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Frazer JL, Norton R. Dengue: A review of laboratory diagnostics in the vaccine age. J Med Microbiol 2024; 73. [PMID: 38722305 DOI: 10.1099/jmm.0.001833] [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: 06/30/2024] Open
Abstract
Background. Dengue is an important arboviral infection of considerable public health significance. It occurs in a wide global belt within a variety of tropical regions. The timely laboratory diagnosis of Dengue infection is critical to inform both clinical management and an appropriate public health response. Vaccination against Dengue virus is being introduced in some areas.Discussion. Appropriate diagnostic strategies will vary between laboratories depending on the available resources and skills. Diagnostic methods available include viral culture, the serological detection of Dengue-specific antibodies in using enzyme immunoassays (EIAs), microsphere immunoassays, haemagglutination inhibition or in lateral flow point of care tests. The results of antibody tests may be influenced by prior vaccination and exposure to other flaviviruses. The detection of non-structural protein 1 in serum (NS1) has improved the early diagnosis of Dengue and is available in point-of-care assays in addition to EIAs. Direct detection of viral RNA from blood by PCR is more sensitive than NS1 antigen detection but requires molecular skills and resources. An increasing variety of isothermal nucleic acid detection methods are in development. Timing of specimen collection and choice of test is critical to optimize diagnostic accuracy. Metagenomics and the direct detection by sequencing of viral RNA from blood offers the ability to rapidly type isolates for epidemiologic purposes.Conclusion. The impact of vaccination on immune response must be recognized as it will impact test interpretation and diagnostic algorithms.
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Affiliation(s)
| | - Robert Norton
- Pathology Queensland, Townsville QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
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Tayyab M, Barrett D, van Riel G, Liu S, Reinius B, Scharfe C, Griffin P, Steinmetz LM, Javanmard M, Pelechano V. Digital assay for rapid electronic quantification of clinical pathogens using DNA nanoballs. SCIENCE ADVANCES 2023; 9:eadi4997. [PMID: 37672583 PMCID: PMC10482329 DOI: 10.1126/sciadv.adi4997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 08/04/2023] [Indexed: 09/08/2023]
Abstract
Fast and accurate detection of nucleic acids is key for pathogen identification. Methods for DNA detection generally rely on fluorescent or colorimetric readout. The development of label-free assays decreases costs and test complexity. We present a novel method combining a one-pot isothermal generation of DNA nanoballs with their detection by electrical impedance. We modified loop-mediated isothermal amplification by using compaction oligonucleotides that self-assemble the amplified target into nanoballs. Next, we use capillary-driven flow to passively pass these nanoballs through a microfluidic impedance cytometer, thus enabling a fully compact system with no moving parts. The movement of individual nanoballs is detected by a change in impedance providing a quantized readout. This approach is flexible for the detection of DNA/RNA of numerous targets (severe acute respiratory syndrome coronavirus 2, HIV, β-lactamase gene, etc.), and we anticipate that its integration into a standalone device would provide an inexpensive (<$5), sensitive (10 target copies), and rapid test (<1 hour).
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Affiliation(s)
- Muhammad Tayyab
- Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Donal Barrett
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Gijs van Riel
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Shujing Liu
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
- International Institute of Tea Industry Innovation for the Belt and Road, Nanjing Agricultural University, Nanjing 210095, China
| | - Björn Reinius
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden
| | | | - Peter Griffin
- Stanford Genome Technology Center, Stanford, CA, USA
| | - Lars M. Steinmetz
- Stanford Genome Technology Center, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Mehdi Javanmard
- Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Vicent Pelechano
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
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Alipanah M, Manzanas C, Hai X, Lednicky JA, Paniz-Mondolfi A, Morris JG, Fan ZH. Mayaro virus detection by integrating sample preparation with isothermal amplification in portable devices. Anal Bioanal Chem 2023; 415:5605-5617. [PMID: 37470813 PMCID: PMC10528734 DOI: 10.1007/s00216-023-04856-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 07/04/2023] [Accepted: 07/06/2023] [Indexed: 07/21/2023]
Abstract
Mayaro virus (MAYV) is an emerging mosquito-borne alphavirus that causes clinical symptoms similar to those caused by Chikungunya virus (CHIKV), Dengue virus (DENV), and Zika virus (ZIKV). To differentiate MAYV from these viruses diagnostically, we have developed a portable device that integrates sample preparation with real-time, reverse-transcription, loop-mediated isothermal amplification (rRT-LAMP). First, we designed a rRT-LAMP assay targeting MAYV's non-structural protein (NS1) gene and determined the limit of detection of at least 10 viral genome equivalents per reaction. The assay was specific for MAYV, without cross-reactions with CHIKV, DENV, or ZIKV. The rRT-LAMP assay was integrated with a sample preparation device (SPD) wherein virus lysis and RNA enrichment/purification were carried out on the spot, without requiring pipetting, while subsequent real-time amplification device (RAD) enables virus detection at the point of care (POC). The functions of our platform were demonstrated using purified MAYV RNA or blood samples containing viable viruses. We have used the devices for detection of MAYV in as short as 13 min, with limit of detection to as low as 10 GEs/reaction.
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Affiliation(s)
- Morteza Alipanah
- Interdisciplinary Microsystems Group, Department of Mechanical and Aerospace Engineering, University of Florida, P.O. Box 116250, Gainesville, FL, 32611, USA
| | - Carlos Manzanas
- Interdisciplinary Microsystems Group, Department of Mechanical and Aerospace Engineering, University of Florida, P.O. Box 116250, Gainesville, FL, 32611, USA
| | - Xin Hai
- Interdisciplinary Microsystems Group, Department of Mechanical and Aerospace Engineering, University of Florida, P.O. Box 116250, Gainesville, FL, 32611, USA
| | - John A Lednicky
- Emerging Pathogens Institute, University of Florida, P.O. Box 100009, Gainesville, FL, 32610, USA.
- Department of Environmental and Global Health, University of Florida, PO Box 100188, Gainesville, FL, 32610, USA.
| | - Alberto Paniz-Mondolfi
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, New York, NY, 10029, USA
| | - J Glenn Morris
- Emerging Pathogens Institute, University of Florida, P.O. Box 100009, Gainesville, FL, 32610, USA
| | - Z Hugh Fan
- Interdisciplinary Microsystems Group, Department of Mechanical and Aerospace Engineering, University of Florida, P.O. Box 116250, Gainesville, FL, 32611, USA.
- Emerging Pathogens Institute, University of Florida, P.O. Box 100009, Gainesville, FL, 32610, USA.
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, P.O. Box 116131, Gainesville, FL, 32611, USA.
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL, 32611, USA.
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4
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Tripathi P. Medical viruses: diagnostic techniques. Virol J 2023; 20:143. [PMID: 37434239 DOI: 10.1186/s12985-023-02108-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/26/2023] [Indexed: 07/13/2023] Open
Abstract
The recent epidemics and pandemics caused by different viruses such as SARS-CoV-2, monkey pox, H1N1, ebola virus etc. have been a cause of mass destruction in the human race, the biggest decline slope in the global economy and mental trauma. A number of viruses have been discovered that may cause serious problems and to overcome this problem, early diagnosis of the viruses and understanding their infection pattern is a must. Early detection of viruses inside the host provides timely management in a strategic manner. Scientists have developed some effective and efficient methods to detect the viruses. In this review, we have explained a few types of diagnostic techniques: Biosensor based, immunological-based, and molecular-based diagnostic techniques that are prominent methodologies to identify and detect the course of infection related to the medical viruses. In biosensor-based diagnostic technique, an analytical device consisting of biological elements and physicochemical component gives a signal upon detection of viral antigen. In immunological-based diagnostic techniques, enzyme-linked antibodies are utilized to find the particular antiviral antibody or viral antigen in human specimens, and nucleic acid-based diagnostic techniques are based on the principle of amplification of the viral genome.
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Affiliation(s)
- Pratima Tripathi
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Bijnor-Sisendi Road, Sarojini Nagar, Near CRPF Base Camp, Lucknow, UP, 226002, India.
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Dutta R, Rajendran K, Jana SK, Saleena LM, Ghorai S. Use of Graphene and Its Derivatives for the Detection of Dengue Virus. BIOSENSORS 2023; 13:349. [PMID: 36979561 PMCID: PMC10046626 DOI: 10.3390/bios13030349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 02/18/2023] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
Every year, the dengue virus and its principal mosquito vector, Aedes sp., have caused massive outbreaks, primarily in equatorial countries. The pre-existing techniques available for dengue detection are expensive and require trained personnel. Graphene and its derivatives have remarkable properties of electrical and thermal conductivity, and are flexible, light, and biocompatible, making them ideal platforms for biosensor development. The incorporation of these materials, along with appropriate nanomaterials, improves the quality of detection methods. Graphene can help overcome the difficulties associated with conventional techniques. In this review, we have given comprehensive details on current graphene-based diagnostics for dengue virus detection. We have also discussed state-of-the-art biosensing technologies and evaluated the advantages and disadvantages of the same.
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Affiliation(s)
- Reshmi Dutta
- Department of Biotechnology, SRM Institute of Science and Technology, College of Engineering and Technology, SRM Nagar, Kattankulathur, Kanchipuram, Chennai 603203, India
| | - Kokilavani Rajendran
- Department of Biotechnology, National Institute of Technology, Arunachal Pradesh 791109, India
| | - Saikat Kumar Jana
- Department of Biotechnology, National Institute of Technology, Arunachal Pradesh 791109, India
| | - Lilly M. Saleena
- Department of Biotechnology, SRM Institute of Science and Technology, College of Engineering and Technology, SRM Nagar, Kattankulathur, Kanchipuram, Chennai 603203, India
| | - Suvankar Ghorai
- Department of Microbiology, Raiganj University, Raiganj 733134, India
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Li X, Wang J, Geng J, Xiao L, Wang H. Emerging Landscape of SARS-CoV-2 Variants and Detection Technologies. Mol Diagn Ther 2023; 27:159-177. [PMID: 36577887 PMCID: PMC9797111 DOI: 10.1007/s40291-022-00631-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/04/2022] [Indexed: 12/29/2022]
Abstract
In 2019, a new coronavirus was identified that has caused significant morbidity and mortality worldwide. Like all RNA viruses, severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2) evolves over time through random mutation resulting in genetic variations in the population. Although the currently approved coronavirus disease 2019 vaccines can be given to those over 5 years of age and older in most countries, strikingly, the number of people diagnosed positive for SARS-Cov-2 is still increasing. Therefore, to prevent and control this epidemic, early diagnosis of infected individuals is of great importance. The current detection of SARS-Cov-2 coronavirus variants are mainly based on reverse transcription-polymerase chain reaction. Although the sensitivity of reverse transcription-polymerase chain reaction is high, it has some disadvantages, for example, multiple temperature changes, long detection time, complicated operation, expensive instruments, and the need for professional personnel, which brings considerable inconvenience to the early diagnosis of this virus. This review comprehensively summarizes the development and application of various current detection technologies for novel coronaviruses, including isothermal amplification, CRISPR-Cas detection, serological detection, biosensor, ensemble, and microfluidic technology, along with next-generation sequencing. Those findings offer us a great potential to replace or combine with reverse transcription-polymerase chain reaction detection to achieve the purpose of allowing predictive diagnostics and targeted prevention of SARS-Cov-2 in the future.
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Affiliation(s)
- Xianghui Li
- Department of Microbiology and Immunology, Medical School, China Three Gorges University, Yichang, 443002, China
| | - Jing Wang
- Institute of Cell Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Jingping Geng
- Department of Microbiology and Immunology, Medical School, China Three Gorges University, Yichang, 443002, China
| | - Liming Xiao
- Institute of Cell Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Hu Wang
- Department of Microbiology and Immunology, Medical School, China Three Gorges University, Yichang, 443002, China.
- Institute of Cell Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD, USA.
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Wang M, Liu H, Ren J, Huang Y, Deng Y, Liu Y, Chen Z, Chow FWN, Leung PHM, Li S. Enzyme-Assisted Nucleic Acid Amplification in Molecular Diagnosis: A Review. BIOSENSORS 2023; 13:bios13020160. [PMID: 36831926 PMCID: PMC9953907 DOI: 10.3390/bios13020160] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 01/03/2023] [Accepted: 01/05/2023] [Indexed: 06/12/2023]
Abstract
Infectious diseases and tumors have become the biggest medical challenges in the 21st century. They are driven by multiple factors such as population growth, aging, climate change, genetic predispositions and more. Nucleic acid amplification technologies (NAATs) are used for rapid and accurate diagnostic testing, providing critical information in order to facilitate better follow-up treatment and prognosis. NAATs are widely used due their high sensitivity, specificity, rapid amplification and detection. It should be noted that different NAATs can be selected according to different environments and research fields; for example, isothermal amplification with a simple operation can be preferred in developing countries or resource-poor areas. In the field of translational medicine, CRISPR has shown great prospects. The core component of NAAT lies in the activity of different enzymes. As the most critical material of nucleic acid amplification, the key role of the enzyme is self-evident, playing the upmost important role in molecular diagnosis. In this review, several common enzymes used in NAATs are compared and described in detail. Furthermore, we summarize both the advances and common issues of NAATs in clinical application.
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Affiliation(s)
- Meiling Wang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Hongna Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Jie Ren
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Yunqi Huang
- 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
| | - Yuan Liu
- Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Zhu Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Franklin Wang-Ngai Chow
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Polly Hang-Mei Leung
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
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Zeyaullah M, Muzammil K, AlShahrani AM, Khan N, Ahmad I, Alam MS, Ahmad R, Khan WH. Preparedness for the Dengue Epidemic: Vaccine as a Viable Approach. Vaccines (Basel) 2022; 10:1940. [PMID: 36423035 PMCID: PMC9697487 DOI: 10.3390/vaccines10111940] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 11/10/2022] [Accepted: 11/12/2022] [Indexed: 08/08/2023] Open
Abstract
Dengue fever is one of the significant fatal mosquito-borne viral diseases and is considered to be a worldwide problem. Aedes mosquito is responsible for transmitting various serotypes of dengue viruses to humans. Dengue incidence has developed prominently throughout the world in the last ten years. The exact number of dengue cases is underestimated, whereas plenty of cases are misdiagnosed as alternative febrile sicknesses. There is an estimation that about 390 million dengue cases occur annually. Dengue fever encompasses a wide range of clinical presentations, usually with undefinable clinical progression and outcome. The diagnosis of dengue depends on serology tests, molecular diagnostic methods, and antigen detection tests. The therapeutic approach relies completely on supplemental drugs, which is far from the real approach. Vaccines for dengue disease are in various stages of development. The commercial formulation Dengvaxia (CYD-TDV) is accessible and developed by Sanofi Pasteur. The vaccine candidate Dengvaxia was inefficient in liberating a stabilized immune reaction toward different serotypes (1-4) of dengue fever. Numerous promising vaccine candidates are now being developed in preclinical and clinical stages even though different serotypes of DENV exist that worsen the situation for a vaccine to be equally effective for all serotypes. Thus, the development of an efficient dengue fever vaccine candidate requires time. Effective dengue fever management can be a multidisciplinary challenge, involving international cooperation from diverse perspectives and expertise to resolve this global concern.
