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Feng X, Liu Y, Zhao Y, Sun Z, Xu N, Zhao C, Xia W. Recombinase Polymerase Amplification-Based Biosensors for Rapid Zoonoses Screening. Int J Nanomedicine 2023; 18:6311-6331. [PMID: 37954459 PMCID: PMC10637217 DOI: 10.2147/ijn.s434197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 10/21/2023] [Indexed: 11/14/2023] Open
Abstract
Recent, outbreaks of new emergency zoonotic diseases have prompted an urgent need to develop fast, accurate, and portable screening assays for pathogen infections. Recombinase polymerase amplification (RPA) is sensitive and specific and can be conducted at a constant low temperature with a short response time, making it especially suitable for on-site screening and making it a powerful tool for preventing or controlling the spread of zoonoses. This review summarizes the design principles of RPA-based biosensors as well as various signal output or readout technologies involved in fluorescence detection, lateral flow assays, enzymatic catalytic reactions, spectroscopic techniques, electrochemical techniques, chemiluminescence, nanopore sequencing technologies, microfluidic digital RPA, and clustered regularly interspaced short palindromic repeats/CRISPR-associated systems. The current status and prospects of the application of RPA-based biosensors in zoonoses screening are highlighted. RPA-based biosensors demonstrate the advantages of rapid response, easy-to-read result output, and easy implementation for on-site detection, enabling development toward greater portability, automation, and miniaturization. Although there are still problems such as high cost with unstable signal output, RPA-based biosensors are increasingly becoming one of the most important means of on-site pathogen screening in complex samples involving environmental, water, food, animal, and human samples for controlling the spread of zoonotic diseases.
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Affiliation(s)
- Xinrui Feng
- College of Public Health, Jilin Medical University, Jilin, 132013, People’s Republic of China
- Medical College, Yanbian University, Yanji, 136200, People’s Republic of China
| | - Yan Liu
- College of Public Health, Jilin Medical University, Jilin, 132013, People’s Republic of China
| | - Yang Zhao
- Department of Emergency and Intensive Medicine, No. 965 Hospital of PLA Joint Logistic Support Force, Jilin, 132013, People’s Republic of China
| | - Zhe Sun
- College of Public Health, Jilin Medical University, Jilin, 132013, People’s Republic of China
- College of Medical Technology, Beihua University, Jilin, 132013, People’s Republic of China
| | - Ning Xu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, 130062, People’s Republic of China
| | - Chen Zhao
- College of Public Health, Jilin Medical University, Jilin, 132013, People’s Republic of China
| | - Wei Xia
- College of Medical Technology, Beihua University, Jilin, 132013, People’s Republic of China
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Pollak NM, Olsson M, Ahmed M, Tan J, Lim G, Setoh YX, Wong JCC, Lai YL, Hobson-Peters J, Macdonald J, McMillan D. Rapid Diagnostic Tests for the Detection of the Four Dengue Virus Serotypes in Clinically Relevant Matrices. Microbiol Spectr 2023; 11:e0279622. [PMID: 36682882 PMCID: PMC9927141 DOI: 10.1128/spectrum.02796-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The efficient and accurate diagnosis of dengue, a major mosquito-borne disease, is of primary importance for clinical care, surveillance, and outbreak control. The identification of specific dengue virus serotype 1 (DENV-1) to DENV-4 can help in understanding the transmission dynamics and spread of dengue disease. The four rapid low-resource serotype-specific dengue tests use a simple sample preparation reagent followed by reverse transcription-isothermal recombinase polymerase amplification (RT-RPA) combined with lateral flow detection (LFD) technology. Results are obtained directly from clinical sample matrices in 35 min, requiring only a heating block and pipettes for liquid handling. In addition, we demonstrate that the rapid sample preparation step inactivates DENV, improving laboratory safety. Human plasma and serum were spiked with DENV, and DENV was detected with analytical sensitivities of 333 to 22,500 median tissue culture infectious doses (TCID50)/mL. The analytical sensitivities in blood were 94,000 to 333,000 TCID50/mL. Analytical specificity testing confirmed that each test could detect multiple serotype-specific strains but did not respond to strains of other serotypes, closely related flaviviruses, or chikungunya virus. Clinical testing on 80 human serum samples demonstrated test specificities of between 94 and 100%, with a DENV-2 test sensitivity of 100%, detecting down to 0.004 PFU/μL, similar to the sensitivity of the PCR test; the other DENV tests detected down to 0.03 to 10.9 PFU/μL. Collectively, our data suggest that some of our rapid dengue serotyping tests provide a potential alternative to conventional labor-intensive RT-quantitative PCR (RT-qPCR) detection, which requires expensive thermal cycling instrumentation, technical expertise, and prolonged testing times. Our tests provide performance and speed without compromising specificity in human plasma and serum and could become promising tools for the detection of high DENV loads in resource-limited settings. IMPORTANCE The efficient and accurate diagnosis of dengue, a major mosquito-borne disease, is of primary importance for clinical care, surveillance, and outbreak control. This study describes the evaluation of four rapid low-resource serotype-specific dengue tests for the detection of specific DENV serotypes in clinical sample matrices. The tests use a simple sample preparation reagent followed by reverse transcription-isothermal recombinase polymerase amplification (RT-RPA) combined with lateral flow detection (LFD) technology. These tests have several advantages compared to RT-qPCR detection, such as a simple workflow, rapid sample processing and turnaround times (35 min from sample preparation to detection), minimal equipment needs, and improved laboratory safety through the inactivation of the virus during the sample preparation step. The low-resource formats of these rapid dengue serotyping tests have the potential to support effective dengue disease surveillance and enhance the diagnostic testing capacity in resource-limited countries with both endemic dengue and intense coronavirus disease 2019 (COVID-19) transmission.
