Evaluation of reopening strategies for educational institutions during COVID-19 through agent based simulation

COVID-19 test-to-stay program for K-12 schools: Opt-in versus opt-out consent model

The Centers for Disease Control and Prevention promoted the Test-to-Stay (TTS) program to facilitate in-person instruction in K-12 schools during COVID-19. This program delineates guidelines for schools to regularly test students and staff to minimize risks of infection transmission. TTS enrollment can be implemented via two different consent models: opt-in, in which students do not test regularly by default, and the opposite, opt-out model. We study the impacts of the two enrollment approaches on testing and positivity rates with data from 259 schools in Illinois. Our results indicate that after controlling for other covariates, schools following the opt-out model are associated with 84% higher testing rate and 30% lower positivity rate. If all schools adopted the opt-out model, 20% of the total lost school days could have been saved. The lower positivity rate among the opt-out group is largely explained by the higher testing rate in these schools, a manifestation of status quo bias.

Optimizing COVID-19 testing strategies on college campuses: Evaluation of the health and economic costs

Colleges and universities in the US struggled to provide safe in-person education throughout the COVID-19 pandemic. Testing coupled with isolation is a nimble intervention strategy that can be tailored to mitigate the changing health and economic risks associated with SARS-CoV-2. We developed a decision-support tool to aid in the design of university-based screening strategies using a mathematical model of SARS-CoV-2 transmission. Applying this framework to a large public university reopening in the fall of 2021 with a 60% student vaccination rate, we find that the optimal strategy, in terms of health and economic costs, is twice weekly antigen testing of all students. This strategy provides a 95% guarantee that, throughout the fall semester, case counts would not exceed twice the CDC's original high transmission threshold of 100 cases per 100k persons over 7 days. As the virus and our medical armament continue to evolve, testing will remain a flexible tool for managing risks and keeping campuses open. We have implemented this model as an online tool to facilitate the design of testing strategies that adjust for COVID-19 conditions as well as campus-specific populations, resources, and priorities.

Readiness of public schools before reopening during COVID-19 pandemic: School-based cross-sectional survey in southern Ethiopia

BACKGROUND

School closures in response to the COVID-19 impacted children's education, protection, and wellbeing. After understanding these impacts and that children were not super spreaders, countries including Ethiopia decided to reopen schools with specified preconditions. But when deciding to reopen schools, the benefits and risks across education, public health and socio-economic factors have to be evaluated. However, there was information gap on status of schools as per preconditions. Hence, this study was designed to investigate status of schools in Southern Ethiopia.

METHODS

School based cross-sectional study was conducted in October 2020 in Southern Ethiopia. Sample of 430 schools were included. National school reopening guideline was used to develop checklist for assessment. Data was collected by public health experts at regional emergency operation center. Descriptive analysis was performed to summarize data.

RESULTS

A total of 430 schools were included. More than two thirds, 298 (69.3%), of schools were from rural areas while 132 (30.7%) were from urban settings. The general infection prevention and water, sanitation and hygiene (IPC-WASH) status of schools were poor and COVID-19 specific preparations were inadequate to meet national preconditions to reopen schools during the pandemic. Total score from 24 items observed ranged from 3 to 22 points with mean score of 11.75 (SD±4.02). No school scored 100% and only 41 (9.5%) scored above 75% while 216 (50.2%%) scored below half point that is 12 items.

CONCLUSION

Both the basic and COVID-19 specific IPC-WASH status of schools were inadequate to implement national school reopening preconditions and general standards. Some of strategies planned to accommodate teaching process and preconditions maximized inequalities in education. Although COVID-19 impact lessened due to vaccination and other factors, it is rational to consider fulfilling water and basic sanitation facilities to schools to prevent communicable diseases of public health importance.

Investigation of airborne spread of COVID-19 using a hybrid agent-based model: a case study of the UK

Agent-based models have been proven to be quite useful in understanding and predicting the SARS-CoV-2 virus-originated COVID-19 infection. Person-to-person contact was considered as the main mechanism of viral transmission in these models. However, recent understanding has confirmed that airborne transmission is the main route to infection spread of COVID-19. We have developed a computationally efficient agent-based hybrid model to study the aerial propagation of the virus and subsequent spread of infection. We considered virus, a continuous variable, spreads diffusively in air and members of populations as discrete agents possessing one of the eight different states at a particular time. The transition from one state to another is probabilistic and age linked. Recognizing that population movement is a key aspect of infection spread, the model allows unbiased movement of agents. We benchmarked the model to recapture the temporal stochastic infection count data of the UK. The model investigates various key factors such as movement, infection susceptibility, new variants, recovery rate and duration, incubation period and vaccination on the infection propagation over time. Furthermore, the model was applied to capture the infection spread in Italy and France.

