performance and to remove any subjectivity associated with operator interpretation of results, we engineered a novel hand-held smart diagnostic device. The robust diagnostic device was further furnished with automated image acquisition and processing algorithms and the collated data was processed through artificial intelligence (AI) pipelines to further reduce the assay run time and the subjectivity of the colorimetric LAMP detection. This advanced AI algorithm-implemented LAMP (ai-LAMP) assay, targeting the RNA-dependent RNA polymerase gene, showed high analytical sensitivity and specificity for SARS-CoV-2. A total of ~200 coronavirus disease (CoVID-19)-suspected NHS patient samples were tested using the platform and it was shown to be reliable, highly specific and significantly more sensitive than the current gold standard qRT-PCR. Therefore, this system could provide an efficient and cost-effective platform to detect SARS-CoV-2 in resource-limited laboratories.
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Affiliation(s)
- Mohammed A. Rohaim
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, The Lancaster University, Lancaster LA1 4YW, UK; (M.A.R.); (E.C.); (I.S.); (J.V.); (M.E.K.); (M.Q.A.-N.); (M.B.); (J.W.-D.); (E.S.); (M.H.); (L.B.); (M.D.B.)
| | - Emily Clayton
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, The Lancaster University, Lancaster LA1 4YW, UK; (M.A.R.); (E.C.); (I.S.); (J.V.); (M.E.K.); (M.Q.A.-N.); (M.B.); (J.W.-D.); (E.S.); (M.H.); (L.B.); (M.D.B.)
| | - Irem Sahin
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, The Lancaster University, Lancaster LA1 4YW, UK; (M.A.R.); (E.C.); (I.S.); (J.V.); (M.E.K.); (M.Q.A.-N.); (M.B.); (J.W.-D.); (E.S.); (M.H.); (L.B.); (M.D.B.)
| | - Julianne Vilela
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, The Lancaster University, Lancaster LA1 4YW, UK; (M.A.R.); (E.C.); (I.S.); (J.V.); (M.E.K.); (M.Q.A.-N.); (M.B.); (J.W.-D.); (E.S.); (M.H.); (L.B.); (M.D.B.)
| | - Manar E. Khalifa
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, The Lancaster University, Lancaster LA1 4YW, UK; (M.A.R.); (E.C.); (I.S.); (J.V.); (M.E.K.); (M.Q.A.-N.); (M.B.); (J.W.-D.); (E.S.); (M.H.); (L.B.); (M.D.B.)
| | - Mohammad Q. Al-Natour
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, The Lancaster University, Lancaster LA1 4YW, UK; (M.A.R.); (E.C.); (I.S.); (J.V.); (M.E.K.); (M.Q.A.-N.); (M.B.); (J.W.-D.); (E.S.); (M.H.); (L.B.); (M.D.B.)
| | - Mahmoud Bayoumi
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, The Lancaster University, Lancaster LA1 4YW, UK; (M.A.R.); (E.C.); (I.S.); (J.V.); (M.E.K.); (M.Q.A.-N.); (M.B.); (J.W.-D.); (E.S.); (M.H.); (L.B.); (M.D.B.)
| | - Aurore C. Poirier
- Department of Pathology and Infectious Diseases, School of Veterinary Medicine, University of Surrey, Guildford GU2 7AL, UK; (A.C.P.); (R.L.R.)
| | - Manoharanehru Branavan
- College of Engineering, Design and Physical Sciences, Brunel University London, Kingston Lane, Uxbridge UB8 3PH, UK; (M.B.); (W.B.)
| | - Mukunthan Tharmakulasingam
- Centre for Vision, Speech and Signal Processing, University of Surrey, Guildford GU2 7XH, UK; (M.T.); (N.S.C.); (A.F.)
| | - Nouman S. Chaudhry
- Centre for Vision, Speech and Signal Processing, University of Surrey, Guildford GU2 7XH, UK; (M.T.); (N.S.C.); (A.F.)