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Affiliation(s)
- Nina M. Pollak
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- DMTC Ltd., Kew, Victoria, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Malin Olsson
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- DMTC Ltd., Kew, Victoria, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Madeeha Ahmed
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Javier Tan
- Environmental Health Institute, National Environment Agency, Singapore, Singapore
| | - George Lim
- Environmental Health Institute, National Environment Agency, Singapore, Singapore
| | - Yin Xiang Setoh
- Environmental Health Institute, National Environment Agency, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland, Australia
| | | | - Yee Ling Lai
- Environmental Health Institute, National Environment Agency, Singapore, Singapore
| | - Jody Hobson-Peters
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland, Australia
| | - Joanne Macdonald
- DMTC Ltd., Kew, Victoria, Australia
- BioCifer Pty. Ltd., Brisbane, Queensland, Australia
| | - David McMillan
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- DMTC Ltd., Kew, Victoria, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
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3
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Pollak NM, Olsson M, Marsh GA, Macdonald J, McMillan D. Evaluation of three rapid low-resource molecular tests for Nipah virus. Front Microbiol 2023; 13:1101914. [PMID: 36845977 PMCID: PMC9949527 DOI: 10.3389/fmicb.2022.1101914] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 12/13/2022] [Indexed: 02/11/2023] Open
Abstract
Accurate and timely diagnosis of Nipah virus (NiV) requires rapid, inexpensive, and robust diagnostic tests to control spread of disease. Current state of the art technologies are slow and require laboratory infrastructure that may not be available in all endemic settings. Here we report the development and comparison of three rapid NiV molecular diagnostic tests based on reverse transcription recombinase-based isothermal amplification coupled with lateral flow detection. These tests include a simple and fast one-step sample processing step that inactivates the BSL-4 pathogen, enabling safe testing without the need for multi-step RNA purification. The rapid NiV tests targeted the Nucleocapsid protein (N) gene with analytical sensitivity down to 1,000 copies/μL for synthetic NiV RNA and did not cross-react with RNA of other flaviviruses or Chikungunya virus, which can clinically present with similar febrile symptoms. Two tests detected 50,000-100,000 TCID50/mL (100-200 RNA copies/reaction) of the two distinct strains of NiV, Bangladesh (NiVB) and Malaysia (NiVM), and took 30 min from sample to result, suggesting these tests are well suited for rapid diagnosis under resource-limited conditions due to rapidity, simplicity, and low equipment requirements. These Nipah tests represent a first step toward development of near-patient NiV diagnostics that are appropriately sensitive for first-line screening, sufficiently robust for a range of peripheral settings, with potential to be safely performed outside of biohazard containment facilities.
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Affiliation(s)
- Nina M. Pollak
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, QLD, Australia,DMTC Limited, Kew, VIC, Australia,School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, Australia,*Correspondence: Nina M. Pollak,
| | - Malin Olsson
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, QLD, Australia,DMTC Limited, Kew, VIC, Australia,School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Glenn A. Marsh
- Commonwealth Scientific and Industrial Research Organisation Health and Biosecurity, Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Joanne Macdonald
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, QLD, Australia,DMTC Limited, Kew, VIC, Australia,School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, Australia,BioCifer Pty Ltd., Brisbane, QLD, Australia,Joanne Macdonald,
| | - David McMillan
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, QLD, Australia,DMTC Limited, Kew, VIC, Australia,School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, Australia,David McMillan,
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Rapid, sensitive, and specific, low-resource molecular detection of Hendra virus. One Health 2023. [DOI: 10.1016/j.onehlt.2023.100504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
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Ahmed M, Nath NS, Hugo LE, Devine GJ, Macdonald J, Pollak NM. Rapid detection of kdr mutation F1534C in Aedes aegypti using recombinase polymerase amplification and lateral flow dipsticks. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2022; 187:105209. [PMID: 36127073 DOI: 10.1016/j.pestbp.2022.105209] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 07/19/2022] [Accepted: 08/08/2022] [Indexed: 06/15/2023]
Abstract
Insecticide resistance monitoring is essential in assessing the efficacy of vector control measures. However, gold standard PCR-based molecular analyses for insecticide resistance detection are often hindered by time-consuming sample processing, as well as considerable infrastructure and resourcing requirements. In this study, we combined a novel one-step sample preparation reagent with a rapid isothermal molecular test that detects a knock down resistance (kdr) mutation (F1534C) that enables pyrethroid resistance in Aedes aegypti mosquitoes. We trialled the rapid F1534C pyrethroid resistance test using insecticide resistant Ae. aegypti mosquito bodies and compared results to a conventional, allele-specific quantitative PCR (AS-qPCR) coupled with melt curve genotyping in corresponding mosquito heads. From a strain of Ae. aegypti established from an insecticide resistant population in Merida, Mexico (n = 27), all the mosquito bodies (n = 27) tested positive with the rapid F1534C test regardless of whether they were homozygous or heterozygous. To assess diagnostic test specificity, we confirmed that F1534 was not detected in laboratory-reared, fully susceptible Ae. aegypti mosquito bodies (n = 28) using the rapid F1534C test or the conventional AS-qPCR melt curve analysis. All corresponding mosquito heads (n = 28) were homozygous wild-type FF1534. The rapid F1534C test thus demonstrated 100% diagnostic sensitivity (95% CI: 87.23% to 100%) and 100% diagnostic specificity (95% CI: 87.66% to 100.00%) for detection of the F1534C pyrethroid resistant single nucleotide polymorphism (SNP) in both heterozygous and homozygous Ae. aegypti. In the collection of mutant mosquitoes from Mexico, CC1534 homozygous mutants occurred at a frequency of 74.1% (n = 20) and FC heterozygous mutants at a frequency of 25.9% (n = 7). The rapid F1534C test significantly reduced the sample processing and testing time from approximately 6 h for the AS-qPCR melt curve analysis to only 25 min. These results demonstrate significant potential for our approach to resistance testing as a field-based, low-resource, rapid alternative to time-consuming and expensive laboratory-based detection.
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Affiliation(s)
- Madeeha Ahmed
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, QLD 4556, Australia; School of Science and Engineering, University of the Sunshine Coast, Sippy Downs, QLD 4556, Australia.
| | - Nisa Suraj Nath
- Mosquito Control Laboratory, QIMR Berghofer Medical Research Institute, 300 Herston Road, 4006 Herston, QLD, Australia.
| | - Leon E Hugo
- Mosquito Control Laboratory, QIMR Berghofer Medical Research Institute, 300 Herston Road, 4006 Herston, QLD, Australia.
| | - Gregor J Devine
- Mosquito Control Laboratory, QIMR Berghofer Medical Research Institute, 300 Herston Road, 4006 Herston, QLD, Australia.
| | - Joanne Macdonald
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, QLD 4556, Australia; School of Science and Engineering, University of the Sunshine Coast, Sippy Downs, QLD 4556, Australia.
| | - Nina M Pollak
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, QLD 4556, Australia; School of Science and Engineering, University of the Sunshine Coast, Sippy Downs, QLD 4556, Australia.
