Your browser doesn't support javascript.
Show: 20 | 50 | 100
Results 1 - 20 de 1.002
Filter
1.
BMC Infect Dis ; 23(1): 398, 2023 Jun 12.
Article in English | MEDLINE | ID: covidwho-20240489

ABSTRACT

BACKGROUND: Children account for a significant proportion of COVID-19 hospitalizations, but data on the predictors of disease severity in children are limited. We aimed to identify risk factors associated with moderate/severe COVID-19 and develop a nomogram for predicting children with moderate/severe COVID-19. METHODS: We identified children ≤ 12 years old hospitalized for COVID-19 across five hospitals in Negeri Sembilan, Malaysia, from 1 January 2021 to 31 December 2021 from the state's pediatric COVID-19 case registration system. The primary outcome was the development of moderate/severe COVID-19 during hospitalization. Multivariate logistic regression was performed to identify independent risk factors for moderate/severe COVID-19. A nomogram was constructed to predict moderate/severe disease. The model performance was evaluated using the area under the curve (AUC), sensitivity, specificity, and accuracy. RESULTS: A total of 1,717 patients were included. After excluding the asymptomatic cases, 1,234 patients (1,023 mild cases and 211 moderate/severe cases) were used to develop the prediction model. Nine independent risk factors were identified, including the presence of at least one comorbidity, shortness of breath, vomiting, diarrhea, rash, seizures, temperature on arrival, chest recessions, and abnormal breath sounds. The nomogram's sensitivity, specificity, accuracy, and AUC for predicting moderate/severe COVID-19 were 58·1%, 80·5%, 76·8%, and 0·86 (95% CI, 0·79 - 0·92) respectively. CONCLUSION: Our nomogram, which incorporated readily available clinical parameters, would be useful to facilitate individualized clinical decisions.


Subject(s)
COVID-19 , Models, Statistical , Humans , Child , Prognosis , Risk Factors , Patient Acuity
2.
Front Public Health ; 11: 1126461, 2023.
Article in English | MEDLINE | ID: covidwho-20236630

ABSTRACT

Background: The lack of precise definitions and terminological consensus about the impact studies of COVID-19 vaccination leads to confusing statements from the scientific community about what a vaccination impact study is. Objective: The present work presents a narrative review, describing and discussing COVID-19 vaccination impact studies, mapping their relevant characteristics, such as study design, approaches and outcome variables, while analyzing their similarities, distinctions, and main insights. Methods: The articles screening, regarding title, abstract, and full-text reading, included papers addressing perspectives about the impact of vaccines on population outcomes. The screening process included articles published before June 10, 2022, based on the initial papers' relevance to this study's research topics. The main inclusion criteria were data analyses and study designs based on statistical modelling or comparison of pre- and post-vaccination population. Results: The review included 18 studies evaluating the vaccine impact in a total of 48 countries, including 32 high-income countries (United States, Israel, and 30 Western European countries) and 16 low- and middle-income countries (Brazil, Colombia, and 14 Eastern European countries). We summarize the main characteristics of the vaccination impact studies analyzed in this narrative review. Conclusion: Although all studies claim to address the impact of a vaccination program, they differ significantly in their objectives since they adopt different definitions of impact, methodologies, and outcome variables. These and other differences are related to distinct data sources, designs, analysis methods, models, and approaches.


Subject(s)
COVID-19 Vaccines , COVID-19 , Humans , United States , COVID-19/prevention & control , Vaccination , Income , Models, Statistical
3.
Stat Med ; 42(12): 1869-1887, 2023 05 30.
Article in English | MEDLINE | ID: covidwho-20236518

ABSTRACT

The ICH E9 (R1) addendum proposes five strategies to define estimands by addressing intercurrent events. However, mathematical forms of these targeted quantities are lacking, which might lead to discordance between statisticians who estimate these quantities and clinicians, drug sponsors, and regulators who interpret them. To improve the concordance, we provide a unified four-step procedure for constructing the mathematical estimands. We apply the procedure for each strategy to derive the mathematical estimands and compare the five strategies in practical interpretations, data collection, and analytical methods. Finally, we show that the procedure can help ease tasks of defining estimands in settings with multiple types of intercurrent events using two real clinical trials.


