Assessing biases in phylodynamic inferences in the presence of super-spreaders.

Phylodynamic analyses using pathogen genetic data have become popular for making epidemiological inferences. However, many methods assume that the underlying host population follows homogenous mixing patterns. Nevertheless, in real disease outbreaks, a small number of individuals infect a disproportionately large number of others (super-spreaders). Our objective was to quantify the degree of bias in estimating the epidemic starting date in the presence of super-spreaders using different sample selection strategies. We simulated 100 epidemics of a hypothetical pathogen (fast evolving foot and mouth disease virus-like) over a real livestock movement network allowing the genetic mutations in pathogen sequence. Genetic sequences were sampled serially over the epidemic, which were then used to estimate the epidemic starting date using Extended Bayesian Coalescent Skyline plot (EBSP) and Birth-death skyline plot (BDSKY) models. Our results showed that the degree of bias varies over different epidemic situations, with substantial overestimations on the epidemic duration occurring in some occasions. While the accuracy and precision of BDSKY were deteriorated when a super-spreader generated a larger proportion of secondary cases, those of EBSP were deteriorated when epidemics were shorter. The accuracies of the inference were similar irrespective of whether the analysis used all sampled sequences or only a subset of them, although the former required substantially longer computational times. When phylodynamic analyses need to be performed under a time constraint to inform policy makers, we suggest multiple phylodynamics models to be used simultaneously for a subset of data to ascertain the robustness of inferences

Optimising the use of new data streams for making epidemiological inferences in veterinary epidemiology : a thesis presented in partial fulfilment of the requirements for the degree of PhD in Veterinary Epidemiology at Massey University, Manawatu, New Zealand

Many ‘big data’ streams have recently become available in animal health disciplines. While these data may be able to provide valuable epidemiological information, researchers are at risk of making erroneous inferences if limitations in these data are overlooked. This thesis focused on understanding the better use of two data streams—livestock movement records and genetic sequence data. The first study analysed national dairy cattle movement data in New Zealand to explore whether regionalisation of the country based on bovine tuberculosis risk influenced trade decisions. The results suggested that the observed livestock movement patterns could be explained by the majority of, but not all, farmers avoiding purchasing cattle from high disease risk areas. The second study took an alternative approach—qualitative interviews—to understanding farmers’ livestock purchasing practices. This study suggested that farmers are not necessarily concerned with disease status of source farms and that it may be the reliance on stock agents to facilitate trade that creates the observed livestock movement patterns in New Zealand. The findings from this study also implied that various demographic and production characteristics of animals may influence farmers’ livestock selling practices, which were quantitatively verified in the third study analysing livestock movement data and animal production data. These studies not only showed that analyses based solely on ‘big data’ can be misleading but also provided useful information necessary to predict future livestock movement patterns. The final study evaluated the performance of various genetic sequence sampling strategies in making phylodynamic inferences. We showed that using all available genetic samples can be not only computationally expensive, but also may lead to erroneous inferences. The results also suggested that strategies for sampling genetic sequences for phylodynamic analyses may need to be tailored based on epidemiological characteristics of each epidemic

Farmers' Decision Making on Livestock Trading Practices: Cowshed Culture and Behavioral Triggers Amongst New Zealand Dairy Farmers.

Studies of farmers' failure to implement biosecurity practices frequently frame their behavior as a lack of intention. More recent studies have argued that farmers' behaviors should be conceptualized as emergent from farming experiences rather than a direct consequence of specific intentions. Drawing on the concepts of "cowshed" culture and the "Trigger Change Model," we explore how farmers' livestock purchasing behavior is shaped by farms' natural and physical environments and identify what triggers behavioral change amongst farmers. Using bovine tuberculosis (bTB) in New Zealand as a case example, qualitative research was conducted with 15 New Zealand dairy producers with varying bTB experiences. We show how farmers' livestock purchasing behavior evolve with culture under a given farm environment. However, established cultures may be disrupted by various triggers such as disease outbreaks, introductions of animals with undesired characteristics, and farm relocation. While dealing with economic and socio-emotional impacts posed by triggers, farmers reorganize their culture and trading behaviors, which may involve holistic biosecurity strategies. Nevertheless, we also show that these triggers instigate only small behavioral changes for some farmers, suggesting the role of the trigger is likely to be context-dependent. Using voluntary disease control schemes such as providing disease status of source farms has attracted great interest as a driver of behavioral change. One hopes such schemes are easily integrated into existing farm practices, however, we speculate such an integration is challenging for many farmers due to path-dependency. We therefore argue that these schemes may fail to bring their intended behavioral changes without a greater understanding of how different types of triggers work in different situations. We need a paradigm shift in how we frame farmers' livestock trading practices. Otherwise, we may not able to answer our questions about farm biosecurity if we continue to approaching these questions solely from a biosecurity point of view

