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Dagens AB, Rojek A, Sigfrid L, Plüddemann A. The diagnostic accuracy of rapid diagnostic tests for Ebola virus disease: a systematic review. Clin Microbiol Infect 2023; 29:171-181. [PMID: 36162724 DOI: 10.1016/j.cmi.2022.09.014] [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: 05/10/2022] [Revised: 08/28/2022] [Accepted: 09/15/2022] [Indexed: 02/07/2023]
Abstract
BACKGROUND Ebola virus disease (EVD) is a dangerous condition that can cause an epidemic. Several rapid diagnostic tests (RDTs) have been developed to diagnose EVD. These RDTs promise to be quicker and easier to use than the current reference standard diagnostic test, PCR. OBJECTIVES To assess the diagnostic accuracy of RDTs for EVD. METHODS A systematic review of diagnostic accuracy studies. DATA SOURCES The following bibliographic databases were searched from inception to present: MEDLINE (Ovid), Embase, Global Health, Cochrane Central Register of Controlled Trials, WHO Global Index Medicus database, Web of Science, PROSPERO register of Systematic Reviews, and Clinical Trials.Gov. STUDY ELIGIBILITY CRITERIA Diagnostic accuracy studies. PARTICIPANTS Patients presenting to the Ebola treatment units with symptoms of EVD. INTERVENTIONS RDTs; reference standard, RT-PCR. ASSESSMENT OF RISK OF BIAS Quality Assessment of Diagnostic Accuracy Studies-2 tool. METHODS OF DATA SYNTHESIS Summary estimates of diagnostic accuracy study were produced for each device type. Subgroup analyses were performed for RDT type and specimen material. A sensitivity analysis was performed to assess the effect of trial design and bias. RESULTS We included 15 diagnostic accuracy studies. The summary estimate of sensitivity for lateral flow assays was 86.1% (95% CI, 86-86.2%), with specificity of 97% (95% CI, 96.1-97.9%). The summary estimate for rapid PCR devices was sensitivity of 96.2% (95% CI, 95.3-97.9%), with a specificity of 96.8% (95% CI, 95.3-97.9%). Pre-specified subgroup analyses demonstrated that RDTs were effective on a range of specimen material. Overall, the risk of bias throughout the included studies was low, but it was high in patient selection and uncertain in the flow and timing domains. CONCLUSIONS RDTs possess both high sensitivity and specificity compared with RT-PCR among symptomatic patients presenting to the Ebola treatment units. Our findings support the use of RDTs as a 'rule in' test to expedite treatment and vaccination.
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Affiliation(s)
- Andrew B Dagens
- Epidemic Research Group Oxford, University of Oxford, Oxford, United Kingdom.
| | - Amanda Rojek
- Epidemic Research Group Oxford, University of Oxford, Oxford, United Kingdom
| | - Louise Sigfrid
- Epidemic Research Group Oxford, University of Oxford, Oxford, United Kingdom
| | - Annette Plüddemann
- Centre for Evidence Based Medicine, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
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Guest PC, Hawkins SFC, Rahmoune H. Rapid Detection of SARS-CoV-2 Variants of Concern by Genomic Surveillance Techniques. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1412:491-509. [PMID: 37378785 DOI: 10.1007/978-3-031-28012-2_27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
This chapter describes the application of genomic, transcriptomic, proteomic, and metabolomic methods in the study of SARS-CoV-2 variants of concern. We also describe the important role of machine learning tools to identify the most significant biomarker signatures and discuss the latest point-of-care devices that can be used to translate these findings to the physician's office or to bedside care. The main emphasis is placed on increasing our diagnostic capacity and predictability of disease outcomes to guide the most appropriate treatment strategies.
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Affiliation(s)
- Paul C Guest
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
- Department of Psychiatry, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
- Laboratory of Translational Psychiatry, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
| | | | - Hassan Rahmoune
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
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Bettini A, Lapa D, Garbuglia AR. Diagnostics of Ebola virus. Front Public Health 2023; 11:1123024. [PMID: 36908455 PMCID: PMC9995846 DOI: 10.3389/fpubh.2023.1123024] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 01/31/2023] [Indexed: 02/25/2023] Open
Abstract
Ebola is a highly pathogenic virus, which in humans reaches a mortality rate above 50%. Due to a lack of laboratories in territories where Ebola viruses are endemic and the limited number of surveillance programmes, tests for the confirmation of suspected cases of Ebola are often performed in Reference Laboratories. While this provides guarantees regarding the accuracy of results, the shipment of samples to a centralized facility where the diagnostic test can be performed and the time required to achieve the results takes several days, which increases costs and entails delays in the isolation of positive subjects and therapeutic intervention with negative consequences both for patients and the community. Molecular tests have been the most frequently used tool in Ebola diagnosis in recent outbreaks. One of the most commonly used molecular tests is the Real-Star Altona, which targets a conserved area of the L gene. This assay showed different sensitivities depending on the Ebola virus: 471 copies/mL (EBOV) and 2871 copies/ml (SUDAN virus). The Cepheid system also showed good sensitivity (232 copies/mL). The LAMP platform is very promising because, being an isothermal reaction, it does not require high-precision instrumentation and can be considered a Point of Care (PoC) tool. Its analytical sensitivity is 1 copy/reaction. However, since data from real life studies are not yet available, it is premature to give any indications on its feasibility. Moreover, in November 2014, the WHO recommended the development of rapid diagnostic tests (RDT) according to ASSURED criteria. Several RDT assays have since been produced, most of which are rapid tests based on the search for antibody anti-Ebola viral proteins with immunochromatographic methods. Several viral antigens are used for this purpose: VP40, NP and GP. These assays show different sensitivities according to the protein used: VP40 57.4-93.1%, GP 53-88.9% and 85% for NP compared to reference molecular assays. From these results, it can be deduced that no RDT reaches the 99% sensitivity recommended by the WHO and therefore any RDT negative results in suspected cases should be confirmed with a molecular test.
