Bayesian inference for the onset time and epidemiological characteristics of emerging infectious diseases.

Background: Emerging infectious diseases pose a significant threat to global public health. Timely detection and response are crucial in mitigating the spread of such epidemics. Inferring the onset time and epidemiological characteristics is vital for accelerating early interventions, but accurately predicting these parameters in the early stages remains challenging. Methods: We introduce a Bayesian inference method to fit epidemic models to time series data based on state-space modeling, employing a stochastic Susceptible-Exposed-Infectious-Removed (SEIR) model for transmission dynamics analysis. Our approach uses the particle Markov chain Monte Carlo (PMCMC) method to estimate key epidemiological parameters, including the onset time, the transmission rate, and the recovery rate. The PMCMC algorithm integrates the advantageous aspects of both MCMC and particle filtering methodologies to yield a computationally feasible and effective means of approximating the likelihood function, especially when it is computationally intractable. Results: To validate the proposed method, we conduct case studies on COVID-19 outbreaks in Wuhan, Shanghai and Nanjing, China, respectively. Using early-stage case reports, the PMCMC algorithm accurately predicted the onset time, key epidemiological parameters, and the basic reproduction number. These findings are consistent with empirical studies and the literature. Conclusion: This study presents a robust Bayesian inference method for the timely investigation of emerging infectious diseases. By accurately estimating the onset time and essential epidemiological parameters, our approach is versatile and efficient, extending its utility beyond COVID-19.

Zoonotic spillover and viral mutations from low and middle-income countries: improving prevention strategies and bridging policy gaps.

The increasing frequency of zoonotic spillover events and viral mutations in low and middle-income countries presents a critical global health challenge. Contributing factors encompass cultural practices like bushmeat consumption, wildlife trade for traditional medicine, habitat disruption, and the encroachment of impoverished settlements onto natural habitats. The existing "vaccine gap" in many developing countries exacerbates the situation by allowing unchecked viral replication and the emergence of novel mutant viruses. Despite global health policies addressing the root causes of zoonotic disease emergence, there is a significant absence of concrete prevention-oriented initiatives, posing a potential risk to vulnerable populations. This article is targeted at policymakers, public health professionals, researchers, and global health stakeholders, particularly those engaged in zoonotic disease prevention and control in low and middle-income countries. The article underscores the importance of assessing potential zoonotic diseases at the animal-human interface and comprehending historical factors contributing to spillover events. To bridge policy gaps, comprehensive strategies are proposed that include education, collaborations, specialized task forces, environmental sampling, and the establishment of integrated diagnostic laboratories. These strategies advocate simplicity and unity, breaking down barriers, and placing humanity at the forefront of addressing global health challenges. Such a strategic and mental shift is crucial for constructing a more resilient and equitable world in the face of emerging zoonotic threats.

Capacity and needs assessment of veterinary services in Vietnam in biosecurity, biosafety and One Health.

The Asia-Pacific region is recognised as an epicentre of emerging infectious diseases (EIDs), of which 75% are zoonotic in nature. Vietnam is recognised as a potential hotspot for zoonotic EIDs. There is a growing recognition that progress towards global health security requires greater focus on collaboration between the human health and animal health sectors to control diseases at their animal source and prevent against human health impacts. Assessment of veterinary epidemiology capacity in Vietnam is paramount to strengthening the health security of Asia-Pacific. This study aims to evaluate the national capacity and needs of veterinary services in Vietnam in biosecurity, biosafety and One Health. A cross-sectional, convergent mixed-methods study was conducted between November 2020 and April 2021. An online questionnaire was administered to government-employed field veterinarians. Descriptive analyses and logistic regression models were performed using survey responses to understand capacity in the field. Semi-structured interviews were also conducted with stakeholders in veterinary services including government, academia, research institutes, non-profit and international organisations. Coding and thematic analysis using a deductive approach was used for data collected from interviews to contextualise findings from the survey and understand institutional capacity. In total, 178 field veterinarians completed the online survey and 25 stakeholders were interviewed. The majority of participants had reported receiving training in biosecurity and biosafety, including use of personal protective equipment. Most respondents reported practicing good biosecurity measures (92%) and good biosafety measures (88%). Physical and socioeconomic barriers to practicing biosecurity were reported to be prevalent for smallholder farmers, which may suggest a gap in the capacity of veterinary services to provide cost-effective and practical biosecurity strategies. Seventy five percent of participants had never or rarely participated in One Health approaches in the field in the last 12 months and 69% reported further training as a high priority. There was a knowledge gap reported amongst district and commune-level veterinary staff about the need for, and awareness of multisectoral collaboration. Respondents that completed postgraduate qualifications in epidemiology or Field Epidemiology Training Programs (adjusted OR: 3.06; 95% CI: 1.01, 9.23, p = 0.046) and had longer job tenure between 10-12 years (OR: 10.38; 95% CI: 3.06, 35.15, p = <0.001) were more likely to have higher levels of experience in One Health. This study identified gaps in knowledge, attitudes and adoption of practices related to biosecurity, biosafety and One Health specifically in lower-level or less experienced veterinary staff without further training opportunities in epidemiology. These findings enable prioritisation of training, policy, and planning activities to further enhance the national capacity of veterinary services in Vietnam.

