Deciphering the introduction and transmission of SARS-CoV-2 in the Colombian Amazon Basin

La pandemia del SARS-CoV-2 ha obligado a las autoridades sanitarias de todo el mundo a tomar importantes decisiones para reducir su propagación. La epidemiología genómica se ha convertido en una herramienta valiosa para comprender las introducciones y la propagación del virus en una ubicación geográfica específica.The SARS-CoV-2 pandemic has forced health authorities across the world to take important decisions to curtail its spread. Genomic epidemiology has emerged as a valuable tool to understand introductions and spread of the virus in a specific geographic location

Spatio-temporal dynamics of Plasmodium falciparum transmission within a spatial unit on the Colombian Pacific Coast

Funder: Newton-Caldas Fund Institutional Links, British Council, award G1854Funder: Newton-Caldas Fund Institutional Links, British Council, award G1854; Faculty of Medicine, Universidad Nacional de Colombia, awards HERMES 35988, 32309Abstract: As malaria control programmes concentrate their efforts towards malaria elimination a better understanding of malaria transmission patterns at fine spatial resolution units becomes necessary. Defining spatial units that consider transmission heterogeneity, human movement and migration will help to set up achievable malaria elimination milestones and guide the creation of efficient operational administrative control units. Using a combination of genetic and epidemiological data we defined a malaria transmission unit as the area contributing 95% of malaria cases diagnosed at the catchment facility located in the town of Guapi in the South Pacific Coast of Colombia. We provide data showing that P. falciparum malaria transmission is heterogeneous in time and space and analysed, using topological data analysis, the spatial connectivity, at the micro epidemiological level, between parasite populations circulating within the unit. To illustrate the necessity to evaluate the efficacy of malaria control measures within the transmission unit in order to increase the efficiency of the malaria control effort, we provide information on the size of the asymptomatic reservoir, the nature of parasite genotypes associated with drug resistance as well as the frequency of the Pfhrp2/3 deletion associated with false negatives when using Rapid Diagnostic Tests

Application of topological data analysis to the hand written digits classification problem

"Aplicamos el algoritmo Mapper a la base de datos MNIST, usando una serie de configuraciones de sus parámetros incluyendo: uso completo y aproximado de la matriz de distancia, coordenadas obtenidas a partir de PCA y t-SNE para la función filtro y representación de los datos en R^784 y RP^\infinito (usando multi-scale projective coordinates). Encontramos que la elección de representar los dígitos escritos a mano en RP^\infinito y usar las coordenadas de t-SNE como filtro, es crucial para obtener resultados interpretables. Mencionamos algunas métricas para comparar configuraciones y decimos algunas interpretaciones útiles de los grafos obtenidos para el conjunto de datos particular. Finalmente, ejecutamos algunas configuraciones sobre la base de datos Fashion-MNIST y desarrollamos una herramienta de visualización usando D3 para explorar los distintos resultados." -- Tomado del Formato de Documento de Grado."We apply Mapper algorithm to the MNIST data set, comparing a range of parameter configurations including: complete and approximate use of the distance matrix, using PCA and t-SNE coordinates as the filter function and representing the data set in both R^784 and RP^\infinity (using multi-scale projective coordinates). Our findings show that using the RP^\infinity representation of the handwritten digits and t-SNE coordinates as a filter, is crucial in obtaining interpretable results. We mention some useful metrics to compare the different configurations and give several useful interpretations and insights on the obtained graphs over the particular data set. Finally we apply selected configurations to the Fashion-MNIST data set and developed a visualizing tool using the D3 framework to explore the different results." -- Tomado del Formato de Documento de Grado.Magíster en MatemáticasMaestrí

Malaria intensity in Colombia by regions and populations

Determining the distribution of disease prevalence among heterogeneous populations at the national scale is fundamental for epidemiology and public health. Here, we use a combination of methods (spatial scan statistic, topological data analysis and epidemic profile) to study measurable differences in malaria intensity by regions and populations of Colombia. This study explores three main questions: What are the regions of Colombia where malaria is epidemic? What are the regions and populations in Colombia where malaria is endemic? What associations exist between epidemic outbreaks between regions in Colombia? Plasmodium falciparum is most prevalent in the Pacific Coast, some regions of the Amazon Basin, and some regions of the Magdalena Basin. Plasmodium vivax is the most prevalent parasite in Colombia, particularly in the Northern Amazon Basin, the Caribbean, and municipalities of Sucre, Antioquia and Cordoba. We find an acute peak of malarial infection at 25 years of age. Indigenous and Afrocolombian populations experience endemic malaria (with household transmission). We find that Plasmodium vivax decreased in the most important hotspots, often with moderate urbanization rate, and was re-introduced to locations with moderate but sustained deforestation. Infection by Plasmodium falciparum, on the other hand, steadily increased in incidence in locations where it was introduced in the 2009-2010 generalized epidemic. Our findings suggest that Colombia is entering an unstable transmission state, where rapid decreases in one location of the country are interconnected with rapid increases in other parts of the country. © 2018 Feged-Rivadeneira et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

