scholarly journals Discovery of ongoing selective sweeps within Anopheles mosquito populations using deep learning

2020 ◽  
Author(s):  
Alexander T Xue ◽  
Daniel R Schrider ◽  
Andrew D Kern ◽  
Keyword(s):  
Deep Learning ◽  
Evolutionary Dynamics ◽  
Mosquito Control ◽  
Sub Saharan Africa ◽  
Supervised Machine Learning ◽  
Selective Sweeps ◽  
Genome Data ◽  
Coalescent Simulations ◽  
Sub Saharan ◽  
Increasing Demand

Abstract Identification of partial sweeps, which include both hard and soft sweeps that have not currently reached fixation, provides crucial information about ongoing evolutionary responses. To this end, we introduce partialS/HIC, a deep learning method to discover selective sweeps from population genomic data. partialS/HIC uses a convolutional neural network for image processing, which is trained with a large suite of summary statistics derived from coalescent simulations incorporating population-specific history, to distinguish between completed versus partial sweeps, hard versus soft sweeps, and regions directly affected by selection versus those merely linked to nearby selective sweeps. We perform several simulation experiments under various demographic scenarios to demonstrate partialS/HIC’s performance, which exhibits excellent resolution for detecting partial sweeps. We also apply our classifier to whole genomes from eight mosquito populations sampled across sub-Saharan Africa by the Anopheles gambiae 1000 Genomes Consortium, elucidating both continent-wide patterns as well as sweeps unique to specific geographic regions. These populations have experienced intense insecticide exposure over the past two decades, and we observe a strong overrepresentation of sweeps at insecticide resistance loci. Our analysis thus provides a list of candidate adaptive loci that may be relevant to mosquito control efforts. More broadly, our supervised machine learning approach introduces a method to distinguish between completed and partial sweeps, as well as between hard and soft sweeps, under a variety of demographic scenarios. As whole-genome data rapidly accumulate for a greater diversity of organisms, partialS/HIC addresses an increasing demand for useful selection scan tools that can track in-progress evolutionary dynamics.

scholarly journals Discovery of ongoing selective sweeps within Anopheles mosquito populations using deep learning

2019 ◽  
Author(s):  
Alexander T. Xue ◽  
Daniel R. Schrider ◽  
Andrew D. Kern ◽  
Keyword(s):  
Deep Learning ◽  
Evolutionary Dynamics ◽  
Mosquito Control ◽  
Sub Saharan Africa ◽  
Supervised Machine Learning ◽  
Selective Sweeps ◽  
Genome Data ◽  
Coalescent Simulations ◽  
Sub Saharan ◽  
Increasing Demand

AbstractIdentification of partial sweeps, which include both hard and soft sweeps that have not currently reached fixation, provides crucial information about ongoing evolutionary responses. To this end, we introduce partialS/HIC, a deep learning method to discover selective sweeps from population genomic data. partialS/HIC uses a convolutional neural network for image processing, which is trained with a large suite of summary statistics derived from coalescent simulations incorporating population-specific history, to distinguish between completed versus partial sweeps, hard versus soft sweeps, and regions directly affected by selection versus those merely linked to nearby selective sweeps. We perform several simulation experiments under various demographic scenarios to demonstrate partialS/HIC’s performance, which exhibits excellent resolution for detecting partial sweeps. We also apply our classifier to whole genomes from eight mosquito populations sampled across sub-Saharan Africa by the Anopheles gambiae 1000 Genomes Consortium, elucidating both continent-wide patterns as well as sweeps unique to specific geographic regions. These populations have experienced intense insecticide exposure over the past two decades, and we observe a strong overrepresentation of sweeps at insecticide resistance loci. Our analysis thus provides a list of candidate adaptive loci that may be relevant to mosquito control efforts. More broadly, our supervised machine learning approach introduces a method to distinguish between completed and partial sweeps, as well as between hard and soft sweeps, under a variety of demographic scenarios. As whole-genome data rapidly accumulate for a greater diversity of organisms, partialS/HIC addresses an increasing demand for useful selection scan tools that can track in-progress evolutionary dynamics.