Subject(s)
Models, Statistical , Research Design , Humans , Data Interpretation, Statistical , Data Collection
4.
PLoS One ; 18(3): e0283452, 2023.
Article in English | MEDLINE | ID: covidwho-2328116

ABSTRACT

In this study, we attempt to anticipate annual rice production in Bangladesh (1961-2020) using both the Autoregressive Integrated Moving Average (ARIMA) and the eXtreme Gradient Boosting (XGBoost) methods and compare their respective performances. On the basis of the lowest Corrected Akaike Information Criteria (AICc) values, a significant ARIMA (0, 1, 1) model with drift was chosen based on the findings. The drift parameter value shows that the production of rice positively trends upward. Thus, the ARIMA (0, 1, 1) model with drift was found to be significant. On the other hand, the XGBoost model for time series data was developed by changing the tunning parameters frequently with the greatest result. The four prominent error measures, such as mean absolute error (MAE), mean percentage error (MPE), root mean square error (RMSE), and mean absolute percentage error (MAPE), were used to assess the predictive performance of each model. We found that the error measures of the XGBoost model in the test set were comparatively lower than those of the ARIMA model. Comparatively, the MAPE value of the test set of the XGBoost model (5.38%) was lower than that of the ARIMA model (7.23%), indicating that XGBoost performs better than ARIMA at predicting the annual rice production in Bangladesh. Hence, the XGBoost model performs better than the ARIMA model in predicting the annual rice production in Bangladesh. Therefore, based on the better performance, the study forecasted the annual rice production for the next 10 years using the XGBoost model. According to our predictions, the annual rice production in Bangladesh will vary from 57,850,318 tons in 2021 to 82,256,944 tons in 2030. The forecast indicated that the amount of rice produced annually in Bangladesh will increase in the years to come.


Subject(s)
Oryza , Bangladesh , Neural Networks, Computer , Incidence , Forecasting , Machine Learning , Models, Statistical
6.
PLoS One ; 18(5): e0285601, 2023.
Article in English | MEDLINE | ID: covidwho-2313969

ABSTRACT

During pandemics like COVID-19, both the quality and quantity of services offered by businesses and organizations have been severely impacted. They often have applied a hybrid home office setup to overcome this problem, although in some situations, working from home lowers employee productivity. So, increasing the rate of presence in the office is frequently desired from the manager's standpoint. On the other hand, as the virus spreads through interpersonal contact, the risk of infection increases when workplace occupancy rises. Motivated by this trade-off, in this paper, we model this problem as a bi-objective optimization problem and propose a practical approach to find the trade-off solutions. We present a new probabilistic framework to compute the expected number of infected employees for a setting of the influential parameters, such as the incidence level in the neighborhood of the company, transmission rate of the virus, number of employees, rate of vaccination, testing frequency, and rate of contacts among the employees. The results show a wide range of trade-offs between the expected number of infections and productivity, for example, from 1 to 6 weekly infections in 100 employees and a productivity level of 65% to 85%. This depends on the configuration of influential parameters and the occupancy level. We implement the model and the algorithm and perform several experiments with different settings of the parameters. Moreover, we developed an online application based on the result in this paper which can be used as a recommender for the optimal rate of occupancy in companies/workplaces.


Subject(s)
COVID-19 , Humans , COVID-19/epidemiology , COVID-19/prevention & control , Pandemics/prevention & control , Workplace , Models, Statistical
7.
PLoS One ; 18(5): e0285407, 2023.
Article in English | MEDLINE | ID: covidwho-2320283