Scaling dynamics of human diseases and urbanization in Colombia

Colombia has one of the largest numbers of internally displaced populations in the world and recently entered a period of post-conflict. These socio-political processes and trends have increased the migration of people towards cities and accordingly are affecting the distribution and occurrence of tropical diseases in its urban and peri-urban areas. Studies have suggested that many human phenomena such as urbanization scale according to the size of human populations regardless of cultural context. But other studies show that health epidemics such as malarial and human immunodeficiency virus infections, follow a scale-free distribution in terms of population size and density. We explore these relationships and dynamics in a tropical context using statistical analyses and available geospatial data to identify the scale dynamics between urbanization processes and disease transmission in Colombia. We found that rural populations and certain disease dynamics were described by power-laws that are frequently mentioned in urbanization studies. However, we found that malaria presented higher intensity of infection in human settlements of less than 50,000 individuals, particularly for ethnic indigenous populations. Results indicate that epidemics and urbanization dynamics do indeed follow scales in Colombia; findings that differ from previous epidemiological studies such as those for malarial infection. Additionally, we identified trends showing that malarial infections become endemic in peri-urban areas. Targeting such peri-urban locations and certain demographic groups are key for managing public health issues in the urbanizing tropics

Malaria Incidents by Municipalities

Malaria incidents by municipality from 2007 to 2015 for species: <i>Plasmodium falciparum </i>and<i> Plasmodium vivax.</i

Políticas públicas, grandes datos, teoría de redes y COVID-19

Technology applied to the use of big data has been an important tool to provide necessary information for public health responses to the COVID-19 pandemic, and Colombia has not been the exception. In this document, we analyze two data inputs (digital contact tracking and aggregate mobility analysis, both based on cell pone data), based on which public health measures have been taken in the Latin American country, such as, for example, determining differential control zones within a city, contact tracking, and identification of potential super spreaders. Based on a simple of the data used, we reflect upon the findings reported so far, especially from the perspective of complex networks of contacts and super spreaders, which have been shown to have a critical role in the behavior of the epidemic. The analyses shown here are part of a complex interaction of political and epidemiological contexts which have led to diverse implementations. We highlight that several examples of public policies in Colombia have been informed by this data.A tecnologia aplicada ao uso de grandes dados tem sido uma ferramenta importante para prover informação necessária para dar respostas aos desafios de saúde pública ante a pandemia de COVID-19, e na Colômbia não tem sido exceção. Neste documento se analisam dois insumos de analítica de dados (rastreio digital de contatos e análise agregado de mobilidade, ambos os dois baseados em dados de telefonia celular) sobre os quais se têm tomado medidas de saúde pública no país latino-americano como, por exemplo, determinar zonas de controle diferencial dentro da cidade, o rastreio de contatos, e a identificação de potenciais superdispersores. Com base em uma amostra dos dados utilizados, se faz uma reflexão à luz dos resultados reportados até agora, especialmente desde uma perspectiva de redes complexas de contatos e superdispersores, as quais se tem mostrado têm um papel crítico no comportamento da epidemia. As análises expostas são parte de uma complexa interação entre o contexto político e epidemiológico que fazem diversas suas respetivas implementações. Finalmente, ressalta-se que a Colômbia conta com diversos exemplos de políticas públicas informadas por dados de última geração.La tecnología aplicada al uso de grandes datos ha sido una herramienta importante para proveer información necesaria para dar respuestas a los retos de salud pública ante la pandemia de COVID-19, y en Colombia no ha sido la excepción. En este documento se analizan dos insumos de analítica de datos (rastreo digital de contactos y análisis agregado de movilidad, ambos basados en datos de telefonía celular) sobre los cuales se han tomado medidas de salud púbica en el país latinoamericano como, por ejemplo, determinar zonas de control diferencial dentro de una ciudad, el rastreo de contactos, y la identificación de potenciales superdispersores. Con base en una muestra de los datos utilizados, se hace una reflexión a la luz de los hallazgos reportados hasta el momento, especialmente desde una perspectiva de redes complejas de contactos y superdispersores, las cuales se ha mostrado tienen un papel crítico en el comportamiento de la epidemia. Los análisis expuestos son parte de una compleja interacción entre el contexto político y epidemiológico que hacen diversas sus respectivas implementaciones. Por último, se resalta que Colombia cuenta con diversos ejemplos de políticas públicas informadas por datos de última generación