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Yalley AK, Ahiatrogah S, Kafintu-Kwashie AA, Amegatcher G, Prah D, Botwe AK, Adusei-Poku MA, Obodai E, Nii-Trebi NI. A Systematic Review on Suitability of Molecular Techniques for Diagnosis and Research into Infectious Diseases of Concern in Resource-Limited Settings. Curr Issues Mol Biol 2022; 44:4367-4385. [PMID: 36286015 PMCID: PMC9601131 DOI: 10.3390/cimb44100300] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/15/2022] [Accepted: 09/16/2022] [Indexed: 11/16/2022] Open
Abstract
Infectious diseases significantly impact the health status of developing countries. Historically, infectious diseases of the tropics especially have received insufficient attention in worldwide public health initiatives, resulting in poor preventive and treatment options. Many molecular tests for human infections have been established since the 1980s, when polymerase chain reaction (PCR) testing was introduced. In spite of the substantial innovative advancements in PCR technology, which currently has found wide application in most viral pathogens of global concern, the development and application of molecular diagnostics, particularly in resource-limited settings, poses potential constraints. This review accessed data from sources including PubMed, Google Scholar, the Web of Knowledge, as well as reports from the World Health Organization’s Annual Meeting on infectious diseases and examined these for current molecular approaches used to identify, monitor, or investigate some neglected tropical infectious diseases. This review noted some growth efforts in the development of molecular techniques for diagnosis of pathogens that appear to be common in resource limited settings and identified gaps in the availability and applicability of most of these molecular diagnostics, which need to be addressed if the One Health goal is to be achieved.
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Affiliation(s)
- Akua K. Yalley
- Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, University of Ghana, Accra P.O. Box KB 143, Ghana
| | - Selasie Ahiatrogah
- Department of Obstetrics and Gynaecology, College of Medicine, Pan African University of Life and Earth Sciences Institute, University of Ibadan, Ibadan P.O. Box 22133, Nigeria
| | - Anna A. Kafintu-Kwashie
- Department of Medical Microbiology, University of Ghana Medical School, Accra GA-221-1570, Ghana
| | - Gloria Amegatcher
- Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, University of Ghana, Accra P.O. Box KB 143, Ghana
| | - Diana Prah
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra P.O. Box LG 54, Ghana
| | - Akua K. Botwe
- Molecular Biology Unit, Kintampo Health Research Centre, Ghana Health Service, Kintampo P.O. Box 200, Ghana
| | - Mildred A. Adusei-Poku
- Department of Medical Microbiology, University of Ghana Medical School, Accra GA-221-1570, Ghana
| | - Evangeline Obodai
- Department of Virology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra P.O. Box LG 581, Ghana
| | - Nicholas I. Nii-Trebi
- Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, University of Ghana, Accra P.O. Box KB 143, Ghana
- Correspondence: ; Tel.: +233-54-827-6424
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Fluorescent Biosensors for the Detection of Viruses Using Graphene and Two-Dimensional Carbon Nanomaterials. BIOSENSORS 2022; 12:bios12070460. [PMID: 35884263 PMCID: PMC9312944 DOI: 10.3390/bios12070460] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/13/2022] [Accepted: 06/14/2022] [Indexed: 11/16/2022]
Abstract
Two-dimensional carbon nanomaterials have been commonly employed in the field of biosensors to improve their sensitivity/limits of detection and shorten the analysis time. These nanomaterials act as efficient transducers because of their unique characteristics, such as high surface area and optical, electrical, and magnetic properties, which in turn have been exploited to create simple, quick, and low-cost biosensing platforms. In this review, graphene and two-dimensional carbon material-based fluorescent biosensors are covered between 2010 and 2021, for the detection of different human viruses. This review specifically focuses on the new developments in graphene and two-dimensional carbon nanomaterials for fluorescent biosensing based on the Förster resonance energy transfer (FRET) mechanism. The high-efficiency quenching capability of graphene via the FRET mechanism enhances the fluorescent-based biosensors. The review provides a comprehensive reference for the different types of carbon nanomaterials employed for the detection of viruses such as Rotavirus, Ebola virus, Influenza virus H3N2, HIV, Hepatitis C virus (HCV), and Hepatitis B virus (HBV). This review covers the various multiplexing detection technologies as a new direction in the development of biosensing platforms for virus detection. At the end of the review, the different challenges in the use of fluorescent biosensors, as well as some insights into how to overcome them, are highlighted.
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Diakou KI, Mitsis T, Pierouli K, Papakonstantinou E, Bongcam-Rudloff E, Wayengera M, Vlachakis D. Ebola Virus Disease and Current Therapeutic Strategies: A Review. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1339:131-137. [PMID: 35023100 DOI: 10.1007/978-3-030-78787-5_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The Ebola virus disease is a severe hemorrhagic fever that affects humans and other primates. Ebola virus, the causative agent of the disease, is transmitted to humans from wild animals and is highly contagious and aggressive with an estimated fatality rate to be around 50%. Since 1976, 11 outbreaks of Ebola virus disease have been reported in total, affecting mostly sub-Saharan Africa, while the most recent ongoing outbreak in the Democratic Republic of the Congo has more than 3000 reported cases and 72 deaths. Although an effective vaccine against Ebola virus disease has become available, no targeted treatment with proven efficacy upon infection is developed. Herein, we review the epidemiology of Ebola virus and the current situation in terms of prevention, diagnosis, and treatment of the disease.
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Affiliation(s)
- Kalliopi Io Diakou
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Thanasis Mitsis
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Katerina Pierouli
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Eleni Papakonstantinou
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Erik Bongcam-Rudloff
- SLU-Global Bioinformatics Centre, Department of Animal Breeding and Genetics Science, University of Agricultural Sciences, Uppsala, Sweden
| | - Misaki Wayengera
- Department of Pathology, Unit of Genetics & Genomics, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
| | - Dimitrios Vlachakis
- DarkDNA Group, Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece. .,Lab of Molecular Endocrinology, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece. .,Department of Informatics, Faculty of Natural and Mathematical Sciences, King's College London, Strand, London, UK.
