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Mukadi-Bamuleka D, Nkuba-Ndaye A, Mbala-Kingebeni P, Ahuka-Mundeke S, Muyembe-Tamfum JJ. Impact of Ebola epidemics on the daily operation of existing systems in Eastern Democratic Republic of the Congo: a brief review. J Med Econ 2024; 27:184-192. [PMID: 38240249 DOI: 10.1080/13696998.2024.2305009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 01/10/2024] [Indexed: 01/23/2024]
Abstract
AIMS to provide insights into the recent Ebola virus disease (EVD) outbreaks on different aspects of daily life in the Democratic Republic of the Congo and propose possible solutions. METHODS We collected information regarding the effects of EVD outbreaks on existing systems in the eastern part of the Democratic Republic of the Congo (DRC). We searched the PubMed database using the terms "impact effect Ebola outbreak system", "Management Ebola Poor Resources Settings", "Health Economic Challenges Ebola" and "Economic impact Ebola systems." Only studies focusing on epidemiology, diagnostics, sequencing, vaccination, therapeutics, ecology, work force, governance, healthcare provision and health system, and social, political, and economic aspects were considered. The search included the electronic archives of EVD outbreak reports from government and partners. RESULTS EVD outbreaks negatively impacts the functions of countries. The disruption in activities is proportional to the magnitude of the epidemic and slows down the transport of goods, decreases the region's tourist appeal, and increases 'brain drain'. Most low- and medium-income countries, such as the DRC, do not have a long-term holistic emergency plan for unexpected situations or sufficient resources to adequately implement countermeasures against EVD outbreaks. Although the DRC has acquired sufficient expertise in diagnostics, genomic sequencing, administration of vaccines and therapeutics, clinical trials, and research activities, deployment, operation, and maintenance of these expertise and associated tools remains a concern. LIMITATIONS Despite the data search extension, additional reports addressing issues related to social aspects of EVD outbreaks in DRC were not retrieved. CONCLUSION National leadership has not yet taken the lead in strategic, operational, or financial aspects. Therefore, national leaders should double their efforts and awareness to encourage local fundraising, sufficient budget al.location, infrastructure construction, equipment provision, and staff training, to effectively support a holistic approach in response to outbreaks, providing effective results, and all types of research activities.
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Affiliation(s)
- Daniel Mukadi-Bamuleka
- Department of Virology, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Rodolphe Mérieux INRB-Goma Laboratory, Institut National de Recherche Biomédicale (INRB), Goma, Democratic Republic of the Congo
- Service of Microbiology, Department of Medical Biology, Kinshasa Teaching School of Medicine, University of Kinshasa, Democratic Republic of the Congo
| | - Antoine Nkuba-Ndaye
- Department of Virology, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Service of Microbiology, Department of Medical Biology, Kinshasa Teaching School of Medicine, University of Kinshasa, Democratic Republic of the Congo
| | - Placide Mbala-Kingebeni
- Department of Virology, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Service of Microbiology, Department of Medical Biology, Kinshasa Teaching School of Medicine, University of Kinshasa, Democratic Republic of the Congo
| | - Steve Ahuka-Mundeke
- Department of Virology, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Service of Microbiology, Department of Medical Biology, Kinshasa Teaching School of Medicine, University of Kinshasa, Democratic Republic of the Congo
| | - Jean-Jacques Muyembe-Tamfum
- Department of Virology, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Service of Microbiology, Department of Medical Biology, Kinshasa Teaching School of Medicine, University of Kinshasa, Democratic Republic of the Congo
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Balinandi S, Whitmer S, Mulei S, Nassuna C, Pimundu G, Muyigi T, Kainulainen M, Shedroff E, Krapiunaya I, Scholte F, Nyakarahuka L, Tumusiime A, Kyondo J, Baluku J, Kiconco J, Harris JR, Ario AR, Kagirita A, Bosa HK, Ssewanyana I, Nabadda S, Mwebesa HG, Aceng JR, Atwine D, Lutwama JJ, Shoemaker TR, Montgomery JM, Kaleebu P, Klena JD. Molecular characterization of the 2022 Sudan virus disease outbreak in Uganda. J Virol 2023; 97:e0059023. [PMID: 37750724 PMCID: PMC10617429 DOI: 10.1128/jvi.00590-23] [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: 04/20/2023] [Accepted: 08/08/2023] [Indexed: 09/27/2023] Open
Abstract
IMPORTANCE Ebola disease (EBOD) is a public health threat with a high case fatality rate. Most EBOD outbreaks have occurred in remote locations, but the 2013-2016 Western Africa outbreak demonstrated how devastating EBOD can be when it reaches an urban population. Here, the 2022 Sudan virus disease (SVD) outbreak in Mubende District, Uganda, is summarized, and the genetic relatedness of the new variant is evaluated. The Mubende variant exhibited 96% amino acid similarity with historic SUDV sequences from the 1970s and a high degree of conservation throughout the outbreak, which was important for ongoing diagnostics and highly promising for future therapy development. Genetic differences between viruses identified during the Mubende SVD outbreak were linked with epidemiological data to better interpret viral spread and contact tracing chains. This methodology should be used to better integrate discrete epidemiological and sequence data for future viral outbreaks.
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Affiliation(s)
| | - Shannon Whitmer
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Sophia Mulei
- Uganda Virus Research Institute, Entebbe, Uganda
| | | | - Godfrey Pimundu
- Uganda National Health Laboratory Services, Ministry of Health, Kampala, Uganda
| | - Tonny Muyigi
- Uganda National Health Laboratory Services, Ministry of Health, Kampala, Uganda
| | - Markus Kainulainen
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Elizabeth Shedroff
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Inna Krapiunaya
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Florine Scholte
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Luke Nyakarahuka
- Uganda Virus Research Institute, Entebbe, Uganda
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | | | | | - Jimmy Baluku
- Uganda Virus Research Institute, Entebbe, Uganda
| | | | | | - Alex R. Ario
- Uganda Public Health Fellowship Program, Kampala, Uganda
| | | | - Henry K. Bosa
- Ministry of Health, Kampala, Uganda
- Kellogg College, University of Oxford, Oxford, United Kingdom
| | - Isaac Ssewanyana
- Uganda National Health Laboratory Services, Ministry of Health, Kampala, Uganda
| | - Susan Nabadda
- Uganda National Health Laboratory Services, Ministry of Health, Kampala, Uganda
| | | | | | | | | | - Trevor R. Shoemaker
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Joel M. Montgomery
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Pontiano Kaleebu
- Uganda Virus Research Institute, Entebbe, Uganda
- MRC/UVRI & LSHTM Uganda Research Unit, Entebbe, Uganda
| | - John D. Klena
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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3
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Doshi RH, Garbern SC, Kulkarni S, Perera SM, Fleming MK, Muhayangabo RF, Ombeni AB, Tchoualeu DD, Kallay R, Song E, Powell J, Gainey M, Glenn B, Mutumwa RM, Hans Bateyi Mustafa S, Earle-Richardson G, Gao H, Abad N, Soke GN, Fitter DL, Hyde TB, Prybylski D, Levine AC, Jalloh MF, Mbong EN. Ebola vaccine uptake and attitudes among healthcare workers in North Kivu, Democratic Republic of the Congo, 2021. Front Public Health 2023; 11:1080700. [PMID: 37559741 PMCID: PMC10408297 DOI: 10.3389/fpubh.2023.1080700] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 06/19/2023] [Indexed: 08/11/2023] Open
Abstract
Introduction During the 2018-2020 Ebola virus disease (EVD) outbreak in the eastern part of the Democratic Republic of the Congo (DRC), prevention and control measures, such as Ebola vaccination were challenging by community mistrust. We aimed to understand perceptions regarding Ebola vaccination and identify determinants of Ebola vaccine uptake among HCWs. Methods In March 2021, we conducted a cross-sectional survey among 438 HCWs from 100 randomly selected health facilities in three health zones (Butembo, Beni, Mabalako) affected by the 10th EVD outbreak in North Kivu, DRC. HCWs were eligible if they were ≥ 18 years and were working in a health facility during the outbreak. We used survey logistic regression to assess correlates of first-offer uptake (i.e., having received the vaccine the first time it was offered vs. after subsequent offers). Results Of the 438 HCWs enrolled in the study, 420 (95.8%) reported that they were eligible and offered an Ebola vaccine. Among those offered vaccination, self-reported uptake of the Ebola vaccine was 99.0% (95% confidence interval (CI) [98.5-99.4]), but first-offer uptake was 70.2% (95% CI [67.1, 73.5]). Nearly all HCWs (94.3%; 95% CI [92.7-95.5]) perceived themselves to be at risk of contracting EVD. The most common concern was that the vaccine would cause side effects (65.7%; 95% CI [61.4-69.7]). In the multivariable analysis, mistrust of the vaccine source or how the vaccine was produced decreased the odds of first-time uptake. Discussion Overall uptake of the Ebola vaccine was high among HCWs, but uptake at the first offer was substantially lower, which was associated with mistrust of the vaccine source. Future Ebola vaccination efforts should plan to make repeated vaccination offers to HCWs and address their underlying mistrust in the vaccines, which can, in turn, improve community uptake.
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Affiliation(s)
- Reena H. Doshi
- Global Immunization Division, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Stephanie C. Garbern
- Department of Emergency Medicine, Brown University, Providence, RI, United States
| | - Shibani Kulkarni
- Global Immunization Division, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | | | - Monica K. Fleming
- Global Immunization Division, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | | | | | | | - Ruth Kallay
- Global Immunization Division, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | | | | | | | - Bailey Glenn
- James A. Ferguson Infectious Disease Program, Baltimore, MD, United States
| | | | | | - Giulia Earle-Richardson
- National Center for Emerging and Zoonotic Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Hongjiang Gao
- Global Immunization Division, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Neetu Abad
- Global Immunization Division, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Gnakub Norbert Soke
- Division of Global Health Protection, Centers for Disease Control and Prevention, Kinshasa, Democratic Republic of Congo
| | - David L. Fitter
- Global Immunization Division, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Terri B. Hyde
- Global Immunization Division, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Dimitri Prybylski
- Global Immunization Division, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Adam C. Levine
- International Medical Corps, Washington, DC, United States
- International Medical Corps, Goma, Democratic Republic of Congo
| | - Mohamed F. Jalloh
- Division of Global HIV and TB, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Eta Ngole Mbong
- International Medical Corps, Goma, Democratic Republic of Congo
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A case for investment in clinical metagenomics in low-income and middle-income countries. THE LANCET. MICROBE 2023; 4:e192-e199. [PMID: 36563703 DOI: 10.1016/s2666-5247(22)00328-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 10/24/2022] [Accepted: 10/25/2022] [Indexed: 12/24/2022]
Abstract
Clinical metagenomics is the diagnostic approach with the broadest capacity to detect both known and novel pathogens. Clinical metagenomics is costly to run and requires infrastructure, but the use of next-generation sequencing for SARS-CoV-2 molecular epidemiology in low-income and middle-income countries (LMICs) offers an opportunity to direct this infrastructure to the establishment of clinical metagenomics programmes. Local implementation of clinical metagenomics is important to create relevant systems and evaluate cost-effective methodologies for its use, as well as to ensure that reference databases and result interpretation tools are appropriate to local epidemiology. Rational implementation, based on the needs of LMICs and the available resources, could ultimately improve individual patient care in instances in which available diagnostics are inadequate and supplement emerging infectious disease surveillance systems to ensure the next pandemic pathogen is quickly identified.
