Abstract
Background
The largest West African monkeypox outbreak began September 2017, in Nigeria. Four individuals traveling from Nigeria to the United Kingdom (n = 2), Israel (n = 1), and Singapore ...(n = 1) became the first human monkeypox cases exported from Africa, and a related nosocomial transmission event in the United Kingdom became the first confirmed human-to-human monkeypox transmission event outside of Africa.
Methods
Epidemiological and molecular data for exported and Nigerian cases were analyzed jointly to better understand the exportations in the temporal and geographic context of the outbreak.
Results
Isolates from all travelers and a Bayelsa case shared a most recent common ancestor and traveled to Bayelsa, Delta, or Rivers states. Genetic variation for this cluster was lower than would be expected from a random sampling of genomes from this outbreak, but data did not support direct links between travelers.
Conclusions
Monophyly of exportation cases and the Bayelsa sample, along with the intermediate levels of genetic variation, suggest a small pool of related isolates is the likely source for the exported infections. This may be the result of the level of genetic variation present in monkeypox isolates circulating within the contiguous region of Bayelsa, Delta, and Rivers states, or another more restricted, yet unidentified source pool.
Molecular and epidemiological data from multiple human monkeypox exportations from Nigeria show no direct linkage between travelers; however, limited genetic variation among sequenced viruses point to a possible common source pool or independently acquired infections within a small geographic area.
Despite recent insights into cholera transmission patterns in Africa, regional and local dynamics in West Africa-where cholera outbreaks occur every few years-are still poorly understood. Coordinated ...genomic surveillance of
in the areas most affected may reveal transmission patterns important for cholera control.
During a regional sequencing workshop in Nigeria, we sequenced 46 recent
isolates from Cameroon, Niger, and Nigeria (37 from 2018 to 2019) to better understand the relationship between the
bacterium circulating in these three countries.
From these isolates, we generated 44 whole
O1 sequences and analyzed them in the context of 1280 published
O1 genomes. All sequences belonged to the T12
seventh pandemic lineage.
Phylogenetic analysis of newly generated and previously published
genomes suggested that the T12 lineage has been continuously transmitted within West Africa since it was first observed in the region in 2009, despite lack of reported cholera in the intervening years. The results from this regional sequencing effort provide a model for future regionally coordinated surveillance efforts.
Funding for this project was provided by Bill and Melinda Gates Foundation OPP1195157.
Melioidosis is a tropical infectious disease caused by the soil-dwelling bacterium Burkholderia pseudomallei with a mortality of up to 50% in low resource settings. Only a few cases have been ...reported from African countries. However, studies on the global burden of melioidosis showed that Africa holds a significant unrecognized disease burden, with Nigeria being at the top of the list. The first World Health Organization African Melioidosis Workshop was organized in Lagos, Nigeria, with representatives of health authorities, microbiology laboratories, and clinical centers from across the continent. Dedicated hands-on training was given on laboratory diagnostics of B. pseudomallei. This report summarises the meeting objectives, including raising awareness of melioidosis and building capacity for the detection, diagnosis, biosafety, treatment, and prevention across Africa. Further, collaboration with regional and international experts provided a platform for sharing ideas on best practices.
Design thinking allows challenging problems to be redefined in order to identify alternative user-center strategies and solutions. To address the many challenges associated with collecting and ...reporting data during the 2014 Ebola outbreak in Guinea, Liberia and Sierra Leone, we used a design thinking approach to build the Global Ebola Laboratory Data collection and reporting system.
We used the five-stage Design Thinking model proposed by Hasso-Plattner Institute of Design at Stanford in Guinea, Liberia and Sierra Leone. This approach offers a flexible model which focuses on empathizing, defining, ideating, prototyping, and testing. A strong focus of the methodology includes end-users' feedback from the beginning to the end of the process. This is an iterative methodology that continues to adapt according to the needs of the system. The stages do not need to be sequential and can be run in parallel, out of order, and repeated as necessary. Design thinking was used to develop a data collection and reporting system, which contains all laboratory data from the three countries during one of the most complicated multi-country outbreaks to date. The data collection and reporting system was used to orient the response interventions at the district, national, and international levels within the three countries including generating situation reports, monitoring the epidemiological and operational situations, providing forecasts of the epidemic, and supporting Ebola-related research and the Ebola National Survivors programs within each country.
