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Cui N, Perez YL, Hume AJ, Nunley BE, Kong K, Mills MG, Xie H, Greninger AL. A high-throughput, polymerase-targeted RT-PCR for broad detection of mammalian filoviruses. Microbiol Spectr 2024; 12:e0101024. [PMID: 39046245 PMCID: PMC11370238 DOI: 10.1128/spectrum.01010-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Accepted: 06/20/2024] [Indexed: 07/25/2024] Open
Abstract
Filoviruses are some of the most lethal viruses in the modern world, and increasing numbers of filovirus species and genera have been discovered in recent years. Despite the potential severity of filovirus outbreaks in the human population, comparably few sensitive pan-filovirus RT-PCR assays have been described that might facilitate early detection and prevention. Here, we present a new pan-filovirus RT-PCR assay targeting the L polymerase gene for detection of all known mammalian filoviruses. We demonstrate the detection of 10 synthetic filovirus RNA templates with analytical sensitivity ranging from 178 to 3,354 copies/mL, without cross-reactivity on 10 non-filoviral human viral species. We verified assay performance on 10 inactivated filovirus isolates, yielding initial sensitivities of 0.012-44.17 TCID50/mL. We coupled this broadly reactive RT-PCR with a deep sequencing workflow that is amenable to high-throughput pooling to maximize detection and discovery potential. In summary, this pan-filovirus RT-PCR assay targets the most conserved filovirus gene, offers the widest breadth of coverage to date, and may help in the detection and discovery of novel filoviruses.IMPORTANCEFiloviruses remain some of the most mysterious viruses known to the world, with extremely high lethality rates and significant pandemic potential. Yet comparably few filovirus species and genera have been discovered to date and questions surround the definitive host species for zoonotic infections. Here, we describe a novel broadly reactive RT-PCR assay targeting the conserved L polymerase gene for high-throughput screening for filoviruses in a variety of clinical and environmental specimens. We demonstrate the assay can detect all known mammalian filoviruses and determine the sensitivity and specificity of the assay on synthetic RNA sequences, inactivated filovirus isolates, and non-filoviral species.
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Affiliation(s)
- Na Cui
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Yael L. Perez
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Adam J. Hume
- Department of Microbiology/National Emerging Infectious Diseases Laboratories, Chobanian & Avedisian School of Medicine, Boston University, Boston, Massachusetts, USA
| | - B. Ethan Nunley
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Kevin Kong
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Margaret G. Mills
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Hong Xie
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Alexander L. Greninger
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
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Choi Y, Kim Y. Application of multiplex realtime PCR detection for hemorrhagic fever syndrome viruses. J Infect Public Health 2023; 16:1933-1941. [PMID: 37866271 DOI: 10.1016/j.jiph.2023.10.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 09/13/2023] [Accepted: 10/05/2023] [Indexed: 10/24/2023] Open
Abstract
BACKGROUND Multiplex real-time PCR is a quick and cost effective method for detection of various gene simultaneously. HFSV (Hemorrhagic Fever Syndrome Virus) is a newly emerging infectious disease because of globalization and climate change. We tried to develop a molecular diagnostic technique for various causative viruses and evaluate its usefulness for improving public health. METHODS Molecular diagnostic test method that qualitatively detects viruses causing viral hemorrhagic fevers hired Taq-Man Real-time RT-PCR technique. The Ct value was experimentally observed three or more times at the RNA concentration before and after the detection limit. After designing a multiplex real-time RT-PCR test for target gene of selected 17 viruses, the detection limit for each target and the presence or absence of cross-reaction and interference reaction were evaluated to determine its availability. RESULTS Six kinds of viruses, including Crimean-Congo hemorrhagic fever virus, Omsk hemorrhagic fever virus, Sabia virus, Chapare virus, Yellow fever virus, and Variola virus (A4L gene, B12R gene), were able to confirm the detection limit of 0.5 copies/μl, and other Ebola virus, Marburg virus, Rift Valley fever virus, Kyasanur Forest disease virus, Junin virus, Guanarito virus, Machupo virus, Chikungunya virus, Hantavirus, Dengue virus types 1-4, and Lassa virus (L gene, GPC gene), and 11 kinds of viruses, the detection limit was confirmed at 5 copies/μl. No cross-reaction or interference between detected genes was observed. CONCLUSION The virus test method developed through this study using multiplex is expected to be used for public health and quarantine as a test method that can be used when a hemorrhagic fever virus of unknown cause is introduced.
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Affiliation(s)
- Yoonhyuk Choi
- Department of Convergence Engineering, Graduate School of Venture, Hoseo University, Seoul, 06724, South Korea; MDx Center, Diagnosis Division, iNtRON Biotechnology, South Korea
| | - Younghee Kim
- Department of Convergence Engineering, Graduate School of Venture, Hoseo University, Seoul, 06724, South Korea.
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Hussein HA. Brief review on ebola virus disease and one health approach. Heliyon 2023; 9:e19036. [PMID: 37600424 PMCID: PMC10432691 DOI: 10.1016/j.heliyon.2023.e19036] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 07/31/2023] [Accepted: 08/07/2023] [Indexed: 08/22/2023] Open
Abstract
Ebola virus disease (EVD) is a severe and highly fatal zoonotic disease caused by viruses in the family Filoviridae and genus Ebolavirus. The disease first appeared in Zaire near the Ebola River in 1976, now in the Democratic Republic of the Congo. Since then, several outbreaks have been reported in different parts of the world, mainly in Africa, leading to the identification of six distinct viral strains that cause disease in humans and other primates. Bats are assumed to be the main reservoir hosts of the virus, and the initial incidence of human epidemics invariably follows exposure to infected forest animals through contact or consumption of bush meat and body fluids of forest animals harboring the disease. Human-to-human transmission occurs when contaminated body fluids, utensils, and equipment come in contact with broken or abraded skin and mucous membranes. EVD is characterized by sudden onset of 'flu-like' symptoms (fever, myalgia, chills), vomiting and diarrhea, then disease rapidly evolves into a severe state with a rapid clinical decline which may lead potential hemorrhagic complications and multiple organ failure. Effective EVD prevention, detection, and response necessitate strong coordination across the animal, human, and environmental health sectors, as well as well-defined roles and responsibilities evidencing the significance of one health approach; the natural history, epidemiology, pathogenesis, and diagnostic procedures of the Ebola virus, as well as prevention and control efforts in light of one health approach, are discussed in this article.
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Affiliation(s)
- Hassan Abdi Hussein
- College of Veterinary Medicine, Department of One Health Tropical Infectious Disease, Jigjiga University, P.O. Box: 1020, Jigjiga, Ethiopia
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4
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Yang S, Xian Q, Liu Y, Zhang Z, Song Q, Gao Y, Wen W. A Silicon-Based PDMS-PEG Copolymer Microfluidic Chip for Real-Time Polymerase Chain Reaction Diagnosis. J Funct Biomater 2023; 14:jfb14040208. [PMID: 37103298 PMCID: PMC10143339 DOI: 10.3390/jfb14040208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/02/2023] [Accepted: 04/07/2023] [Indexed: 04/28/2023] Open
Abstract
Polydimethylsiloxane (PDMS) has been widely used to make lab-on-a-chip devices, such as reactors and sensors, for biological research. Real-time nucleic acid testing is one of the main applications of PDMS microfluidic chips due to their high biocompatibility and transparency. However, the inherent hydrophobicity and excessive gas permeability of PDMS hinder its applications in many fields. This study developed a silicon-based polydimethylsiloxane-polyethylene-glycol (PDMS-PEG) copolymer microfluidic chip, the PDMS-PEG copolymer silicon chip (PPc-Si chip), for biomolecular diagnosis. By adjusting the modifier formula for PDMS, the hydrophilic switch occurred within 15 s after contact with water, resulting in only a 0.8% reduction in transmittance after modification. In addition, we evaluated the transmittance at a wide range of wavelengths from 200 nm to 1000 nm to provide a reference for its optical property study and application in optical-related devices. The improved hydrophilicity was achieved by introducing a large number of hydroxyl groups, which also resulted in excellent bonding strength of PPc-Si chips. The bonding condition was easy to achieve and time-saving. Real-time PCR tests were successfully conducted with higher efficiency and lower non-specific absorption. This chip has a high potential for a wide range of applications in point-of-care tests (POCT) and rapid disease diagnosis.
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Affiliation(s)
- Siyu Yang
- Division of Emerging Interdisciplinary Areas, Interdisciplinary Program Office, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Thrust of Advanced Materials, The Hong Kong University of Science and Technology (Guangzhou), Nansha, Guangzhou 511400, China
- HKUST Shenzhen-Hong Kong Collaborative Innovation Research Institute, Futian, Shenzhen 518000, China
| | - Qingyue Xian
- Division of Emerging Interdisciplinary Areas, Interdisciplinary Program Office, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Thrust of Advanced Materials, The Hong Kong University of Science and Technology (Guangzhou), Nansha, Guangzhou 511400, China
| | - Yiteng Liu
- Division of Emerging Interdisciplinary Areas, Interdisciplinary Program Office, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Thrust of Advanced Materials, The Hong Kong University of Science and Technology (Guangzhou), Nansha, Guangzhou 511400, China
| | - Ziyi Zhang
- Division of Emerging Interdisciplinary Areas, Interdisciplinary Program Office, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Thrust of Advanced Materials, The Hong Kong University of Science and Technology (Guangzhou), Nansha, Guangzhou 511400, China
| | - Qi Song
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Yibo Gao
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Weijia Wen
- Thrust of Advanced Materials, The Hong Kong University of Science and Technology (Guangzhou), Nansha, Guangzhou 511400, China
- HKUST Shenzhen-Hong Kong Collaborative Innovation Research Institute, Futian, Shenzhen 518000, China
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
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Patel SK, Surve J, Parmar J, Aliqab K, Alsharari M, Armghan A. SARS-CoV-2 detecting rapid metasurface-based sensor. DIAMOND AND RELATED MATERIALS 2023; 132:109644. [PMID: 36575667 PMCID: PMC9780024 DOI: 10.1016/j.diamond.2022.109644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/30/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
We have proposed a novel approach to detect COVID-19 by detecting the ethyl butanoate which high volume ratio is present in the exhaled breath of a COVID-19 infected person. We have employed a refractive index sensor (RIS) with the help of a metasurface-based slotted T-shape perfect absorber that can detect ethyl butanoate present in exhaled breath of COVID-19 infected person with high sensitivity and in-process SARS-CoV-2. The optimized structure of the sensor is obtained by varying several structure parameters including structure length and thickness, slotted T-shape resonator length, width, and thickness. Sensor's performance is evaluated based on numerous factors comprising of sensitivity, Q factor, detection limit, a figure of merit (FOM), detection accuracy, and other performance defining parameters. The proposed slotted T-shape RIS achieved the largest sensitivity of 2500 nm/RIU, Q factor of 131.06, a FOM of 131.58 RIU-1, detection limit of 0.0224 RIU.