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Affiliation(s)
- Md. Zeyaullah
- Department of Basic Medical Science, College of Applied Medical Sciences, Khamis Mushayt Campus, King Khalid University (KKU), Abha 62561, Saudi Arabia
| | - Khursheed Muzammil
- Department of Public Health, College of Applied Medical Sciences, Khamis Mushayt Campus, King Khalid University (KKU), Abha 62561, Saudi Arabia
| | - Abdullah M. AlShahrani
- Department of Basic Medical Science, College of Applied Medical Sciences, Khamis Mushayt Campus, King Khalid University (KKU), Abha 62561, Saudi Arabia
| | - Nida Khan
- Department of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Irfan Ahmad
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University (KKU), Abha 62561, Saudi Arabia
| | - Md. Shane Alam
- Department of Medical Laboratory Technology, College of Applied Medical Sciences, Jazan University, Jazan 45142, Saudi Arabia
| | - Razi Ahmad
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Wajihul H. Khan
- Department of Microbiology, All India Institute of Medical Sciences Delhi, New Delhi 110029, India
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Iqbal BN, Arunasalam S, Divarathna MVM, Jabeer AAOM, Sirisena PDNN, Senaratne T, Muthugala R, Noordeen F. Diagnostic utility and validation of a newly developed real time loop mediated isothermal amplification method for the detection of SARS CoV-2 infection. JOURNAL OF CLINICAL VIROLOGY PLUS 2022; 2:100081. [PMID: 35540180 PMCID: PMC9069985 DOI: 10.1016/j.jcvp.2022.100081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 04/23/2022] [Accepted: 05/04/2022] [Indexed: 01/17/2023] Open
Abstract
Background Detecting SARS-CoV-2 using a simple real time molecular assay will be helpful for the mitigation efforts in low / middle income countries during the pandemic. We have developed and validated a rapid and simple real time loop mediated isothermal amplification assay (LAMP) for screening of SARS-CoV-2 infection in known infected and non-infected individuals. Methods Six sets of primers were designed targeting the N-gene of the SARS-CoV-2 (Accession ID MN994468). LAMP reactions were performed using Warm Start 2X Master Mix and real-time PCR machine at 65 °C for 60 cycles with 15 s for each cycle. Results were read by visualizing turbidity under ultraviolet light and real time fluorescence detection through FAM channel of the real time PCR machine. We tested a total of 320 including 240 SARS CoV-2 positive (Ct values <40) and 80 SARS CoV-2 negative samples as tested by a real time RT-PCR using the newly developed LAMP assay. Results A total of 206 out of 240 SARS CoV-2 positive samples were tested positive by the newly developed LAMP assay with a sensitivity of 86%. All 80 SARS CoV-2 negative samples were tested negative by the newly developed LAMP assay with a specificity of 100%. Conclusion The newly developed real time LAMP assay has a sensitivity of 86% and specificity of 100% compared to the real time RT-PCR for the detection of SARS CoV-2. The new assay will be useful to screen large number of samples if adopted to minimize the time and cost.
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Affiliation(s)
- Bushran N Iqbal
- Diagnostic and Research Virology Laboratory, Department of Microbiology, Faculty of Medicine, University of Peradeniya, Peradeniya 20400, Sri Lanka
| | - Shiyamalee Arunasalam
- Diagnostic and Research Virology Laboratory, Department of Microbiology, Faculty of Medicine, University of Peradeniya, Peradeniya 20400, Sri Lanka
| | - Maduja V M Divarathna
- Diagnostic and Research Virology Laboratory, Department of Microbiology, Faculty of Medicine, University of Peradeniya, Peradeniya 20400, Sri Lanka
| | - AAOM Jabeer
- Diagnostic and Research Virology Laboratory, Department of Microbiology, Faculty of Medicine, University of Peradeniya, Peradeniya 20400, Sri Lanka
| | | | - Thamarasi Senaratne
- Department of Multidisciplinary Sciences, Faculty of Allied Health Sciences, General Sir John Kotelawala Defense University, Werahera, Ratmalana 10390, Sri Lanka
| | - Rohitha Muthugala
- Diagnostic and Reference Virology Laboratory, National Hospital, Kandy 20000, Sri Lanka
| | - Faseeha Noordeen
- Diagnostic and Research Virology Laboratory, Department of Microbiology, Faculty of Medicine, University of Peradeniya, Peradeniya 20400, Sri Lanka,Corresponding author
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A molecular beacon biosensor for viral RNA detection based on HyCaSD strategy. Anal Chim Acta 2022; 1221:340134. [DOI: 10.1016/j.aca.2022.340134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 06/26/2022] [Indexed: 11/24/2022]
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Islam MM, Koirala D. Toward a next-generation diagnostic tool: A review on emerging isothermal nucleic acid amplification techniques for the detection of SARS-CoV-2 and other infectious viruses. Anal Chim Acta 2022; 1209:339338. [PMID: 35569864 PMCID: PMC8633689 DOI: 10.1016/j.aca.2021.339338] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 11/22/2021] [Accepted: 11/27/2021] [Indexed: 01/09/2023]
Abstract
As the COVID-19 pandemic continues to affect human health across the globe rapid, simple, point-of-care (POC) diagnosis of infectious viruses such as SARS-CoV-2 remains challenging. Polymerase chain reaction (PCR)-based diagnosis has risen to meet these demands and despite its high-throughput and accuracy, it has failed to gain traction in the rapid, low-cost, point-of-test settings. In contrast, different emerging isothermal amplification-based detection methods show promise in the rapid point-of-test market. In this comprehensive study of the literature, several promising isothermal amplification methods for the detection of SARS-CoV-2 are critically reviewed that can also be applied to other infectious viruses detection. Starting with a brief discussion on the SARS-CoV-2 structure, its genomic features, and the epidemiology of the current pandemic, this review focuses on different emerging isothermal methods and their advancement. The potential of isothermal amplification combined with the revolutionary CRISPR/Cas system for a more powerful detection tool is also critically reviewed. Additionally, the commercial success of several isothermal methods in the pandemic are highlighted. Different variants of SARS-CoV-2 and their implication on isothermal amplifications are also discussed. Furthermore, three most crucial aspects in achieving a simple, fast, and multiplexable platform are addressed.
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Farrera‐Soler L, Gonse A, Kim KT, Barluenga S, Winssinger N. Combining recombinase polymerase amplification and DNA-templated reaction for SARS-CoV-2 sensing with dual fluorescence and lateral flow assay output. Biopolymers 2022; 113:e23485. [PMID: 35023571 PMCID: PMC9011641 DOI: 10.1002/bip.23485] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 12/17/2021] [Accepted: 12/20/2021] [Indexed: 12/17/2022]
Abstract
The early phase of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic was exacerbated by a diagnostic challenge of unprecedented magnitude. In the absence of effective therapeutics or vaccines, breaking the chain of transmission through early disease detection and patient isolation was the only means to control the growing pandemic. While polymerase chain reaction (PCR)-based methods and rapid-antigen tests rose to the occasion, the analytical challenge of rapid and sequence-specific nucleic acid-sensing at a point-of-care or home setting stimulated intense developments. Herein we report a method that combines recombinase polymerase amplification and a DNA-templated reaction to achieve a dual readout with either fluorescence (microtiter plate) or naked eye (lateral flow assay: LFA) detection. The nucleic acid templated reaction is based on an SN Ar that simultaneously transfers biotin from one Peptide Nucleic Acid (PNA) strand to another PNA strand, enabling LFA detection while uncaging a coumarin for fluorescence readout. This methodology has been applied to the detection of a DNA or RNA sequence uniquely attributed to the SARS-CoV-2.
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Affiliation(s)
- Lluc Farrera‐Soler
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of ScienceUniversity of GenevaGenevaSwitzerland
| | - Arthur Gonse
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of ScienceUniversity of GenevaGenevaSwitzerland
| | - Ki Tae Kim
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of ScienceUniversity of GenevaGenevaSwitzerland
| | - Sofia Barluenga
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of ScienceUniversity of GenevaGenevaSwitzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of ScienceUniversity of GenevaGenevaSwitzerland
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Leon F, Pinchon E, Mayran C, Daynès A, Morvan F, Molès JP, Cantaloube JF, Fournier-Wirth C. Magnetic Field-Enhanced Agglutination Readout Combined With Isothermal Reverse Transcription Recombinase Polymerase Amplification for Rapid and Sensitive Molecular Detection of Dengue Virus. Front Chem 2022; 9:817246. [PMID: 35141206 PMCID: PMC8819590 DOI: 10.3389/fchem.2021.817246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 12/24/2021] [Indexed: 11/13/2022] Open
Abstract
Among the numerous molecular diagnostic methods, isothermal reverse transcription recombinase polymerase amplification (RT-RPA) is a simple method that has high sensitivity and avoids the use of expensive instruments. However, detection of amplified genomes often requires a fluorescence readout on costly readers or migration on a lateral flow strip with a subjective visual reading. Aiming to establish a new approach to rapidly and sensitively detect viruses, we combined RT-RPA with a magnetic field-enhanced agglutination (MFEA) assay and assessed the ability of this method to detect the dengue virus (DENV). Magnetization cycles accelerated the capture of amplified DENV genomes between functionalized magnetic nanoparticles by a fast chaining process to less than 5 min; the agglutination was quantified by simple turbidimetry. A total of 37 DENV RNA+ and 30 DENV RNA− samples were evaluated with this combined method. The sensitivity and specificity were 89.19% (95% CI, 72.75–100.00%) and 100% (95% CI, 81.74–100.00%), respectively. This approach provides a solution for developing innovative diagnostic assays for the molecular detection of emerging infections.
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Affiliation(s)
- Fanny Leon
- Pathogénèse et Contrôle des Infections Chroniques et Emergentes, Université de Montpellier, Etablissement Français du Sang, Inserm, Université des Antilles, Montpellier, France
| | - Elena Pinchon
- Pathogénèse et Contrôle des Infections Chroniques et Emergentes, Université de Montpellier, Etablissement Français du Sang, Inserm, Université des Antilles, Montpellier, France
| | - Charly Mayran
- Pathogénèse et Contrôle des Infections Chroniques et Emergentes, Université de Montpellier, Etablissement Français du Sang, Inserm, Université des Antilles, Montpellier, France
| | | | - François Morvan
- Institut des Biomolecules Max Mousseron (IBMM), Université de Montpellier, CNRS, ENSCM, Montpellier, France
| | - Jean-Pierre Molès
- Pathogénèse et Contrôle des Infections Chroniques et Emergentes, Université de Montpellier, Etablissement Français du Sang, Inserm, Université des Antilles, Montpellier, France
| | - Jean-François Cantaloube
- Pathogénèse et Contrôle des Infections Chroniques et Emergentes, Université de Montpellier, Etablissement Français du Sang, Inserm, Université des Antilles, Montpellier, France
| | - Chantal Fournier-Wirth
- Pathogénèse et Contrôle des Infections Chroniques et Emergentes, Université de Montpellier, Etablissement Français du Sang, Inserm, Université des Antilles, Montpellier, France
- *Correspondence: Chantal Fournier-Wirth,
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14
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Rasmi Y. Testing and diagnosis of SARS-CoV-2 infection. CORONAVIRUS DRUG DISCOVERY 2022. [PMCID: PMC9217735 DOI: 10.1016/b978-0-323-85156-5.00012-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The recent outbreak of the coronavirus disease 2019 (COVID-19) has rapidly spread around the world since its discovery in China, in December 2019. The current standard method for determining whether a patient is infected with the SARS-CoV-2 virus involves taking a nasal or throat swab sample, which is then sent to laboratories for testing. The laboratories then use polymerase chain reaction (PCR)-based technology on respiratory specimens remain the gold standard to determine if the genetic material of the virus is present in the sample and use this information to diagnose the patient. However, serologic immunoassays and point-of-care technologies are rapidly emerging with high specificity and sensitivity as well. Even if there are excellent techniques for diagnosing symptomatic patients with COVID-19 in equipped laboratories, critical gaps still exist in the screening of asymptomatic individuals who are in the incubation phase of the virus, as well as in the accurate determination of live virus shedding during convalescence to inform decisions for ending isolation.
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15
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Burkhalter KL, O'Keefe M, Holbert-Watson Z, Green T, Savage HM, Markowski DM. Laboratory and Field Evaluations of a Commercially Available Real-Time Loop-Mediated Isothermal Amplification Assay for the Detection of West Nile Virus in Mosquito Pools. JOURNAL OF THE AMERICAN MOSQUITO CONTROL ASSOCIATION 2021; 37:256-262. [PMID: 34817603 DOI: 10.2987/21-7033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Although the specific cDNA amplification mechanisms of reverse-transcriptase polymerase chain reaction (RT-PCR) and RT loop-mediated isothermal amplification (RT-LAMP) are very different, both molecular assays serve as options to detect arboviral RNA in mosquito pools. Like RT-PCR, RT-LAMP uses a reverse transcription step to synthesize complementary DNA (cDNA) from an RNA template and then uses target-specific primers to amplify cDNA to detectable levels in a single-tube reaction. Using laboratory-generated West Nile virus (WNV) samples and field-collected mosquito pools, we evaluated the sensitivity and specificity of a commercially available WNV real-time RT-LAMP assay (Pro-AmpRT™ WNV; Pro-Lab Diagnostics, Inc., Round Rock, Texas) and compared the results to a validated real-time RT-PCR assay. Laboratory generated virus stock samples containing ≥ 2.3 log10 plaque-forming units (PFU)/ml and intrathoracically inoculated mosquitoes containing ≥ 2.4 log10 PFU/ml produced positive results in the Pro-AmpRT WNV assay. Of field-collected pools that were WNV positive by real-time RT-PCR, 74.5% (70 of 94) were also positive by the Pro-AmpRT WNV assay, resulting in an overall Cohen's kappa agreement of 79.4% between the 2 tests. The Pro-AmpRT WNV assay shows promise as a suitable virus screening tool for vector surveillance programs provided agencies are aware of its characteristics and limitations.
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16
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Buultjens AH, Vandelannoote K, Sharkey LK, Howden BP, Monk IR, Lee JYH, Stinear TP. Low-Cost, Open-Source Device for High-Performance Fluorescence Detection of Isothermal Nucleic Acid Amplification Reactions. ACS Biomater Sci Eng 2021; 7:4982-4990. [PMID: 34521204 DOI: 10.1021/acsbiomaterials.1c01105] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The ability to detect SARS-CoV-2 is critical to implementing evidence-based strategies to address the COVID-19 global pandemic. Expanding SARS-CoV-2 diagnostic ability beyond well-equipped laboratories widens the opportunity for surveillance and control efforts. However, such advances are predicated on the availability of rapid, scalable, accessible, yet high-performance diagnostic platforms. Methods to detect viral RNA using reverse transcription loop-mediated isothermal amplification (RT-LAMP) show promise as rapid and field-deployable tests; however, the per-unit costs of the required diagnostic hardware can be a barrier for scaled deployment. Here, we describe a diagnostic hardware configuration for LAMP technology, named the FABL-8, that can be built for approximately US$380 per machine and provide results in under 30 min. Benchmarking showed that FABL-8 has a similar performance to a high-end commercial instrument for detecting fluorescence-based LAMP reactions. Performance testing of the instrument with RNA extracted from a SARS-CoV-2 virus dilution series revealed an analytical detection sensitivity of 50 virus copies per microliter-a detection threshold suitable to detect patient viral load in the first few days following symptom onset. In addition to the detection of SARS-CoV-2, we show that the system can be used to detect the presence of two bacterial pathogens, demonstrating the versatility of the platform for the detection of other pathogens. This cost-effective and scalable hardware alternative allows democratization of the instrumentation required for high-performance molecular diagnostics, such that it could be available to laboratories anywhere-supporting infectious diseases surveillance and research activities in resource-limited settings.