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Ahmed M, Pollak NM, Hugo LE, van den Hurk AF, Hobson-Peters J, Macdonald J. Rapid molecular assays for the detection of the four dengue viruses in infected mosquitoes. Gates Open Res 2022; 6:81. [PMID: 36636741 PMCID: PMC9816563 DOI: 10.12688/gatesopenres.13534.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2022] [Indexed: 12/24/2022] Open
Abstract
The pantropic emergence of severe dengue disease can partly be attributed to the co-circulation of different dengue viruses (DENVs) in the same geographical location. Effective monitoring for circulation of each of the four DENVs is critical to inform disease mitigation strategies. In low resource settings, this can be effectively achieved by utilizing inexpensive, rapid, sensitive and specific assays to detect viruses in mosquito populations. In this study, we developed four rapid DENV tests with direct applicability for low-resource virus surveillance in mosquitoes. The test protocols utilize a novel sample preparation step, a single-temperature isothermal amplification, and a simple lateral flow detection. Analytical sensitivity testing demonstrated tests could detect down to 1,000 copies/µL of virus-specific DENV RNA, and analytical specificity testing indicated tests were highly specific for their respective virus, and did not detect closely related flaviviruses. All four DENV tests showed excellent diagnostic specificity and sensitivity when used for detection of both individually infected mosquitoes and infected mosquitoes in pools of uninfected mosquitoes. With individually infected mosquitoes, the rapid DENV-1, -2 and -3 tests showed 100% diagnostic sensitivity (95% CI = 69% to 100%, n=8 for DENV-1; n=10 for DENV 2,3) and the DENV-4 test showed 92% diagnostic sensitivity (CI: 62% to 100%, n=12) along with 100% diagnostic specificity (CI: 48-100%) for all four tests. Testing infected mosquito pools, the rapid DENV-2, -3 and -4 tests showed 100% diagnostic sensitivity (95% CI = 69% to 100%, n=10) and the DENV-1 test showed 90% diagnostic sensitivity (55.50% to 99.75%, n=10) together with 100% diagnostic specificity (CI: 48-100%). Our tests reduce the operational time required to perform mosquito infection status surveillance testing from > two hours to only 35 minutes, and have potential to improve accessibility of mosquito screening, improving monitoring and control strategies in low-income countries most affected by dengue outbreaks.
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Affiliation(s)
- Madeeha Ahmed
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, QLD, 4556, Australia.,School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, 4556, Australia
| | - Nina M Pollak
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, QLD, 4556, Australia.,School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, 4556, Australia.,DMTC Limited, Hawthorn, Victoria, 3122, Australia
| | - Leon E Hugo
- Mosquito Control Laboratory, QIMR Berghofer Medical Research Institute, Herston, QLD, 4006, Australia
| | - Andrew F van den Hurk
- Public Health Virology, Forensic and Scientific Services, Department of Health, Queensland Government, Coopers Plains, QLD, 4108, Australia
| | - Jody Hobson-Peters
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Joanne Macdonald
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, QLD, 4556, Australia.,School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, 4556, Australia.,DMTC Limited, Hawthorn, Victoria, 3122, Australia
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Ahmed M, Pollak NM, Hugo LE, van den Hurk AF, Hobson-Peters J, Macdonald J. Rapid molecular assays for the detection of the four dengue viruses in infected mosquitoes. Gates Open Res 2022; 6:81. [PMID: 36636741 PMCID: PMC9816563 DOI: 10.12688/gatesopenres.13534.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/31/2022] [Indexed: 01/16/2023] Open
Abstract
The pantropic emergence of severe dengue disease can partly be attributed to the co-circulation of different dengue viruses (DENVs) in the same geographical location. Effective monitoring for circulation of each of the four DENVs is critical to inform disease mitigation strategies. In low resource settings, this can be effectively achieved by utilizing inexpensive, rapid, sensitive and specific assays to detect viruses in mosquito populations. In this study, we developed four rapid DENV tests with direct applicability for low-resource virus surveillance in mosquitoes. The test protocols utilize a novel sample preparation step, a single-temperature isothermal amplification, and a simple lateral flow detection. Analytical sensitivity testing demonstrated tests could detect down to 1,000 copies/µL of virus-specific DENV RNA, and analytical specificity testing indicated tests were highly specific for their respective virus, and did not detect closely related flaviviruses. All four DENV tests showed excellent diagnostic specificity and sensitivity when used for detection of both individually infected mosquitoes and infected mosquitoes in pools of uninfected mosquitoes. With individually infected mosquitoes, the rapid DENV-1, -2 and -3 tests showed 100% diagnostic sensitivity (95% CI = 69% to 100%, n=8 for DENV-1; n=10 for DENV 2,3) and the DENV-4 test showed 92% diagnostic sensitivity (CI: 62% to 100%, n=12) along with 100% diagnostic specificity (CI: 48-100%) for all four tests. Testing infected mosquito pools, the rapid DENV-2, -3 and -4 tests showed 100% diagnostic sensitivity (95% CI = 69% to 100%, n=10) and the DENV-1 test showed 90% diagnostic sensitivity (55.50% to 99.75%, n=10) together with 100% diagnostic specificity (CI: 48-100%). Our tests reduce the operational time required to perform mosquito infection status surveillance testing from > two hours to only 35 minutes, and have potential to improve accessibility of mosquito screening, improving monitoring and control strategies in low-income countries most affected by dengue outbreaks.
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Affiliation(s)
- Madeeha Ahmed
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, QLD, 4556, Australia.,School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, 4556, Australia
| | - Nina M Pollak
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, QLD, 4556, Australia.,School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, 4556, Australia.,DMTC Limited, Hawthorn, Victoria, 3122, Australia
| | - Leon E Hugo
- Mosquito Control Laboratory, QIMR Berghofer Medical Research Institute, Herston, QLD, 4006, Australia
| | - Andrew F van den Hurk
- Public Health Virology, Forensic and Scientific Services, Department of Health, Queensland Government, Coopers Plains, QLD, 4108, Australia
| | - Jody Hobson-Peters
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Joanne Macdonald
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, QLD, 4556, Australia.,School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, 4556, Australia.,DMTC Limited, Hawthorn, Victoria, 3122, Australia
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11
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Guaman-Bautista LP, Moreta-Urbano E, Oña-Arias CG, Torres-Arias M, Kyriakidis NC, Malcı K, Jonguitud-Borrego N, Rios-Solis L, Ramos-Martinez E, López-Cortés A, Barba-Ostria C. Tracking SARS-CoV-2: Novel Trends and Diagnostic Strategies. Diagnostics (Basel) 2021; 11:1981. [PMID: 34829328 PMCID: PMC8621220 DOI: 10.3390/diagnostics11111981] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 09/18/2021] [Accepted: 09/23/2021] [Indexed: 12/26/2022] Open
Abstract
The COVID-19 pandemic has had an enormous impact on economies and health systems globally, therefore a top priority is the development of increasingly better diagnostic and surveillance alternatives to slow down the spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In order to establish massive testing and contact tracing policies, it is crucial to have a clear view of the diagnostic options available and their principal advantages and drawbacks. Although classical molecular methods such as RT-qPCR are broadly used, diagnostic alternatives based on technologies such as LAMP, antigen, serological testing, or the application of novel technologies such as CRISPR-Cas for diagnostics, are also discussed. The present review also discusses the most important automation strategies employed to increase testing capability. Several serological-based diagnostic kits are presented, as well as novel nanotechnology-based diagnostic methods. In summary, this review provides a clear diagnostic landscape of the most relevant tools to track COVID-19.