| | - Ravinder Sodi
- Department of Biochemistry, Poole & Bournemouth Hospitals NHS Trust, Longfleet Road, Poole BH15 2JB, UK;
| | - Amy Brown
- The Royal Lancaster Infirmary, University Hospitals of Morecambe Bay NHS, Foundation Trust, Kendal LA9 7RG, UK; (A.B.); (P.B.); (W.H.); (J.B.); (J.B.); (H.W.); (C.W.)
| | - Peter Burkhart
- The Royal Lancaster Infirmary, University Hospitals of Morecambe Bay NHS, Foundation Trust, Kendal LA9 7RG, UK; (A.B.); (P.B.); (W.H.); (J.B.); (J.B.); (H.W.); (C.W.)
| | - Wendy Hacking
- The Royal Lancaster Infirmary, University Hospitals of Morecambe Bay NHS, Foundation Trust, Kendal LA9 7RG, UK; (A.B.); (P.B.); (W.H.); (J.B.); (J.B.); (H.W.); (C.W.)
| | - Judy Botham
- The Royal Lancaster Infirmary, University Hospitals of Morecambe Bay NHS, Foundation Trust, Kendal LA9 7RG, UK; (A.B.); (P.B.); (W.H.); (J.B.); (J.B.); (H.W.); (C.W.)
| | - Joe Boyce
- The Royal Lancaster Infirmary, University Hospitals of Morecambe Bay NHS, Foundation Trust, Kendal LA9 7RG, UK; (A.B.); (P.B.); (W.H.); (J.B.); (J.B.); (H.W.); (C.W.)
| | - Hayley Wilkinson
- The Royal Lancaster Infirmary, University Hospitals of Morecambe Bay NHS, Foundation Trust, Kendal LA9 7RG, UK; (A.B.); (P.B.); (W.H.); (J.B.); (J.B.); (H.W.); (C.W.)
| | - Craig Williams
- The Royal Lancaster Infirmary, University Hospitals of Morecambe Bay NHS, Foundation Trust, Kendal LA9 7RG, UK; (A.B.); (P.B.); (W.H.); (J.B.); (J.B.); (H.W.); (C.W.)
| | - Jayde Whittingham-Dowd
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, The Lancaster University, Lancaster LA1 4YW, UK; (M.A.R.); (E.C.); (I.S.); (J.V.); (M.E.K.); (M.Q.A.-N.); (M.B.); (J.W.-D.); (E.S.); (M.H.); (L.B.); (M.D.B.)
| | - Elisabeth Shaw
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, The Lancaster University, Lancaster LA1 4YW, UK; (M.A.R.); (E.C.); (I.S.); (J.V.); (M.E.K.); (M.Q.A.-N.); (M.B.); (J.W.-D.); (E.S.); (M.H.); (L.B.); (M.D.B.)
| | - Matt Hodges
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, The Lancaster University, Lancaster LA1 4YW, UK; (M.A.R.); (E.C.); (I.S.); (J.V.); (M.E.K.); (M.Q.A.-N.); (M.B.); (J.W.-D.); (E.S.); (M.H.); (L.B.); (M.D.B.)
| | - Lisa Butler
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, The Lancaster University, Lancaster LA1 4YW, UK; (M.A.R.); (E.C.); (I.S.); (J.V.); (M.E.K.); (M.Q.A.-N.); (M.B.); (J.W.-D.); (E.S.); (M.H.); (L.B.); (M.D.B.)
| | - Michelle D. Bates
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, The Lancaster University, Lancaster LA1 4YW, UK; (M.A.R.); (E.C.); (I.S.); (J.V.); (M.E.K.); (M.Q.A.-N.); (M.B.); (J.W.-D.); (E.S.); (M.H.); (L.B.); (M.D.B.)
| | - Roberto La Ragione
- Department of Pathology and Infectious Diseases, School of Veterinary Medicine, University of Surrey, Guildford GU2 7AL, UK; (A.C.P.); (R.L.R.)
| | - Wamadeva Balachandran
- College of Engineering, Design and Physical Sciences, Brunel University London, Kingston Lane, Uxbridge UB8 3PH, UK; (M.B.); (W.B.)
| | - Anil Fernando
- Centre for Vision, Speech and Signal Processing, University of Surrey, Guildford GU2 7XH, UK; (M.T.); (N.S.C.); (A.F.)
| | - Muhammad Munir
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, The Lancaster University, Lancaster LA1 4YW, UK; (M.A.R.); (E.C.); (I.S.); (J.V.); (M.E.K.); (M.Q.A.-N.); (M.B.); (J.W.-D.); (E.S.); (M.H.); (L.B.); (M.D.B.)