Comparative effectiveness of contact tracing interventions in the context of the COVID-19 pandemic: a systematic review

Contact tracing is a non-pharmaceutical intervention (NPI) widely used in the control of the COVID-19 pandemic. Its effectiveness may depend on a number of factors including the proportion of contacts traced, delays in tracing, the mode of contact tracing (e.g. forward, backward or bidirectional contact training), the types of contacts who are traced (e.g. contacts of index cases or contacts of contacts of index cases), or the setting where contacts are traced (e.g. the household or the workplace). We performed a systematic review of the evidence regarding the comparative effectiveness of contact tracing interventions. 78 studies were included in the review, 12 observational (ten ecological studies, one retrospective cohort study and one pre-post study with two patient cohorts) and 66 mathematical modelling studies. Based on the results from six of the 12 observational studies, contact tracing can be effective at controlling COVID-19. Two high quality ecological studies showed the incremental effectiveness of adding digital contact tracing to manual contact tracing. One ecological study of intermediate quality showed that increases in contact tracing were associated with a drop in COVID-19 mortality, and a pre-post study of acceptable quality showed that prompt contact tracing of contacts of COVID-19 case clusters / symptomatic individuals led to a reduction in the reproduction number R. Within the seven observational studies exploring the effectiveness of contact tracing in the context of the implementation of other non-pharmaceutical interventions, contact tracing was found to have an effect on COVID-19 epidemic control in two studies and not in the remaining five studies. However, a limitation in many of these studies is the lack of description of the extent of implementation of contact tracing interventions. Based on the results from the mathematical modelling studies, we identified the following highly effective policies: (1) manual contact tracing with high tracing coverage and either medium-term immunity, highly efficacious isolation/quarantine and/ or physical distancing (2) hybrid manual and digital contact tracing with high app adoption with highly effective isolation/ quarantine and social distancing, (3) secondary contact tracing, (4) eliminating contact tracing delays, (5) bidirectional contact tracing, (6) contact tracing with high coverage in reopening educational institutions. We also highlighted the role of social distancing to enhance the effectiveness of some of these interventions in the context of 2020 lockdown reopening. While limited, the evidence from observational studies shows a role for manual and digital contact tracing in controlling the COVID-19 epidemic. More empirical studies accounting for the extent of contact tracing implementation are required.

Implementation and effectiveness of a COVID-19 case investigation and contact tracing program at a large, urban midwestern university

BACKGROUND

The University of Illinois Chicago (UIC) COVID-19 Contact Tracing and Epidemiology Program was critical to the university's COVID-19 incident response during the 2020-2021 academic year. We are a team of epidemiologists and student contact tracers who perform COVID-19 contact tracing among campus members. Literature is sparse on models for mobilizing non-clinical students as contact tracers; therefore, we aim to disseminate strategies that are adaptable by other institutions.

METHODS

We described essential aspects of our program including surveillance testing, staffing and training models, interdepartmental partnerships, and workflows. Additionally, we analyzed the epidemiology of COVID-19 at UIC and measures of contact tracing effectiveness.

RESULTS

The program was responsible for promptly quarantining 120 cases prior to converting and potentially infecting others, thereby preventing at least 132 downstream exposures and 22 COVID-19 infections from occurring.

DISCUSSION

Features central to program success included routine data translation and dissemination and utilizing students as indigenous campus contact tracers. Major operational challenges included high staff turnover and adjusting to rapidly evolving public health guidance.

CONCLUSIONS

Institutes of higher education provide fertile ground for effective contact tracing, particularly when comprehensive networks of partners facilitate compliance with institution-specific public health requirements.