Uptrend in global managed honey bee colonies and production based on a six-decade viewpoint, 1961-2017

We conducted a retrospective study to examine the long-term trends for the global honey bee population and its two main products: honey and beeswax. Our analysis was based on the data collected by the Food and Agriculture Organization of the United Nations from 1961 to 2017. During this period, there were increases in the number of managed honey bee colonies (85.0%), honey production (181.0%) and beeswax production (116.0%). The amount of honey produced per colony increased by 45.0%, signifying improvements in the efficiency for producing honey. Concurrently, the human population grew by 144.0%. Whilst the absolute number of managed colonies increased globally, the number per capita declined by 19.9% from 13.6 colonies per 1000 population in 1961 to 10.9 colonies per 1000 population in 2017. Beeswax had a similar trend as the global production per capita reduced by 8.5% from 8.2 to 7.5 kg per 1000 population. In contrast, the global honey production per capita increased by 42.9% at the global level. The global human population growth outpaced that of managed honey bee colonies. Continuation of this trend raises the possibility of having a shortfall of pollinators to meet the increasing consumer demand for pollinated crops. To mitigate these challenges locally driven solutions will be key as influencing factors differed geographically

Luck perception is associated with less frequent preventive practices and a higher number of social contacts among adults during the SARS-CoV-2 pandemic

Objectives Non-pharmaceutical interventions have been crucial to reduce transmission of the SARS-CoV-2 virus in many countries including the United Kingdom. A key research priority has been to better understand psychological and social determinants of health behaviours. We aimed to quantify the impact of luck perception on contact and preventive behaviours among adults in the UK, adjusting for key confounders. Study design A cross-sectional study. Methods Data were collected between the 28th July and the 31st August 2020. Luck perception, which refers to a belief whether individual's SARS-CoV-2 infection status is determined by fate or chance, was measured using Chance score, drawing on Health Locus of Control Theory. Self-reporting online questionnaires were administered to obtain participants' contact patterns and frequencies of avoiding crowds, washed hands and wore a mask. Associations between luck perception and protective behaviours and contact patterns were quantified using regression models. Results Data from 233 survey respondents were analysed. Chance score was negatively associated with all protective behaviours; avoiding crowds (adjusted odds ratio (aOR) 0.46, 95% confidence interval (CI) 0.25–0.86, p = 0.02), washing hands (aOR 0.35, 95%CI 0.17–0.70, p = 0.003), and wearing masks (aOR 0.58, 95%CI 0.34–0.99, p = 0.046). For non-physical contacts (with or without distancing), a significant interaction was identified between Chance score and ethnicity. Chance score increased the number of non-physical contacts among white British, an opposite trend was observed for non-white participants. Conclusions Luck perception during the pandemic may affect individuals’ health protection behaviours and contact patterns. Further mechanistic understandings of human behaviours against infectious diseases are indispensable for effective response to future pandemics

Effectiveness and implementation challenges of a livestock asset transfer intervention for smallholders in community-protected areas in Cambodia

BACKGROUND: Limited opportunities to generate income in community-protected areas (CPAs) often lead to the illegal harvesting of wildlife and natural resources, undermining the aim of protected areas. Sustained livestock production can be an alternative income source. OBJECTIVES: To understand the effectiveness and feasibility of livestock production in CPAs. METHODS: We conducted a livestock asset transfer intervention in 25 CPAs across three agroecological zones in Cambodia. We monitored livestock mortality, consumption and sales of livestock over 2 years. Participant observations and structured questionnaires were conducted to elicit information about constraints for livestock production perceived by the participants. A total of 756 households were recruited and 320, 184 and 252 households received chicken, pigs and cattle, respectively. All participants received technical training in livestock production and biosecurity management practices. RESULTS: After the intervention, the number of chickens, pigs and cattle increased on average by 5.9 (range: 0.3-26.3), 0.5 (-1 to 2.7) and 0.12 (0-0.35) per 1 input animal, respectively. The extent of increase was significantly different between zones only for chickens (Kruskal-Wallis test p = 0.004). The number of chickens and pigs sold per household was significantly different among zones. We observed that training was ineffective to alter livestock management practices in some CPAs, which partially explains their suboptimal performance of livestock production. CONCLUSIONS: Understanding contextual factors required for successful livestock production in CPAs is crucial for improving livelihoods and preventing biodiversity loss in Cambodia

Current research and future directions for realizing the ideal One-Health approach: A summary of key-informant interviews in Japan and a literature review

