Genetic characterization of influenza A(H3N2) viruses circulating in coastal Kenya, 2009-2017

Background Influenza viruses evolve rapidly and undergo immune driven selection, especially in the hemagglutinin (HA) protein. We report amino acid changes affecting antigenic epitopes and receptor‐binding sites of A(H3N2) viruses circulating in Kilifi, Kenya, from 2009 to 2017. Methods Next‐generation sequencing (NGS) was used to generate A(H3N2) virus genomic data from influenza‐positive specimens collected from hospital admissions and health facility outpatients presenting with acute respiratory illness to health facilities within the Kilifi Health and Demographic Surveillance System. Full‐length HA sequences were utilized to characterize A(H3N2) virus genetic and antigenic changes. Results From 186 (90 inpatient and 96 outpatient) influenza A virus‐positive specimens processed, 101 A(H3N2) virus whole genomes were obtained. Among viruses identified in inpatient specimens from 2009 to 2015, divergence of circulating A(H3N2) viruses from the vaccine strains A/Perth/16/2009, A/Texas/50/2012, and A/Switzerland/9715293/2013 formed 6 genetic clades (A/Victoria/208/2009‐like, 3B, 3C, 3C.2a, 4, and 7). Among viruses identified in outpatient specimens from 2015 to 2017, divergence of circulating A(H3N2) viruses from vaccine strain A/Hong Kong/4801/2014 formed clade 3C.2a, subclades 3C.2a2 and 3C.2a3, and subgroup 3C.2a1b. Several amino acid substitutions were associated with the continued genetic evolution of A(H3N2) strains in circulation. Conclusions Our results suggest continuing evolution of currently circulating A(H3N2) viruses in Kilifi, coastal Kenya and suggest the need for continuous genetic and antigenic viral surveillance of circulating seasonal influenza viruses with broad geographic representation to facilitate prompt and efficient selection of influenza strains for inclusion in future influenza vaccines

Epidemiological and evolutionary dynamics of influenza B virus in coastal Kenya as revealed by genomic analysis of strains sampled over a single season

The genomic epidemiology of influenza B virus (IBV) remains understudied in Africa despite significance to design of effective local and global control strategies. We undertook surveillance throughout 2016 in coastal Kenya, recruiting individuals presenting with acute respiratory illness at nine outpatient health facilities (any age) or admitted to the Kilifi County Hospital (<5-year-old). Whole genomes were sequenced for a select 111 positives; 94 (84.7%) of B/Victoria lineage and 17 (15.3%) of B/Yamagata lineage. Inter-Lineage reassortment was detected in 10 viruses; nine with B/Yamagata backbone but B/Victoria NA and NP segments and one with a B/Victoria backbone but B/Yamagata PB2, PB1, PA and MP segments. Five phylogenomic clusters were identified among the sequenced viruses; (i) pure B/Victoria clade 1A (n = 93, 83.8%), (ii) reassortant B/Victoria clade 1A (n = 1, 0.9%), (iii) pure B/Yamagata clade 2 (n = 2, 1.8%), (iv) pure B/Yamagata clade 3 (n = 6, 5.4%) and (v) reassortant B/Yamagata clade 3 (n = 9, 8.1%). Using divergence dates and clustering patterns in the presence of global background sequences, we counted up to 29 independent IBV strain introductions into the study area (∼900 km2) in 2016. Local viruses, including the reassortant B/Yamagata strains, clustered closely with viruses from neighbouring Tanzania and Uganda. Our study demonstrated that genomic analysis provides a clearer picture of locally circulating IBV diversity. The high number of IBV introductions highlights the challenge in controlling local influenza epidemics by targeted approaches e.g. sub-population vaccination or patient quarantine. The finding of divergent IBV strains co-circulating within a single season emphasizes why broad immunity vaccines are the most ideal for influenza control in Kenya

Adaptation Actions in Africa: Evidence that Gender Matters

This paper presents the initial data analyses of the CCAFS gender survey implemented in four sites in Africa. Using descriptive statistics we show gender differences in terms of perceptions of climate change, awareness and adoption of climate smart agricultural (CSA) practices, and types and sources of agro-climatic information in the four sites.We find that both men and women are experiencing changes in long-run weather patterns and that they are changing their behaviours in response; albeit relatively minor shifts in existing agricultural practices. For example, the most prevalent changes reported include switching crop varieties, switching types of crops and changing planting dates. As expected, women are less aware of many CSA practices. Encouragingly, this same pattern does not hold when it comes to adoption; in many cases, in East Africa in particular, women, when aware, are more likely than or just as likely as men to adopt CSA practices. In West Africa, overall, the adoption of these practices was much lower. In addition, we see that access to information from different sources varies greatly between men and women and among the sites; however, promisingly, those with access to information report using it to make changes to their agricultural practices. Our findings suggest that targeting women with climate and agricultural information is likely to result in uptake of new agricultural practices for adaptation