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Affiliation(s)
- Andrew H Buultjens
- Department of Microbiology and Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Melbourne 3000, Victoria, Australia
| | - Koen Vandelannoote
- Department of Microbiology and Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Melbourne 3000, Victoria, Australia
| | - Liam K Sharkey
- Department of Microbiology and Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Melbourne 3000, Victoria, Australia
| | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Level 1, The University of Melbourne at The Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Melbourne 3000, Victoria, Australia.,Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Melbourne 3000, Victoria, Australia.,Department of Infectious Diseases, Austin Hospital, 145 Studley Road, Heidelberg 3084, Victoria, Australia
| | - Ian R Monk
- Department of Microbiology and Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Melbourne 3000, Victoria, Australia
| | - Jean Y H Lee
- Department of Microbiology and Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Melbourne 3000, Victoria, Australia.,Department of Infectious Diseases, Monash Health, 246 Clayton Road, Clayton 3168, Victoria, Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Melbourne 3000, Victoria, Australia.,Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Melbourne 3000, Victoria, Australia
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17
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Taguchi array optimization of the reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for sensitive and rapid detection of dengue virus serotype 2. Biotechnol Lett 2021; 43:2149-2160. [PMID: 34533679 DOI: 10.1007/s10529-021-03175-1] [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: 05/19/2021] [Accepted: 08/26/2021] [Indexed: 10/20/2022]
Abstract
OBJECTIVES Serotype 2 of dengue virus (DENV-2) is the most prevalent cause of dengue fevers. In this study, the C-prM gene was used for specific detection of DENV-2 by RT-LAMP assay. The RT-LAMP assay was optimized using the Taguchi design of experiments. RESULTS The efficiency of the assay in such optimal conditions resulted in 100% sensitivity, 100% specificity, and 100% overall accuracy for detection of 4 copies/μL of the genome of DENV-2. In addition, the detection of 2 copies/μL of the genome of DENV-2 was feasible, although the sensitivity was 50%. Considering the importance of the specific detection of the dengue virus serotypes, the cost-effective RT-LAMP approach can be used for rapid, specific, and sensitive detection of DENV-2. CONCLUSION RT-LAMP, as a cost-effective method, was optimized using Taguchi array approach for specific and rapid detection of DENV-2. Such methods can facilitate the diagnosis procedure in remote regions.
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18
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JEV-nanobarcode and colorimetric reverse transcription loop-mediated isothermal amplification (cRT-LAMP). Mikrochim Acta 2021; 188:333. [PMID: 34498149 DOI: 10.1007/s00604-021-04986-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 08/11/2021] [Indexed: 10/20/2022]
Abstract
Nucleic acid amplification tests (NAATs) are powerful tools for the Japanese encephalitis virus (JEV). We demonstrated highly sensitive, specific, and rapid detection of JEV by colorimetric reverse-transcription loop-mediated isothermal amplification (cRT-LAMP). Under optimized conditions, the RT-LAMP assay results showed that the limit of detection was approximately equivalent to 1 RNA genome copy/μL with an assay time of 30 min. The assay was highly specific to JEV when tested with other mosquito-borne virus panels (Zika virus and dengue virus types 2-4). The ability to detect JEV directly from crude human sample matrices (serum and urine) demonstrated the suitability of our JEV RT-LAMP for widespread clinical application. The JEV RT-LAMP provides combination of rapid colorimetric determination of true-positive JEV RT-LAMP amplicons with our recently developed JEV-nanobarcodes, measured at absorbance wavelenght of 530 (A530) and 650 (A650), which have a limit of detection of 23.3 ng/μL. The AuNP:polyA10-JEV RT-LAMP nanobarcodes exhibited superior capability for stabilizing the true-positive JEV RT-LAMP amplicons against salt-induced AuNP aggregation, which improved the evaluation of true/false positive signals in the assay. These advances enable to expand the use of RT-LAMP for point-of-care tests, which will greatly bolster JEV clinical programs. The JEV RT-LAMP nanobarcode assay targeting the envelope (E) gene and MgSO4 induced AuNP aggregation, indicated by an instant pink-to-violet colorimetric read-out.
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19
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Matute T, Nuñez I, Rivera M, Reyes J, Blázquez-Sánchez P, Arce A, Brown AJ, Gandini C, Molloy J, Ramírez-Sarmiento CA, Federici F. Homebrew reagents for low-cost RT-LAMP. J Biomol Tech 2021; 32:114-120. [PMID: 35027869 PMCID: PMC8730520 DOI: 10.7171/jbt.21-3203-006] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/18/2023]
Abstract
Reverse transcription-loop-mediated isothermal amplification (RT-LAMP) has gained popularity for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The high specificity, sensitivity, simple protocols, and potential to deliver results without the use of expensive equipment has made it an attractive alternative to RT-PCR. However, the high cost per reaction, the centralized manufacturing of required reagents, and their distribution under cold chain shipping limit RT-LAMP's applicability in low-income settings. The preparation of assays using homebrew enzymes and buffers has emerged worldwide as a response to these limitations and potential shortages. Here, we describe the production of Moloney murine leukemia virus reverse transcriptase and BstLF DNA polymerase for the local implementation of RT-LAMP reactions at low cost. These reagents compared favorably to commercial kits, and optimum concentrations were defined in order to reduce time to threshold, increase ON/OFF range, and minimize enzyme quantities per reaction. As a validation, we tested the performance of these reagents in the detection of SARS-CoV-2 from RNA extracted from clinical nasopharyngeal samples, obtaining high agreement between RT-LAMP and RT-PCR clinical results. The in-house preparation of these reactions results in an order of magnitude reduction in costs; thus, we provide protocols and DNA to enable the replication of these tests at other locations. These results contribute to the global effort of developing open and low-cost diagnostics that enable technological autonomy and distributed capacities in viral surveillance.
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Affiliation(s)
- Tamara Matute
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Isaac Nuñez
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Maira Rivera
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Javiera Reyes
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Paula Blázquez-Sánchez
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Aníbal Arce
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alexander J. Brown
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, Colorado, USA
- Department of Immunology & Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Chiara Gandini
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
| | - Jennifer Molloy
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
| | - César A. Ramírez-Sarmiento
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Fernán Federici
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
- FONDAP Center for Genome Regulation, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
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20
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Kabir MA, Zilouchian H, Younas MA, Asghar W. Dengue Detection: Advances in Diagnostic Tools from Conventional Technology to Point of Care. BIOSENSORS 2021; 11:206. [PMID: 34201849 PMCID: PMC8301808 DOI: 10.3390/bios11070206] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/05/2021] [Accepted: 06/15/2021] [Indexed: 06/02/2023]
Abstract
The dengue virus (DENV) is a vector-borne flavivirus that infects around 390 million individuals each year with 2.5 billion being in danger. Having access to testing is paramount in preventing future infections and receiving adequate treatment. Currently, there are numerous conventional methods for DENV testing, such as NS1 based antigen testing, IgM/IgG antibody testing, and Polymerase Chain Reaction (PCR). In addition, novel methods are emerging that can cut both cost and time. Such methods can be effective in rural and low-income areas throughout the world. In this paper, we discuss the structural evolution of the virus followed by a comprehensive review of current dengue detection strategies and methods that are being developed or commercialized. We also discuss the state of art biosensing technologies, evaluated their performance and outline strategies to address challenges posed by the disease. Further, we outline future guidelines for the improved usage of diagnostic tools during recurrence or future outbreaks of DENV.
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Affiliation(s)
- Md Alamgir Kabir
- Asghar-Lab, Micro and Nanotechnology in Medicine, College of Engineering and Computer Science, Boca Raton, FL 33431, USA; (M.A.K.); (H.Z.)
- Department of Computer & Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Hussein Zilouchian
- Asghar-Lab, Micro and Nanotechnology in Medicine, College of Engineering and Computer Science, Boca Raton, FL 33431, USA; (M.A.K.); (H.Z.)
- College of Medicine, University of Central Florida, Orlando, FL 32827, USA
| | | | - Waseem Asghar
- Asghar-Lab, Micro and Nanotechnology in Medicine, College of Engineering and Computer Science, Boca Raton, FL 33431, USA; (M.A.K.); (H.Z.)
- Department of Computer & Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA
- Department of Biological Sciences (Courtesy Appointment), Florida Atlantic University, Boca Raton, FL 33431, USA
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21
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Mori A, Pomari E, Deiana M, Perandin F, Caldrer S, Formenti F, Mistretta M, Orza P, Ragusa A, Piubelli C. Molecular techniques for the genomic viral RNA detection of West Nile, Dengue, Zika and Chikungunya arboviruses: a narrative review. Expert Rev Mol Diagn 2021; 21:591-612. [PMID: 33910444 DOI: 10.1080/14737159.2021.1924059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Introduction: Molecular technology has played an important role in arboviruses diagnostics. PCR-based methods stand out in terms of sensitivity, specificity, cost, robustness, and accessibility, and especially the isothermal amplification (IA) method is ideal for field-adaptable diagnostics in resource-limited settings (RLS).Areas covered: In this review, we provide an overview of the various molecular methods for West Nile, Zika, Dengue and Chikungunya. We summarize literature works reporting the assessment and use of in house and commercial assays. We describe limitations and challenges in the usage of methods and opportunities for novel approaches such as NNext-GenerationSequencing (NGS).Expert opinion: The rapidity and accuracy of differential diagnosis is essential for a successful clinical management, particularly in co-circulation area of arboviruses. Several commercial diagnostic molecular assays are available, but many are not affordable by RLS and not usable as Point-of-care/Point-of-need (POC/PON) such as RReal-TimeRT-PCR, Array-based methods and NGS. In contrast, the IA-based system fits better for POC/PON but it is still not ideal for the multiplexing detection system. Improvement in the characterization and validation of current molecular assays is needed to optimize their translation to the point of care.
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Affiliation(s)
- Antonio Mori
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy.,Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Elena Pomari
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Michela Deiana
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Francesca Perandin
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Sara Caldrer
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Fabio Formenti
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Manuela Mistretta
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Pierantonio Orza
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Andrea Ragusa
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Chiara Piubelli
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
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22
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Oishee MJ, Ali T, Jahan N, Khandker SS, Haq MA, Khondoker MU, Sil BK, Lugova H, Krishnapillai A, Abubakar AR, Kumar S, Haque M, Jamiruddin MR, Adnan N. COVID-19 Pandemic: Review of Contemporary and Forthcoming Detection Tools. Infect Drug Resist 2021; 14:1049-1082. [PMID: 33762831 PMCID: PMC7982560 DOI: 10.2147/idr.s289629] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/30/2021] [Indexed: 01/10/2023] Open
Abstract
Recent severe acute respiratory syndrome 2 (SARS-CoV-2) known as COVID-19, presents a deadly challenge to the global healthcare system of developing and developed countries, exposing the limitations of health facilities preparedness for emerging infectious disease pandemic. Opportune detection, confinement, and early treatment of infected cases present the first step in combating COVID-19. In this review, we elaborate on various COVID-19 diagnostic tools that are available or under investigation. Consequently, cell culture, followed by an indirect fluorescent antibody, is one of the most accurate methods for detecting SARS-CoV-2 infection. However, restrictions imposed by the regulatory authorities prevented its general use and implementation. Diagnosis via radiologic imaging and reverse transcriptase PCR assay is frequently employed, considered as standard procedures, whereas isothermal amplification methods are currently on the verge of clinical introduction. Notably, techniques such as CRISPR-Cas and microfluidics have added new dimensions to the SARS-CoV-2 diagnosis. Furthermore, commonly used immunoassays such as enzyme-linked immunosorbent assay (ELISA), lateral flow immunoassay (LFIA), neutralization assay, and the chemiluminescent assay can also be used for early detection and surveillance of SARS-CoV-2 infection. Finally, advancement in the next generation sequencing (NGS) and metagenomic analysis are smoothing the viral detection further in this global challenge.
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Affiliation(s)
| | - Tamanna Ali
- Gonoshasthaya-RNA Molecular Diagnostic and Research Center, Dhaka, Bangladesh
| | - Nowshin Jahan
- Gonoshasthaya-RNA Molecular Diagnostic and Research Center, Dhaka, Bangladesh
| | | | - Md Ahsanul Haq
- Gonoshasthaya-RNA Molecular Diagnostic and Research Center, Dhaka, Bangladesh
| | | | | | - Halyna Lugova
- Faculty of Medicine and Defence Health, National Defence University of Malaysia, Kuala Lumpur, Malaysia
| | - Ambigga Krishnapillai
- Faculty of Medicine and Defence Health, National Defence University of Malaysia, Kuala Lumpur, Malaysia
| | - Abdullahi Rabiu Abubakar
- Department of Pharmacology and Therapeutics, Faculty of Pharmaceutical Sciences, Bayero University, Kano, 700233, Kano, Nigeria
| | - Santosh Kumar
- Department of Periodontology and Implantology, Karnavati University, Gandhinagar, 382422, India
| | - Mainul Haque
- The Unit of Pharmacology, Faculty of Medicine and Defence Health Universiti Pertahanan, Nasional Malaysia (National Defence University of Malaysia), Kuala Lumpur, Malaysia
| | | | - Nihad Adnan
- Department of Microbiology, Jahangirnagar University, Dhaka, 1342, Bangladesh
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23
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An innovative and user-friendly smartphone-assisted molecular diagnostic approach for rapid detection of canine vector-borne diseases. Parasitol Res 2021; 120:1799-1809. [PMID: 33649963 PMCID: PMC7920752 DOI: 10.1007/s00436-021-07077-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 02/01/2021] [Indexed: 11/17/2022]
Abstract
Present-day diagnostic tools and technologies for canine diseases and other vector-borne parasitic diseases hardly meet the requirements of an efficient and rapid diagnostic tool, which can be suitable for use at the point-of-care in resource-limited settings. Loop-mediated isothermal amplification (LAMP) technique has been always a method of choice in the development and validation of quick, precise, and sensitive diagnostic assays for pathogen detection and to reorganize point-of-care (POC) molecular diagnostics. In this study, we have demonstrated an efficient detection system for parasitic vector-borne pathogens like Ehrlichia canis and Hepatozoon canis by linking the LAMP assay to a smartphone via a simple, inexpensive, and a portable “LAMP box,” All the components of the LAMP box were connected to each other wirelessly. This LAMP box was made up of an isothermal heating pad mounted below an aluminum base which served as a platform for the reaction tubes and LAMP assay. The entire setup could be connected to a smartphone via an inbuilt Wi-Fi that allowed the user to establish the connection to control the LAMP box. A 5 V USB power source was used as a power supply. The sensitivity of the LAMP assay was estimated to be up to 10−6 dilution limit using the amplified, purified, and quantified specific DNA templates. It can also serve as an efficient diagnostic platform for many other veterinary infectious or parasitic diseases of zoonotic origin majorly towards field-based diagnostics.