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Vandenbogaert M, Kwasiborski A, Gonofio E, Descorps-Declère S, Selekon B, Nkili Meyong AA, Ouilibona RS, Gessain A, Manuguerra JC, Caro V, Nakoune E, Berthet N. Nanopore sequencing of a monkeypox virus strain isolated from a pustular lesion in the Central African Republic. Sci Rep 2022; 12:10768. [PMID: 35750759 PMCID: PMC9232561 DOI: 10.1038/s41598-022-15073-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 06/17/2022] [Indexed: 12/16/2022] Open
Abstract
Monkeypox is an emerging and neglected zoonotic disease whose number of reported cases has been gradually increasing in Central Africa since 1980. This disease is caused by the monkeypox virus (MPXV), which belongs to the genus Orthopoxvirus in the family Poxviridae. Obtaining molecular data is particularly useful for establishing the relationships between the viral strains involved in outbreaks in countries affected by this disease. In this study, we evaluated the use of the MinION real-time sequencer as well as different polishing tools on MinION-sequenced genome for sequencing the MPXV genome originating from a pustular lesion in the context of an epidemic in a remote area of the Central African Republic. The reads corresponding to the MPXV genome were identified using two taxonomic classifiers, Kraken2 and Kaiju. Assembly of these reads led to a complete sequence of 196,956 bases, which is 6322 bases longer than the sequence previously obtained with Illumina sequencing from the same sample. The comparison of the two sequences showed mainly indels at the homopolymeric regions. However, the combined use of Canu with specific polishing tools such as Medaka and Homopolish was the best combination that reduced their numbers without adding mismatches. Although MinION sequencing is known to introduce a number of characteristic errors compared to Illumina sequencing, the new polishing tools allow a better-quality MinION-sequenced genome, thus to be used to help determine strain origin through phylogenetic analysis.
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Affiliation(s)
- Mathias Vandenbogaert
- Unité Environnement et Risque Infectieux, Cellule d'Intervention Biologique d'Urgence, Institut Pasteur, Paris, France
| | - Aurélia Kwasiborski
- Unité Environnement et Risque Infectieux, Cellule d'Intervention Biologique d'Urgence, Institut Pasteur, Paris, France
| | - Ella Gonofio
- Institut Pasteur de Bangui, Bangui, Central African Republic
| | - Stéphane Descorps-Declère
- Centre of Bioinformatics, Biostatistics and Integrative Biology (C3BI), Institut Pasteur, Paris, France
| | | | | | | | - Antoine Gessain
- Unité d'Epidémiologie et Physiopathologie des Virus Oncogènes, Département de Virologie, UMR3569, Institut Pasteur, Centre National de la Recherche Scientifique (CNRS, Paris, France
| | - Jean-Claude Manuguerra
- Unité Environnement et Risque Infectieux, Cellule d'Intervention Biologique d'Urgence, Institut Pasteur, Paris, France
| | - Valérie Caro
- Unité Environnement et Risque Infectieux, Cellule d'Intervention Biologique d'Urgence, Institut Pasteur, Paris, France
| | | | - Nicolas Berthet
- Unité Environnement et Risque Infectieux, Cellule d'Intervention Biologique d'Urgence, Institut Pasteur, Paris, France.
- The Center for Microbes, Development and Health, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai-Chinese Academy of Sciences, Discovery and Molecular Characterization of Pathogens, No. 320 Yueyang Road, XuHui District, Shanghai, 200031, China.
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6
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Seifert SN, Fischer RJ, Kuisma E, Badzi Nkoua C, Bounga G, Akongo MJ, Schulz JE, Escudero-Pérez B, Akoundzie BJ, Ampiri VRB, Dieudonne A, Indolo GD, Kaba SD, Louzolo I, Macosso LN, Mavoungou Y, Miegakanda VBB, Nina RA, Samabide KT, Ondzie AI, Ntoumi F, Muñoz-Fontela C, Mombouli JV, Olson SH, Walzer C, Niama FR, Munster VJ. Zaire ebolavirus surveillance near the Bikoro region of the Democratic Republic of the Congo during the 2018 outbreak reveals presence of seropositive bats. PLoS Negl Trop Dis 2022; 16:e0010504. [PMID: 35731800 PMCID: PMC9255767 DOI: 10.1371/journal.pntd.0010504] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/05/2022] [Accepted: 05/16/2022] [Indexed: 11/18/2022] Open
Abstract
On the 8th of May, 2018, an outbreak of Ebola virus disease (EVD) was declared, originating in the Bikoro region of the Democratic Republic of the Congo (DRC) near the border with neighboring Republic of the Congo (ROC). Frequent trade and migration occur between DRC and ROC-based communities residing along the Congo River. In June 2018, a field team was deployed to determine whether Zaire ebolavirus (Ebola virus (EBOV)) was contemporaneously circulating in local bats at the human-animal interface in ROC near the Bikoro EVD outbreak. Samples were collected from bats in the Cuvette and Likouala departments, ROC, bordering the Équateur Province in DRC where the Bikoro EVD outbreak was first detected. EBOV genomic material was not detected in bat-derived samples by targeted quantitative reverse transcription-polymerase chain reaction or by family-level consensus polymerase chain reaction; however, serological data suggests recent exposure to EBOV in bats in the region. We collected serum from 144 bats in the Cuvette department with 6.9% seropositivity against the EBOV glycoprotein and 14.3% seropositivity for serum collected from 27 fruit bats and one Molossinae in the Likouala department. We conclude that proactive investment in longitudinal sampling for filoviruses at the human-animal interface, coupled with ecological investigations are needed to identify EBOV wildlife reservoirs.
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Affiliation(s)
- Stephanie N. Seifert
- Paul G. Allen School for Global Health, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States
- Virus Ecology Section, Laboratory of Virology, Rocky Mountain Laboratories, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States
- * E-mail:
| | - Robert J. Fischer
- Virus Ecology Section, Laboratory of Virology, Rocky Mountain Laboratories, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States
| | - Eeva Kuisma
- Wildlife Health Program, Wildlife Conservation Society, Brazzaville, Republic of the Congo
| | - Cynthia Badzi Nkoua
- Département de la Recherche et de la Production, Laboratoire National de Santé Publique, Brazzaville, Republic of the Congo
| | - Gerard Bounga
- Wildlife Health Program, Wildlife Conservation Society, Brazzaville, Republic of the Congo
| | - Marc-Joël Akongo
- Wildlife Health Program, Wildlife Conservation Society, Brazzaville, Republic of the Congo
| | - Jonathan E. Schulz
- Virus Ecology Section, Laboratory of Virology, Rocky Mountain Laboratories, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States
| | - Beatriz Escudero-Pérez
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Centre for Infection Research (DZIF), Partner Site Hamburg-Luebeck-Borstel, Germany
| | - Beal-Junior Akoundzie
- Département de la Recherche et de la Production, Laboratoire National de Santé Publique, Brazzaville, Republic of the Congo
| | - Vishnou Reize Bani Ampiri
- Département de la Recherche et de la Production, Laboratoire National de Santé Publique, Brazzaville, Republic of the Congo
| | - Ankara Dieudonne
- Direction de la Santé Animale, Ministére de L’Agriculture et de L’Élevage, Brazzaville, Republic of the Congo
| | - Ghislain Dzeret Indolo
- Département de la Recherche et de la Production, Laboratoire National de Santé Publique, Brazzaville, Republic of the Congo
| | - Serge D. Kaba
- Wildlife Health Program, Wildlife Conservation Society, Brazzaville, Republic of the Congo
| | - Igor Louzolo
- Département de la Recherche et de la Production, Laboratoire National de Santé Publique, Brazzaville, Republic of the Congo
| | - Lucette Nathalie Macosso
- Département de la Recherche et de la Production, Laboratoire National de Santé Publique, Brazzaville, Republic of the Congo
| | - Yanne Mavoungou
- Département de la Recherche et de la Production, Laboratoire National de Santé Publique, Brazzaville, Republic of the Congo
| | - Valchy Bel-bebi Miegakanda
- Département de la Recherche et de la Production, Laboratoire National de Santé Publique, Brazzaville, Republic of the Congo
| | - Rock Aimé Nina
- Direction de la Santé Animale, Ministére de L’Agriculture et de L’Élevage, Brazzaville, Republic of the Congo
| | - Kevin Tolovou Samabide
- Département de la Recherche et de la Production, Laboratoire National de Santé Publique, Brazzaville, Republic of the Congo
- Faculty of Sciences and Techniques, Université Marien N’Gouabi, Brazzaville, Republic of the Congo
| | - Alain I. Ondzie
- Wildlife Health Program, Wildlife Conservation Society, Brazzaville, Republic of the Congo
| | - Francine Ntoumi
- Faculty of Sciences and Techniques, Université Marien N’Gouabi, Brazzaville, Republic of the Congo
- Fondation Congolaise pour la Recherche Médicale, Brazzaville, Republic of the Congo
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
| | | | - Jean-Vivien Mombouli
- Département de la Recherche et de la Production, Laboratoire National de Santé Publique, Brazzaville, Republic of the Congo
| | - Sarah H. Olson
- Health Program, Wildlife Conservation Society, New York, New York, United States
| | - Chris Walzer
- Health Program, Wildlife Conservation Society, New York, New York, United States
- Research Institute of Wildlife Ecology, University of Veterinary Medicine, Vienna, Austria
| | - Fabien Roch Niama
- Département de la Recherche et de la Production, Laboratoire National de Santé Publique, Brazzaville, Republic of the Congo
| | - Vincent J. Munster
- Virus Ecology Section, Laboratory of Virology, Rocky Mountain Laboratories, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States
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7
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Stefan CP, Hall AT, Graham AS, Minogue TD. Comparison of Illumina and Oxford Nanopore Sequencing Technologies for Pathogen Detection from Clinical Matrices Using Molecular Inversion Probes. J Mol Diagn 2022; 24:395-405. [PMID: 35085783 DOI: 10.1016/j.jmoldx.2021.12.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 11/19/2021] [Accepted: 12/22/2021] [Indexed: 11/16/2022] Open
Abstract
Next-generation sequencing is rapidly finding footholds in numerous microbiological fields, including infectious disease diagnostics. Here, we describe a molecular inversion probe panel for the identification of bacterial, viral, and parasitic pathogens. We describe the ability of Illumina and Oxford Nanopore Technologies (ONT) to sequence small amplicons originating from this panel for the identification of pathogens in complex matrices. The panel correctly classified 31 bacterial pathogens directly from positive blood culture bottles with a genus-level concordance of 96.7% and 90.3% on the Illumina and ONT platforms, respectively. Both sequencing platforms detected 18 viral and parasitic organisms directly from mock clinical samples of plasma and whole blood at concentrations of 104 PFU/mL with few exceptions. In general, Illumina sequencing exhibited greater read counts with lower percent mapped reads; however, this resulted in no effect on limits of detection compared with ONT sequencing. Mock clinical evaluation of the probe panel on the Illumina and ONT platforms resulted in positive predictive values of 0.91 and 0.88 and negative predictive values of 1 and 1 from de-identified human chikungunya virus samples compared with gold standard quantitative RT-PCR. Overall, these data show that molecular inversion probes are an adaptable technology capable of pathogen detection from complex sample matrices on current next-generation sequencing platforms.