- Correspondence:
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Bonney LC, Watson RJ, Slack GS, Bosworth A, Wand NIV, Hewson R. A flexible format LAMP assay for rapid detection of Ebola virus. PLoS Negl Trop Dis 2020; 14:e0008496. [PMID: 32735587 PMCID: PMC7423149 DOI: 10.1371/journal.pntd.0008496] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 08/12/2020] [Accepted: 06/16/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The unprecedented 2013/16 outbreak of Zaire ebolavirus (Ebola virus) in West Africa has highighted the need for rapid, high-throughput and POC diagnostic assays to enable timely detection and appropriate triaging of Ebola Virus Disease (EVD) patients. Ebola virus is highly infectious and prompt diagnosis and triage is crucial in preventing further spread within community and healthcare settings. Moreover, due to the ecology of Ebola virus it is important that newly developed diagnostic assays are suitable for use in both the healthcare environment and low resource rural locations. METHODOLOGY/PRINCIPLE FINDINGS A LAMP assay was successfully developed with three detection formats; a real-time intercalating dye-based assay, a real-time probe-based assay to enable multiplexing and an end-point colourimetric assay to simplify interpretation for the field. All assay formats were sensitive and specific, detecting a range of Ebola virus strains isolated in 1976-2014; with Probit analysis predicting limits of detection of 243, 290 and 75 copies/reaction respectively and no cross-detection of related strains or other viral haemorrhagic fevers (VHF's). The assays are rapid, (as fast as 5-7.25 mins for real-time formats) and robust, detecting Ebola virus RNA in presence of minimally diluted bodily fluids. Moreover, when tested on patient samples from the 2013/16 outbreak, there were no false positives and 93-96% of all new case positives were detected, with only a failure to detect very low copy number samples. CONCLUSION/SIGNIFICANCE These are a set of robust and adaptable diagnostic solutions, which are fast, easy-to-perform-and-interpret and are suitable for use on a range of platforms including portable low-power devices. They can be readily transferred to field-laboratory settings, with no specific equipment needs and are therefore ideally placed for use in locations with limited resources.
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Affiliation(s)
- Laura C. Bonney
- Public Health England, National Infection Service, Porton Down, Salisbury, Wiltshire, United Kingdom
| | - Robert J. Watson
- Public Health England, National Infection Service, Porton Down, Salisbury, Wiltshire, United Kingdom
| | - Gillian S. Slack
- Public Health England, National Infection Service, Porton Down, Salisbury, Wiltshire, United Kingdom
| | - Andrew Bosworth
- Public Health England, National Infection Service, Porton Down, Salisbury, Wiltshire, United Kingdom
| | - Nadina I. Vasileva Wand
- Public Health England, National Infection Service, Porton Down, Salisbury, Wiltshire, United Kingdom
| | - Roger Hewson
- Public Health England, National Infection Service, Porton Down, Salisbury, Wiltshire, United Kingdom
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Fast and Parallel Detection of Four Ebola Virus Species on a Microfluidic-Chip-Based Portable Reverse Transcription Loop-Mediated Isothermal Amplification System. MICROMACHINES 2019; 10:mi10110777. [PMID: 31739456 PMCID: PMC6915550 DOI: 10.3390/mi10110777] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 11/08/2019] [Accepted: 11/11/2019] [Indexed: 12/31/2022]
Abstract
Considering the lack of official vaccines and medicines for Ebola virus infection, reliable diagnostic methods are necessary for the control of the outbreak and the spread of the disease. We developed a microfluidic-chip-based portable system for fast and parallel detection of four Ebola virus species. The system is based on reverse transcription loop-mediated isothermal amplification (RT-LAMP) and consists of four specific LAMP primers, a disc microfluidic chip, and a portable real-time fluorescence detector. It could specifically and parallelly distinguish four species of the Ebola virus after only one sampling, including the Zaire Ebola virus, the Sudan Ebola virus, the Bundibugyo Ebola virus, and the Tai Forest Ebola virus, without cross-contamination. The limit of detection was as small as 10 copies per reaction, while the total consumption of sample and reagent was 0.94 μL per reaction. The final results could be obtained in 50 min after one addition of sample and reagent mixture. This approach provides simplicity, high sensitivity, and multi-target parallel detection at a low cost, which could enable convenient and effective on-site detections of the Ebola virus in the outdoors, remote areas, and modern hospitals.