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24
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Abd-Jamil J, Azizan NS, Che-Mat-Seri NAA, Yaacob CN, Samsudin NI, Mahfodz NH, Zulkifli MMS, Poh HS, Teoh BT, AbuBakar S. Detection and confirmation of dengue pre- and postintroduction of dengue NS1-antigen test at the University Malaya Medical Centre: An observational study. J Med Virol 2021; 93:4714-4719. [PMID: 33421159 DOI: 10.1002/jmv.26790] [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: 12/03/2020] [Revised: 12/11/2020] [Accepted: 01/07/2021] [Indexed: 11/10/2022]
Abstract
Early diagnosis of dengue is important to ensure proper management of patients and effective implementation of control measures. The present study was undertaken to determine the outcome of the implementation of dengue NS1-antigen (Ag) rapid diagnostic test (RDT) in the confirmation of dengue at the first patient hospital visit at the University Malaya Medical Centre. A total of 1036 and 1097 sera from the year 2008 and 2015 were used, representing samples from before and after dengue NS1-Ag RDT was implemented as routine diagnostic at the hospital. Results showed that similar dengue confirmation percentage (56%) was made in 2008 and 2015, regardless of the main laboratory diagnostic method used. Confirmation of dengue, however, increased to 68% and 73% when dengue NS1-Ag test or dengue immunoglobulin M-capture enzyme-linked immunosorbent assay was used as the second test for the 2008 and 2015 samples, respectively. Detection of dengue virus (DENV) using multiplex reverse transcription-polymerase chain reaction (RT-PCR) showed that DENV-1 was the highest in circulation in 2008 and that both DENV-1 and DENV-2 were dominant in 2015. In summary, the present study demonstrated that the introduction and use of the dengue NS1-Ag RDT did not change or compromise confirmation of dengue, highlighting the advantage of using the method. With the reducing cost of molecular detection tools, DENV detection using RT-PCR remains a viable option for further confirmation of dengue in hospital settings.
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Affiliation(s)
- Juraina Abd-Jamil
- Tropical Infectious Diseases Research & Education Centre (TIDREC), University Malaya, Kuala Lumpur, Malaysia
| | - Noor-Syahida Azizan
- Tropical Infectious Diseases Research & Education Centre (TIDREC), University Malaya, Kuala Lumpur, Malaysia
| | | | - Che-Norainon Yaacob
- Tropical Infectious Diseases Research & Education Centre (TIDREC), University Malaya, Kuala Lumpur, Malaysia
| | - Nur-Izyan Samsudin
- Tropical Infectious Diseases Research & Education Centre (TIDREC), University Malaya, Kuala Lumpur, Malaysia
| | - Nur-Hidayana Mahfodz
- Tropical Infectious Diseases Research & Education Centre (TIDREC), University Malaya, Kuala Lumpur, Malaysia
| | - Mulya-Mustika-Sari Zulkifli
- Tropical Infectious Diseases Research & Education Centre (TIDREC), University Malaya, Kuala Lumpur, Malaysia
| | - Hooi-Sim Poh
- Diagnostic Virology Laboratory, University Malaya Medical Centre, University Malaya, Kuala Lumpur, Malaysia
| | - Boon-Teong Teoh
- Tropical Infectious Diseases Research & Education Centre (TIDREC), University Malaya, Kuala Lumpur, Malaysia
| | - Sazaly AbuBakar
- Tropical Infectious Diseases Research & Education Centre (TIDREC), University Malaya, Kuala Lumpur, Malaysia
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25
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Moehling TJ, Choi G, Dugan LC, Salit M, Meagher RJ. LAMP Diagnostics at the Point-of-Care: Emerging Trends and Perspectives for the Developer Community. Expert Rev Mol Diagn 2021; 21:43-61. [PMID: 33474990 DOI: 10.1080/14737159.2021.1873769] [Citation(s) in RCA: 106] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Introduction: Over the past decade, loop-mediated isothermal amplification (LAMP) technology has played an important role in molecular diagnostics. Amongst numerous nucleic acid amplification assays, LAMP stands out in terms of sample-to-answer time, sensitivity, specificity, cost, robustness, and accessibility, making it ideal for field-deployable diagnostics in resource-limited regions.Areas covered: In this review, we outline the front-end LAMP design practices for point-of-care (POC) applications, including sample handling and various signal readout methodologies. Next, we explore existing LAMP technologies that have been validated with clinical samples in the field. We summarize recent work that utilizes reverse transcription (RT) LAMP to rapidly detect SARS-CoV-2 as an alternative to standard PCR protocols. Finally, we describe challenges in translating LAMP from the benchtop to the field and opportunities for future LAMP assay development and performance reporting.Expert opinion: Despite the popularity of LAMP in the academic research community and a recent surge in interest in LAMP due to the COVID-19 pandemic, there are numerous areas for improvement in the fundamental understanding of LAMP, which are needed to elevate the field of LAMP assay development and characterization.
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Affiliation(s)
- Taylor J Moehling
- Sandia National Laboratories, Biotechnology & Bioengineering Dept., Livermore, CA, USA
| | - Gihoon Choi
- Sandia National Laboratories, Biotechnology & Bioengineering Dept., Livermore, CA, USA
| | - Lawrence C Dugan
- Lawrence Livermore National Laboratory, Biosciences & Biotechnology Div., Livermore, CA, USA
| | - Marc Salit
- Joint Initiative for Metrology in Biology, SLAC National Accelerator Lab and Departments of Bioengineering and Pathology, Stanford University, Stanford, CA, USA
| | - Robert J Meagher
- Sandia National Laboratories, Biotechnology & Bioengineering Dept., Livermore, CA, USA
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26
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Zhang S, Shin J, Shin S, Chung YJ. Development of reverse transcription loop-mediated isothermal amplification assays for point-of-care testing of avian influenza virus subtype H5 and H9. Genomics Inform 2021; 18:e40. [PMID: 33412756 PMCID: PMC7808867 DOI: 10.5808/gi.2020.18.4.e40] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 10/16/2020] [Indexed: 12/01/2022] Open
Abstract
Avian influenza (AIV) outbreaks can induce fatal human pulmonary infections in addition to economic losses to the poultry industry. In this study, we aimed to develop a rapid and sensitive point-of-care AIV test using loop-mediated isothermal amplification (LAMP) technology. We designed three sets of reverse transcription LAMP (RT-LAMP) primers targeting the matrix (M) and hemagglutinin (HA) genes of the H5 and H9 subtypes. RT-LAMP targeting the universal M gene was designed to screen for the presence of AIV and RT-LAMP assays targeting H5-HA and H9-HA were designed to discriminate between the H5 and H9 subtypes. All three RT-LAMP assays showed specific amplification results without nonspecific reactions. In terms of sensitivity, the detection limits of our RT-LAMP assays were 100 to 1,000 RNA copies per reaction, which were 10 times more sensitive than the detection limits of the reference reverse‒transcription polymerase chain reaction (RT-PCR) (1,000 to 10,000 RNA copies per reaction). The reaction time of our RT-LAMP assays was less than 30 min, which was approximately four times quicker than that of conventional RT-PCR. Altogether, these assays successfully detected the existence of AIV and discriminated between the H5 or H9 subtypes with higher sensitivity and less time than the conventional RT-PCR assay.
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Affiliation(s)
- Songzi Zhang
- Department of Biomedicine & Health Sciences, Graduate School, The Catholic University of Korea, Seoul 06591, Korea.,Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea.,Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea.,Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | | | - Sun Shin
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea.,Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea.,Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | - Yeun-Jun Chung
- Department of Biomedicine & Health Sciences, Graduate School, The Catholic University of Korea, Seoul 06591, Korea.,Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea.,Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea.,Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
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27
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Teoh BT, Chin KL, Samsudin NI, Loong SK, Sam SS, Tan KK, Khor CS, Abd-Jamil J, Zainal N, Wilder-Smith A, Zandi K, AbuBakar S. A reverse transcription loop-mediated isothermal amplification for broad coverage detection of Asian and African Zika virus lineages. BMC Infect Dis 2020; 20:947. [PMID: 33308203 PMCID: PMC7731766 DOI: 10.1186/s12879-020-05585-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 11/04/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Early detection of Zika virus (ZIKV) infection during the viremia and viruria facilitates proper patient management and mosquito control measurement to prevent disease spread. Therefore, a cost-effective nucleic acid detection method for the diagnosis of ZIKV infection, especially in resource-deficient settings, is highly required. METHODS In the present study, a single-tube reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed for the detection of both the Asian and African-lineage ZIKV. The detection limit, strain coverage and cross-reactivity of the ZIKV RT-LAMP assay was evaluated. The sensitivity and specificity of the RT-LAMP were also evaluated using a total of 24 simulated clinical samples. The ZIKV quantitative reverse transcription-polymerase chain reaction (qRT-PCR) assay was used as the reference assay. RESULTS The detection limit of the RT-LAMP assay was 3.73 ZIKV RNA copies (probit analysis, P ≤ 0.05). The RT-LAMP assay detected the ZIKV genomes of both the Asian and African lineages without cross-reacting with other arthropod-borne viruses. The sensitivity and specificity of the RT-LAMP assay were 90% (95% CI = 59.6-98.2) and 100% (95% CI = 78.5-100.0), respectively. The RT-LAMP assay detected ZIKV genome in 9 of 24 (37.5%) of the simulated clinical samples compared to 10 of 24 (41.7%) by qRT-PCR assay with a high level of concordance (κ = 0.913, P < 0.001). CONCLUSION The RT-LAMP assay is applicable for the broad coverage detection of both the Asian and African ZIKV strains in resource-deficient settings.
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Affiliation(s)
- Boon-Teong Teoh
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Universiti Malaya, Kuala Lumpur, Malaysia.
| | - Kim-Ling Chin
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Universiti Malaya, Kuala Lumpur, Malaysia.,Institute for Advanced Studies (IAS), Universiti Malaya, Kuala Lumpur, Malaysia
| | - Nur-Izyan Samsudin
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Universiti Malaya, Kuala Lumpur, Malaysia
| | - Shih-Keng Loong
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Universiti Malaya, Kuala Lumpur, Malaysia
| | - Sing-Sin Sam
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Universiti Malaya, Kuala Lumpur, Malaysia
| | - Kim-Kee Tan
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Universiti Malaya, Kuala Lumpur, Malaysia
| | - Chee-Sieng Khor
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Universiti Malaya, Kuala Lumpur, Malaysia
| | - Juraina Abd-Jamil
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Universiti Malaya, Kuala Lumpur, Malaysia
| | - Nurhafiza Zainal
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Annelies Wilder-Smith
- Department of Public Health and Clinical Medicine, Epidemiology and Global Health, Umeå University, Umeå, Sweden.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Republic of Singapore
| | - Keivan Zandi
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia.,Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Sazaly AbuBakar
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Universiti Malaya, Kuala Lumpur, Malaysia. .,Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia.
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28
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Hanpanich O, Saito K, Shimada N, Maruyama A. One-step isothermal RNA detection with LNA-modified MNAzymes chaperoned by cationic copolymer. Biosens Bioelectron 2020; 165:112383. [PMID: 32729508 PMCID: PMC7836245 DOI: 10.1016/j.bios.2020.112383] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/13/2020] [Accepted: 06/08/2020] [Indexed: 12/21/2022]
Abstract
RNA detection permits early diagnosis of several infectious diseases and cancers, which prevent propagation of diseases and improve treatment efficacy. However, standard technique for RNA detection such as reverse transcription-quantitative polymerase chain reaction has complicated procedure and requires well-trained personnel and specialized lab equipment. These shortcomings limit the application for point-of-care analysis which is critical for rapid and effective disease management. The multicomponent nucleic acid enzymes (MNAzymes) are one of the promising biosensors for simple, isothermal and enzyme-free RNA detection. Herein, we demonstrate simple yet effective strategies that significantly enhance analytical performance of MNAzymes. The addition of the cationic copolymer and structural modification of MNAzyme significantly enhanced selectivity and activity of MNAzymes by 250 fold and 2,700 fold, respectively. The highly simplified RNA detection system achieved a detection limit of 73 fM target concentration without additional amplification. The robustness of MNAzyme in the presence of non-target RNA was also improved. Our finding opens up a route toward the development of an alternative rapid, sensitive, isothermal, and protein-free RNA diagnostic tool, which expected to be of great clinical significance.
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Affiliation(s)
- Orakan Hanpanich
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259 B-57, Yokohama, 226-8501, Japan
| | - Ken Saito
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259 B-57, Yokohama, 226-8501, Japan
| | - Naohiko Shimada
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259 B-57, Yokohama, 226-8501, Japan
| | - Atsushi Maruyama
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259 B-57, Yokohama, 226-8501, Japan.
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29
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Cui F, Zhou HS. Diagnostic methods and potential portable biosensors for coronavirus disease 2019. Biosens Bioelectron 2020; 165:112349. [PMID: 32510340 PMCID: PMC7266610 DOI: 10.1016/j.bios.2020.112349] [Citation(s) in RCA: 218] [Impact Index Per Article: 54.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 05/26/2020] [Accepted: 06/01/2020] [Indexed: 12/14/2022]
Abstract
Timely detection and diagnosis are urgently needed to guide epidemiological measures, infection control, antiviral treatment, and vaccine research. In this review, biomarkers/indicators for diagnosis of coronavirus disease 2019 (COVID-19) or detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the environment are summarized and discussed. It is concluded that the detection methods targeting antibodies are not suitable for screening of early and asymptomatic cases since most patients had an antibody response at about 10 days after onset of symptoms. However, antibody detection methods can be combined with quantitative real-time reverse transcriptase-polymerase chain reaction (RT-qPCR) to significantly improve the sensitivity and specificity of diagnosis, and boost vaccine research. Fast, sensitive and accurate detection methods targeting antigens need to be developed urgently. Various specimens for diagnosis or detection are compared and analyzed. Among them, deep throat saliva and induced sputum are desired for RT-qPCR test or other early detection technologies. Chest computerized tomography (CT) scan, RT-qPCR, lateral flow immunochromatographic strip (LFICS) for diagnosis of COVID-19 are summarized and compared. Specially, potential electrochemical (EC) biosensor, surface enhanced Raman scattering (SERS)-based biosensor, field-effect transistor (FET)-based biosensor, surface plasmon resonance (SPR)-based biosensor and artificial intelligence (AI) assisted diagnosis of COVID-19 are emphasized. Finally, some commercialized portable detection device, current challenges and future directions are discussed.
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Affiliation(s)
- Feiyun Cui
- Department of Chemical Engineering, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA, 01609, United States
| | - H Susan Zhou
- Department of Chemical Engineering, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA, 01609, United States.