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Affiliation(s)
- Shobhit K Patel
- Department of Computer Engineering, Marwadi University, Rajkot, Gujarat - 360003, India
| | - Jaymit Surve
- Department of Electrical Engineering, Marwadi University, Rajkot, Gujarat - 360003, India
| | - Juveriya Parmar
- Department of Mechanical and Materials Engineering, University of Nebraska-Lincoln, 1400 R St., NE 68588, USA
| | - Khaled Aliqab
- Department of Electrical Engineering, College of Engineering, Jouf University, Sakaka 72388, Saudi Arabia
| | - Meshari Alsharari
- Department of Electrical Engineering, College of Engineering, Jouf University, Sakaka 72388, Saudi Arabia
| | - Ammar Armghan
- Department of Electrical Engineering, College of Engineering, Jouf University, Sakaka 72388, Saudi Arabia
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Yang S, Zhang Z, Xian Q, Song Q, Liu Y, Gao Y, Wen W. An Aluminum-Based Microfluidic Chip for Polymerase Chain Reaction Diagnosis. Molecules 2023; 28:molecules28031085. [PMID: 36770751 PMCID: PMC9921548 DOI: 10.3390/molecules28031085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/13/2023] [Accepted: 01/18/2023] [Indexed: 01/24/2023] Open
Abstract
Real-time polymerase chain reaction (real-time PCR) tests were successfully conducted in an aluminum-based microfluidic chip developed in this work. The reaction chamber was coated with silicone-modified epoxy resin to isolate the reaction system from metal surfaces, preventing the metal ions from interfering with the reaction process. The patterned aluminum substrate was bonded with a hydroxylated glass mask using silicone sealant at room temperature. The effect of thermal expansion was counteracted by the elasticity of cured silicone. With the heating process closely monitored, real-time PCR testing in reaction chambers proceeded smoothly, and the results show similar quantification cycle values to those of traditional test sets. Scanning electron microscope (SEM) and atomic force microscopy (AFM) images showed that the surface of the reaction chamber was smoothly coated, illustrating the promising coating and isolating properties. Energy-dispersive X-ray spectroscopy (EDS), X-ray photoelectron spectroscopy (XPS), and inductively coupled plasma-optical emission spectrometer (ICP-OES) showed that no metal ions escaped from the metal to the chip surface. Fourier-transform infrared spectroscopy (FTIR) was used to check the surface chemical state before and after tests, and the unchanged infrared absorption peaks indicated the unreacted, antifouling surface. The limit of detection (LOD) of at least two copies can be obtained in this chip.
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Affiliation(s)
- Siyu Yang
- Division of Emerging Interdisciplinary Areas, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR 999077, China
| | - Ziyi Zhang
- Division of Emerging Interdisciplinary Areas, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR 999077, China
| | - Qingyue Xian
- Division of Emerging Interdisciplinary Areas, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR 999077, China
| | - Qi Song
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR 999077, China
| | - Yiteng Liu
- Division of Emerging Interdisciplinary Areas, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR 999077, China
| | - Yibo Gao
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR 999077, China
| | - Weijia Wen
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR 999077, China
- Thrust of Advanced Materials, The Hong Kong University of Science and Technology (Guangzhou), Nansha, Guangzhou 511400, China
- HKUST Shenzhen-Hong Kong Collaborative Innovation Research Institute, Futian, Shenzhen 518000, China
- Correspondence: ; Tel.: +852-2358-5781
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Patel SK, Surve J, Parmar J, Ahmed K, Bui FM, Al-Zahrani FA. Recent Advances in Biosensors for Detection of COVID-19 and Other Viruses. IEEE Rev Biomed Eng 2023; 16:22-37. [PMID: 36197867 PMCID: PMC10009816 DOI: 10.1109/rbme.2022.3212038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 06/28/2022] [Accepted: 09/23/2022] [Indexed: 11/06/2022]
Abstract
This century has introduced very deadly, dangerous, and infectious diseases to humankind such as the influenza virus, Ebola virus, Zika virus, and the most infectious SARS-CoV-2 commonly known as COVID-19 and have caused epidemics and pandemics across the globe. For some of these diseases, proper medications, and vaccinations are missing and the early detection of these viruses will be critical to saving the patients. And even the vaccines are available for COVID-19, the new variants of COVID-19 such as Delta, and Omicron are spreading at large. The available virus detection techniques take a long time, are costly, and complex and some of them generates false negative or false positive that might cost patients their lives. The biosensor technique is one of the best qualified to address this difficult challenge. In this systematic review, we have summarized recent advancements in biosensor-based detection of these pandemic viruses including COVID-19. Biosensors are emerging as efficient and economical analytical diagnostic instruments for early-stage illness detection. They are highly suitable for applications related to healthcare, wearable electronics, safety, environment, military, and agriculture. We strongly believe that these insights will aid in the study and development of a new generation of adaptable virus biosensors for fellow researchers.
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Affiliation(s)
- Shobhit K. Patel
- Department of Computer EngineeringMarwadi UniversityRajkot360003India
| | - Jaymit Surve
- Department of Electrical EngineeringMarwadi UniversityRajkot360003India
| | - Juveriya Parmar
- Department of Mechanical and Materials EngineeringUniversity of Nebraska - LincolnNebraska68588USA
- Department of Electronics and Communication EngineeringMarwadi UniversityRajkot360003India
| | - Kawsar Ahmed
- Department of Electrical and Computer EngineeringUniversity of SaskatchewanSaskatoonSKS79 5A9Canada
- Group of Bio-PhotomatiX, Department of Information and Communication TechnologyMawlana Bhashani Science and Technology UniversitySantoshTangail1902Bangladesh
| | - Francis M. Bui
- Department of Electrical and Computer EngineeringUniversity of SaskatchewanSaskatoonSKS79 5A9Canada
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Zhao M, Xu Y, Zhang D, Li G, Gao H, Zeng X, Tie Y, Wu Y, Dai E, Feng Z. Establishment and evaluation of a quadruple quantitative real-time PCR assay for simultaneous detection of human coronavirus subtypes. Virol J 2022; 19:67. [PMID: 35410305 PMCID: PMC8995687 DOI: 10.1186/s12985-022-01793-3] [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: 01/11/2022] [Accepted: 03/22/2022] [Indexed: 01/08/2023] Open
Abstract
Background The newly discovered severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and four seasonal human coronaviruses (HCoVs) (HCoV-229E, HCoV-OC43, HCoV-NL63 and HCoV-HKU1) still circulate worldwide. The early clinical symptoms of SARS-CoV-2 and seasonal HCoV infections are similar, so rapid and accurate identification of the subtypes of HCoVs is crucial for early diagnosis, early treatment, prevention and control of these infections. However, current multiplex molecular diagnostic techniques for HCoV subtypes including SARS-CoV-2 are limited. Methods We designed primers and probes specific for the S and N genes of SARS-CoV-2, the N gene of severe acute respiratory syndrome coronavirus (SARS-CoV), and the ORF1ab gene of four seasonal HCoVs, as well as the human B2M gene product. We developed and optimized a quadruple quantitative real-time PCR assay (qq-PCR) for simultaneous detection of SARS-CoV-2, SARS-CoV and four seasonal HCoVs. This assay was further tested for specificity and sensitivity, and validated using 184 clinical samples. Results The limit of detection of the qq-PCR assay was in the range 2.5 × 101 to 6.5 × 101 copies/μL for each gene and no cross-reactivity with other common respiratory viruses was observed. The intra-assay and inter-assay coefficients of variation were 0.5–2%. The qq-PCR assay had a 91.9% sensitivity and 100.0% specificity for SARS-CoV-2 and a 95.7% sensitivity and 100% specificity for seasonal HCoVs, using the approved commercial kits as the reference. Compared to the commercial kits, total detection consistency was 98.4% (181/184) for SARS-CoV-2 and 98.6% (142/144) for seasonal HCoVs. Conclusion With the advantages of sensitivity, specificity, rapid detection, cost-effectiveness, and convenience, this qq-PCR assay has potential for clinical use for rapid discrimination between SARS-CoV-2, SARS-CoV and seasonal HCoVs. Supplementary Information The online version contains supplementary material available at 10.1186/s12985-022-01793-3.
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Ebola Virus Disease, Diagnostics and Therapeutics: Where is the Consensus in Over Three Decades of Clinical Research? SCIENTIFIC AFRICAN 2021. [DOI: 10.1016/j.sciaf.2021.e00862] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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10
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Huang Y, Xiao S, Yuan Z. Comparison and Evaluation of Real-Time Taqman PCR for Detection and Quantification of Ebolavirus. Viruses 2021; 13:1575. [PMID: 34452440 PMCID: PMC8402893 DOI: 10.3390/v13081575] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 08/05/2021] [Accepted: 08/05/2021] [Indexed: 01/12/2023] Open
Abstract
Given that ebolavirus causes severe and frequently lethal disease, its rapid and accurate detection using available and validated methods is essential for controlling infection. Real-time reverse-transcription PCR (RT-PCR) has proven to be an invaluable tool for ebolaviruses diagnostics. Many assays with different targets have been developed, but they have not been externally compared or validated, and limits of detection are not uniformly reported. Here we compared and evaluated the sensitivity, reproducibility and specificity of 23 in-house assays under the same conditions. Our results showed that these assays were highly gene- and species- specific when evaluated using in vitro RNA transcripts and viral RNA, and the potential limits of detection were uniformly reported ranging from 102 to 106 in vitro synthesized RNA transcripts copies perμL and 1-100 TCID50/mL. The comparison of these assays indicated that those targeting the more conservative NP gene could be the better option for EVD case definition and quantitative measurement because of its higher sensitivity for the same species. Our analysis could contribute to the standardization of ebolavirus detection and quantification assays, which can offer a better understanding of the meaning of results across laboratories and time points, as well as make them easy to implement, especially under outbreak conditions.
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Affiliation(s)
- Yi Huang
- National Biosafety Laboratory, Chinese Academy of Sciences, Wuhan 430020, China
| | - Shuqi Xiao
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430020, China;
| | - Zhiming Yuan
- National Biosafety Laboratory, Chinese Academy of Sciences, Wuhan 430020, China
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Jiang N, Tansukawat ND, Gonzalez-Macia L, Ates HC, Dincer C, Güder F, Tasoglu S, Yetisen AK. Low-Cost Optical Assays for Point-of-Care Diagnosis in Resource-Limited Settings. ACS Sens 2021; 6:2108-2124. [PMID: 34076428 DOI: 10.1021/acssensors.1c00669] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Readily deployable, low-cost point-of-care medical devices such as lateral flow assays (LFAs), microfluidic paper-based analytical devices (μPADs), and microfluidic thread-based analytical devices (μTADs) are urgently needed in resource-poor settings. Governed by the ASSURED criteria (affordable, sensitive, specific, user-friendly, rapid and robust, equipment-free, and deliverability) set by the World Health Organization, these reliable platforms can screen a myriad of chemical and biological analytes including viruses, bacteria, proteins, electrolytes, and narcotics. The Ebola epidemic in 2014 and the ongoing pandemic of SARS-CoV-2 have exemplified the ever-increasing importance of timely diagnostics to limit the spread of diseases. This review provides a comprehensive survey of LFAs, μPADs, and μTADs that can be deployed in resource-limited settings. The subsequent commercialization of these technologies will benefit the public health, especially in areas where access to healthcare is limited.