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Affiliation(s)
- Christopher P Stefan
- Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Disease, Fort Detrick, Maryland
| | - Adrienne T Hall
- Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Disease, Fort Detrick, Maryland
| | - Amanda S Graham
- Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Disease, Fort Detrick, Maryland
| | - Timothy D Minogue
- Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Disease, Fort Detrick, Maryland.
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8
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Djomsi DM, Mba Djonzo FA, Ndong Bass I, Champagne M, Lacroix A, Thaurignac G, Esteban A, De Nys H, Bourgarel M, Akoachere JF, Delaporte E, Ayouba A, Cappelle J, Mpoudi Ngole E, Peeters M. Dynamics of Antibodies to Ebolaviruses in an Eidolon helvum Bat Colony in Cameroon. Viruses 2022; 14:560. [PMID: 35336967 PMCID: PMC8951055 DOI: 10.3390/v14030560] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 02/24/2022] [Accepted: 02/25/2022] [Indexed: 11/16/2022] Open
Abstract
The ecology of ebolaviruses is still poorly understood and the role of bats in outbreaks needs to be further clarified. Straw-colored fruit bats (Eidolon helvum) are the most common fruit bats in Africa and antibodies to ebolaviruses have been documented in this species. Between December 2018 and November 2019, samples were collected at approximately monthly intervals in roosting and feeding sites from 820 bats from an Eidolon helvum colony. Dried blood spots (DBS) were tested for antibodies to Zaire, Sudan, and Bundibugyo ebolaviruses. The proportion of samples reactive with GP antigens increased significantly with age from 0-9/220 (0-4.1%) in juveniles to 26-158/225 (11.6-70.2%) in immature adults and 10-225/372 (2.7-60.5%) in adult bats. Antibody responses were lower in lactating females. Viral RNA was not detected in 456 swab samples collected from 152 juvenile and 214 immature adult bats. Overall, our study shows that antibody levels increase in young bats suggesting that seroconversion to Ebola or related viruses occurs in older juvenile and immature adult bats. Multiple year monitoring would be needed to confirm this trend. Knowledge of the periods of the year with the highest risk of Ebolavirus circulation can guide the implementation of strategies to mitigate spill-over events.
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Affiliation(s)
- Dowbiss Meta Djomsi
- Laboratoire de Virologie-Cremer, Institut de Recherches Médicales et d’Études des Plantes Médicinales (IMPM), Yaoundé P.O. Box 13033, Cameroon; (D.M.D.); (F.A.M.D.); (I.N.B.)
| | - Flaubert Auguste Mba Djonzo
- Laboratoire de Virologie-Cremer, Institut de Recherches Médicales et d’Études des Plantes Médicinales (IMPM), Yaoundé P.O. Box 13033, Cameroon; (D.M.D.); (F.A.M.D.); (I.N.B.)
| | - Innocent Ndong Bass
- Laboratoire de Virologie-Cremer, Institut de Recherches Médicales et d’Études des Plantes Médicinales (IMPM), Yaoundé P.O. Box 13033, Cameroon; (D.M.D.); (F.A.M.D.); (I.N.B.)
| | - Maëliss Champagne
- Transvihmi, Institut de Recherche pour le Développement (IRD), University of Montpellier, Inserm, 34394 Montpellier, France; (M.C.); (A.L.); (G.T.); (A.E.); (E.D.); (A.A.)
| | - Audrey Lacroix
- Transvihmi, Institut de Recherche pour le Développement (IRD), University of Montpellier, Inserm, 34394 Montpellier, France; (M.C.); (A.L.); (G.T.); (A.E.); (E.D.); (A.A.)
| | - Guillaume Thaurignac
- Transvihmi, Institut de Recherche pour le Développement (IRD), University of Montpellier, Inserm, 34394 Montpellier, France; (M.C.); (A.L.); (G.T.); (A.E.); (E.D.); (A.A.)
| | - Amandine Esteban
- Transvihmi, Institut de Recherche pour le Développement (IRD), University of Montpellier, Inserm, 34394 Montpellier, France; (M.C.); (A.L.); (G.T.); (A.E.); (E.D.); (A.A.)
| | - Helene De Nys
- ASTRE, CIRAD, Harare, Zimbabwe; (H.D.N.); (M.B.)
- ASTRE, CIRAD, INRAE, University of Montpellier, 34398 Montpellier, France
| | - Mathieu Bourgarel
- ASTRE, CIRAD, Harare, Zimbabwe; (H.D.N.); (M.B.)
- ASTRE, CIRAD, INRAE, University of Montpellier, 34398 Montpellier, France
| | - Jane-Francis Akoachere
- Department of Microbiology and Parasitology, University of Buea, Buea P.O. Box 63, Cameroon; (J.-F.A.); (J.C.)
| | - Eric Delaporte
- Transvihmi, Institut de Recherche pour le Développement (IRD), University of Montpellier, Inserm, 34394 Montpellier, France; (M.C.); (A.L.); (G.T.); (A.E.); (E.D.); (A.A.)
| | - Ahidjo Ayouba
- Transvihmi, Institut de Recherche pour le Développement (IRD), University of Montpellier, Inserm, 34394 Montpellier, France; (M.C.); (A.L.); (G.T.); (A.E.); (E.D.); (A.A.)
| | - Julien Cappelle
- Department of Microbiology and Parasitology, University of Buea, Buea P.O. Box 63, Cameroon; (J.-F.A.); (J.C.)
| | - Eitel Mpoudi Ngole
- Laboratoire de Virologie-Cremer, Institut de Recherches Médicales et d’Études des Plantes Médicinales (IMPM), Yaoundé P.O. Box 13033, Cameroon; (D.M.D.); (F.A.M.D.); (I.N.B.)
| | - Martine Peeters
- Transvihmi, Institut de Recherche pour le Développement (IRD), University of Montpellier, Inserm, 34394 Montpellier, France; (M.C.); (A.L.); (G.T.); (A.E.); (E.D.); (A.A.)
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9
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OUEMBA TASSÉ AJ, TSANOU B, LUBUMA J, WOUKENG JEANLOUIS, SIGNING FRANCIS. EBOLA VIRUS DISEASE DYNAMICS WITH SOME PREVENTIVE MEASURES: A CASE STUDY OF THE 2018–2020 KIVU OUTBREAK. J BIOL SYST 2022. [DOI: 10.1142/s0218339022500048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
To fight against Ebola virus disease, several measures have been adopted. Among them, isolation, safe burial and vaccination occupy a prominent place. In this paper, we present a model which takes into account these three control strategies as well as the indirect transmission through a polluted environment. The asymptotic behavior of our model is achieved. Namely, we determine a threshold value [Formula: see text] of the control reproduction number [Formula: see text], below which the disease is eliminated in the long run. Whenever the value of [Formula: see text] ranges from [Formula: see text] and 1, we prove the existence of a backward bifurcation phenomenon, which corresponds to the case, where a locally asymptotically stable positive equilibrium co-exists with the disease-free equilibrium, which is also locally asymptotically stable. The existence of this bifurcation complicates the control of Ebola, since the requirement of [Formula: see text] below one, although necessary, is no longer sufficient for the elimination of Ebola, more efforts need to be deployed. When the value of [Formula: see text] is greater than one, we prove the existence of a unique endemic equilibrium, locally asymptotically stable. That is the disease may persist and become endemic. Numerically, we fit our model to the reported data for the 2018–2020 Kivu Ebola outbreak which occurred in Democratic Republic of Congo. Through the sensitivity analysis of the control reproduction number, we prove that the transmission rates of infected alive who are outside hospital are the most influential parameters. Numerically, we explore the usefulness of isolation, safe burial combined with vaccination and investigate the importance to combine the latter control strategies to the educational campaigns or/and case finding.
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Affiliation(s)
- A. J. OUEMBA TASSÉ
- Department of Mathematics and Computer Science, University of Dschang, P. O. Box 67, Dschang, Cameroon
| | - B. TSANOU
- Department of Mathematics and Computer Science, University of Dschang, P. O. Box 67, Dschang, Cameroon
- Department of Science, Mathematics and Applied Mathematics, University of Pretoria, Private Bag X20, Pretoria 0028, South Africa
- IRD Sorbonne University, UMMISCO, F-93143, Bondy, France
| | - J. LUBUMA
- School of Computer Science and Applied Mathematics, University of the Witwatersrand, Johannesburg, South Africa
| | - JEAN LOUIS WOUKENG
- Department of Mathematics and Computer Science, University of Dschang, P. O. Box 67, Dschang, Cameroon
| | - FRANCIS SIGNING
- Department of Mathematics and Computer Science, University of Dschang, P. O. Box 67, Dschang, Cameroon
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10
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Tiper I, Kourout M, Lanning B, Fisher C, Konduru K, Purkayastha A, Kaplan G, Duncan R. Tracking ebolavirus genomic drift with a resequencing microarray. PLoS One 2022; 17:e0263732. [PMID: 35143574 PMCID: PMC8830711 DOI: 10.1371/journal.pone.0263732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 01/25/2022] [Indexed: 11/17/2022] Open
Abstract
Filoviruses are emerging pathogens that cause acute fever with high fatality rate and present a global public health threat. During the 2013–2016 Ebola virus outbreak, genome sequencing allowed the study of virus evolution, mutations affecting pathogenicity and infectivity, and tracing the viral spread. In 2018, early sequence identification of the Ebolavirus as EBOV in the Democratic Republic of the Congo supported the use of an Ebola virus vaccine. However, field-deployable sequencing methods are needed to enable a rapid public health response. Resequencing microarrays (RMA) are a targeted method to obtain genomic sequence on clinical specimens rapidly, and sensitively, overcoming the need for extensive bioinformatic analysis. This study presents the design and initial evaluation of an ebolavirus resequencing microarray (Ebolavirus-RMA) system for sequencing the major genomic regions of four Ebolaviruses that cause disease in humans. The design of the Ebolavirus-RMA system is described and evaluated by sequencing repository samples of three Ebolaviruses and two EBOV variants. The ability of the system to identify genetic drift in a replicating virus was achieved by sequencing the ebolavirus glycoprotein gene in a recombinant virus cultured under pressure from a neutralizing antibody. Comparison of the Ebolavirus-RMA results to the Genbank database sequence file with the accession number given for the source RNA and Ebolavirus-RMA results compared to Next Generation Sequence results of the same RNA samples showed up to 99% agreement.
