Reactions of the inhabitants of Alicante against yellow fever epidemic of 1804

Este trabajo es una parte de la Memoria de Investigación titulada Hambre, enfermedad y muerte. La sociedad alicantina frente a la epidemia de fiebre amarilla de 1804, dirigida por el doctor Josep Bernabeu.El trabajo analiza a través de la revisión de diversas fuentes manuscritas, las reacciones suscitadas en el seno de la población alicantina a raíz de la epidemia de fiebre amarilla de 1804. Los resultados ponen de manifiesto la diversidad socioeconómica de los comportamientos. Mientras los hacendados y comerciantes emigraron en su mayor parte, otros colectivos, como los militares o parte del clero, permanecieron en la ciudad al frente de muchas de las iniciativas político-administrativas o filantrópicas que se tomaron. Las clases populares fueron las que más padecieron los efectos de la epidemia, lo que provocó el resentimiento y la rebeldía a la hora de aceptar y de cumplir las órdenes impuestas por las autoridades. La aparición de la fiebre amarilla, con la consiguiente paralización de la vida comercial y laboral, agravó los problemas que acompañaban a la población alicantina en 1804: crisis agraria, conflicto bélico, desabastecimiento, condiciones higiénico-sanitarias deficientes, etc.This study analizes, through a revision of numerous varied handwritten documents. the reaction of the Alicantine population stemming from the yellow fever epidemic of 1804. The results of this investigation reveal a great diversity of behaviours throughout the socio-economic strata. While the majority of Alicante's landowners and merchants emigrated, other groups, such as members of the military and part of the clergy, remained in the city, at the head of many of the political and administrative initiatives that were adopted. The lower classes suffered most the effects of the epidemic. provoking resentment and rebellion when it came time to accept and act on the orders of the authorities. The arrival of the yellow fever and the subsequent paralization of commerce and work in the city aggravated the problems already faced by the people of Alicante in 1804: a national agrarian crisis, war with England, a scarcity of provisions, deplorable health and hygienic conditions, etc

Nonparametric Bayesian grouping methods for spatial time-series data

We describe an approach for identifying groups of dynamically similar locations in spatial time-series data based on a simple Markov transition model. We give maximum-likelihood, empirical Bayes, and fully Bayesian formulations of the model, and describe exhaustive, greedy, and MCMC-based inference methods. The approach has been employed successfully in several studies to reveal meaningful relationships between environmental patterns and disease dynamics.Comment: 11 pages, no figure

Strength and tempo of selection revealed in viral gene genealogies

BACKGROUND: RNA viruses evolve extremely quickly, allowing them to rapidly adapt to new environmental conditions. Viral pathogens, such as influenza virus, exploit this capacity for evolutionary change to persist within the human population despite substantial immune pressure. Understanding the process of adaptation in these viral systems is essential to our efforts to combat infectious disease. RESULTS: Through analysis of simulated populations and sequence data from influenza A (H3N2) and measles virus, we show how phylogenetic and population genetic techniques can be used to assess the strength and temporal pattern of adaptive evolution. The action of natural selection affects the shape of the genealogical tree connecting members of an evolving population, causing deviations from the neutral expectation. The magnitude and distribution of these deviations lends insight into the historical pattern of evolution and adaptation in the viral population. We quantify the degree of ongoing adaptation in influenza and measles virus through comparison of census population size and effective population size inferred from genealogical patterns, finding a 60-fold greater deviation in influenza than in measles. We also examine the tempo of adaptation in influenza, finding evidence for both continuous and episodic change. CONCLUSIONS: Our results have important consequences for understanding the epidemiological and evolutionary dynamics of the influenza virus. Additionally, these general techniques may prove useful to assess the strength and pattern of adaptive evolution in a variety of evolving systems. They are especially powerful when assessing selection in fast-evolving populations, where temporal patterns become highly visible

Quantifying asymptomatic infection and transmission of COVID-19 in New York City using observed cases, serology, and testing capacity

The contributions of asymptomatic infections to herd immunity and community transmission are key to the resurgence and control of COVID-19, but are difficult to estimate using current models that ignore changes in testing capacity. Using a model that incorporates daily testing information fit to the case and serology data from New York City, we show that the proportion of symptomatic cases is low, ranging from 13 to 18%, and that the reproductive number may be larger than often assumed. Asymptomatic infections contribute substantially to herd immunity, and to community transmission together with presymptomatic ones. If asymptomatic infections transmit at similar rates as symptomatic ones, the overall reproductive number across all classes is larger than often assumed, with estimates ranging from 3.2 to 4.4. If they transmit poorly, then symptomatic cases have a larger reproductive number ranging from 3.9 to 8.1. Even in this regime, presymptomatic and asymptomatic cases together comprise at least 50% of the force of infection at the outbreak peak. We find no regimes in which all infection subpopulations have reproductive numbers lower than three. These findings elucidate the uncertainty that current case and serology data cannot resolve, despite consideration of different model structures. They also emphasize how temporal data on testing can reduce and better define this uncertainty, as we move forward through longer surveillance and second epidemic waves. Complementary information is required to determine the transmissibility of asymptomatic cases, which we discuss. Regardless, current assumptions about the basic reproductive number of severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2) should be reconsidered