scholarly journals Development of an Insecticide-Free Trapping Bednet to Control Mosquitoes and Manage Resistance in Malaria Vector Control: A New Way of Thinking

Insects ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 732
Author(s):  
Chouaibou S. Mouhamadou ◽  
Kun Luan ◽  
Behi K. Fodjo ◽  
Andre J. West ◽  
Marian G. McCord ◽  
...  
Keyword(s):  
Mosquito Control ◽  
Pyrethroid Resistance ◽  
Three Dimensional ◽  
Field Testing ◽  
Sub Saharan Africa ◽  
Malaria Vector Control ◽  
Worst Case ◽  
Crowd Modeling ◽  
Single Chemical ◽  
Sub Saharan

Mosquito-borne malaria kills 429,000 people each year with the problem being acute in sub-Saharan Africa. The successes gained with long-lasting pyrethroid-treated bednets are now in jeopardy because of wide-spread, pyrethroid resistance in mosquitoes. Using crowd modeling theory normalized for standard bednet architecture, we were able to design an attract–trap–kill technology for mosquitoes that does not require insecticides. Using three-dimensional polyester knitting and heat fixation, trap funnels were developed with high capture efficacy with no egression under worst-case laboratory conditions. Field testing in Africa in WHO huts with Gen1-3 T (trap)-Nets validated our model, and as predicted, Gen3 had the highest efficacy with a 4.3-fold greater trap–kill rate with no deterrence or repellency compared to Permanet 2.0, the most common bednet in Africa. A T-Net population model was developed based on field data to predict community-level mosquito control compared to a pyrethroid bednet. This model showed the Gen3 non-insecticidal T-Net under field conditions in Africa against pyrethroid resistant mosquitoes was 12.7-fold more efficacious than single chemical, pyrethroid-treated nets.

scholarly journals Aquaponics for Improved Food Security in Africa: A Review

2021 ◽  
Vol 5 ◽  
Author(s):  
Kwasi Adu Obirikorang ◽  
Wonder Sekey ◽  
Benjamin Apraku Gyampoh ◽  
George Ashiagbor ◽  
Winston Asante
Keyword(s):  
Food Security ◽  
Sub Saharan Africa ◽  
Vegetable Production ◽  
Limited Information ◽  
Start Up ◽  
The Face ◽  
Sub Saharan ◽  
Plant Yields ◽  
Increasing Demand ◽  
Benefit Cost

Increasing demand on water resources, reduced land water availability, and concerns over food security have spurred the evolution of many innovative and complex food production. An aquaponic system is a productive, innovative, and sustainable fish and vegetable production system that is revolutionizing agriculture in the face of drought, soil fertility losses, and climate change. Aquaponics, as an advanced aquaculture-agriculture system, is expected to improve food security in developing countries. However, as an emerging technology, there is very limited information on the system in Africa. Questions about the ecological and socio-economic sustainability of aquaponics are answered in this comprehensive review. This review considers aquaponics projects in Africa, categorizes the technology by evidences of their effectiveness, fish and plant yields, and juxtaposes the technology within best-use practices to make recommendations that will inform evidence-based policymaking. It also maps the present spatial adoption of the technology in sub-Saharan Africa and highlights the system's contribution to improving food security on the continent. Egypt and South Africa are countries where aquaponics is emerging and being adopted at faster rates and contributing to food security. In West Africa, significantly lower net-discounted benefit-cost ratios were realized when aquaponics systems were constructed using imported materials compared to using locally available materials. Despite aquaponics systems generally having higher start-up costs currently, its potential to be economically viable when undertaken with local materials is very high.

scholarly journals Using Supervised Machine Learning and Empirical Bayesian Kriging to reveal Correlates and Patterns of COVID-19 Disease outbreak in sub-Saharan Africa: Exploratory Data Analysis

