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MeSH Disease

Human Phenotype

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    Time is of the essence: containment of the SARS-CoV-2 epidemic in Switzerland from February to May 2020

    Authors: Christian L Althaus; Daniel Probst; Anthony Hauser; Julien L Riou

    doi:10.1101/2020.07.21.20158014 Date: 2020-07-25 Source: medRxiv

    AIM: In late February and early March 2020, Switzerland experienced rapid growth of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections MESHD with 30,243 confirmed cases TRANS and 1,860 deaths as of 10 May 2020. The sequential introduction of non-pharmaceutical interventions (NPIs) resulted in successful containment of the epidemic. A better understanding of how the timing of implementing NPIs influences the dynamics and outcome of SARS-CoV-2 epidemics will be crucial for the management of a potential resurgence in Switzerland. METHODS: We developed a dynamic transmission TRANS model that describes infection MESHD, hospitalization, recovery and death MESHD due to SARS-CoV-2 in Switzerland. Using a maximum likelihood framework, we fitted the model to aggregated daily numbers of hospitalized patients, ICU occupancy MESHD and death MESHD from 25 February to 10 May 2020. We estimated critical parameters of SARS-CoV-2 transmission TRANS in Switzerland and explored counterfactual scenarios of an earlier and later implementation of NPIs. RESULTS: We estimated the basic reproduction number TRANS R0 TRANS = 2.61 (95% compatibility interval, CI: 2.51-2.71) during the early exponential phase of the SARS-CoV-2 epidemic MESHD in Switzerland. After the implementation of NPIs, the effective reproduction number TRANS approached Re = 0.64 (95% CI: 0.61-0.66). Based on the observed doubling times of the epidemic before and after the implementation of NPIs, we estimated that one week of early exponential spread required 3.1 weeks (95% CI: 2.8-3.3 weeks) of 'lockdown' to reduce the number of infections to the same level. Introducing the same sequence of NPIs one week earlier or later would have resulted in substantially lower (399, 95% prediction interval, PI: 347-458) and higher (8,683, 95% PI: 8,038-9,453) numbers of deaths, respectively. CONCLUSIONS: The introduction of NPIs in March 2020 prevented thousands of SARS-CoV-2-related deaths in Switzerland. Early implementation of NPIs during SARS-CoV-2 outbreaks can reduce the number of deaths MESHD and the necessary duration of strict control measures considerably.

    An Analysis of Outbreak Dynamics and Intervention Effects for COVID-19 Transmission TRANS in Europe

    Authors: Wei Wang

    doi:10.1101/2020.07.21.20158873 Date: 2020-07-25 Source: medRxiv

    As of March 13, 2020, Europe became the center of COVID-19 pandemic. In order to prevent further spread and slow down the increase in confirmed cases TRANS and deaths MESHD, many countries in European Union have taken some interventions since mid-March. In this study, a metapopulation model was used to model the outbreak of COVID-19 in Europe and the effectiveness of these interventions were also estimated. The findings suggested that many countries successfully kept the reproduction number TRANS R_t less than 1 (e.g., Belgium, Germany, Spain, and France) while other countries exhibited R_t greater than 1 (e.g., United Kingdom, Cyprus). Based on the assumed reopen strategy, this study also revealed that a 2-week delay in response predicted approximately 2,000 deaths and 200,000 cases (daily peak value), while a 3-week delay predicted approximately 5,000 deaths MESHD and 600,000 cases (daily peak value). Therefore, a quick response upon signs of a re-emerging pandemic in the world is highly imperative to mitigate potential loss of life and to keep transmission TRANS of Covid-19 under control.

    Modelling COVID-19 cases in Nigeria: Forecasts, uncertainties, projections and the link with weather

    Authors: Adeyeri O.E.; Oyekan K.S.A.; Ige S.O.; Akinbobola A.; Okogbue E.C.