ABSTRACT

Improving forecasting particularly time series forecasting accuracy, efficiency and precisely become crucial for the authorities to forecast, monitor, and prevent the COVID-19 cases so that its spread can be controlled more effectively. However, the results obtained from prediction models are inaccurate, imprecise as well as inefficient due to linear and non-linear patterns exist in the data set, respectively. Therefore, to produce more accurate and efficient COVID-19 prediction value that is closer to the true COVID-19 value, a hybrid approach has been implemented. Thus, aims of this study is (1) to propose a hybrid ARIMA-SVM model to produce better forecasting results. (2) to investigate in terms of the performance of the proposed models and percentage improvement against ARIMA and SVM models. statistical measurements such as MSE, RMSE, MAE, and MAPE then conducted to verify that the proposed models are better than ARIMA and SVM models. Empirical results with three real datasets of well-known cases of COVID-19 in Malaysia show that, compared to the ARIMA and SVM models, the proposed model generates the smallest MSE, RMSE, MAE and MAPE values for the training and testing datasets, means that the predicted value from the proposed model is closer to the actual value. These results prove that the proposed model can generate estimated values more accurately and efficiently. As compared to ARIMA and SVM, our proposed models perform much better in terms of error reduction percentages for all datasets. This is demonstrated by the maximum scores of 73.12%, 74.6%, 90.38%, and 68.99% in the MAE, MAPE, MSE, and RMSE, respectively. Therefore, the proposed model can be the best and effective way to improve prediction performance with a higher level of accuracy and efficiency in predicting cases of COVID-19.


Subject(s)
COVID-19 , Humans , COVID-19/epidemiology , Models, Statistical , Pandemics , Forecasting , Malaysia
8.
J Biomed Inform ; 141: 104364, 2023 05.
Article in English | MEDLINE | ID: covidwho-2294058

ABSTRACT

In the three years since SARS-CoV-2 was first detected in China, hundreds of millions of people have been infected and millions have died. Along with the immediate need for treatment solutions, the COVID-19 epidemic has reinforced the need for mathematical models that can predict the spread of the pandemic in an ever-changing environment. The susceptible-infectious-removed (SIR) model has been widely used to model COVID-19 transmission, however, with limited success. Here, we present a novel, dynamic Monte-Carlo Agent-based Model (MAM), which is based on the basic principles of statistical physics. Using public aggregative data from Israel on three major outbreaks, we compare predictions made by SIR and MAM, and show that MAM outperforms SIR in all aspects. Furthermore, MAM is a flexible model and allows to accurately examine the effects of vaccinations in different subgroups, and the effects of the introduction of new variants.


Subject(s)
COVID-19 , Humans , COVID-19/epidemiology , SARS-CoV-2 , Models, Statistical , Models, Theoretical , Disease Outbreaks
9.
Accid Anal Prev ; 187: 107038, 2023 Jul.
Article in English | MEDLINE | ID: covidwho-2299632

ABSTRACT

Stay-at-home orders - imposed to prevent the spread of COVID-19 - drastically changed the way highways operate. Despite lower traffic volumes during these times, the rate of fatal and serious injury crashes increased significantly across the United States due to increased speeding on roads with less traffic congestion and lower levels of speed enforcement. This paper uses a mixed effect binomial regression model to investigate the impact of stay-at-home orders on odds of speeding on urban limited access highway segments in Maine and Connecticut. This paper also establishes a link between traffic density and the odds of speeding. For this purpose, hourly speed and volume probe data were collected on limited access highway segments for the U.S. states of Maine and Connecticut to estimate the traffic density. The traffic density was then combined with the roadway geometric characteristics, speed limit, as well as dummy variables denoting the time of the week, time of the day, COVID-19 phases (before, during and after stay-at-home order), and the interactions between them. Density, represented in the model as Level of Service, was found to be associated with the odds of speeding, with better levels of service such as A, or B (low density) resulting in the higher odds that drivers would speed. We also found that narrower shoulder width could result in lower odds of speeding. Furthermore, we found that during the stay-at-home order, the odds of speeding by more than 10, 15, and 20 mph increased respectively by 54%, 71% and 85% in Connecticut, and by 15%, 36%, and 65% in Maine during evening peak hours. Additionally, one year after the onset of the pandemic, during evening peak hours, the odds of speeding greater than 10, 15, and 20 mph were still 35%, 29%, and 19% greater in Connecticut and 35% 35% and 20% greater in Maine compared to before pandemic.