Políticas públicas, grandes dados, teoria de redes e COVID-19

La tecnología aplicada al uso de grandes datos ha sido una herramienta importante para proveer información necesaria para dar respuestas a los retos de salud pública ante la pandemia de COVID-19, y en Colombia no ha sido la excepción. En este documento se analizan dos insumos de analítica de datos (rastreo digital de contactos y análisis agregado de movilidad, ambos basados en datos de telefonía celular) sobre los cuales se han tomado medidas de salud púbica en el país latinoamericano como, por ejemplo, determinar zonas de control diferencial dentro de una ciudad, el rastreo de contactos, y la identificación de potenciales superdispersores. Con base en una muestra de los datos utilizados, se hace una reflexión a la luz de los hallazgos reportados hasta el momento, especialmente desde una perspectiva de redes complejas de contactos y superdispersores, las cuales se ha mostrado tienen un papel crítico en el comportamiento de la epidemia. Los análisis expuestos son parte de una compleja interacción entre el contexto político y epidemiológico que hacen diversas sus respectivas implementaciones. Por último, se resalta que Colombia cuenta con diversos ejemplos de políticas públicas informadas por datos de última generación.Technology applied to the use of big data has been an important tool to provide necessary information for public health responses to the COVID-19 pandemic, and Colombia has not been the exception. In this document, we analyze two data inputs (digital contact tracking and aggregate mobility analysis, both based on cell pone data), based on which public health measures have been taken in the Latin American country, such as, for example, determining differential control zones within a city, contact tracking, and identification of potential super spreaders. Based on a simple of the data used, we reflect upon the findings reported so far, especially from the perspective of complex networks of contacts and super spreaders, which have been shown to have a critical role in the behavior of the epidemic. The analyses shown here are part of a complex interaction of political and epidemiological contexts which have led to diverse implementations. We highlight that several examples of public policies in Colombia have been informed by this data

Políticas públicas, grandes dados, teoria de redes e COVID-19

La tecnología aplicada al uso de grandes datos ha sido una herramienta importante para proveer información necesaria para dar respuestas a los retos de salud pública ante la pandemia de COVID-19, y en Colombia no ha sido la excepción. En este documento se analizan dos insumos de analítica de datos (rastreo digital de contactos y análisis agregado de movilidad, ambos basados en datos de telefonía celular) sobre los cuales se han tomado medidas de salud púbica en el país latinoamericano como, por ejemplo, determinar zonas de control diferencial dentro de una ciudad, el rastreo de contactos, y la identificación de potenciales superdispersores. Con base en una muestra de los datos utilizados, se hace una reflexión a la luz de los hallazgos reportados hasta el momento, especialmente desde una perspectiva de redes complejas de contactos y superdispersores, las cuales se ha mostrado tienen un papel crítico en el comportamiento de la epidemia. Los análisis expuestos son parte de una compleja interacción entre el contexto político y epidemiológico que hacen diversas sus respectivas implementaciones. Por último, se resalta que Colombia cuenta con diversos ejemplos de políticas públicas informadas por datos de última generación.Technology applied to the use of big data has been an important tool to provide necessary information for public health responses to the COVID-19 pandemic, and Colombia has not been the exception. In this document, we analyze two data inputs (digital contact tracking and aggregate mobility analysis, both based on cell pone data), based on which public health measures have been taken in the Latin American country, such as, for example, determining differential control zones within a city, contact tracking, and identification of potential super spreaders. Based on a simple of the data used, we reflect upon the findings reported so far, especially from the perspective of complex networks of contacts and super spreaders, which have been shown to have a critical role in the behavior of the epidemic. The analyses shown here are part of a complex interaction of political and epidemiological contexts which have led to diverse implementations. We highlight that several examples of public policies in Colombia have been informed by this data

Spatio-temporal dynamics of Plasmodium falciparum transmission within a spatial unit on the Colombian Pacific Coast

As malaria control programmes concentrate their efforts towards malaria elimination a better understanding of malaria transmission patterns at fine spatial resolution units becomes necessary. Defining spatial units that consider transmission heterogeneity, human movement and migration will help to set up achievable malaria elimination milestones and guide the creation of efficient operational administrative control units. Using a combination of genetic and epidemiological data we defined a malaria transmission unit as the area contributing 95% of malaria cases diagnosed at the catchment facility located in the town of Guapi in the South Pacific Coast of Colombia. We provide data showing that P. falciparum malaria transmission is heterogeneous in time and space and analysed, using topological data analysis, the spatial connectivity, at the micro epidemiological level, between parasite populations circulating within the unit. To illustrate the necessity to evaluate the efficacy of malaria control measures within the transmission unit in order to increase the efficiency of the malaria control effort, we provide information on the size of the asymptomatic reservoir, the nature of parasite genotypes associated with drug resistance as well as the frequency of the Pfhrp2/3 deletion associated with false negatives when using Rapid Diagnostic Tests. © 2020, The Author(s)