Financial influence on global risks of zoonotic emerging and re-emerging diseases: an integrative analysis.

BACKGROUND: Emerging and re-emerging infectious diseases (EIDs), such as Ebola virus disease and highly pathogenic influenza, are serious threats to human health and wellbeing worldwide. The financial sector has an important, yet often ignored, influence as owners and investors in industries that are associated with anthropogenic land-use changes in ecosystems linked to increased EIDs risks. We aimed to analyse financial influence associated with EIDs risks that are affected by anthropogenic land-use changes. We also aimed to provide empirical assessments of such influence to help guide engagements by governments, private organisations, and non-governmental organisations with the financial sector to advance a planetary health agenda. METHODS: For this integrative analysis, we identified regions in the world where there was evidence of a connection between EIDs and anthropogenic land-use changes between Nov 9, 1999, and Oct 25, 2021, through a targeted literature review of academic literature and grey literature to identify evidence of drivers of anthropogenic land-use change and their association with commodity production in these regions. We only included publications in English that showed a connection between deforestation and the production of one or more commodities. Publications merely describing spatial or temporal land-use change dynamics (eg, a reduction of forest or an increase of palm-oil plantations) were excluded. As we were assessing financial influence on corporate activities through ownership specifically, we focused our analysis on publicly listed companies. Equity data and data about ownership structure were extracted from Orbis, a company information database. We assessed financial influence by identifying financial entities with the largest equity ownership, descriptively mapping transboundary connections between investors and publicly listed companies. FINDINGS: 227 public and private companies operating in five economic sectors (ie, production of palm oil, pulp and wood products, cocoa, soybeans, and beef) between Dec 15, 2020, and March 8, 2021, were identified. Of these 227, 99 (44%) were publicly listed companies, with 2310 unique shareholders. These publicly listed companies operated in six geographical regions, resulting in nine case-study regions. 54 (55%) companies with complete geographical information were included in the countries network. Four financial entities (ie, Dimensional, Vanguard, BlackRock, and Norway's sovereign wealth fund) each had ownership in 39 companies or more in three of the case-study regions (ie, north America, east Asia, and Europe). Four large US-based asset managers (ie, Vanguard, BlackRock, T Rowe Price, and State Street) were the largest owners of publicly listed companies in terms of total equity size, with ownership amounts for these four entities ranging from US$8 billion to $21 billion. The specific patterns of cross-national ownership depended on the region of interest; for example, financial influence on EIDs risks that was associated with commodity production in southeast and east Asia came from not only global asset managers but also Malaysian, Chinese, Japanese, and Korean financial entities. India, Brazil, the USA, Mexico, and Argentina were the countries towards which investments were most directed. INTERPRETATION: Although commodity supply chains and financial markets are highly globalised, a small number of investors and countries could be viewed as disproportionally influential in sectors that increase EIDs risks. Such financial influence could be used to develop and implement effective policies to reduce ecological degradation and mitigate EIDs risks and their effects on population health. FUNDING: Formas and Networks of Financial Rupture-how cascading changes in the climate and ecosystems could impact on the financial sector.

Enfermedades emergentes, pobreza y hambre / Emerging diseases, poverty and hunger