2020 ◽  
Author(s):  
Amobi Andrew Onovo ◽  
Akinyemi Atobatele ◽  
Abiye Kalaiwo ◽  
Christopher Obanubi ◽  
Ezekiel James ◽  
...  
Keyword(s):  
Machine Learning ◽  
Positive Impact ◽  
Disease Outbreak ◽  
Rate Of Change ◽  
Sub Saharan Africa ◽  
Supervised Machine Learning ◽  
Empirical Bayesian ◽  
Bayesian Kriging ◽  
Empirical Bayesian Kriging ◽  
Sub Saharan

AbstractIntroductionCoronavirus disease 2019 (COVID-19) is an emerging infectious disease that was first reported in Wuhan1,2, China, and has subsequently spread worldwide. Knowledge of coronavirus-related risk factors can help countries build more systematic and successful responses to COVID-19 disease outbreak. Here we used Supervised Machine Learning and Empirical Bayesian Kriging (EBK) techniques to reveal correlates and patterns of COVID-19 Disease outbreak in sub-Saharan Africa (SSA).MethodsWe analyzed time series aggregate data compiled by Johns Hopkins University on the outbreak of COVID-19 disease across SSA. COVID-19 data was merged with additional data on socio-demographic and health indicator survey data for 39 of SSA’s 48 countries that reported confirmed cases and deaths from coronavirus between February 28, 2020 through March 26, 2020. We used supervised machine learning algorithm, Lasso for variable selection and statistical inference. EBK was used to also create a raster estimating the spatial distribution of COVID-19 disease outbreak.ResultsThe lasso Cross-fit partialing out predictive model ascertained seven variables significantly associated with the risk of coronavirus infection (i.e. new HIV infections among pediatric, adolescent, and middle-aged adult PLHIV, time (days), pneumococcal conjugate-based vaccine, incidence of malaria and diarrhea treatment). Our study indicates, the doubling time in new coronavirus cases was 3 days. The steady three-day decrease in coronavirus outbreak rate of change (ROC) from 37% on March 23, 2020 to 23% on March 26, 2020 indicates the positive impact of countries’ steps to stymie the outbreak. The interpolated maps show that coronavirus is rising every day and appears to be severely confined in South Africa. In the West African region (i.e. Burkina Faso, Ghana, Senegal, Cote d’Iviore, Cameroon, and Nigeria), we predict that new cases and deaths from the virus are most likely to increase.InterpretationIntegrated and efficiently delivered interventions to reduce HIV, pneumonia, malaria and diarrhea, are essential to accelerating global health efforts. Scaling up screening and increasing COVID-19 testing capacity across SSA countries can help provide better understanding on how the pandemic is progressing and possibly ensure a sustained decline in the ROC of coronavirus outbreak.FundingAuthors were wholly responsible for the costs of data collation and analysis.

scholarly journals Beta-globin gene haplotypes and selected Malaria-associated variants among black Southern African populations

2017 ◽  
Vol 2 ◽  
Author(s):  
G. D. Pule ◽  
E. R. Chimusa ◽  
K. Mnika ◽  
K. Mhandire ◽  
E. Kampira ◽  
...  
Keyword(s):  
Positive Selection ◽  
Sickle Cell ◽  
Evolutionary Dynamics ◽  
Globin Gene ◽  
Sub Saharan Africa ◽  
Migration Route ◽  
Beta Globin ◽  
African Populations ◽  
Sub Saharan ◽  
Selection Of

