Modelling COVID-19 transmission in a hemodialysis centre using simulation generated contacts matrices.
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ABSTRACT:
SUBMITTER: Tofighi M
PROVIDER: S-EPMC8604317 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundClose-contact rates are thought to be a driving force behind the transmission of many infectious respiratory diseases. Yet, contact rates and their relation to transmission and the impact of control measures, are seldom quantified. We quantify the response of contact rates, reported cases and transmission of COVID-19, to public health contact-restriction orders, and examine the associations among these three variables in the province of British Columbia, Canada.MethodsWe derived time series data for contact rates, daily cases and transmission of COVID-19 from a social contacts survey, reported case counts and by fitting a transmission model to reported cases, respectively. We used segmented regression to investigate impacts of public health orders; Pearson correlation to determine associations between contact rates and transmission; and vector autoregressive modeling to quantify lagged associations between contacts rates, daily cases, and transmission.ResultsDeclines in contact rates and transmission occurred concurrently with the announcement of public health orders, whereas declines in cases showed a reporting delay of about 2 weeks. Contact rates were a significant driver of COVID-19 and explained roughly 19 and 20% of the variation in new cases and transmission, respectively. Interestingly, increases in COVID-19 transmission and cases were followed by reduced contact rates: overall, daily cases explained about 10% of the variation in subsequent contact rates.ConclusionWe showed that close-contact rates were a significant time-series driver of transmission and ultimately of reported cases of COVID-19 in British Columbia, Canada and that they varied in response to public health orders. Our results also suggest possible behavioral feedback, by which increased reported cases lead to reduced subsequent contact rates. Our findings help to explain and validate the commonly assumed, but rarely measured, response of close contact rates to public health guidelines and their impact on the dynamics of infectious diseases.
| S-EPMC9110764 | biostudies-literature
Project description:Since the outbreak of COVID-19 in early March 2020, supermarkets around the world have implemented different policies to reduce the virus transmission in stores to protect both customers and staff, such as restricting the maximum number of customers in a store, changes to the store layout, or enforcing a mandatory face covering policy. To quantitatively assess these mitigation methods, we formulate an agent-based model of customer movement in a supermarket (which we represent by a network) with a simple virus transmission model based on the amount of time a customer spends in close proximity to infectious customers (which we call the exposure time). We apply our model to synthetic store and shopping data to show how one can use our model to estimate exposure time and thereby the number of infections due to human-to-human contact in stores and how to model different store interventions. The source code is openly available under https://github.com/fabianying/covid19-supermarket-abm. We encourage retailers to use the model to find the most effective store policies that reduce virus transmission in stores and thereby protect both customers and staff.
| S-EPMC8034715 | biostudies-literature
Project description:There is a continuing debate on relative benefits of various mitigation and suppression strategies aimed to control the spread of COVID-19. Here we report the results of agent-based modelling using a fine-grained computational simulation of the ongoing COVID-19 pandemic in Australia. This model is calibrated to match key characteristics of COVID-19 transmission. An important calibration outcome is the age-dependent fraction of symptomatic cases, with this fraction for children found to be one-fifth of such fraction for adults. We apply the model to compare several intervention strategies, including restrictions on international air travel, case isolation, home quarantine, social distancing with varying levels of compliance, and school closures. School closures are not found to bring decisive benefits unless coupled with high level of social distancing compliance. We report several trade-offs, and an important transition across the levels of social distancing compliance, in the range between 70% and 80% levels, with compliance at the 90% level found to control the disease within 13-14 weeks, when coupled with effective case isolation and international travel restrictions.
| S-EPMC7659014 | biostudies-literature
Project description:ObjectivesMathematical modelling is of interest to study the dynamics of coronavirus disease 2019 (COVID-19), and models such as SEIR (Susceptible-Exposed-Infected-Recovered) have been considered. This article describes the development of a compartmental transmission network model - Susceptible-Exposed-Quarantine-Infectious-Infectious, undetected-Infectious, home-based care-Hospitalized-Vaccinated-Recovered-Dead - to simulate the dynamics of COVID-19 in order to account for specific measures put into place by the Government of Rwanda to prevent further spread of the disease.MethodsThe compartments of this model are connected by parameters, some of which are known from the literature, and others are estimated from available data using the least squares method. For the stability of the model, equilibrium points were determined and the basic reproduction number R0 was studied; R 0 is an indicator for contagiousness.ResultsThe model showed that secondary infections are generated from the exposed group, the asymptomatic group, the infected (symptomatic) group, the infected (undetected) group, the infected (home-based care) group and the hospitalized group. The formulated model was reliable and fit the data. Furthermore, the estimated R0 of 2.16 shows that COVID-19 will persist without the application of control measures.ConclusionsThis article presents results regarding predicted spread of COVID-19 in Rwanda.