La pobreza y el hambre son elementos significativos para la prevalencia de las enfermedades emergentes, además de la ignorancia, la indigencia, las falencias sanitarias y los cambios ambientales debidos al calentamiento global. La desnutrición es consecuencia de la pobreza y ésta es causa de desnutrición. Los niños que viven en condiciones de mayor vulnerabilidad tienen un riesgo alto de morir por diarrea, neumonía y enfermedades emergentes. La mayoría son desnutridos. Su futuro en la adultez guarda relación con la desnutrición en la infancia. En el mundo 820 millones de niños padecen hambre y mueren anualmente 3 millones de menores de 5 años, según datos del Fondo de las Naciones Unidas para la Infancia. En Argentina, según datos del segundo semestre de 2022, un 39,2% de la población es pobre (Instituto Nacional de Estadísticas y Censos). El 15,5% de niños y adolescentes padecen inseguridad alimentaria y 2 millones de niños padecen hambre (Médicos sin Fronteras). La tasa de mortalidad infantil en menores de 5 años tiene una prevalencia del 0,4%. Los cambios climáticos ejercen influencia sobre la salud, produciendo cambios en la epidemiologia de las enfermedades emergentes, mientras que la insuficiente alimentación ocasiona efectos negativos sobre la salud. El calentamiento global aumenta las inundaciones y las sequías, incidiendo en la escasez de alimentos e incrementando las enfermedades emergentes. La situación debe ser revertida mediante el desarrollo sostenido de la educación, el bienestar social y los proyectos sanitarios. (AU)

Poverty and hunger are significant elements for the prevalence of emerging diseases, in addition to ignorance, indigence, sanitary deficiencies and environmental changes due to global warming. Malnutrition is a consequence of poverty and poverty is a cause of malnutrition. Children living in more vulnerable conditions are at greater risk of dying from diarrhea, pneumonia and emerging diseases. Most are malnourished. Their future in adulthood is related to malnutrition in childhood. Worldwide, 820 million children suffer from hunger and 3 million children under 5 die annually (United Nations Children's Fund). In Argentina, according to data from the second half of 2022, 39.2% of the population is poor (Instituto Nacional de Estadísticas y Censos). 15.5% of children and adolescents are food insecure and 2 million children are hungry (Médecins Sans Frontières). The infant mortality rate in children under 5 years of age has a prevalence of 0.4%. Climate change influences health, producing changes in the epidemiology of emerging diseases, while insufficient food has negative effects on health. Global warming increases floods and droughts, leading to food shortages and increasing emerging diseases. The situation must be reversed through sustained development of education, social welfare and health projects. (AU)

Policies to prevent zoonotic spillover: a systematic scoping review of evaluative evidence.

BACKGROUND: Emerging infectious diseases of zoonotic origin present a critical threat to global population health. As accelerating globalisation makes epidemics and pandemics more difficult to contain, there is a need for effective preventive interventions that reduce the risk of zoonotic spillover events. Public policies can play a key role in preventing spillover events. The aim of this review is to identify and describe evaluations of public policies that target the determinants of zoonotic spillover. Our approach is informed by a One Health perspective, acknowledging the inter-connectedness of human, animal and environmental health. METHODS: In this systematic scoping review, we searched Medline, SCOPUS, Web of Science and Global Health in May 2021 using search terms combining animal health and the animal-human interface, public policy, prevention and zoonoses. We screened titles and abstracts, extracted data and reported our process in line with PRISMA-ScR guidelines. We also searched relevant organisations' websites for evaluations published in the grey literature. All evaluations of public policies aiming to prevent zoonotic spillover events were eligible for inclusion. We summarised key data from each study, mapping policies along the spillover pathway. RESULTS: Our review found 95 publications evaluating 111 policies. We identified 27 unique policy options including habitat protection; trade regulations; border control and quarantine procedures; farm and market biosecurity measures; public information campaigns; and vaccination programmes, as well as multi-component programmes. These were implemented by many sectors, highlighting the cross-sectoral nature of zoonotic spillover prevention. Reports emphasised the importance of surveillance data in both guiding prevention efforts and enabling policy evaluation, as well as the importance of industry and private sector actors in implementing many of these policies. Thoughtful engagement with stakeholders ranging from subsistence hunters and farmers to industrial animal agriculture operations is key for policy success in this area. CONCLUSION: This review outlines the state of the evaluative evidence around policies to prevent zoonotic spillover in order to guide policy decision-making and focus research efforts. Since we found that most of the existing policy evaluations target 'downstream' determinants, additional research could focus on evaluating policies targeting 'upstream' determinants of zoonotic spillover, such as land use change, and policies impacting infection intensity and pathogen shedding in animal populations, such as those targeting animal welfare.

Rapid On-Site Detection of SARS-CoV-2 Using RT-LAMP Assay with a Portable Low-Cost Device.

Emerging infectious diseases pose a serious threat to human health and affect social stability. In recent years, the epidemic situation of emerging infectious diseases is very serious; among these infectious diseases, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has affected many countries and regions in a short time. The prevention and treatment of these diseases require rapid on-site detection methods. However, the common detection method, RT-PCR, requires expensive instruments, complex operations, and professional operators. Here, we developed a portable low-cost assay for rapid on-site detection of viral nucleic acid using reverse transcription-loop-mediated isothermal amplification (RT-LAMP). The SARS-CoV-2 RNA can be successfully amplified within 15 min in a thermos, and the detection result is read rapidly in a portable low-cost device with a sensitivity of 100 copies/µL. The portable low-cost device consists of a black box, a laser or LED and a filter, costing only a few cents. The rapid on-site detection method can provide strong support for the control of biological threats such as infectious diseases. It is also an emergency detection method for low-resource settings, relieving the huge pressure on health care.