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Affiliation(s)
- Aurora Bettini
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani (IRCCS), Rome, Italy
| | - Daniele Lapa
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani (IRCCS), Rome, Italy
| | - Anna Rosa Garbuglia
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani (IRCCS), Rome, Italy
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Relich RF, Abbott AN. Syndromic and Point-of-Care Molecular Testing. Clin Lab Med 2022; 42:507-531. [PMID: 36368779 DOI: 10.1016/j.cll.2022.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ryan F Relich
- Division of Clinical Microbiology, Indiana University Health Pathology Laboratory, Indiana University Health and Indiana University School of Medicine, Suite 6027E, 350 West 11th Street, Indianapolis, IN 46202, USA.
| | - April N Abbott
- Department of Laboratory Medicine, Deaconess Hospital, 600 Mary Street, Evansville, IN 47747, USA
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Bentahir M, Barry MD, Koulemou K, Gala JL. Providing On-Site Laboratory and Biosafety Just-In-Time Training Inside a Box-Based Laboratory during the West Africa Ebola Outbreak: Supporting Better Preparedness for Future Health Emergencies. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph191811566. [PMID: 36141839 PMCID: PMC9517019 DOI: 10.3390/ijerph191811566] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/09/2022] [Accepted: 09/09/2022] [Indexed: 06/13/2023]
Abstract
The Biological Light Fieldable Laboratory for Emergencies (B-LiFE) is a box-based modular laboratory with the capacity to quickly deploy on-site in cases of uncontrolled spread of infectious disease. During the 2014-2015 West Africa Ebola outbreak, this tent laboratory provided diagnostic support to the N'Zerekore Ebola Treatment Center (ETC), Guinea, for three months. One of the objectives of B-LiFE deployment was to contribute, as much as possible, to national capacity building by training local scientists. Two Guinean biologists were selected according to their basic biological knowledge and laboratory skills among 50 candidate trainees, and were integrated into the team through "just-in-time training" (JiTT), which helped the biologists acquire knowledge and laboratory skills beyond their expertise. The JiTT program was conducted according to standard laboratory procedures, in line with international biosafety guidelines adapted to field conditions. Supervised acquisition of field-laboratory practices mainly focused on biochemical testing and Ebola viral load quantification using routine PCR-based detection, including the Biofire FilmArray® system (BFA), a novel, as yet non-validated, automated assay for diagnostic testing of Ebola virus disease at the time of B-LiFE deployment. During the JiTT, the two biologists were closely involved in all laboratory activities, including BFA validation and biosafety procedures. Meanwhile, this successful JiTT enhanced the B-LiFE in-field operational capacity and contributed to national capacity building. A post-training evaluation and contacts were organised to assess the evolution and technical skills gained by the two researchers during the B-LiFE mission. At the end of the B-LiFE mission, both biologists were enrolled in follow-on programmes to curb the epidemic spreading in Africa. These results demonstrate that during infectious disease outbreaks or major crises, the JiTT approach can rapidly expand access to critical diagnostic testing and train local staff to do so.