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Affiliation(s)
- Irina Tiper
- Division of Emerging and Transfusion-Transmitted Diseases, Office of Blood Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, United States of America
| | - Moussa Kourout
- Division of Emerging and Transfusion-Transmitted Diseases, Office of Blood Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, United States of America
| | - Bryan Lanning
- Division of Emerging and Transfusion-Transmitted Diseases, Office of Blood Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, United States of America
| | - Carolyn Fisher
- Division of Emerging and Transfusion-Transmitted Diseases, Office of Blood Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, United States of America
| | - Krishnamurthy Konduru
- Division of Emerging and Transfusion-Transmitted Diseases, Office of Blood Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, United States of America
| | | | - Gerardo Kaplan
- Division of Emerging and Transfusion-Transmitted Diseases, Office of Blood Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, United States of America
| | - Robert Duncan
- Division of Emerging and Transfusion-Transmitted Diseases, Office of Blood Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, United States of America
- * E-mail:
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11
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Resurgence of Ebola virus in 2021 in Guinea suggests a new paradigm for outbreaks. Nature 2021; 597:539-543. [PMID: 34526718 DOI: 10.1038/s41586-021-03901-9] [Citation(s) in RCA: 104] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 08/11/2021] [Indexed: 02/08/2023]
Abstract
Seven years after the declaration of the first epidemic of Ebola virus disease in Guinea, the country faced a new outbreak-between 14 February and 19 June 2021-near the epicentre of the previous epidemic1,2. Here we use next-generation sequencing to generate complete or near-complete genomes of Zaire ebolavirus from samples obtained from 12 different patients. These genomes form a well-supported phylogenetic cluster with genomes from the previous outbreak, which indicates that the new outbreak was not the result of a new spillover event from an animal reservoir. The 2021 lineage shows considerably lower divergence than would be expected during sustained human-to-human transmission, which suggests a persistent infection with reduced replication or a period of latency. The resurgence of Zaire ebolavirus from humans five years after the end of the previous outbreak of Ebola virus disease reinforces the need for long-term medical and social care for patients who survive the disease, to reduce the risk of re-emergence and to prevent further stigmatization.
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12
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Li Z, Li Y, Chen L, Li S, Yu L, Zhu A, Yang F, Jiang Q, Chen L, Zhao J, Lu W, Zhong N, Ye F. A Confirmed Case of SARS-CoV-2 Pneumonia With Negative Routine Reverse Transcriptase-Polymerase Chain Reaction and Virus Variation in Guangzhou, China. Clin Infect Dis 2021; 73:e426-e433. [PMID: 32642757 PMCID: PMC7454436 DOI: 10.1093/cid/ciaa941] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 07/03/2020] [Indexed: 01/08/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pneumonia is a newly recognized disease, and its diagnosis is primarily confirmed by routine RT-PCR detection of SARS-CoV-2. However, we report a confirmed case of SARS-CoV-2 pneumonia with routine RT-PCR negative. This case has been finally diagnosed by Nanopore sequencing combined with antibody of SARS-CoV-2. Simultaneously, the ORF and NP gene variation of SARS-CoV-2 were found. This case has highlighted that false negative results could be present in the routine RT-PCR diagnosis, especially with virus variation. At the moment, Nanopore pathogen sequencing and antibody detection have been found effective in clinical diagnosis.
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Affiliation(s)
- Zhengtu Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yinhu Li
- Beijing YuanShengKangTai (ProtoDNA) Genetech Co Ltd, Beijing, China
| | - Lingdan Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Shaoqiang Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Le Yu
- Beijing YuanShengKangTai (ProtoDNA) Genetech Co Ltd, Beijing, China
| | - Airu Zhu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Feng Yang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Qian Jiang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Liyan Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wenju Lu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Nanshan Zhong
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Feng Ye
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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13
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Fairhead J, Leach M, Millimouno D. Spillover or endemic? Reconsidering the origins of Ebola virus disease outbreaks by revisiting local accounts in light of new evidence from Guinea. BMJ Glob Health 2021; 6:bmjgh-2021-005783. [PMID: 33893144 PMCID: PMC8074560 DOI: 10.1136/bmjgh-2021-005783] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/02/2021] [Accepted: 04/05/2021] [Indexed: 12/22/2022] Open
Affiliation(s)
- James Fairhead
- Department of Anthropology, University of Sussex, Brighton, UK
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14
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Lacroix A, Mbala Kingebeni P, Ndimbo Kumugo SP, Lempu G, Butel C, Serrano L, Vidal N, Thaurignac G, Esteban A, Mukadi Bamuleka D, Likofata J, Delaporte E, Muyembe Tamfum JJ, Ayouba A, Peeters M, Ahuka Mundeke S. Investigating the Circulation of Ebola Viruses in Bats during the Ebola Virus Disease Outbreaks in the Equateur and North Kivu Provinces of the Democratic Republic of Congo from 2018. Pathogens 2021; 10:pathogens10050557. [PMID: 34064424 PMCID: PMC8147758 DOI: 10.3390/pathogens10050557] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/28/2021] [Accepted: 04/30/2021] [Indexed: 02/04/2023] Open
Abstract
With 12 of the 31 outbreaks, the Democratic Republic of Congo (DRC) is highly affected by Ebolavirus disease (EVD). To better understand the role of bats in the ecology of Ebola viruses, we conducted surveys in bats during two recent EVD outbreaks and in two areas with previous outbreaks. Dried blood spots were tested for antibodies to ebolaviruses and oral and rectal swabs were screened for the presence of filovirus using a broadly reactive semi-nested RT-PCR. Between 2018 and 2020, 892 (88.6%) frugivorous and 115 (11.4%) insectivorous bats were collected. Overall, 11/925 (1.2%) to 100/925 (10.8%) bats showed antibodies to at least one Ebolavirus antigen depending on the positivity criteria. Antibodies were detected in fruit bats from the four sites and from species previously documented to harbor Ebola antibodies or RNA. We tested for the first time a large number of bats during ongoing EVD outbreaks in DRC, but no viral RNA was detected in the 676 sampled bats. Our study illustrates the difficulty to document the role of bats as a source of Ebolaviruses as they might clear quickly the virus. Given the increasing frequency of EVD outbreaks, more studies on the animal reservoir are urgently needed.
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Affiliation(s)
- Audrey Lacroix
- TransVIHMI (Recherches Translationnelles sur VIH et Maladies Infectieuses), Université de Montpellier, Institut de Recherche pour le Développement, INSERM, 34394 Montpellier, France; (A.L.); (C.B.); (L.S.); (N.V.); (G.T.); (A.E.); (E.D.); (A.A.)
| | - Placide Mbala Kingebeni
- Institut National de Recherche Biomédicale (INRB), 1197 Kinshasa, Democratic Republic of the Congo; (P.M.K.); (S.P.N.K.); (G.L.); (J.-J.M.T.)
- Service de Microbiologie, Cliniques Universitaires de Kinshasa, 1197 Kinshasa, Democratic Republic of the Congo;
| | - Simon Pierre Ndimbo Kumugo
- Institut National de Recherche Biomédicale (INRB), 1197 Kinshasa, Democratic Republic of the Congo; (P.M.K.); (S.P.N.K.); (G.L.); (J.-J.M.T.)
| | - Guy Lempu
- Institut National de Recherche Biomédicale (INRB), 1197 Kinshasa, Democratic Republic of the Congo; (P.M.K.); (S.P.N.K.); (G.L.); (J.-J.M.T.)
| | - Christelle Butel
- TransVIHMI (Recherches Translationnelles sur VIH et Maladies Infectieuses), Université de Montpellier, Institut de Recherche pour le Développement, INSERM, 34394 Montpellier, France; (A.L.); (C.B.); (L.S.); (N.V.); (G.T.); (A.E.); (E.D.); (A.A.)
| | - Laetitia Serrano
- TransVIHMI (Recherches Translationnelles sur VIH et Maladies Infectieuses), Université de Montpellier, Institut de Recherche pour le Développement, INSERM, 34394 Montpellier, France; (A.L.); (C.B.); (L.S.); (N.V.); (G.T.); (A.E.); (E.D.); (A.A.)
| | - Nicole Vidal
- TransVIHMI (Recherches Translationnelles sur VIH et Maladies Infectieuses), Université de Montpellier, Institut de Recherche pour le Développement, INSERM, 34394 Montpellier, France; (A.L.); (C.B.); (L.S.); (N.V.); (G.T.); (A.E.); (E.D.); (A.A.)
| | - Guillaume Thaurignac
- TransVIHMI (Recherches Translationnelles sur VIH et Maladies Infectieuses), Université de Montpellier, Institut de Recherche pour le Développement, INSERM, 34394 Montpellier, France; (A.L.); (C.B.); (L.S.); (N.V.); (G.T.); (A.E.); (E.D.); (A.A.)
| | - Amandine Esteban
- TransVIHMI (Recherches Translationnelles sur VIH et Maladies Infectieuses), Université de Montpellier, Institut de Recherche pour le Développement, INSERM, 34394 Montpellier, France; (A.L.); (C.B.); (L.S.); (N.V.); (G.T.); (A.E.); (E.D.); (A.A.)
| | - Daniel Mukadi Bamuleka
- Service de Microbiologie, Cliniques Universitaires de Kinshasa, 1197 Kinshasa, Democratic Republic of the Congo;
- Institut National de Recherche Biomédicale (INRB), Goma, Democratic Republic of the Congo
| | - Jacques Likofata
- Laboratoire Provincial de Mbandaka, Equateur, Democratic Republic of the Congo;
| | - Eric Delaporte
- TransVIHMI (Recherches Translationnelles sur VIH et Maladies Infectieuses), Université de Montpellier, Institut de Recherche pour le Développement, INSERM, 34394 Montpellier, France; (A.L.); (C.B.); (L.S.); (N.V.); (G.T.); (A.E.); (E.D.); (A.A.)
| | - Jean-Jacques Muyembe Tamfum
- Institut National de Recherche Biomédicale (INRB), 1197 Kinshasa, Democratic Republic of the Congo; (P.M.K.); (S.P.N.K.); (G.L.); (J.-J.M.T.)
- Service de Microbiologie, Cliniques Universitaires de Kinshasa, 1197 Kinshasa, Democratic Republic of the Congo;
| | - Ahidjo Ayouba
- TransVIHMI (Recherches Translationnelles sur VIH et Maladies Infectieuses), Université de Montpellier, Institut de Recherche pour le Développement, INSERM, 34394 Montpellier, France; (A.L.); (C.B.); (L.S.); (N.V.); (G.T.); (A.E.); (E.D.); (A.A.)
| | - Martine Peeters
- TransVIHMI (Recherches Translationnelles sur VIH et Maladies Infectieuses), Université de Montpellier, Institut de Recherche pour le Développement, INSERM, 34394 Montpellier, France; (A.L.); (C.B.); (L.S.); (N.V.); (G.T.); (A.E.); (E.D.); (A.A.)
