COVID-19 spread, detection, and dynamics in Bogota, Colombia.
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ABSTRACT:
SUBMITTER: Laajaj R
PROVIDER: S-EPMC8342514 | biostudies-literature | 2021 Aug
REPOSITORIES: biostudies-literature
Publications
COVID-19 spread, detection, and dynamics in Bogota, Colombia.
Laajaj Rachid R De Los Rios Camilo C Sarmiento-Barbieri Ignacio I Aristizabal Danilo D Behrentz Eduardo E Bernal Raquel R Buitrago Giancarlo G Cucunubá Zulma Z de la Hoz Fernando F Gaviria Alejandro A Hernández Luis Jorge LJ León Leonardo L Moyano Diane D Osorio Elkin E Varela Andrea Ramírez AR Restrepo Silvia S Rodriguez Rodrigo R Schady Norbert N Vives Martha M Webb Duncan D
Nature communications 20210805 1
Latin America has been severely affected by the COVID-19 pandemic but estimations of rates of infections are very limited and lack the level of detail required to guide policy decisions. We implemented a COVID-19 sentinel surveillance study with 59,770 RT-PCR tests on mostly asymptomatic individuals and combine this data with administrative records on all detected cases to capture the spread and dynamics of the COVID-19 pandemic in Bogota from June 2020 to early March 2021. We describe various f ...[more]
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Project description:The COVID-19 pandemic has affected millions of people around the world. In Colombia, 1.65 million cases and 43,495 deaths were reported in 2020. Schools were closed in many places around the world to slow down the spread of SARS-CoV-2. In Bogotá, Colombia, most of the public schools were closed from March 2020 until the end of the year. School closures can exacerbate poverty, particularly in low- and middle-income countries. To reconcile these two priorities in health and fighting poverty, we estimated the impact of school reopening for in-person instruction in 2021. We used an agent-based model of SARS-CoV-2 transmission calibrated to the daily number of deaths. The model includes schools that represent private and public schools in terms of age, enrollment, location, and size. We simulated school reopening at different capacities, assuming a high level of face-mask use, and evaluated the impact on the number of deaths in the city. We also evaluated the impact of reopening schools based on grade and multidimensional poverty index. We found that school at 35% capacity, assuming face-mask adherence at 75% in>8 years of age, had a small impact on the number of deaths reported in the city during a third wave. The increase in deaths was smallest when only pre-kinder was opened, and largest when secondary school was opened. At larger capacities, the impact on the number of deaths of opening pre-kinder was below 10%. In contrast, reopening other grades above 50% capacity substantially increased the number of deaths. Reopening schools based on their multidimensional poverty index resulted in a similar impact, irrespective of the level of poverty of the schools that were reopened. The impact of schools reopening was lower for pre-kinder grades and the magnitude of additional deaths associated with school reopening can be minimized by adjusting capacity in older grades.
| S-EPMC10021412 | biostudies-literature
Project description:The transmission dynamics of the coronavirus-COVID-19-have challenged humankind at almost every level. Currently, research groups around the globe are trying to figure out such transmission dynamics under special conditions such as separation policies enforced by governments. Mathematical and computational models, like the compartmental model or the agent-based model, are being used for this purpose. This paper proposes an agent-based model, called INFEKTA, for simulating the transmission of infectious diseases, not only the COVID-19, under social distancing policies. INFEKTA combines the transmission dynamic of a specific disease, (according to parameters found in the literature) with demographic information (population density, age, and genre of individuals) of geopolitical regions of the real town or city under study. Agents (virtual persons) can move, according to its mobility routines and the enforced social distancing policy, on a complex network of accessible places defined over an Euclidean space representing the town or city. The transmission dynamics of the COVID-19 under different social distancing policies in Bogotá city, the capital of Colombia, is simulated using INFEKTA with one million virtual persons. A sensitivity analysis of the impact of social distancing policies indicates that it is possible to establish a 'medium' (i.e., close 40% of the places) social distancing policy to achieve a significant reduction in the disease transmission.
