Complete Genome Sequence of a New Ebola Virus Strain Isolated during the 2017 Likati Outbreak in the Democratic Republic of the Congo.
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ABSTRACT:
SUBMITTER: Wawina-Bokalanga T
PROVIDER: S-EPMC6522791 | biostudies-literature | 2019 May
REPOSITORIES: biostudies-literature
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Complete Genome Sequence of a New Ebola Virus Strain Isolated during the 2017 Likati Outbreak in the Democratic Republic of the Congo.
Wawina-Bokalanga Tony T Vanmechelen Bert B Martí-Carreras Joan J Vergote Valentijn V Vermeire Kurt K Muyembe-Tamfum Jean-Jacques JJ Ahuka-Mundeke Steve S Maes Piet P
Microbiology resource announcements 20190516 20
Genomic sequencing for early identification of Ebola virus remains a big challenge in low-income countries. Here, we report the complete genome sequence of an Ebola virus strain obtained during the 2017 Likati outbreak in the Democratic Republic of the Congo (DRC) by using the Oxford Nanopore Technologies (ONT) MinION sequencer. ...[more]
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Project description:While the clinical, laboratory and epidemiological investigation results of the Ebola outbreak in Likati Health Zone, Democratic Republic of the Congo (DRC) in May 2017 have been previously reported, we provide novel commentary on the contextual, social, and epidemiological characteristics of the epidemic. As first responders with the outbreak Surveillance Team, we explain the procedures that led to a successful epidemiological investigation and ultimately a rapid end to the epidemic. We discuss the role that several factors played in the trajectory of the epidemic, including traditional healers, insufficient knowledge of epidemiological case definitions, a lack of community-based surveillance systems and tools, and remote geography. We also demonstrate how a collaborative Rapid Response Team and implementation of community-based surveillance methods helped counter contextual challenges during the Likati epidemic and aid in identifying and reporting suspected cases and contacts in remote and rural settings. Understanding these factors can hinder or help in the rapid detection, notification, and response to future epidemics in the DRC.
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| S-EPMC8972744 | biostudies-literature
Project description:The Democratic Republic of Congo (DRC) experienced a confined rural outbreak of Ebola virus disease (EVD) with 69 reported cases from July to October 2014. Understanding the transmission dynamics during the outbreak can provide important information for anticipating and controlling future EVD epidemics. I fitted an EVD transmission model to previously published data of this outbreak and estimated the basic reproduction number R 0 = 5.2 (95% CI [4.0-6.7]). The model suggests that the net reproduction number Rt fell below unity 28 days (95% CI [25-34] days) after the onset of symptoms in the index case. This study adds to previous epidemiological descriptions of the 2014 EVD outbreak in DRC, and is consistent with the notion that a rapid implementation of control interventions helped reduce further spread.
| S-EPMC4655090 | biostudies-literature
Project description:BackgroundThe 2018-2019 Ebola virus disease (EVD) outbreak in North Kivu and Ituri provinces in the Democratic Republic of the Congo (DRC) is the largest ever recorded in the DRC. It has been declared a Public Health Emergency of International Concern. The outbreak emerged in a region of chronic conflict and insecurity, and directed attacks against health care workers may have interfered with disease response activities. Our study characterizes and quantifies the broader conflict dynamics over the course of the outbreak by pairing epidemiological and all available spatial conflict data.MethodsWe build a set of conflict variables by mapping the spatial locations of all conflict events and their associated deaths in each of the affected health zones in North Kivu and Ituri, eastern DRC, before and during the outbreak. Using these data, we compare patterns of conflict before and during the outbreak in affected health zones and those not affected. We then test whether conflict is correlated with increased EVD transmission at the health zone level.FindingsThe incidence of conflict events per capita is ~ 600 times more likely in Ituri and North Kivu than for the rest of the DRC. We identified 15 time periods of substantial uninterrupted transmission across 11 health zones and a total of 120 bi-weeks. We do not find significant short-term associations between the bi-week reproduction numbers and the number of conflicts. However, we do find that the incidence of conflict per capita was correlated with the incidence of EVD per capita at the health zone level for the entire outbreak (Pearson's r = 0.33, 95% CI 0.05-0.57). In the two provinces, the monthly number of conflict events also increased by a factor of 2.7 in Ebola-affected health zones (p value < 0.05) compared to 2.0 where no transmission was reported and 1.3 in the rest of the DRC, in the period between February 2019 and July 2019.ConclusionWe characterized the association between variables documenting broad conflict levels and EVD transmission. Such assessment is important to understand if and how such conflict variables could be used to inform the outbreak response. We found that while these variables can help characterize long-term challenges and susceptibilities of the different regions they provide little insight on the short-term dynamics of EVD transmission.