Subject(s)
Automobile Driving , COVID-19 , Humans , Accidents, Traffic/prevention & control , Pandemics , COVID-19/epidemiology , COVID-19/prevention & control , Models, Statistical , Connecticut/epidemiology
10.
Rev Salud Publica (Bogota) ; 22(2): 123-131, 2020 03 01.
Article in Spanish | MEDLINE | ID: covidwho-2299528

ABSTRACT

OBJECTIVE: To develop a prognostic SIR model of the COVID-19 pandemic in Colombia. MATERIALS AND METHODS: A SIR model with a deterministic approach was used to forecast the development of the COVID-19 pandemic in Colombia. The states considered were susceptible (S), infectious (i) and recovered or deceased (R). Population data were obtained from the National Administrative Department of Statistics (DANE) - Population Projections 2018-2020, released in January 2020-, and data on daily confirmed cases of COVID-19 from the National Institute of Health. Different models were proposed varying the basic reproduction number (R0). RESULTS: Based on the cases reported by the Ministry of Health, 4 simulated environments were created in an epidemiological SIR model. The time series was extended until May 30, the probable date when 99% of the population will be infected. R0=2 is the basic reproduction number and the closest approximation to the behavior of the pandemic during the first 15 days since the first case report; the worst scenario would occur in the first week of April with R0=3. CONCLUSIONS: Further mitigation and suppression measures are necessary in the containment and sustained transmission phases, such as increased diagnostic capacity through testing and disinfection of populated areas and homes in isolation.


Subject(s)
COVID-19 , Humans , COVID-19/epidemiology , Pandemics , SARS-CoV-2 , Epidemiological Models , Colombia/epidemiology , Models, Statistical
11.
Elife ; 122023 04 21.
Article in English | MEDLINE | ID: covidwho-2303644