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Affiliation(s)
- Nan Jiang
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
- Department of Chemical Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Natha Dean Tansukawat
- Department of Chemical Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Laura Gonzalez-Macia
- Department of Bioengineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - H. Ceren Ates
- Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, Freiburg 79110, Germany
- Department of Microsystems Engineering (IMTEK), Laboratory for Sensors, University of Freiburg, Freiburg 79110, Germany
| | - Can Dincer
- Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, Freiburg 79110, Germany
- Department of Microsystems Engineering (IMTEK), Laboratory for Sensors, University of Freiburg, Freiburg 79110, Germany
| | - Firat Güder
- Department of Bioengineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Savas Tasoglu
- Department of Mechanical Engineering, Koc University, Sariyer, Istanbul 34450, Turkey
| | - Ali K. Yetisen
- Department of Chemical Engineering, Imperial College London, London SW7 2AZ, United Kingdom
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Widodo WT, Huda C. Detection of Escherichia Coli Using PCR Analysis Without DNA Extraction. FOLIA MEDICA INDONESIANA 2021. [DOI: 10.20473/fmi.v57i2.22097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
This study aimed to detect Escherichia coli directly without DNA extraction. The nucleus membrane and cell membranes of the Escherichia coli are composed of a phospholipid bilayer, damaged if heated at 950C. Pre-denaturation and denaturation of PCR were carried out at 950C. The two stages are thought to break down the Escherichia coli cells, so that the DNA that comes out of the cells can directly become a template in the PCR analysis. In this study, PCR analysis was carried out using Escherichia coli culture, Escherichia coli bacteria culture incubated at 950C, and Escherichia coli bacteria cultures incubated at 650C + on ice as templates. The results showed that PCR analysis using Escherichia coli culture directly and Escherichia coli culture incubated at 650C + on ice as templates produced very thin DNA bands with a size of 580 bp. while PCR analysis using Escherichia coli bacteria culture incubated at 950C as a template produced thick DNA bands with a size of 580 bp. This study's results are very useful for saving time and costs in the detection of Escherichia coli bacteria. The sample to be tested does not need DNA isolation as usual, but only needs to be incubated at 950C for 10 minutes.
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Medina‐Rivera M, Centeno‐Tablante E, Finkelstein JL, Rayco‐Solon P, Peña‐Rosas JP, Garcia‐Casal MN, Rogers L, Ridwan P, Martinez SS, Andrade J, Layden AJ, Chang J, Zambrano MP, Ghezzi‐Kopel K, Mehta S. Presence of Ebola virus in breast milk and risk of mother-to-child transmission: synthesis of evidence. Ann N Y Acad Sci 2021; 1488:33-43. [PMID: 33113592 PMCID: PMC8048832 DOI: 10.1111/nyas.14519] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 09/16/2020] [Accepted: 10/08/2020] [Indexed: 12/28/2022]
Abstract
To help inform global guidelines on infant feeding, this systematic review synthesizes evidence related to the presence of the Ebola virus (EBOV) in breast milk and its potential risk of viral transmission to the infant when breastfeeding. We relied on a comprehensive search strategy to identify studies including women with suspected, probable, or confirmed EBOV infection, intending to breastfeed or give breast milk to an infant. Our search identified 10,454 records, and after deduplication and screening, we assessed 148 full texts. We included eight studies reporting on 10 breastfeeding mothers and their children (one mother with twins), who provided breast milk samples for assessment. EBOV was detected via RT-PCR or viral culture in seven out of ten breast milk samples. Four out of the five-breastfed infants with EBOV-positive breast milk were found positive for EBOV infection, and all of these EBOV-positive infants died. Since previous reports have detected EBOV in tears, saliva, sweat, and contaminated surfaces, with the current evidence, it is not possible to conclude with certainty that breast milk was the main route of EBOV transmission.
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Affiliation(s)
| | | | | | - Pura Rayco‐Solon
- Department of Maternal, Newborn, Child and Adolescent Health and AgeingWorld Health OrganizationGenevaSwitzerland
| | | | | | - Lisa Rogers
- Department of Nutrition and Food SafetyWorld Health OrganizationGenevaSwitzerland
| | - Pratiwi Ridwan
- Division of Nutritional SciencesCornell UniversityIthacaNew York
| | - Sabrina Sales Martinez
- Department of Dietetics and Nutrition, Robert Stempel College of Public Health and Social WorkFlorida International UniversityMiamiFlorida
| | - Joyce Andrade
- Hospital de Niños Roberto Gilbert ElizaldeGuayaquilEcuador
| | | | - Juan Chang
- Hospital de Niños Roberto Gilbert ElizaldeGuayaquilEcuador
| | | | | | - Saurabh Mehta
- Division of Nutritional SciencesCornell UniversityIthacaNew York
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14
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Development of an Enzyme-Linked Immunosorbent Assay to Determine the Expression Dynamics of Ebola Virus Soluble Glycoprotein during Infection. Microorganisms 2020; 8:microorganisms8101535. [PMID: 33036194 PMCID: PMC7600751 DOI: 10.3390/microorganisms8101535] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/02/2020] [Accepted: 10/03/2020] [Indexed: 01/17/2023] Open
Abstract
Ebola virus (EBOV) is a highly pathogenic virus with human case fatality rates of up to 90%. EBOV uses transcriptional editing to express three different glycoproteins (GPs) from its GP gene: soluble GP (sGP), GP, and small sGP (ssGP). The molecular ratio of unedited to edited mRNA is about 70% (sGP): 25% (GP): 5% (ssGP), indicating that sGP is produced more abundantly than GP. While the presence of sGP has been confirmed in the blood during human EBOV infection, there is no report about its expression dynamics. In this study, we developed an EBOV-sGP-specific sandwich enzyme-linked immunosorbent assay (ELISA) using two different available antibodies and tested several animal serum samples to determine the concentration of sGP. EBOV-sGP was detected in nonhuman primate serum samples as early as 4 days after EBOV infection, correlating with RT-qPCR positivity. This ELISA might be further developed into a diagnostic tool for detection of EBOV in patients. Furthermore, this study provides insights into the expression dynamics of sGP during infection, which are important to decipher the function that sGP plays during infection.
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15
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Goncharova EA, Dedkov VG, Dolgova AS, Kassirov IS, Safonova MV, Voytsekhovskaya Y, Totolian AA. One-step quantitative RT-PCR assay with armored RNA controls for detection of SARS-CoV-2. J Med Virol 2020; 93:1694-1701. [PMID: 32966645 PMCID: PMC7537076 DOI: 10.1002/jmv.26540] [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] [Received: 08/27/2020] [Revised: 09/16/2020] [Accepted: 09/18/2020] [Indexed: 01/08/2023]
Abstract
Coronavirus disease 2019 (COVID‐19) has become pandemic since March 11, 2020. Thus, development and integration in clinics of fast and sensitive diagnostic tools are essential. The aim of the study is a development and evaluation of a one‐step quantitative reverse transcription‐polymerase chain reaction (RT‐qPCR) assay (COVID‐19 Amp) for severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) detection with an armored positive control and internal controls constructed from synthetic MS2‐phage‐based RNA particles. The COVID‐19 Amp assay limit of detection was 103 copies/ml, the analytical specificity was 100%. A total of 109 biological samples were examined using COVID‐19 Amp and World Health Organization (WHO)‐based assay. Discordance in nine samples was observed (negative by the WHO‐based assay) and discordant samples were retested as positive according to the results obtained from the Vector‐PCRrv‐2019‐nCoV‐RG assay. The developed COVID‐19 Amp assay has high sensitivity and specificity, includes virus particles‐based controls, provides the direct definition of the SARS‐CoV‐2 RdRp gene partial sequence, and is suitable for any hospital and laboratory equipped for RT‐qPCR. One‐step RT‐qPCR assay (COVID‐19 Amp) contains an armored positive control (ARC+) and an armored internal control (ICS) constructed from synthetic MS2‐phage‐based RNA particles. Displays high specificity and selectivity rendering it a powerful diagnostic test Suitable for any hospital and laboratory equipped for RT‐qPCR.
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Affiliation(s)
- Ekaterina A Goncharova
- Department of Epidemiology, Pasteur Institute, Federal Service on Consumers' Rights Protection and Human Well-Being Surveillance, Saint Petersburg, Russia
| | - Vladimir G Dedkov
- Department of Epidemiology, Pasteur Institute, Federal Service on Consumers' Rights Protection and Human Well-Being Surveillance, Saint Petersburg, Russia.,Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Anna S Dolgova
- Department of Epidemiology, Pasteur Institute, Federal Service on Consumers' Rights Protection and Human Well-Being Surveillance, Saint Petersburg, Russia
| | - Ilia S Kassirov
- Department of Epidemiology, Pasteur Institute, Federal Service on Consumers' Rights Protection and Human Well-Being Surveillance, Saint Petersburg, Russia
| | - Marina V Safonova
- Department of Particularly Dangerous Diseases, Anti-Plague Center, Federal Service on Consumers' Rights Protection and Human Well-Being Surveillance, Moscow, Russia
| | - Yana Voytsekhovskaya
- Department of Molecular Diagnostics and Epidemiology, Central Research Institute for Epidemiology, Federal Service on Consumers' Rights Protection and Human Well-Being Surveillance, Moscow, Russia
| | - Areg A Totolian
- Department of Epidemiology, Pasteur Institute, Federal Service on Consumers' Rights Protection and Human Well-Being Surveillance, Saint Petersburg, Russia
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16
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17
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Grimes KEL, Ngoyi BF, Stolka KB, Hemingway-Foday JJ, Lubula L, Mossoko M, Okitandjate A, MacDonald PDM, Nelson A, Rhea S, Ilunga BK. Contextual, Social and Epidemiological Characteristics of the Ebola Virus Disease Outbreak in Likati Health Zone, Democratic Republic of the Congo, 2017. Front Public Health 2020; 8:349. [PMID: 32850587 PMCID: PMC7417652 DOI: 10.3389/fpubh.2020.00349] [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: 08/27/2019] [Accepted: 06/22/2020] [Indexed: 11/13/2022] Open
Abstract
While the clinical, laboratory and epidemiological investigation results of the Ebola outbreak in Likati Health Zone, Democratic Republic of the Congo (DRC) in May 2017 have been previously reported, we provide novel commentary on the contextual, social, and epidemiological characteristics of the epidemic. As first responders with the outbreak Surveillance Team, we explain the procedures that led to a successful epidemiological investigation and ultimately a rapid end to the epidemic. We discuss the role that several factors played in the trajectory of the epidemic, including traditional healers, insufficient knowledge of epidemiological case definitions, a lack of community-based surveillance systems and tools, and remote geography. We also demonstrate how a collaborative Rapid Response Team and implementation of community-based surveillance methods helped counter contextual challenges during the Likati epidemic and aid in identifying and reporting suspected cases and contacts in remote and rural settings. Understanding these factors can hinder or help in the rapid detection, notification, and response to future epidemics in the DRC.
