Spatiotemporal dynamics of epidemiology diseases: mobility based risk and short-term prediction modeling of COVID-19

Nowadays, epidemiological modeling is applied to a wide range of diseases, communicable and non-communicable, namely AIDS, Ebola, influenza, Dengue, Malaria, Zika. More recently, in the context of the last pandemic declared by the World Health Organization (WHO), several studies applied these models to SARS-CoV-2. Despite the increasing number of researches using spatial analysis, some constraints persist that prevent more complex modeling such as capturing local epidemiological dynamics or capturing the real patterns and dynamics. For example, the unavailability of: (i) epidemiological information such as the frequency with which it is made available; (ii) sociodemographic and environmental factors (e.g., population density and population mobility) at a finer scale which influence the evolution patterns of infectious diseases; or (iii) the number of cases information that is also very dependent on the degree of testing performed, often with severe territorial disparities and influenced by context factors. Moreover, the delay in case reporting and the lack of quality control in epidemiological information is responsible for biases in the data that lead to many results obtained being subject to the ecological fallacy, making it difficult to identify causal relationships. Other important methodological limitations are the control of spatiotemporal dependence, management of non-linearity, ergodicy, among others, which can impute inconsistencies to the results. In addition to these issues, social contact, is still difficult to quantify in order to be incorporated into modeling processes. This study aims to explore a modeling framework that can overcome some of these modeling methodological limitations to allow more accurate modeling of epidemiological diseases. Based on Geographic Information Systems (GIS) and spatial analysis, our model is developed to identify group of municipalities where population density (vulnerability) has a stronger relationship with incidence (hazard) and commuting movements (exposure). Specifically, our framework shows how to operate a model over data with no clear trend or seasonal pattern which is suitable for a short-term predicting (i.e., forecasting) of cases based on few determinants. Our tested models provide a good alternative for when explanatory data is few and the time component is not available, once they have shown a good fit and good short-term forecast ability.

Exploring potential risk pathways with high risk groups for urban Rift Valley fever virus introduction, transmission, and persistence in two urban centers of Kenya

Rift Valley fever virus (RVFV) is a zoonotic arbovirus that has profound impact on domestic ruminants and can also be transmitted to humans via infected animal secretions. Urban areas in endemic regions across Africa have susceptible animal and human hosts, dense vector distributions, and source livestock (often from high risk locations to meet the demand for animal protein). Yet, there has never been a documented urban outbreak of RVF. To understand the likely risk of RVFV introduction to urban communities from their perspective and guide future initiatives, we conducted focus group discussions with slaughterhouse workers, slaughterhouse animal product traders, and livestock owners in Kisumu City and Ukunda Town in Kenya. For added perspective and data triangulation, in-depth interviews were conducted one-on-one with meat inspector veterinarians from selected slaughterhouses. A theoretical framework relevant to introduction, transmission, and potential persistence of RVF in urban areas is presented here. Urban livestock were primarily mentioned as business opportunities, but also had personal sentiment. In addition to slaughtering risks, perceived risk factors included consumption of fresh milk. High risk groups' knowledge and experience with RVFV and other zoonotic diseases impacted their consideration of personal risk, with consensus towards lower risk in the urban setting compared to rural areas as determination of health risk was said to primarily rely on hygiene practices rather than the slaughtering process. Groups relied heavily on veterinarians to confirm animal health and meat safety, yet veterinarians reported difficulty in accessing RVFV diagnostics. We also identified vulnerable public health regulations including corruption in meat certification outside of the slaughterhouse system, and blood collected during slaughter being used for food and medicine, which could provide a means for direct RVFV community transmission. These factors, when compounded by diverse urban vector breeding habitats and dense human and animal populations, could create suitable conditions for RVFV to arrive an urban center via a viremic imported animal, transmit to locally owned animals and humans, and potentially adapt to secondary vectors and persist in the urban setting. This explorative qualitative study proposes risk pathways and provides initial insight towards determining how urban areas could adapt control measures and plan future initiatives to better understand urban RVF potential.

Risk assessment and preventive health behaviours toward COVID-19 amongst bushmeat handlers in Nigerian wildlife markets: Drivers and One Health challenge