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Hu J, Xiao K, Jin B, Zheng X, Ji F, Bai D. Paper-based point-of-care test with xeno nucleic acid probes. Biotechnol Bioeng 2019; 116:2764-2777. [PMID: 31282991 DOI: 10.1002/bit.27106] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 06/20/2019] [Accepted: 06/24/2019] [Indexed: 01/09/2023]
Abstract
Bridging the unmet need of efficient point-of-care testing (POCT) in biomedical engineering research and practice with the emerging development in artificial synthetic xeno nucleic acids (XNAs), this review summarized the recent development in paper-based POCT using XNAs as sensing probes. Alongside the signal transducing mode and immobilization methods of XNA probes, a detailed evaluation of probe performance was disclosed. With these new aspects, both researchers in synthetic chemistry / biomedical engineering and physicians in clinical practice could gain new insights in designing, manufacturing and choosing suitable reagents and techniques for POCT.
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Affiliation(s)
- Jie Hu
- Singapore Institute of Manufacturing Technology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Kang Xiao
- Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, Beijing, P. R. China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou, P. R. China
| | - Birui Jin
- School of Materials and Chemical Engineering, Xi'an Technological University, Xi'an, P. R. China
| | - Xuyang Zheng
- Department of Infectious Diseases, Tangdu Hospital, The Fourth Military Medical University, Xi'an, Shaanxi, P. R. China
| | - Fanpu Ji
- Department of Infectious Diseases, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
| | - Dan Bai
- Xi'an Institute of Flexible Electronics (IFE) & Xi'an Key Laboratory of Flexible Electronics (KLoFE), MIIT Key Laboratory of Flexible Electronics (KLoFE), Shaanxi Key Laboratory of Flexible Electronics (KLoFE), Northwestern Polytechnical University (NPU), Xi'an, Shaanxi, P. R. China.,Xi'an Institute of Biomedical Materials and Engineering (IBME) & Xi'an Key Laboratory of Biomedical Materials and Engineering (KLBME), Northwestern Polytechnical University (NPU), Xi'an, Shaanxi, P. R. China
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16
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Tembo J, Simulundu E, Changula K, Handley D, Gilbert M, Chilufya M, Asogun D, Ansumana R, Kapata N, Ntoumi F, Ippolito G, Zumla A, Bates M. Recent advances in the development and evaluation of molecular diagnostics for Ebola virus disease. Expert Rev Mol Diagn 2019; 19:325-340. [PMID: 30916590 DOI: 10.1080/14737159.2019.1595592] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
INTRODUCTION The 2014-16 outbreak of ebola virus disease (EVD) in West Africa resulted in 11,308 deaths. During the outbreak only 60% of patients were laboratory confirmed and global health authorities have identified the need for accurate and readily deployable molecular diagnostics as an important component of the ideal response to future outbreaks, to quickly identify and isolate patients. Areas covered: Currently PCR-based techniques and rapid diagnostic tests (RDTs) that detect antigens specific to EVD infections dominate the diagnostic landscape, but recent advances in biosensor technologies have led to novel approaches for the development of EVD diagnostics. This review summarises the literature and available performance data of currently available molecular diagnostics for ebolavirus, identifies knowledge gaps and maps out future priorities for research in this field. Expert opinion: While there are now a plethora of diagnostic tests for EVD at various stages of development, there is an acute need for studies to compare their clinical performance, but the sporadic nature of EVD outbreaks makes this extremely challenging, demanding pragmatic new modalities of research funding and ethical/institutional approval, to enable responsive research in outbreak settings. Retrospective head-to-head diagnostic comparisons could also be implemented using biobanked specimens, providing this can be done safely.