ABSTRACT

Background: Short-term forecasts of infectious disease burden can contribute to situational awareness and aid capacity planning. Based on best practice in other fields and recent insights in infectious disease epidemiology, one can maximise the predictive performance of such forecasts if multiple models are combined into an ensemble. Here, we report on the performance of ensembles in predicting COVID-19 cases and deaths across Europe between 08 March 2021 and 07 March 2022. Methods: We used open-source tools to develop a public European COVID-19 Forecast Hub. We invited groups globally to contribute weekly forecasts for COVID-19 cases and deaths reported by a standardised source for 32 countries over the next 1-4 weeks. Teams submitted forecasts from March 2021 using standardised quantiles of the predictive distribution. Each week we created an ensemble forecast, where each predictive quantile was calculated as the equally-weighted average (initially the mean and then from 26th July the median) of all individual models' predictive quantiles. We measured the performance of each model using the relative Weighted Interval Score (WIS), comparing models' forecast accuracy relative to all other models. We retrospectively explored alternative methods for ensemble forecasts, including weighted averages based on models' past predictive performance. Results: Over 52 weeks, we collected forecasts from 48 unique models. We evaluated 29 models' forecast scores in comparison to the ensemble model. We found a weekly ensemble had a consistently strong performance across countries over time. Across all horizons and locations, the ensemble performed better on relative WIS than 83% of participating models' forecasts of incident cases (with a total N=886 predictions from 23 unique models), and 91% of participating models' forecasts of deaths (N=763 predictions from 20 models). Across a 1-4 week time horizon, ensemble performance declined with longer forecast periods when forecasting cases, but remained stable over 4 weeks for incident death forecasts. In every forecast across 32 countries, the ensemble outperformed most contributing models when forecasting either cases or deaths, frequently outperforming all of its individual component models. Among several choices of ensemble methods we found that the most influential and best choice was to use a median average of models instead of using the mean, regardless of methods of weighting component forecast models. Conclusions: Our results support the use of combining forecasts from individual models into an ensemble in order to improve predictive performance across epidemiological targets and populations during infectious disease epidemics. Our findings further suggest that median ensemble methods yield better predictive performance more than ones based on means. Our findings also highlight that forecast consumers should place more weight on incident death forecasts than incident case forecasts at forecast horizons greater than 2 weeks. Funding: AA, BH, BL, LWa, MMa, PP, SV funded by National Institutes of Health (NIH) Grant 1R01GM109718, NSF BIG DATA Grant IIS-1633028, NSF Grant No.: OAC-1916805, NSF Expeditions in Computing Grant CCF-1918656, CCF-1917819, NSF RAPID CNS-2028004, NSF RAPID OAC-2027541, US Centers for Disease Control and Prevention 75D30119C05935, a grant from Google, University of Virginia Strategic Investment Fund award number SIF160, Defense Threat Reduction Agency (DTRA) under Contract No. HDTRA1-19-D-0007, and respectively Virginia Dept of Health Grant VDH-21-501-0141, VDH-21-501-0143, VDH-21-501-0147, VDH-21-501-0145, VDH-21-501-0146, VDH-21-501-0142, VDH-21-501-0148. AF, AMa, GL funded by SMIGE - Modelli statistici inferenziali per governare l'epidemia, FISR 2020-Covid-19 I Fase, FISR2020IP-00156, Codice Progetto: PRJ-0695. AM, BK, FD, FR, JK, JN, JZ, KN, MG, MR, MS, RB funded by Ministry of Science and Higher Education of Poland with grant 28/WFSN/2021 to the University of Warsaw. BRe, CPe, JLAz funded by Ministerio de Sanidad/ISCIII. BT, PG funded by PERISCOPE European H2020 project, contract number 101016233. CP, DL, EA, MC, SA funded by European Commission - Directorate-General for Communications Networks, Content and Technology through the contract LC-01485746, and Ministerio de Ciencia, Innovacion y Universidades and FEDER, with the project PGC2018-095456-B-I00. DE., MGu funded by Spanish Ministry of Health / REACT-UE (FEDER). DO, GF, IMi, LC funded by Laboratory Directed Research and Development program of Los Alamos National Laboratory (LANL) under project number 20200700ER. DS, ELR, GG, NGR, NW, YW funded by National Institutes of General Medical Sciences (R35GM119582; the content is solely the responsibility of the authors and does not necessarily represent the official views of NIGMS or the National Institutes of Health). FB, FP funded by InPresa, Lombardy Region, Italy. HG, KS funded by European Centre for Disease Prevention and Control. IV funded by Agencia de Qualitat i Avaluacio Sanitaries de Catalunya (AQuAS) through contract 2021-021OE. JDe, SMo, VP funded by Netzwerk Universitatsmedizin (NUM) project egePan (01KX2021). JPB, SH, TH funded by Federal Ministry of Education and Research (BMBF; grant 05M18SIA). KH, MSc, YKh funded by Project SaxoCOV, funded by the German Free State of Saxony. Presentation of data, model results and simulations also funded by the NFDI4Health Task Force COVID-19 (https://www.nfdi4health.de/task-force-covid-19-2) within the framework of a DFG-project (LO-342/17-1). LP, VE funded by Mathematical and Statistical modelling project (MUNI/A/1615/2020), Online platform for real-time monitoring, analysis and management of epidemic situations (MUNI/11/02202001/2020); VE also supported by RECETOX research infrastructure (Ministry of Education, Youth and Sports of the Czech Republic: LM2018121), the CETOCOEN EXCELLENCE (CZ.02.1.01/0.0/0.0/17-043/0009632), RECETOX RI project (CZ.02.1.01/0.0/0.0/16-013/0001761). NIB funded by Health Protection Research Unit (grant code NIHR200908). SAb, SF funded by Wellcome Trust (210758/Z/18/Z).


Subject(s)
COVID-19 , Communicable Diseases , Epidemics , Humans , COVID-19/diagnosis , COVID-19/epidemiology , Forecasting , Models, Statistical , Retrospective Studies
12.
PLoS One ; 18(4): e0283618, 2023.
Article in English | MEDLINE | ID: covidwho-2294639

ABSTRACT

This paper provides a novel model that is more relevant than the well-known conventional distributions, which stand for the two-parameter distribution of the lifetime modified Kies Topp-Leone (MKTL) model. Compared to the current distributions, the most recent one gives an unusually varied collection of probability functions. The density and hazard rate functions exhibit features, demonstrating that the model is flexible to several kinds of data. Multiple statistical characteristics have been obtained. To estimate the parameters of the MKTL model, we employed various estimation techniques, including maximum likelihood estimators (MLEs) and the Bayesian estimation approach. We compared the traditional reliability function model to the fuzzy reliability function model within the reliability analysis framework. A complete Monte Carlo simulation analysis is conducted to determine the precision of these estimators. The suggested model outperforms competing models in real-world applications and may be chosen as an enhanced model for building a statistical model for the COVID-19 data and other data sets with similar features.