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Affiliation(s)
| | | | | | | | - Leopold Lubula
- Directorate of Disease Control, Ministry of Public Health, Kinshasa, Congo
| | - Mathias Mossoko
- Directorate of Disease Control, Ministry of Public Health, Kinshasa, Congo
| | | | - Pia D M MacDonald
- RTI International, Durham, NC, United States.,Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, United States
| | - Amy Nelson
- RTI International, Durham, NC, United States
| | - Sarah Rhea
- RTI International, Durham, NC, United States
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18
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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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19
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Ward MD, Kenny T, Bruggeman E, Kane CD, Morrell CL, Kane MM, Bixler S, Grady SL, Quizon RS, Astatke M, Cazares LH. Early detection of Ebola virus proteins in peripheral blood mononuclear cells from infected mice. Clin Proteomics 2020; 17:11. [PMID: 32194356 PMCID: PMC7077124 DOI: 10.1186/s12014-020-09273-y] [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: 09/26/2019] [Accepted: 02/27/2020] [Indexed: 01/09/2023] Open
Abstract
Background Detection of viral ribo-nucleic acid (RNA) via real-time polymerase chain reaction (RT-PCR) is the gold standard for the detection of Ebola virus (EBOV) during acute infection. However, the earliest window for viral RNA detection in blood samples is 48–72 h post-onset of symptoms. Therefore, efforts to develop additional orthogonal assays using complementary immunological and serological technologies are still needed to provide simplified methodology for field diagnostics. Furthermore, unlike RT-PCR tests, immunoassays that target viral proteins and/or early host responses are less susceptible to sequence erosion due to viral genetic drift. Although virus is shed into the bloodstream from infected cells, the wide dynamic range of proteins in blood plasma makes this a difficult sample matrix for the detection of low-abundant viral proteins. We hypothesized that the isolation of peripheral blood mononuclear cells (PBMCs), which are the first cellular targets of the Ebola virus (EBOV), may provide an enriched source of viral proteins. Methods A mouse infection model that employs a mouse-adapted EBOV (MaEBOV) was chosen as a proof-of-principal experimental paradigm to determine if viral proteins present in PBMCs can help diagnose EBOV infection pre-symptomatically. We employed a liquid chromatography coupled with tandem mass spectrometry (LC–MS/MS) platform to provide both high sensitivity and specificity for the detection and relative quantitation of viral proteins in PBMCs collected during MaEBOV infection. Blood samples pooled from animals at the post-infection time-points were used to determine the viral load by RT-PCR and purify PBMCs. Results Using quantitative LC-MS/MS, we detected two EBOV proteins (vp40 and nucleoprotein) in samples collected on Day 2 post-infection, which was also the first day of detectable viremia via RT-PCR. These results were confirmed via western blot which was performed on identical PBMC lysates from each post-infection time point. Conclusions While mass spectrometry is not currently amenable to field diagnostics, these results suggest that viral protein enrichment in PBMCs in tandem with highly sensitive immunoassays platforms, could lead to the development of a rapid, high-throughput diagnostic platform for pre-symptomatic detection of EBOV infection.
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Affiliation(s)
- Michael D Ward
- 1Systems and Stuctural Biology Division, Protein Sciences Branch, U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD USA
| | - Tara Kenny
- 1Systems and Stuctural Biology Division, Protein Sciences Branch, U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD USA
| | - Ernie Bruggeman
- 1Systems and Stuctural Biology Division, Protein Sciences Branch, U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD USA
| | - Christopher D Kane
- 2Therapeutic Development Center, U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD USA
| | - Courtney L Morrell
- 1Systems and Stuctural Biology Division, Protein Sciences Branch, U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD USA
| | - Molly M Kane
- 2Therapeutic Development Center, U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD USA
| | - Sandra Bixler
- 2Therapeutic Development Center, U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD USA
| | - Sarah L Grady
- 3Applied Biological Sciences, The Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Road, Laurel, MD USA
| | - Rachel S Quizon
- 3Applied Biological Sciences, The Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Road, Laurel, MD USA
| | - Mekbib Astatke
- 3Applied Biological Sciences, The Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Road, Laurel, MD USA
| | - Lisa H Cazares
- 1Systems and Stuctural Biology Division, Protein Sciences Branch, U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD USA.,2Therapeutic Development Center, U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD USA
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20
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Artika IM, Wiyatno A, Ma'roef CN. Pathogenic viruses: Molecular detection and characterization. INFECTION GENETICS AND EVOLUTION 2020; 81:104215. [PMID: 32006706 PMCID: PMC7106233 DOI: 10.1016/j.meegid.2020.104215] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 01/23/2020] [Accepted: 01/28/2020] [Indexed: 12/14/2022]
Abstract
Pathogenic viruses are viruses that can infect and replicate within human cells and cause diseases. The continuous emergence and re-emergence of pathogenic viruses has become a major threat to public health. Whenever pathogenic viruses emerge, their rapid detection is critical to enable implementation of specific control measures and the limitation of virus spread. Further molecular characterization to better understand these viruses is required for the development of diagnostic tests and countermeasures. Advances in molecular biology techniques have revolutionized the procedures for detection and characterization of pathogenic viruses. The development of PCR-based techniques together with DNA sequencing technology, have provided highly sensitive and specific methods to determine virus circulation. Pathogenic viruses potentially having global catastrophic consequences may emerge in regions where capacity for their detection and characterization is limited. Development of a local capacity to rapidly identify new viruses is therefore critical. This article reviews the molecular biology of pathogenic viruses and the basic principles of molecular techniques commonly used for their detection and characterization. The principles of good laboratory practices for handling pathogenic viruses are also discussed. This review aims at providing researchers and laboratory personnel with an overview of the molecular biology of pathogenic viruses and the principles of molecular techniques and good laboratory practices commonly implemented for their detection and characterization. The continous emergence and re-emergence of pathogenic viruses has become a major threat to public health. PCR-based techniques together with DNA sequencing technology have provided highly sensitive and specific methods to determine virus circulation. Southeast Asia is considered to be vulnerable to potential outbreaks of pathogenic viruses. A number of pathogenic viruses have been reported to circulate in this region. The 2019 novel coronavirus has also been identified in Southeast Asia. Development of local capacity to rapidly identify new viruses is very important.
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Affiliation(s)
- I Made Artika
- Biosafety Level 3 Unit, Eijkman Institute for Molecular Biology, Jalan Diponegoro 69, Jakarta 10430, Indonesia; Department of Biochemistry, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University, Darmaga Campus, Bogor 16680, Indonesia.
| | - Ageng Wiyatno
- Emerging Virus Research Unit, Eijkman Institute for Molecular Biology, Jalan Diponegoro 69, Jakarta 10430, Indonesia
| | - Chairin Nisa Ma'roef
- Emerging Virus Research Unit, Eijkman Institute for Molecular Biology, Jalan Diponegoro 69, Jakarta 10430, Indonesia
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21
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Deng X, Achari A, Federman S, Yu G, Somasekar S, Bártolo I, Yagi S, Mbala-Kingebeni P, Kapetshi J, Ahuka-Mundeke S, Muyembe-Tamfum JJ, Ahmed AA, Ganesh V, Tamhankar M, Patterson JL, Ndembi N, Mbanya D, Kaptue L, McArthur C, Muñoz-Medina JE, Gonzalez-Bonilla CR, López S, Arias CF, Arevalo S, Miller S, Stone M, Busch M, Hsieh K, Messenger S, Wadford DA, Rodgers M, Cloherty G, Faria NR, Thézé J, Pybus OG, Neto Z, Morais J, Taveira N, R Hackett J, Chiu CY. Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance. Nat Microbiol 2020; 5:443-454. [PMID: 31932713 PMCID: PMC7047537 DOI: 10.1038/s41564-019-0637-9] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 11/08/2019] [Indexed: 12/27/2022]
Abstract
Metagenomic next-generation sequencing (mNGS), the shotgun sequencing of RNA and DNA from clinical samples, has proved useful for broad-spectrum pathogen detection and the genomic surveillance of viral outbreaks. An additional target enrichment step is generally needed for high-sensitivity pathogen identification in low-titre infections, yet available methods using PCR or capture probes can be limited by high cost, narrow scope of detection, lengthy protocols and/or cross-contamination. Here, we developed metagenomic sequencing with spiked primer enrichment (MSSPE), a method for enriching targeted RNA viral sequences while simultaneously retaining metagenomic sensitivity for other pathogens. We evaluated MSSPE for 14 different viruses, yielding a median tenfold enrichment and mean 47% (±16%) increase in the breadth of genome coverage over mNGS alone. Virus detection using MSSPE arboviral or haemorrhagic fever viral panels was comparable in sensitivity to specific PCR, demonstrating 95% accuracy for the detection of Zika, Ebola, dengue, chikungunya and yellow fever viruses in plasma samples from infected patients. Notably, sequences from re-emerging and/or co-infecting viruses that have not been specifically targeted a priori, including Powassan and Usutu, were successfully enriched using MSSPE. MSSPE is simple, low cost, fast and deployable on either benchtop or portable nanopore sequencers, making this method directly applicable for diagnostic laboratory and field use. This study describes a new method that improves the sensitivity of viral detection compared with next-generation sequencing and enables the detection of emerging flaviviruses not specifically targeted a priori. Metagenomic sequencing with spiked primer enrichment is simple, low cost, fast and deployable on either benchtop or portable nanopore sequencers, making it applicable for diagnostic laboratory and field use.
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Affiliation(s)
- Xianding Deng
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Asmeeta Achari
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Scot Federman
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Guixia Yu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Sneha Somasekar
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Inês Bártolo
- Research Institute for Medicines, Faculty of Pharmacy, University of Lisbon, Lisbon, Portugal
| | - Shigeo Yagi
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, USA
| | | | - Jimmy Kapetshi
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | - Steve Ahuka-Mundeke
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | | | - Asim A Ahmed
- Boston Children's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Vijay Ganesh
- Massachussetts General Hospital, Boston, MA, USA
| | - Manasi Tamhankar
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Jean L Patterson
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Nicaise Ndembi
- Institute for Human Virology Nigeria, Abuja, Nigeria.,Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Dora Mbanya
- Universite de Yaoundé I, Yaoundé, Cameroon.,University of Bamenda, Bamenda, Cameroon
| | | | | | | | | | - Susana López
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Carlos F Arias
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Shaun Arevalo
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Steve Miller
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Mars Stone
- Blood Systems Research Institute, San Francisco, CA, USA
| | - Michael Busch
- Blood Systems Research Institute, San Francisco, CA, USA
| | - Kristina Hsieh
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, USA
| | - Sharon Messenger
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, USA
| | - Debra A Wadford
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, USA
| | | | | | - Nuno R Faria
- Department of Zoology, University of Oxford, Oxford, UK
| | - Julien Thézé
- Department of Zoology, University of Oxford, Oxford, UK
| | | | - Zoraima Neto
- Angolan National Institute of Health Research, Luanda, Angola
| | - Joana Morais
- Angolan National Institute of Health Research, Luanda, Angola
| | - Nuno Taveira
- Research Institute for Medicines, Faculty of Pharmacy, University of Lisbon, Lisbon, Portugal.,Instituto Universitário Egas Moniz (IUEM), Monte de Caparica, Portugal
| | | | - Charles Y Chiu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA. .,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA. .,Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, CA, USA.
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22
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Thirion L, Charrel RN, Boehmann Y, Corcostegui I, Raoul H, de Lamballerie X. Development and Evaluation of a Duo Zaire ebolavirus Real-Time RT-PCR Assay Targeting Two Regions within the Genome. Microorganisms 2019; 7:microorganisms7120652. [PMID: 31817185 PMCID: PMC6956279 DOI: 10.3390/microorganisms7120652] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 11/27/2019] [Accepted: 11/29/2019] [Indexed: 12/23/2022] Open
Abstract
Preparedness and response actions to mitigate Ebola virus disease (EVD) outbreaks rely on rapid diagnosis to be implemented locally to sort suspect patients attending health centers. Our aim was (i) to develop and evaluate an RT-qPCR assay combining primers and probes derived from two reference assays targeting different genomic regions; (ii) to study whether sensitivity and specificity of this dual-target assay were at least equal or better to the parental assays; (iii) to implement this dual-target assay onto the Cepheid GeneXpert open cartridge as a proof of principle for technological transfer aiming at bedsite testing locally. To do so, three home-made published RT-qPCR assays were selected to be compared with the RealStar® Filovirus Screen RT-PCR kit 1.0 (Altona Diagnostics, Hamburg, Germany), a technique that was largely deployed during the 2014–2015 West African EVD outbreak. Primers and probes sequences of the custom-made assays were analyzed in silico against a multiple sequence alignment, including >250 complete sequences corresponding to strains that have caused EVD epidemics in the past. Genomic RNA purified from the Mekambo strain of Zaire ebolavirus (EBOV) was used to study the sensitivity of the five methods. Based on these results, two in-house methods were selected and adapted to design the dual-target assay, which performances were compared to those of the parental assays using a synthetic RNA control. The dual-target assay showed better sensitivity and limit of detection (LoD95 at 0.4 copies/µL) than the parental methods (1.7 and 2.2 copies/µL). Ultimately, the dual-target assay was transferred onto the GeneXpert Flex-03 open cartridge, demonstrating a LoD95 at 0.75 copies/µL. Together these results indicate that EBOV dual-target assay has the potential to be used during EVD outbreak in the laboratory having performed molecular testing during the recent outbreaks.