Climate Smart Agriculture in the African Context

Agriculture remains vital to the economy of most African countries and its development has significant implications for food security and poverty reduction in the region. Increase in agricultural production over the past decades has mainly been due to land area expansion, with very little change in production techniques and limited improvement in yields. Currently one in four people remains malnourished in Africa. CSA integrates all three dimensions of sustainable development and is aimed at (1) sustainably increasing agricultural productivity and incomes; (2) adapting and building resilience to climate change from the farm to national levels; and (3) developing opportunities to reduce greenhouse gas emissions from agriculture compared with past trends. It is an approach to identify the most suitable strategies according to national and local priorities and conditions to meet these three objectives. There is no such thing as an agricultural practice that is climate smart per se. Whether or not a particular practice or production system is climate smart depends upon the particular local climatic, biophysical, socio-economic and development context, which determines how far a particular practice or system can deliver on productivity increase, resilience and mitigation benefits. For Africa to reap the potential benefits CSA, concrete actions must be taken to: enhance the evidence base to underpin strategic choices, promote and facilitate wider adoption by farmers of appropriate technologies; develop institutional arrangements to support, apply and scale-out CSA from the farm level to the agricultural landscape level; manage tradeoffs in perspectives of farmers and policymakers; strengthen technical, analytical and implementation capacities; ensure policy frameworks and public investments are supportive of CSA; develop and implement effective risk-sharing schemes

The potential of agroecology to build climate-resilient livelihoods and food systems

Climate change has severe negative impacts on livelihoods and food systems worldwide. Our future climate according to latest scenarios seriously undermine current efforts to improve the state of food security and nutrition, especially in sub-Sahara Africa. To address this to its full extent, there is an urgent need for transformational change of our food systems towards more sustainability and resilience. Agroecology could play a vital role here. As a response to FAO’s governing bodies’ call for increased evidence-based work on agroecology, this study aims to elaborate on existing links between agroecology and climate change. It provides evidence on the technical and policy potential of agroecology to build resilient food systems. Inspired by the idea that transformation will only happen through a coordinated approach among all levels, this study was jointly developed by a broad set of actors from UN agencies (FAO), research institutes (FIBL, Bioversity, ISRA) and CSOs (Biovision, Enda Pronat, ICE) and thus combines evidence from a broad range of backgrounds and perspectives. The overall research question of this study was: How can agroecology foster climate change adaptation, mitigation and resilience through practices and policies? To provide a robust and evidence based answer to this we analysed three different dimensions: 1. International policy arena, in particular in the United Nations Framework Convention on Climate Change and the Koronivia Joint Work on Agriculture; 2. Peer-reviewed scientific studies on agroecology applying a meta-analysis; and 3. Two case studies in Kenya and Senegal that assess both, the policy potential of agroecology in respective national settings and the technical potential of agroecology to foster climate resilience on farm-level. The main findings of the study are: - Robust scientific evidence demonstrates that agroecology increases climate resilience. Success factors for this are that agroecology builds on: a) ecological principles, in particular on biodiversity, overall diversity and healthy soils (meta-analysis and case studies results); b) social aspects, in particular on the co-creation and sharing of knowledge and fostering traditions (case study results). - More than ten percent of the nationally determined contributions (NDCs) by UNFCCC member states mention agroecology and consider it a valid approach to address climate change. The climate potential of agroecology is furthermore backed by the IPCC Special Report on Climate Change and Land and the 2019 HLPE report of the Committee on World Food Security (CFS) (int. policy analysis result). - The interdisciplinary and systemic nature of agroecology is key for its true transformational power. However these characteristics are also the main challenges for both, conducting comprehensive research and policy revisions: typically research concepts and policy processes focus on the productive dimension with selective sectorial views (meta-analysis and policy analysis results). The key recommendations from this study are: - Given the sound knowledge base, fostering agroecology to build resilience should be recognized as a viable climate change adaptation strategy. - Barriers to the scaling-up of agroecology need to be addressed: amongst others, improved access to knowledge and understanding of systemic approaches should be fostered across sectors, stakeholders and scales. - Further comparative research on the multidimensional effects of agroecology is needed. - Agroecology’s transformative resilience-building potential depends on its holistic and systemic nature which goes beyond a set of practices and includes: a social movement for producers’ empowerment and a multidisciplinary scientific paradigm

Household Welfare Effects of Stress-Tolerant Varieties in Northern Uganda

This study assessed the adoption of stress-tolerant varieties and their effect on household welfare, measured by net crop income per capita in Nwoya District, Uganda. The stress-tolerant varieties were considered to be climate-smart because they stabilise and increase crop income in the presence of climatic shocks. However, the uptake of the stress-tolerant varieties was still low in northern Uganda, due to bad past experience in terms of the performance of other improved varieties. Using data from a random sample of 585 households, a logistic model was estimated to assess the drivers for adoption of stress-tolerant varieties. In addition, a propensity score matching model was employed to assess causal effects. The second model was estimated because it controls for unobserved heterogeneity caused by self-selection bias. Results showed that adoption of stress-tolerant varieties was positively influenced by household size, access to information from non-governmental organizations (NGOs), the perception of future climate change, the number of years an individual had lived in the village, and the number and type of assets owned as an indicator of household well-being. Average treatment effect from results showed that stress-tolerant varieties can increase crop income within a range of United States Dollars (USD) 500–864 per hectare per year, representing an 18–32% increase in crop income. The findings offer justification for scaling up stress tolerant varieties among smallholder farmers in northern Uganda to improve their welfare