Subject(s)
COVID-19 , Humans , Bayes Theorem , Reproducibility of Results , Computer Simulation , Models, Statistical , Likelihood Functions , Data Analysis
13.
Stat Methods Med Res ; 31(9): 1641-1655, 2022 09.
Article in English | MEDLINE | ID: covidwho-2280342

ABSTRACT

Time-to-event data are right-truncated if only individuals who have experienced the event by a certain time can be included in the sample. For example, we may be interested in estimating the distribution of time from onset of disease symptoms to death and only have data on individuals who have died. This may be the case, for example, at the beginning of an epidemic. Right truncation causes the distribution of times to event in the sample to be biased towards shorter times compared to the population distribution, and appropriate statistical methods should be used to account for this bias. This article is a review of such methods, particularly in the context of an infectious disease epidemic, like COVID-19. We consider methods for estimating the marginal time-to-event distribution, and compare their efficiencies. (Non-)identifiability of the distribution is an important issue with right-truncated data, particularly at the beginning of an epidemic, and this is discussed in detail. We also review methods for estimating the effects of covariates on the time to event. An illustration of the application of many of these methods is provided, using data on individuals who had died with coronavirus disease by 5 April 2020.


Subject(s)
COVID-19 , Models, Statistical , Bias , COVID-19/epidemiology , Data Interpretation, Statistical , Humans , Survival Analysis
14.
Eur J Health Econ ; 23(6): 917-940, 2022 Aug.
Article in English | MEDLINE | ID: covidwho-2276237

ABSTRACT

The coronavirus disease (COVID-19) is a severe, ongoing, novel pandemic that emerged in Wuhan, China, in December 2019. As of January 21, 2021, the virus had infected approximately 100 million people, causing over 2 million deaths. This article analyzed several time series forecasting methods to predict the spread of COVID-19 during the pandemic's second wave in Italy (the period after October 13, 2020). The autoregressive moving average (ARIMA) model, innovations state space models for exponential smoothing (ETS), the neural network autoregression (NNAR) model, the trigonometric exponential smoothing state space model with Box-Cox transformation, ARMA errors, and trend and seasonal components (TBATS), and all of their feasible hybrid combinations were employed to forecast the number of patients hospitalized with mild symptoms and the number of patients hospitalized in the intensive care units (ICU). The data for the period February 21, 2020-October 13, 2020 were extracted from the website of the Italian Ministry of Health ( www.salute.gov.it ). The results showed that (i) hybrid models were better at capturing the linear, nonlinear, and seasonal pandemic patterns, significantly outperforming the respective single models for both time series, and (ii) the numbers of COVID-19-related hospitalizations of patients with mild symptoms and in the ICU were projected to increase rapidly from October 2020 to mid-November 2020. According to the estimations, the necessary ordinary and intensive care beds were expected to double in 10 days and to triple in approximately 20 days. These predictions were consistent with the observed trend, demonstrating that hybrid models may facilitate public health authorities' decision-making, especially in the short-term.


Subject(s)
COVID-19 , COVID-19/epidemiology , Forecasting , Hospitalization , Humans , Models, Statistical , Neural Networks, Computer , Pandemics
15.
Proc Natl Acad Sci U S A ; 119(33): e2203042119, 2022 08 16.
Article in English | MEDLINE | ID: covidwho-2268839

ABSTRACT

A common feature of large-scale extreme events, such as pandemics, wildfires, and major storms is that, despite their differences in etiology and duration, they significantly change routine human movement patterns. Such changes, which can be major or minor in size and duration and which differ across contexts, affect both the consequences of the events and the ability of governments to mount effective responses. Based on naturally tracked, anonymized mobility behavior from over 90 million people in the United States, we document these mobility differences in space and over time in six large-scale crises, including wildfires, major tropical storms, winter freeze and pandemics. We introduce a model that effectively captures the high-dimensional heterogeneity in human mobility changes following large-scale extreme events. Across five different metrics and regardless of spatial resolution, the changes in human mobility behavior exhibit a consistent hyperbolic decline, a pattern we characterize as "spatiotemporal decay." When applied to the case of COVID-19, our model also uncovers significant disparities in mobility changes-individuals from wealthy areas not only reduce their mobility at higher rates at the start of the pandemic but also maintain the change longer. Residents from lower-income regions show a faster and greater hyperbolic decay, which we suggest may help account for different COVID-19 rates. Our model represents a powerful tool to understand and forecast mobility patterns post emergency, and thus to help produce more effective responses.


