Integration of genomic sequencing into the response to the Ebola virus outbreak in Nord Kivu, Democratic Republic of the Congo

Kinganda-Lusamaki, Eddy; Black, Allison; Mukadi, Daniel; Hadfield, James; Mbala-Kingebeni, Placide; Pratt, Catherine; Aziza, Amuri; Diagne, Moussa Moïse; White, Brian; Bisento, Nella; Nsunda, Bibiche; Akonga, Marceline; Faye, Martin; Faye, Ousmane; Edidi-Atani, François; Matondo-Kuamfumu, Meris; Mambu-Mbika, Fabrice; Bulabula, Junior; Paola, Nicholas Di; Pauthner, Matthias G.; Andersen, Kristian G.; Palacios, Gustavo; Delaporte, Éric; Sall, Amadou Alpha; Peeters, Martine; Wiley, Michael R.; Ahuka‐Mundeke, Steve; Bedford, Trevor; Tamfum, Jean Jacques Muyembe

doi:10.1038/s41591-021-01302-z

Cited by 45 publications

(25 citation statements)

References 17 publications

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“…Direct sequencing in the field can provide actionable data to identify and characterize transmission chains and assist contact tracing in near real time [12,13]. Furthermore, sequencing analyses performed on patient samples early in an outbreak can provide critical information as to whether currently available MCMs may be effective based on the species and strain of the virus in circulation; the data can also help monitor for the development of resistance to deployed countermeasures [14]. Inclusion of Next Generation Sequencing (NGS) technologies into the field laboratory, however, is not without its challenges, including necessary increases in the laboratory footprint and the requirement that laboratorians with specialized skills be deployed.…”

Section: Evd Diagnostics: Ebov-specific Assays and Genome Sequencingmentioning

confidence: 99%

The Evolution of Medical Countermeasures for Ebola Virus Disease: Lessons Learned and Next Steps

et al. 2022

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The Ebola virus disease outbreak that occurred in Western Africa from 2013–2016, and subsequent smaller but increasingly frequent outbreaks of Ebola virus disease in recent years, spurred an unprecedented effort to develop and deploy effective vaccines, therapeutics, and diagnostics. This effort led to the U.S. regulatory approval of a diagnostic test, two vaccines, and two therapeutics for Ebola virus disease indications. Moreover, the establishment of fieldable diagnostic tests improved the speed with which patients can be diagnosed and public health resources mobilized. The United States government has played and continues to play a key role in funding and coordinating these medical countermeasure efforts. Here, we describe the coordinated U.S. government response to develop medical countermeasures for Ebola virus disease and we identify lessons learned that may improve future efforts to develop and deploy effective countermeasures against other filoviruses, such as Sudan virus and Marburg virus.

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Section: Evd Diagnostics: Ebov-specific Assays and Genome Sequencingmentioning

confidence: 99%

The Evolution of Medical Countermeasures for Ebola Virus Disease: Lessons Learned and Next Steps

et al. 2022

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“…Reads were mapped to an EBOV Ituri reference genome (MK007329) using in-house scripts-consisting of adaptor removal (cutadapt), quality trimming (printseq-lite -min_qual_mean 25 -trim_qual_right 20 -min_len 50), read mapping (BWA-mem), PCR-de-duplication (picard MarkDuplicates) and consensus genomes were called using Geneious (threshold = 0%, Assign Quality = total, minimum coverage > 2; version 10). Evolutionary history was inferred with EBOV genomes from Genbank and INRB [16][17][18] ((using raxml (-m GTRGAMMA -p $RANDOM -f a -x $RAN-DOM -N 1000) with bootstrap support provided by 1000 iterations. EBOV genomes were deposited to Genbank: MZ854250-3.…”

Section: Laboratory Testingmentioning

confidence: 99%

First laboratory confirmation and sequencing of Zaire ebolavirus in Uganda following two independent introductions of cases from the 10th Ebola Outbreak in the Democratic Republic of the Congo, June 2019

et al. 2022

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Uganda established a domestic Viral Hemorrhagic Fever (VHF) testing capacity in 2010 in response to the increasing occurrence of filovirus outbreaks. In July 2018, the neighboring Democratic Republic of Congo (DRC) experienced its 10th Ebola Virus Disease (EVD) outbreak and for the duration of the outbreak, the Ugandan Ministry of Health (MOH) initiated a national EVD preparedness stance. Almost one year later, on 10th June 2019, three family members who had contracted EVD in the DRC crossed into Uganda to seek medical treatment. Samples were collected from all the suspected cases using internationally established biosafety protocols and submitted for VHF diagnostic testing at Uganda Virus Research Institute. All samples were initially tested by RT-PCR for ebolaviruses, marburgviruses, Rift Valley fever (RVF) virus and Crimean-Congo hemorrhagic fever (CCHF) virus. Four people were identified as being positive for Zaire ebolavirus, marking the first report of Zaire ebolavirus in Uganda. In-country Next Generation Sequencing (NGS) and phylogenetic analysis was performed for the first time in Uganda, confirming the outbreak as imported from DRC at two different time point from different clades. This rapid response by the MoH, UVRI and partners led to the control of the outbreak and prevention of secondary virus transmission.

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“…Whole-genome sequencing technology and networks available, which have been driven by viral research to provide real-time data on the mutation and evolution of viral pathogens [ 16 ], also have the potential to improve fungal vaccine and antifungal targets research in Africa. Data from Democratic Republic of Congo on Ebola virus response and research have shown that a combination of genomic and epidemiological surveillance can be used in response to infectious disease outbreak and containment [ 17 ]. The African Pathogen Genomics Initiative network, which links genomic sequencing laboratories in Africa, holds great promise in fungal genomics research and surveillance of emerging infections such as emergomycosis and mucormycosis, data sharing, and can improve fungal genome sequencing capability across the continent.…”

Section: Africa: Current Statisticsmentioning

confidence: 99%

The impact of COVID-19 pandemic on invasive fungal infections in Africa: What have we learned?

Ibe

2022

PLoS Negl Trop Dis

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Invasive fungal infections (IFIs) have been described as diseases of the poor. The mortality rate of the infections is comparable to that of malaria, HIV, and TB, yet the infections remain poorly funded, neglected in research, and policy at all levels of human resources. The Coronavirus Disease 2019 (COVID-19) pandemic has further worsened the current state of management for IFIs. At the same time, response to COVID-19 has stirred and boosted vaccine production, vaccine substance manufacturing, and building of next-generation sequencing capacity and genomics data sharing network in the continent. Through collaboration and transdisciplinary research effort, these network and technology can be extended to encourage fungal research to address health issues of existing and emerging fungal pathogens.

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Integration of genomic sequencing into the response to the Ebola virus outbreak in Nord Kivu, Democratic Republic of the Congo

Cited by 45 publications

References 17 publications

The Evolution of Medical Countermeasures for Ebola Virus Disease: Lessons Learned and Next Steps

The Evolution of Medical Countermeasures for Ebola Virus Disease: Lessons Learned and Next Steps

First laboratory confirmation and sequencing of Zaire ebolavirus in Uganda following two independent introductions of cases from the 10th Ebola Outbreak in the Democratic Republic of the Congo, June 2019

The impact of COVID-19 pandemic on invasive fungal infections in Africa: What have we learned?

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