| S-EPMC7894857 | biostudies-literature
Project description:BackgroundDespite a wealth of data from high-income countries, there is limited information on the distinct epidemiological patterns observed in diverse, densely populated regions within Latin America. This retrospective analysis of COVID-19's four major waves in Bogotá, Colombia, evaluates 1.77 million cases in detail.MethodsA comprehensive suite of statistical methods was employed. Transmission dynamics were assessed by estimating the instantaneous reproduction number R(t) , while variant-specific transmission advantages were estimated using multinomial logistic regression models. Disease severity was assessed through a suite of indicators: Hospitalisation Case Ratio (HCR), intensive care unit case ratio (ICU-CR), case fatality ratio (CFR), hospitalisation fatality ratio (HFR), and ICU fatality ratio (ICU-FR). Additionally, we analysed the distribution of hospitalisations, ICU admissions, and fatalities by age group and wave. We employed a Bayesian hierarchical model to capture epidemiological delays-such as onset-to-death, hospitalisation, and ICU admission durations to estimate hospital and ICU stay durations.ResultsOur findings reveal substantial variation in R(t) , with peaks exceeding 2.5 during the ancestral and Omicron waves. Over the course of the pandemic, we observed a 78% reduction in CFR, underscoring shifts in clinical severity. The third wave, associated with the Mu variant, recorded the highest case and death counts, alongside a decreased CFR, an elevated HFR, and a shift in the most affected age group towards younger populations. In contrast, the fourth wave, driven by the Omicron variant, exhibited the highest reproduction number and the lowest overall severity. This wave was characterised by a significant increase in pediatric hospitalisations. The study reveals a continued decline in the mean durations of hospital and ICU stays across the four waves, with hospital stays decreasing from 10.84 to 7.85 days and ICU stays dropping from 16.2 to 12.4 days.ConclusionsThis study reveals significant shifts in transmission and severity metrics-including mortality, hospitalisation, and ICU rates and stays-across age groups during Bogotá's four COVID-19 waves. These insights underscore the value of retrospective analyses to understand the pandemic's varied impact and inform public health strategies in diverse urban settings.
| S-EPMC11629508 | biostudies-literature
Project description:Introduction SARS-CoV-2 infection is an emerging disease that represents a threat to life globally, with more than 179 million confirmed cases and 3 million deaths. In Colombia, where almost 5 million infections and approximately 127 thousand deaths have been reported, it presents a wide variety of neurological manifestations that range from mild to severe symptoms. Objective This study describes the characteristics of neurological manifestations in patients with COVID-19 in the period March–September 2020 at a tertiary hospital in Bogota. Methods We performed a cross-sectional descriptive study. We selected patients by non-probability sampling, including all patients attended by the neurology service at our hospital. We included all patients with infection confirmed by RT-PCR test and neurological disease confirmed by tomography, study of cerebrospinal fluid, and clinical manifestations reported in the medical history. We excluded epileptic patients who presented seizures as the only clinical manifestation. Results In a total of 58 patients, the mean age was 58 years, with 60.3% of patients being men; 65.5% were alert at admission. The main neurological symptom was brain ischaemia, in 36.2%, followed by seizures, in 25.9%. Arterial hypertension was observed in 58.6%. We observed no alterations in the cerebrospinal fluid; the mean hospital stay was 35 days, and 41.4% of patients died. Conclusions SARS-CoV-2 infection not only affects the respiratory system, but can also cause a range of neurological manifestations ranging from mild symptoms such as headache, dysgeusia, and anosmia to severe complications such as seizures, brain ischaemia/haemorrhage, encephalopathy, or death.
| S-EPMC8860473 | biostudies-literature
Project description:We sought to explore mental health and psychosocial impact among young people (18 to 24 years old) in Bogotá during the first months of the COVID-19 pandemic.MethodsWe carried a cross sectional study using a web-based survey to assess mental health and personal impact among 18 to 24 years old living in Bogotá during the first 4 months of the 2020 COVID-19 pandemic lockdown. The depressive symptoms were measured with PHQ-8 and anxiety symptoms with (GAD-7). We also designed a questionnaire exploring changes in personal, family and social life.ResultsOverall, 23% of the sample (n = 834) reported mild depressive symptoms (males 24% and females 23%); 29% reported moderate depressive symptoms (males 28%, females 30%); 22% moderate-severe symptoms (males 20%, females 23%) and 17% severe symptoms (males 15%, females 17%). Mild anxiety symptoms were reported by 29% of the sample (males 30%, females 29%); moderate anxiety symptoms by 29% (males 26%, females 30%); moderate-severe 18% (males 15%, females 20%) and severe anxiety by 6.0% (males 6.0% and females 6.0%). High symptoms of depression (PHQ-8 ≥ 10) were associated with being female, considering that the quarantine was stressful, having one member of the family losing their job, worsening of family relationships, decrease of physical activity and having a less nutritious diet. Having high anxiety symptoms (GAD-7 ≥ 10) were associated with sometimes not having enough money to buy food.ConclusionsThe first months of the pandemic lockdown were associated with high depressive and anxiety symptoms among young persons living in Bogotá, Colombia. Increasing public health measures to provide support for young people is needed during lockdowns and it is necessary to further explore the long-term mental health impact due to personal, family and social changes brought by the COVID-19 pandemic.