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Affiliation(s)
- Linda P. Guaman-Bautista
- Centro de Investigación Biomédica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito 170147, Ecuador; (L.P.G.-B.); (E.M.-U.); (C.G.O.-A.)
| | - Erick Moreta-Urbano
- Centro de Investigación Biomédica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito 170147, Ecuador; (L.P.G.-B.); (E.M.-U.); (C.G.O.-A.)
| | - Claudia G. Oña-Arias
- Centro de Investigación Biomédica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito 170147, Ecuador; (L.P.G.-B.); (E.M.-U.); (C.G.O.-A.)
| | - Marbel Torres-Arias
- Immunology and Virology Laboratory, Department of Life Science and Agriculture, Universidad de las Fuerzas Armadas, Quito 171103, Ecuador;
| | - Nikolaos C. Kyriakidis
- Grupo de Investigación en Biotecnología Aplicada a Biomedicina (BIOMED), Universidad de Las Américas, Quito 170125, Ecuador;
- One Health Research Group, Faculty of Medicine, Universidad de Las Américas (UDLA), Quito 170125, Ecuador
| | - Koray Malcı
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Edinburgh EH8 9LE, UK; (K.M.); (N.J.-B.); (L.R.-S.)
- Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Edinburgh EH8 9LE, UK
| | - Nestor Jonguitud-Borrego
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Edinburgh EH8 9LE, UK; (K.M.); (N.J.-B.); (L.R.-S.)
- Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Edinburgh EH8 9LE, UK
| | - Leonardo Rios-Solis
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Edinburgh EH8 9LE, UK; (K.M.); (N.J.-B.); (L.R.-S.)
- Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Edinburgh EH8 9LE, UK
| | - Espiridion Ramos-Martinez
- Experimental Medicine Research Unit, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City 4510, Mexico;
| | - Andrés López-Cortés
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito 170147, Ecuador;
| | - Carlos Barba-Ostria
- Escuela de Medicina, Colegio de Ciencias de la Salud Quito, Universidad San Francisco de Quito USFQ, Quito 170901, Ecuador
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12
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Stambaugh A, Stott MA, Meena GG, Tamhankar M, Carrion R, Patterson JL, Hawkins AR, Schmidt H. Optofluidic Amplification-free Multiplex Detection of Viral Hemorrhagic Fevers. IEEE JOURNAL OF SELECTED TOPICS IN QUANTUM ELECTRONICS : A PUBLICATION OF THE IEEE LASERS AND ELECTRO-OPTICS SOCIETY 2021; 27:7200206. [PMID: 33390686 PMCID: PMC7774596 DOI: 10.1109/jstqe.2020.3024239] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Infectious disease outbreaks such as Ebola and other Viral Hemorrhagic Fevers (VHF) require low-complexity, specific, and differentiated diagnostics as illustrated by the recent outbreak in the Democratic Republic of Congo. Here, we describe amplification-free spectrally multiplex detection of four different VHF total RNA samples using multi-spot excitation on a multimode interference waveguide platform along with combinatorial fluorescence labeling of target nucleic acids. In these experiments, we observed an average of 8-fold greater fluorescence signal amplitudes for the Ebola total RNA sample compared to three other total RNA samples: Lake Victoria Marburg Virus, Ravn Marburg Virus, and Crimean-Congo Hemorrhagic Fever. We have attributed this amplitude amplification to an increased amount of RNA during synthesis of soluble glycoprotein in infection. This hypothesis is confirmed by single molecule detection of the total RNA sample after heat-activated release from the carrier microbeads. From these experiments, we observed at least a 5.3x higher RNA mass loading on the Ebola carrier microbeads compared to the Lake Victoria Marburg carrier microbeads, which is consistent with the known production of soluble glycoprotein during infection.
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Affiliation(s)
- Alexandra Stambaugh
- School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064 USA
| | - Matthew A Stott
- Department of Electrical and Computer Engineering, Brigham Young University, Provo UT 84602 USA
| | - Gopikrishnan G Meena
- School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064 USA
| | - Manasi Tamhankar
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX 78227 USA
| | - Ricardo Carrion
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX 78227 USA
| | - Jean L Patterson
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX 78227 USA
| | - Aaron R Hawkins
- Department of Electrical and Computer Engineering, Brigham Young University, Provo UT 84602 USA
| | - Holger Schmidt
- School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064 USA
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13
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Harrison AR, Todd S, Dearnley M, David CT, Green D, Rawlinson SM, Au GG, Marsh GA, Moseley GW. Antagonism of STAT3 signalling by Ebola virus. PLoS Pathog 2021; 17:e1009636. [PMID: 34166464 PMCID: PMC8224886 DOI: 10.1371/journal.ppat.1009636] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 05/12/2021] [Indexed: 12/25/2022] Open
Abstract
Many viruses target signal transducers and activators of transcription (STAT) 1 and 2 to antagonise antiviral interferon signalling, but targeting of signalling by other STATs/cytokines, including STAT3/interleukin 6 that regulate processes important to Ebola virus (EBOV) haemorrhagic fever, is poorly defined. We report that EBOV potently inhibits STAT3 responses to interleukin-6 family cytokines, and that this is mediated by the interferon-antagonist VP24. Mechanistic analysis indicates that VP24 effects a unique strategy combining distinct karyopherin-dependent and karyopherin-independent mechanisms to antagonise STAT3-STAT1 heterodimers and STAT3 homodimers, respectively. This appears to reflect distinct mechanisms of nuclear trafficking of the STAT3 complexes, revealed for the first time by our analysis of VP24 function. These findings are consistent with major roles for global inhibition of STAT3 signalling in EBOV infection, and provide new insights into the molecular mechanisms of STAT3 nuclear trafficking, significant to pathogen-host interactions, cell physiology and pathologies such as cancer. Ebola virus (EBOV) continues to pose a significant risk to human health globally, causing ongoing disease outbreaks with case-fatality rates between 40 and 65%. Suppression of immune responses is a critical component of EBOV haemorrhagic fever, but understanding of EBOV impact on signalling by cytokines other than interferon is limited. We find that infectious EBOV inhibits interleukin-6 cytokine signalling via antagonism of STAT3. The antagonistic strategy uniquely combines two distinct mechanisms, which appear to reflect differing nuclear trafficking mechanisms of critical STAT3 complexes. This provides fundamental insights into the mechanisms of pathogenesis of a lethal virus, and biology of STAT3, a critical player in immunity, development, growth and cancer.