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Affiliation(s)
- Mostafa Bentahir
- Centre for Applied Molecular Technologies (CTMA), Institute of Clinical and Experimental Research, Université Catholique de Louvain, Avenue Hippocrate 54-55, B1.54.01, B-1200 Brussels, Belgium
| | - Mamadou Diouldé Barry
- Laboratoire des Fièvres Hémorragiques Virales de Guinée, N’Zérékoré P.O. Box 50, Guinea
| | - Kekoura Koulemou
- Laboratory of the Prefectural Hospital of Gueckedou, Gueckedou P.O. Box 82, Guinea
| | - Jean-Luc Gala
- Centre for Applied Molecular Technologies (CTMA), Institute of Clinical and Experimental Research, Université Catholique de Louvain, Avenue Hippocrate 54-55, B1.54.01, B-1200 Brussels, Belgium
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Manabe YC, Betz J, Jackson O, Asoala V, Bazan I, Blair PW, Chang A, Chusri S, Crump JA, Edgel KA, Faix DJ, Fernandez S, Fox AT, Garcia JA, Grogl M, Hansen EA, Heang V, House SL, Jongsakul K, Kaburise MB, Klungthong C, Lamorde M, Letizia AG, Lorenzana I, Luy M, Maro VP, Mores CN, Myers CA, Oduro AR, Parham L, Porzucek AJ, Prouty M, Rabiger DS, Rubach MP, Siles C, Silva M, Ukachu C, Waitumbi JN, Phillips CL, Jones BW. Clinical evaluation of the BioFire Global Fever Panel for the identification of malaria, leptospirosis, chikungunya, and dengue from whole blood: a prospective, multicentre, cross-sectional diagnostic accuracy study. THE LANCET. INFECTIOUS DISEASES 2022; 22:1356-1364. [PMID: 35716700 PMCID: PMC9420791 DOI: 10.1016/s1473-3099(22)00290-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/27/2022] [Accepted: 04/12/2022] [Indexed: 12/29/2022]
Abstract
BACKGROUND Acute febrile illness is a common presentation for patients at hospitals globally. Assays that can diagnose a variety of common pathogens in blood could help to establish a diagnosis for targeted disease management. We aimed to evaluate the performance of the BioFire Global Fever Panel (GF Panel), a multiplex nucleic acid amplification test performed on whole blood specimens run on the BioFire FilmArray System, in the diagnosis of several pathogens that cause acute febrile illness. METHODS We did a prospective, multicentre, cross-sectional diagnostic accuracy study to evaluate the GF Panel. Consenting adults and children older than 6 months presenting with fever in the previous 2 days were enrolled consecutively in sub-Saharan Africa (Ghana, Kenya, Tanzania, Uganda), southeast Asia (Cambodia, Thailand), central and South America (Honduras, Peru), and the USA (Washington, DC; St Louis, MO). We assessed the performance of six analytes (chikungunya virus, dengue virus [serotypes 1-4], Leptospira spp, Plasmodium spp, Plasmodium falciparum, and Plasmodium vivax or Plasmodium ovale) on the GF Panel. The performance of the GF Panel was assessed using comparator PCR assays with different primers followed by bidirectional sequencing on nucleic acid extracts from the same specimen. We calculated the positive percent agreement and negative percent agreement of the GF Panel with respect to the comparator assays. This study is registered with ClinicalTrials.gov, NCT02968355. FINDINGS From March 26, 2018, to Sept 30, 2019, 1965 participants were enrolled at ten sites worldwide. Of the 1875 participants with analysable results, 980 (52·3%) were female and the median age was 22 years (range 0-100). At least one analyte was detected in 657 (35·0%) of 1875 specimens. The GF Panel had a positive percent agreement for the six analytes evaluated as follows: chikungunya virus 100% (95% CI 86·3-100), dengue virus 94·0% (90·6-96·5), Leptospira spp 93·8% (69·8-99·8), Plasmodium spp 98·3% (96·3-99·4), P falciparum 92·7% (88·8-95·6), and P vivax or P ovale 92·7% (86·7-96·6). The GF Panel had a negative percent agreement equal to or greater than 99·2% (98·6-99·6) for all analytes. INTERPRETATION This 1 h sample-to-answer, molecular device can detect common causative agents of acute febrile illness with excellent positive percent agreement and negative percent agreement directly in whole blood. The targets of the assay are prevalent in tropical and subtropical regions globally, and the assay could help to provide both public health surveillance and individual diagnoses. FUNDING BioFire Defense, Joint Project Manager for Medical Countermeasure Systems and US Army Medical Materiel Development Activity, and National Institute of Allergy and Infectious Diseases.
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Affiliation(s)
- Yukari C Manabe
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Infectious Diseases Institute, Makerere University College of Health Sciences, Kampala, Uganda.
| | - Joshua Betz
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | | - Victor Asoala
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
| | - Isabel Bazan
- Virology and Emerging Infections Department, US Naval Medical Research Unit Six, Lima, Peru
| | - Paul W Blair
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Aileen Chang
- Department of Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC, USA
| | - Sarunyou Chusri
- Faculty of Medicine, Prince of Songkhla University, Songkhla, Thailand
| | - John A Crump
- Division of Infectious Diseases & International Health, Department of Medicine, Duke University, Durham, NC, USA; Centre for International Health, University of Otago, Dunedin, New Zealand
| | | | - Dennis J Faix
- US Naval Medical Research Unit Two, Phnom Penh, Cambodia
| | - Stefan Fernandez
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Anne T Fox
- US Naval Medical Research Unit Three, Ghana Detachment, Accra, Ghana
| | - Jose A Garcia
- US Naval Medical Research Unit Two, Phnom Penh, Cambodia
| | - Max Grogl
- Virology and Emerging Infections Department, US Naval Medical Research Unit Six, Lima, Peru
| | - Erin A Hansen
- Operational Infectious Diseases, Naval Health Research Center, San Diego, CA, USA
| | - Vireak Heang
- US Naval Medical Research Unit Two, Phnom Penh, Cambodia
| | - Stacey L House