CROI 2023: Epidemiology, Diagnosis, and Management of MPox.

The 2023 Conference on Retroviruses and Opportunistic Infections (CROI) emphasized emerging infectious diseases such as COVID-19 and mpox. Despite emerging from countries in which it was endemic only 9 months before the conference, mpox was well covered, with more than 60 presentations addressing various topics. There was a focus on the rapid development and implementation of tests to reduce the time to diagnosis, as well as multiplex panels to increase the accuracy of differential diagnosis. Presenters also highlighted the ability to diagnose mpox from multiple compartments, such as with rectal and pharyngeal swabs, and provided crucial information on the duration of positivity that may impact isolation requirements. Clinical experiences were described, including risk factors for severe disease and syndemic management. High rates of concomitant sexually transmitted infection (STI) were reported. Finally, prevention was a key topic, with presenters pointing to the contributions of individual behavioral changes and vaccine efficacy to reducing new cases.

Surveillance and risk assessment for early detection of emerging infectious diseases in livestock.

Those who work in the area of surveillance and prevention of emerging infectious diseases (EIDs) face a challenge in accurately predicting where infection will occur and who (or what) it will affect. Establishing surveillance and control programmes for EIDs requires substantial and long-term commitment of resources that are limited in nature. This contrasts with the unquantifiable number of possible zoonotic and non-zoonotic infectious diseases that may emerge, even when the focus is restricted to diseases involving livestock. Such diseases may emerge from many combinations of, and changes in, host species, production systems, environments/habitats and pathogen types. Given these multiple elements, risk prioritisation frameworks should be used more widely to support decision-making and resource allocation for surveillance. In this paper, the authors use recent examples of EID events in livestock to review surveillance approaches for the early detection of EIDs, and highlight the need for surveillance programmes to be informed and prioritised by regularly updated risk assessment frameworks. They conclude by discussing some unmet needs in risk assessment practices for EIDs, and the need for improved coordination in global infectious disease surveillance.

Les personnes travaillant dans le domaine de la surveillance et de la prévention des maladies infectieuses émergentes (MIE) sont confrontées à la difficulté de prédire avec exactitude le lieu d'émergence d'une maladie, ainsi que l'espèce, le système ou le site affectés. La mise en place de programmes de surveillance et de lutte contre les MIE exige une mobilisation conséquente et durable de ressources nécessairement limitées. Par contraste, le nombre des maladies infectieuses zoonotiques et non zoonotiques pouvant se déclarer est impossible à quantifier, même si l'on s'en tient aux seules maladies affectant les animaux d'élevage. Ces maladies surviennent à la faveur des nombreuses et diverses configurations, associations ou modifications qui peuvent se produire parmi les espèces hôtes, les systèmes de production, les environnements ou habitats et les types d'agents pathogènes. Compte tenu de la multiplicité de ces éléments, il devrait être fait plus largement appel à des cadres de priorisation du risque afin de soutenir les processus de prise de décision et d'allocation des ressources en matière de surveillance. Les auteurs s'appuient sur des exemples récents d'événements liés à des MIE pour faire le point sur les méthodes de surveillance appliquées pour la détection précoce de ces maladies et soulignent l'importance de documenter et de prioriser les programmes de surveillance en procédant à des mises à jour régulières des cadres utilisés pour l'évaluation du risque. Ils concluent en évoquant certains aspects importants que les pratiques actuelles d'évaluation du risque ne permettent pas de couvrir lorsqu'il s'agit de MIE, ainsi que l'importance d'améliorer la coordination de la surveillance des maladies infectieuses au niveau mondial.