Partial carrier-resistance toPlasmodium falciparummalaria conferred by the sickle cell (HbS) mutation has resulted in the local amplification and positive selection of sickle cell disease (SCD) in malaria-endemic regions and particularly in sub-Saharan Africa (SSA). The present study investigated theβ-globin gene haplotypes, and selected malaria-associated variants among three cohorts of Bantu-speaking individuals from Malawi, Zimbabwe and South Africa compared with reports with data from others SSA populations. The data suggest a south-ward frequency decrease of malaria-associated variants in SSA linked to the evolutionary dynamics of various African populations’ genomes through selective pressure of malaria. These selected genomics differences, positive selection of SCD in malaria-endemic regions among ‘Bantus’ from various part of Africa emphasise the evidence of the dissociation between genetics, anthropology and culture. The present study also showed a relatively prevalent Benin haplotype, which is mostly found in West Africa, among Southern African Blacks and very low Bantu haplotype, which could suggest a major migration route, of Southern Africa Bantu, along the African west coast, post-occurrence of the Sickle cell mutation, which date remain to be fully elucidated.

scholarly journals EPIDEMIOLOGY OF IMPORTED MALARIA IN THE MEDITERRANEAN REGION

2012 ◽  
Vol 4 (1) ◽  
pp. e2012031 ◽  
Author(s):  
Silvia Odolini ◽  
Philippe Gautret ◽  
Philippe Parola
Keyword(s):  
Health Professionals ◽  
Climate Changes ◽  
Mosquito Control ◽  
International Travel ◽  
Imported Malaria ◽  
Sub Saharan Africa ◽  
Actual Knowledge ◽  
Mediterranean Countries ◽  
Sub Saharan ◽  
Ongoing Surveillance

Malaria is one of the most widespread infectious diseases of our time, causing approximately one million deaths, most of them in sub-Saharan Africa and under the age of 5. During the last few years the number of imported malaria cases in Europe has decreased, but several imported malaria cases are still reported in Europe and Mediterranean countries, probably supported by the increasing number of international travel in association with the enormous influx of immigrants from malaria-endemic countries. Moreover, the presence of Anopheline vectors in Mediterranean countries, the returned infected travellers as a source of parasite and climate changes may result in the reappearance of malaria in countries where it was previously eradicated, such as Greece in the recent years. Several cases of autochthonous malaria have recently been reported to support the need of an ongoing surveillance for mosquito control and an increased vigilance by health professionals. Aim of this review is to explore all literature about imported malaria in Mediterranean areas and the potential consequences of this, providing a critical comprehensive revision of actual knowledge.

Yellow fever from Angola and Congo: a storm gathers

2017 ◽  
Vol 47 (2) ◽  
pp. 92-96 ◽  
Author(s):  
Qanta A Ahmed ◽  
Ziad A Memish
Keyword(s):  
Yellow Fever ◽  
Mosquito Control ◽  
Case Fatality ◽  
Sub Saharan Africa ◽  
Urban Migration ◽  
Political Will ◽  
Principal Vector ◽  
Control Programmes ◽  
Sub Saharan ◽  
Modern Technologies

In common with Zika, Chikungunya and Dengue, Yellow Fever (YF) is an arthropod-borne flavivirus. It is transmitted between humans and from monkeys by mosquitoes of the Aedes aegypti (its principal vector), haemogogus and albopictus varieties. Three cycles of transmission may occur: urban; sylvatic; and intermediate. Recently, sub-Saharan Africa has seen the resurgence of this neglected disease. The current YF outbreak in Angola began in December 2015 in the capital Luanda and by October 2016 there had been > 4300 suspected cases, with 376 deaths (case fatality rate = 8.8%). A total of 884 were laboratory confirmed but it is likely that case numbers may be seriously underestimated. YF has subsequently quickly spread to neighbouring Congo and further afield to Kenya and also China, this being of grave concern as this was a first introduction of YF to Asia. YF has recently hit Brazil, with 555 suspected cases and 107 deaths reported by the end of January 2017. Extremely rapid unplanned urban migration in Africa by non-immune rural populations to already densely populated cities, where high densities of mosquitoes co-exist with city dwellers in makeshift flimsy accommodation, poses a ready recipe for an epidemic of massive proportion. In such conditions, with enormously strained public services existing among the most needy and vulnerable populations, mosquito control programmes are nearly impossible. YF in Congo is a tempest barely restrained. However, it is one that can be controlled by focused and committed international collaboration, by intense and united political will and by the marriage of old and trusted techniques: a vaccine almost a century old and some of the most modern technologies available to man.