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Affiliation(s)
- Laurence Thirion
- Unité des Virus Emergents (UVE: Aix Marseille Univ, IRD 190, INSERM U1207, IHU Méditerranée Infection), Aix Marseille Universite, Marseille 13000, France; (L.T.); (Y.B.); (I.C.); (X.d.L.)
| | - Remi N. Charrel
- Unité des Virus Emergents (UVE: Aix Marseille Univ, IRD 190, INSERM U1207, IHU Méditerranée Infection), Aix Marseille Universite, Marseille 13000, France; (L.T.); (Y.B.); (I.C.); (X.d.L.)
- Correspondence:
| | - Yannik Boehmann
- Unité des Virus Emergents (UVE: Aix Marseille Univ, IRD 190, INSERM U1207, IHU Méditerranée Infection), Aix Marseille Universite, Marseille 13000, France; (L.T.); (Y.B.); (I.C.); (X.d.L.)
| | - Iban Corcostegui
- Unité des Virus Emergents (UVE: Aix Marseille Univ, IRD 190, INSERM U1207, IHU Méditerranée Infection), Aix Marseille Universite, Marseille 13000, France; (L.T.); (Y.B.); (I.C.); (X.d.L.)
| | - Hervé Raoul
- Laboratory P4-Jean Mérieux, INSERM, Lyon 69007, France;
| | - Xavier de Lamballerie
- Unité des Virus Emergents (UVE: Aix Marseille Univ, IRD 190, INSERM U1207, IHU Méditerranée Infection), Aix Marseille Universite, Marseille 13000, France; (L.T.); (Y.B.); (I.C.); (X.d.L.)
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23
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Reusken CB, Mögling R, Smit PW, Grunow R, Ippolito G, Di Caro A, Koopmans M. Status, quality and specific needs of Ebola virus diagnostic capacity and capability in laboratories of the two European preparedness laboratory networks EMERGE and EVD-LabNet. ACTA ACUST UNITED AC 2019; 23. [PMID: 29766839 PMCID: PMC5954606 DOI: 10.2807/1560-7917.es.2018.23.19.17-00404] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
From December 2013 to March 2016, West Africa experienced the largest Ebola virus (EBOV) outbreak to date, leading to a European-wide activation of laboratory preparedness and response. At the end of the outbreak, laboratories associated with the two European preparedness networks of expert laboratories EMERGE JA and EVD-LabNet were invited to participate in an assessment of the response of European laboratories to the EBOV outbreak, to identify learning points and training needs to strengthen future outbreak responses. Response aspects assessed included diagnostics, biorisk management and quality assurance. The overall coverage of EBOV diagnostics in the European Union/European Economic Area (EU/EEA) was found to be adequate although some points for quality improvement were identified. These included the need for relevant International Organization for Standardization (ISO) accreditation, the provision of EBOV external quality assessments (EQA) in periods where there is no emergency, facilitating access to controls and knowledge, biorisk management without compromising biosafety and a rapid public health response, and the need for both sustained and contingency funding for preparedness and response activities.
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Affiliation(s)
- Chantal B Reusken
- Department of Viroscience, World Health Organization Collaborating Centre for Arbovirus and Viral Haemorrhagic Fever Reference and Research, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Ramona Mögling
- Department of Viroscience, World Health Organization Collaborating Centre for Arbovirus and Viral Haemorrhagic Fever Reference and Research, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Pieter W Smit
- Department of Viroscience, World Health Organization Collaborating Centre for Arbovirus and Viral Haemorrhagic Fever Reference and Research, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | | | - Giuseppe Ippolito
- National Institute for Infectious Diseases (INMI) Lazzaro Spallanzani, Rome, Italy
| | - Antonino Di Caro
- National Institute for Infectious Diseases (INMI) Lazzaro Spallanzani, Rome, Italy
| | - Marion Koopmans
- Department of Viroscience, World Health Organization Collaborating Centre for Arbovirus and Viral Haemorrhagic Fever Reference and Research, Erasmus University Medical Centre, Rotterdam, the Netherlands
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24
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Dedkov VG, Magassouba N'F, Safonova MV, Naydenova EV, Ayginin AA, Soropogui B, Kourouma F, Camara AB, Camara J, Kritzkiy AA, Tuchkov IV, Shchelkanov MY, Maleev VV. Development and Evaluation of a One-Step Quantitative RT-PCR Assay for Detection of Lassa Virus. J Virol Methods 2019; 271:113674. [PMID: 31170468 PMCID: PMC7113850 DOI: 10.1016/j.jviromet.2019.113674] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 06/01/2019] [Accepted: 06/01/2019] [Indexed: 11/01/2022]
Abstract
Lassa fever is a severe viral hemorrhagic illness caused by Lassa virus. Based on estimates, the number of LASV infections ranges from 300,000 to 500,000 cases in endemic areas with a fatality rate of 1%. Development of fast and sensitive tools for the control and prevention of Lassa virus infection as well as for clinical diagnostics of Lassa fever are crucial. Here we reported development and evaluation of a one-step quantitative RT-qPCR assay for the Lassa virus detection - LASV-Fl. This assay is suitable for the detection of lineages I-IV of Lassa virus. The limit of detection of the assay ranged from 103 copies/ml to 105 copies/ml and has 96.4% diagnostic sensitivity, whereas analytical and diagnostic specificities both were 100%. Serum, whole blood and tissue are suitable for use with the assay. The assay contains all the necessary components to perform the analysis, including an armored positive control (ARC+) and an armored internal control (IC). The study was done during the mission of specialized anti-epidemic team of the Russian Federation (SAET) in the Republic of Guinea in 2015-2018. Based on sequencing data, LASV-specific assay was developed using synthetic MS2-phage-based armored RNA particles, RNA from Lassa virus strain Josiah, and further, evaluated in field conditions using samples from patients and Mastomys natalensis rodents.
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Affiliation(s)
- Vladimir G Dedkov
- Pasteur Institute, Federal Service on Consumers' Rights Protection and Human Well-Being Surveillance, Saint-Petersburg, Russia; Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, Moscow, Russia.
| | - N 'Faly Magassouba
- Laboratorie de Virologic B1568, Université Gamal Abdel Nasser de Conakry, Projet de Recherche sur les Fièvres Hémorragiques en Guinée, Conakry, Guinea
| | - Marina V Safonova
- Anti-Plague Center, Federal Service on Consumers' Rights Protection and Human Well-Being Surveillance, Moscow, Russia
| | - Ekaterina V Naydenova
- Russian Research Anti-Plague Institute «Microbe», Federal Service on Consumers' Rights Protection and Human Well-Being Surveillance, Saratov, Russia
| | - Andrey A Ayginin
- Central Research Institute for Epidemiology, Federal Service on Consumers' Rights Protection and Human Well-Being Surveillance, Moscow, Russia
| | - Barre Soropogui
- Laboratorie de Virologic B1568, Université Gamal Abdel Nasser de Conakry, Projet de Recherche sur les Fièvres Hémorragiques en Guinée, Conakry, Guinea
| | - Fode Kourouma
- Laboratorie de Virologic B1568, Université Gamal Abdel Nasser de Conakry, Projet de Recherche sur les Fièvres Hémorragiques en Guinée, Conakry, Guinea
| | - Amara B Camara
- Laboratorie de Virologic B1568, Université Gamal Abdel Nasser de Conakry, Projet de Recherche sur les Fièvres Hémorragiques en Guinée, Conakry, Guinea
| | - Jacob Camara
- Laboratorie de Virologic B1568, Université Gamal Abdel Nasser de Conakry, Projet de Recherche sur les Fièvres Hémorragiques en Guinée, Conakry, Guinea
| | - Andrey A Kritzkiy
- Russian Research Anti-Plague Institute «Microbe», Federal Service on Consumers' Rights Protection and Human Well-Being Surveillance, Saratov, Russia
| | - Igor V Tuchkov
- Russian Research Anti-Plague Institute «Microbe», Federal Service on Consumers' Rights Protection and Human Well-Being Surveillance, Saratov, Russia
| | | | - Victor V Maleev
- Central Research Institute for Epidemiology, Federal Service on Consumers' Rights Protection and Human Well-Being Surveillance, Moscow, Russia
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25
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Racine T, Kobinger GP. Challenges and perspectives on the use of mobile laboratories during outbreaks and their use for vaccine evaluation. Hum Vaccin Immunother 2019; 15:2264-2268. [PMID: 30893007 PMCID: PMC6816390 DOI: 10.1080/21645515.2019.1597595] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
Mobile laboratories provide diagnostic capabilities for routine surveillance and patient identification during an outbreak. In either situation, they face many challenges including identification of the appropriate assay(s) to employ, logistical arrangements, and providing for the health and safety of the laboratory staff. Great strides have been made over the last decade in the development of mobile laboratories with assays that require minimal infrastructure and technical experience. This knowledge and expertise have been developed in partnership with many researchers and public health officials who live in regions prone to infectious disease outbreaks. Mobile laboratories should now also be used in the evaluation of novel vaccines and therapeutics in remote locations. Clinical mobile laboratories will include similar diagnostic capabilities as outbreak response mobile labs, but will also include additional point-of-care instruments operated under Good Clinical Practice guidelines. They will also operate rigorous data management plans so that the data collected will satisfy regulatory agencies during the licensure process. Failure to deploy an adequate clinical mobile laboratory when administering a novel biological product in a remote location is a significant limitation to any collected scientific data that could ultimately undermine clinical development and availability of life-saving interventions.