A Participatory Approach to Assessing the Climate-Smartness of Agricultural Interventions: The Lushoto Case

The concept of climate-smart agriculture (CSA) is gaining momentum across the globe. However, it is not specific on what should be covered under its three pillars—productivity, resilience and mitigation. Consequently, CSA encompasses many different agricultural practices/technologies, making it difficult to prioritise CSA objectives. Firstly, there is a lack of clear and workable criteria as well as methods for assessing the climate-smartness of interventions. Secondly, little information exists about the impact of the various interventions already promoted as CSA, especially in the developing world. Finally, CSA prioritisation does not take into account stakeholders’ perspectives to ensure that the interventions are applicable, suitable and of high adoption-potential. Here, we describe a new participatory protocol for assessing the climate-smartness of agricultural interventions in smallholder practices. This identifies farm-level indicators (and indices) for the food security and adaptation pillars of CSA. It also supports the participatory scoring of indicators, enabling baseline and future assessments of climate-smartness to be made. The protocol was tested among 72 farmers implementing a variety of CSA interventions in the climate-smart village of Lushoto, Tanzania. Farmers especially valued interventions that improved soil fertility and structure, reduced surface runoff, and reclaimed degraded land due to the positive impacts on yield and off-season crop agriculture. Mostly, the CSA interventions increased animal production, food production, consumption and income. The protocol is easy to adapt to different regions and farming systems and allows for the better prioritisation of interventions. But we recommend that CSA is adopted as part of a monitoring, evaluation and learning process

Inclusion of gender in Africa’s climate change policies and strategies

Concerns of climate change impacts and adaptations have continued to receive much attention in both local and international climate change debate. It is now understood that the challenge of climate change cannot be addressed as a standalone issue but within different social, economic, and environmental contexts. It is currently acknowledged that Africa’s contribution to greenhouse gas emissions is insignificant. Except for South Africa, all the countries in Africa contribute below the global average of 3.5 m/ton of CO2 per capita. However, Africa is very vulnerable to climate change given its low capacity to respond and adapt. Furthermore, progress in enhancing better understanding of gender variations on the impacts and adaptation to climate change has been relatively limited. The differentiated impacts of climate change at local level add to the complexities of developing gender sensitive response strategies. With the endorsement of the Paris Climate agreement of 2015, African countries are now gearing up to implement international and national climate change adaptation and mitigation initiatives. While progress has been in developing polices and strategies for climate change adaptation and mitigation, it is critical to ensure that these do not lead to further inequalities during implementation. This chapter, therefore, aims at reviewing climate change related policies and strategies in East and West Africa through a gendered lens. The countries are Kenya, Uganda, Tanzania in East Africa, and Ghana and Nigeria in West Africa. Drawing upon a common framework/guideline, we examined commonality in policies, while recognizing the complexity in the social, economic and ecological systems of each country. The chapter further assesses the importance of integrating and mainstreaming gender into Africa’s national adaptations plans of actions (NAPAs), and Intended Nationally Distributed Contributions (INDCs), and the need for better gender oriented climate change policies, programs and plans

Changing rainfall patterns and farmers ’ adaptation through soil water management practices in semi- arid eastern Kenya

There is limited documentation of soil and water management technologies that enhance adaptation to climate change in drylands of Kenya. Rainfall patterns were analyzed in the semi-arid Machakos and Makueni counties of eastern Kenya using historical data. A total of forty-three smallholder farmers implementing soil water management practices were sampled, and an estimate of the seasonal water budget for current crop and livestock production systems computed. Analysis of rainfall amounts and distribution shows increasing variability, with the average annual total amounts decreasing over the past 50 years. Furthermore, the number of rainy days within the March-April-May season that can support crop growth is gradually decreasing. These decreases are however not significant at P <0.05. There were more seasons with low rainfall amounts compared to those with high rainfall amounts. All these subject the smallholder crop and livestock production system to limited soil moisture. Farmers address the risk by harnessing and utilizing green (rainfall stored in soil) and blue (rainfall collected into storage tanks) water technologies. The study found that farmers in these semi-arid counties practice fifteen diverse soil and water management interventions on their farms. The most popular practices are cut-off drains, retention ditches, terracing, run-off harvesting, and agroforestry. The estimated seasonal water budget indicates the need for integrated soil and water management interventions to address the crop and livestock production constraints