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The goal of public health is to improve the overall health of a population by reducing the burden of disease and premature death. In order to monitor our progress towards eliminating existing problems and to identify the emergence of new problems, we need to be able to quantify the levels of ill health or disease in a population. Researchers and policy makers use many different measures to describe the health of populations. In this chapter we introduce more of the most commonly used measures so that you can use and interpret them correctly. We first discuss the three fundamental measures that underlie both the attack rate and most of the other health statistics that you will come across in health-related reports, the incidence rate, incidence proportion (also called risk or cumulative incidence) and prevalence, and then look at how they are calculated and used in practice. We finish by considering other, more elaborate measures that attempt to get closer to describing the overall health of a population. As you will see, this is not always as straightforward as it might seem.
The extent to which the oro-faecal route contributes to the transmission of SARS-CoV-2 is not established.
We systematically reviewed the evidence on the presence of infectious SARS-CoV-2 in faeces and other gastrointestinal sources by examining studies that used viral culture to investigate the presence of replication-competent virus in these samples. We conducted searches in the WHO COVID-19 Database, LitCovid, medRxiv, and Google Scholar for SARS-CoV-2 using keywords and associated synonyms, with a search date up to 28 November 2023.
We included 13 studies involving 229 COVID-19 subjects – providing 308 faecal or rectal swab SARS-CoV2 reverse transcription-polymerase chain reaction (RT-PCR)-positive samples tested with viral culture. The methods used for viral culture across the studies were heterogeneous. Three studies (two cohorts and one case series) reported observing replication-competent SARS-CoV-2 confirmed by quantitative RT-PCR (qPCR) and whole-genome sequencing, and qPCR including appropriate cycle threshold changes. Overall, six (1.9%) of 308 faecal samples subjected to cell culture showed replication-competent virus. One study found replication-competent samples from one immunocompromised patient. No studies were identified demonstrating direct evidence of oro-faecal transmission to humans.
Our review found a relatively low frequency of replication-competent SARS-CoV-2 in faecal and other gastrointestinal sources. Although it is biologically plausible, more research is needed using standardized cell culture methods, control groups, adequate follow-up, and robust epidemiologic methods, including whether secondary infections occurred, to determine the role of the oro-faecal route in the transmission of SARS-CoV-2.
Epidemiology is about measuring disease or other aspects of health in populations, identifying the causes of ill-health and intervening to improve health, and we come back to these three fundamental components later in the chapter. But what do we mean by ‘health’? Back in 1948, the World Health Organization defined it as ‘… a state of complete physical, mental and social well-being’ (WHO, 1948). In practice, what we usually measure is physical health, and this focus is reflected in the content of most routine reports of health data and in many of the health measures that we will consider here; however, there are now methods to capture the more elusive components of mental and social well-being as well. Importantly, the WHO recognised that it is not longevity per se that we seek, but a long and healthy life. So, instead of simply measuring ‘life expectancy’, WHO introduced the concepts of ‘health-adjusted life expectancy’ (HALE) and subsequently ‘disability-adjusted life years’ (DALYs) to enable better international comparisons of the effectiveness of health systems.
People live complicated lives and, unlike laboratory scientists who can control all aspects of their experiments, epidemiologists have to work with that complexity. As a result, no epidemiological study can ever be perfect. Even an apparently straightforward survey of, say, alcohol consumption in a community, can be fraught with problems. Who should be included in the survey? How do you measure alcohol consumption reliably? All we can do when we conduct a study is aim to minimise error as far as possible, and then assess the practical effects of any unavoidable error. A critical aspect of epidemiology is, therefore, the ability to recognise potential sources of error and, more importantly, to assess the likely effects of any error, both in your own work and in the work of others. If we publish or use flawed or biased research we spread misinformation that could hinder decision-making, harm patients and adversely affect health policy. Future research may also be misdirected, delaying discoveries that can enhance public health.