Subject(s)
COVID-19 , Human Migration , Models, Statistical , Natural Disasters , Pandemics , COVID-19/epidemiology , Forecasting , Human Migration/trends , Humans , Income , Seasons , Spatio-Temporal Analysis , United States
16.
Philos Trans A Math Phys Eng Sci ; 380(2214): 20210121, 2022 Jan 10.
Article in English | MEDLINE | ID: covidwho-2250742

ABSTRACT

We develop a statistical model for the testing of disease prevalence in a population. The model assumes a binary test result, positive or negative, but allows for biases in sample selection and both type I (false positive) and type II (false negative) testing errors. Our model also incorporates multiple test types and is able to distinguish between retesting and exclusion after testing. Our quantitative framework allows us to directly interpret testing results as a function of errors and biases. By applying our testing model to COVID-19 testing data and actual case data from specific jurisdictions, we are able to estimate and provide uncertainty quantification of indices that are crucial in a pandemic, such as disease prevalence and fatality ratios. This article is part of the theme issue 'Data science approach to infectious disease surveillance'.


Subject(s)
COVID-19 Testing , COVID-19 , Bias , False Positive Reactions , Humans , Models, Statistical , SARS-CoV-2 , Selection Bias , Sensitivity and Specificity
17.
PLoS One ; 15(12): e0239455, 2020.
Article in English | MEDLINE | ID: covidwho-2282847

ABSTRACT

BACKGROUND: To control the COVID-19 outbreak in Japan, sports and entertainment events were canceled and schools were closed throughout Japan from February 26 through March 19. That policy has been designated as voluntary event cancellation and school closure (VECSC). OBJECT: This study assesses VECSC effectiveness based on predicted outcomes. METHODS: A simple susceptible-infected-recovered model was applied to data of patients with symptoms in Japan during January 14 through March 26. The respective reproduction numbers for periods before VECSC (R0), during VECSC (Re), and after VECSC (Ra) were estimated. RESULTS: Results suggest R0 before VECSC as 2.534 [2.449, 2.598], Re during VECSC as 1.077 [0.948, 1.228], and Ra after VECSC as 4.455 [3.615, 5.255]. DISCUSSION AND CONCLUSION: Results demonstrated that VECSC can reduce COVID-19 infectiousness considerably, but after VECSC, the value of the reproduction number rose to exceed 4.0.


Subject(s)
COVID-19/prevention & control , Disease Outbreaks , Humans , Japan , Models, Statistical , Pandemics , Schools
18.
Infect Dis Poverty ; 9(1): 69, 2020 Jun 18.
Article in English | MEDLINE | ID: covidwho-2269139

ABSTRACT

BACKGROUND: The outbreak of coronavirus disease 2019 (COVID-19) has become a pandemic causing global health problem. We provide estimates of the daily trend in the size of the epidemic in Wuhan based on detailed information of 10 940 confirmed cases outside Hubei province. METHODS: In this modelling study, we first estimate the epidemic size in Wuhan from 10 January to 5 April 2020 with a newly proposed model, based on the confirmed cases outside Hubei province that left Wuhan by 23 January 2020 retrieved from official websites of provincial and municipal health commissions. Since some confirmed cases have no information on whether they visited Wuhan before, we adjust for these missing values. We then calculate the reporting rate in Wuhan from 20 January to 5 April 2020. Finally, we estimate the date when the first infected case occurred in Wuhan. RESULTS: We estimate the number of cases that should be reported in Wuhan by 10 January 2020, as 3229 (95% confidence interval [CI]: 3139-3321) and 51 273 (95% CI: 49 844-52 734) by 5 April 2020. The reporting rate has grown rapidly from 1.5% (95% CI: 1.5-1.6%) on 20 January 2020, to 39.1% (95% CI: 38.0-40.2%) on 11 February 2020, and increased to 71.4% (95% CI: 69.4-73.4%) on 13 February 2020, and reaches 97.6% (95% CI: 94.8-100.3%) on 5 April 2020. The date of first infection is estimated as 30 November 2019. CONCLUSIONS: In the early stage of COVID-19 outbreak, the testing capacity of Wuhan was insufficient. Clinical diagnosis could be a good complement to the method of confirmation at that time. The reporting rate is very close to 100% now and there are very few cases since 17 March 2020, which might suggest that Wuhan is able to accommodate all patients and the epidemic has been controlled.