| S-EPMC9827742 | biostudies-literature
Project description:ObjectivesThe aims of this study were to obtain insights into the current coronavirus disease 2019 (COVID-19) epidemic in the city of Daegu, which accounted for 6,482 of the 9,241 confirmed cases in Korea as of March 26, 2020, to predict the future spread, and to analyze the impact of school opening.MethodsUsing an individual-based model, we simulated the spread of COVID-19 in Daegu. An individual can be infected through close contact with infected people in a household, at work/school, and at religious and social gatherings. We created a synthetic population from census sample data. Then, 9,000 people were randomly selected from the entire population of Daegu and set as members of the Shincheonji Church. We did not take into account population movements to and from other regions in Korea.ResultsUsing the individual-based model, the cumulative confirmed cases in Daegu through March 26, 2020, were reproduced, and it was confirmed that the hotspot, i.e., the Shincheonji Church had a different probability of infection than non-hotspot, i.e., the Daegu community. For 3 scenarios (I: school closing, II: school opening after April 6, III: school opening after April 6 and the mean period from symptom onset to hospitalization increasing to 4.3 days), we predicted future changes in the pattern of COVID-19 spread in Daegu.ConclusionsCompared to scenario I, it was found that in scenario III, the cumulative number of patients would increase by 107 and the date of occurrence of the last patient would be delayed by 92 days.
| S-EPMC7644934 | biostudies-literature
Project description:Increasing evidence indicates that superspreading plays a dominant role in COVID-19 transmission. Recent estimates suggest that the dispersion parameter k for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is on the order of 0.1, which corresponds to about 10% of cases being the source of 80% of infections. To investigate how overdispersion might affect the outcome of various mitigation strategies, we developed an agent-based model with a social network that allows transmission through contact in three sectors: "close" (a small, unchanging group of mutual contacts as might be found in a household), "regular" (a larger, unchanging group as might be found in a workplace or school), and "random" (drawn from the entire model population and not repeated regularly). We assigned individual infectivity from a gamma distribution with dispersion parameter k We found that when k was low (i.e., greater heterogeneity, more superspreading events), reducing random sector contacts had a far greater impact on the epidemic trajectory than did reducing regular contacts; when k was high (i.e., less heterogeneity, no superspreading events), that difference disappeared. These results suggest that overdispersion of COVID-19 transmission gives the virus an Achilles' heel: Reducing contacts between people who do not regularly meet would substantially reduce the pandemic, while reducing repeated contacts in defined social groups would be less effective.
| S-EPMC8040586 | biostudies-literature
Project description:BackgroundThe purpose was to analyse the associations between dental and trait anxiety, fear of COVID-19 and the duration and frequency of spontaneous hand-to-face contact (self-contact).MethodsA cross-sectional design was carried out with 128 adult patients from four dental clinics in Madrid, during the confinement, from March 15 to May 15. The patients' movements in the waiting room were monitored with Microsoft Kinect Software, also completed the Trait anxiety subscale of the STAI, the COVID-19 Fear and the S-DAI questionnaire.ResultsAssociations were observed between the duration and frequency of facial, mask and eye contact with trait anxiety and dental fear was determined only by the frequency of this self-contact. Trait anxiety is associated with dental anxiety and with fear of COVID-19. Although facial self-contact is higher in women, it also rises in men as dental fear increases. Moreover, dental anxiety is a good predictor of trait anxiety and the incidence of facial self-contact.ConclusionsUnderstanding the possible associations between biopsychosocial factors, such as trait anxiety, dental anxiety and self-contact is important. It may help to prevent the spread of COVID-19 in the population as well as enabling the formulation of effective interventions to improve oral health care through the implementation of dental care programmes.
