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https://www.readbyqxmd.com/read/29136087/the-utility-and-perspectives-of-ngs-based-methods-in-bsl-3-and-bsl-4-laboratory-sequencing-and-analysis-strategies
#1
Tomasz Wolkowicz
Modern diagnostics is in general based on molecular biology methods. Nowadays sequencing-based methods, especially whole genome sequencing, are becoming increasingly important. Implementation of such methods into routine diagnostic of highly dangerous pathogens, like Bacillus anthracis, Francisella tularensis, Yersinia pestis, Ebola virus, MERS, Lassa virus etc. would be very helpful. The best diagnostic strategy would be the metagenomic sequencing directly from the clinical sample. Implementation of majority of currently available WGS platforms inside the BSL-3 or 4 laboratory is impractical because of the size of the equipment and time consuming wet lab part (e...
November 10, 2017: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/29129921/towards-a-genomics-informed-real-time-global-pathogen-surveillance-system
#2
REVIEW
Jennifer L Gardy, Nicholas J Loman
The recent Ebola and Zika epidemics demonstrate the need for the continuous surveillance, rapid diagnosis and real-time tracking of emerging infectious diseases. Fast, affordable sequencing of pathogen genomes - now a staple of the public health microbiology laboratory in well-resourced settings - can affect each of these areas. Coupling genomic diagnostics and epidemiology to innovative digital disease detection platforms raises the possibility of an open, global, digital pathogen surveillance system. When informed by a One Health approach, in which human, animal and environmental health are considered together, such a genomics-based system has profound potential to improve public health in settings lacking robust laboratory capacity...
November 13, 2017: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/29107122/ebola-ag-k-set-rapid-test-field-evaluation-in-sierra-leone
#3
Francesca Colavita, Mirella Biava, Pascal Mertens, Quentin Gilleman, Céline Borlon, Michela Delli Guanti, Antonio Petrocelli, Gianluca Cataldi, Alhaji T Kamara, Santige A Kamara, Kelfala Konneh, Donatella Vincenti, Concetta Castilletti, Samir Abdurahman, Ali Mirazimi, Maria Rosaria Capobianchi, Giuseppe Ippolito, Rossella Miccio, Antonino Di Caro
OBJECTIVES: Efficient interruption of Ebola virus disease (EVD) transmission chains critically depends on reliable and fast laboratory diagnosis. We evaluated the performance of the EBOLA Virus Antigen Detection K-SeT (EBOLA Ag K-SeT), a new rapid diagnostic antigen test (RDT)in field settings. METHODS: The study was conducted in a field laboratory located in Freetown (Sierra Leone) by the Italian National Institute for Infectious Diseases "L. Spallanzani" and EMERGENCY Onlus NGO...
October 26, 2017: Clinical Microbiology and Infection
https://www.readbyqxmd.com/read/29047428/symptom-and-laboratory-based-ebola-risk-scores-to-differentiate-likely-ebola-infections
#4
Shefali Oza, Alieu A Sesay, Neal J Russell, Kevin Wing, Sabah Boufkhed, Lahai Vandi, Sahr C Sebba, Rachael Cummings, Francesco Checchi
Rapidly identifying likely Ebola patients is difficult because of a broad case definition, overlap of symptoms with common illnesses, and lack of rapid diagnostics. However, rapid identification is critical for care and containment of contagion. We analyzed retrospective data from 252 Ebola-positive and 172 Ebola-negative patients at a Sierra Leone Ebola treatment center to develop easy-to-use risk scores, based on symptoms and laboratory tests (if available), to stratify triaged patients by their likelihood of having Ebola infection...
November 2017: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/29031848/local-national-and-regional-viral-haemorrhagic-fever-pandemic-potential-in-africa-a-multistage-analysis
#5
David M Pigott, Aniruddha Deshpande, Ian Letourneau, Chloe Morozoff, Robert C Reiner, Moritz U G Kraemer, Shannon E Brent, Isaac I Bogoch, Kamran Khan, Molly H Biehl, Roy Burstein, Lucas Earl, Nancy Fullman, Jane P Messina, Adrian Q N Mylne, Catherine L Moyes, Freya M Shearer, Samir Bhatt, Oliver J Brady, Peter W Gething, Daniel J Weiss, Andrew J Tatem, Luke Caley, Tom De Groeve, Luca Vernaccini, Nick Golding, Peter Horby, Jens H Kuhn, Sandra J Laney, Edmond Ng, Peter Piot, Osman Sankoh, Christopher J L Murray, Simon I Hay
BACKGROUND: Predicting when and where pathogens will emerge is difficult, yet, as shown by the recent Ebola and Zika epidemics, effective and timely responses are key. It is therefore crucial to transition from reactive to proactive responses for these pathogens. To better identify priorities for outbreak mitigation and prevention, we developed a cohesive framework combining disparate methods and data sources, and assessed subnational pandemic potential for four viral haemorrhagic fevers in Africa, Crimean-Congo haemorrhagic fever, Ebola virus disease, Lassa fever, and Marburg virus disease...