Over 70% of emerging infectious diseases are zoonotic and 72% of them have wildlife reservoirs with consequent global health impacts. Both SARS-CoV-1 and SARS-CoV-2 emerged certainly through wildlife market routes. We assessed wildlife handlers' zoonotic risk perceptions and preventive health behaviour measures toward COVID-19 during pandemic waves, and its drivers at wildlife markets using Health Belief Model (HBM) constructs. A cross-sectional study was conducted at purposively selected wildlife markets in Nigeria between November 2020 and October 2021. Descriptive, univariate, and multivariable logistic regressions analyses were performed at 95% confidence interval. Of the 600 targeted handlers in 97 wildlife markets, 97.2% (n = 583) participated. Consumers were the majority (65.3%), followed by hunters (18.4) and vendors (16.3%). Only 10.3% hunters, 24.3% vendors and 21.0% consumers associated COVID-19 with high zoonotic risk. Also, only few handlers practiced social/physical distancing at markets. Avoidance of handshaking or hugging and vaccination was significantly (p = 0.001) practiced by few handlers as preventive health behaviours at the markets. All the socio-demographic variables were significantly (p<0.05) associated with their knowledge, risk perceptions, and practice of preventive health behaviours toward COVID-19 at univariate analysis. Poor markets sanitation, hygiene, and biosecurity (OR=3.35, 95% CI: 2.33, 4.82); and poor butchering practices and exchange of wildlife species between shops [(OR=1.87; 95% CI: 1.34, 2.60) and (OR=2.03; 95% CI: 1.43, 2.88), respectively] were more likely to significantly influence COVID-19 emergence and spread at the markets. To tackle the highlighted gaps, collaborations between the public health, anthropologists, and veterinary and wildlife authorities through the One Health approach are advocated to intensify awareness and health education programmes that will improve perceptions and behaviours toward the disease and other emerging diseases control and prevention.

Examining the paradox of urban disease ecology by linking the perspectives of Urban One Health and Ecology with Cities

The ecology of zoonotic, including vector-borne, diseases in urban social-ecological systems is influenced by complex interactions among human and environmental factors. Several characteristics contribute to the emergence and spread of infectious diseases in urban places, such as high human population densities, favorable habitat for vectors, and humans' close proximity to animals and their pathogens. On the other hand, urban living can contribute to the improvement of public health through better access to health services and creation of ecological and technological infrastructure that reduces disease burdens. Therefore, urbanization creates a disease ecology paradox through the interplay of urban health penalties and advantages for individual and community outcomes. To address this contradiction, we advocate a holistic Urban One Health perspective for managing urban systems, especially their green spaces and animal populations, in ways that more effectively control the spread of zoonotic diseases. This view should be coupled with an Ecology with Cities approach which emphasizes actionable science needed for urban planning, management and policymaking; developing disease and vector surveillance programs using citizen and community science methods; and improving education and communication actions that help diverse stakeholders understand the complexities of urban disease ecology. Such measures will enable scholars from many disciplines to collaborate with professionals, government officials, and others to tackle challenges of the urban disease paradox and create more sustainable, health-promoting environments.

Population genomics of Escherichia coli in livestock-keeping households across a rapidly developing urban landscape

Quantitative evidence for the risk of zoonoses and the spread of antimicrobial resistance remains lacking. Here, as part of the UrbanZoo project, we sampled Escherichia coli from humans, livestock and peri-domestic wildlife in 99 households across Nairobi, Kenya, to investigate its distribution among host species in this rapidly developing urban landscape. We performed whole-genome sequencing of 1,338 E. coli isolates and found that the diversity and sharing patterns of E. coli were heavily structured by household and strongly shaped by host type. We also found evidence for inter-household and inter-host sharing and, importantly, between humans and animals, although this occurs much less frequently. Resistome similarity was differently distributed across host and household, consistent with being driven by shared exposure to antimicrobials. Our results indicate that a large, epidemiologically structured sampling framework combined with WGS is needed to uncover strain-sharing events among different host populations in complex environments and the major contributing pathways that could ultimately drive the emergence of zoonoses and the spread of antimicrobial resistance.

Phylogeography and phylogenomic analyses of E. coli isolates collected from humans and domesticated and wild animals across 99 households in Nairobi reveal strong intra-household, and lower but detectable inter-household and inter-host, strain-sharing patterns.

Home gardens can be more important than other urban green infrastructure for mental well-being during COVID-19 pandemics

The current COVID-19 pandemics is a major threat to human populations. The disease has rapidly spread, causing mass hospitalization and the loss of millions of people mainly in urban areas which are hubs for contagion. At the same time, the social distancing practices required for containing the outbreak have caused an eruption of mental illnesses that include symptoms of depression, anxiety and stress. The severity of such mental distress is modulated by the context of media coverage and the information and guidelines from local health authorities. Different urban green infrastructures, such as gardens, parks, and green views can be important for mitigating mental distress during the pandemics. However, it is unclear whether some urban green infrastructures are more efficient than others in reducing mental distress or whether their effectiveness changes with the context. Here we assess the relative importance of different urban green infrastructures on the mental distress of residents of Rio de Janeiro, Brazil. We show that although urban parks and green views are important, home gardens are the most efficient in mitigating mental distress. This is likely related to the practice of self-isolation seen for the residents of Rio de Janeiro. Information on the efficiency of different urban green infrastructures in mitigating mental distress can be important to help guide programs to inform the public about the best practices for maintaining mental health during the current outbreak. This can also help planning cities that are more resilient to future pandemics.