Effective screening strategies for safe opening of universities under Omicron and Delta variants of COVID-19

As new COVID-19 variants emerge, and disease and population characteristics change, screening strategies may also need to change. We develop a decision-making model that can assist a college to determine an optimal screening strategy based on their characteristics and resources, considering COVID-19 infections/hospitalizations/deaths; peak daily hospitalizations; and the tests required. We also use this tool to generate screening guidelines for the safe opening of college campuses. Our compartmental model simulates disease spread on a hypothetical college campus under co-circulating variants with different disease dynamics, considering: (i) the heterogeneity in disease transmission and outcomes for faculty/staff and students based on vaccination status and level of natural immunity; and (ii) variant- and dose-dependent vaccine efficacy. Using the Spring 2022 academic semester as a case study, we study routine screening strategies, and find that screening the faculty/staff less frequently than the students, and/or the boosted and vaccinated less frequently than the unvaccinated, may avert a higher number of infections per test, compared to universal screening of the entire population at a common frequency. We also discuss key policy issues, including the need to revisit the mitigation objective over time, effective strategies that are informed by booster coverage, and if and when screening alone can compensate for low booster coverage.

Optimizing COVID-19 testing strategies on college campuses: evaluation of the health and economic costs

Colleges and universities in the US struggled to provide safe in-person education throughout the COVID-19 pandemic. Testing coupled with isolation is a nimble intervention strategy that can be tailored to mitigate health and economic costs, as the virus and our arsenal of medical countermeasures continue to evolve. We developed a decision-support tool to aid in the design of university-based testing strategies using a mathematical model of SARS-CoV-2 transmission. Applying this framework to a large public university reopening in the fall of 2021 with a 60% student vaccination rate, we find that the optimal strategy, in terms of health and economic costs, is twice weekly antigen testing of all students. This strategy provides a 95% guarantee that, throughout the fall semester, case counts would not exceed the CDC's original high transmission threshold of 100 cases per 100k persons over 7 days. As the virus and our medical armament continue to evolve, testing will remain a flexible tool for managing risks and keeping campuses open. We have implemented this model as an online tool to facilitate the design of testing strategies that adjust for COVID-19 conditions, university-specific parameters, and institutional goals.

Impact of government policies on the COVID-19 pandemic unraveled by mathematical modelling

Since the very beginning of the COVID-19 pandemic, control policies and restrictions have been the hope for containing the rapid spread of the virus. However, the psychological and economic toll they take on society entails the necessity to develop an optimal control strategy. Assessment of the effectiveness of these interventions aided with mathematical modelling remains a non-trivial issue in terms of numerical conditioning due to the high number of parameters to estimate from a highly noisy dataset and significant correlations between policy timings. We propose a solution to the problem of parameter non-estimability utilizing data from a set of European countries. Treating a subset of parameters as common for all countries and the rest as country-specific, we construct a set of individualized models incorporating 13 different pandemic control measures, and estimate their parameters without prior assumptions. We demonstrate high predictive abilities of these models on an independent validation set and rank the policies by their effectiveness in reducing transmission rates. We show that raising awareness through information campaigns, providing income support, closing schools and workplaces, cancelling public events, and maintaining an open testing policy have the highest potential to mitigate the pandemic.

Using simulation modelling and systems science to help contain COVID-19: A systematic review

This study systematically reviews applications of three simulation approaches, that is, system dynamics model (SDM), agent-based model (ABM) and discrete event simulation (DES), and their hybrids in COVID-19 research and identifies theoretical and application innovations in public health. Among the 372 eligible papers, 72 focused on COVID-19 transmission dynamics, 204 evaluated both pharmaceutical and non-pharmaceutical interventions, 29 focused on the prediction of the pandemic and 67 investigated the impacts of COVID-19. ABM was used in 275 papers, followed by 54 SDM papers, 32 DES papers and 11 hybrid model papers. Evaluation and design of intervention scenarios are the most widely addressed area accounting for 55% of the four main categories, that is, the transmission of COVID-19, prediction of the pandemic, evaluation and design of intervention scenarios and societal impact assessment. The complexities in impact evaluation and intervention design demand hybrid simulation models that can simultaneously capture micro and macro aspects of the socio-economic systems involved.

