Dataset Information

Rapid outbreak sequencing of Ebola virus in Sierra Leone identifies transmission chains linked to sporadic cases.

ABSTRACT: To end the largest known outbreak of Ebola virus disease (EVD) in West Africa and to prevent new transmissions, rapid epidemiological tracing of cases and contacts was required. The ability to quickly identify unknown sources and chains of transmission is key to ending the EVD epidemic and of even greater importance in the context of recent reports of Ebola virus (EBOV) persistence in survivors. Phylogenetic analysis of complete EBOV genomes can provide important information on the source of any new infection. A local deep sequencing facility was established at the Mateneh Ebola Treatment Centre in central Sierra Leone. The facility included all wetlab and computational resources to rapidly process EBOV diagnostic samples into full genome sequences. We produced 554 EBOV genomes from EVD cases across Sierra Leone. These genomes provided a detailed description of EBOV evolution and facilitated phylogenetic tracking of new EVD cases. Importantly, we show that linked genomic and epidemiological data can not only support contact tracing but also identify unconventional transmission chains involving body fluids, including semen. Rapid EBOV genome sequencing, when linked to epidemiological information and a comprehensive database of virus sequences across the outbreak, provided a powerful tool for public health epidemic control efforts.

SUBMITTER: Arias A

PROVIDER: S-EPMC5499387 | biostudies-literature | 2016 Jan

REPOSITORIES: biostudies-literature

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Rapid outbreak sequencing of Ebola virus in Sierra Leone identifies transmission chains linked to sporadic cases.

Arias Armando A Watson Simon J SJ Asogun Danny D Tobin Ekaete Alice EA Lu Jia J Phan My V T MVT Jah Umaru U Wadoum Raoul Emeric Guetiya REG Meredith Luke L Thorne Lucy L Caddy Sarah S Tarawalie Alimamy A Langat Pinky P Dudas Gytis G Faria Nuno R NR Dellicour Simon S Kamara Abdul A Kargbo Brima B Kamara Brima Osaio BO Gevao Sahr S Cooper Daniel D Newport Matthew M Horby Peter P Dunning Jake J Sahr Foday F Brooks Tim T Simpson Andrew J H AJH Groppelli Elisabetta E Liu Guoying G Mulakken Nisha N Rhodes Kate K Akpablie James J Yoti Zabulon Z Lamunu Margaret M Vitto Esther E Otim Patrick P Owilli Collins C Boateng Isaac I Okoror Lawrence L Omomoh Emmanuel E Oyakhilome Jennifer J Omiunu Racheal R Yemisis Ighodalo I Adomeh Donatus D Ehikhiametalor Solomon S Akhilomen Patience P Aire Chris C Kurth Andreas A Cook Nicola N Baumann Jan J Gabriel Martin M Wölfel Roman R Di Caro Antonino A Carroll Miles W MW Günther Stephan S Redd John J Naidoo Dhamari D Pybus Oliver G OG Rambaut Andrew A Kellam Paul P Goodfellow Ian I Cotten Matthew M

Virus evolution 20160101 1

To end the largest known outbreak of Ebola virus disease (EVD) in West Africa and to prevent new transmissions, rapid epidemiological tracing of cases and contacts was required. The ability to quickly identify unknown sources and chains of transmission is key to ending the EVD epidemic and of even greater importance in the context of recent reports of Ebola virus (EBOV) persistence in survivors. Phylogenetic analysis of complete EBOV genomes can provide important information on the source of any ...[more]

PMID: 28694998

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Project description:BackgroundPerceived susceptibility to a disease threat (risk perception) can influence protective behaviour. This study aims to determine how exposure to information sources, knowledge and behaviours potentially influenced risk perceptions during the 2014-2015 Ebola Virus Disease outbreak in Sierra Leone.MethodsThe study is based on three cross-sectional, national surveys (August 2014, n = 1413; October 2014, n = 2086; December 2014, n = 3540) that measured Ebola-related knowledge, attitudes, and practices in Sierra Leone. Data were pooled and composite variables were created for knowledge, misconceptions and three Ebola-specific behaviours. Risk perception was measured using a Likert-item and dichotomised into 'no risk perception' and 'some risk perception'. Exposure to five information sources was dichotomised into a binary variable for exposed and unexposed. Multilevel logistic regression models were fitted to examine various associations.ResultsExposure to new media (e.g. internet) and community-level information sources (e.g. religious leaders) were positively associated with expressing risk perception. Ebola-specific knowledge and hand washing were positively associated with expressing risk perception (Adjusted OR [AOR] 1.4, 95% Confidence Interval [CI] 1.2-1.8 and AOR 1.4, 95% CI 1.1-1.7 respectively), whereas misconceptions and avoiding burials were negatively associated with risk perception, (AOR 0.7, 95% CI 0.6-0.8 and AOR 0.8, 95% CI 06-1.0, respectively).ConclusionsOur results illustrate the complexity of how individuals perceived their Ebola acquisition risk based on the way they received information, what they knew about Ebola, and actions they took to protect themselves. Community-level information sources may help to align the public's perceived risk with their actual epidemiological risk. As part of global health security efforts, increased investments are needed for community-level engagements that allow for two-way communication during health emergencies.

Dataset Information

Rapid outbreak sequencing of Ebola virus in Sierra Leone identifies transmission chains linked to sporadic cases.

Publications

Rapid outbreak sequencing of Ebola virus in Sierra Leone identifies transmission chains linked to sporadic cases.

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