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Affiliation(s)
- Trina Racine
- Department of Medical Microbiology, University of Manitoba , Winnipeg , Manitoba , Canada.,Centre de Recherche en Infectiologie, Centre Hospitalier Universitaire de Québec, Université Laval , Québec City , Québec , Canada
| | - Gary P Kobinger
- Department of Medical Microbiology, University of Manitoba , Winnipeg , Manitoba , Canada.,Centre de Recherche en Infectiologie, Centre Hospitalier Universitaire de Québec, Université Laval , Québec City , Québec , Canada.,Department of Immunology, University of Manitoba , Winnipeg , Manitoba , Canada.,Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine , Philadelphia , PA , USA
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26
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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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27
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Jain S, Baranwal M. Computational analysis in designing T cell epitopes enriched peptides of Ebola glycoprotein exhibiting strong binding interaction with HLA molecules. J Theor Biol 2019; 465:34-44. [DOI: 10.1016/j.jtbi.2019.01.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 12/28/2018] [Accepted: 01/09/2019] [Indexed: 01/13/2023]
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28
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Strong JE, Feldmann H. The Crux of Ebola Diagnostics. J Infect Dis 2019; 216:1340-1342. [PMID: 29029148 DOI: 10.1093/infdis/jix490] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 09/20/2017] [Indexed: 11/12/2022] Open
Affiliation(s)
- James E Strong
- Special Pathogens, National Microbiology Laboratory, Public Health Agency of Canada.,Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada.,Department of Paediatrics and Child Health, College of Medicine, Faculty of Health Sciences, University of Manitoba, Winnipeg, Canada
| | - Heinz Feldmann
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada.,Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana
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29
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Paper-Based Microfluidics for Point-of-Care Medical Diagnostics. Bioanalysis 2019. [DOI: 10.1007/978-981-13-6229-3_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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30
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Gürtler C, Laible M, Schwabe W, Steinhäuser H, Li X, Liu S, Schlombs K, Sahin U. Transferring a Quantitative Molecular Diagnostic Test to Multiple Real-Time Quantitative PCR Platforms. J Mol Diagn 2018; 20:398-414. [DOI: 10.1016/j.jmoldx.2018.02.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 01/16/2018] [Accepted: 02/28/2018] [Indexed: 12/22/2022] Open
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31
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Filovirus – Auslöser von hämorrhagischem Fieber. Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz 2018; 61:894-907. [DOI: 10.1007/s00103-018-2757-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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32
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Duy J, Honko AN, Altamura LA, Bixler SL, Wollen-Roberts S, Wauquier N, O'Hearn A, Mucker EM, Johnson JC, Shamblin JD, Zelko J, Botto MA, Bangura J, Coomber M, Pitt ML, Gonzalez JP, Schoepp RJ, Goff AJ, Minogue TD. Virus-encoded miRNAs in Ebola virus disease. Sci Rep 2018; 8:6480. [PMID: 29691416 PMCID: PMC5915558 DOI: 10.1038/s41598-018-23916-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 03/15/2018] [Indexed: 12/31/2022] Open
Abstract
Ebola virus (EBOV) is a negative-strand RNA virus that replicates in the cytoplasm and causes an often-fatal hemorrhagic fever. EBOV, like other viruses, can reportedly encode its own microRNAs (miRNAs) to subvert host immune defenses. miRNAs are short noncoding RNAs that can regulate gene expression by hybridizing to multiple mRNAs, and viral miRNAs can enhance viral replication and infectivity by regulating host or viral genes. To date, only one EBOV miRNA has been examined in human infection. Here, we assayed mouse, rhesus macaque, cynomolgus macaque, and human samples infected with three EBOV variants for twelve computationally predicted viral miRNAs using RT-qPCR. Ten miRNAs aligned to EBOV variants and were detectable in the four species during disease with several viral miRNAs showing presymptomatic amplification in animal models. miRNA abundances in both the mouse and nonhuman primate models mirrored the human cohort, with miR-1-5p, miR-1-3p, and miR-T3-3p consistently at the highest levels. These striking similarities in the most abundant miRNAs during infection with different EBOV variants and hosts indicate that these miRNAs are potential valuable diagnostic markers and key effectors of EBOV pathogenesis.
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Affiliation(s)
- Janice Duy
- Diagnostic Systems Division, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Anna N Honko
- Virology Division, U.S. Army Medical Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Louis A Altamura
- Diagnostic Systems Division, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Sandra L Bixler
- Virology Division, U.S. Army Medical Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Suzanne Wollen-Roberts
- Virology Division, U.S. Army Medical Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Nadia Wauquier
- Metabiota, Kenema, Sierra Leone.,MRIGlobal - Global Health Surveillance and Diagnostics, Gaithersburg, MD, USA
| | - Aileen O'Hearn
- Diagnostic Systems Division, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Eric M Mucker
- Virology Division, U.S. Army Medical Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Joshua C Johnson
- Virology Division, U.S. Army Medical Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Joshua D Shamblin
- Virology Division, U.S. Army Medical Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Justine Zelko
- Virology Division, U.S. Army Medical Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Miriam A Botto
- Virology Division, U.S. Army Medical Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | | | | | - M Louise Pitt
- Virology Division, U.S. Army Medical Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Jean-Paul Gonzalez
- Metabiota, Washington, DC, USA.,Center of Excellence for Emerging & Zoonotic Animal Disease, Kansas State University, Manhattan, KS, USA
| | - Randal J Schoepp
- Diagnostic Systems Division, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Arthur J Goff
- Virology Division, U.S. Army Medical Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Timothy D Minogue
- Diagnostic Systems Division, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA.
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33
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Raabe V, O'Neal JP, Drenzek C, Kraft CS. Reply to Nicastri et al. Clin Infect Dis 2018; 66:638-639. [PMID: 29186318 DOI: 10.1093/cid/cix865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Vanessa Raabe
- Division of Infectious Diseases, Emory University, Atlanta, Georgia
| | - J Patrick O'Neal
- Georgia Department of Public Health, Emory University, Atlanta, Georgia
| | - Cherie Drenzek
- Georgia Department of Public Health, Emory University, Atlanta, Georgia
| | - Colleen S Kraft
- Division of Infectious Diseases, Emory University, Atlanta, Georgia.,Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia
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34
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Dedkov VG, Magassouba N, Safonova MV, Bodnev SA, Pyankov OV, Camara J, Sylla B, Agafonov AP, Maleev VV, Shipulin GA. Sensitive Multiplex Real-time RT-qPCR Assay for the Detection of Filoviruses. Health Secur 2018; 16:14-21. [DOI: 10.1089/hs.2017.0027] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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35
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Logue CH, Lewis SM, Lansley A, Fraser S, Shieber C, Shah S, Semper A, Bailey D, Busuttil J, Evans L, Carroll MW, Silman NJ, Brooks T, Shallcross JA. Case study: design and implementation of training for scientists deploying to Ebola diagnostic field laboratories in Sierra Leone: October 2014 to February 2016. Philos Trans R Soc Lond B Biol Sci 2017; 372:rstb.2016.0299. [PMID: 28396470 DOI: 10.1098/rstb.2016.0299] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/14/2017] [Indexed: 11/12/2022] Open
Abstract
As part of the UK response to the 2013-2016 Ebola virus disease (EVD) epidemic in West Africa, Public Health England (PHE) were tasked with establishing three field Ebola virus (EBOV) diagnostic laboratories in Sierra Leone by the UK Department for International Development (DFID). These provided diagnostic support to the Ebola Treatment Centre (ETC) facilities located in Kerry Town, Makeni and Port Loko. The Novel and Dangerous Pathogens (NADP) Training group at PHE, Porton Down, designed and implemented a pre-deployment Ebola diagnostic laboratory training programme for UK volunteer scientists being deployed to the PHE EVD laboratories. Here, we describe the training, workflow and capabilities of these field laboratories for use in response to disease epidemics and in epidemiological surveillance. We discuss the training outcomes, the laboratory outputs, lessons learned and the legacy value of the support provided. We hope this information will assist in the recruitment and training of staff for future responses and in the design and implementation of rapid deployment diagnostic field laboratories for future outbreaks of high consequence pathogens.This article is part of the themed issue 'The 2013-2016 West African Ebola epidemic: data, decision-making and disease control'.
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Affiliation(s)
- Christopher H Logue
- Novel and Dangerous Pathogens Training, Public Health England, Porton Down, Salisbury, Wiltshire, SP4 0JG, UK
| | - Suzanna M Lewis
- Novel and Dangerous Pathogens Training, Public Health England, Porton Down, Salisbury, Wiltshire, SP4 0JG, UK
| | - Amber Lansley
- Novel and Dangerous Pathogens Training, Public Health England, Porton Down, Salisbury, Wiltshire, SP4 0JG, UK
| | - Sara Fraser
- Novel and Dangerous Pathogens Training, Public Health England, Porton Down, Salisbury, Wiltshire, SP4 0JG, UK
| | - Clare Shieber
- Novel and Dangerous Pathogens Training, Public Health England, Porton Down, Salisbury, Wiltshire, SP4 0JG, UK
| | - Sonal Shah
- Novel and Dangerous Pathogens Training, Public Health England, Porton Down, Salisbury, Wiltshire, SP4 0JG, UK
| | - Amanda Semper
- Novel and Dangerous Pathogens Training, Public Health England, Porton Down, Salisbury, Wiltshire, SP4 0JG, UK
| | - Daniel Bailey
- Novel and Dangerous Pathogens Training, Public Health England, Porton Down, Salisbury, Wiltshire, SP4 0JG, UK
| | - Jason Busuttil
- Novel and Dangerous Pathogens Training, Public Health England, Porton Down, Salisbury, Wiltshire, SP4 0JG, UK
| | - Liz Evans
- Novel and Dangerous Pathogens Training, Public Health England, Porton Down, Salisbury, Wiltshire, SP4 0JG, UK
| | - Miles W Carroll
- Novel and Dangerous Pathogens Training, Public Health England, Porton Down, Salisbury, Wiltshire, SP4 0JG, UK
| | - Nigel J Silman
- Novel and Dangerous Pathogens Training, Public Health England, Porton Down, Salisbury, Wiltshire, SP4 0JG, UK
| | - Tim Brooks
- Novel and Dangerous Pathogens Training, Public Health England, Porton Down, Salisbury, Wiltshire, SP4 0JG, UK
| | - Jane A Shallcross
- Novel and Dangerous Pathogens Training, Public Health England, Porton Down, Salisbury, Wiltshire, SP4 0JG, UK
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36
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Mérens A, Bigaillon C, Delaune D. Ebola virus disease: Biological and diagnostic evolution from 2014 to 2017. Med Mal Infect 2017; 48:83-94. [PMID: 29224715 DOI: 10.1016/j.medmal.2017.11.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 11/14/2017] [Indexed: 10/18/2022]
Abstract
The Ebola virus disease outbreak observed in West Africa from March 2014 to June 2016 has led to many fundamental and applied research works. Knowledge of this virus has substantially increased. Treatment of many patients in epidemic countries and a few imported cases in developed countries led to developing new diagnostic methods and to adapt laboratory organization and biosafety precautions to perform conventional biological analyses. Clinical and biological monitoring of patients infected with Ebola virus disease helped to determine severity criteria and bad prognosis markers. It also contributed to showing the possibility of viral sanctuaries in patients and the risk of transmission after recovery. After a summary of recent knowledge of environmental and clinical viral persistence, we aimed to present new diagnostic methods and other biological tests that led to highlighting the pathophysiological consequences of Ebola virus disease and its prognostic markers. We also aimed to describe our lab experience in the care of Ebola virus-infected patients, especially technical and logistical changes between 2014 and 2017.