The search for the causes of disease is an obvious central step in the pursuit of better health through disease prevention. In the previous chapters we looked at how we measure health (or disease) and how we look for associations between exposure and disease. Being able to identify a relation between a potential cause of disease and the disease itself is not enough, though. If our goal is to change practice or policy in order to improve health, then we need to go one step further and decide whether the relation is causal because, if it is not, intervening will have no effect. As in previous chapters, we discuss causation mainly in the context of an exposure causing disease but, as you will see when we come to assessing causation in practice, the concepts apply equally to a consideration of whether a potential preventive measure really does improve health.
With global wind energy capacity ramping up, accurately predicting damage equivalent loads (DELs) and fatigue across wind turbine populations is critical, not only for ensuring the longevity of existing wind farms but also for the design of new farms. However, the estimation of such quantities of interests is hampered by the inherent complexity in modeling critical underlying processes, such as the aerodynamic wake interactions between turbines that increase mechanical stress and reduce useful lifetime. While high-fidelity computational fluid dynamics and aeroelastic models can capture these effects, their computational requirements limits real-world usage. Recently, fast machine learning-based surrogates which emulate more complex simulations have emerged as a promising solution. Yet, most surrogates are task-specific and lack flexibility for varying turbine layouts and types. This study explores the use of graph neural networks (GNNs) to create a robust, generalizable flow and DEL prediction platform. By conceptualizing wind turbine populations as graphs, GNNs effectively capture farm layout-dependent relational data, allowing extrapolation to novel configurations. We train a GNN surrogate on a large database of PyWake simulations of random wind farm layouts to learn basic wake physics, then fine-tune the model on limited data for a specific unseen layout simulated in HAWC2Farm for accurate adapted predictions. This transfer learning approach circumvents data scarcity limitations and leverages fundamental physics knowledge from the source low-resolution data. The proposed platform aims to match simulator accuracy, while enabling efficient adaptation to new higher-fidelity domains, providing a flexible blueprint for wake load forecasting across varying farm configurations.
The importance of simple descriptive data was recognised by William Farr, whom we mentioned briefly in Chapter 1 for his seminal work using the newly established vital statistics register of England in the nineteenth century. As we discussed in Chapter 1, this descriptive epidemiology, concerned as it is with ‘person, place and time’, attempts to answer the questions ‘Who?’, ‘What?’, ‘Where?’ and ‘When?’. This can include anything from a description of disease in a single person (a case report) or a special survey conducted to measure the prevalence of a particular health issue in a specific population, to reports from national surveys and data collection systems showing how rates of disease or other health-related factors vary in different geographical areas or over time (time trends). In this chapter we look in more detail at some of the most common types of descriptive data and where they come from. However, before embarking on a data hunt, we first need to decide exactly what it is we want to know, and this can pose a challenge. To make good use of the most relevant descriptive data, it is critical to formulate our question as precisely as possible.
While it is important to be able to read and interpret individual papers, the results of a single study are never going to provide the complete answer to a question. To move towards this, we need to review the literature more widely. There can be a number of reasons for doing this, some of which require a more comprehensive approach than others. If the aim is simply to increase our personal understanding of a new area, then a few papers might provide adequate background material. Traditional narrative reviews have value for exploring areas of uncertainty or novelty but give less emphasis to complete coverage of the literature and tend to be more qualitative, so it is harder to scrutinise them for flaws. Scoping reviews are more systematic but still exploratory. They are conducted to identify the breadth of evidence available on a particular topic, clarify key concepts and identify the knowledge gaps. In contrast, a major decision regarding policy or practice should be based on a systematic review and perhaps a meta-analysis of all the relevant literature, and it is this approach that we focus on here.
The global pandemic of COVID-19 that began in late 2019 highlighted the importance of rapid and thorough investigations of outbreaks. The response to COVID-19 was at a scale not previously seen, involving all sectors of society, including government and private industry. To control and minimise the impact of COVID-19, huge and costly efforts were required to effectively coordinate many different organisations, many of which were not primarily concerned with public health. This type of re-focusing of resources is common in outbreak and public health emergency settings, but is rarely seen at such scale.In this chapter we look at outbreak investigation in more detail and, in doing so, focus on infectious diseases, although not exclusively, because other agents such as toxins and chemicals can also result in ‘outbreaks’ of non-communicable intoxications, injuries and cancer.