| S-EPMC9807414 | biostudies-literature
Project description:Urban wetlands are essential to the longstanding health and well-being of cities. Acknowledged as rich in biodiversity and highly productive ecosystems, they provide ecosystem services represented in aspects such as air purification, urban climate regulation, physical and mental health, recreation, and contemplation, among a wide variety of other goods and services on which the quality of life of the inhabitants of large cities such as Bogota depends largely. We used cellular automata to model and simulate urban wetland changes in Bogota, Colombia. The study applied the coupled Markov-Future Land Use Simulation (FLUS) model to simulate and analyze land use/land cover (LULC) change over 20 years. First, we used an orthomosaic (1998) and two WorldView-2 satellite images (2004 and 2010), to detect land cover changes. Then, using the artificial neural network FLUS module, we calculated the relationships between land classes and associated drivers and estimated the probability of occurrence of each land class. Finally, we applied Intensity Analysis to examine the observed and projected LULC change (1998-2034). Results indicate that gains in areas of crops and pastures are at the expense of wetlands. In addition, simulation outputs show that wetlands will likely represent less than 2% of the total study area in 2034, representing a 14% decrease in 24 years. The importance of this project lies in its potential contribution to the decision-making process within the city and as an instrument of natural resource management. Additionally, the results of this study could contribute to the United Nations Sustainable Development Goal 6, "Clean water and sanitation," and climate change mitigation.
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Project description:BackgroundEnterococcus faecium is ranked worldwide as one of the top ten pathogens identified in healthcare-associated infections (HAI) and is classified as one of the high priority pathogens for research and development of new antibiotics worldwide. Due to molecular biology techniques' higher costs, the approach for identifying and controlling infectious diseases in developing countries has been based on clinical and epidemiological perspectives. Nevertheless, after an abrupt vancomycin-resistant Enterococcus faecium dissemination in the Méderi teaching hospital, ending up in an outbreak, further measures needed to be taken into consideration. The present study describes the vancomycin-resistant Enterococcus faecium pattern within Colombian's largest installed-bed capacity hospital in 2016.MethodsThirty-three vancomycin-resistant Enterococcus faecium isolates were recovered during a 5-month period in 2016. Multilocus variable-number tandem-repeat analysis was used for molecular typing to determine clonality amongst strains. A modified time-place-sequence algorithm was used to trace VREfm spread patterns during the outbreak period and estimate transmission routes.ResultsFour clonal profiles were identified. Chronological clonal profile follow-up suggested a transitional spread from profile "A" to profile "B", returning to a higher prevalence of "A" by the end of the study. Antibiotic susceptibility indicated high-level vancomycin-resistance in most isolates frequently matching vanA gene identification.DiscussionTransmission analysis suggested cross-contamination via healthcare workers. Despite epidemiological control of the outbreak, post-outbreak isolates were still being identified as having outbreak-related clonal profile (A), indicating reduction but not eradication of this clonality. This study supports the use of combined molecular and epidemiological strategies in an approach to controlling infectious diseases. It contributes towards a more accurate evaluation of the effectiveness of the epidemiological measures taken regarding outbreak control and estimates the main cause related to the spread of this microorganism.
| S-EPMC6419805 | biostudies-literature
Project description:BackgroundThe incidence of invasive pneumococcal disease (IPD) varies depending on a number of factors, including vaccine uptake, in both children and adults, the geographic location, and local serotype prevalence. There are limited data about the burden of Streptococcus pneumoniae (Spn), serotype distribution, and clinical characteristics of adults hospitalized due to IPD in Colombia. The objectives of this study included assessment of Spn serotype distribution, clinical characteristics, mortality, ICU admission, and the need for mechanical ventilation.MethodsThis was an observational, retrospective, a citywide study conducted between 2012 and 2019 in Bogotá, Colombia. We analyzed reported positive cases of IPD from 55 hospitals in a governmental pneumococcal surveillance program. Pneumococcal strains were isolated in each hospital and typified in a centralized laboratory. This is a descriptive study stratified by age and subtypes of IPD obtained through the analysis of medical records.ResultsA total of 310 patients with IPD were included, of whom 45.5% were female. The leading cause of IPD was pneumonia (60%, 186/310), followed by meningitis. The most frequent serotypes isolated were 19A (13.87%, 43/310) and 3 (11.94%, 37/310). The overall hospital mortality rate was 30.3% (94/310). Moreover, 52.6% (163/310 patients) were admitted to the ICU, 45.5% (141/310) required invasive mechanical ventilation and 5.1% (16/310) non-invasive mechanical ventilation.ConclusionPneumococcal pneumonia is the most prevalent cause of IPD, with serotypes 19A and 3 being the leading cause of IPD in Colombian adults. Mortality due to IPD in adults continues to be very high.
| S-EPMC8507327 | biostudies-literature