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Affiliation(s)
- A Mérens
- Laboratoire de biologie, hôpital d'instruction des Armées-Bégin, 69, avenue de Paris, 94160 Saint-Mandé, France.
| | - C Bigaillon
- Laboratoire de biologie, hôpital d'instruction des Armées-Bégin, 69, avenue de Paris, 94160 Saint-Mandé, France
| | - D Delaune
- Laboratoire de biologie, hôpital d'instruction des Armées-Bégin, 69, avenue de Paris, 94160 Saint-Mandé, France
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37
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Hu J, Jiang YZ, Wu LL, Wu Z, Bi Y, Wong G, Qiu X, Chen J, Pang DW, Zhang ZL. Dual-Signal Readout Nanospheres for Rapid Point-of-Care Detection of Ebola Virus Glycoprotein. Anal Chem 2017; 89:13105-13111. [DOI: 10.1021/acs.analchem.7b02222] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Jiao Hu
- Key Laboratory of
Analytical Chemistry for Biology and Medicine (Ministry of Education),
College of Chemistry and Molecular Sciences, State Key Laboratory
of Virology, The Institute for Advanced Studies, and Wuhan Institute
of Biotechnology, Wuhan University, Wuhan 430072, People’s Republic of China
| | - Yong-Zhong Jiang
- Key Laboratory of
Analytical Chemistry for Biology and Medicine (Ministry of Education),
College of Chemistry and Molecular Sciences, State Key Laboratory
of Virology, The Institute for Advanced Studies, and Wuhan Institute
of Biotechnology, Wuhan University, Wuhan 430072, People’s Republic of China
| | - Ling-Ling Wu
- Key Laboratory of
Analytical Chemistry for Biology and Medicine (Ministry of Education),
College of Chemistry and Molecular Sciences, State Key Laboratory
of Virology, The Institute for Advanced Studies, and Wuhan Institute
of Biotechnology, Wuhan University, Wuhan 430072, People’s Republic of China
| | - Zhen Wu
- Key Laboratory of
Analytical Chemistry for Biology and Medicine (Ministry of Education),
College of Chemistry and Molecular Sciences, State Key Laboratory
of Virology, The Institute for Advanced Studies, and Wuhan Institute
of Biotechnology, Wuhan University, Wuhan 430072, People’s Republic of China
| | - Yuhai Bi
- Shenzhen
Key Laboratory of Pathogen and Immunity, State Key Discipline of Infectious
Disease, Shenzhen Third People’s Hospital, Shenzhen 518112, People’s Republic of China
- Chinese Academy of Sciences
Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Beijing 100101, People’s Republic of China
- Chinese Academy of Sciences
Center for Influenza Research and Early Warning, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Gary Wong
- Chinese Academy of Sciences
Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Beijing 100101, People’s Republic of China
- Chinese Academy of Sciences
Center for Influenza Research and Early Warning, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Xiangguo Qiu
- Special Pathogens Program, National
Microbiology Laboratory, Public Health Agency of Canada, Department
of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba R3E 3R2, Canada
| | - Jianjun Chen
- Chinese Academy of Sciences Key Laboratory of Special Pathogens and
Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Hubei 430071, People’s Republic of China
- Chinese Academy of Sciences
Center for Influenza Research and Early Warning, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Dai-Wen Pang
- Key Laboratory of
Analytical Chemistry for Biology and Medicine (Ministry of Education),
College of Chemistry and Molecular Sciences, State Key Laboratory
of Virology, The Institute for Advanced Studies, and Wuhan Institute
of Biotechnology, Wuhan University, Wuhan 430072, People’s Republic of China
| | - Zhi-Ling Zhang
- Key Laboratory of
Analytical Chemistry for Biology and Medicine (Ministry of Education),
College of Chemistry and Molecular Sciences, State Key Laboratory
of Virology, The Institute for Advanced Studies, and Wuhan Institute
of Biotechnology, Wuhan University, Wuhan 430072, People’s Republic of China
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Du K, Park M, Griffiths A, Carrion R, Patterson J, Schmidt H, Mathies R. Microfluidic System for Detection of Viral RNA in Blood Using a Barcode Fluorescence Reporter and a Photocleavable Capture Probe. Anal Chem 2017; 89:12433-12440. [PMID: 29073356 PMCID: PMC5990416 DOI: 10.1021/acs.analchem.7b03527] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A microfluidic sample preparation multiplexer (SPM) and assay procedure is developed to improve amplification-free detection of Ebola virus RNA from blood. While a previous prototype successfully detected viral RNA following off-chip RNA extraction from infected cells, the new device and protocol can detect Ebola virus in raw blood with clinically relevant sensitivity. The Ebola RNA is hybridized with sequence specific capture and labeling DNA probes in solution and then the complex is pulled down onto capture beads for purification and concentration. After washing, the captured RNA target is released by irradiating the photocleavable DNA capture probe with ultraviolet (UV) light. The released, labeled, and purified RNA is detected by a sensitive and compact fluorometer. Exploiting these capabilities, a detection limit of 800 attomolar (aM) is achieved without target amplification. The new SPM can run up to 80 assays in parallel using a pneumatic multiplexing architecture. Importantly, our new protocol does not require time-consuming and problematic off-chip probe conjugation and washing. This improved SPM and labeling protocol is an important step toward a useful POC device and assay.
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Affiliation(s)
- Ke Du
- Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, United States
| | - Myeongkee Park
- Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, United States
| | - Anthony Griffiths
- Department of Virology and Immunology, Texas Biomedical Research Institute, 7620 NW Loop 410, San Antonio, Texas 78227, United States
| | - Ricardo Carrion
- Department of Virology and Immunology, Texas Biomedical Research Institute, 7620 NW Loop 410, San Antonio, Texas 78227, United States
| | - Jean Patterson
- Department of Virology and Immunology, Texas Biomedical Research Institute, 7620 NW Loop 410, San Antonio, Texas 78227, United States
| | - Holger Schmidt
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Richard Mathies
- Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, United States
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Coarsey CT, Esiobu N, Narayanan R, Pavlovic M, Shafiee H, Asghar W. Strategies in Ebola virus disease (EVD) diagnostics at the point of care. Crit Rev Microbiol 2017; 43:779-798. [PMID: 28440096 PMCID: PMC5653233 DOI: 10.1080/1040841x.2017.1313814] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 10/21/2016] [Accepted: 03/25/2017] [Indexed: 12/13/2022]
Abstract
Ebola virus disease (EVD) is a devastating, highly infectious illness with a high mortality rate. The disease is endemic to regions of Central and West Africa, where there is limited laboratory infrastructure and trained staff. The recent 2014 West African EVD outbreak has been unprecedented in case numbers and fatalities, and has proven that such regional outbreaks can become a potential threat to global public health, as it became the source for the subsequent transmission events in Spain and the USA. The urgent need for rapid and affordable means of detecting Ebola is crucial to control the spread of EVD and prevent devastating fatalities. Current diagnostic techniques include molecular diagnostics and other serological and antigen detection assays; which can be time-consuming, laboratory-based, often require trained personnel and specialized equipment. In this review, we discuss the various Ebola detection techniques currently in use, and highlight the potential future directions pertinent to the development and adoption of novel point-of-care diagnostic tools. Finally, a case is made for the need to develop novel microfluidic technologies and versatile rapid detection platforms for early detection of EVD.
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Affiliation(s)
- Chad T. Coarsey
- Department of Computer and Electrical Engineering & Computer Science, Florida Atlantic University, Boca Raton, FL, United States
- Asghar-Lab: Micro and Nanotechnology in Medicine, Florida Atlantic University, Boca Raton, FL, United States
| | - Nwadiuto Esiobu
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, FL, United States
| | - Ramswamy Narayanan
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, FL, United States
| | - Mirjana Pavlovic
- Department of Computer and Electrical Engineering & Computer Science, Florida Atlantic University, Boca Raton, FL, United States
| | - Hadi Shafiee
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Waseem Asghar
- Department of Computer and Electrical Engineering & Computer Science, Florida Atlantic University, Boca Raton, FL, United States
- Asghar-Lab: Micro and Nanotechnology in Medicine, Florida Atlantic University, Boca Raton, FL, United States
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, FL, United States
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40
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Magro L, Escadafal C, Garneret P, Jacquelin B, Kwasiborski A, Manuguerra JC, Monti F, Sakuntabhai A, Vanhomwegen J, Lafaye P, Tabeling P. Paper microfluidics for nucleic acid amplification testing (NAAT) of infectious diseases. LAB ON A CHIP 2017. [PMID: 28632278 DOI: 10.1039/c7lc00013h] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The diagnosis of infectious diseases is entering a new and interesting phase. Technologies based on paper microfluidics, coupled to developments in isothermal amplification of Nucleic Acids (NAs) raise opportunities for bringing the methods of molecular biology in the field, in a low setting environment. A lot of work has been performed in the domain over the last few years and the landscape of contributions is rich and diverse. Most often, the level of sample preparation differs, along with the sample nature, the amplification and detection methods, and the design of the device, among other features. In this review, we attempt to offer a structured description of the state of the art. The domain is not mature and there exist bottlenecks that hamper the realization of Nucleic Acid Amplification Tests (NAATs) complying with the constraints of the field in low and middle income countries. In this domain however, the pace of progress is impressively fast. This review is written for a broad Lab on a Chip audience.
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Affiliation(s)
- Laura Magro
- MMN, Gulliver Laboratory, UMR CNRS 7083, ESPCI Paris, PSL Research University, Paris, France.
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41
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Gay-Andrieu F, Magassouba N, Picot V, Phillips CL, Peyrefitte CN, Dacosta B, Doré A, Kourouma F, Ligeon-Ligeonnet V, Gauby C, Longuet C, Scullion M, Faye O, Machuron JL, Miller M. Clinical evaluation of the BioFire FilmArray ® BioThreat-E test for the diagnosis of Ebola Virus Disease in Guinea. J Clin Virol 2017; 92:20-24. [DOI: 10.1016/j.jcv.2017.04.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 04/09/2017] [Accepted: 04/28/2017] [Indexed: 02/06/2023]
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43
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Magro L, Jacquelin B, Escadafal C, Garneret P, Kwasiborski A, Manuguerra JC, Monti F, Sakuntabhai A, Vanhomwegen J, Lafaye P, Tabeling P. Paper-based RNA detection and multiplexed analysis for Ebola virus diagnostics. Sci Rep 2017; 7:1347. [PMID: 28465576 PMCID: PMC5431003 DOI: 10.1038/s41598-017-00758-9] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 03/13/2017] [Indexed: 11/09/2022] Open
Abstract
The most performing techniques enabling early diagnosis of infectious diseases rely on nucleic acid detection. Today, because of their high technicality and cost, nucleic acid amplification tests (NAAT) are of benefit only to a small fraction of developing countries population. By reducing costs, simplifying procedures and enabling multiplexing, paper microfluidics has the potential to considerably facilitate their accessibility. However, most of the studies performed in this area have not quit the lab. This letter brings NAAT on paper closer to the field, by using clinical samples and operating in a resource-limited setting. We first performed isothermal reverse transcription and Recombinase Polymerase Amplification (RT-RPA) of synthetic Ribonucleic Acid (RNA) of Ebola virus using paper microfluidics devices. We further applied this method in Guinea to detect the presence of Ebola virus in human sample RNA extracts, with minimal facilities (carry-on detection device and freeze-dried reagents on paper). RT-RPA results were available in few minutes and demonstrate a sensitivity of 90.0% compared to the gold-standard RT-PCR on a set of 43 patient samples. Furthermore, the realization of a nine-spot multilayered device achieving the parallel detection of three distinct RNA sequences opens a route toward the detection of multiple viral strains or pathogens.
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Affiliation(s)
- Laura Magro
- MMN laboratory CNRS UMR7083 Gulliver, ESPCI Paris, PSL Research University, Paris, France
| | | | - Camille Escadafal
- Institut Pasteur, Laboratory for Urgent Response to Biological Threats, Paris, France
| | - Pierre Garneret
- MMN laboratory CNRS UMR7083 Gulliver, ESPCI Paris, PSL Research University, Paris, France
| | - Aurélia Kwasiborski
- Institut Pasteur, Laboratory for Urgent Response to Biological Threats, Paris, France
| | | | - Fabrice Monti
- MMN laboratory CNRS UMR7083 Gulliver, ESPCI Paris, PSL Research University, Paris, France
| | - Anavaj Sakuntabhai
- Institut Pasteur, Functional Genetics of Infectious Diseases Unit, CNRS URA3012, Paris, France
| | - Jessica Vanhomwegen
- Institut Pasteur, Laboratory for Urgent Response to Biological Threats, Paris, France
| | - Pierre Lafaye
- Institut Pasteur, Antibody Engineering Platform, UtechS proteins, Paris, France
| | - Patrick Tabeling
- MMN laboratory CNRS UMR7083 Gulliver, ESPCI Paris, PSL Research University, Paris, France.