Our study demonstrates the numerous benefits that arise when using a design thinking methodology during an outbreak to solve acute challenges within the national health information system and the authors recommend it's use during future complex outbreaks.
In 2017 the Nigerian Ministry of Health notified the World Health Organization (WHO) of an outbreak of hepatitis E located in the north-east region of the country with 146 cases with 2 deaths. The ...analysis of the hepatitis E virus (HEV) genotypes responsible for the outbreak revealed the predominance of HEV genotypes 1 (HEV-1) and 2 (HEV-2). Molecular data of HEV-2 genomes are limited; therefore we characterized a HEV-2 strain of the outbreak in more detail.
The full-length genome sequence of an HEV-2 strain (NG/17-0500) from the outbreak was amplified using newly designed consensus primers. Comparison with other HEV complete genome sequences, including the only HEV-2 strain (Mex-14) with available complete genome sequences and the availability of data of partial HEV-2 sequences from Sub-Saharan Africa, suggests that NG/17-0500 belongs to HEV subtype 2b (HEV-2b).
We identified a novel HEV-2b strain from Sub-Saharan Africa, which is the second complete HEV-2 sequence to date, whose natural history and epidemiology merit further investigation.
Following cessation of continuous Ebola virus (EBOV) transmission within Western Africa, sporadic EBOV disease (EVD) cases continued to re-emerge beyond the viral incubation period. Epidemiological ...and genomic evidence strongly suggests that this represented transmission from EVD survivors. To investigate whether persistent infections are characterized by ongoing viral replication, we sequenced EBOV from the semen of nine EVD survivors and a subset of corresponding acute specimens. EBOV evolutionary rates during persistence were either similar to or reduced relative to acute infection rates. Active EBOV replication/transcription continued during convalescence, but decreased over time, consistent with viral persistence rather than viral latency. Patterns of genetic divergence suggest a moderate relaxation of selective constraints within the sGP carboxy-terminal tail during persistent infections, but do not support widespread diversifying selection. Altogether, our data illustrate that EBOV persistence in semen, urine, and aqueous humor is not a quiescent or latent infection.
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•During persistence, EBOV exhibits heterogeneous evolutionary rates•Active EBOV transcription and replication occurs during persistence•RNA hyper-editing observed during viral persistence•No evidence for significant selective pressure during persistence
Whitmer et al. find that Ebola virus continues replication/transcription within the eye and male genital tract of Ebola virus disease survivors. They describe viral replication, evolutionary rates, and selective pressures experienced during acute and persistent infection.
Lassa fever cases have increased in Nigeria since 2016 with the highest number, 633 cases, reported in 2018. From 1 January to 28 April 2019, 554 laboratory-confirmed cases including 124 deaths were ...reported in 21 states in Nigeria. A public health emergency was declared on 22 January by the Nigeria Centre for Disease Control. We describe the various outbreak responses that have been implemented, including establishment of emergency thresholds and guidelines for case management.
During the recent Ebola outbreak in West Africa several international mobile laboratories were deployed to the mainly affected countries Guinea, Sierra Leone and Liberia to provide ebolavirus ...diagnostic capacity. Additionally, imported cases and small outbreaks in other countries required global preparedness for Ebola diagnostics. Detection of viral RNA by reverse transcription polymerase chain reaction has proven effective for diagnosis of ebolavirus disease and several assays are available. However, reliability of these assays is largely unknown and requires serious evaluation. Therefore, a proficiency test panel of 11 samples was generated and distributed on a global scale. Panels were analyzed by 83 expert laboratories and 106 data sets were returned. From these 78 results were rated optimal and 3 acceptable, 25 indicated need for improvement. While performance of the laboratories deployed to West Africa was superior to the overall performance there was no significant difference between the different assays applied.
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