Assessment of community led total sanitation uptake in rural Kenya

Background: Community Led Total Sanitation (CLTS) is an innovative community led drive to set up pit latrines in rural Kenya with an aim of promoting sustainable sanitation through behaviour change. It’s a behaviour change approach based on social capital that triggers households to build pit latrines without subsidy. The Ministry of Health introduced the CLTS campaign in 2007 and the first road map to ODF ended in 2013. Since the commencement of the CLTS Programme in, there is little documentation on assessment of its uptake from triggering to the certification of open defecation free villages.Objective: To assess the magnitude of Community Led Total Sanitation (CLTS) triggering to certification of Open Defecation free (ODF) villages in rural Kenya.Design: A retrospective descriptive study.Setting: The 47 counties in Kenya. Kenya is projected to have a population of 46 million people with the majority as rural populace. The study unit were Villages across the 47 counties from the data generated in the CLTS monitoring and evaluation dataset.Results: The number of triggered villages (11641) compared to those that reached certification stage (3131) reduced significantly. Busia County achieved the 100% target for triggering. There was a significant decline of the proportions per county in the process of claiming, verifying and certifying ODF villages however Busia, Siaya and Vihiga were leading across the counties. The proportion of CLTS facilitators and CLTS certified villages per county were incongruent.Conclusion: There was low uptake of CLTS from the triggering phase to the certification phase due to plausible factors such as inadequate monitoring of the CLTS process, inadequate funding of CLTS programmeming and conflicting work demands on the CLTS facilitators leading to reduced momentum as observed in Uganda

An assessment of water, sanitation and hygiene (wash) practices and quality of routinely collected data in Machakos County Kenya

Background: Poor water, sanitation, and hygiene (WASH) practices, predispose to childhood morbidity and mortality globally, and especially from diarrhoeal diseases. Machakos County in its community strategy utilises Community Health Workers (CHWs) to promote WASH practices and to collect household based data using a structured reporting tool. There is no published data on WASH in Machakos County.Objectives: To assess (i) WASH practices, and (ii) completeness and accuracy of routinely collected data on household water, sanitation and hygiene with reported childhood diarrhoea cases of all community units in Machakos County, Kenya.Design: Descriptive ecological studySetting: Machakos County, KenyaSubjects: Household unitsResults: A total of 137,540 households were served by the CHWs between January and December 2014. The number of households was not updated as per ministry of health recommendation, after six months hence the denominator remained constant. There was a high uptake of households with treated drinking water (92%), availability of hand washing facilities in (89%) and availability of functional pit latrines (98%). A total of 4,012 diarrhoea cases were reported in the County, with an average of 90 cases every month, except in the month of August where 3,020 cases of diarrhoea were reported. There was no apparent relationship observed between WASH practices and occurrence of under five diarrhoea cases.Conclusion: Water, sanitation and hygiene practices at community level in Machakos County are in keeping with post 2015 WASH targets and indicators, with few cases of under-five diarrhoea reported. Data quality and completeness need to be addressed for effective programme evaluation

User guide to the toolbox for working with root, tuber and banana seed systems. RTB User guide

This user guide to the Toolbox for working with root, tuber and banana seed systems introduces tools to diagnose, evaluate, and improve seed systems of banana, cassava, potato, sweetpotato, and yam. As a whole, these crops are called roots, tubers and bananas, and they are crucial for food security and income generation, especially in developing countries. All of these crops are reproduced vegetatively, from roots, tubers, stems, suckers or vines. This bulky planting material is expensive to transport. Vegetative seed is perishable and (except for potatoes, yams and a few other exceptions) must be planted as fresh as possible, and it is more likely to carry pests and diseases than true seed. Besides these unique challenges, improved seed systems of root, tuber and banana crops give farmers the opportunity to boost their livelihoods by accessing better quality planting material from landraces or improved varieties that are high yielding, resistant to stresses, more nutritious or more responsive to consumer demand

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

New technologies provide innovative opportunities to enhance understanding of major virus diseases threatening global food security

Open Access ArticlePlant viruses pose a continuous and serious threat to crop production worldwide, and globalization and climate change are exacerbating the establishment and rapid spread of new viruses. Simultaneously, developments in genome sequencing technology, nucleic acid amplification methods, and epidemiological modeling are providing plant health specialists with unprecedented opportunities to confront these major threats to the food security and livelihoods of millions of resource-constrained smallholders. In this perspective, we have used recent examples of integrated application of these technologies to enhance understanding of the emergence of plant viral diseases of key food security crops in low- and middle-income countries. We highlight how international funding and collaboration have enabled high-throughput sequencing-based surveillance approaches, targeted field and lab-based diagnostic tools, and modeling approaches that can be effectively used to support surveillance and preparedness against existing and emerging plant viral threats. The importance of national and international collaboration and the future role of CGIAR in further supporting these efforts, including building capabilities to make optimal use of these technologies in low- and middle-income countries, are discussed

The effectiveness of consistent roguing in managing banana bunchy top disease in smallholder production in Africa

The removal of infected individuals is a common practice in the management of plant disease outbreaks. It minimizes the contact between healthy individuals and inoculum sources by reducing the infectious window of contaminated individuals. This requires early detection and consistent removal at landscape scale. Roguing of mats with symptoms of banana bunchy top disease (BBTD) in Cavendish banana production systems has been tested in Australia, using trained personnel, but has never been tested in smallholder systems. We studied the effectiveness of long-term consistent roguing in prolonging the productivity of banana orchards under smallholder farming systems in highland banana and plantain dominated production systems in Africa. We assessed the possibility of low-risk seed sourcing from the managed plots. Roguing reduced BBTD incidence to 2% in managed farmer fields and to 10% in experimental field plots, while a nonmanaged field eventually collapsed in the same period. With roguing, new infections decreased monthly compared to an exponential increase in a non managed field. The emergence of new infections in both managed and non managed farms followed a seasonal cycle. BBTD managed plots were a source of low-risk seed for replacing the rogued mats in the same fields, but perhaps not safe for use in nonendemic areas. We conclude that it is possible for smallholder farmers to recover and maintain banana productivity with rigorous roguing, which would entail early identification of symptoms and early removal of diseased mats. Studies are needed on the intensity of roguing under different disease and production conditions