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Affiliation(s)
- Angela R. Harrison
- Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Shawn Todd
- Australian Centre for Disease Preparedness, CSIRO, Geelong, Victoria, Australia
| | - Megan Dearnley
- Australian Centre for Disease Preparedness, CSIRO, Geelong, Victoria, Australia
| | - Cassandra T. David
- Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Diane Green
- Australian Centre for Disease Preparedness, CSIRO, Geelong, Victoria, Australia
| | - Stephen M. Rawlinson
- Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Gough G. Au
- Australian Centre for Disease Preparedness, CSIRO, Geelong, Victoria, Australia
| | - Glenn A. Marsh
- Australian Centre for Disease Preparedness, CSIRO, Geelong, Victoria, Australia
| | - Gregory W. Moseley
- Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- * E-mail:
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14
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Ayfan AKS, Macdonald J, Harris PNA, Heney C, Paterson DL, Trembizki E, Wang CYT, Whiley DM, Zowawi HM, Irwin AD. Rapid detection of NDM and VIM carbapenemase encoding genes by recombinase polymerase amplification and lateral flow-based detection. Eur J Clin Microbiol Infect Dis 2021; 40:2447-2453. [PMID: 33974185 DOI: 10.1007/s10096-021-04267-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 04/29/2021] [Indexed: 12/26/2022]
Abstract
Carbapenemase-producing organisms (CPOs) pose a serious clinical threat and rapid detection tools are essential to aid in patient management. We developed rapid and simple molecular tests to detect blaNDM-type and blaVIM-type carbapenemase genes using recombinase polymerase amplification (RPA) combined with a lateral flow detection. The tests could provide results in approximately 15 min when using DNA extracts, with limits of detection of 9.2 copies/μl for the blaNDM-type assay and 7.5 copies/μl for blaVIM-type assay, and successfully detected all isolates harbouring the carbapenemase encoding genes in a panel of 57 isolates. These RPA tests may be suitable for use in low-resource settings to tailor rapid implementation of infection control precautions and antibiotic stewardship.
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Affiliation(s)
- Abdulrahman K S Ayfan
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Royal Brisbane and Women's Hospital Campus, Brisbane, Australia
- Faculty of Science, Biochemistry Department, King Abdul-Aziz University (KAU), Jeddah, Saudi Arabia
| | - Joanne Macdonald
- School of Science and Engineering, Genecology Research Centre, University of Sunshine Coast (USC), Sunshine Coast, Australia
| | - Patrick N A Harris
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Royal Brisbane and Women's Hospital Campus, Brisbane, Australia
- Department of Microbiology, Pathology Queensland, Brisbane, Australia
| | - Claire Heney
- Department of Microbiology, Pathology Queensland, Brisbane, Australia
| | - David L Paterson
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Royal Brisbane and Women's Hospital Campus, Brisbane, Australia
| | - Ella Trembizki
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Royal Brisbane and Women's Hospital Campus, Brisbane, Australia
| | - Claire Y T Wang
- Infection Management and Prevention Service, Queensland Children's Hospital, Brisbane, Australia
| | - David M Whiley
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Royal Brisbane and Women's Hospital Campus, Brisbane, Australia
- Department of Microbiology, Pathology Queensland, Brisbane, Australia
| | - Hosam M Zowawi
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Royal Brisbane and Women's Hospital Campus, Brisbane, Australia
- College of Medicine, King Saud bin Abdul-Aziz University for Health Science (KSAU-HS), Riyadh, Saudi Arabia
- King Abdullah International Medical Research Centre (KAIMRC), Riyadh, Saudi Arabia
| | - Adam D Irwin
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Royal Brisbane and Women's Hospital Campus, Brisbane, Australia.
- Infection Management and Prevention Service, Queensland Children's Hospital, Brisbane, Australia.
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15
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Brunauer A, Verboket RD, Kainz DM, von Stetten F, Früh SM. Rapid Detection of Pathogens in Wound Exudate via Nucleic Acid Lateral Flow Immunoassay. BIOSENSORS-BASEL 2021; 11:bios11030074. [PMID: 33800856 PMCID: PMC8035659 DOI: 10.3390/bios11030074] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 02/24/2021] [Accepted: 03/03/2021] [Indexed: 12/15/2022]
Abstract
The rapid detection of pathogens in infected wounds can significantly improve the clinical outcome. Wound exudate, which can be collected in a non-invasive way, offers an attractive sample material for the detection of pathogens at the point-of-care (POC). Here, we report the development of a nucleic acid lateral flow immunoassay for direct detection of isothermally amplified DNA combined with fast sample preparation. The streamlined protocol was evaluated using human wound exudate spiked with the opportunistic pathogen Pseudomonas aeruginosa that cause severe health issues upon wound colonization. A detection limit of 2.1 × 105 CFU per mL of wound fluid was achieved, and no cross-reaction with other pathogens was observed. Furthermore, we integrated an internal amplification control that excludes false negative results and, in combination with the flow control, ensures the validity of the test result. The paper-based approach with only three simple hands-on steps has a turn-around time of less than 30 min and covers the complete analytical process chain from sample to answer. This newly developed workflow for wound fluid diagnostics has tremendous potential for reliable pathogen POC testing and subsequent target-oriented therapy.
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Affiliation(s)
- Anna Brunauer
- Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - René D Verboket
- Department of Trauma-, Hand- and Reconstructive Surgery, University Hospital Frankfurt, Johann Wolfgang Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Daniel M Kainz
- Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Felix von Stetten
- Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Susanna M Früh
- Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
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16
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Zhang J, Liu J, An D, Fan Y, Cheng Z, Tang Y, Diao Y. A novel recombinase polymerase amplification assay for rapid detection of epidemic fowl adenovirus. Poult Sci 2020; 99:6446-6453. [PMID: 33248559 PMCID: PMC7449135 DOI: 10.1016/j.psj.2020.08.021] [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: 03/08/2020] [Revised: 07/28/2020] [Accepted: 08/15/2020] [Indexed: 11/30/2022] Open
Abstract
Fowl adenovirus (FAdV) has posed a grave threat to the health of poultry, and the sudden outbreak highlights the importance of the new rapid diagnostic method for the control and prevention of transmission. Hence, in the present study, a novel recombinase polymerase amplification (RPA) assay, which was suitable for all 12 serotypes (FAdV-1 to 8a and 8b to 11) had been successfully launched to detect FAdV. Also, the entire amplification process could be completed in the isothermal condition when temperature ranged from 26 to 42°C within no more than 14 min, which was remarkably superior to endpoint polymerase chain reaction (98 min) with the same detecting sensitivity (as low as 0.1 fg viral DNA), avoiding sophisticated thermal cyclers with simple operation. Additionally, the same primers did not produce positive reactions with other viruses tested, demonstrating that the specificity of the RPA assay was acceptable. Moreover, this developed method could be efficiently used in the diagnosis of FAdV references and epidemic strains from different avian origins, thus making it a rapid, reliable, and point-of-care FAdV diagnostics tool, as well as an alternative to endpoint PCR.