Estimates of COVID-19 Risk Factors among Social Strata and Predictors for a Vulnerability to the Infection

Coronavirus disease 2019 (COVID-19) has emerged as a potentially severe disease, especially for individuals presenting with certain underlying medical conditions. We analyzed the rates of comorbidities and symptoms to reveal the potential severity of the pandemic in Volos, one of the most air-polluted cities in Greece. Environmental and health-related predictors for SARS-CoV-2 infection were investigated. A web-based questionnaire was disseminated through social media in the first half of March 2021 during a five-month strict lockdown. Sociodemographic data, preexisting medical conditions, frequency of clinical symptoms, and COVID-19 information were recorded. The study population consisted of 2000 responders. Four-fifths of the participants reported comorbidities that could increase vulnerability to severe COVID-19. Respiratory symptoms were reported from the unemployed and from retirees, and cold-related symptoms were reported in the education sector and in undergraduates. Women and younger generations shaped social vulnerability to respiratory infections similar to the elderly. SARS-CoV-2 infection was reported in 3.7% of the study population. Common headache (OR 2; CI 1189-3013; p = 0.007) and prior pneumonia (OR 1.9; CI 1024-2898; p = 0.04) were significant predictors for susceptibility to SARS-CoV-2 infection. The importance of monitoring society through community-based questionnaires is highlighted, for predicting and preventing future widespread transmission of infectious diseases.

The Pandemic City: Urban Issues in the Time of COVID-19

Pandemics have shaped the way cities are planned and configured. Throughout history, cities have evolved to solve problems of sanitation, hygiene, and health access while providing space and opportunities for the urban dwellers. COVID-19 will have significant implications in the way cities are planned. This recent crisis highlights a number of issues. This paper looks at the context for the pandemic and then reviews studies and debates in four areas: transformations in the configuration of public spaces, transportation, urban connectivities, and urban economies. This pandemic, like other similar episodes in the past, is forcing us to rethink the nature of urban space and may be an opportunity to plan for safer, more sustainable cities.

Drivers of Infectious Disease Seasonality: Potential Implications for COVID-19

Not 1 year has passed since the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19). Since its emergence, great uncertainty has surrounded the potential for COVID-19 to establish as a seasonally recurrent disease. Many infectious diseases, including endemic human coronaviruses, vary across the year. They show a wide range of seasonal waveforms, timing (phase), and amplitudes, which differ depending on the geographical region. Drivers of such patterns are predominantly studied from an epidemiological perspective with a focus on weather and behavior, but complementary insights emerge from physiological studies of seasonality in animals, including humans. Thus, we take a multidisciplinary approach to integrate knowledge from usually distinct fields. First, we review epidemiological evidence of environmental and behavioral drivers of infectious disease seasonality. Subsequently, we take a chronobiological perspective and discuss within-host changes that may affect susceptibility, morbidity, and mortality from infectious diseases. Based on photoperiodic, circannual, and comparative human data, we not only identify promising future avenues but also highlight the need for further studies in animal models. Our preliminary assessment is that host immune seasonality warrants evaluation alongside weather and human behavior as factors that may contribute to COVID-19 seasonality, and that the relative importance of these drivers requires further investigation. A major challenge to predicting seasonality of infectious diseases are rapid, human-induced changes in the hitherto predictable seasonality of our planet, whose influence we review in a final outlook section. We conclude that a proactive multidisciplinary approach is warranted to predict, mitigate, and prevent seasonal infectious diseases in our complex, changing human-earth system.

The COVID-19 pandemic: local to global implications as perceived by urban ecologists

The global COVID-19 pandemic is affecting everyone, but in many different ways, stimulating contrasting reactions and responses: opportunities for some, difficulties for many. A simple survey of how individual workers in urban ecology have been coping with COVID-19 constraints found divergent responses to COVID-19 on people’s activities, both within countries and between continents. Many academics felt frustrated at being unable to do fieldwork, but several saw opportunities to change ways of working and review their engagement with the natural world. Some engaging with social groups found new ways of sharing ideas and developing aspirations without face-to-face contact. Practitioners creating and managing urban greenspaces had to devise ways to work and travel while maintaining social distancing. Many feared severe funding impacts from changed local government priorities. Around the world, the COVID-19 pandemic has amplified issues, such as environmental injustice, disaster preparation and food security, that have been endemic in most countries across the global south in modern times. However, developing and sustaining the strong community spirit shown in many places will speed economic recovery and make cities more resilient against future geophysical and people-made disasters. Significantly, top-down responses and one-size-fits-all solutions, however good the modelling on which they are based, are unlikely to succeed without the insights that local knowledge and community understanding can bring. We all will have to look at disaster preparation in a more comprehensive, caring and consistent way in future.