| S-EPMC7184697 | biostudies-literature
Project description:After the 2017 Ebola virus (EBOV) outbreak in Likati, a district in northern Democratic Republic of the Congo, we sampled small mammals from the location where the primary case-patient presumably acquired the infection. None tested positive for EBOV RNA or antibodies against EBOV, highlighting the ongoing challenge in detecting animal reservoirs for EBOV.
| S-EPMC7454093 | biostudies-literature
Project description:BackgroundThe Democratic Republic of the Congo has had 15 Ebola virus disease (EVD) outbreaks, from 1976 to 2023. On June 1, 2020, the Democratic Republic of the Congo declared an outbreak of EVD in the western Équateur Province (11th outbreak), proximal to the 2018 Tumba and Bikoro outbreak and concurrent with an outbreak in the eastern Nord Kivu Province. In this Article, we assessed whether the 11th outbreak was genetically related to previous or concurrent EVD outbreaks and connected available epidemiological and genetic data to identify sources of possible zoonotic spillover, uncover additional unreported cases of nosocomial transmission, and provide a deeper investigation into the 11th outbreak.MethodsWe analysed epidemiological factors from the 11th EVD outbreak to identify patient characteristics, epidemiological links, and transmission modes to explore virus spread through space, time, and age groups in the Équateur Province, Democratic Republic of the Congo. Trained field investigators and health professionals recorded data on suspected, probable, and confirmed cases, including demographic characteristics, possible exposures, symptom onset and signs and symptoms, and potentially exposed contacts. We used blood samples from individuals who were live suspected cases and oral swabs from individuals who were deceased to diagnose EVD. We applied whole-genome sequencing of 87 available Ebola virus genomes (from 130 individuals with EVD between May 19 and Sept 16, 2020), phylogenetic divergence versus time, and Bayesian reconstruction of phylogenetic trees to calculate viral substitution rates and study viral evolution. We linked the available epidemiological and genetic datasets to conduct a genomic and epidemiological study of the 11th EVD outbreak.FindingsBetween May 19 and Sept 16, 2020, 130 EVD (119 confirmed and 11 probable) cases were reported across 13 Équateur Province health zones. The individual identified as the index case reported frequent consumption of bat meat, suggesting the outbreak started due to zoonotic spillover. Sequencing revealed two circulating Ebola virus variants associated with this outbreak-a Mbandaka variant associated with the majority (97%) of cases and a Tumba-like variant with similarity to the ninth EVD outbreak in 2018. The Tumba-like variant exhibited a reduced substitution rate, suggesting transmission from a previous survivor of EVD.InterpretationIntegrating genetic and epidemiological data allowed for investigative fact-checking and verified patient-reported sources of possible zoonotic spillover. These results demonstrate that rapid genetic sequencing combined with epidemiological data can inform responders of the mechanisms of viral spread, uncover novel transmission modes, and provide a deeper understanding of the outbreak, which is ultimately needed for infection prevention and control during outbreaks.FundingWHO and US Centers for Disease Control and Prevention.