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Affiliation(s)
- John Tembo
- a HerpeZ , University Teaching hospital , Lusaka , Zambia
| | - Edgar Simulundu
- b Department of Disease Control , University of Zambia School of Veterinary Medicine , Lusaka , Zambia
| | - Katendi Changula
- b Department of Disease Control , University of Zambia School of Veterinary Medicine , Lusaka , Zambia
| | - Dale Handley
- c School of Life Sciences , University of Lincoln , Lincoln , UK
| | - Matthew Gilbert
- c School of Life Sciences , University of Lincoln , Lincoln , UK
| | - Moses Chilufya
- a HerpeZ , University Teaching hospital , Lusaka , Zambia
| | - Danny Asogun
- d Lassa fever research institute , Irrua University Teaching Hospital , Irrua , Nigeria
| | | | - Nathan Kapata
- f Zambia National Public Health Institute , Lusaka , Zambia
| | - Francine Ntoumi
- g Fondation Congolaise pour la Recherche Médicale , Brazzaville , Republic of Congo
| | - Giuseppe Ippolito
- h National Institute for Infectious Diseases , Lazzaro Spallanzani, IRCCS , Rome , Italy
| | - Alimuddin Zumla
- i Centre for Clinical Microbiology, Division of Infection and Immunity , University College London (UCL) , London , UK.,j National Institute of Health and Research Biomedical Research Centre , UCL Hospitals National Health Service Foundation Trust , London , UK
| | - Matthew Bates
- a HerpeZ , University Teaching hospital , Lusaka , Zambia.,c School of Life Sciences , University of Lincoln , Lincoln , UK.,i Centre for Clinical Microbiology, Division of Infection and Immunity , University College London (UCL) , London , UK
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Filovirus – Auslöser von hämorrhagischem Fieber. Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz 2018; 61:894-907. [DOI: 10.1007/s00103-018-2757-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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18
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Huang P, Wang H, Cao Z, Jin H, Chi H, Zhao J, Yu B, Yan F, Hu X, Wu F, Jiao C, Hou P, Xu S, Zhao Y, Feng N, Wang J, Sun W, Wang T, Gao Y, Yang S, Xia X. A Rapid and Specific Assay for the Detection of MERS-CoV. Front Microbiol 2018; 9:1101. [PMID: 29896174 PMCID: PMC5987675 DOI: 10.3389/fmicb.2018.01101] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 05/08/2018] [Indexed: 12/21/2022] Open
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) is a novel human coronavirus that can cause human respiratory disease. The development of a detection method for this virus that can lead to rapid and accurate diagnosis would be significant. In this study, we established a nucleic acid visualization technique that combines the reverse transcription loop-mediated isothermal amplification technique and a vertical flow visualization strip (RT-LAMP-VF) to detect the N gene of MERS-CoV. The RT-LAMP-VF assay was performed in a constant temperature water bath for 30 min, and the result was visible by the naked eye within 5 min. The RT-LAMP-VF assay was capable of detecting 2 × 101 copies/μl of synthesized RNA transcript and 1 × 101 copies/μl of MERS-CoV RNA. The method exhibits no cross-reactivities with multiple CoVs including SARS-related (SARSr)-CoV, HKU4, HKU1, OC43 and 229E, and thus exhibits high specificity. Compared to the real-time RT-PCR (rRT-PCR) method recommended by the World Health Organization (WHO), the RT-LAMP-VF assay is easy to handle, does not require expensive equipment and can rapidly complete detection within 35 min.