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Affiliation(s)
- Ji Zhang
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Jie Liu
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Da An
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Yunhao Fan
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Ziqiang Cheng
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an, Shandong, 271018, China.
| | - Yi Tang
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an, Shandong, 271018, China.
| | - Youxiang Diao
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an, Shandong, 271018, China.
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17
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Bonney LC, Watson RJ, Slack GS, Bosworth A, Wand NIV, Hewson R. A flexible format LAMP assay for rapid detection of Ebola virus. PLoS Negl Trop Dis 2020; 14:e0008496. [PMID: 32735587 PMCID: PMC7423149 DOI: 10.1371/journal.pntd.0008496] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 08/12/2020] [Accepted: 06/16/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The unprecedented 2013/16 outbreak of Zaire ebolavirus (Ebola virus) in West Africa has highighted the need for rapid, high-throughput and POC diagnostic assays to enable timely detection and appropriate triaging of Ebola Virus Disease (EVD) patients. Ebola virus is highly infectious and prompt diagnosis and triage is crucial in preventing further spread within community and healthcare settings. Moreover, due to the ecology of Ebola virus it is important that newly developed diagnostic assays are suitable for use in both the healthcare environment and low resource rural locations. METHODOLOGY/PRINCIPLE FINDINGS A LAMP assay was successfully developed with three detection formats; a real-time intercalating dye-based assay, a real-time probe-based assay to enable multiplexing and an end-point colourimetric assay to simplify interpretation for the field. All assay formats were sensitive and specific, detecting a range of Ebola virus strains isolated in 1976-2014; with Probit analysis predicting limits of detection of 243, 290 and 75 copies/reaction respectively and no cross-detection of related strains or other viral haemorrhagic fevers (VHF's). The assays are rapid, (as fast as 5-7.25 mins for real-time formats) and robust, detecting Ebola virus RNA in presence of minimally diluted bodily fluids. Moreover, when tested on patient samples from the 2013/16 outbreak, there were no false positives and 93-96% of all new case positives were detected, with only a failure to detect very low copy number samples. CONCLUSION/SIGNIFICANCE These are a set of robust and adaptable diagnostic solutions, which are fast, easy-to-perform-and-interpret and are suitable for use on a range of platforms including portable low-power devices. They can be readily transferred to field-laboratory settings, with no specific equipment needs and are therefore ideally placed for use in locations with limited resources.
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Affiliation(s)
- Laura C. Bonney
- Public Health England, National Infection Service, Porton Down, Salisbury, Wiltshire, United Kingdom
| | - Robert J. Watson
- Public Health England, National Infection Service, Porton Down, Salisbury, Wiltshire, United Kingdom
| | - Gillian S. Slack
- Public Health England, National Infection Service, Porton Down, Salisbury, Wiltshire, United Kingdom
| | - Andrew Bosworth
- Public Health England, National Infection Service, Porton Down, Salisbury, Wiltshire, United Kingdom
| | - Nadina I. Vasileva Wand
- Public Health England, National Infection Service, Porton Down, Salisbury, Wiltshire, United Kingdom
| | - Roger Hewson
- Public Health England, National Infection Service, Porton Down, Salisbury, Wiltshire, United Kingdom
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18
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James AS, Alwneh JI. COVID-19 Infection Diagnosis: Potential Impact of Isothermal Amplification Technology to Reduce Community Transmission of SARS-CoV-2. Diagnostics (Basel) 2020; 10:E399. [PMID: 32545412 PMCID: PMC7345291 DOI: 10.3390/diagnostics10060399] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 05/30/2020] [Accepted: 06/05/2020] [Indexed: 01/08/2023] Open
Abstract
The current coronavirus disease 2019 (COVID-19) pandemic is largely driven by community transmission, after 2019 novel Coronavirus (2019-nCoV or SARS-CoV-2) crosses the borders. To stop the spread, rapid testing is required at community clinics and hospitals. These rapid tests should be comparable with the standard PCR technology. Isothermal amplification technology provides an excellent alternative that is highly amenable to resource limited settings, where expertise and infrastructure to support PCR are not available. In this review, we provide a brief description of isothermal amplification technology, its potential and the gaps that need to be considered for SARS-CoV-2 detection. Among this emerging technology, loop-mediated amplification (LAMP), recombinase polymerase amplification (RPA) and Nicking enzyme-assisted reaction (NEAR) technologies have been identified as potential platforms that could be implemented at community level, without samples referral to a centralized laboratory and prolonged turnaround time associated with the standard COVID-19 RT-PCR test. LAMP, for example, has recently been shown to be comparable with PCR and could be performed in less than 30 min by non-laboratory staff, without RNA extractions commonly associated with PCR. Interestingly, NEAR (ID NOW™ COVID-19 (Abbott, IL, USA) was able to detect the virus in 5 min. More so, isothermal platforms are cost effective and could easily be scaled up to resource limited settings. Diagnostics developers, scientific community and commercial companies could consider this alternative method to help stop the spread of COVID-19.
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Affiliation(s)
- Ameh S. James
- Good Clinical Practice Research Group, School of Veterinary Science, The University of Queensland, Gatton Campus, Gatton, QLD 4343, Australia;
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19
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Chen Z, Huang J, Zhang F, Zhou Y, Huang H. Detection of shrimp hemocyte iridescent virus by recombinase polymerase amplification assay. Mol Cell Probes 2019; 49:101475. [PMID: 31655105 DOI: 10.1016/j.mcp.2019.101475] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/27/2019] [Accepted: 10/22/2019] [Indexed: 12/23/2022]
Abstract
Shrimp hemocyte iridescent virus (SHIV), which was first identified in white leg shrimp (Litopenaeus vannamei) in China in 2014, can cause extensive shrimp mortality and major economic losses in the shrimp farming industry in China. In this study, a novel real-time isothermal recombinase polymerase amplification (RPA) assay was developed using a TwistAmp exo kit for SHIV detection. First, five primers and a probe were designed for the major capsid protein gene (GenBank: KY681039.1) according to the TwistDx manual; next, the optimal primers were selected by a comparison experiment. The primers and probe were specific for SHIV and did not react with shrimp white spot syndrome virus (WSSV), shrimp infectious hypodermal and hematopoietic necrosis virus (IHHNV), shrimp enterocytozoon hepatopenaei (EHP), and macrobrachium rosenbergii nodavirus (MrNV) samples, as well as pathogens of acute hepatopancreatic necrosis disease (AHPND). The RPA assay reached a detection limit of 11 copies per reaction according to probit regression analysis. In addition, RPA assay detected the positive plasmid samples at concentration of 1000 copies/μL within 16.04 ± 0.72 min at a single low operation temperature (39 °C). The results proved that the proposed RPA method was an accurate, sensitive, affordable, and rapid detection tool that can be suitably applied for the diagnosis of SHIV in field conditions and in resource-poor settings.