Screening for SARS-CoV-2 Infection in Students at the Medical University of Warsaw, Poland Between November 15 and December 10, 2021 Using a Single Lateral Flow Test, the Panbio™ COVID-19 Ag Rapid Test

BACKGROUND Education was significantly affected by the coronavirus disease 2019 (COVID-19) pandemic, caused by the SARS-CoV-2 virus. Online learning affects the quality of learning as well as the mental health status of students. Regular screening for COVID-19 may be crucial to provide practical classes during the pandemic. The present study aimed to analyze the usefulness of rapid antigen tests for on-campus COVID-19 screening in real-life conditions at a medical university in Poland. MATERIAL AND METHODS This screening study was carried out among students attending practical classes at the Medical University of Warsaw, Poland between November 15 and December 10, 2021, during which a series of rapid antigen tests (Panbio™ COVID-19 Ag Rapid Test Device, nasal) were performed by healthcare professionals (nurses). Out of 104 student groups selected for the study (n=1847 students), 423 individuals from 63 student groups were tested at least once (22.9% response rate). A total of 2295 samples were collected. RESULTS Among the participants, 3.4% (n=15) had positive test results. Out of 15 COVID-19 cases, 14 were vaccinated. At least 1 positive COVID-19 case was detected in 8 student groups. In 3 student groups, we observed ≥2 infections that occurred at intervals, which may suggest student-to-student SARS-CoV-2 transmission. CONCLUSIONS This study produced real-world data from a COVID-19 screening study and confirmed the usefulness of the rapid antigen test (Panbio™ COVID-19 Ag Rapid Test Device nasal) for on-campus COVID-19 screening prior to practical classes. Maintaining a high percentage of participants is crucial to ensuring the effectiveness of on-campus COVID-19 screening.

Heterogeneity in testing for infectious diseases

Testing strategies have varied widely between nation states during the COVID-19 pandemic, in intensity as well as methodology. Some countries have mainly performed diagnostic testing while others have opted for mass-screening for the presence of SARS-CoV-2 as well. COVID passport solutions have been introduced, in which access to several aspects of public life requires either testing, proof of vaccination or a combination thereof. This creates a coupling between personal activity levels and testing behaviour which, as we show in a mathematical model, leverages heterogeneous behaviours in a population and turns this heterogeneity from a disadvantage to an advantage for epidemic control.

Evaluating efficacy of indoor non-pharmaceutical interventions against COVID-19 outbreaks with a coupled spatial-SIR agent-based simulation framework

Contagious respiratory diseases, such as COVID-19, depend on sufficiently prolonged exposures for the successful transmission of the underlying pathogen. It is important that organizations evaluate the efficacy of non-pharmaceutical interventions aimed at mitigating viral transmission among their personnel. We have developed a operational risk assessment simulation framework that couples a spatial agent-based model of movement with an agent-based SIR model to assess the relative risks of different intervention strategies. By applying our model on MIT's Stata center, we assess the impacts of three possible dimensions of intervention: one-way vs unrestricted movement, population size allowed onsite, and frequency of leaving designated work location for breaks. We find that there is no significant impact made by one-way movement restrictions over unrestricted movement. Instead, we find that reducing the frequency at which individuals leave their workstations combined with lowering the number of individuals admitted below the current recommendations lowers the likelihood of highly connected individuals within the contact networks that emerge, which in turn lowers the overall risk of infection. We discover three classes of possible interventions based on their epidemiological effects. By assuming a direct relationship between data on secondary attack rates and transmissibility in the agent-based SIR model, we compare relative infection risk of four respiratory illnesses, MERS, SARS, COVID-19, and Measles, within the simulated area, and recommend appropriate intervention guidelines.

Evaluating the mitigation strategies of COVID-19 by the application of the CO2 emission data through high-resolution agent-based computational experiments

The negative consequences, such as healthy and environmental issues, brought by rapid urbanization and interactive human activities result in increasing social uncertainties, unreliable predictions, and poor management decisions. For instance, the Coronavirus Disease (COVID-19) occurred in 2019 has been plaguing many countries. Aiming at controlling the spread of COVID-19, countries around the world have adopted various mitigation and suppression strategies. However, how to comprehensively eva luate different mitigation strategies remains unexplored. To this end, based on the Artificial societies, Computational experiments, Parallel execution (ACP) approach, we proposed a system model, which clarifies the process to collect the necessary data and conduct large-scale computational experiments to evaluate the effectiveness of different mitigation strategies. Specifically, we established an artificial society of Wuhan city through geo-environment modeling, population modeling, contact behavior modeling, disease spread modeling and mitigation strategy modeling. Moreover, we established an evaluation model in terms of the control effects and economic costs of the mitigation strategy. With respect to the control effects, it is directly reflected by indicators such as the cumulative number of diseases and deaths, while the relationship between mitigation strategies and economic costs is built based on the CO2 emission. Finally, large-scale simulation experiments are conducted to evaluate the mitigation strategies of six countries. The results reveal that the more strict mitigation strategies achieve better control effects and less economic costs.