Cuantos trabajan en el ámbito de la vigilancia y la prevención de enfermedades infecciosas emergentes (EIE) tienen dificultades para predecir con precisión dónde va a surgir y a quién (o qué) afectará una infección. La instauración de programas de vigilancia y control de EIE exige una inversión sustancial y duradera de recursos que por definición son escasos, sobre todo teniendo en cuenta el número incalculable de enfermedades infecciosas zoonóticas y no zoonóticas que pueden aparecer, aun considerando solo aquellas que afectan al ganado. Este tipo de enfermedades pueden surgir como resultado de muchas combinaciones distintas de especie hospedadora, sistema productivo, medio/hábitat y tipo de patógeno o por efecto de cambios que se den en cualquiera de estos elementos. En vista de la multiplicidad de factores que concurren, convendría emplear de modo más generalizado un sistema de jerarquización de los riesgos en el cual fundamentar las decisiones de vigilancia y la distribución de los recursos destinados a ella. Los autores, valiéndose de ejemplos recientes de episodios infecciosos emergentes que afectaron al ganado, pasan revista a distintos métodos de vigilancia para la detección temprana de EIE y recalcan que los programas de vigilancia deben reposar en procedimientos de determinación del riesgo periódicamente actualizados y en las prioridades fijadas a partir de estos procedimientos. Por último, los autores se detienen en algunas necesidades desatendidas en la praxis de la determinación del riesgo de EIE y en la necesidad de una mejor coordinación de la vigilancia mundial de las enfermedades infecciosas.

Development of animal models for emerging infectious diseases by breaking the barrier of species susceptibility to human pathogens.

Outbreaks of emerging infectious diseases pose a serious threat to public health security, human health and economic development. After an outbreak, an animal model for an emerging infectious disease is urgently needed for studying the etiology, host immune mechanisms and pathology of the disease, evaluating the efficiency of vaccines or drugs against infection, and minimizing the time available for animal model development, which is usually hindered by the nonsusceptibility of common laboratory animals to human pathogens. Thus, we summarize the technologies and methods that induce animal susceptibility to human pathogens, which include viral receptor humanization, pathogen-targeted tissue humanization, immunodeficiency induction and screening for naturally susceptible animal species. Furthermore, the advantages and deficiencies of animal models developed using each method were analyzed, and these will guide the selection of susceptible animals and potentially reduce the time needed to develop animal models during epidemics.

Exploring spatiotemporal pattern in the association between short-term exposure to fine particulate matter and COVID-19 incidence in the continental United States: a Leroux-conditional-autoregression-based strategy.

Background: Numerous studies have demonstrated that fine particulate matter (PM2.5) is adversely associated with COVID-19 incidence. However, few studies have explored the spatiotemporal heterogeneity in this association, which is critical for developing cost-effective pollution-related policies for a specific location and epidemic stage, as well as, understanding the temporal change of association between PM2.5 and an emerging infectious disease like COVID-19. Methods: The outcome was state-level daily COVID-19 cases in 49 native United States between April 1, 2020 and December 31, 2021. The exposure variable was the moving average of PM2.5 with a lag range of 0-14 days. A latest proposed strategy was used to investigate the spatial distribution of PM2.5-COVID-19 association in state level. First, generalized additive models were independently constructed for each state to obtain the rough association estimations, which then were smoothed using a Leroux-prior-based conditional autoregression. Finally, a modified time-varying approach was used to analyze the temporal change of association and explore the potential causes spatiotemporal heterogeneity. Results: In all states, a positive association between PM2.5 and COVID-19 incidence was observed. Nearly one-third of these states, mainly located in the northeastern and middle-northern United States, exhibited statistically significant. On average, a 1 µg/m3 increase in PM2.5 concentration led to an increase in COVID-19 incidence by 0.92% (95%CI: 0.63-1.23%). A U-shaped temporal change of association was examined, with the strongest association occurring in the end of 2021 and the weakest association occurring in September 1, 2020 and July 1, 2021. Vaccination rate was identified as a significant cause for the association heterogeneity, with a stronger association occurring at a higher vaccination rate. Conclusion: Short-term exposure to PM2.5 and COVID-19 incidence presented positive association in the United States, which exhibited a significant spatiotemporal heterogeneity with strong association in the eastern and middle regions and with a U-shaped temporal change.

Achieving Global Vaccine Equity: The Case for an International Pandemic Treaty.

This paper presents an ethical argument in support of an international Pandemic Treaty. It argues that an international Pandemic Treaty is the best way to mark progress on global vaccine equity and broader issues of global pandemic preparedness and response which came to light during the coronavirus disease 2019 (COVID-19) pandemic. Section I evaluates principles of multilateral charity, national security, and international diplomacy standardly invoked in debates about global vaccine allocation and argues that these approaches fall short. Section II explicates notions of solidarity, duties to the least well-off, and mutual aid as ethical values more fitting for an era of emerging infectious diseases. Section III relates the discussion to an international Pandemic Treaty and presents legal, pragmatic, and ethical reasons to support it. The paper concludes that in an interconnected world, fair sharing of vaccines between nations is morally mandatory.