- Washington University School of Medicine, Department of Emergency Medicine, St Louis, MO, USA
| | - Krisada Jongsakul
- Department of Bacterial and Parasitic Diseases, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | | | - Chonticha Klungthong
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Mohammed Lamorde
- Infectious Diseases Institute, Makerere University College of Health Sciences, Kampala, Uganda
| | - Andrew G Letizia
- US Naval Medical Research Unit Three, Ghana Detachment, Accra, Ghana
| | - Ivette Lorenzana
- Universidad Nacional Autónoma de Honduras, Centro de Investigaciones Geneticas, Instituto de Investigacion en Microdbiologia, Tegucigalpa, Honduras
| | - Malen Luy
- US Naval Medical Research Unit Two, Phnom Penh, Cambodia
| | - Vanance P Maro
- Department of Medicine, Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Christopher N Mores
- Virology and Emerging Infections Department, US Naval Medical Research Unit Six, Lima, Peru; Department of Global Health, Milken Institute School of Public Health, George Washington University, Washington, DC, USA
| | - Christopher A Myers
- Operational Infectious Diseases, Naval Health Research Center, San Diego, CA, USA
| | - Abraham R Oduro
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
| | - Leda Parham
- Universidad Nacional Autónoma de Honduras, Centro de Investigaciones Geneticas, Instituto de Investigacion en Microdbiologia, Tegucigalpa, Honduras
| | - Abigail J Porzucek
- Department of Global Health, Milken Institute School of Public Health, George Washington University, Washington, DC, USA
| | - Michael Prouty
- Virology and Emerging Infections Department, US Naval Medical Research Unit Six, Lima, Peru
| | | | - Matthew P Rubach
- Division of Infectious Diseases & International Health, Department of Medicine, Duke University, Durham, NC, USA
| | - Crystyan Siles
- Virology and Emerging Infections Department, US Naval Medical Research Unit Six, Lima, Peru
| | - Maria Silva
- Virology and Emerging Infections Department, US Naval Medical Research Unit Six, Lima, Peru
| | - Chinaka Ukachu
- Operational Infectious Diseases, Naval Health Research Center, San Diego, CA, USA
| | - John N Waitumbi
- US Army Medical Research Directorate-Africa, Kenya Medical Research Institute, Nairobi, Kenya
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Muzembo BA, Kitahara K, Ohno A, Ntontolo NP, Ngatu NR, Okamoto K, Miyoshi SI. Rapid diagnostic tests versus RT-PCR for Ebola virus infections: a systematic review and meta-analysis. Bull World Health Organ 2022; 100:447-458. [PMID: 35813519 PMCID: PMC9243686 DOI: 10.2471/blt.21.287496] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 05/08/2022] [Accepted: 05/16/2022] [Indexed: 11/27/2022] Open
Abstract
Objective To evaluate the clinical accuracy of rapid diagnostic tests for the detection of Ebola virus. Methods We searched MEDLINE®, Embase® and Web of Science for articles published between 1976 and October 2021 reporting on clinical studies assessing the performance of Ebola virus rapid diagnostic tests compared with reverse transcription polymerase chain reaction (RT-PCR). We assessed study quality using the QUADAS-2 criteria. To estimate the pooled sensitivity and specificity of these rapid diagnostic tests, we used a bivariate random-effects meta-analysis. Findings Our search identified 113 unique studies, of which nine met the inclusion criteria. The studies were conducted in the Democratic Republic of the Congo, Guinea, Liberia and Sierra Leone and they evaluated 12 rapid diagnostic tests. We included eight studies in the meta-analysis. The pooled sensitivity and specificity of the rapid tests were 86% (95% confidence interval, CI: 80-91) and 95% (95% CI: 91-97), respectively. However, pooled sensitivity decreased to 83% (95% CI: 77-88) after removing outliers. Pooled sensitivity increased to 90% (95% CI: 82-94) when analysis was restricted to studies using the RT-PCR from altona Diagnostics as gold standard. Pooled sensitivity increased to 99% (95% CI: 67-100) when the analysis was restricted to studies using whole or capillary blood specimens. Conclusion The included rapid diagnostic tests did not detect all the Ebola virus disease cases. While the sensitivity and specificity of these tests are moderate, they are still valuable tools, especially useful for triage and detecting Ebola virus in remote areas.
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Affiliation(s)
- Basilua Andre Muzembo
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1 Tsushimanaka, Kita Ward, Okayama, 700-8530, Japan
| | - Kei Kitahara
- Collaborative Research Center of Okayama University for Infectious Diseases in India, Kolkata, India
| | - Ayumu Ohno
- Collaborative Research Center of Okayama University for Infectious Diseases in India, Kolkata, India
| | | | - Nlandu Roger Ngatu
- Department of Public Health, Kagawa University Faculty of Medicine, Miki, Japan
| | - Keinosuke Okamoto
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1 Tsushimanaka, Kita Ward, Okayama, 700-8530, Japan
| | - Shin-Ichi Miyoshi
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1 Tsushimanaka, Kita Ward, Okayama, 700-8530, Japan
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Roth S, Thurner L, Becker SL. Application of the FilmArray® BioThreat Panel for molecular diagnosis of human tularemia. Ticks Tick Borne Dis 2021; 12:101792. [PMID: 34330678 DOI: 10.1016/j.ttbdis.2021.101792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/04/2021] [Accepted: 07/09/2021] [Indexed: 11/25/2022]
Affiliation(s)
- Sophie Roth
- Institute of Medical Microbiology and Hygiene, Saarland University, Homburg/Saar, Germany
| | - Lorenz Thurner
- Department of Hematology, Oncology, Clinical Immunology, Rheumatology, Saarland University, Homburg, Germany
| | - Sören L Becker
- Institute of Medical Microbiology and Hygiene, Saarland University, Homburg/Saar, Germany; Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland.