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30
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Reta DH, Tessema TS, Ashenef AS, Desta AF, Labisso WL, Gizaw ST, Abay SM, Melka DS, Reta FA. Molecular and Immunological Diagnostic Techniques of Medical Viruses. Int J Microbiol 2020; 2020:8832728. [PMID: 32908530 PMCID: PMC7474384 DOI: 10.1155/2020/8832728] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 06/24/2020] [Accepted: 08/15/2020] [Indexed: 01/12/2023] Open
Abstract
Viral infections are causing serious problems in human population worldwide. The recent outbreak of coronavirus disease 2019 caused by SARS-CoV-2 is a perfect example how viral infection could pose a great threat to global public health and economic sectors. Therefore, the first step in combating viral pathogens is to get a timely and accurate diagnosis. Early and accurate detection of the viral presence in patient sample is crucial for appropriate treatment, control, and prevention of epidemics. Here, we summarize some of the molecular and immunological diagnostic approaches available for the detection of viral infections of humans. Molecular diagnostic techniques provide rapid viral detection in patient sample. They are also relatively inexpensive and highly sensitive and specific diagnostic methods. Immunological-based techniques have been extensively utilized for the detection and epidemiological studies of human viral infections. They can detect antiviral antibodies or viral antigens in clinical samples. There are several commercially available molecular and immunological diagnostic kits that facilitate the use of these methods in the majority of clinical laboratories worldwide. In developing countries including Ethiopia where most of viral infections are endemic, exposure to improved or new methods is highly limited as these methods are very costly to use and also require technical skills. Since researchers and clinicians in all corners of the globe are working hard, it is hoped that in the near future, they will develop good quality tests that can be accessible in low-income countries.
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Affiliation(s)
- Daniel Hussien Reta
- School of Veterinary Medicine, Wollo University, Dessie, Ethiopia
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | | | | | - Adey Feleke Desta
- Department of Microbial, Cellular and Molecular Biology, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Wajana Lako Labisso
- Department of Pathology, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Solomon Tebeje Gizaw
- Department of Medical Biochemistry, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Solomon Mequanente Abay
- Department of Pharmacology and Clinical Pharmacy, School of Pharmacy, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Daniel Seifu Melka
- Department of Medical Biochemistry, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Fisseha Alemu Reta
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Biology, College of Natural and Computational Sciences, Jigjiga University, Jigjiga, Ethiopia
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31
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Augustine R, Hasan A, Das S, Ahmed R, Mori Y, Notomi T, Kevadiya BD, S. Thakor A. Loop-Mediated Isothermal Amplification (LAMP): A Rapid, Sensitive, Specific, and Cost-Effective Point-of-Care Test for Coronaviruses in the Context of COVID-19 Pandemic. BIOLOGY 2020; 9:E182. [PMID: 32707972 PMCID: PMC7464797 DOI: 10.3390/biology9080182] [Citation(s) in RCA: 123] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/01/2020] [Accepted: 07/07/2020] [Indexed: 12/21/2022]
Abstract
The rampant spread of COVID-19 and the worldwide prevalence of infected cases demand a rapid, simple, and cost-effective Point of Care Test (PoCT) for the accurate diagnosis of this pandemic. The most common molecular tests approved by regulatory bodies across the world for COVID-19 diagnosis are based on Polymerase Chain Reaction (PCR). While PCR-based tests are highly sensitive, specific, and remarkably reliable, they have many limitations ranging from the requirement of sophisticated laboratories, need of skilled personnel, use of complex protocol, long wait times for results, and an overall high cost per test. These limitations have inspired researchers to search for alternative diagnostic methods that are fast, economical, and executable in low-resource laboratory settings. The discovery of Loop-mediated isothermal Amplification (LAMP) has provided a reliable substitute platform for the accurate detection of low copy number nucleic acids in the diagnosis of several viral diseases, including epidemics like Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS). At present, a cocktail of LAMP assay reagents along with reverse transcriptase enzyme (Reverse Transcription LAMP, RT-LAMP) can be a robust solution for the rapid and cost-effective diagnosis for COVID-19, particularly in developing, and low-income countries. In summary, the development of RT-LAMP based diagnostic tools in a paper/strip format or the integration of this method into a microfluidic platform such as a Lab-on-a-chip may revolutionize the concept of PoCT for COVID-19 diagnosis. This review discusses the principle, technology and past research underpinning the success for using this method for diagnosing MERS and SARS, in addition to ongoing research, and the prominent prospect of RT-LAMP in the context of COVID-19 diagnosis.
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Affiliation(s)
- Robin Augustine
- Department of Mechanical and Industrial Engineering, College of Engineering, Qatar University, Doha 2713, Qatar;
- Biomedical Research Center (BRC), Qatar University, Doha PO Box 2713, Qatar
| | - Anwarul Hasan
- Department of Mechanical and Industrial Engineering, College of Engineering, Qatar University, Doha 2713, Qatar;
- Biomedical Research Center (BRC), Qatar University, Doha PO Box 2713, Qatar
| | - Suvarthi Das
- Department of Medicine, Stanford University Medical Center, Palo Alto, CA 94304, USA;
| | - Rashid Ahmed
- Department of Mechanical and Industrial Engineering, College of Engineering, Qatar University, Doha 2713, Qatar;
- Biomedical Research Center (BRC), Qatar University, Doha PO Box 2713, Qatar
| | - Yasuyoshi Mori
- Eiken Chemical Co., Ltd., Research and Development Division, Taito-ku 110-8408, Japan; (Y.M.); (T.N.)
| | - Tsugunori Notomi
- Eiken Chemical Co., Ltd., Research and Development Division, Taito-ku 110-8408, Japan; (Y.M.); (T.N.)
| | - Bhavesh D. Kevadiya
- Interventional Regenerative Medicine and Imaging Laboratory, Department of Radiology, School of Medicine, Stanford University, Palo Alto, CA 94304, USA; (B.D.K.); (A.S.T.)
| | - Avnesh S. Thakor
- Interventional Regenerative Medicine and Imaging Laboratory, Department of Radiology, School of Medicine, Stanford University, Palo Alto, CA 94304, USA; (B.D.K.); (A.S.T.)
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32
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Yu L, Wu S, Hao X, Dong X, Mao L, Pelechano V, Chen WH, Yin X. Rapid Detection of COVID-19 Coronavirus Using a Reverse Transcriptional Loop-Mediated Isothermal Amplification (RT-LAMP) Diagnostic Platform. Clin Chem 2020; 66:975-977. [PMID: 32315390 PMCID: PMC7188121 DOI: 10.1093/clinchem/hvaa102] [Citation(s) in RCA: 311] [Impact Index Per Article: 77.8] [Reference Citation Analysis] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/17/2020] [Indexed: 01/19/2023]
Affiliation(s)
- Lin Yu
- Applied Biology Laboratory, Shenyang University of Chemical Technology, Shenyang, China
| | - Shanshan Wu
- Applied Biology Laboratory, Shenyang University of Chemical Technology, Shenyang, China
| | - Xiaowen Hao
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xue Dong
- Shenyang Center for Disease Control and Prevention, Shenyang, Liaoning, China
| | - Lingling Mao
- Liaoning Center for Disease Control and Prevention, Shenyang, Liaoning, China
| | - Vicent Pelechano
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology. Karolinska Institute, Solna, Sweden
| | - Wei-Hua Chen
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China.,College of Life Science, HeNan Normal University, Xinxiang, Henan, China.,Pluri Biotech Co.Ltd, Xuzhou, China.,Biotech & Biomedicine Science (Shenyang) Co. Ltd, Shenyang, China.,Biotech & Biomedicine Science (Jiangxi)Co. Ltd, Ganzhou, China
| | - Xiushan Yin
- Applied Biology Laboratory, Shenyang University of Chemical Technology, Shenyang, China.,SciLifeLab, Department of Microbiology, Tumor and Cell Biology. Karolinska Institute, Solna, Sweden.,Pluri Biotech Co.Ltd, Xuzhou, China.,Biotech & Biomedicine Science (Shenyang) Co. Ltd, Shenyang, China.,Biotech & Biomedicine Science (Jiangxi)Co. Ltd, Ganzhou, China.,Nanog Biotech Co. Ltd, Shanghai, China
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33
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Yu L, Wu S, Hao X, Dong X, Mao L, Pelechano V, Chen WH, Yin X. Rapid Detection of COVID-19 Coronavirus Using a Reverse Transcriptional Loop-Mediated Isothermal Amplification (RT-LAMP) Diagnostic Platform. Clin Chem 2020. [PMID: 32315390 DOI: 10.1101/2020.02.20.20025874] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
AbstractThe recent outbreak of a novel coronavirus SARS-CoV-2 (also known as 2019-nCoV) threatens global health, given serious cause for concern. SARS-CoV-2 is a human-to-human pathogen that caused fever, severe respiratory disease and pneumonia (known as COVID-19). By press time, more than 70,000 infected people had been confirmed worldwide. SARS-CoV-2 is very similar to the severe acute respiratory syndrome (SARS) coronavirus broke out 17 years ago. However, it has increased transmissibility as compared with the SARS-CoV, e.g. very often infected individuals without any symptoms could still transfer the virus to others. It is thus urgent to develop a rapid, accurate and onsite diagnosis methods in order to effectively identify these early infects, treat them on time and control the disease spreading. Here we developed an isothermal LAMP based method-iLACO (isothermal LAMP based method for COVID-19) to amplify a fragment of the ORF1ab gene using 6 primers. We assured the species-specificity of iLACO by comparing the sequences of 11 related viruses by BLAST (including 7 similar coronaviruses, 2 influenza viruses and 2 normal coronaviruses). The sensitivity is comparable to Taqman based qPCR detection method, detecting synthesized RNA equivalent to 10 copies of 2019-nCoV virus. Reaction time varied from 15-40 minutes, depending on the loading of virus in the collected samples. The accuracy, simplicity and versatility of the new developed method suggests that iLACO assays can be conveniently applied with for 2019-nCoV threat control, even in those cases where specialized molecular biology equipment is not available.
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Affiliation(s)
- Lin Yu
- Applied Biology Laboratory, Shenyang University of Chemical Technology, Shenyang, China
| | - Shanshan Wu
- Applied Biology Laboratory, Shenyang University of Chemical Technology, Shenyang, China
| | - Xiaowen Hao
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xue Dong
- Shenyang Center for Disease Control and Prevention, Shenyang, Liaoning, China
| | - Lingling Mao
- Liaoning Center for Disease Control and Prevention, Shenyang, Liaoning, China
| | - Vicent Pelechano
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology. Karolinska Institute, Solna, Sweden
| | - Wei-Hua Chen
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
- College of Life Science, HeNan Normal University, Xinxiang, Henan, China
- Pluri Biotech Co.Ltd, Xuzhou, China
- Biotech & Biomedicine Science (Shenyang) Co. Ltd, Shenyang, China
- Biotech & Biomedicine Science (Jiangxi)Co. Ltd, Ganzhou, China
| | - Xiushan Yin
- Applied Biology Laboratory, Shenyang University of Chemical Technology, Shenyang, China
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology. Karolinska Institute, Solna, Sweden
- Pluri Biotech Co.Ltd, Xuzhou, China
- Biotech & Biomedicine Science (Shenyang) Co. Ltd, Shenyang, China
- Biotech & Biomedicine Science (Jiangxi)Co. Ltd, Ganzhou, China
- Nanog Biotech Co. Ltd, Shanghai, China
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Karthikeyan PA, Hoti SL, Kanungo R. Evaluation of loop-mediated isothermal amplification assay for detection of scrub typhus in patients with acute febrile illness presenting to a Tertiary Care Center in Puducherry, India. J Lab Physicians 2020; 11:82-86. [PMID: 30983808 PMCID: PMC6437831 DOI: 10.4103/jlp.jlp_148_18] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
PURPOSE Scrub typhus an acute febrile illness has diverse clinical manifestations, which overlap with other febrile illnesses. Due to this reason, it is misdiagnosed, leading to inappropriate treatment, sometimes resulting in fatality. Thus, accurate diagnosis of scrub typhus is important for appropriate treatment. This study evaluated the loop-mediated isothermal amplification (LAMP) assay as a diagnostic test for scrub typhus among patients with fever. MATERIALS AND METHODS A total of 50 cases of acute febrile illness clinically resembling scrub typhus, with or without an eschar, or cases of pyrexia of unknown origin were included in the study. Blood samples collected from these cases were subjected to detection of IgM antibodies to Orientia tsutsugamushi by ELISA, conventional groEL polymerase chain reaction (PCR), and the LAMP assay. RESULTS Twelve cases had fever for less than a week, and two had fever for more than 3 weeks. IgM antibodies to O. tsutsugamushi were detected in 37 out of 50 samples (74%). LAMP assay was positive in 33 samples (66%). groEL gene-based PCR detected 35 (70%) samples as positive. Two samples negative by LAMP assay were positive by this PCR. Twenty samples collected from patients with dengue, typhoid, and malaria tested by the LAMP assay were negative, indicating its good specificity. LAMP assay and the conventional groEL-based PCR could detect 72.7% and 74.3% of the samples, respectively before the 10th day after onset of fever, whereas IgM ELISA could detect only 40.5% of the 37 samples. CONCLUSION This study suggests that LAMP assay could be a useful diagnostic test for detecting scrub typhus in the acute phase of the illness and a cheaper alternative to other molecular methods in resource poor settings.
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Affiliation(s)
| | | | - Reba Kanungo
- Department of Microbiology, Pondicherry Institute of Medical Sciences, Puducherry, India
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Bui TT, Moi ML, Morita K, Hasebe F. Development of Universal and Lineage-Specific Primer Sets for Rapid Detection of the Zika Virus (ZIKV) in Blood and Urine Samples Using One-Step Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP). Jpn J Infect Dis 2019; 73:153-156. [PMID: 31666491 DOI: 10.7883/yoken.jjid.2019.073] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Zika is a mosquito-borne disease that has been posing a significant threat to public health in recent years. The Zika virus (ZIKV), the causative agent of this disease, is classified into 2 distinct genetic lineages, namely Asian and African. While molecular nucleic acid analysis methods have been shown to be useful for the diagnosis of ZIKV infection, the development of assays based on one-step reverse transcription loop-mediated isothermal amplification (RT-LAMP) offers several advantages, such as shorter incubation times, ease of handling, and rapid detection. In this study, a universal LAMP primer set was developed to target conserved sequences of known ZIKV lineages. Additionally, the Af7462 and As1788 primer sets were designed based on LAMP-based single-nucleotide polymorphism (SNPs) typing for the specific detection of the African and Asian lineages. The developed RT-LAMP assays could specifically detect the African and Asian lineages of ZIKV, with a detection limit ranging from 0.17 FFU/mL to 2.3×102 FFU/mL. As ZIKV viremia ranges between 102 to 106 PFU/mL or 103 to 106 copies/mL, the data indicate that the viremia range of clinical samples is within the detection range of our assay. Due to the high specificity and sensitivity, as well as the ease of use of our assay, it could potentially be used for early clinical diagnosis applications.