October 11, 2017: Lancet
https://www.readbyqxmd.com/read/29029148/the-crux-of-ebola-diagnostics
#6
James E Strong, Heinz Feldmann
No abstract text is available yet for this article.
September 23, 2017: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/29026397/role-of-contact-tracing-in-containing-the-2014-ebola-outbreak-a-review
#7
Shrivastava Saurabh, Shrivastava Prateek
BACKGROUND: The 2014 outbreak of Ebola virus disease which emerged in the month of March in the year 2014 in Guinea has been declared as a public health emergency of international concern. OBJECTIVES: The objectives of the review article are to assess the role of contact tracing in the Ebola outbreak and to identify the challenges faced by the health workers while performing contact tracing. METHODS: An extensive search of all materials related to the Ebola outbreak and contact tracing was carried out in PubMed, Medline, World Health Organization website and Google Scholar search engines...
March 2017: African Health Sciences
https://www.readbyqxmd.com/read/29024445/a-rapid-bio-optical-sensor-for-diagnosing-q-fever-in-clinical-specimens
#8
Bonhan Koo, Choong Eun Jin, Se Yoon Park, Tae Yoon Lee, Jeonghun Nam, Young-Rock Jang, Sun Mi Kim, Ji Yeun Kim, Sung-Han Kim, Yong Shin
Recent zoonotic outbreaks, such as Zika, Middle East Respiratory Syndrome, and Ebola, have highlighted the need for rapid and accurate diagnostic assays that can be used to aid pathogen control. Q-fever is a zoonotic disease caused by the transmission of Coxiella burnetii that can cause serious illness in humans via aerosols and is considered a potential bioterrorism agent. However the existing assays are not suitable for the detection of this pathogen due to its low levels in real samples. We here describe a rapid bio-optical sensor for the accurate detection of Q fever and validate its clinical utility...
October 10, 2017: Journal of Biophotonics
https://www.readbyqxmd.com/read/28961947/ebola-virus-inactivation-by-detergents-is-annulled-in-serum
#9
Jeroen J A van Kampen, Andrei Tintu, Henk Russcher, Pieter L A Fraaij, Chantal B E M Reusken, Mikel Rijken, Jaap J van Hellemond, Perry J J van Genderen, Rob Koelewijn, Menno D de Jong, Elaine Haddock, Robert J Fischer, Vincent J Munster, Marion P G Koopmans
Background: Treatment of blood samples from hemorrhagic fever virus (HFV)-infected patients with 0.1% detergents has been recommended for virus inactivation and subsequent safe laboratory testing. However, data on virus inactivation by this procedure are lacking. Here we show the effect of this procedure on diagnostic test results and infectious Ebola virus (EBOV) titers. Methods: Serum and whole-blood samples were treated with 0.1% or 1% sodium dodecyl sulfate (SDS) or 0...
October 17, 2017: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/28941617/the-effect-of-a-non-denaturing-detergent-and-a-guanidinium-based-inactivation-agent-on-the-viability-of-ebola-virus-in-mock-clinical-serum-samples
#10
J E Burton, L Easterbrook, J Pitman, D Anderson, S Roddy, D Bailey, R Vipond, C B Bruce, A D Roberts
The 2014 Ebola outbreak in West Africa required the rapid testing of clinical material for the presence of potentially high titre Ebola virus (EBOV). Safe, fast and effective methods for the inactivation of such clinical samples are required so that rapid diagnostic tests including downstream analysis by RT-qPCR or nucleotide sequencing can be carried out. One of the most commonly used guanidinium - based denaturing agents, AVL (Qiagen) has been shown to fully inactivate EBOV once ethanol is added, however this is not compatible with the use of automated nucleic acid extraction systems...
September 20, 2017: Journal of Virological Methods
https://www.readbyqxmd.com/read/28879148/implementation-of-broad-screening-with-ebola-rapid-diagnostic-tests-in-for%C3%A3-cariah-guinea
#11
Frantz Jean Louis, Jennifer Y Huang, Yacouba K Nebie, Lamine Koivogui, Gayatri Jayaraman, Nadine Abiola, Amanda Vansteelandt, Mary C Worrel, Judith Shang, Louise B Murphy, David L Fitter, Barbara J Marston, Lise Martel
BACKGROUND: Laboratory-enhanced surveillance is critical for rapidly detecting the potential re-emergence of Ebola virus disease. Rapid diagnostic tests (RDT) for Ebola antigens could expand diagnostic capacity for Ebola virus disease. OBJECTIVES: The Guinean National Coordination for Ebola Response conducted a pilot implementation to determine the feasibility of broad screening of patients and corpses with the OraQuick(®) Ebola RDT. METHODS: The implementation team developed protocols and trained healthcare workers to screen patients and corpses in Forécariah prefecture, Guinea, from 15 October to 30 November 2015...