The COVID-19 pandemic has highlighted the importance of the One Health (OH) approach, which considers the health of humans, animals, and the environment in preventing future pandemics. A wide range of sustainable interdisciplinary collaborations are required to truly fulfill the purpose of the OH approach. It is well-recognized, however, that such collaborations are challenging. In this study, we undertook key-informant interviews with a panel of stakeholders from Japan to identify their perceived needs and challenges related to OH research. This panel included scientists, government officials, journalists, and industry stakeholders. By combining a thematic analysis of these interviews and a literature review, we summarized two key themes pertinent to the effective implementation of OH research: types of required research and systems to support that research. As a technological issue, interviewees suggested the importance of research and development of methodologies that can promote the integration and collaboration of research fields that are currently fragmented. An example of such a methodology would allow researchers to obtain high-resolution metadata (e.g. ecological and wildlife data) with high throughput and then maximize the use of the obtained metadata in research, such as in environmental DNA analysis, database construction, or the use of computational algorithms to find novel viral genomes. In terms of systems surrounding OH research, some interviewees stressed the importance of creating a sustainable research system, such as one that has continuous budget support and allows researchers to pursue their academic careers and interests. These perceptions and challenges held by Japanese stakeholders may be common to others around the world. We hope this review will encourage more researchers and others to work together to create a resilient society against future pandemics

Exploring why animal health practices are (not) adopted among smallholders in low and middle-income countries: a realist framework and scoping review protocol

BackgroundImproving livestock health is considered critical to address poverty, malnutrition and food insecurity in low- and middle-income countries (LMICs). Modifications of livestock management practices is also increasingly recognized as an important strategy to mitigate global threats such as climate change and novel disease emergence. Smallholders are, however, under various constraints which prohibit them from altering health practices for livestock and little is known about how the adoption of these practices may be promoted. The proposed scoping review aims to systematically map evidence around “what practices are (not) adopted by smallholders under what circumstances, how and why?.”Method and analysisWe conducted initial scoping searches to broadly define types of animal health practices relevant for smallholders in LMICs and formulated search terms. A scoping review protocol was designed and registered. A systematic literature search will be conducted using electronic databases including CAB Abstract, Scopus, MEDLINE, EMBASE, and Web of Science Core Collection. Gray literature will be searched from AGRIS and Standards for Supporting Agricultural Livelihoods in Emergencies. Articles in English, pertaining to the animal health practices considered highly relevant will be considered eligible for inclusion. Articles will be screened at two stages by two independent reviewers; screening of titles, abstracts, and keywords, followed by full-article screening. The first reviewer will review 100% of the articles at both stages. The second reviewer will review a random sample of 20% of the articles at both stages. Any disagreements will be resolved using inputs from the third reviewer. A thematic analysis will be conducted to catalog contexts and mechanisms for adoption and discussed under a realist framework.DiscussionUnderstanding of the mechanisms underlying the adoption of animal health practices by livestock smallholders in LMICs is crucial for successful implementation of interventions including those which are based on a One Health approach. This review will identify the extent of this knowledge across disciplines and inform future research priorities for the design of effective and feasible interventions which can contribute toward Sustainable Development Goal 2.RegistrationThis protocol is registered within the Open Science Framework (https://doi.org/10.17605/OSF.IO/FUQAX)

Movement Behaviour of Traditionally Managed Cattle in the Eastern Province of Zambia Captured Using Two-Dimensional Motion Sensors

Two-dimensional motion sensors use electronic accelerometers to record the lying, standing and walking activity of cattle. Movement behaviour data collected automatically using these sensors over prolonged periods of time could be of use to stakeholders making management and disease control decisions in rural sub-Saharan Africa leading to potential improvements in animal health and production. Motion sensors were used in this study with the aim of monitoring and quantifying the movement behaviour of traditionally managed Angoni cattle in Petauke District in the Eastern Province of Zambia. This study was designed to assess whether motion sensors were suitable for use on traditionally managed cattle in two veterinary camps in Petauke District in the Eastern Province of Zambia. In each veterinary camp, twenty cattle were selected for study. Each animal had a motion sensor placed on its hind leg to continuously measure and record its movement behaviour over a two week period. Analysing the sensor data using principal components analysis (PCA) revealed that the majority of variability in behaviour among studied cattle could be attributed to their behaviour at night and in the morning. The behaviour at night was markedly different between veterinary camps; while differences in the morning appeared to reflect varying behaviour across all animals. The study results validate the use of such motion sensors in the chosen setting and highlight the importance of appropriate data summarisation techniques to adequately describe and compare animal movement behaviours if association to other factors, such as location, breed or health status are to be assessed