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Barbieri R, Signoli M, Chevé D, Costedoat C, Tzortzis S, Aboudharam G, Raoult D, Drancourt M. Yersinia pestis: the Natural History of Plague. Clin Microbiol Rev 2020; 34:e00044-19. [PMID: 33298527 PMCID: PMC7920731 DOI: 10.1128/cmr.00044-19] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The Gram-negative bacterium Yersinia pestis is responsible for deadly plague, a zoonotic disease established in stable foci in the Americas, Africa, and Eurasia. Its persistence in the environment relies on the subtle balance between Y. pestis-contaminated soils, burrowing and nonburrowing mammals exhibiting variable degrees of plague susceptibility, and their associated fleas. Transmission from one host to another relies mainly on infected flea bites, inducing typical painful, enlarged lymph nodes referred to as buboes, followed by septicemic dissemination of the pathogen. In contrast, droplet inhalation after close contact with infected mammals induces primary pneumonic plague. Finally, the rarely reported consumption of contaminated raw meat causes pharyngeal and gastrointestinal plague. Point-of-care diagnosis, early antibiotic treatment, and confinement measures contribute to outbreak control despite residual mortality. Mandatory primary prevention relies on the active surveillance of established plague foci and ectoparasite control. Plague is acknowledged to have infected human populations for at least 5,000 years in Eurasia. Y. pestis genomes recovered from affected archaeological sites have suggested clonal evolution from a common ancestor shared with the closely related enteric pathogen Yersinia pseudotuberculosis and have indicated that ymt gene acquisition during the Bronze Age conferred Y. pestis with ectoparasite transmissibility while maintaining its enteric transmissibility. Three historic pandemics, starting in 541 AD and continuing until today, have been described. At present, the third pandemic has become largely quiescent, with hundreds of human cases being reported mainly in a few impoverished African countries, where zoonotic plague is mostly transmitted to people by rodent-associated flea bites.
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Affiliation(s)
- R Barbieri
- Aix-Marseille University, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- Aix-Marseille University, CNRS, EFS, ADES, Marseille, France
- Fondation Méditerranée Infection, Marseille, France
| | - M Signoli
- Aix-Marseille University, CNRS, EFS, ADES, Marseille, France
| | - D Chevé
- Aix-Marseille University, CNRS, EFS, ADES, Marseille, France
| | - C Costedoat
- Aix-Marseille University, CNRS, EFS, ADES, Marseille, France
| | - S Tzortzis
- Ministère de la Culture, Direction Régionale des Affaires Culturelles de Provence-Alpes-Côte d'Azur, Service Régional de l'Archéologie, Aix-en-Provence, France
| | - G Aboudharam
- Aix-Marseille University, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- Aix-Marseille University, Faculty of Odontology, Marseille, France
| | - D Raoult
- Aix-Marseille University, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- Fondation Méditerranée Infection, Marseille, France
| | - M Drancourt
- Aix-Marseille University, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- Fondation Méditerranée Infection, Marseille, France
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Emperador DM, Mazzola LT, Kelly-Cirino C. An open-source molecular diagnostic platform approach for outbreak and epidemic preparedness. Afr J Lab Med 2020; 9:1017. [PMID: 33102172 PMCID: PMC7564747 DOI: 10.4102/ajlm.v9i2.1017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 07/08/2020] [Indexed: 12/11/2022] Open
Abstract
Background Diagnostic development for outbreak pathogens has typically followed a disease-specific reactive rather than proactive response. Given the diversity of outbreak pathogens, particularly those prioritised by the World Health Organization Research and Development Blueprint, a more flexible and proactive approach to epidemic preparedness is needed to expand access to critical molecular diagnostic tests in peripheral and resource-constrained deployment settings. Objective New and more sustainable directives are needed to spur the development of high-quality products, particularly for epidemics more often found in low- and middle-income countries. To leverage and de-risk the development process, we present the benefits and challenges of an open-source business model for co-development of molecular diagnostic tests for decentralised settings. Methods We identify key outbreak pathogens that are available only for testing in high infrastructure laboratories and compare in-country installed base platforms that could be leveraged for menu expansion. Key strengths and challenges for development are highlighted for both platform and assay developers, with discussion of how to leverage and de-risk the process through an open-source development model. Results Depending on the specific partner strengths, options for partnership roles are presented. The proposed open-source business model addresses the particular challenges in the detection of outbreak- and epidemic-prone pathogens in low- and middle-income countries, reduces development and deployment risks to support outbreak response, strengthens diagnostic capacity and creates a viable market for product developers. Conclusion We hope this model for a collaborative and open-source approach for molecular diagnostics serves to encourage stakeholders to consider co-development partnerships to improve outbreak preparedness and epidemic/pandemic response.
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Affiliation(s)
- Devy M Emperador
- Foundation for Innovative and New Diagnostics, Geneva, Switzerland
| | - Laura T Mazzola
- Foundation for Innovative and New Diagnostics, San Francisco, California, United States
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Zhu H, Zhang H, Ni S, Korabečná M, Yobas L, Neuzil P. The vision of point-of-care PCR tests for the COVID-19 pandemic and beyond. Trends Analyt Chem 2020; 130:115984. [PMID: 32834243 PMCID: PMC7369599 DOI: 10.1016/j.trac.2020.115984] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Infectious diseases, such as the most recent case of coronavirus disease 2019, have brought the prospect of point-of-care (POC) diagnostic tests into the spotlight. A rapid, accurate, low-cost, and easy-to-use test in the field could stop epidemics before they develop into full-blown pandemics. Unfortunately, despite all the advances, it still does not exist. Here, we critically review the limited number of prototypes demonstrated to date that is based on a polymerase chain reaction (PCR) and has come close to fulfill this vision. We summarize the requirements for the POC-PCR tests and then go on to discuss the PCR product-detection methods, the integration of their functional components, the potential applications, and other practical issues related to the implementation of lab-on-a-chip technologies. We conclude our review with a discussion of the latest findings on nucleic acid-based diagnosis.