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Affiliation(s)
- Pei Huang
- Animal Science and Technology College, Jilin Agricultural University, Changchun, China.,Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Hualei Wang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China.,College of Veterinary Medicine, Jilin University, Changchun, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou, China
| | - Zengguo Cao
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China.,College of Veterinary Medicine, Jilin University, Changchun, China
| | - Hongli Jin
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China.,College of Veterinary Medicine, Jilin University, Changchun, China
| | - Hang Chi
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Heath, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Guangzhou Eighth People's Hospital of Guangzhou Medical University, Guangzhou, China
| | - Beibei Yu
- Department of Clinical Laboratory, College of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Feihu Yan
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Xingxing Hu
- Animal Science and Technology College, Jilin Agricultural University, Changchun, China.,Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Fangfang Wu
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Cuicui Jiao
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Pengfei Hou
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China.,College of Veterinary Medicine, Jilin University, Changchun, China
| | - Shengnan Xu
- Animal Science and Technology College, Jilin Agricultural University, Changchun, China.,Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Yongkun Zhao
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou, China
| | - Na Feng
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou, China
| | - Jianzhong Wang
- Animal Science and Technology College, Jilin Agricultural University, Changchun, China
| | - Weiyang Sun
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou, China
| | - Tiecheng Wang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou, China
| | - Yuwei Gao
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou, China
| | - Songtao Yang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou, China
| | - Xianzhu Xia
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou, China
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19
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Clark DJ, Tyson J, Sails AD, Krishna S, Staines HM. The current landscape of nucleic acid tests for filovirus detection. J Clin Virol 2018; 103:27-36. [PMID: 29625392 PMCID: PMC5958242 DOI: 10.1016/j.jcv.2018.03.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 03/14/2018] [Indexed: 11/03/2022]
Abstract
Filoviruses can cause severe hemorrhagic fever in humans and non-human primates. There is an urgent need for rapid diagnosis of filoviruses during outbreaks. Filovirus diagnostics have advanced since the 2014–2016 Ebolavirus outbreak. NATs are the gold standard for filovirus detection. NAT-based diagnostic speed, portability and multiplexing have all improved.
Nucleic acid testing (NAT) for pathogenic filoviruses plays a key role in surveillance and to control the spread of infection. As they share clinical features with other pathogens, the initial spread of these viruses can be misdiagnosed. Tests that can identify a pathogen in the initial stages of infection are essential to control outbreaks. Since the Ebola virus disease (EVD) outbreak in 2014–2016 several tests have been developed that are faster than previous tests and more suited for field use. Furthermore, the ability to test for a range of pathogens simultaneously has been expanded to improve clinical pathway management of febrile syndromes. This review provides an overview of these novel diagnostic tests.
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Affiliation(s)
- David J Clark
- Centre for Diagnostics & Antimicrobial Resistance, Institute for Infection & Immunity, St. George's University of London, Cranmer Terrace, London SW17 0RE, UK; Institute for Infection & Immunity, St. George's University of London, Cranmer Terrace, London SW17 0RE, UK.
| | - John Tyson
- QuantuMDx, Lugano Building, 57 Melbourne Street, Newcastle-upon-Tyne, NE1 2JQ, UK
| | - Andrew D Sails
- QuantuMDx, Lugano Building, 57 Melbourne Street, Newcastle-upon-Tyne, NE1 2JQ, UK
| | - Sanjeev Krishna
- Centre for Diagnostics & Antimicrobial Resistance, Institute for Infection & Immunity, St. George's University of London, Cranmer Terrace, London SW17 0RE, UK; Institute for Infection & Immunity, St. George's University of London, Cranmer Terrace, London SW17 0RE, UK; St. George's University Hospitals NHS Foundation Trust, Blackshaw Road, Tooting, London SW17 0QT, UK
| | - Henry M Staines
- Centre for Diagnostics & Antimicrobial Resistance, Institute for Infection & Immunity, St. George's University of London, Cranmer Terrace, London SW17 0RE, UK; Institute for Infection & Immunity, St. George's University of London, Cranmer Terrace, London SW17 0RE, UK
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20