| S-EPMC8056369 | biostudies-literature
Project description:BACKGROUND:Voluntary individual quarantine and voluntary active monitoring of contacts are core disease control strategies for emerging infectious diseases such as COVID-19. Given the impact of quarantine on resources and individual liberty, it is vital to assess under what conditions individual quarantine can more effectively control COVID-19 than active monitoring. As an epidemic grows, it is also important to consider when these interventions are no longer feasible and broader mitigation measures must be implemented. METHODS:To estimate the comparative efficacy of individual quarantine and active monitoring of contacts to control severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), we fit a stochastic branching model to reported parameters for the dynamics of the disease. Specifically, we fit a model to the incubation period distribution (mean 5·2 days) and to two estimates of the serial interval distribution: a shorter one with a mean serial interval of 4·8 days and a longer one with a mean of 7·5 days. To assess variable resource settings, we considered two feasibility settings: a high-feasibility setting with 90% of contacts traced, a half-day average delay in tracing and symptom recognition, and 90% effective isolation; and a low-feasibility setting with 50% of contacts traced, a 2-day average delay, and 50% effective isolation. FINDINGS:Model fitting by sequential Monte Carlo resulted in a mean time of infectiousness onset before symptom onset of 0·77 days (95% CI -1·98 to 0·29) for the shorter serial interval, and for the longer serial interval it resulted in a mean time of infectiousness onset after symptom onset of 0·51 days (95% CI -0·77 to 1·50). Individual quarantine in high-feasibility settings, where at least 75% of infected contacts are individually quarantined, contains an outbreak of SARS-CoV-2 with a short serial interval (4·8 days) 84% of the time. However, in settings where the outbreak continues to grow (eg, low-feasibility settings), so too will the burden of the number of contacts traced for active monitoring or quarantine, particularly uninfected contacts (who never develop symptoms). When resources are prioritised for scalable interventions such as physical distancing, we show active monitoring or individual quarantine of high-risk contacts can contribute synergistically to mitigation efforts. Even under the shorter serial interval, if physical distancing reduces the reproductive number to 1·25, active monitoring of 50% of contacts can result in overall outbreak control (ie, effective reproductive number <1). INTERPRETATION:Our model highlights the urgent need for more data on the serial interval and the extent of presymptomatic transmission to make data-driven policy decisions regarding the cost-benefit comparisons of individual quarantine versus active monitoring of contacts. To the extent that these interventions can be implemented, they can help mitigate the spread of SARS-CoV-2. FUNDING:National Institute of General Medical Sciences, National Institutes of Health.
| S-EPMC7239635 | biostudies-literature
Project description:The coronavirus disease 2019 (COVID-19) has now spread throughout most countries in the world causing heavy life losses and damaging social-economic impacts. Following a stochastic point process modelling approach, a Monte Carlo simulation model was developed to represent the COVID-19 spread dynamics. First, we examined various expected performances (theoretical properties) of the simulation model assuming a number of arbitrarily defined scenarios. Simulation studies were then performed on the real COVID-19 data reported (over the period of 1 March to 1 May) for Australia and United Kingdom (UK). Given the initial number of COVID-19 infection active cases were around 10 for both countries, the model estimated that the number of active cases would peak around 29 March in Australia (≈ 1,700 cases) and around 22 April in UK (≈ 22,860 cases); ultimately the total confirmed cases could sum to 6,790 for Australia in about 75 days and 206,480 for UK in about 105 days. The results of the estimated COVID-19 reproduction numbers were consistent with what was reported in the literature. This simulation model was considered an effective and adaptable decision making/what-if analysis tool in battling COVID-19 in the immediate need, and for modelling any other infectious diseases in the future.
| S-EPMC7403316 | biostudies-literature
Project description:This work aims to provide insights on the COVID-19 pandemic in three prime aspects. First, we attempted to understand the association between the COVID-19 transmission rate, environmental factors (air pollution, weather, mobility), and socio-political parameters (Government Stringency Index, GSI). Second, we evaluated the efficiency of various strategies, including radical opening, intermittent lockdown, phase lift, and contact tracing, to exit the COVID-19 pandemic and get back to pre-pandemic conditions using a stochastic individual-based epidemiology model. Third, we used a deep learning approach and simulated the vaccination rate and the time for reaching herd immunity. The analysis was done based on the collected data from eight countries in Asia, including Iran, Turkey, India, Saudi Arabia, United Arab Emirates, the Philippines, South Korea, and Russia (as a transcontinental country). Our findings in the first part highlighted a noninfluential impact from the weather-driven parameters and short-term exposure to pollutants on the transmission rate; however, long-term exposure could potentially increase the risk of COVID-19 mortality rates (based on 1998-2017 p.m.2.5 data). Mobility was highly correlated with the COVID-19 transmission and based on our causal analysis reducing mobility could curb the COVID-19 transmission rate with a 6-day lag time (on average). Secondly, among all the tested policies for exiting the COVID-19 pandemic, the contact tracing was the most efficient if executed correctly. With a 2-day delay in tracing the virus hosts, a 60% successful host tracing, and a 70% contact reduction with the hosts, a pandemic will end in a year without overburdening a healthcare system with 6000 hospital beds capacity per million. Lastly, our vaccine simulations showed that the target date for achieving herd immunity significantly varied among the countries and could be delayed to October-november 2022 in countries like India and Iran (based on 60% immunized population and assuming no intermediate factors affecting the vaccination rate).
| S-EPMC8265190 | biostudies-literature