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Affiliation(s)
- Zhengwei Chen
- Laboratory of Information Optics and Optoelectronic Technology, Shanghai Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Shanghai, P.R. China; University of Chinese Academy of Sciences, Beijing, P.R. China; Center of Engineering Training, Zhejiang University of Science and Technology, Hangzhou, P.R. China.
| | - Jun Huang
- College of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, P.R. China
| | - Fang Zhang
- Laboratory of Information Optics and Optoelectronic Technology, Shanghai Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Shanghai, P.R. China.
| | - Yang Zhou
- College of Information and Electronic Engineering, Zhejiang University of Science and Technology, Hangzhou, P.R. China
| | - Huijie Huang
- Laboratory of Information Optics and Optoelectronic Technology, Shanghai Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Shanghai, P.R. China; University of Chinese Academy of Sciences, Beijing, P.R. China.
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20
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Tembo J, Simulundu E, Changula K, Handley D, Gilbert M, Chilufya M, Asogun D, Ansumana R, Kapata N, Ntoumi F, Ippolito G, Zumla A, Bates M. Recent advances in the development and evaluation of molecular diagnostics for Ebola virus disease. Expert Rev Mol Diagn 2019; 19:325-340. [PMID: 30916590 DOI: 10.1080/14737159.2019.1595592] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
INTRODUCTION The 2014-16 outbreak of ebola virus disease (EVD) in West Africa resulted in 11,308 deaths. During the outbreak only 60% of patients were laboratory confirmed and global health authorities have identified the need for accurate and readily deployable molecular diagnostics as an important component of the ideal response to future outbreaks, to quickly identify and isolate patients. Areas covered: Currently PCR-based techniques and rapid diagnostic tests (RDTs) that detect antigens specific to EVD infections dominate the diagnostic landscape, but recent advances in biosensor technologies have led to novel approaches for the development of EVD diagnostics. This review summarises the literature and available performance data of currently available molecular diagnostics for ebolavirus, identifies knowledge gaps and maps out future priorities for research in this field. Expert opinion: While there are now a plethora of diagnostic tests for EVD at various stages of development, there is an acute need for studies to compare their clinical performance, but the sporadic nature of EVD outbreaks makes this extremely challenging, demanding pragmatic new modalities of research funding and ethical/institutional approval, to enable responsive research in outbreak settings. Retrospective head-to-head diagnostic comparisons could also be implemented using biobanked specimens, providing this can be done safely.
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Affiliation(s)
- John Tembo
- a HerpeZ , University Teaching hospital , Lusaka , Zambia
| | - Edgar Simulundu
- b Department of Disease Control , University of Zambia School of Veterinary Medicine , Lusaka , Zambia
| | - Katendi Changula
- b Department of Disease Control , University of Zambia School of Veterinary Medicine , Lusaka , Zambia
| | - Dale Handley
- c School of Life Sciences , University of Lincoln , Lincoln , UK
| | - Matthew Gilbert
- c School of Life Sciences , University of Lincoln , Lincoln , UK
| | - Moses Chilufya
- a HerpeZ , University Teaching hospital , Lusaka , Zambia
| | - Danny Asogun
- d Lassa fever research institute , Irrua University Teaching Hospital , Irrua , Nigeria
| | | | - Nathan Kapata
- f Zambia National Public Health Institute , Lusaka , Zambia
| | - Francine Ntoumi
- g Fondation Congolaise pour la Recherche Médicale , Brazzaville , Republic of Congo
| | - Giuseppe Ippolito
- h National Institute for Infectious Diseases , Lazzaro Spallanzani, IRCCS , Rome , Italy
| | - Alimuddin Zumla
- i Centre for Clinical Microbiology, Division of Infection and Immunity , University College London (UCL) , London , UK.,j National Institute of Health and Research Biomedical Research Centre , UCL Hospitals National Health Service Foundation Trust , London , UK
| | - Matthew Bates
- a HerpeZ , University Teaching hospital , Lusaka , Zambia.,c School of Life Sciences , University of Lincoln , Lincoln , UK.,i Centre for Clinical Microbiology, Division of Infection and Immunity , University College London (UCL) , London , UK
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Reed AJ, Connelly RP, Williams A, Tran M, Shim BS, Choe H, Gerasimova YV. Label-Free Pathogen Detection by a Deoxyribozyme Cascade with Visual Signal Readout. SENSORS AND ACTUATORS. B, CHEMICAL 2019; 282:945-951. [PMID: 31462856 PMCID: PMC6713451 DOI: 10.1016/j.snb.2018.11.147] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
A colorimetric nucleic acid based test for label-free pathogen detection has been developed and used for the detection of the Zika virus. The test relies on nucleic acid sequence-based amplification (NASBA) of a viral RNA followed by interrogation of the amplicon by a cascade of deoxyribozymes constituting a visual split deoxyribozyme (vsDz) probe. The probe consists of a split phosphodiesterase deoxyribozyme, which forms its catalytic core upon binding to a specific amplicon fragment. The catalytically active complex recognizes and cleaves an inhibited peroxidase-like deoxyribozyme (PDz), thereby activating it. Active PDz catalyzes hydrogen peroxide-mediated oxidation of a colorless substrate into a colored product, thereby generating a visible signal. Viral RNA (106 copies/mL or higher) triggers intense color within 2 hr. The test selectively differentiates between Zika and closely related dengue and West Nile viruses. The reported technology combines isothermal amplification and visual detection and therefore represents a basis for the future development of a cost-efficient and instrument-free method for point-of-care nucleic acid analysis.
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Affiliation(s)
- Adam J. Reed
- Chemistry Department, University of Central Florida, Orlando, Florida 32816, United States
| | - Ryan P. Connelly
- Chemistry Department, University of Central Florida, Orlando, Florida 32816, United States
| | - Allison Williams
- Chemistry Department, University of Central Florida, Orlando, Florida 32816, United States
| | - Maithi Tran
- Chemistry Department, University of Central Florida, Orlando, Florida 32816, United States
| | - Byoung-Shik Shim
- Department of Immunology and Microbiology, Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Hyeryun Choe
- Department of Immunology and Microbiology, Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Yulia V. Gerasimova
- Chemistry Department, University of Central Florida, Orlando, Florida 32816, United States
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