Interactions of Co, Cu, and non-metal phthalocyanines with external structures of SARS-CoV-2 using docking and molecular dynamics

The new coronavirus, SARS-CoV-2, caused the COVID-19 pandemic, characterized by its high rate of contamination, propagation capacity, and lethality rate. In this work, we approach the use of phthalocyanines as an inhibitor of SARS-CoV-2, as they present several interactive properties of the phthalocyanines (Pc) of Cobalt (CoPc), Copper (CuPc) and without a metal group (NoPc) can interact with SARS-CoV-2, showing potential be used as filtering by adsorption on paints on walls, masks, clothes, and air conditioning filters. Molecular modeling techniques through Molecular Docking and Molecular Dynamics were used, where the target was the external structures of the virus, but specifically the envelope protein, main protease, and Spike glycoprotein proteases. Using the g_MM-GBSA module and with it, the molecular docking studies show that the ligands have interaction characteristics capable of adsorbing the structures. Molecular dynamics provided information on the root-mean-square deviation of the atomic positions provided values between 1 and 2.5. The generalized Born implicit solvation model, Gibbs free energy, and solvent accessible surface area approach were used. Among the results obtained through molecular dynamics, it was noticed that interactions occur since Pc could bind to residues of the active site of macromolecules, demonstrating good interactions; in particular with CoPc. Molecular couplings and free energy showed that S-gly active site residues interacted strongly with phthalocyanines with values ​​of - 182.443 kJ/mol (CoPc), 158.954 kJ/mol (CuPc), and - 129.963 kJ/mol (NoPc). The interactions of Pc's with SARS-CoV-2 may predict some promising candidates for antagonists to the virus, which if confirmed through experimental approaches, may contribute to resolving the global crisis of the COVID-19 pandemic.

When Do We Need Massive Computations to Perform Detailed COVID-19 Simulations?

The COVID-19 pandemic has infected over 250 million people worldwide and killed more than 5 million as of November 2021. Many intervention strategies are utilized (e.g., masks, social distancing, vaccinations), but officials making decisions have a limited time to act. Computer simulations can aid them by predicting future disease outcomes, but they also require significant processing power or time. It is examined whether a machine learning model can be trained on a small subset of simulation runs to inexpensively predict future disease trajectories resembling the original simulation results. Using four previously published agent-based models (ABMs) for COVID-19, a decision tree regression for each ABM is built and its predictions are compared to the corresponding ABM. Accurate machine learning meta-models are generated from ABMs without strong interventions (e.g., vaccines, lockdowns) using small amounts of simulation data: the root-mean-square error (RMSE) with 25% of the data is close to the RMSE for the full dataset (0.15 vs 0.14 in one model; 0.07 vs 0.06 in another). However, meta-models for ABMs employing strong interventions require much more training data (at least 60%) to achieve a similar accuracy. In conclusion, machine learning meta-models can be used in some scenarios to assist in faster decision-making.

SARS-CoV-2 Variants of Concern Increased Transmission and Decrease Vaccine Efficacy in the COVID-19 Pandemic in Palembang Indonesia

BACKGROUND AND AIM

The number of COVID-19 cases surging despite the large scale of health promotion campaigns. This study aimed to find disease transmissibility and affected vaccine efficacy associated with the mutation of the SARS-CoV-2 variant of concern.

METHODS

The study was a descriptive temporal survey design with secondary ecological data: the whole-genome sequence (WGS) from the Global Initiative on Sharing Avian Influenza (GISAID) and COVID-19 data from the Palembang City Health Office website. Bioinformatics software was used to detect mutations.

RESULTS

Palembang submitted 43 whole genome sequences, 13 of which were Pangoline sequences classifications.