Subject(s)
Betacoronavirus , Coronavirus Infections/epidemiology , Epidemiologic Methods , Models, Statistical , Pneumonia, Viral/epidemiology , Adolescent , Adult , Aged , Aged, 80 and over , COVID-19 , Child , Child, Preschool , China/epidemiology , Female , Humans , Infant , Infant, Newborn , Male , Middle Aged , Pandemics , SARS-CoV-2 , Young Adult
19.
Swiss Med Wkly ; 150: w20295, 2020 05 18.
Article in English | MEDLINE | ID: covidwho-2268435

ABSTRACT

Following the rapid dissemination of COVID-19 cases in Switzerland, large-scale non-pharmaceutical interventions (NPIs) were implemented by the cantons and the federal government between 28 February and 20 March 2020. Estimates of the impact of these interventions on SARS-CoV-2 transmission are critical for decision making in this and future outbreaks. We here aim to assess the impact of these NPIs on disease transmission by estimating changes in the basic reproduction number (R0) at national and cantonal levels in relation to the timing of these NPIs. We estimated the time-varying R0 nationally and in eleven cantons by fitting a stochastic transmission model explicitly simulating within-hospital dynamics. We used individual-level data from more than 1000 hospitalised patients in Switzerland and public daily reports of hospitalisations and deaths. We estimated the national R0 to be 2.8 (95% confidence interval 2.1–3.8) at the beginning of the epidemic. Starting from around 7 March, we found a strong reduction in time-varying R0 with a 86% median decrease (95% quantile range [QR] 79–90%) to a value of 0.40 (95% QR 0.3–0.58) in the period of 29 March to 5 April. At the cantonal level, R0 decreased over the course of the epidemic between 53% and 92%. Reductions in time-varying R0 were synchronous with changes in mobility patterns as estimated through smartphone activity, which started before the official implementation of NPIs. We inferred that most of the reduction of transmission is attributable to behavioural changes as opposed to natural immunity, the latter accounting for only about 4% of the total reduction in effective transmission. As Switzerland considers relaxing some of the restrictions of social mixing, current estimates of time-varying R0 well below one are promising. However, as of 24 April 2020, at least 96% (95% QR 95.7–96.4%) of the Swiss population remains susceptible to SARS-CoV-2. These results warrant a cautious relaxation of social distance practices and close monitoring of changes in both the basic and effective reproduction numbers.


Subject(s)
Betacoronavirus/isolation & purification , Communicable Disease Control , Coronavirus Infections , Disease Transmission, Infectious , Pandemics/statistics & numerical data , Pneumonia, Viral , COVID-19 , Communicable Disease Control/methods , Communicable Disease Control/organization & administration , Communicable Disease Control/statistics & numerical data , Communicable Diseases, Emerging/prevention & control , Coronavirus Infections/epidemiology , Coronavirus Infections/prevention & control , Coronavirus Infections/transmission , Disease Transmission, Infectious/prevention & control , Disease Transmission, Infectious/statistics & numerical data , Hospitalization/statistics & numerical data , Humans , Models, Statistical , Mortality , Pandemics/prevention & control , Pneumonia, Viral/epidemiology , Pneumonia, Viral/prevention & control , Pneumonia, Viral/transmission , SARS-CoV-2 , Space-Time Clustering , Stochastic Processes
SELECTION OF CITATIONS
SEARCH DETAIL