    doi:10.21203/ Date: 2020-07-11 Source: ResearchSquare

    The World Health Organization (WHO) declared COVID-19 a global pandemic on 11 March 2020 due to its global spread. In Nigeria, the first case was documented on 27 February 2020. Since then, it has spread to most parts of the country. This study models, forecasts and projects COVID-19 incidence, cumulative incidence and death MESHD cases in Nigeria using six estimation methods i.e. the attack rate TRANS, maximum likelihood, exponential growth, Markov chain monte Carlo (MCMC), time-dependent and the sequential Bayesian approaches. A sensitivity SERO analysis with respect to the mean generation time is used to quantify the associated reproduction number TRANS uncertainties. The relationship between the COVID-19 incidence and five meteorological variables are further assessed. The result shows that the highest incidences are recorded in days with either religious activities or market days while the weekday trend decreases towards the weekend. It is also established that COVID-19 incidence significantly increases with increasing sea level pressure (0.7 correlation coefficient) and significantly decreases with increasing maximum temperature (-0.3 correlation coefficient). Also, selecting an optimal period for reproduction number TRANS estimates reduces the variability between estimates. As an example, in the EG approach, the epidemic curve that optimally fits the exponential growth is between 1- and 53-time units with reproduction number TRANS estimate of 1.60 [1.58; 1.62] at 95% confidence interval. However, this optimal reproduction number TRANS estimate is different from the default reproduction number TRANS estimate.  Using the MCMC approach, the correlation coefficients between the observed and forecasted incidence, cumulative death MESHD and cumulative confirmed cases TRANS are 0.66, 0.92 and 0.90 respectively. The projections till December shows values approaching 1,000,000, 120,000 and 3,000,000 respectively. Therefore, timely intervention and effective preventive measures are immediately needed to mitigate a full-scale epidemic in the country. 

    Impact of public health measures to control SARS-CoV-2Outbreak: a data-driven analysis

    Authors: Hugues Turbe; Mina Bjelogrlic; Arnaud Robert; Christophe Gaudet-Blavignac; Christian Lovis; Jean-Philippe Goldman

    doi:10.1101/2020.06.10.20126870 Date: 2020-06-11 Source: medRxiv

    With the rapid spread of the SARS-CoV-2 virus since Fall HP 2019, public health confinement measures to contain the propagation of the pandemic are taken. Our method to estimate the reproductive number TRANS using Bayesian inference with time-dependent priors enhances previous approaches by considering a dynamic prior continuously updated as restrictive measures and comportments within the society evolve. In addition, to allow direct comparison between reproductive number TRANS and introduction of public health measures in a specific country, the infection dates are inferred from daily confirmed cases TRANS and death MESHD with the mean time between a case being declared as positive and its death estimated on 1430 cases at 10.7 days. The evolution of the reproductive rate in combination with the stringency index is analyzed on 31 European countries. We show that most countries required tough state interventions with a stringency index equal to 83.6 out of 100 to reduce the reproductive number TRANS below one and control the progression of the epidemic. In addition, we show a direct correlation between the time taken to introduce restrictive measures and the time required to contain the spread of the epidemic with a median time of 8 days. Our analysis reinforces the importance of having a fast response with a coherent and comprehensive set of confinement measures to control the epidemic. Only combinations of non-pharmaceutical interventions (NPIs) have shown to be effective.

    Scrutinizing the heterogeneous spreading of COVID-19 outbreak in Brazilian territory

    Authors: Rafael Marques Da Silva; Carlos Fabio de Oliveira Mendes; Cesar Manchein

    doi:10.1101/2020.06.05.20123604 Date: 2020-06-09 Source: medRxiv

    After the spread of COVID-19 out of China, the evolution of the pandemic shows remarkable similarities and differences among countries across the world. Eventually, such characteristics are also observed between different regions of the same country. Herewith, we study the heterogeneous spreading of the confirmed infected cases and deaths by the COVID-19 until May 30th, 2020, in the Brazilian territory, which has been seen as the current epicenter of the pandemic in South America. Our first set of results is related to the similarities and it shows that: (i) a power-law growth of the cumulative number of infected people MESHD is observed for federative units of the five regions of Brazil; and (ii) the Distance Correlation (DC) calculated between the time series of the most affected federative units and the curve that describes the evolution of the pandemic in Brazil remains about 1 in most of the time, while such quantity calculated for the federative units with a low incidence of newly infected people remains about 0.95. In the second set of results, we focus on the heterogeneous distribution of the confirmed cases TRANS and deaths MESHD, which is demonstrated by the fact that only three regions concentrate 92% of the cases. By applying the epidemiological SIRD model we estimated the effective reproduction number TRANS Re during the pandemic evolution and found that: (i) the mean value of Re for the eight most affected federative units in Brazil is about 2; (ii) the current value of Re for Brazil is greater than 1, which indicates that the epidemic peak is far; and (iii) Ceara was the only federative unit for which the current Re < 1. Based on these findings, we projected the effects of increase or decrease the effective reproduction number TRANS and concluded that if the value of Re increases 20%, not only the peak might grow at least 40% but also its occurrence might be anticipated, which hastens the collapse of the public health care system. In all cases, to keep the effective reproduction number TRANS 20% below the current one can save thousands of people in the long term.