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Affiliation(s)
- Hanliang Zhu
- Department of Microsystem Engineering, School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, 710072 Shaanxi, PR China
| | - Haoqing Zhang
- Department of Microsystem Engineering, School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, 710072 Shaanxi, PR China
| | - Sheng Ni
- Department of Electronic and Computer Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, S.A.R., PR China
| | - Marie Korabečná
- Institute of Biology and Medical Genetics, 1st Faculty of Medicine, Charles University and General University Hospital in Prague, Albertov 4, Prague 2, Czech Republic
| | - Levent Yobas
- Department of Electronic and Computer Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, S.A.R., PR China,Corresponding author
| | - Pavel Neuzil
- Department of Microsystem Engineering, School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, 710072 Shaanxi, PR China,CEITEC Brno University of Technology, Purkyňova 123, 612 00 Brno, Czech Republic,Faculty of Electrical Engineering and Communications, Brno University of Technology, Technická 3058/10, 616 00 Brno, Czech Republic,Corresponding author. Department of Microsystem Engineering, School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, 710072 Shaanxi, PR China
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12
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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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Wang YM, Trinh MP, Zheng Y, Guo K, Jimenez LA, Zhong W. Analysis of circulating non-coding RNAs in a non-invasive and cost-effective manner. Trends Analyt Chem 2019; 117:242-262. [PMID: 32292220 PMCID: PMC7156030 DOI: 10.1016/j.trac.2019.07.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Non-coding RNAs (ncRNAs) participate in regulation of gene expression, and are highly relevant to pathological development. They are found to be stably present in diverse body fluids, including those in the circulatory system, which can be sampled non-invasively for clinical tests. Thus, circulating ncRNAs have great potential to be disease biomarkers. However, tremendous efforts are desired to discover and utilize ncRNAs as biomarkers in clinical diagnosis, calling for technological advancement in analysis of circulating ncRNAs in biospecimens. Hence, this review summarizes the recent developments in this area, highlighting the works devoted to cancer diagnosis and prognosis. Three main directions are focused: 1) Extraction and purification of ncRNAs from body fluids; 2) Quantification of the purified circulating ncRNAs; and 3) Microfluidic platforms for integration of both steps to enable point-of-care diagnostics. These technologies have laid a solid foundation to move forward the applications of circulating ncRNAs in disease diagnosis and cure.
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Affiliation(s)
- Yu-Min Wang
- Department of Chemistry, University of California at Riverside, Riverside, California 92521, United States
- Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, School of Chemistry and Environment, South China Normal University, Guangzhou, Guangdong 510006, P. R. China
| | - Michael Patrick Trinh
- Department of Chemistry, University of California at Riverside, Riverside, California 92521, United States
| | - Yongzan Zheng
- Department of Chemistry, University of California at Riverside, Riverside, California 92521, United States
| | - Kaizhu Guo
- Department of Chemistry, University of California at Riverside, Riverside, California 92521, United States
| | - Luis A. Jimenez
- Program in Biomedical Sciences, University of California at Riverside, Riverside, California 92521, United States
| | - Wenwan Zhong
- Department of Chemistry, University of California at Riverside, Riverside, California 92521, United States
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Deshpande SV, Reed TM, Sullivan RF, Kerkhof LJ, Beigel KM, Wade MM. Offline Next Generation Metagenomics Sequence Analysis Using MinION Detection Software (MINDS). Genes (Basel) 2019; 10:genes10080578. [PMID: 31366182 PMCID: PMC6723491 DOI: 10.3390/genes10080578] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 07/25/2019] [Accepted: 07/25/2019] [Indexed: 12/14/2022] Open
Abstract
Field laboratories interested in using the MinION often need the internet to perform sample analysis. Thus, the lack of internet connectivity in resource-limited or remote locations renders downstream analysis problematic, resulting in a lack of sample identification in the field. Due to this dependency, field samples are generally transported back to the lab for analysis where internet availability for downstream analysis is available. These logistics problems and the time lost in sample characterization and identification, pose a significant problem for field scientists. To address this limitation, we have developed a stand-alone data analysis packet using open source tools developed by the Nanopore community that does not depend on internet availability. Like Oxford Nanopore Technologies’ (ONT) cloud-based What’s In My Pot (WIMP) software, we developed the offline MinION Detection Software (MINDS) based on the Centrifuge classification engine for rapid species identification. Several online bioinformatics applications have been developed surrounding ONT’s framework for analysis of long reads. We have developed and evaluated an offline real time classification application pipeline using open source tools developed by the Nanopore community that does not depend on internet availability. Our application has been tested on ATCC’s 20 strain even mix whole cell (ATCC MSA-2002) sample. Using the Rapid Sequencing Kit (SQK-RAD004), we were able to identify all 20 organisms at species level. The analysis was performed in 15 min using a Dell Precision 7720 laptop. Our offline downstream bioinformatics application provides a cost-effective option as well as quick turn-around time when analyzing samples in the field, thus enabling researchers to fully utilize ONT’s MinION portability, ease-of-use, and identification capability in remote locations.