Simple temporal models for ecological systems with complex spatial patterns

Spatial patterns are ubiquitous in nature. Because these patterns modify the temporal dynamics and stability properties of population densities at a range of spatial scales, their effects must be incorporated in temporal ecological models that do not represent space explicitly. We demonstrate a connection between a simple parameterization of spatial effects and the geometry of clusters in an individual-based predator–prey model that is both nonlinear and stochastic. Specifically we show that clusters exhibit a power-law scaling of perimeter to area with an exponent close to unity. In systems with a high degree of patchiness, similar power-law scalings can provide a basis for applying simple temporal models that assume well-mixed conditions.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/72011/1/j.1461-0248.2002.00334.x.pd

Strength and tempo of selection revealed in viral gene genealogies

Abstract Background RNA viruses evolve extremely quickly, allowing them to rapidly adapt to new environmental conditions. Viral pathogens, such as influenza virus, exploit this capacity for evolutionary change to persist within the human population despite substantial immune pressure. Understanding the process of adaptation in these viral systems is essential to our efforts to combat infectious disease. Results Through analysis of simulated populations and sequence data from influenza A (H3N2) and measles virus, we show how phylogenetic and population genetic techniques can be used to assess the strength and temporal pattern of adaptive evolution. The action of natural selection affects the shape of the genealogical tree connecting members of an evolving population, causing deviations from the neutral expectation. The magnitude and distribution of these deviations lends insight into the historical pattern of evolution and adaptation in the viral population. We quantify the degree of ongoing adaptation in influenza and measles virus through comparison of census population size and effective population size inferred from genealogical patterns, finding a 60-fold greater deviation in influenza than in measles. We also examine the tempo of adaptation in influenza, finding evidence for both continuous and episodic change. Conclusions Our results have important consequences for understanding the epidemiological and evolutionary dynamics of the influenza virus. Additionally, these general techniques may prove useful to assess the strength and pattern of adaptive evolution in a variety of evolving systems. They are especially powerful when assessing selection in fast-evolving populations, where temporal patterns become highly visible.http://deepblue.lib.umich.edu/bitstream/2027.42/112626/1/12862_2011_Article_1838.pd

Climate Cycles and Forecasts of Cutaneous Leishmaniasis, a Nonstationary Vector-Borne Disease

BACKGROUND: Cutaneous leishmaniasis (CL) is one of the main emergent diseases in the Americas. As in other vector-transmitted diseases, its transmission is sensitive to the physical environment, but no study has addressed the nonstationary nature of such relationships or the interannual patterns of cycling of the disease. METHODS AND FINDINGS: We studied monthly data, spanning from 1991 to 2001, of CL incidence in Costa Rica using several approaches for nonstationary time series analysis in order to ensure robustness in the description of CL's cycles. Interannual cycles of the disease and the association of these cycles to climate variables were described using frequency and time-frequency techniques for time series analysis. We fitted linear models to the data using climatic predictors, and tested forecasting accuracy for several intervals of time. Forecasts were evaluated using “out of fit” data (i.e., data not used to fit the models). We showed that CL has cycles of approximately 3 y that are coherent with those of temperature and El Niño Southern Oscillation indices (Sea Surface Temperature 4 and Multivariate ENSO Index). CONCLUSIONS: Linear models using temperature and MEI can predict satisfactorily CL incidence dynamics up to 12 mo ahead, with an accuracy that varies from 72% to 77% depending on prediction time. They clearly outperform simpler models with no climate predictors, a finding that further supports a dynamical link between the disease and climate

La ciudad ante el contagio: medidas políticas y administrativas dictadas en la epidemia de fiebre amarilla de 1804 en Alicante

Since 1800 the yellow fever started producing epidemic incidents in the Iberian Peninsula. In this article the measures that were established by the different sanitary assemblies implied in the control of the epìdemic outbreak that affected the city of Alicante in 1804 are shown and analysed. The study of this case in Alicante has allowed to put in context this analysis in the framework of what happened in other places during this and other epidemies. It is proved the coexistence of traditional measures of prevention and of new ones. The political and sanitary speech focused on assuring the isolation of the population affected in order to avoid the spreading of this disease and to extend it as long as possible, as a quarantee for the surrounding cities.el artículo se presentan y analizan las medidas que instauraron las diversas Juntas de Sanidad implicadas en el control del brote epidémico que afectó a la ciudad de Alicante en 1804. El estudio del caso alicantino ha permitido contextualizar dicho análisis en el marco de lo sucedido en otras localidades durante ésta y otras epidemias. Se constata la coexistencia de medidas tradicionales de prevención y de nuevas medidas. Las medidas administrativas y sanitarias se centraron en asegurar el aislamiento de la población afectada para evitar la extensión de la enfermedad y prolongarlo el mayor tiempo posible, como una garantía para las localidades vecinas