    An epidemiological model for the spread of COVID-19: A South African case study

    Authors: L. E. Olivier; I. K. Craig

    id:2005.08012v2 Date: 2020-05-16 Source: arXiv

    An epidemiological model is developed for the spread of COVID-19 in South Africa. A variant of the classical compartmental SEIR model, called the SEIQRDP model, is used. As South Africa is still in the early phases of the global COVID-19 pandemic with the confirmed infectious cases not having peaked, the SEIQRDP model is first parameterized on data for Germany, Italy, and South Korea - countries for which the number of infectious cases are well past their peaks. Good fits MESHD are achieved with reasonable predictions of where the number of COVID-19 confirmed cases TRANS, deaths MESHD, and recovered cases will end up and by when. South African data for the period from 23 March to 8 May 2020 is then used to obtain SEIQRDP model parameters. It is found that the model fits the initial disease progression well, but that the long-term predictive capability of the model is rather poor. The South African SEIQRDP model is subsequently recalculated with the basic reproduction number TRANS constrained to reported values. The resulting model fits the data well, and long-term predictions appear to be reasonable. The South African SEIQRDP model predicts that the peak in the number of confirmed infectious individuals will occur at the end of October 2020, and that the total number of deaths will range from about 10,000 to 90,000, with a nominal value of about 22,000. All of these predictions are heavily dependent on the disease control measures in place, and the adherence to these measures. These predictions are further shown to be particularly sensitive to parameters used to determine the basic reproduction number TRANS. The future aim is to use a feedback control approach together with the South African SEIQRDP model to determine the epidemiological impact of varying lockdown levels proposed by the South African Government.

    Emerging Polynomial Growth Trends MESHD in COVID-19 Pandemic Data and Their Reconciliation with Compartment Based Models

    Authors: Katarina Bodova; Richard Kollar

    id:2005.06933v1 Date: 2020-05-14 Source: arXiv

    We study the reported data from the COVID-19 pandemic outbreak in January - May 2020 in 119 countries. We observe that the time series of active cases in individual countries (the difference of the total number of confirmed infections TRANS infections MESHD and the sum of the total number of reported deaths MESHD and recovered cases) display a strong agreement with polynomial growth and at a later epidemic stage also with a combined polynomial growth with exponential decay. Our results are also formulated in terms of compartment type mathematical models of epidemics. Within these models the universal scaling characterizing the observed regime in an advanced epidemic stage can be interpreted as an algebraic decay of the relative reproduction number TRANS $ R_0 TRANS$ as $T_M/t$, where $T_M$ is a constant and $t$ is the duration of the epidemic outbreak. We show how our findings can be applied to improve predictions of the reported pandemic data and estimate some epidemic parameters. Note that although the model shows a good agreement with the reported data we do not make any claims about the real size of the pandemics as the relation of the observed reported data to the total number of infected in the population is still unknown.

    Better Strategies for Containing COVID-19 Epidemics --- A Study of 25 Countries via an Extended Varying Coefficient SEIR Model

    Authors: Jia Gu; Han Yan; Ya Huang; Yu Zhu; Hao Sun; Xin Zhang; Yu Wang; Yumou Qiu; Song Chen

    doi:10.1101/2020.04.27.20081232 Date: 2020-05-03 Source: medRxiv

    We evaluate the effectiveness of COVID-19 control strategies of 25 countries which have endured more than four weeks of community infections. With an extended SEIR model that allows infections MESHD in both the exposed and infected states, the key epidemic parameters are estimated from each country's data, which facilitate the evaluation and cross-country comparison. It is found quicker control measures significantly reduce the average reproduction numbers TRANS and shorten the time length to infection peaks. If the swift control measures of Korea and China were implemented, average reductions of 88% in the confirmed cases TRANS and 80% in deaths would had been attained for the other 23 countries from start to April 10. Effects of earlier or delayed interventions in the US and the UK are experimented which show at least 75% (29%) less infections MESHD and deaths can be attained for the US (the UK) under a Five-Day Earlier experiment. The impacts of two removal regimes (Korea and Italy) on the total infection MESHD and death tolls on the other countries are compared with the naturally forecast ones, which suggest there are still ample opportunity for countries to reduce the final death MESHD numbers by improving the removal process.