- Correspondence: (M.P.); (S.A.M.)
| | - Steve Ahuka Mundeke
- Institut National de Recherche Biomédicale (INRB), 1197 Kinshasa, Democratic Republic of the Congo; (P.M.K.); (S.P.N.K.); (G.L.); (J.-J.M.T.)
- Service de Microbiologie, Cliniques Universitaires de Kinshasa, 1197 Kinshasa, Democratic Republic of the Congo;
- Correspondence: (M.P.); (S.A.M.)
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15
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Dixit D, Masumbuko Claude K, Kjaldgaard L, Hawkes MT. Review of Ebola virus disease in children - how far have we come? Paediatr Int Child Health 2021; 41:12-27. [PMID: 32894024 DOI: 10.1080/20469047.2020.1805260] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Ebola virus (EBOV) causes an extremely contagious viral haemorrhagic fever associated with high mortality. While, historically, children have represented a small number of total cases of Ebolavirus disease (EVD), in recent outbreaks up to a quarter of cases have been in children. They pose unique challenges in clinical management and infection prevention and control. In this review of paediatric EVD, the epidemiology of past EVD outbreaks with specific focus on children is discussed, the clinical manifestations and laboratory findings are described and key developments in clinical management including specific topics such as viral persistence and breastfeeding while considering unique psychosocial and anthropological considerations for paediatric care including of survivors and orphans and the stigma they face are discussed. In addition to summarising the literature, perspectives based on the authors' experience of EVD outbreaks in the Democratic Republic of the Congo (DRC) are described.Abbreviations: ARDS: acute respiratory distress syndrome; aOR: adjusted odds ratio; ALT: alanine transferase; ALIMA: Alliance for International Medical Action; AST: aspartate transaminase; BUN: blood urea nitrogen; CNS: central nervous system; CUBE: chambre d'urgence biosécurisée pour épidémie; COVID-19: coronavirus disease 2019; Ct: cycle threshold; DRC: Democratic Republic of Congo; ETC: ebola treatment centre; ETU: ebola treatment unit; EBOV: ebola virus; EVD: ebolavirus disease; FEAST: fluid expansion as supportive therapy; GP: glycoprotein; IV: intravenous; MEURI: monitored emergency use of unregistered interventions; NETEC: National Ebola Training and Education Centre; NP: nucleoprotein; ORS: oral rehydration solution; PALM: Pamoja Tulinde Maisha; PREVAIL: Partnership for Research on Ebola Virus in Liberia; PPE: personal protective equipment; PCR: polymerase chain reaction; PEP: post-exposure prophylaxis; RDTs: rapid diagnostic tests; RT: reverse transcriptase; RNA: ribonucleic acid; UNICEF: United Nations International Children's Emergency Fund; USA: United States of America; WHO: World Health Organization.
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Affiliation(s)
- Devika Dixit
- Department of Medicine and Pediatrics. Division of Infectious Diseases, University of Saskatchewan, Saskatoon, SK, Canada
| | | | | | - Michael T Hawkes
- Department of Pediatrics. Division of Infectious Diseases, University of Alberta, Edmonton, Alberta, Canada.,School of Public Health, University of Alberta, Edmonton, Canada.,Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Canada.,Stollery Science Laboratory, Edmonton, Alberta, Canada.,Women and Children's Health Research Institute, Edmonton, Alberta, Canada
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16
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Chen B, Li QX, Zhang H, Zhu JY, Yang X, Wu YH, Xiong J, Li F, Wang H, Chen ZT. The psychological impact of COVID-19 outbreak on medical staff and the general public. CURRENT PSYCHOLOGY 2020; 41:5631-5639. [PMID: 33046955 PMCID: PMC7539749 DOI: 10.1007/s12144-020-01109-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/02/2020] [Indexed: 12/12/2022]
Abstract
To assess the psychological effects of the novel coronavirus disease (COVID-19) on medical staff and the general public. During the outbreak of COVID-19, an internet-based questionnaire included The Self-rating Depression Scale (SDS), Perceived Stress Scale (PSS-10), and Impact of Event Scale-Revised (IES-R) was used to assess the impact of the pandemic situation on the mental health of medical staff and general population in Wuhan and its surrounding areas. Among the 1493 questionnaires completed, 827 (55.39%) of these were men, and 422 (28.27%) of these were medical personnel. The results suggest that the outbreak of COVID-19 has affected individuals significantly, the degree of which is related to age, sex, occupation and mental illness. There was a significant difference in PSS-10 and IES-R scores between the medical staff and the general population. The medical staff showed higher PSS-10 scores (16.813 ± 4.87) and IES-R scores (22.40 ± 12.12) compared to members of the general population PSS-10 (14.80 ± 5.60) and IES-R scores (17.89 ± 13.08). However, there was no statistically significant difference between the SDS scores of medical staff (44.52 ± 12.36) and the general public (43.08 ± 11.42). In terms of the need for psychological assistance, 50.97% of interviewees responded that they needed psychological counseling, of which medical staff accounted for 65.87% and non-medical staff accounted for 45.10%. During the ongoing COVID-19 outbreak, great attention should be paid to the mental health of the population, especially medical staff, and measures such as psychological intervention should be actively carried out for reducing the psychosocial effects.
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Affiliation(s)
- Biao Chen
- Department of Orthopedic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071 China
| | - Qing-Xian Li
- Department of Orthopedic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071 China
| | - Heng Zhang
- Department of Gastroenterology, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430014 China
| | - Jia-Yong Zhu
- Department of Orthopedic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071 China
| | - Xu Yang
- Department of Orthopedic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071 China
| | - Yu-Hang Wu
- Applied Statistics, School of mathematics and statistics, Wuhan University, Wuhan, 430072 China
| | - Jie Xiong
- The Mental Health Center of Wuhan, Wuhan, 430022 China
| | - Fu Li
- The Mental Health Center of Wuhan, Wuhan, 430022 China
| | - Hua Wang
- Department of Orthopedic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071 China
| | - Zhi-Tao Chen
- Department of Gastroenterology, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430014 China
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Chang JJM, Ip YCA, Ng CSL, Huang D. Takeaways from Mobile DNA Barcoding with BentoLab and MinION. Genes (Basel) 2020; 11:E1121. [PMID: 32987804 PMCID: PMC7598690 DOI: 10.3390/genes11101121] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 09/17/2020] [Accepted: 09/22/2020] [Indexed: 12/13/2022] Open
Abstract
Since the release of the MinION sequencer in 2014, it has been applied to great effect in the remotest and harshest of environments, and even in space. One of the most common applications of MinION is for nanopore-based DNA barcoding in situ for species identification and discovery, yet the existing sample capability is limited (n ≤ 10). Here, we assembled a portable sequencing setup comprising the BentoLab and MinION and developed a workflow capable of processing 32 samples simultaneously. We demonstrated this enhanced capability out at sea, where we collected samples and barcoded them onboard a dive vessel moored off Sisters' Islands Marine Park, Singapore. In under 9 h, we generated 105 MinION barcodes, of which 19 belonged to fresh metazoans processed immediately after collection. Our setup is thus viable and would greatly fortify existing portable DNA barcoding capabilities. We also tested the performance of the newly released R10.3 nanopore flow cell for DNA barcoding, and showed that the barcodes generated were ~99.9% accurate when compared to Illumina references. A total of 80% of the R10.3 nanopore barcodes also had zero base ambiguities, compared to 50-60% for R9.4.1, suggesting an improved homopolymer resolution and making the use of R10.3 highly recommended.
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Affiliation(s)
- Jia Jin Marc Chang
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore; (Y.C.A.I.); (C.S.L.N.)
| | - Yin Cheong Aden Ip
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore; (Y.C.A.I.); (C.S.L.N.)
| | - Chin Soon Lionel Ng
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore; (Y.C.A.I.); (C.S.L.N.)
- Tropical Marine Science Institute, National University of Singapore, 18 Kent Ridge Road, Singapore 119227, Singapore
| | - Danwei Huang
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore; (Y.C.A.I.); (C.S.L.N.)
- Tropical Marine Science Institute, National University of Singapore, 18 Kent Ridge Road, Singapore 119227, Singapore
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18
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Di Paola N, Sanchez-Lockhart M, Zeng X, Kuhn JH, Palacios G. Viral genomics in Ebola virus research. Nat Rev Microbiol 2020; 18:365-378. [PMID: 32367066 PMCID: PMC7223634 DOI: 10.1038/s41579-020-0354-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/09/2020] [Indexed: 12/20/2022]
Abstract
Filoviruses such as Ebola virus continue to pose a substantial health risk to humans. Advances in the sequencing and functional characterization of both pathogen and host genomes have provided a wealth of knowledge to clinicians, epidemiologists and public health responders during outbreaks of high-consequence viral disease. Here, we describe how genomics has been historically used to investigate Ebola virus disease outbreaks and how new technologies allow for rapid, large-scale data generation at the point of care. We highlight how genomics extends beyond consensus-level sequencing of the virus to include intra-host viral transcriptomics and the characterization of host responses in acute and persistently infected patients. Similar genomics techniques can also be applied to the characterization of non-human primate animal models and to known natural reservoirs of filoviruses, and metagenomic sequencing can be the key to the discovery of novel filoviruses. Finally, we outline the importance of reverse genetics systems that can swiftly characterize filoviruses as soon as their genome sequences are available.
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Affiliation(s)
- Nicholas Di Paola
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Mariano Sanchez-Lockhart
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Xiankun Zeng
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA
| | - Gustavo Palacios
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA.
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19
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Identification of Novel Adjuvants for Ebola Virus-Like Particle Vaccine. Vaccines (Basel) 2020; 8:vaccines8020215. [PMID: 32397625 PMCID: PMC7349346 DOI: 10.3390/vaccines8020215] [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: 04/17/2020] [Revised: 05/03/2020] [Accepted: 05/05/2020] [Indexed: 11/16/2022] Open
Abstract
Ebola virus disease is a severe disease, often fatal, with a mortality rate of up to 90%. Presently, effective treatment and safe prevention options for Ebola virus disease are not available. Therefore, there is an urgent need to develop control measures to prevent or limit future Ebola virus outbreaks. Ebola virus protein-based virus-like particle (VLP) and inactivated whole virion vaccines have demonstrated efficacy in animal models, and the addition of appropriate adjuvants may provide additional benefits to these vaccines, including enhanced immune responses. In this study, we screened 24 compounds from injectable excipients approved for human use in Japan and identified six compounds that significantly enhanced the humoral response to Ebola VLP vaccine in a murine model. Our novel adjuvant candidates for Ebola VLP vaccine have already been demonstrated to be safe when administered intramuscularly or subcutaneously, and therefore, they are closer to clinical trials than adjuvants whose safety profiles are unknown.
