Reaching for the low hanging fruits: One health benefits of joint crop-livestock services for small-scale farmers

Crop protection practices and viral zoonotic risks within a One Health framework

Recent viral zoonotic epidemics have been attributed partially to the negative impact of human activities on ecosystem biodiversity. Agricultural activities, particularly conventional crop protection (CP) practices, are a major threat to global biodiversity, ecosystem health and human health. Here we review interactions between CP practices and viral zoonoses (VZs), the first time this has been done. It should be noted that a) VZs stand at the interface between human, animal and ecosystem health; b) some VZs involve arthropod vectors that are affected by CP practices; and c) some crop pests, or their natural enemies are vertebrate reservoirs/carriers of certain VZs, and their contact with humans or domestic animals is affected by CP practices. Our review encompasses examples highlighting interactions between VZs and CP practices, both efficiency improvement-based (i.e. conventional with agrochemical insecticides and rodenticides), substitution-based (i.e. mainly with physical/mechanical or biopesticidal pest control), and redesign-based (i.e. mainly with conservation biological pest control, including some forms of crop-livestock integration). These CP practices mainly target arthropod and vertebrate pests. They also target, to a lesser extent, weeds and plant pathogens. Conventional and some physical/mechanical control methods and some forms of biopesticidal and crop-livestock integration practices were found to have mixed outcomes in terms of VZ risk management. Conversely, practices based on biological control by habitat conservation of arthropod or vertebrate natural enemies, falling within the Agroecological Crop Protection (ACP) framework, result in VZ prevention at various scales (local to global, and short-term to long-term). ACP addresses major global challenges including climate resilience, biodiversity conservation and animal welfare, and helps integrate plant health within the extended "One Health" concept.

Rapid in-country sequencing of whole virus genomes to inform rabies elimination programmes

Genomic surveillance is an important aspect of contemporary disease management but has yet to be used routinely to monitor endemic disease transmission and control in low- and middle-income countries. Rabies is an almost invariably fatal viral disease that causes a large public health and economic burden in Asia and Africa, despite being entirely vaccine preventable. With policy efforts now directed towards achieving a global goal of zero dog-mediated human rabies deaths by 2030, establishing effective surveillance tools is critical. Genomic data can provide important and unique insights into rabies spread and persistence that can direct control efforts. However, capacity for genomic research in low- and middle-income countries is held back by limited laboratory infrastructure, cost, supply chains and other logistical challenges. Here we present and validate an end-to-end workflow to facilitate affordable whole genome sequencing for rabies surveillance utilising nanopore technology. We used this workflow in Kenya, Tanzania and the Philippines to generate rabies virus genomes in two to three days, reducing costs to approximately £60 per genome. This is over half the cost of metagenomic sequencing previously conducted for Tanzanian samples, which involved exporting samples to the UK and a three- to six-month lag time. Ongoing optimization of workflows are likely to reduce these costs further. We also present tools to support routine whole genome sequencing and interpretation for genomic surveillance. Moreover, combined with training workshops to empower scientists in-country, we show that local sequencing capacity can be readily established and sustainable, negating the common misperception that cutting-edge genomic research can only be conducted in high resource laboratories. More generally, we argue that the capacity to harness genomic data is a game-changer for endemic disease surveillance and should precipitate a new wave of researchers from low- and middle-income countries.

Rapid in-country sequencing of whole virus genomes to inform rabies elimination programmes

Genomic surveillance is an important aspect of contemporary disease management but has yet to be used routinely to monitor endemic disease transmission and control in low- and middle-income countries. Rabies is an almost invariably fatal viral disease that causes a large public health and economic burden in Asia and Africa, despite being entirely vaccine preventable. With policy efforts now directed towards achieving a global goal of zero dog-mediated human rabies deaths by 2030, establishing effective surveillance tools is critical. Genomic data can provide important and unique insights into rabies spread and persistence that can direct control efforts. However, capacity for genomic research in low- and middle-income countries is held back by limited laboratory infrastructure, cost, supply chains and other logistical challenges. Here we present and validate an end-to-end workflow to facilitate affordable whole genome sequencing for rabies surveillance utilising nanopore technology. We used this workflow in Kenya, Tanzania and the Philippines to generate rabies virus genomes in two to three days, reducing costs to approximately £60 per genome. This is over half the cost of metagenomic sequencing previously conducted for Tanzanian samples, which involved exporting samples to the UK and a three- to six-month lag time. Ongoing optimization of workflows are likely to reduce these costs further. We also present tools to support routine whole genome sequencing and interpretation for genomic surveillance. Moreover, combined with training workshops to empower scientists in-country, we show that local sequencing capacity can be readily established and sustainable, negating the common misperception that cutting-edge genomic research can only be conducted in high resource laboratories. More generally, we argue that the capacity to harness genomic data is a game-changer for endemic disease surveillance and should precipitate a new wave of researchers from low- and middle-income countries.

A one health exploration of the reasons for low cocoa productivity in West Sulawesi

We conducted an interdisciplinary One Health study of potential links between agricultural, health and associated livelihood factors on the livelihoods of smallholder cocoa-growing families in West Sulawesi. Our 2017 survey of 509 cocoa smallholder family members in 120 households in Polewali-Mandar District, West Sulawesi, Indonesia showed that farmers face many challenges to improving their livelihoods, including land management, agricultural practices, nutrition and human health, animal health, aging and demographic changes. Price fluctuations, limited access to capital and poor health deterred farmers from applying agricultural inputs and resulted in levels of low cocoa production (275 kg/annum per household). While market demand for live goats in the region is substantial and expected to increase, uptake of mixed farming with goats by smallholders was low. However, most households kept chickens. Bank accounts were held by 31% of households. Inadequate sanitation and unsafe water were reported in >50% households. Anthropometric measures showed that 42% of children under five years were significantly stunted and 32% of women were overweight. Joint, back pain and blurry vision were reported by 30% of adult respondents. High blood pressure contributed to complications in 20% of pregnancies. Primary health care provided by district health services mainly focuses on maternal and child health, leaving chronic health problems such as Type 2 diabetes, cataracts, arthritis and mental illness under-diagnosed, and if diagnosed, with inadequate treatment. Availability of food was a source of worry for 58% of households with 63% reporting limited food variety. Dietary diversity was low with an average of four out of ten food categories consumed in each household. Positive correlations were recorded for household cocoa productivity, land size, dietary diversity and perceptions that food availability and variety was sufficient. The results showed that an integrated One Health approach provides deep understanding of priority areas for improving livelihoods.

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A household survey of a cocoa-dependent community in Sulawesi indicated low productivity, incomes and uptake of mixed farming.

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Results showed variable health services, chronic health conditions and childhood stunting.

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Dietary diversity and perceptions of food availability were low.

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The interdependency of problems facing smallholders supports an integrated (One Health) approach.