    Shortages of hospital beds exacerbate severity of COVID-19 outbreaks

    Authors: Weike Zhou; Aili Wang; Xia Wang; Robert A Cheke; Sanyi Tang

    doi:10.21203/ Date: 2020-04-23 Source: ResearchSquare

    Background: The global outbreak of COVID-19 has caused worrying concern amongst the public and health authorities. The first and foremost problem that many countries face is a shortage of medical resources. The experience of Wuhan, China, in fighting against COVID-19 provides a model for other countries to learn from. Methods: We formulated a piecewise smooth model to describe the limitation of hospital beds, based on the transmission TRANS progression of COVID-19, and the strengthening prevention and control strategies implemented in Wuhan, China. We used data of the cumulative numbers of confirmed cases TRANS, cured cases and deaths MESHD in Wuhan city from 10 January to 20 March, 2020 to estimate unknown parameters and the effective reproduction number TRANS. Sensitivity SERO analysis was conducted to investigate the impact of a shortage of hospital beds on the COVID-19 outbreak. Results: Even with strong prevention and control measures in Wuhan, slowing down of the supply rate, reducing the maximum capacity and delaying the intervention time of supplementing hospital beds aggravated the outbreak severity by magnifying the cumulative numbers of confirmed cases TRANS and deaths MESHD, prolonging the period of the outbreak in Wuhan, enlarging the value of the effective reproduction number TRANS during the outbreak and postponing the time when the threshold value is reduced to 1. Conclusions: The quick establishment of the Huoshenshan and Leishenshan Hospitals in a short time and the deployment of mobile cabin hospitals played important roles in containing the COVID-19 outbreak in Wuhan, providing a model for other countries to provide more hospital beds for COVID-19 patients faster and earlier. 

    Incidence, clinical outcomes, and transmission TRANS dynamics of hospitalized 2019 coronavirus disease MESHD among 9,596,321 individuals residing in California and Washington MESHD, United States: a prospective cohort study

    Authors: Joseph A Lewnard; Vincent X Liu; Michael L Jackson; Mark A Schmidt; Britta L Jewell; Jean P Flores; Chris Jentz; Graham R Northrup; Ayesha Mahmud; Arthur L Reingold; Maya Petersen; Nicholas P Jewell; Scott Young; Jim Bellows

    doi:10.1101/2020.04.12.20062943 Date: 2020-04-16 Source: medRxiv

    Background: The United States is now the country reporting the highest number of 2019 coronavirus disease MESHD (COVID-19) cases and deaths MESHD. However, little is known about the epidemiology and burden of severe COVID-19 to inform planning within healthcare systems and modeling of intervention impact. Methods: We assessed incidence, duration of hospitalization, and clinical outcomes of acute COVID-19 inpatient admissions in a prospectively-followed cohort of 9,596,321 individuals enrolled in comprehensive, integrated healthcare delivery plans from Kaiser Permanente in California MESHD and Washington state. We also estimated the effective reproductive number TRANS (RE) describing transmission TRANS in the study populations. Results: Data covered 1277 hospitalized patients with laboratory- or clinically-confirmed COVID-19 diagnosis by April 9, 2020. Cumulative incidence of first COVID-19 acute inpatient admission was 10.6-12.4 per 100,000 cohort members across the study regions. Mean censoring-adjusted duration of hospitalization was 10.7 days (2.5-97.5%iles: 0.8-30.1) among survivors and 13.7 days (2.5-97.5%iles: 1.7-34.6) among non-survivors. Among all hospitalized confirmed cases TRANS, censoring-adjusted probabilities of ICU admission and mortality were 41.9% (95% confidence interval: 34.1-51.4%) and 17.8% (14.3-22.2%), respectively, and higher among men than women. We estimated RE was 1.43 (1.17-1.73), 2.09 (1.63-2.69), and 1.47 (0.07-2.59) in Northern California, Southern California, and Washington, respectively, for infections acquired March 1, 2020. RE declined to 0.98 (0.76-1.27), 0.89 (0.74-1.06), and 0.92 (0.05-1.55) respectively, for infections MESHD acquired March 20, 2020. Conclusions: We identify high probability of ICU admission, long durations of stay, and considerable mortality risk among hospitalized COVID-19 cases in the western United States. Reductions in RE have occurred in conjunction with implementation of non-pharmaceutical interventions.

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MeSH Disease
Human Phenotype

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