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20
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Forna A, Dorigatti I, Nouvellet P, Donnelly CA. Spatiotemporal variability in case fatality ratios for the 2013-2016 Ebola epidemic in West Africa. Int J Infect Dis 2020; 93:48-55. [PMID: 32004692 PMCID: PMC7191269 DOI: 10.1016/j.ijid.2020.01.046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 01/21/2020] [Accepted: 01/22/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND For the 2013-2016 Ebola epidemic in West Africa, the largest Ebola virus disease (EVD) epidemic to date, we aim to analyse the patient mix in detail to characterise key sources of spatiotemporal heterogeneity in the case fatality ratios (CFR). METHODS We applied a non-parametric Boosted Regression Trees (BRT) imputation approach for patients with missing survival outcomes and adjusted for model imperfection. Semivariogram analysis and kriging were used to investigate spatiotemporal heterogeneities. RESULTS CFR estimates varied significantly between districts and over time over the course of the epidemic. BRT modelling accounted for most of the spatiotemporal variation and interactions in CFR, but moderate spatial autocorrelation remained for distances up to approximately 90 km. Combining district-level CFR estimates and kriged district-level residuals provided the best linear unbiased predicted map of CFR accounting for the both explained and unexplained spatial variation. Temporal autocorrelation was not observed in the district-level residuals from the BRT estimates. CONCLUSIONS This study provides new insight into the epidemiology of the 2013-2016 West African Ebola epidemic with a view of informing future public health contingency planning, resource allocation and impact assessment. The analytical framework developed in this analysis, coupled with key domain knowledge, could be deployed in real time to support the response to ongoing and future outbreaks.
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Affiliation(s)
- Alpha Forna
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK.
| | - Ilaria Dorigatti
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Pierre Nouvellet
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK; School of Life Sciences, University of Sussex, Brighton, UK
| | - Christl A Donnelly
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK; Department of Statistics, University of Oxford, Oxford, UK
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21
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Augier C, Beyne E, Villabona-Arenas CJ, Mpoudi Ngole E, Peeters M, Ayouba A. Identification of a Novel Simian Immunodeficiency Virus-Infected African Green Monkey ( Chlorocebus tantalus) Confirms that Tantalus Monkeys in Cameroon Are Infected with a Mosaic SIVagm Lineage. AIDS Res Hum Retroviruses 2020; 36:167-170. [PMID: 31547667 DOI: 10.1089/aid.2019.0216] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In this study we report on the identification of a simian immunodeficiency virus (SIV) infecting a Chlorocebus tantalus from Cameroon. The isolate, SIVagmTAN-CA1, was molecularly characterized by sequencing partial genome (∼4,000 bp) using the conventional Sanger method and the Oxford Nanopore Technology (ONT). In pol and gp41/nef SIVagmTAN-CA1 clusters with SIVagmSAB infecting Chlorocebus sabaeus from West Africa, whereas in env-gp120 it clusters with SIVagmTAN infecting C. tantalus from Central Africa. This mosaic structure is similar to that of a previously reported isolate infecting another tantalus monkey from Cameroon and confirms that the evolution of SIVagm is complex. Our data show that ONT sequencing gives results comparable with conventional Sanger sequencing on SIV and could help in distinguishing recombination and coinfection.
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Affiliation(s)
- Camille Augier
- Recherches Translationnelles sur le VIH et Maladies Infectieuses, Institut National de la Santé et de la Recherche Médicale 1175, Institut de Recherche pour le Développement, University of Montpellier, Montpellier, France
| | - Emmanuelle Beyne
- Recherches Translationnelles sur le VIH et Maladies Infectieuses, Institut National de la Santé et de la Recherche Médicale 1175, Institut de Recherche pour le Développement, University of Montpellier, Montpellier, France
| | - Christian Julian Villabona-Arenas
- Recherches Translationnelles sur le VIH et Maladies Infectieuses, Institut National de la Santé et de la Recherche Médicale 1175, Institut de Recherche pour le Développement, University of Montpellier, Montpellier, France
| | - Eitel Mpoudi Ngole
- Centre de Recherches sur les Maladies Émergentes, Ré-émergentes et la Médecine Nucléaire, Institut de Recherches Médicales et D'études des Plantes Médicinales, Yaoundé, Cameroun
| | - Martine Peeters
- Recherches Translationnelles sur le VIH et Maladies Infectieuses, Institut National de la Santé et de la Recherche Médicale 1175, Institut de Recherche pour le Développement, University of Montpellier, Montpellier, France
| | - Ahidjo Ayouba
- Recherches Translationnelles sur le VIH et Maladies Infectieuses, Institut National de la Santé et de la Recherche Médicale 1175, Institut de Recherche pour le Développement, University of Montpellier, Montpellier, France
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22
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23
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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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24
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Sherwood LJ, Taylor AB, Hart PJ, Hayhurst A. Paratope Duality and Gullying are Among the Atypical Recognition Mechanisms Used by a Trio of Nanobodies to Differentiate Ebolavirus Nucleoproteins. J Mol Biol 2019; 431:4848-4867. [PMID: 31626803 PMCID: PMC6990103 DOI: 10.1016/j.jmb.2019.10.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 09/28/2019] [Accepted: 10/07/2019] [Indexed: 02/08/2023]
Abstract
We had previously shown that three anti–Marburg virus nanobodies (VHH or single-domain antibody [sdAb]) targeted a cryptotope within an alpha-helical assembly at the nucleoprotein (NP) C-terminus that was conserved through half a century of viral evolution. Here, we wished to determine whether an anti–Ebola virus sdAb, that was cross-reactive within the Ebolavirus genus, recognized a similar structural feature upstream of the ebolavirus NP C-terminus. In addition, we sought to determine whether the specificities of a less cross-reactive anti–Zaire ebolavirus sdAb and a totally specific anti–Sudan ebolavirus sdAb were the result of exclusion from this region. Binding and X-ray crystallographic studies revealed that the primary determinant of cross-reactivity did indeed appear to be a preference for the helical feature. Specificity, in the case of the Zaire ebolavirus–specific sdAb, arose from the footprint shifting away from the helices to engage more variable residues. While both sdAbs used CDRs, they also had atypical side-on approaches, with framework 2 helping to accommodate parts of the epitope in sizeable paratope gullies. The Sudan ebolavirus–specific sdAb was more remarkable and appeared to bind two C-terminal domains simultaneously via nonoverlapping epitopes—“paratope duality.” One mode involved paratope gullying, whereas the other involved only CDRs, with CDR3 restructuring to wedge in between opposing walls of an interdomain crevice. The varied routes used by sdAbs to engage antigens discovered here deepen our appreciation of the small scaffold’s architectural versatility and also reveal lucrative opportunities within the ebolavirus NP C-termini that might be leveraged for diagnostics and novel therapeutic targeting.
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Affiliation(s)
- Laura Jo Sherwood
- Disease Intervention and Prevention, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Alexander Bryan Taylor
- X-ray Crystallography Core Laboratory, Institutional Research Cores and Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Peter John Hart
- X-ray Crystallography Core Laboratory, Institutional Research Cores and Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA; Department of Veterans Affairs, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
| | - Andrew Hayhurst
- Disease Intervention and Prevention, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA. http://
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25
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Polyclonal and convergent antibody response to Ebola virus vaccine rVSV-ZEBOV. Nat Med 2019; 25:1589-1600. [PMID: 31591605 DOI: 10.1038/s41591-019-0602-4] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 09/04/2019] [Indexed: 11/08/2022]
Abstract
Recombinant vesicular stomatitis virus-Zaire Ebola virus (rVSV-ZEBOV) is the most advanced Ebola virus vaccine candidate and is currently being used to combat the outbreak of Ebola virus disease (EVD) in the Democratic Republic of the Congo (DRC). Here we examine the humoral immune response in a subset of human volunteers enrolled in a phase 1 rVSV-ZEBOV vaccination trial by performing comprehensive single B cell and electron microscopy structure analyses. Four studied vaccinees show polyclonal, yet reproducible and convergent B cell responses with shared sequence characteristics. EBOV-targeting antibodies cross-react with other Ebolavirus species, and detailed epitope mapping revealed overlapping target epitopes with antibodies isolated from EVD survivors. Moreover, in all vaccinees, we detected highly potent EBOV-neutralizing antibodies with activities comparable or superior to the monoclonal antibodies currently used in clinical trials. These include antibodies combining the IGHV3-15/IGLV1-40 immunoglobulin gene segments that were identified in all investigated individuals. Our findings will help to evaluate and direct current and future vaccination strategies and offer opportunities for novel EVD therapies.
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26
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Jerome H, Taylor C, Sreenu VB, Klymenko T, Filipe ADS, Jackson C, Davis C, Ashraf S, Wilson-Davies E, Jesudason N, Devine K, Harder L, Aitken C, Gunson R, Thomson EC. Metagenomic next-generation sequencing aids the diagnosis of viral infections in febrile returning travellers. J Infect 2019; 79:383-388. [PMID: 31398374 PMCID: PMC6859916 DOI: 10.1016/j.jinf.2019.08.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 07/18/2019] [Accepted: 08/03/2019] [Indexed: 01/20/2023]
Abstract
OBJECTIVES Travel-associated infections are challenging to diagnose because of the broad spectrum of potential aetiologies. As a proof-of-principle study, we used MNGS to identify viral pathogens in clinical samples from returning travellers in a single center to explore its suitability as a diagnostic tool. METHODS Plasma samples from 40 returning travellers presenting with a fever of ≥38°C were sequenced using MNGS on the Illumina MiSeq platform and compared with standard-of-care diagnostic assays. RESULTS In total, 11/40 patients were diagnosed with a viral infection. Standard of care diagnostics revealed 5 viral infections using plasma samples; dengue virus 1 (n = 2), hepatitis E (n = 1), Ebola virus (n = 1) and hepatitis A (n = 1), all of which were detected by MNGS. Three additional patients with Chikungunya virus (n = 2) and mumps virus were diagnosed by MNGS only. Respiratory infections detected by nasal/throat swabs only were not detected by MNGS of plasma. One patient had infection with malaria and mumps virus during the same admission. CONCLUSIONS MNGS analysis of plasma samples improves the sensitivity of diagnosis of viral infections and has potential as an all-in-one diagnostic test. It can be used to identify infections that have not been considered by the treating physician, co-infections and new or emerging pathogens. SUMMARY Next generation sequencing (NGS) has potential as an all-in-one diagnostic test. In this study we used NGS to diagnose returning travellers with acute febrile illness in the UK, highlighting cases where the diagnosis was missed using standard methods.