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44
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Ro YT, Ticer A, Carrion R, Patterson JL. Rapid detection and quantification of Ebola Zaire virus by one-step real-time quantitative reverse transcription-polymerase chain reaction. Microbiol Immunol 2017; 61:130-137. [PMID: 28332721 DOI: 10.1111/1348-0421.12475] [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] [Received: 11/14/2016] [Revised: 02/09/2017] [Accepted: 03/02/2017] [Indexed: 11/26/2022]
Abstract
Given that Ebola virus causes severe hemorrhagic fever in humans with mortality rates as high as 90%, rapid and accurate detection of this virus is essential both for controlling infection and preventing further transmission. Here, a one-step qRT-PCR assay for rapid and quantitative detection of an Ebola Zaire strain using GP, VP24 or VP40 genes as a target is introduced. Routine assay conditions for hydrolysis probe detection were established from the manufacturer's protocol used in the assays. The analytical specificity and sensitivity of each assay was evaluated using in vitro synthesized viral RNA transcripts. The assays were highly specific for the RNA transcripts, no cross-reactivity being observed among them. The limits of detection of the assays ranged from 102 to 103 copies per reaction. The assays were also evaluated using viral RNAs extracted from cell culture-propagated viruses (Ebola Zaire, Sudan and Reston strains), confirming that they are gene- and strain-specific. The RT-PCR assays detected viral RNAs in blood samples from virus-infected animal, suggesting that they can be also a useful method for identifying Ebola virus in clinical samples.
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Affiliation(s)
- Young-Tae Ro
- Department of Biochemistry, Graduate School of Medicine, Konkuk University, Seoul 143-701, Korea.,Department of Virology and Immunology, Texas Biomedical Research Institute 7620 NW Loop 410, San Antonio, TX78227, USA
| | - Anysha Ticer
- Department of Virology and Immunology, Texas Biomedical Research Institute 7620 NW Loop 410, San Antonio, TX78227, USA
| | - Ricardo Carrion
- Department of Virology and Immunology, Texas Biomedical Research Institute 7620 NW Loop 410, San Antonio, TX78227, USA
| | - Jean L Patterson
- Department of Virology and Immunology, Texas Biomedical Research Institute 7620 NW Loop 410, San Antonio, TX78227, USA
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Maehira Y, Kurosaki Y, Saito T, Yasuda J, Tarui M, Malvy DJM, Takeuchi T. Responding to ever-changing epidemiological dynamics of Ebola virus disease. BMJ Glob Health 2016; 1:e000180. [PMID: 28588973 PMCID: PMC5321369 DOI: 10.1136/bmjgh-2016-000180] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 10/27/2016] [Indexed: 11/03/2022] Open
Abstract
With the incidence and mortality rates of Ebola virus disease (EVD) in Guinea, Liberia and Sierra Leone now at zero and reports of the largest and most complex EVD outbreak in history no longer on the front pages of newspapers worldwide, the urgency of that crisis seems to have subsided. During this lull after the storm and before the next one, the international community needs to engage in a 'lessons-learned' exercise with respect to our collective scientific, clinical and public health preparedness. This engagement must identify pragmatic, innovative mechanisms at multinational, national and community levels that allow research and development of next generation diagnostics and therapeutics, the safe and effective practice of medicine, and the maintenance of public health to keep pace with the rapid epidemiological dynamics of EVD and other deadly infectious diseases.
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Affiliation(s)
- Yuki Maehira
- St. Luke's International University, Tokyo, Japan
| | - Yohei Kurosaki
- Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Tomoya Saito
- National Institute of Public Health, Saitama, Japan
| | - Jiro Yasuda
- Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | | | - Denis J M Malvy
- Inserm 1219, University of Bordeaux & Division of Clinical Tropical Medicine, CHU de Bordeaux, Bordeaux, France
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Shorten RJ, Brown CS, Jacobs M, Rattenbury S, Simpson AJ, Mepham S. Diagnostics in Ebola Virus Disease in Resource-Rich and Resource-Limited Settings. PLoS Negl Trop Dis 2016; 10:e0004948. [PMID: 27788135 PMCID: PMC5082928 DOI: 10.1371/journal.pntd.0004948] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The Ebola virus disease (EVD) outbreak in West Africa was unprecedented in scale and location. Limited access to both diagnostic and supportive pathology assays in both resource-rich and resource-limited settings had a detrimental effect on the identification and isolation of cases as well as individual patient management. Limited access to such assays in resource-rich settings resulted in delays in differentiating EVD from other illnesses in returning travellers, in turn utilising valuable resources until a diagnosis could be made. This had a much greater impact in West Africa, where it contributed to the initial failure to contain the outbreak. This review explores diagnostic assays of use in EVD in both resource-rich and resource-limited settings, including their respective limitations, and some novel assays and approaches that may be of use in future outbreaks.
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Affiliation(s)
- Robert J Shorten
- Public Health Laboratory Manchester, Manchester Royal Infirmary, Manchester, United Kingdom
- University College London, Centre for Clinical Microbiology, Department of Infection, London United Kingdom
| | - Colin S Brown
- Hospital for Tropical Diseases, University College London Hospital, London, United Kingdom
- King’s Sierra Leone Partnership, King’s Centre for Global Health, King’s College London, and King’s Health Partners, London, United Kingdom
| | - Michael Jacobs
- Department of Infection, Royal Free London NHS Foundation Trust, London, United Kingdom
| | - Simon Rattenbury
- Department of Infection, Royal Free London NHS Foundation Trust, London, United Kingdom
| | - Andrew J. Simpson
- University College London, Centre for Clinical Microbiology, Department of Infection, London United Kingdom
- Rare and Imported Pathogens Laboratory, Public Health England, Salisbury, United Kingdom
| | - Stephen Mepham
- Department of Infection, Royal Free London NHS Foundation Trust, London, United Kingdom
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47
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Broadhurst MJ, Brooks TJG, Pollock NR. Diagnosis of Ebola Virus Disease: Past, Present, and Future. Clin Microbiol Rev 2016; 29:773-93. [PMID: 27413095 PMCID: PMC5010747 DOI: 10.1128/cmr.00003-16] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Laboratory diagnosis of Ebola virus disease plays a critical role in outbreak response efforts; however, establishing safe and expeditious testing strategies for this high-biosafety-level pathogen in resource-poor environments remains extremely challenging. Since the discovery of Ebola virus in 1976 via traditional viral culture techniques and electron microscopy, diagnostic methodologies have trended toward faster, more accurate molecular assays. Importantly, technological advances have been paired with increasing efforts to support decentralized diagnostic testing capacity that can be deployed at or near the point of patient care. The unprecedented scope of the 2014-2015 West Africa Ebola epidemic spurred tremendous innovation in this arena, and a variety of new diagnostic platforms that have the potential both to immediately improve ongoing surveillance efforts in West Africa and to transform future outbreak responses have reached the field. In this review, we describe the evolution of Ebola virus disease diagnostic testing and efforts to deploy field diagnostic laboratories in prior outbreaks. We then explore the diagnostic challenges pervading the 2014-2015 epidemic and provide a comprehensive examination of novel diagnostic tests that are likely to address some of these challenges moving forward.
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Affiliation(s)
- M Jana Broadhurst
- Department of Pathology, Stanford University School of Medicine, Palo Alto, California, USA
| | - Tim J G Brooks
- Public Health England, Porton Down, Salisbury, United Kingdom
| | - Nira R Pollock
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, Massachusetts, USA
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48
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Benzine JW, Brown KM, Agans KN, Godiska R, Mire CE, Gowda K, Converse B, Geisbert TW, Mead DA, Chander Y. Molecular Diagnostic Field Test for Point-of-Care Detection of Ebola Virus Directly From Blood. J Infect Dis 2016; 214:S234-S242. [PMID: 27638947 DOI: 10.1093/infdis/jiw330] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A molecular diagnostic method for robust detection of Ebola virus (EBOV) at the point of care (POC) directly from blood samples is described. This assay is based on reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) of the glycoprotein gene of EBOV. Complete reaction formulations were lyophilized in 0.2-mL polymerase chain reaction tubes. RT-LAMP reactions were performed on a battery-operated isothermal instrument. Limit of detection of this RT-LAMP assay was 2.8 × 102 plaque-forming units (PFU)/test and 1 × 103 PFU/test within 40 minutes for EBOV-Kikwit and EBOV-Makona, respectively. This assay was found to be specific for the detection of EBOV, as no nonspecific amplification was detected in blood samples spiked with closely related viruses and other pathogens. These results showed that this diagnostic test can be used at the point of care for rapid and specific detection of EBOV directly from blood with high sensitivity within 40 minutes.
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Affiliation(s)
| | | | - Krystle N Agans
- Department of Microbiology and Immunology Galveston National Laboratory, University of Texas Medical Branch at Galveston
| | | | - Chad E Mire
- Department of Microbiology and Immunology Galveston National Laboratory, University of Texas Medical Branch at Galveston
| | | | | | - Thomas W Geisbert
- Department of Microbiology and Immunology Galveston National Laboratory, University of Texas Medical Branch at Galveston
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Rieger T, Kerber R, El Halas H, Pallasch E, Duraffour S, Günther S, Ölschläger S. Evaluation of RealStar Reverse Transcription-Polymerase Chain Reaction Kits for Filovirus Detection in the Laboratory and Field. J Infect Dis 2016; 214:S243-S249. [PMID: 27549586 PMCID: PMC5050472 DOI: 10.1093/infdis/jiw246] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Background. Diagnosis of Ebola virus (EBOV) disease (EVD) requires laboratory testing. Methods. The RealStar Filovirus Screen reverse transcription–polymerase chain reaction (RT-PCR) kit and the derived RealStar Zaire Ebolavirus RT-PCR kit were validated using in vitro transcripts, supernatant of infected cell cultures, and clinical specimens from patients with EVD. Results. The Filovirus Screen kit detected EBOV, Sudan virus, Taï Forest virus, Bundibugyo virus, Reston virus, and Marburg virus and differentiated between the genera Ebolavirus and Marburgvirus. The amount of filovirus RNA that could be detected with a probability of 95% ranged from 11 to 67 RNA copies/reaction on a LightCycler 480 II. The Zaire Ebolavirus kit is based on the Filovirus Screen kit but was optimized for detection of EBOV. It has an improved signal-to-noise ratio at low EBOV RNA concentrations and is somewhat more sensitive than the Filovirus kit. Both kits show significantly lower analytical sensitivity on a SmartCycler II. Clinical evaluation revealed that the SmartCycler II, compared with other real-time PCR platforms, decreases the clinical sensitivity of the Filovirus Screen kit to diagnose EVD at an early stage. Conclusions. The Filovirus Screen kit detects all human-pathogenic filoviruses with good analytical sensitivity if performed on an appropriate real-time PCR platform. High analytical sensitivity is important for early diagnosis of EVD.
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Affiliation(s)
- Toni Rieger
- Department of Virology, Bernhard Nocht Institute for Tropical Medicine
| | - Romy Kerber
- Department of Virology, Bernhard Nocht Institute for Tropical Medicine
| | | | - Elisa Pallasch
- Department of Virology, Bernhard Nocht Institute for Tropical Medicine German Center for Infection Research, Hamburg, Germany
| | - Sophie Duraffour
- Department of Virology, Bernhard Nocht Institute for Tropical Medicine
| | - Stephan Günther
- Department of Virology, Bernhard Nocht Institute for Tropical Medicine German Center for Infection Research, Hamburg, Germany
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50
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EbolaID: An Online Database of Informative Genomic Regions for Ebola Identification and Treatment. PLoS Negl Trop Dis 2016; 10:e0004757. [PMID: 27441375 PMCID: PMC4956216 DOI: 10.1371/journal.pntd.0004757] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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