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Affiliation(s)
- Thu Thuy Bui
- Department of Virology, Institute of Tropical Medicine, Nagasaki University
| | - Meng Ling Moi
- Department of Virology, Institute of Tropical Medicine, Nagasaki University
| | - Kouichi Morita
- Department of Virology, Institute of Tropical Medicine, Nagasaki University
| | - Futoshi Hasebe
- Vietnam Research station, Center for Infectious Disease Research in Asia and Africa, Institute of Tropical Medicine, Nagasaki University
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Singh MP, Rungta T, Kumar A, Goyal K, Bharti B, Ratho RK. Institutional outbreak of varicella in a child welfare institute in Chandigarh, North India. Indian J Med Microbiol 2019; 37:24-28. [PMID: 31424006 DOI: 10.4103/ijmm.ijmm_18_264] [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: 11/04/2022]
Abstract
Introduction Varicella outbreaks are known to occur in developing nations as vaccine coverage is still low. Material and Methods In the present study, an institutional outbreak from Chandigarh, India, is reported wherein the utility of non-invasive samples such as saliva and urine was studied for the molecular diagnosis of varicella by conventional polymerase chain reaction (PCR), real-time PCR and real-time loop-mediated isothermal amplification (real-time LAMP). Results The results of the present study showed that saliva and urine samples can be used for outbreak investigation of varicella compared to varicella-zoster virus DNA in vesicular swab samples with reasonable sensitivity. Conclusion Thus, molecular techniques may be useful in the early identification of the outbreak and timely isolation, and the treatment of cases can further prevent its spread.
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Affiliation(s)
- Mini P Singh
- Department of Virology, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - Tripti Rungta
- Department of Virology, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - Archit Kumar
- Department of Virology, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - Kapil Goyal
- Department of Virology, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - Bhavneet Bharti
- Department of Paediatrics, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - R K Ratho
- Department of Virology, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
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Sigera PC, Amarasekara R, Rodrigo C, Rajapakse S, Weeratunga P, De Silva NL, Huang CH, Sahoo MK, Pinsky BA, Pillai DR, Tissera HA, Jayasinghe S, Handunnetti S, Fernando SD. Risk prediction for severe disease and better diagnostic accuracy in early dengue infection; the Colombo dengue study. BMC Infect Dis 2019; 19:680. [PMID: 31370795 PMCID: PMC6676631 DOI: 10.1186/s12879-019-4304-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 07/22/2019] [Indexed: 01/14/2023] Open
Abstract
Background A major challenge in dengue management in resource limited settings is the confirmation of diagnosis. Clinical features of dengue often overlap with other infections and molecular diagnostic tools are not readily accessible to clinicians at hospitals. In addition, the prediction of plasma leakage in dengue is also difficult. Hematocrit level and ultrasound scans (combined with clinical parameters) are helpful to detect plasma leakage once it has happened, not before. Methods Colombo Dengue Study (CDS) is a prospective cohort study of clinically suspected adult dengue patients recruited from the National hospital of Sri Lanka (within the first 3 days of fever) that aimed to a) identify clinical and basic laboratory test parameters to differentiate dengue from non-dengue fever, b) evaluate the comparative efficacy of loop-mediated isothermal amplification (LAMP) for dengue diagnosis (vs. NS1 antigen test and RT-qPCR) and c) identify early associations that are predictive of plasma leakage or severe dengue. The basic laboratory tests considered here included hematological parameters, serum biochemistry and inflammatory markers. Results Only 70% of clinically suspected patients were confirmed as having dengue by either the NS1 antigen test or RT-qPCR. On a Bayesian latent class model which assumes no “gold standard”, LAMP performed equally or better than RT-qPCR and NS1 antigen test respectively. When confirmed dengue patients were compared with others, the earlier group had significantly lower lymphocyte counts and higher aspartate aminotransferase levels (AST) within the first 3 days of fever. Confirmed dengue patients with plasma leakage had a lower mean age and a higher median baseline AST level compared to those without plasma leakage (p < 0.05). Conclusion Clinical suspicion overestimates the true number of dengue patients. RT-LAMP is a potentially useful low-cost diagnostic tool for dengue diagnosis. Confirmed dengue patients had significantly higher AST levels and lower lymphocyte counts in early disease compared to others. In confirmed dengue patients, younger age and a higher AST level in early infection were associated with subsequent plasma leakage. Electronic supplementary material The online version of this article (10.1186/s12879-019-4304-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Ranmalee Amarasekara
- Department of Microbiology, Immunology, and Infectious Diseases, University of Calgary, Calgary, Canada
| | - Chaturaka Rodrigo
- Department of Pathology, School of Medical Sciences, UNSW Sydney, Kensington, Australia
| | - Senaka Rajapakse
- Department of Clinical Medicine, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka
| | - Praveen Weeratunga
- Department of Clinical Medicine, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka
| | - Nipun Lakshita De Silva
- Department of Clinical Medicine, Faculty of Medicine, General Sir John Kotelawala Defence University, Colombo, Sri Lanka
| | - Chun Hong Huang
- Department of Pathology, Stanford University School of Medicine, Standford, USA
| | - Malaya K Sahoo
- Department of Pathology, Stanford University School of Medicine, Standford, USA
| | - Benjamin A Pinsky
- Department of Pathology, Stanford University School of Medicine, Standford, USA.,Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Standford, USA
| | - Dylan R Pillai
- Department of Microbiology, Immunology, and Infectious Diseases, University of Calgary, Calgary, Canada
| | | | - Saroj Jayasinghe
- Department of Clinical Medicine, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka
| | - Shiroma Handunnetti
- The Institute of Biochemistry, Molecular Biology and Biotechnology, Colombo, Sri Lanka
| | - Sumadhya D Fernando
- Department of Parasitology, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka.
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38
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Zhou Y, Wan Z, Yang S, Li Y, Li M, Wang B, Hu Y, Xia X, Jin X, Yu N, Zhang C. A Mismatch-Tolerant Reverse Transcription Loop-Mediated Isothermal Amplification Method and Its Application on Simultaneous Detection of All Four Serotype of Dengue Viruses. Front Microbiol 2019; 10:1056. [PMID: 31139171 PMCID: PMC6518337 DOI: 10.3389/fmicb.2019.01056] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 04/26/2019] [Indexed: 11/25/2022] Open
Abstract
Loop-mediated isothermal amplification (LAMP) has been widely used in the detection of pathogens causing infectious diseases. However, mismatches between primers (especially in the 3′-end) and templates significantly reduced the amplification efficiency of LAMP, and limited its application to genetically diverse viruses. Here, we reported a novel mismatch-tolerant LAMP assay and its application in the detection of dengue viruses (DENV). The novel method features the addition of as little as 0.15 U of high-fidelity DNA polymerase to the standard 25 μl LAMP reaction mixture. This amount was sufficient to remove the mismatched bases at the 3′-end of primers, thereby resulting in excellent tolerance for various mismatches occurring at the 3′-end of the LAMP primers during amplification. This novel LAMP assay has a markedly improved amplification efficiency especially for the mutants forming mismatches with internal primers (FIP/BIP) and loop primers (FLP/BLP). The reaction time of the novel method was about 5.6–22.6 min faster than the conventional LAMP method regardless of the presence or absence of mismatches between primers and templates. Using the novel method, we improved a previously established pan-serotype assay for DENV, and demonstrated greater sensitivity for detection of four DENV serotypes than the previous one. The limit of detection (LOD) of the novel assay was 74, 252, 78, and 35 virus RNA copies per reaction for DENV-1, DENV-2, DENV-3, and DENV-4, respectively. Among 153 clinical samples from patients with suspected DENV infection, the novel assay detected 94.8% samples being DENV positive, higher than that detected by the commercial NS1 antigen assay (92.2%), laboratory-based RT-PCR method (78.4%), and the conventional RT-LAMP assay (86.9%). Furthermore, the novel RT-LAMP assay has been developed into a visual determination method by adding colorimetric dyes. Because of its simplicity, all LAMP-based diagnostic assays may be easily updated to the newly improved version. The novel mismatch-tolerant LAMP method represents a simple, sensitive and promising approach for molecular diagnosis of highly variable viruses, and it is especially suited for application in resource-limited settings.
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Affiliation(s)
- Yi Zhou
- School of Life Sciences, East China Normal University, Shanghai, China.,Pathogen Discovery and Big Data Center, Chinese Academy of Sciences (CAS) Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Zhenzhou Wan
- Medical Laboratory of Taizhou Fourth People's Hospital, Taizhou, China
| | - Shuting Yang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Yingxue Li
- Pathogen Discovery and Big Data Center, Chinese Academy of Sciences (CAS) Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Min Li
- Viral Disease and Vaccine Translational Research Unit, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Binghui Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Yihong Hu
- Pathogen Discovery and Big Data Center, Chinese Academy of Sciences (CAS) Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Xueshan Xia
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Xia Jin
- Viral Disease and Vaccine Translational Research Unit, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Na Yu
- School of Life Sciences, East China Normal University, Shanghai, China
| | - Chiyu Zhang
- Pathogen Discovery and Big Data Center, Chinese Academy of Sciences (CAS) Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
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Imai K, Tarumoto N, Runtuwene LR, Sakai J, Hayashida K, Eshita Y, Maeda R, Tuda J, Ohno H, Murakami T, Maesaki S, Suzuki Y, Yamagishi J, Maeda T. An innovative diagnostic technology for the codon mutation C580Y in kelch13 of Plasmodium falciparum with MinION nanopore sequencer. Malar J 2018; 17:217. [PMID: 29843734 PMCID: PMC5975513 DOI: 10.1186/s12936-018-2362-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Accepted: 05/22/2018] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND The recent spread of artemisinin (ART)-resistant Plasmodium falciparum represents an emerging global threat to public health. In Southeast Asia, the C580Y mutation of kelch13 (k13) is the dominant mutation of ART-resistant P. falciparum. Therefore, a simple method for the detection of C580Y mutation is urgently needed to enable widespread routine surveillance in the field. The aim of this study is to develop a new diagnostic procedure for the C580Y mutation using loop-mediated isothermal amplification (LAMP) combined with the MinION nanopore sequencer. RESULTS A LAMP assay for the k13 gene of P. falciparum to detect the C580Y mutation was successfully developed. The detection limit of this procedure was 10 copies of the reference plasmid harboring the k13 gene within 60 min. Thereafter, amplicon sequencing of the LAMP products using the MinION nanopore sequencer was performed to clarify the nucleotide sequences of the gene. The C580Y mutation was identified based on the sequence data collected from MinION reads 30 min after the start of sequencing. Further, clinical evaluation of the LAMP assay in 34 human blood samples collected from patients with P. falciparum malaria in Indonesia revealed a positive detection rate of 100%. All LAMP amplicons of up to 12 specimens were simultaneously sequenced using MinION. The results of sequencing were consistent with those of the conventional PCR and Sanger sequencing protocol. All procedures from DNA extraction to variant calling were completed within 3 h. The C580Y mutation was not found among these 34 P. falciparum isolates in Indonesia. CONCLUSIONS An innovative method combining LAMP and MinION will enable simple, rapid, and high-sensitivity detection of the C580Y mutation of P. falciparum, even in resource-limited situations in developing countries.
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Affiliation(s)
- Kazuo Imai
- Department of Infectious Disease and Infection Control, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama, 350-0495, Japan.,Center for Clinical Infectious Diseases and Research, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama, 350-0495, Japan
| | - Norihito Tarumoto
- Department of Infectious Disease and Infection Control, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama, 350-0495, Japan.,Center for Clinical Infectious Diseases and Research, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama, 350-0495, Japan
| | - Lucky Ronald Runtuwene
- Department of Computational Biology and Medical Science, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan
| | - Jun Sakai
- Department of Infectious Disease and Infection Control, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama, 350-0495, Japan.,Center for Clinical Infectious Diseases and Research, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama, 350-0495, Japan
| | - Kyoko Hayashida
- Research Center for Zoonosis Control, Hokkaido University, North 20, West 10 Kita-ku, Sapporo, Hokkaido, 001-0020, Japan
| | - Yuki Eshita
- Research Center for Zoonosis Control, Hokkaido University, North 20, West 10 Kita-ku, Sapporo, Hokkaido, 001-0020, Japan.,Faculty of Medicine, Oita University, 1-1 Hasama-machi, Yufu, Oita, 879-5593, Japan.,Department of Medical Entomology, Faculty of Tropical Medicine, Mahidol University, 420/6 Ratchawithi Road, Thung Phaya, Ratchathewi, Bangkok, 10400, Thailand.,Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Ryuichiro Maeda
- Division of Biomedical Sciences, Department of Basic Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine, 2-11 Inada-cho, Obihiro, Hokkaido, 080-8555, Japan
| | - Josef Tuda
- Department of Parasitology, Faculty of Medicine, Sam Ratulangi University, Kampus Unsrat, Bahu Manado, 95115, Indonesia
| | - Hideaki Ohno
- Department of Infectious Diseases and Infection Control, Saitama Medical Center, Saitama Medical University, 1981 Kamoda, Kawagoe, Saitama, 350-8550, Japan
| | - Takashi Murakami
- Center for Clinical Infectious Diseases and Research, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama, 350-0495, Japan.,Department of Microbiology, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama, 350-0495, Japan
| | - Shigefumi Maesaki
- Department of Infectious Disease and Infection Control, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama, 350-0495, Japan.,Center for Clinical Infectious Diseases and Research, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama, 350-0495, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Science, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan
| | - Junya Yamagishi
- Research Center for Zoonosis Control, Hokkaido University, North 20, West 10 Kita-ku, Sapporo, Hokkaido, 001-0020, Japan.,Global Station for Zoonosis Control, GI-CoRE, Hokkaido University, North 20, West 10 Kita-ku, Sapporo, Hokkaido, 001-0020, Japan
| | - Takuya Maeda
- Center for Clinical Infectious Diseases and Research, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama, 350-0495, Japan. .,Department of Microbiology, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama, 350-0495, Japan.
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Lopez-Jimena B, Bekaert M, Bakheit M, Frischmann S, Patel P, Simon-Loriere E, Lambrechts L, Duong V, Dussart P, Harold G, Fall C, Faye O, Sall AA, Weidmann M. Development and validation of four one-step real-time RT-LAMP assays for specific detection of each dengue virus serotype. PLoS Negl Trop Dis 2018; 12:e0006381. [PMID: 29813062 PMCID: PMC5973574 DOI: 10.1371/journal.pntd.0006381] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 03/12/2018] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND 4 one-step, real-time, reverse transcription loop-mediated isothermal amplification (RT-LAMP) assays were developed for the detection of dengue virus (DENV) serotypes by considering 2,056 full genome DENV sequences. DENV1 and DENV2 RT-LAMP assays were validated with 31 blood and 11 serum samples from Tanzania, Senegal, Sudan and Mauritania. DENV3 and DENV4 RT-LAMP assays were validated with 25 serum samples from Cambodia. METHODOLOGY/PRINCIPAL FINDINGS 4 final reaction primer mixes were obtained by using a combination of Principal Component Analysis of the full DENV genome sequences, and LAMP primer design based on sequence alignments using the LAVA software. These mixes contained 14 (DENV1), 12 (DENV2), 8 (DENV3) and 3 (DENV4) LAMP primer sets. The assays were evaluated with an External Quality Assessment panel from Quality Control for Molecular Diagnostics. The assays were serotype-specific and did not cross-detect with other flaviviruses. The limits of detection, with 95% probability, were 22 (DENV1), 542 (DENV2), 197 (DENV3) and 641 (DENV4) RNA molecules, and 100% reproducibility in the assays was obtained with up to 102 (DENV1) and 103 RNA molecules (DENV2, DENV3 and DENV4). Validation of the DENV2 assay with blood samples from Tanzania resulted in 23 samples detected by RT-LAMP, demonstrating that the assay is 100% specific and 95.8% sensitive (positive predictive value of 100% and a negative predictive value of 85.7%). All serum samples from Senegal, Sudan and Mauritania were detected and 3 untyped as DENV1. The sensitivity of RT-LAMP for DENV4 samples from Cambodia did not quite match qRT-PCR. CONCLUSIONS/SIGNIFICANCE We have shown a novel approach to design LAMP primers that makes use of fast growing sequence databases. The DENV1 and DENV2 assays were validated with viral RNA extracted clinical samples, showing very good performance parameters.