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Affiliation(s)
- Hanna Jerome
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow G61 1QH, UK
| | - Callum Taylor
- Department of Infectious Diseases, Queen Elizabeth University Hospital, 1345 Govan Rd, Govan, Glasgow G51 4TF, UK
| | - Vattipally B. Sreenu
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow G61 1QH, UK
| | - Tanya Klymenko
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow G61 1QH, UK
| | - Ana Da Silva Filipe
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow G61 1QH, UK
| | - Celia Jackson
- West of Scotland Specialist Virology Centre, Level 5, New Lister Building, Glasgow Royal Infirmary, 10-16 Alexandra Parade, Glasgow G31 2ER, UK
| | - Chris Davis
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow G61 1QH, UK
| | - Shirin Ashraf
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow G61 1QH, UK
| | - Eleri Wilson-Davies
- West of Scotland Specialist Virology Centre, Level 5, New Lister Building, Glasgow Royal Infirmary, 10-16 Alexandra Parade, Glasgow G31 2ER, UK
| | - Natasha Jesudason
- Queen Elizabeth University Hospital, 1345 Govan Rd, Govan, Glasgow G51 4TF, UK
| | - Karen Devine
- Department of Infectious Diseases, Queen Elizabeth University Hospital, 1345 Govan Rd, Govan, Glasgow G51 4TF, UK
| | - Lisbeth Harder
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow G61 1QH, UK
| | - Celia Aitken
- West of Scotland Specialist Virology Centre, Level 5, New Lister Building, Glasgow Royal Infirmary, 10-16 Alexandra Parade, Glasgow G31 2ER, UK
| | - Rory Gunson
- West of Scotland Specialist Virology Centre, Level 5, New Lister Building, Glasgow Royal Infirmary, 10-16 Alexandra Parade, Glasgow G31 2ER, UK
| | - Emma C. Thomson
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow G61 1QH, UK
- Department of Infectious Diseases, Queen Elizabeth University Hospital, 1345 Govan Rd, Govan, Glasgow G51 4TF, UK
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27
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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: 16] [Impact Index Per Article: 3.2] [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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Mbala-Kingebeni P, Pratt CB, Wiley MR, Diagne MM, Makiala-Mandanda S, Aziza A, Di Paola N, Chitty JA, Diop M, Ayouba A, Vidal N, Faye O, Faye O, Karhemere S, Aruna A, Nsio J, Mulangu F, Mukadi D, Mukadi P, Kombe J, Mulumba A, Duraffour S, Likofata J, Pukuta E, Caviness K, Bartlett ML, Gonzalez J, Minogue T, Sozhamannan S, Gross SM, Schroth GP, Kuhn JH, Donaldson EF, Delaporte E, Sanchez-Lockhart M, Peeters M, Muyembe-Tamfum JJ, Alpha Sall A, Palacios G, Ahuka-Mundeke S. 2018 Ebola virus disease outbreak in Équateur Province, Democratic Republic of the Congo: a retrospective genomic characterisation. THE LANCET. INFECTIOUS DISEASES 2019; 19:641-647. [PMID: 31000465 DOI: 10.1016/s1473-3099(19)30124-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 02/09/2019] [Accepted: 02/15/2019] [Indexed: 01/08/2023]
Abstract
BACKGROUND The 2018 Ebola virus disease (EVD) outbreak in Équateur Province, Democratic Republic of the Congo, began on May 8, and was declared over on July 24; it resulted in 54 documented cases and 33 deaths. We did a retrospective genomic characterisation of the outbreak and assessed potential therapeutic agents and vaccine (medical countermeasures). METHODS We used target-enrichment sequencing to produce Ebola virus genomes from samples obtained in the 2018 Équateur Province outbreak. Combining these genomes with genomes associated with known outbreaks from GenBank, we constructed a maximum-likelihood phylogenetic tree. In-silico analyses were used to assess potential mismatches between the outbreak strain and the probes and primers of diagnostic assays and the antigenic sites of the experimental rVSVΔG-ZEBOV-GP vaccine and therapeutics. An in-vitro flow cytometry assay was used to assess the binding capability of the individual components of the monoclonal antibody cocktail ZMapp. FINDINGS A targeted sequencing approach produced 16 near-complete genomes. Phylogenetic analysis of these genomes and 1011 genomes from GenBank revealed a distinct cluster, confirming a new Ebola virus variant, for which we propose the name "Tumba". This new variant appears to have evolved at a slower rate than other Ebola virus variants (0·69 × 10-3 substitutions per site per year with "Tumba" vs 1·06 × 10-3 substitutions per site per year without "Tumba"). We found few sequence mismatches in the assessed assay target regions and antigenic sites. We identified nine amino acid changes in the Ebola virus surface glycoprotein, of which one resulted in reduced binding of the 13C6 antibody within the ZMapp cocktail. INTERPRETATION Retrospectively, we show the feasibility of using genomics to rapidly characterise a new Ebola virus variant within the timeframe of an outbreak. Phylogenetic analysis provides further indications that these variants are evolving at differing rates. Rapid in-silico analyses can direct in-vitro experiments to quickly assess medical countermeasures. FUNDING Defense Biological Product Assurance Office.
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Affiliation(s)
- Placide Mbala-Kingebeni
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo; TransVIHMI, Institut de Recherche pour le Développement, Institut National de la Santé et de la Recherche Médicale, Université de Montpellier, Montpellier, France; Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Catherine B Pratt
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA; College of Public Health, University of Nebraska Medical Center, Omaha, NE, USA
| | - Michael R Wiley
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA; College of Public Health, University of Nebraska Medical Center, Omaha, NE, USA
| | | | - Sheila Makiala-Mandanda
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo; Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Amuri Aziza
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | - Nicholas Di Paola
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Joseph A Chitty
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | | | - Ahidjo Ayouba
- TransVIHMI, Institut de Recherche pour le Développement, Institut National de la Santé et de la Recherche Médicale, Université de Montpellier, Montpellier, France
| | - Nicole Vidal
- TransVIHMI, Institut de Recherche pour le Développement, Institut National de la Santé et de la Recherche Médicale, Université de Montpellier, Montpellier, France
| | | | - Oumar Faye
- Institut Pasteur de Dakar, Dakar, Senegal
| | - Stormy Karhemere
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | - Aaron Aruna
- Direction Générale de Lutte contre la Maladie, Kinshasa, Democratic Republic of the Congo
| | - Justus Nsio
- Direction Générale de Lutte contre la Maladie, Kinshasa, Democratic Republic of the Congo
| | - Felix Mulangu
- Direction Générale de Lutte contre la Maladie, Kinshasa, Democratic Republic of the Congo
| | - Daniel Mukadi
- Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Patrick Mukadi
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | - John Kombe
- Direction Générale de Lutte contre la Maladie, Kinshasa, Democratic Republic of the Congo
| | - Anastasie Mulumba
- Monsieur le Représentant de l'Organisation Mondiale de la Santé, Democratic Republic of the Congo
| | - Sophie Duraffour
- Monsieur le Représentant de l'Organisation Mondiale de la Santé, Democratic Republic of the Congo; Bernhard-Nocht-Institut für Tropenmedizin, Hamburg, Germany
| | - Jacques Likofata
- Laboratoire Provinciale, Mbandaka, Democratic Republic of the Congo
| | - Elisabeth Pukuta
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | - Katie Caviness
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Maggie L Bartlett
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA; Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Jeanette Gonzalez
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Timothy Minogue
- Diagnostics Services Division, US Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Shanmuga Sozhamannan
- Defense Biological Product Assurance Office, Joint Program Executive Office for Chemical, Biological, Radiological and Nuclear Defense-Joint Project Management Office for Guardian, Frederick, MD, USA; Logistics Management Institute, Tysons, VA, USA
| | | | | | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA
| | - Eric F Donaldson
- Division of Antiviral Products, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Eric Delaporte
- TransVIHMI, Institut de Recherche pour le Développement, Institut National de la Santé et de la Recherche Médicale, Université de Montpellier, Montpellier, France
| | - Mariano Sanchez-Lockhart
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA; Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Martine Peeters
- TransVIHMI, Institut de Recherche pour le Développement, Institut National de la Santé et de la Recherche Médicale, Université de Montpellier, Montpellier, France
| | - Jean-Jacques Muyembe-Tamfum
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo; Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | | | - Gustavo Palacios
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA.
| | - Steve Ahuka-Mundeke
- Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa, Democratic Republic of the Congo; Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
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Mbala-Kingebeni P, Aziza A, Di Paola N, Wiley MR, Makiala-Mandanda S, Caviness K, Pratt CB, Ladner JT, Kugelman JR, Prieto K, Chitty JA, Larson PA, Beitzel B, Ayouba A, Vidal N, Karhemere S, Diop M, Diagne MM, Faye M, Faye O, Aruna A, Nsio J, Mulangu F, Mukadi D, Mukadi P, Kombe J, Mulumba A, Villabona-Arenas CJ, Pukuta E, Gonzalez J, Bartlett ML, Sozhamannan S, Gross SM, Schroth GP, Tim R, Zhao JJ, Kuhn JH, Diallo B, Yao M, Fall IS, Ndjoloko B, Mossoko M, Lacroix A, Delaporte E, Sanchez-Lockhart M, Sall AA, Muyembe-Tamfum JJ, Peeters M, Palacios G, Ahuka-Mundeke S. Medical countermeasures during the 2018 Ebola virus disease outbreak in the North Kivu and Ituri Provinces of the Democratic Republic of the Congo: a rapid genomic assessment. THE LANCET. INFECTIOUS DISEASES 2019; 19:648-657. [PMID: 31000464 DOI: 10.1016/s1473-3099(19)30118-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 02/21/2019] [Accepted: 03/06/2019] [Indexed: 11/30/2022]
Abstract
BACKGROUND The real-time generation of information about pathogen genomes has become a vital goal for transmission analysis and characterisation in rapid outbreak responses. In response to the recently established genomic capacity in the Democratic Republic of the Congo, we explored the real-time generation of genomic information at the start of the 2018 Ebola virus disease (EVD) outbreak in North Kivu Province. METHODS We used targeted-enrichment sequencing to produce two coding-complete Ebola virus genomes 5 days after declaration of the EVD outbreak in North Kivu. Subsequent sequencing efforts yielded an additional 46 genomes. Genomic information was used to assess early transmission, medical countermeasures, and evolution of Ebola virus. FINDINGS The genomic information demonstrated that the EVD outbreak in the North Kivu and Ituri Provinces was distinct from the 2018 EVD outbreak in Équateur Province of the Democratic Republic of the Congo. Primer and probe mismatches to Ebola virus were identified in silico for all deployed diagnostic PCR assays, with the exception of the Cepheid GeneXpert GP assay. INTERPRETATION The first two coding-complete genomes provided actionable information in real-time for the deployment of the rVSVΔG-ZEBOV-GP Ebola virus envelope glycoprotein vaccine, available therapeutics, and sequence-based diagnostic assays. Based on the mutations identified in the Ebola virus surface glycoprotein (GP12) observed in all 48 genomes, deployed monoclonal antibody therapeutics (mAb114 and ZMapp) should be efficacious against the circulating Ebola virus variant. Rapid Ebola virus genomic characterisation should be included in routine EVD outbreak response procedures to ascertain efficacy of medical countermeasures. FUNDING Defense Biological Product Assurance Office.