| S-EPMC10849974 | biostudies-literature
Project description:We applied metagenomic next-generation sequencing (mNGS) to detect Zaire Ebola virus (EBOV) and other potential pathogens from whole-blood samples from 70 patients with suspected Ebola hemorrhagic fever during a 2014 outbreak in Boende, Democratic Republic of the Congo (DRC) and correlated these findings with clinical symptoms. Twenty of 31 patients (64.5%) tested in Kinshasa, DRC, were EBOV positive by quantitative reverse transcriptase PCR (qRT-PCR). Despite partial degradation of sample RNA during shipping and handling, mNGS followed by EBOV-specific capture probe enrichment in a U.S. genomics laboratory identified EBOV reads in 22 of 70 samples (31.4%) versus in 21 of 70 (30.0%) EBOV-positive samples by repeat qRT-PCR (overall concordance = 87.1%). Reads from Plasmodium falciparum (malaria) were detected in 21 patients, of which at least 9 (42.9%) were coinfected with EBOV. Other positive viral detections included hepatitis B virus (n = 2), human pegivirus 1 (n = 2), Epstein-Barr virus (n = 9), and Orungo virus (n = 1), a virus in the Reoviridae family. The patient with Orungo virus infection presented with an acute febrile illness and died rapidly from massive hemorrhage and dehydration. Although the patient's blood sample was negative by EBOV qRT-PCR testing, identification of viral reads by mNGS confirmed the presence of EBOV coinfection. In total, 9 new EBOV genomes (3 complete genomes, and an additional 6 ≥50% complete) were assembled. Relaxed molecular clock phylogenetic analysis demonstrated a molecular evolutionary rate for the Boende strain 4 to 10× slower than that of other Ebola lineages. These results demonstrate the utility of mNGS in broad-based pathogen detection and outbreak surveillance.
| S-EPMC6711896 | biostudies-literature
Project description:ImportanceIn 2018 to 2020, the Democratic Republic of the Congo experienced the world's second largest Ebola virus disease (EVD) outbreak, killing 2290 individuals; women were disproportionately infected (57% of all cases) despite no evidence of differential biological EVD risk. Understanding how gender norms may influence exposure to EVD, intensity, and prognosis as well as personal protective behaviors against the virus is important to disease risk reduction and control interventions.ObjectiveTo assess whether men and women differ in personal protective behaviors (vaccine acceptance, health-seeking behaviors, physical distancing) and the mediating role of EVD information and knowledge, perceived disease risk, and social relations.Design, setting, and participantsThis cross-sectional, multistage cluster survey study of 1395 randomly selected adults was conducted in the Ebola-affected regions of North Kivu from April 20, 2019, to May 10, 2019. Path analyses were conducted using structural equation modeling to examine associations among study variables. Statistical analysis was conducted from August 2019 to May 2020.Main outcomes and measuresThe main behavioral outcomes of interest were (1) vaccine acceptance, (2) formal health care seeking, and (3) self-protective behaviors. The primary factor of interest was self-reported gender identity. We also assessed sociodemographic factors.ResultsAmong the study's 1395 participants, 1286 (93%) had Nande ethnicity and 698 (50%) were women; the mean (SD) age was 34.5 (13.1) years. Compared with female participants, male participants reported significantly higher levels of education, wealth, and mobile phone access. There were associations found between gender and all EVD preventive behavioral outcomes, with evidence for mediation through EVD knowledge and belief in rumors. Men reported greater EVD knowledge accuracy compared with women (mean [SE] score for men: 12.06 [0.13] vs women: 11.08 [0.16]; P < .001), and greater knowledge accuracy was associated with increases in vaccine acceptance (β = 0.37; P < .001), formal care seeking (β = 0.39; P < .001), and self-protective behaviors (β = 0.35; P < .001). Lower belief in rumors was associated with greater vaccine acceptance (β = -0.30; P < .001), and greater EVD information awareness was associated with increased adoption of self-protective behaviors (β = 0.23; P < .001).Conclusions and relevanceThis survey study found gender differences in adopting preventive protective behaviors against EVD. These findings suggest that it is critical to design gender-sensitive communication and vaccination strategies, while engaging women and their community as a whole in any response to infectious disease outbreaks. Research on the potential link between gender and sociodemographics factors associated with disease risk and outcomes is needed.
| S-EPMC8851299 | biostudies-literature