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Affiliation(s)
- Samir V Deshpande
- Science and Technology Corporation, 111 Bata Blvd, Suite C, Belcamp, MD 21017, USA
| | - Timothy M Reed
- US Army, 20th CBRNE, Aberdeen Proving Ground, MD 21010, USA
| | - Raymond F Sullivan
- US Army, CCDC-Chemical Biological Center, Aberdeen Proving Ground, MD 21010, USA
| | - Lee J Kerkhof
- Department of Marine and Coastal Sciences, Rutgers University, 71 Dudley Rd, New Brunswick, NJ 08901-8521, USA
| | - Keith M Beigel
- US Army, 20th CBRNE, Aberdeen Proving Ground, MD 21010, USA.
| | - Mary M Wade
- US Army, CCDC-Chemical Biological Center, Aberdeen Proving Ground, MD 21010, USA.
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Trotter AJ, Aydin A, Strinden MJ, O'Grady J. Recent and emerging technologies for the rapid diagnosis of infection and antimicrobial resistance. Curr Opin Microbiol 2019; 51:39-45. [PMID: 31077935 DOI: 10.1016/j.mib.2019.03.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 02/04/2019] [Accepted: 03/08/2019] [Indexed: 10/26/2022]
Abstract
The rise in antimicrobial resistance (AMR) is predicted to cause 10 million deaths per year by 2050 unless steps are taken to prevent this looming crisis. Microbiological culture is the gold standard for the diagnosis of bacterial/fungal pathogens and antimicrobial resistance and takes 48 hours or longer. Hence, antibiotic prescriptions are rarely based on a definitive diagnosis and patients often receive inappropriate treatment. Rapid diagnostic tools are urgently required to guide appropriate antimicrobial therapy, thereby improving patient outcomes and slowing AMR development. We discuss new technologies for rapid infection diagnosis including: sample-in-answer-out PCR-based tests, BioFire FilmArray and Curetis Unyvero; rapid susceptibility tests, Accelerate Pheno and microfluidic tests; and sequencing-based approaches, focusing on targeted and clinical metagenomic nanopore sequencing.
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Affiliation(s)
- Alexander J Trotter
- University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK; Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
| | - Alp Aydin
- University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK; Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
| | - Michael J Strinden
- University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK; Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
| | - Justin O'Grady
- University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK; Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK.
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16
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Colón-López DD, Stefan CP, Koehler JW. Emerging viral infections. GENOMIC AND PRECISION MEDICINE 2019. [PMCID: PMC7150306 DOI: 10.1016/b978-0-12-801496-7.00010-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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17
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Kost GJ. Molecular and point-of-care diagnostics for Ebola and new threats: National POCT policy and guidelines will stop epidemics. Expert Rev Mol Diagn 2018; 18:657-673. [DOI: 10.1080/14737159.2018.1491793] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Gerald J. Kost
- Point-of-Care Center for Teaching and Research (POCT•CTRTM), School of Medicine, UC Davis, and Knowledge Optimization®, Davis, CA
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18
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Xiong Y, McQuistan TJ, Stanek JW, Summerton JE, Mata JE, Squier TC. Detection of unique Ebola virus oligonucleotides using fluorescently-labeled phosphorodiamidate morpholino oligonucleotide probe pairs. Anal Biochem 2018; 557:84-90. [PMID: 30030994 DOI: 10.1016/j.ab.2018.07.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 07/12/2018] [Indexed: 12/22/2022]
Abstract
Here we identify a low-cost diagnostic platform using fluorescently-labeled phosphorodiamidate morpholino oligonucleotide (PMO) probe pairs, which upon binding target oligonucleotides undergo fluorescence resonance energy transfer (FRET). Using a target oligonucleotide derived from the Ebola virus (EBOV), we have derivatized PMO probes with either Alexa Fluor488 (donor) or tetramethylrhodamine (acceptor). Upon EBOV target oligonulceotide binding, observed changes in FRET between PMO probe pairs permit a 25 pM lower limit of detection; there is no off-target binding within a complex mixture of nucleic acids and other biomolecules present in human saliva. Equivalent levels of FRET occur using PMO probe pairs for single or double stranded oligonucleotide targets. High-affinity binding is retained under low-ionic strength conditions that disrupt oligonucleotide secondary structures (e.g., stem-loop structures), ensuring reliable target detection. Under these low-ionic strength conditions, rates of PMO probe binding to target oligonucleotides are increased 3-fold relative to conventional high-ionic strength conditions used for nucleic acid hybridization, with half-maximal binding occurring within 10 min. Our results indicate an ability to use PMO probe pairs to detect clinically relevant levels of EBOV and other oligonucleotide targets in complex biological samples without the need for nucleic acid amplification, and open the possibility of population screening that includes assays for the genomic integration of DNA based copies of viral RNA.