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Affiliation(s)
- Benjamin Lopez-Jimena
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, United Kingdom
| | - Michaël Bekaert
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, United Kingdom
| | | | | | - Pranav Patel
- Robert Koch Institute, Centre for biological security 1 (ZBS1), Berlin, Germany
| | - Etienne Simon-Loriere
- Functional Genetics of Infectious Diseases Unit, Department of Genomes and Genetics, Institut Pasteur, Paris, France
- Centre National de la Recherche Scientifique, Unité de Recherche Associée, Paris, France
| | - Louis Lambrechts
- Centre National de la Recherche Scientifique, Unité de Recherche Associée, Paris, France
- Insect-Virus Interactions Group, Department of Genomes and Genetics, Institut Pasteur, Paris, France
| | - Veasna Duong
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
| | - Philippe Dussart
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
| | - Graham Harold
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, United Kingdom
| | - Cheikh Fall
- Arbovirus and viral haemorrhagic fever unit, Institut Pasteur de Dakar, Institut Pasteur International Network, Dakar, Senegal
| | - Oumar Faye
- Arbovirus and viral haemorrhagic fever unit, Institut Pasteur de Dakar, Institut Pasteur International Network, Dakar, Senegal
| | - Amadou Alpha Sall
- Arbovirus and viral haemorrhagic fever unit, Institut Pasteur de Dakar, Institut Pasteur International Network, Dakar, Senegal
| | - Manfred Weidmann
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, United Kingdom
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Tan KK, Azizan NS, Yaacob CN, Che Mat Seri NAA, Samsudin NI, Teoh BT, Sam SS, AbuBakar S. Operational utility of the reverse-transcription recombinase polymerase amplification for detection of dengue virus. BMC Infect Dis 2018; 18:169. [PMID: 29642856 PMCID: PMC5896040 DOI: 10.1186/s12879-018-3065-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 03/26/2018] [Indexed: 02/02/2023] Open
Abstract
Background A method for rapid detection of dengue virus using the reverse-transcription recombinase polymerase amplification (RT-RPA) was recently developed, evaluated and made ready for deployment. However, reliance solely on the evaluation performed by experienced researchers in a well-structured and well-equipped reference laboratory may overlook the potential intrinsic problems that may arise during deployment of the assay into new application sites, especially for users unfamiliar with the test. Appropriate assessment of this newly developed assay by users who are unfamiliar with the assay is, therefore, vital. Methods An operational utility test to elucidate the efficiency and effectiveness of the dengue RT-RPA assay was conducted among a group of researchers new to the assay. Nineteen volunteer researchers with different research experience were recruited. The participants performed the RT-RPA assay and interpreted the test results according to the protocol provided. Deviation from the protocol was identified and tabulated by trained facilitators. Post-test questionnaires were conducted to determine the user satisfaction and acceptability of the dengue RT-RPA assay. Results All the participants completed the test and successfully interpreted the results according to the provided instructions, regardless of their research experience. Of the 19 participants, three (15.8%) performed the assay with no deviations and 16 (84.2%) performed the assay with only 1 to 5 deviations. The number of deviations from protocol, however, was not correlated with the user laboratory experience. The accuracy of the results was also not affected by user laboratory experience. The concordance of the assay results against that of the expected was at 89.3%. The user satisfaction towards the RT-RPA protocol and interpretation of results was 90% and 100%, respectively. Conclusions The dengue RT-RPA assay can be successfully performed by simply following the provided written instructions. Deviations from the written protocols did not adversely affect the outcome of the assay. These suggest that the RT-RPA assay is indeed a simple, robust and efficient laboratory method for detection of dengue virus. Furthermore, high new user acceptance of the RT-RPA assay suggests that this assay could be successfully deployed into new laboratories where RT-RPA was not previously performed. Electronic supplementary material The online version of this article (10.1186/s12879-018-3065-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kim-Kee Tan
- Tropical Infectious Diseases Research and Education Centre (TIDREC), University of Malaya, 50603, Kuala Lumpur, Malaysia.,WHO Collaborating Centre for Arbovirus Research and Reference (Dengue and Severe Dengue), University of Malaya, 50603, Kuala Lumpur, Malaysia.,Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Noor Syahida Azizan
- Tropical Infectious Diseases Research and Education Centre (TIDREC), University of Malaya, 50603, Kuala Lumpur, Malaysia.,WHO Collaborating Centre for Arbovirus Research and Reference (Dengue and Severe Dengue), University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Che Norainon Yaacob
- Tropical Infectious Diseases Research and Education Centre (TIDREC), University of Malaya, 50603, Kuala Lumpur, Malaysia.,WHO Collaborating Centre for Arbovirus Research and Reference (Dengue and Severe Dengue), University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Nurul Asma Anati Che Mat Seri
- Tropical Infectious Diseases Research and Education Centre (TIDREC), University of Malaya, 50603, Kuala Lumpur, Malaysia.,WHO Collaborating Centre for Arbovirus Research and Reference (Dengue and Severe Dengue), University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Nur Izyan Samsudin
- Tropical Infectious Diseases Research and Education Centre (TIDREC), University of Malaya, 50603, Kuala Lumpur, Malaysia.,WHO Collaborating Centre for Arbovirus Research and Reference (Dengue and Severe Dengue), University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Boon-Teong Teoh
- Tropical Infectious Diseases Research and Education Centre (TIDREC), University of Malaya, 50603, Kuala Lumpur, Malaysia.,WHO Collaborating Centre for Arbovirus Research and Reference (Dengue and Severe Dengue), University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Sing-Sin Sam
- Tropical Infectious Diseases Research and Education Centre (TIDREC), University of Malaya, 50603, Kuala Lumpur, Malaysia.,WHO Collaborating Centre for Arbovirus Research and Reference (Dengue and Severe Dengue), University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Sazaly AbuBakar
- Tropical Infectious Diseases Research and Education Centre (TIDREC), University of Malaya, 50603, Kuala Lumpur, Malaysia. .,WHO Collaborating Centre for Arbovirus Research and Reference (Dengue and Severe Dengue), University of Malaya, 50603, Kuala Lumpur, Malaysia. .,Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia.
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Wilder-Smith A, Tissera H, AbuBakar S, Kittayapong P, Logan J, Neumayr A, Rocklöv J, Byass P, Louis VR, Tozan Y, Massad E, Preet R. Novel tools for the surveillance and control of dengue: findings by the DengueTools research consortium. Glob Health Action 2018; 11:1549930. [PMID: 30560735 PMCID: PMC6282436 DOI: 10.1080/16549716.2018.1549930] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 11/10/2018] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Dengue fever persists as a major global disease burden, and may increase as a consequence of climate change. Along with other measures, research actions to improve diagnosis, surveillance, prevention, and predictive models are highly relevant. The European Commission funded the DengueTools consortium to lead a major initiative in these areas, and this review synthesises the outputs and findings of this work conducted from 2011 to 2016. Research areas: DengueTools organised its work into three research areas, namely [1] Early warning and surveillance systems; [2] Strategies to prevent dengue in children; and [3] Predictive models for the global spread of dengue. Research area 1 focused on case-studies undertaken in Sri Lanka, including developing laboratory-based sentinel surveillance, evaluating economic impact, identifying drivers of transmission intensity, evaluating outbreak prediction capacity and developing diagnostic capacity. Research area 2 addressed preventing dengue transmission in school children, with case-studies undertaken in Thailand. Insecticide-treated school uniforms represented an intriguing potential approach, with some encouraging results, but which were overshadowed by a lack of persistence of insecticide on the uniforms with repeated washing. Research area 3 evaluated potential global spread of dengue, particularly into dengue-naïve areas such as Europe. The role of international travel, changing boundaries of vectors, developing models of vectorial capacity under different climate change scenarios and strategies for vector control in outbreaks was all evaluated. CONCLUDING REMARKS DengueTools was able to make significant advances in methods for understanding and controlling dengue transmission in a range of settings. These will have implications for public health agendas to counteract dengue, including vaccination programmes. OUTLOOK Towards the end of the DengueTools project, Zika virus emerged as an unexpected epidemic in the central and southern America. Given the similarities between the dengue and Zika viruses, with vectors in common, some of the DengueTools thinking translated readily into the Zika situation.
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Affiliation(s)
- Annelies Wilder-Smith
- Unit of Epidemiology and Global Health, Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | - Hasitha Tissera
- Epidemiological Unit, Ministry of Health, Colombo, Sri Lanka
| | - Sazaly AbuBakar
- WHO Collaborating Centre for Arbovirus Reference and Research (Dengue/Severe Dengue), Tropical Infectious Diseases Research and Education Centre (TIDREC) University of Malaya, Kuala Lumpur, Malaysia
| | - Pattamaporn Kittayapong
- Center of Excellence for Vectors and Vector-Borne Diseases, Department of Biology, Faculty of Science, Mahidol University, Salaya, Nakhon Pathom, Bangkok, Thailand
| | - James Logan
- Department of Disease Control, London School of Hygiene and Tropical Medicine, London, UK
| | - Andreas Neumayr
- Department of Medical Services, Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Joacim Rocklöv
- Unit of Epidemiology and Global Health, Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | - Peter Byass
- Unit of Epidemiology and Global Health, Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | - Valérie R. Louis
- Heidelberg Institute of Global Health, Heidelberg University Medical School, Heidelberg, Germany
| | - Yesim Tozan
- Heidelberg Institute of Global Health, Heidelberg University Medical School, Heidelberg, Germany
- NYU College of Global Public Health, New York, NY, USA
| | - Eduardo Massad
- School of Applied Mathematics, Fundacao Getulio Vargas, Rio de Janeiro, Brazil
| | - Raman Preet
- Unit of Epidemiology and Global Health, Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
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Calvert AE, Biggerstaff BJ, Tanner NA, Lauterbach M, Lanciotti RS. Rapid colorimetric detection of Zika virus from serum and urine specimens by reverse transcription loop-mediated isothermal amplification (RT-LAMP). PLoS One 2017; 12:e0185340. [PMID: 28945787 PMCID: PMC5612724 DOI: 10.1371/journal.pone.0185340] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 09/11/2017] [Indexed: 12/22/2022] Open
Abstract
Zika virus (ZIKV) has emerged as a major global public health concern in the last two years due to its link as a causative agent of human birth defects. Its rapid expansion into the Western Hemisphere as well as the ability to be transmitted from mother to fetus, through sexual transmission and possibly through blood transfusions has increased the need for a rapid and expansive public health response to this unprecedented epidemic. A non-invasive and rapid ZIKV diagnostic screening assay that can be performed in a clinical setting throughout pregnancy is vital for prenatal care of women living in areas of the world where exposure to the virus is possible. To meet this need we have developed a sensitive and specific reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) assay to detect ZIKV RNA in urine and serum with a simple visual detection. RT-LAMP results were shown to have a limit of detection 10-fold higher than qRT-PCR. As little as 1.2 RNA copies/μl was detected by RT-LAMP from a panel of 178 diagnostic specimens. The assay was shown to be highly specific for ZIKV RNA when tested with diagnostic specimens positive for dengue virus (DENV) and chikungunya virus (CHIKV). The assay described here illustrates the potential for a fast, reliable, sensitive and specific assay for the detection of ZIKV from urine or serum that can be performed in a clinical or field setting with minimal equipment and technological expertise.
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Affiliation(s)
- Amanda E. Calvert
- Arboviral Diseases Branch, Division of Vector-Borne Diseases, U.S. Centers for Disease Control and Prevention, Fort Collins, CO, United States of America
- * E-mail:
| | - Brad J. Biggerstaff
- Arboviral Diseases Branch, Division of Vector-Borne Diseases, U.S. Centers for Disease Control and Prevention, Fort Collins, CO, United States of America
| | | | - Molly Lauterbach
- Arboviral Diseases Branch, Division of Vector-Borne Diseases, U.S. Centers for Disease Control and Prevention, Fort Collins, CO, United States of America
| | - Robert S. Lanciotti
- Arboviral Diseases Branch, Division of Vector-Borne Diseases, U.S. Centers for Disease Control and Prevention, Fort Collins, CO, United States of America
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44
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Joanne S, Vythilingam I, Teoh BT, Leong CS, Tan KK, Wong ML, Yugavathy N, AbuBakar S. Vector competence of Malaysian Aedes albopictus with and without Wolbachia to four dengue virus serotypes. Trop Med Int Health 2017; 22:1154-1165. [PMID: 28653334 DOI: 10.1111/tmi.12918] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
OBJECTIVE To determine the susceptibility status of Aedes albopictus with and without Wolbachia to the four dengue virus serotypes. METHODS Two newly colonised colonies of Ae. albopictus from the wild were used for the study. One colony was naturally infected with Wolbachia while in the other Wolbachia was removed by tetracycline treatment. Both colonies were orally infected with dengue virus-infected fresh blood meal. Dengue virus load was measured using quantitative RT-PCR at four-time intervals in the salivary glands, midguts and ovaries. RESULTS Wolbachia did not significantly affect Malaysian Ae. albopictus dengue infection or the dissemination rate for all four dengue virus serotypes. Malaysian Ae. albopictus had the highest replication kinetics for DENV-1 and the highest salivary gland and midgut infection rate for DENV-4. CONCLUSION Wolbachia, which naturally exists in Malaysian Ae. albopictus, does not significantly affect dengue virus replication. Malaysian Ae. albopictus is susceptible to dengue virus infections and capable of transmitting dengue virus, especially DENV-1 and DENV-4. Removal of Wolbachia from Malaysian Ae. albopictus would not reduce their susceptibility status.