2017: African Journal of Laboratory Medicine
https://www.readbyqxmd.com/read/28861524/deep-sequencing-of-rna-from-blood-and-oral-swab-samples-reveals-the-presence-of-nucleic-acid-from-a-number-of-pathogens-in-patients-with-acute-ebola-virus-disease-and-is-consistent-with-bacterial-translocation-across-the-gut
#12
Miles W Carroll, Sam Haldenby, Natasha Y Rickett, Bernadett Pályi, Isabel Garcia-Dorival, Xuan Liu, Gary Barker, Joseph Akoi Bore, Fara Raymond Koundouno, E Diane Williamson, Thomas R Laws, Romy Kerber, Daouda Sissoko, Nóra Magyar, Antonino Di Caro, Mirella Biava, Tom E Fletcher, Armand Sprecher, Lisa F P Ng, Laurent Rénia, N'faly Magassouba, Stephan Günther, Roman Wölfel, Kilian Stoecker, David A Matthews, Julian A Hiscox
In this study, samples from the 2013-2016 West African Ebola virus outbreak from patients in Guinea with Ebola virus disease (EVD) were analyzed to discover and classify what other pathogens were present. Throat swabs were taken from deceased EVD patients, and peripheral blood samples were analyzed that had been taken from patients when they presented at the treatment center with acute illness. High-throughput RNA sequencing (RNA-seq) and bioinformatics were used to identify the potential microorganisms. This approach confirmed Ebola virus (EBOV) in all samples from patients diagnosed as acute positive for the virus by quantitative reverse transcription-PCR in deployed field laboratories...
July 2017: MSphere
https://www.readbyqxmd.com/read/28813542/the-african-cholera-surveillance-network-africhol-consortium-meeting-10-11-june-2015-lom%C3%A3-togo
#13
Aline Munier, Berthe-Marie Njanpop-Lafourcade, Delphine Sauvageot, Raymond B Mhlanga, Léonard Heyerdahl, Johara Nadri, Richard Wood, Issaka Ouedraogo, Alexandre Blake, Laurent Akilimali Mukelenge, Jean-Claude B Anné, Abiba Banla Kere, Lucienne Dempouo, Sakoba Keita, José P M Langa, Issa Makumbi, Elibariki R Mwakapeje, Ian J Njeru, Olubunmi E Ojo, Isaac Phiri, Lorenzo Pezzoli, Bradford D Gessner, Martin Mengel
The fifth annual meeting of the African cholera surveillance network (Africhol) took place on 10-11 June 2015 in Lomé, Togo. Together with international partners, representatives from the 11 member countries -Cameroon, Côte d'Ivoire, Democratic Republic of Congo, Guinea, Kenya, Mozambique, Nigeria, Tanzania, Togo, Uganda, Zimbabwe- and an invited country (Malawi) shared their experience. The meeting featured three sessions: i) cholera surveillance, prevention and control in participating countries, ii) cholera surveillance methodology, such as cholera mapping, cost-effectiveness studies and the issue of overlapping epidemics from different diseases, iii) cholera laboratory diagnostics tools and capacity building...
2017: BMC Proceedings
https://www.readbyqxmd.com/read/28791241/ebola-virus-disease-essential-clinical-knowledge
#14
REVIEW
Mahmoud Tawfik Khalafallah, Omar Ali Aboshady, Shaban Ahmed Moawed, Menna Said Ramadan
Since its initial outbreak in 1976, Ebola virus disease (EVD) has affected thousands of people, causing severe illness with high mortality rates. In the absence of a vaccine or effective specific treatment, as well as the lack of early diagnostic and detective methods, the EVD outbreak has generated a significant worldwide health concern. Insufficient health-care system resources, deficient infection control measures, and the shortage of appropriate personal protective equipment acted as amplifiers of the outbreak extension, especially in poorly resourced and unprepared communities...
July 2017: Avicenna Journal of Medicine
https://www.readbyqxmd.com/read/28732038/analysis-of-patient-data-from-laboratories-during-the-ebola-virus-disease-outbreak-in-liberia-april-2014-to-march-2015
#15
Yuki Furuse, Mosoka Fallah, Hitoshi Oshitani, Ling Kituyi, Nuha Mahmoud, Emmanuel Musa, Alex Gasasira, Tolbert Nyenswah, Bernice Dahn, Luke Bawo
An outbreak of Ebola virus disease (EVD) in Liberia began in March 2014 and ended in January 2016. Epidemiological information on the EVD cases was collected and managed nationally; however, collection and management of the data were challenging at the time because surveillance and reporting systems malfunctioned during the outbreak. EVD diagnostic laboratories, however, were able to register basic demographic and clinical information of patients more systematically. Here we present data on 16,370 laboratory samples that were tested between April 4, 2014 and March 29, 2015...