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Affiliation(s)
- Yijia Xiong
- Department of Basic Medical Sciences, Western University of Health Sciences, 200 Mullins Drive, Lebanon, OR, 97355, United States
| | - Tammie J McQuistan
- Department of Basic Medical Sciences, Western University of Health Sciences, 200 Mullins Drive, Lebanon, OR, 97355, United States
| | - James W Stanek
- Department of Basic Medical Sciences, Western University of Health Sciences, 200 Mullins Drive, Lebanon, OR, 97355, United States
| | - James E Summerton
- Gene Tools, LLC, One Summerton Way, Philomath, OR, 97370, United States
| | - John E Mata
- Department of Basic Medical Sciences, Western University of Health Sciences, 200 Mullins Drive, Lebanon, OR, 97355, United States; Takena Technologies Inc, 405 West First Street, Albany, OR, 97321, United States
| | - Thomas C Squier
- Department of Basic Medical Sciences, Western University of Health Sciences, 200 Mullins Drive, Lebanon, OR, 97355, United States.
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Frequency of Instrument, Environment, and Laboratory Technologist Contamination during Routine Diagnostic Testing of Infectious Specimens. J Clin Microbiol 2018; 56:JCM.00225-18. [PMID: 29563204 DOI: 10.1128/jcm.00225-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 03/14/2018] [Indexed: 02/03/2023] Open
Abstract
Laboratory testing to support the care of patients with highly infectious diseases may pose a risk for laboratory workers. However, data on the risk of virus transmission during routine laboratory testing conducted using standard personal protective equipment (PPE) are sparse. Our objective was to measure laboratory contamination during routine analysis of patient specimens. Remnant specimens were spiked with the nonpathogenic bacteriophage MS2 at 1.0 × 107 PFU/ml, and contamination was assessed using reverse transcriptase PCR (RT-PCR) for MS2. Specimen containers were exteriorly coated with a fluorescent powder to enable the visualization of gross contamination using UV light. Testing was performed by two experienced laboratory technologists using standard laboratory PPE and sample-to-answer instrumentation. Fluorescence was noted on the gloves, bare hands, and laboratory coat cuffs of the laboratory technologist in 36/36 (100%), 13/36 (36%), and 4/36 (11%) tests performed, respectively. Fluorescence was observed in the biosafety cabinet (BSC) in 8/36 (22%) tests, on test cartridges/devices in 14/32 (44%) tests, and on testing accessory items in 29/32 (91%) tests. Fluorescence was not observed on or in laboratory instrumentation or adjacent surfaces. In contrast to fluorescence detection, MS2 detection was infrequent (3/286 instances [1%]) and occurred during test setup for the FilmArray instrument and on FilmArray accessory equipment. The information from this study may provide opportunities for the improvement of clinical laboratory safety practices so as to reduce the risk of pathogen transmission to laboratory workers.
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20
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Clark DJ, Tyson J, Sails AD, Krishna S, Staines HM. The current landscape of nucleic acid tests for filovirus detection. J Clin Virol 2018; 103:27-36. [PMID: 29625392 PMCID: PMC5958242 DOI: 10.1016/j.jcv.2018.03.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 03/14/2018] [Indexed: 11/03/2022]
Abstract
Filoviruses can cause severe hemorrhagic fever in humans and non-human primates. There is an urgent need for rapid diagnosis of filoviruses during outbreaks. Filovirus diagnostics have advanced since the 2014–2016 Ebolavirus outbreak. NATs are the gold standard for filovirus detection. NAT-based diagnostic speed, portability and multiplexing have all improved.
Nucleic acid testing (NAT) for pathogenic filoviruses plays a key role in surveillance and to control the spread of infection. As they share clinical features with other pathogens, the initial spread of these viruses can be misdiagnosed. Tests that can identify a pathogen in the initial stages of infection are essential to control outbreaks. Since the Ebola virus disease (EVD) outbreak in 2014–2016 several tests have been developed that are faster than previous tests and more suited for field use. Furthermore, the ability to test for a range of pathogens simultaneously has been expanded to improve clinical pathway management of febrile syndromes. This review provides an overview of these novel diagnostic tests.
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Affiliation(s)
- David J Clark
- Centre for Diagnostics & Antimicrobial Resistance, Institute for Infection & Immunity, St. George's University of London, Cranmer Terrace, London SW17 0RE, UK; Institute for Infection & Immunity, St. George's University of London, Cranmer Terrace, London SW17 0RE, UK.
| | - John Tyson
- QuantuMDx, Lugano Building, 57 Melbourne Street, Newcastle-upon-Tyne, NE1 2JQ, UK
| | - Andrew D Sails
- QuantuMDx, Lugano Building, 57 Melbourne Street, Newcastle-upon-Tyne, NE1 2JQ, UK
| | - Sanjeev Krishna
- Centre for Diagnostics & Antimicrobial Resistance, Institute for Infection & Immunity, St. George's University of London, Cranmer Terrace, London SW17 0RE, UK; Institute for Infection & Immunity, St. George's University of London, Cranmer Terrace, London SW17 0RE, UK; St. George's University Hospitals NHS Foundation Trust, Blackshaw Road, Tooting, London SW17 0QT, UK
| | - Henry M Staines
- Centre for Diagnostics & Antimicrobial Resistance, Institute for Infection & Immunity, St. George's University of London, Cranmer Terrace, London SW17 0RE, UK; Institute for Infection & Immunity, St. George's University of London, Cranmer Terrace, London SW17 0RE, UK
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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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