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Hu L, Ma L, Zheng S, He X, Wang H, Brown E, Hammack T, Zhang G. Evaluation of 3M Molecular Detection System and ANSR Pathogen Detection System for rapid detection of Salmonella from egg products. Poult Sci 2017; 96:1410-1418. [DOI: 10.3382/ps/pew399] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 10/13/2016] [Indexed: 01/22/2023] Open
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Oloniniyi OK, Kurosaki Y, Miyamoto H, Takada A, Yasuda J. Rapid detection of all known ebolavirus species by reverse transcription-loop-mediated isothermal amplification (RT-LAMP). J Virol Methods 2017; 246:8-14. [PMID: 28356221 DOI: 10.1016/j.jviromet.2017.03.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 03/22/2017] [Accepted: 03/24/2017] [Indexed: 11/26/2022]
Abstract
Ebola virus disease (EVD), a highly virulent infectious disease caused by ebolaviruses, has a fatality rate of 25-90%. Without a licensed chemotherapeutic agent or vaccine for the treatment and prevention of EVD, control of outbreaks requires accurate and rapid diagnosis of cases. In this study, five sets of six oligonucleotide primers targeting the nucleoprotein gene were designed for specific identification of each of the five ebolavirus species using reverse transcription-loop mediated isothermal amplification (RT-LAMP) assay. The detection limits of the ebolavirus species-specific primer sets were evaluated using in vitro transcribed RNAs. The detection limit of species-specific RT-LAMP assays for Zaire ebolavirus, Sudan ebolavirus, Taï Forest ebolavirus, and Bundibugyo ebolavirus was 256 copies/reaction, while the detection limit for Reston ebolavirus was 64 copies/reaction, and the detection time for each of the RT-LAMP assays was 13.3±3.0, 19.8±4.6, 14.3±0.6, 16.1±4.7, and 19.8±2.4min (mean±SD), respectively. The sensitivity of the species-specific RT-LAMP assays were similar to that of the established RT-PCR and quantitative RT-PCR assays for diagnosis of EVD and are suitable for field or point-of-care diagnosis. The RT-LAMP assays were specific for the detection of the respective species of ebolavirus with no cross reaction with other species of ebolavirus and other viral hemorrhagic fever viruses such as Marburg virus, Lassa fever virus, and Dengue virus. The species-specific RT-LAMP assays developed in this study are rapid, sensitive, and specific and could be useful in case of an EVD outbreak.
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Affiliation(s)
- Olamide K Oloniniyi
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan; Graduate School of Biomedical Sciences and Program for Nurturing Global Leaders in Tropical and Emerging Communicable Diseases, Nagasaki University, Nagasaki, Japan.
| | - Yohei Kurosaki
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan.
| | - Hiroko Miyamoto
- Division of Global Epidemiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.
| | - Ayato Takada
- Division of Global Epidemiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan; Global station for Zoonosis Control, Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo, Japan.
| | - Jiro Yasuda
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan; Graduate School of Biomedical Sciences and Program for Nurturing Global Leaders in Tropical and Emerging Communicable Diseases, Nagasaki University, Nagasaki, Japan.
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22
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Benzine JW, Brown KM, Agans KN, Godiska R, Mire CE, Gowda K, Converse B, Geisbert TW, Mead DA, Chander Y. Molecular Diagnostic Field Test for Point-of-Care Detection of Ebola Virus Directly From Blood. J Infect Dis 2016; 214:S234-S242. [PMID: 27638947 DOI: 10.1093/infdis/jiw330] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A molecular diagnostic method for robust detection of Ebola virus (EBOV) at the point of care (POC) directly from blood samples is described. This assay is based on reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) of the glycoprotein gene of EBOV. Complete reaction formulations were lyophilized in 0.2-mL polymerase chain reaction tubes. RT-LAMP reactions were performed on a battery-operated isothermal instrument. Limit of detection of this RT-LAMP assay was 2.8 × 102 plaque-forming units (PFU)/test and 1 × 103 PFU/test within 40 minutes for EBOV-Kikwit and EBOV-Makona, respectively. This assay was found to be specific for the detection of EBOV, as no nonspecific amplification was detected in blood samples spiked with closely related viruses and other pathogens. These results showed that this diagnostic test can be used at the point of care for rapid and specific detection of EBOV directly from blood with high sensitivity within 40 minutes.
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Affiliation(s)
| | | | - Krystle N Agans
- Department of Microbiology and Immunology Galveston National Laboratory, University of Texas Medical Branch at Galveston
| | | | - Chad E Mire
- Department of Microbiology and Immunology Galveston National Laboratory, University of Texas Medical Branch at Galveston
| | | | | | - Thomas W Geisbert
- Department of Microbiology and Immunology Galveston National Laboratory, University of Texas Medical Branch at Galveston
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