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Affiliation(s)
- Placide Mbala-Kingebeni
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo; TransVIHMI, Institut de Recherche pour le Développement, Institut National de la Santé et de la Recherche Médicale, Université de Montpellier, Montpellier, France; Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Amuri Aziza
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | - Nicholas Di Paola
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Michael R Wiley
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA; College of Public Health, Northern Arizona University, Flagstaff, AZ, USA
| | - Sheila Makiala-Mandanda
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo; Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Katie Caviness
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Catherine B Pratt
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA; College of Public Health, Northern Arizona University, Flagstaff, AZ, USA
| | - Jason T Ladner
- University of Nebraska Medical Center, Omaha, NE, USA; The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | | | - Karla Prieto
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA; College of Public Health, Northern Arizona University, Flagstaff, AZ, USA
| | - Joseph A Chitty
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Peter A Larson
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Brett Beitzel
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Ahidjo Ayouba
- TransVIHMI, Institut de Recherche pour le Développement, Institut National de la Santé et de la Recherche Médicale, Université de Montpellier, Montpellier, France
| | - Nicole Vidal
- TransVIHMI, Institut de Recherche pour le Développement, Institut National de la Santé et de la Recherche Médicale, Université de Montpellier, Montpellier, France
| | - Stomy Karhemere
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | | | | | | | | | - Aaron Aruna
- Direction Générale de Lutte contre la Maladie, Kinshasa, Democratic Republic of the Congo
| | - Justus Nsio
- Direction Générale de Lutte contre la Maladie, Kinshasa, Democratic Republic of the Congo
| | - Felix Mulangu
- Direction Générale de Lutte contre la Maladie, Kinshasa, Democratic Republic of the Congo
| | - Daniel Mukadi
- Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Patrick Mukadi
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | - John Kombe
- Direction Générale de Lutte contre la Maladie, Kinshasa, Democratic Republic of the Congo
| | - Anastasie Mulumba
- l'Organisation Mondiale de la Santé, Kinshasa, Democratic Republic of the Congo
| | | | - Elisabeth Pukuta
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | - Jeanette Gonzalez
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Maggie L Bartlett
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA; Department of Pathology and Microbiology, Northern Arizona University, Flagstaff, AZ, USA
| | - Shanmuga Sozhamannan
- Defense Biological Product Assurance Office, Joint Program Executive Office for Chemical, Biological, Radiological and Nuclear Defense-Joint Project Management Office for Guardian, Frederick, MA, USA; The Tauri Group, Alexandria, VA, USA
| | | | | | | | | | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA
| | | | - Michel Yao
- World Health Organization, Geneva, Switzerland
| | | | - Bathe Ndjoloko
- Direction Générale de Lutte contre la Maladie, Kinshasa, Democratic Republic of the Congo
| | - Mathias Mossoko
- Direction Générale de Lutte contre la Maladie, Kinshasa, Democratic Republic of the Congo
| | - Audrey Lacroix
- TransVIHMI, Institut de Recherche pour le Développement, Institut National de la Santé et de la Recherche Médicale, Université de Montpellier, Montpellier, France
| | - Eric Delaporte
- TransVIHMI, Institut de Recherche pour le Développement, Institut National de la Santé et de la Recherche Médicale, Université de Montpellier, Montpellier, France
| | - Mariano Sanchez-Lockhart
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA; Department of Pathology and Microbiology, Northern Arizona University, Flagstaff, AZ, USA
| | | | - Jean-Jacques Muyembe-Tamfum
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo; Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Martine Peeters
- TransVIHMI, Institut de Recherche pour le Développement, Institut National de la Santé et de la Recherche Médicale, Université de Montpellier, Montpellier, France
| | - Gustavo Palacios
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA.
| | - Steve Ahuka-Mundeke
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo; Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa, Democratic Republic of the Congo
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Nsio J, Kapetshi J, Makiala S, Raymond F, Tshapenda G, Boucher N, Corbeil J, Okitandjate A, Mbuyi G, Kiyele M, Mondonge V, Kikoo MJ, Van Herp M, Barboza P, Petrucci R, Benedetti G, Formenty P, Muyembe Muzinga B, Ilunga Kalenga O, Ahuka S, Fausther-Bovendo H, Ilunga BK, Kobinger GP, Muyembe JJT. 2017 Outbreak of Ebola Virus Disease in Northern Democratic Republic of Congo. J Infect Dis 2019; 221:701-706. [DOI: 10.1093/infdis/jiz107] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 03/22/2019] [Indexed: 11/12/2022] Open
Affiliation(s)
- Justus Nsio
- Ministry of Health, Kinshasa, Democratic Republic of the Congo
| | - Jimmy Kapetshi
- Institut National de Recherche Biomedicale, Kinshasa, Democratic Republic of the Congo
| | - Sheila Makiala
- Institut National de Recherche Biomedicale, Kinshasa, Democratic Republic of the Congo
| | | | | | | | | | | | - Gisele Mbuyi
- Ministry of Health, Kinshasa, Democratic Republic of the Congo
| | - Musa Kiyele
- Ministry of Health, Kinshasa, Democratic Republic of the Congo
| | - Vital Mondonge
- World Health Organization (WHO), Kinshasa, Democratic Republic of the Congo
| | - Marie Jose Kikoo
- World Health Organization (WHO), Kinshasa, Democratic Republic of the Congo
| | | | | | | | - Guido Benedetti
- Medical Department, Operational Centre–Brussels, MSF, Luxembourg, Luxembourg
| | | | - Baby Muyembe Muzinga
- Institut National de Recherche Biomedicale, Kinshasa, Democratic Republic of the Congo
| | | | - Steve Ahuka
- Institut National de Recherche Biomedicale, Kinshasa, Democratic Republic of the Congo
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Malvy D, McElroy AK, de Clerck H, Günther S, van Griensven J. Ebola virus disease. Lancet 2019; 393:936-948. [PMID: 30777297 DOI: 10.1016/s0140-6736(18)33132-5] [Citation(s) in RCA: 246] [Impact Index Per Article: 49.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 11/12/2018] [Accepted: 11/28/2018] [Indexed: 12/17/2022]
Abstract
Ebolaviruses are pathogenic agents associated with a severe, potentially fatal, systemic disease in man and great apes. Four species of ebolaviruses have been identified in west or equatorial Africa. Once the more virulent forms enter the human population, transmission occurs primarily through contact with infected body fluids and can result in major epidemics in under-resourced settings. These viruses cause a disease characterised by systemic viral replication, immune suppression, abnormal inflammatory responses, major fluid and electrolyte losses, and high mortality. Despite recent progress on vaccines, and with no licensed prophylaxis or treatment available, case management is essentially supportive with management of severe multiple organ failure resulting from immune-mediated cell damage. The 2013-16 outbreak was classified by WHO as a Public Health Emergency of International Concern, which drew attention to the challenges of diseases caused by infections with ebolaviruses and questioned scientific, clinical, and societal preparation to handle future epidemics.
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Affiliation(s)
- Denis Malvy
- Department for Infectious and Tropical Diseases, University Hospital Centre of Bordeaux, Bordeaux, France; INSERM 1219, University of Bordeaux, Bordeaux, France.
| | - Anita K McElroy
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | | | - Stephan Günther
- Department of Virology, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Germany
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Shabardina V, Kischka T, Manske F, Grundmann N, Frith MC, Suzuki Y, Makałowski W. NanoPipe-a web server for nanopore MinION sequencing data analysis. Gigascience 2019; 8:giy169. [PMID: 30689855 PMCID: PMC6377397 DOI: 10.1093/gigascience/giy169] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 12/10/2018] [Accepted: 12/23/2018] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND The fast-moving progress of the third-generation long-read sequencing technologies will soon bring the biological and medical sciences to a new era of research. Altogether, the technique and experimental procedures are becoming more straightforward and available to biologists from diverse fields, even without any profound experience in DNA sequencing. Thus, the introduction of the MinION device by Oxford Nanopore Technologies promises to "bring sequencing technology to the masses" and also allows quick and operative analysis in field studies. However, the convenience of this sequencing technology dramatically contrasts with the available analysis tools, which may significantly reduce enthusiasm of a "regular" user. To really bring the sequencing technology to every biologist, we need a set of user-friendly tools that can perform a powerful analysis in an automatic manner. FINDINGS NanoPipe was developed in consideration of the specifics of the MinION sequencing technologies, providing accordingly adjusted alignment parameters. The range of the target species/sequences for the alignment is not limited, and the descriptive usage page of NanoPipe helps a user to succeed with NanoPipe analysis. The results contain alignment statistics, consensus sequence, polymorphisms data, and visualization of the alignment. Several test cases are used to demonstrate the efficiency of the tool. CONCLUSIONS Freely available NanoPipe software allows effortless and reliable analysis of MinION sequencing data for experienced bioinformaticians, as well for wet-lab biologists with minimum bioinformatics knowledge. Moreover, for the latter group, we describe the basic algorithm necessary for MinION sequencing analysis from the first to last step.
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Affiliation(s)
- Victoria Shabardina
- Institue of Bioinformatics, University of Muenster, Niels-Stensen-Strasse 14, Muenster, 48149, Germany
| | - Tabea Kischka
- Institue of Bioinformatics, University of Muenster, Niels-Stensen-Strasse 14, Muenster, 48149, Germany
| | - Felix Manske
- Institue of Bioinformatics, University of Muenster, Niels-Stensen-Strasse 14, Muenster, 48149, Germany
| | - Norbert Grundmann
- Institue of Bioinformatics, University of Muenster, Niels-Stensen-Strasse 14, Muenster, 48149, Germany
| | - Martin C Frith
- Artificial Intelligence Research Center, AIST, 2-3-26, Aomi, Koto-ku, Tokyo, 135-0064, Japan
- Department of Computational Biology and Medical Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan
- AIST-Waseda University Computational Bio Big Data Open Innovation Laboratory, 3-4-1 Ookubo, Shinjuku-ku, Tokyo, 169-8555, Japan
| | - Yutaka Suzuki
- Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan
| | - Wojciech Makałowski
- Institue of Bioinformatics, University of Muenster, Niels-Stensen-Strasse 14, Muenster, 48149, Germany
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Phylodynamic Analysis of Ebola Virus Disease Transmission in Sierra Leone. Viruses 2019; 11:v11010071. [PMID: 30654482 PMCID: PMC6356631 DOI: 10.3390/v11010071] [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: 12/27/2018] [Revised: 01/11/2019] [Accepted: 01/14/2019] [Indexed: 12/20/2022] Open
Abstract
We generated genome sequences from 218 cases of Ebola virus disease (EVD) in Sierra Leone (SLE) during 2014–2015 to complement available datasets, particularly by including cases from a period of low sequence coverage during peak transmission of Ebola virus (EBOV) in the highly-affected Western Area division of SLE. The combined dataset was utilized to produce phylogenetic and phylodynamic inferences, to study sink–source dynamics and virus dispersal from highly-populated transmission hotspots. We identified four districts in SLE where EBOV was introduced and transmission occurred without onward exportation to other districts. We also identified six districts that substantially contributed to the dispersal of the virus and prolonged the EVD outbreak: five of these served as major hubs, with lots of movement in and out, and one acted primarily as a source, exporting the virus to other areas of the country. Positive correlations between case numbers, inter-district transition events, and district population sizes reaffirm that population size was a driver of EBOV transmission dynamics in SLE. The data presented here confirm the role of urban hubs in virus dispersal and of a delayed laboratory response in the expansion and perpetuation of the EVD outbreak in SLE.
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