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

Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern-particularly Alpha, Beta, Delta, and Omicron-on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

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

Assessment of developing-country urban consumers’ willingness to pay for quality of leafy vegetables: The case of middle and high income consumers in Nairobi, Kenya

The improvement in income in developing countries has led to emergence of middle and high income consumers in urban centers. Improvement in income usually causes the shift to consumption of non-staples including leafy vegetables. Thus in major developing country urban centers there has been rapid expansion of the grocery sections featuring leafy vegetables in leading retail stores. Specialty stores have also emerged featuring broad range vegetables. Many middle and high income consumers shop these stores. This study examines the willing of the middle and high income consumers who shop specialized stores to pay for quality of leafy vegetables and drivers of willingness to pay for quality. The study uses contingent valuation and the payment card method in eliciting consumers’ WTP. It considers a broad range of quality attributes including safety, nutrition, environmental friendliness, hygiene in handling. The study finds that mean willingness to pay for quality is higher among high income consumers (>60%). It also finds that income, age of children the consumer has, access to information of food safety are among the significant drivers of kale consumers’ willingness to pay for quality of kales. The study concludes that there is demand for quality of leafy vegetables and discusses policy implications

Gender, livestock and livelihood indicators. Version 2

This guide is a reference point for some of the important indicators that ILRI can use to monitor the changing role of livestock in livelihoods in different production systems and the impact of livestock-related interventions. While this list of indicators is not comprehensive in covering all the areas in which ILRI works, it provides a starting point for the common objectives which most of our projects, be they in markets, biotechnology or the environment, hope to achieve. Some of these indicators are already commonly used in different surveys but their application has not always been consistent or comparable. With time, we expect to develop further common indicators around other areas of research in ILRI. This document should therefore be considered as a living document to which we will add core indicators around the thematic areas covered by ILRI’s research including such areas as partnerships, capacity building and the key thematic areas of markets, biotechnology and environment. This document should be used to guide your data collection within projects. These may include baseline data, evaluation (both internal and external), impact assessments, project appraisals and any other data collection within the projects and programs across the institute, including surveys conducted by students where possible. Currently, the indicators are designed for data collection at household level and for integration into household surveys. Project teams should ask for assistance in adapting these indicators for use in other types of surveys such as community surveys, focus group discussions, market agent surveys and key informant interviews. Livestock play multiple roles in livelihoods. In deriving these indicators, we have used both the sustainable livelihoods framework, placing livestock within an assets and capital framework, and as a pathway out of poverty. The latter recognizes that for livestock to translate into poverty reduction the necessary conditions i.e. technologies and services to generate productive, sustainable and profitable markets are a pre-requisit

Providing “a beam of light to see the gaps”: determinants of implementation of the Systems Analysis and Improvement Approach applied to the pediatric and adolescent HIV cascade in Kenya

Abstract Background Children and adolescents living with HIV have poorer rates of HIV testing, treatment, and virologic suppression than adults. Strategies that use a systems approach to optimize these multiple, linked steps simultaneously are critical to close these gaps. Methods The Systems Analysis and Improvement Approach (SAIA) was adapted and piloted for the pediatric and adolescent HIV care and treatment cascade (SAIA-PEDS) at 6 facilities in Kenya. SAIA-PEDS includes three tools: continuous quality improvement (CQI), flow mapping, and pediatric cascade analysis (PedCAT). A predominately qualitative evaluation utilizing focus group discussions (N = 6) and in-depth interviews (N = 19) was conducted with healthcare workers after implementation to identify determinants of implementation. Data collection and analysis were grounded in the Consolidated Framework for Implementation Research (CFIR). Results Overall, the adapted SAIA-PEDS strategy was acceptable, and the three tools complemented one another and provided a relative advantage over existing processes. The flow mapping and CQI tools were compatible with existing workflows and resonated with team priorities and goals while providing a structure for group problem solving that transcended a single department’s focus. The PedCAT was overly complex, making it difficult to use. Leadership and hierarchy were complex determinants. All teams reported supportive leadership, with some describing in detail how their leadership was engaged and enthusiastic about the SAIA-PEDS process, by providing recognition, time, and resources. Hierarchy was similarly complex: in some facilities, leadership stifled rapid innovation by insisting on approving each change, while at other facilities, leadership had strong and supportive oversight of processes, checking on the progress frequently and empowering teams to test innovative ideas. Conclusion CQI and flow mapping were core components of SAIA-PEDS, with high acceptability and consistent use, but the PedCAT was too complex. Leadership and hierarchy had a nuanced role in implementation. Future SAIA-PEDS testing should address PedCAT complexity and further explore the modifiability of leadership engagement to maximize implementation

Resilience of routine childhood immunization services in two counties in Kenya in the face of the COVID-19 pandemic

This work was funded by the US Centers for Disease Control and Prevention grant (Cooperative Agreement 5U01GH002143) and the Task Force for Global Health (TFGH) through the Partnership for Influenza Vaccine Introduction (PIVI).The recently emerged coronavirus disease 2019 (COVID-19) has caused considerable morbidity and mortality worldwide and disrupted health services. We describe the effect of the COVID-19 pandemic on utilization of childhood vaccination services during the pandemic. Using a mixed methods approach combining retrospective data review, a cross-sectional survey, focus group discussions among care givers and key informant interviews among nurses, we collected data between May and September 2021 in Mombasa and Nakuru counties. Overall, there was a <2 % decline in the number of vaccine doses administered during the pandemic period compared to the pre-pandemic period but this was statistically insignificant, both for the pentavalent-1 vaccine (ß = −0.013, p = 0.505) and the pentavalent-3 vaccine (ß = −0.012, p = 0.440). In government health facilities, there was 7.7 % reduction in the number of pentavalent-1 (ß = −0.08, p = 0.010) and 10.4 % reduction in the number of pentavalent-3 (ß = −0.11, p < 0.001) vaccine doses that were administered during the pandemic period. In non-government facilities, there was a 25.8 % increase in the number of pentavalent-1 (ß=0.23, p < 0.001) and 31.0 % increase in the number of pentavalent-3 (ß = −0.27, p < 0.001) vaccine doses that were administered facilities during the pandemic period. The strategies implemented to maintain immunization services during the pandemic period included providing messaging on the availability and importance of staying current with routine vaccination and conducting catch-up vaccinations and vaccination outreaches. Our findings suggest that the COVID-19 pandemic did not impact childhood vaccination services in Mombasa and Nakuru counties in Kenya. The private health facilities cushioned vaccination services against the effects of the pandemic and the strategies that were put in place by the ministry of health ensured continuation of vaccination services and encouraged uptake of the services during the pandemic period in the two counties in Kenya. These findings provide useful information to safeguard vaccination services during future pandemics.Publisher PDFPeer reviewe