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Affiliation(s)
- Sylvia Joanne
- Department of Parasitology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Indra Vythilingam
- Department of Parasitology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Boon-Teong Teoh
- Department of Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Cherng-Shii Leong
- Department of Parasitology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Kim-Kee Tan
- Department of Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Meng-Li Wong
- Department of Parasitology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Nava Yugavathy
- Department of Parasitology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Sazaly AbuBakar
- Department of Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
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45
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Chotiwan N, Brewster CD, Magalhaes T, Weger-Lucarelli J, Duggal NK, Rückert C, Nguyen C, Garcia Luna SM, Fauver JR, Andre B, Gray M, Black WC, Kading RC, Ebel GD, Kuan G, Balmaseda A, Jaenisch T, Marques ETA, Brault AC, Harris E, Foy BD, Quackenbush SL, Perera R, Rovnak J. Rapid and specific detection of Asian- and African-lineage Zika viruses. Sci Transl Med 2017; 9:eaag0538. [PMID: 28469032 PMCID: PMC5654541 DOI: 10.1126/scitranslmed.aag0538] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 08/12/2016] [Accepted: 02/15/2017] [Indexed: 01/23/2023]
Abstract
Understanding the dynamics of Zika virus transmission and formulating rational strategies for its control require precise diagnostic tools that are also appropriate for resource-poor environments. We have developed a rapid and sensitive loop-mediated isothermal amplification (LAMP) assay that distinguishes Zika viruses of Asian and African lineages. The assay does not detect chikungunya virus or flaviviruses such as dengue, yellow fever, or West Nile viruses. The assay conditions allowed direct detection of Zika virus RNA in cultured infected cells; in mosquitoes; in virus-spiked samples of human blood, plasma, saliva, urine, and semen; and in infected patient serum, plasma, and semen samples without the need for RNA isolation or reverse transcription. The assay offers rapid, specific, sensitive, and inexpensive detection of the Asian-lineage Zika virus strain that is currently circulating in the Western hemisphere, and can also detect the African-lineage Zika virus strain using separate, specific primers.
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Affiliation(s)
- Nunya Chotiwan
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
- Arthropod-borne Infectious Disease Laboratories, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Connie D Brewster
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Tereza Magalhaes
- Arthropod-borne Infectious Disease Laboratories, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
- Laboratory of Virology and Experimental Therapeutics, Centro de Pesquisas Aggeu Magalhaes, Fundacao Oswaldo Cruz, Recife-PE, Brazil
| | - James Weger-Lucarelli
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
- Arthropod-borne Infectious Disease Laboratories, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Nisha K Duggal
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, CO 80521, USA
| | - Claudia Rückert
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
- Arthropod-borne Infectious Disease Laboratories, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Chilinh Nguyen
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
- Arthropod-borne Infectious Disease Laboratories, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Selene M Garcia Luna
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
- Arthropod-borne Infectious Disease Laboratories, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Joseph R Fauver
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
- Arthropod-borne Infectious Disease Laboratories, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Barb Andre
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Meg Gray
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
- Arthropod-borne Infectious Disease Laboratories, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - William C Black
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
- Arthropod-borne Infectious Disease Laboratories, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Rebekah C Kading
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
- Arthropod-borne Infectious Disease Laboratories, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Gregory D Ebel
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
- Arthropod-borne Infectious Disease Laboratories, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Guillermina Kuan
- Centro de Salud Sócrates Flores Vivas, Ministry of Health, Managua, Nicaragua
| | - Angel Balmaseda
- Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministry of Health, Managua, Nicaragua
| | - Thomas Jaenisch
- Section Clinical Tropical Medicine, Department for Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
- German Centre for Infection Research (DZIF), partner site Heidelberg, Heidelberg, Germany
| | - Ernesto T A Marques
- Laboratory of Virology and Experimental Therapeutics, Centro de Pesquisas Aggeu Magalhaes, Fundacao Oswaldo Cruz, Recife-PE, Brazil
- Center for Vaccine Research, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Aaron C Brault
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, CO 80521, USA
| | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA 94720-7360, USA
| | - Brian D Foy
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
- Arthropod-borne Infectious Disease Laboratories, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Sandra L Quackenbush
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Rushika Perera
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
- Arthropod-borne Infectious Disease Laboratories, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Joel Rovnak
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA.
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Genotypic detection of the bla CTX-M-1 gene among extended-spectrum β-lactamase-producing Enterobacteriaceae. J Glob Antimicrob Resist 2017; 9:87-93. [PMID: 28438685 DOI: 10.1016/j.jgar.2017.01.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 01/06/2017] [Accepted: 01/09/2017] [Indexed: 11/22/2022] Open
Abstract
OBJECTIVES Extended-spectrum β-lactamases (ESBLs), a group of β-lactamase enzymes produced by bacteria in the family Enterobacteriaceae, are becoming a major problem in the healthcare community worldwide. Although many attempts have been made in the detection of ESBL-producing bacteria, the cost and speed of detection remains an important challenge. Therefore, this study aimed to develop a rapid, effective and affordable method for detection of the blaCTX-M-1 ESBL gene by a loop-mediated isothermal amplification (LAMP) technique. METHODS Clinical ESBL-producing Enterobacteriaceae, including Escherichia coli and Klebsiella pneumoniae, were isolated and were used as representative strains. The double-disk synergy method was performed to detect ESBL-producing Enterobacteriaceae. Performance of the LAMP method in the detection of blaCTX-M-1 was compared with conventional PCR in terms of sensitivity and specificity. RESULTS The developed LAMP method efficiently identified the presence of the blaCTX-M-1 gene in ESBL-producing Enterobacteriaceae. It provided similar results to conventional PCR, but the LAMP technique required only 20min of testing time. The accuracy of the LAMP method was confirmed by restriction digestion, which showed the predicted size of the blaCTX-M-1 gene. In addition, the developed method was comparable with PCR that amplified only the target blaCTX-M-1 gene in terms of specificity, but LAMP was ca. 1000-fold more sensitive than PCR. CONCLUSIONS A rapid assay to detect ESBL-producing Enterobacteriaceae by a LAMP technique was developed in this study. The developed method is sensitive and suitable for rapid screening of blaCTX-M-1 in routine laboratories with limited resources.
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Muller DA, Depelsenaire ACI, Young PR. Clinical and Laboratory Diagnosis of Dengue Virus Infection. J Infect Dis 2017; 215:S89-S95. [PMID: 28403441 DOI: 10.1093/infdis/jiw649] [Citation(s) in RCA: 193] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Infection with any of the 4 dengue virus serotypes results in a diverse range of symptoms, from mild undifferentiated fever to life-threatening hemorrhagic fever and shock. Given that dengue virus infection elicits such a broad range of clinical symptoms, early and accurate laboratory diagnosis is essential for appropriate patient management. Virus detection and serological conversion have been the main targets of diagnostic assessment for many years, however cross-reactivity of antibody responses among the flaviviruses has been a confounding issue in providing a differential diagnosis. Furthermore, there is no single, definitive diagnostic biomarker that is present across the entire period of patient presentation, particularly in those experiencing a secondary dengue infection. Nevertheless, the development and commercialization of point-of-care combination tests capable of detecting markers of infection present during different stages of infection (viral nonstructural protein 1 and immunoglobulin M) has greatly simplified laboratory-based dengue diagnosis. Despite these advances, significant challenges remain in the clinical management of dengue-infected patients, especially in the absence of reliable biomarkers that provide an effective prognostic indicator of severe disease progression. This review briefly summarizes some of the complexities and issues surrounding clinical dengue diagnosis and the laboratory diagnostic options currently available.
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Affiliation(s)
- David A Muller
- Australian Institute for Bioengineering and Nanotechnology and.,Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Australia
| | | | - Paul R Young
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane,Australia
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48
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A smartphone-based diagnostic platform for rapid detection of Zika, chikungunya, and dengue viruses. Sci Rep 2017; 7:44778. [PMID: 28317856 PMCID: PMC5357913 DOI: 10.1038/srep44778] [Citation(s) in RCA: 179] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 01/24/2017] [Indexed: 12/27/2022] Open
Abstract
Current multiplexed diagnostics for Zika, dengue, and chikungunya viruses are situated outside the intersection of affordability, high performance, and suitability for use at the point-of-care in resource-limited settings. Consequently, insufficient diagnostic capabilities are a key limitation facing current Zika outbreak management strategies. Here we demonstrate highly sensitive and specific detection of Zika, chikungunya, and dengue viruses by coupling reverse-transcription loop-mediated isothermal amplification (RT-LAMP) with our recently developed quenching of unincorporated amplification signal reporters (QUASR) technique. We conduct reactions in a simple, inexpensive and portable "LAMP box" supplemented with a consumer class smartphone. The entire assembly can be powered by a 5 V USB source such as a USB power bank or solar panel. Our smartphone employs a novel algorithm utilizing chromaticity to analyze fluorescence signals, which improves the discrimination of positive/negative signals by 5-fold when compared to detection with traditional RGB intensity sensors or the naked eye. The ability to detect ZIKV directly from crude human sample matrices (blood, urine, and saliva) demonstrates our device's utility for widespread clinical deployment. Together, these advances enable our system to host the key components necessary to expand the use of nucleic acid amplification-based detection assays towards point-of-care settings where they are needed most.
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49
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Carter C, Akrami K, Hall D, Smith D, Aronoff-Spencer E. Lyophilized visually readable loop-mediated isothermal reverse transcriptase nucleic acid amplification test for detection Ebola Zaire RNA. J Virol Methods 2017; 244:32-38. [PMID: 28242293 DOI: 10.1016/j.jviromet.2017.02.013] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 02/18/2017] [Accepted: 02/23/2017] [Indexed: 11/28/2022]
Abstract
Recent viral outbreaks highlight the need for reliable, yet broadly deployable diagnostics for detection of epidemic and emerging pathogens. In this study we designed and optimized methods to visually detect viral nucleic acid by isothermal amplification and SYBR dye intercalation. We designed and tested loop-mediated isothermal amplification (LAMP) primers and lyophilized reactions to optimize the detection of Zaire Ebola Virus (ZEBOV) and further evolved the LAMP platform to allow room-temperature storage for deployment in resource limited settings. Our results demonstrated excellent sensitivity and specificity for viral nucleic acid sequences with lower limits of detection of less than 100 copies. Moreover, lyophilized reaction mixtures retained activity for prolonged periods under dry conditions at room temperature. This approach offers a way for detection of emerging viruses in resource limited settings.
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Affiliation(s)
- Christoph Carter
- University of California, Department of Medicine, Division of Infectious Disease, 9500 Gilman Drive # 0711, La Jolla, San Diego, CA 92093-0711, USA.
| | - Kevan Akrami
- University of California, Electrical and Computer Engineering, 9500 Gilman Drive, Jacobs Hall, Room 4805, La Jolla, San Diego, CA, USA.
| | - Drew Hall
- University of California, Department of Medicine, Division of Infectious Disease, 9500 Gilman Drive # 0711, La Jolla, San Diego, CA 92093-0711, USA; University of California, Electrical and Computer Engineering, 9500 Gilman Drive, Jacobs Hall, Room 4805, La Jolla, San Diego, CA, USA.
| | - Davey Smith
- University of California, Electrical and Computer Engineering, 9500 Gilman Drive, Jacobs Hall, Room 4805, La Jolla, San Diego, CA, USA.
| | - Eliah Aronoff-Spencer
- University of California, Electrical and Computer Engineering, 9500 Gilman Drive, Jacobs Hall, Room 4805, La Jolla, San Diego, CA, USA.
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50
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Choi JR, Yong KW, Tang R, Gong Y, Wen T, Yang H, Li A, Chia YC, Pingguan-Murphy B, Xu F. Lateral Flow Assay Based on Paper-Hydrogel Hybrid Material for Sensitive Point-of-Care Detection of Dengue Virus. Adv Healthc Mater 2017; 6. [PMID: 27860384 DOI: 10.1002/adhm.201600920] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 10/09/2016] [Indexed: 11/09/2022]
Abstract
Paper-based devices have been broadly used for the point-of-care detection of dengue viral nucleic acids due to their simplicity, cost-effectiveness, and readily observable colorimetric readout. However, their moderate sensitivity and functionality have limited their applications. Despite the above-mentioned advantages, paper substrates are lacking in their ability to control fluid flow, in contrast to the flow control enabled by polymer substrates (e.g., agarose) with readily tunable pore size and porosity. Herein, taking the benefits from both materials, the authors propose a strategy to create a hybrid substrate by incorporating agarose into the test strip to achieve flow control for optimal biomolecule interactions. As compared to the unmodified test strip, this strategy allows sensitive detection of targets with an approximately tenfold signal improvement. Additionally, the authors showcase the potential of functionality improvement by creating multiple test zones for semi-quantification of targets, suggesting that the number of visible test zones is directly proportional to the target concentration. The authors further demonstrate the potential of their proposed strategy for clinical assessment by applying it to their prototype sample-to-result test strip to sensitively and semi-quantitatively detect dengue viral RNA from the clinical blood samples. This proposed strategy holds significant promise for detecting various targets for diverse future applications.
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Affiliation(s)
- Jane Ru Choi
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education; School of Life Science and Technology; Xi'an Jiaotong University; Xi'an 710049 P. R. China
- Bioinspired Engineering and Biomechanics Center (BEBC); Xi'an Jiaotong University; Xi'an 710049 P. R. China
- Department of Biomedical Engineering; Faculty of Engineering; University of Malaya; Lembah Pantai; 50603 Kuala Lumpur Malaysia
| | - Kar Wey Yong
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education; School of Life Science and Technology; Xi'an Jiaotong University; Xi'an 710049 P. R. China
- Bioinspired Engineering and Biomechanics Center (BEBC); Xi'an Jiaotong University; Xi'an 710049 P. R. China
- Department of Biomedical Engineering; Faculty of Engineering; University of Malaya; Lembah Pantai; 50603 Kuala Lumpur Malaysia
| | - Ruihua Tang
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education; School of Life Science and Technology; Xi'an Jiaotong University; Xi'an 710049 P. R. China
- Bioinspired Engineering and Biomechanics Center (BEBC); Xi'an Jiaotong University; Xi'an 710049 P. R. China
- School of Life Sciences; Northwestern Polytechnical University; Xi'an 710072 P. R. China
| | - Yan Gong
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education; School of Life Science and Technology; Xi'an Jiaotong University; Xi'an 710049 P. R. China
- Bioinspired Engineering and Biomechanics Center (BEBC); Xi'an Jiaotong University; Xi'an 710049 P. R. China
- Xi'an Diandi Biotech Company; Xi'an 710049 P. R. China
| | - Ting Wen
- Xi'an Diandi Biotech Company; Xi'an 710049 P. R. China
| | - Hui Yang
- School of Life Sciences; Northwestern Polytechnical University; Xi'an 710072 P. R. China
| | - Ang Li
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research; College of Stomatology; Xi'an Jiaotong University; Xi'an 710049 P. R. China
| | - Yook Chin Chia
- Department of Primary Care Medicine; University of Malaya Primary Care Research Group; Faculty of Medicine; University of Malaya; Lembah Pantai; 50603 Kuala Lumpur Malaysia
| | - Belinda Pingguan-Murphy
- Department of Biomedical Engineering; Faculty of Engineering; University of Malaya; Lembah Pantai; 50603 Kuala Lumpur Malaysia
| | - Feng Xu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education; School of Life Science and Technology; Xi'an Jiaotong University; Xi'an 710049 P. R. China
- Bioinspired Engineering and Biomechanics Center (BEBC); Xi'an Jiaotong University; Xi'an 710049 P. R. China
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