scholarly journals Proceedings of an expert workshop on community agreement for gene drive research in Africa - Co-organised by KEMRI, PAMCA and Target Malaria

2021 ◽  
Vol 5 ◽  
pp. 19
Author(s):  
Delphine Thizy ◽  
Lea Pare Toe ◽  
Charles Mbogo ◽  
Damaris Matoke-Muhia ◽  
Vincent Pius Alibu ◽  
...  
Keyword(s):  
Mosquito Control ◽  
Genetically Modified ◽  
Field Evaluation ◽  
Epidemiological Studies ◽  
Sub Saharan Africa ◽  
Gene Drive ◽  
P Gene ◽  
Individual Informed Consent ◽  
Sub Saharan ◽  
Control Association

Gene drive research is progressing towards future field evaluation of modified mosquitoes for malaria control in sub-Saharan Africa. While many literature sources and guidance point to the inadequacy of individual informed consent for any genetically modified mosquito release, including gene drive ones, (outside of epidemiological studies that might require blood samples) and at the need for a community-level decision, researchers often find themselves with no specific guidance on how that decision should be made, expressed and by whom. Target Malaria, the Kenya Medical Research Institute and the Pan African Mosquito Control Association co-organised a workshop with researchers and practitioners on this topic to question the model proposed by Target Malaria in its research so far that involved the release of genetically modified sterile male mosquitoes and how this could be adapted to future studies involving gene drive mosquito releases for them to offer reflections about potential best practices. This paper shares the outcomes of that workshop and highlights the remaining topics for discussion before a comprehensive model can be designed.

scholarly journals ImergardTMWP: A Non-Chemical Alternative for an Indoor Residual Spray, Effective against Pyrethroid-Resistant Anopheles gambiae (s.l.) in Africa

Insects ◽  
2020 ◽  
Vol 11 (5) ◽  
pp. 322 ◽  
Author(s):  
Jean M. Deguenon ◽  
Roseric Azondekon ◽  
Fiacre R. Agossa ◽  
Gil G. Padonou ◽  
Rodrigue Anagonou ◽  
...  
Keyword(s):  
Anopheles Gambiae ◽  
Mosquito Control ◽  
Residual Activity ◽  
Sub Saharan Africa ◽  
World Health ◽  
Wild Type ◽  
Anopheles Gambiae S.L ◽  
Sub Saharan ◽  
Health Organization ◽  
Assay Conditions

Malaria is the deadliest mosquito-borne disease and kills predominantly people in sub-Saharan Africa (SSA). The now widespread mosquito resistance to pyrethroids, with rapidly growing resistance to other insecticide classes recommended by the World Health Organization (WHO), may overturn the successes gained in mosquito control in recent years. It is of utmost importance to search for new, inexpensive, and safe alternatives, with new modes of action, that might improve the efficacy of current insecticides. The efficacy of a novel mechanical insecticidal mineral derived from volcanic rock, ImergardTMWP, was investigated to determine its efficacy as a stand-alone residual wall spray and as a mixture with deltamethrin (K-Othrine® Polyzone) in experimental huts in Cove, Benin. The evaluation was conducted with susceptible (Kisumu) and wild-type Anopheles gambiae (s.l.). Deltamethrin applied alone demonstrated 40–45% mortality (at 72 h post-exposure) during the first four months, which declined to 25% at six months for wild An. gambiae from Cove. ImergardTMWP alone and mixed with deltamethrin, under the same assay conditions, produced 79–82% and 73–81% mortality, respectively, during the same six-month period. ImergardTMWP met the 80% WHO bio-efficacy threshold for residual activity for the first five months with 78% residual activity at six months. ImergardTMWP can be used as a mixture with chemical insecticides or as a stand-alone pesticide for mosquito control in Africa.

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