July 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28726603/clinical-laboratory-values-as-early-indicators-of-ebola-virus-infection-in-nonhuman-primates
#16
Ronald B Reisler, Chenggang Yu, Michael J Donofrio, Travis K Warren, Jay B Wells, Kelly S Stuthman, Nicole L Garza, Sean A Vantongeren, Ginger C Donnelly, Christopher D Kane, Mark G Kortepeter, Sina Bavari, Anthony P Cardile
The Ebola virus (EBOV) outbreak in West Africa during 2013-2016 demonstrated the need to improve Ebola virus disease (EVD) diagnostics and standards of care. This retrospective study compared laboratory values and clinical features of 3 nonhuman primate models of lethal EVD to assess associations with improved survival time. In addition, the study identified laboratory values useful as predictors of survival, surrogates for EBOV viral loads, and triggers for initiation of therapeutic interventions in these nonhuman primate models...
August 2017: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/28665950/mortality-among-pcr-negative-admitted-ebola-suspects-during-the-2014-15-outbreak-in-conakry-guinea-a-retrospective-cohort-study
#17
Brecht Ingelbeen, Elhadj Ibrahima Bah, Tom Decroo, Idrissa Balde, Helena Nordenstedt, Johan van Griensven, Anja De Weggheleire
Non-cases are suspect Ebola Virus Disease (EVD) cases testing negative by EVD RT-PCR after admission to an Ebola Treatment Centre (ETC). Admitting non-cases to an ETC prompts concerns on case- and workload in the ETC, risk for nosocomial EVD infection, and delays in diagnosis and disease-specific treatment. We retrospectively analysed characteristics, outcomes and determinants of death of EVD cases and non-cases admitted to the Conakry ETC in Guinea between 03/2014 and 09/2015. Of the 2362 admitted suspects who underwent full confirmatory PCR testing, 1540 (65...
2017: PloS One
https://www.readbyqxmd.com/read/28628619/south-african-ebola-diagnostic-response-in-sierra-leone-a-modular-high-biosafety-field-laboratory
#18
Janusz T Paweska, Petrus Jansen van Vuren, Gunther H Meier, Chantel le Roux, Ousman S Conteh, Alan Kemp, Cardia Fourie, Prabha Naidoo, Serisha Naicker, Phumza Ohaebosim, Nadia Storm, Orienka Hellferscee, Lisa K Ming Sun, Busisiwe Mogodi, Nishi Prabdial-Sing, Desiree du Plessis, Deidre Greyling, Shayne Loubser, Mark Goosen, Stewart D McCulloch, Terence P Scott, Alexandra Moerdyk, Wesley Dlamini, Kelfala Konneh, Idrissa L Kamara, Dauda Sowa, Samuel Sorie, Brima Kargbo, Shabir A Madhi
BACKGROUND: In August 2014, the National Institute for Communicable Diseases (NICD) in South Africa established a modular high-biosafety field Ebola diagnostic laboratory (SA FEDL) near Freetown, Sierra Leone in response to the rapidly increasing number of Ebola virus disease (EVD) cases. METHODS AND FINDINGS: The SA FEDL operated in the Western Area of Sierra Leone, which remained a "hotspot" of the EVD epidemic for months. The FEDL was the only diagnostic capacity available to respond to the overwhelming demand for rapid EVD laboratory diagnosis for several weeks in the initial stages of the EVD crisis in the capital of Sierra Leone...
June 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28588973/responding-to-ever-changing-epidemiological-dynamics-of-ebola-virus-disease
#19
Yuki Maehira, Yohei Kurosaki, Tomoya Saito, Jiro Yasuda, Masayoshi Tarui, Denis J M Malvy, Tsutomu Takeuchi
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...
November 2016: BMJ Global Health
https://www.readbyqxmd.com/read/28577861/diagnostic-preparedness-for-infectious-disease-outbreaks
#20
Mark D Perkins, Christopher Dye, Manica Balasegaram, Christian Bréchot, Jean-Vivien Mombouli, John-Arne Røttingen, Marcel Tanner, Catharina C Boehme
Diagnostics are crucial in mitigating the effect of disease outbreaks. Because diagnostic development and validation are time consuming, they should be carried out in anticipation of epidemics rather than in response to them. The diagnostic response to the 2014-15 Ebola epidemic, although ultimately effective, was slow and expensive. If a focused mechanism had existed with the technical and financial resources to drive its development ahead of the outbreak, point-of-care Ebola tests supporting a less costly and more mobile response could have been available early on in the diagnosis process...
May 31, 2017: Lancet
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