CONCLUSIONS

The two concern variations, Alpha and Delta, were associated with increased transmissions and decreased vaccination efficacy using temporal analysis. Regulations governing the relaxation of mobility restrictions should be based on high rates of testing and tracing, and universal vaccination programs should require that all received two doses of any vaccines as fast as possible.

Evaluating the Dynamics of Bluetooth Low Energy Based COVID-19 Risk Estimation for Educational Institutes

COVID-19 tracing applications have been launched in several countries to track and control the spread of viruses. Such applications utilize Bluetooth Low Energy (BLE) transmissions, which are short range and can be used to determine infected and susceptible persons near an infected person. The COVID-19 risk estimation depends on an epidemic model for the virus behavior and Machine Learning (ML) model to classify the risk based on time series distance of the nodes that may be infected. The BLE technology enabled smartphones continuously transmit beacons and the distance is inferred from the received signal strength indicators (RSSI). The educational activities have shifted to online teaching modes due to the contagious nature of COVID-19. The government policy makers decide on education mode (online, hybrid, or physical) with little technological insight on actual risk estimates. In this study, we analyze BLE technology to debate the COVID-19 risks in university block and indoor class environments. We utilize a sigmoid based epidemic model with varying thresholds of distance to label contact data with high risk or low risk based on features such as contact duration. Further, we train multiple ML classifiers to classify a person into high risk or low risk based on labeled data of RSSI and distance. We analyze the accuracy of the ML classifiers in terms of F-score, receiver operating characteristic (ROC) curve, and confusion matrix. Lastly, we debate future research directions and limitations of this study. We complement the study with open source code so that it can be validated and further investigated.

covid19.Explorer: a web application and R package to explore United States COVID-19 data

Appearing at the end of 2019, a novel virus (later identified as SARS-CoV-2) was characterized in the city of Wuhan in Hubei Province, China. As of the time of writing, the disease caused by this virus (known as COVID-19) has already resulted in over three million deaths worldwide. SARS-CoV-2 infections and deaths, however, have been highly unevenly distributed among age groups, sexes, countries, and jurisdictions over the course of the pandemic. Herein, I present a tool (the covid19.Explorer R package and web application) that has been designed to explore and analyze publicly available United States COVID-19 infection and death data from the 2020/21 U.S. SARS-CoV-2 pandemic. The analyses and visualizations that this R package and web application facilitate can help users better comprehend the geographic progress of the pandemic, the effectiveness of non-pharmaceutical interventions (such as lockdowns and other measures, which have varied widely among U.S. states), and the relative risks posed by COVID-19 to different age groups within the U.S. population. The end result is an interactive tool that will help its users develop an improved understanding of the temporal and geographic dynamics of the SARS-CoV-2 pandemic, accessible to lay people and scientists alike.

Adaptive Susceptible-Infectious-Removed Model for Continuous Estimation of the COVID-19 Infection Rate and Reproduction Number in the United States: Modeling Study

BACKGROUND

The dynamics of the COVID-19 pandemic vary owing to local population density and policy measures. During decision-making, policymakers consider an estimate of the effective reproduction number Rt, which is the expected number of secondary infections spread by a single infected individual.

OBJECTIVE

We propose a simple method for estimating the time-varying infection rate and the Rt.

METHODS

We used a sliding window approach with a Susceptible-Infectious-Removed (SIR) model. We estimated the infection rate from the reported cases over a 7-day window to obtain a continuous estimation of Rt. A proposed adaptive SIR (aSIR) model was applied to analyze the data at the state and county levels.

RESULTS

The aSIR model showed an excellent fit for the number of reported COVID-19 cases, and the 1-day forecast mean absolute prediction error was <2.6% across all states. However, the 7-day forecast mean absolute prediction error approached 16.2% and strongly overestimated the number of cases when the Rt was rapidly decreasing. The maximal Rt displayed a wide range of 2.0 to 4.5 across all states, with the highest values for New York (4.4) and Michigan (4.5). We found that the aSIR model can rapidly adapt to an increase in the number of tests and an associated increase in the reported cases of infection. Our results also suggest that intensive testing may be an effective method of reducing Rt.

CONCLUSIONS

The aSIR model provides a simple and accurate computational tool for continuous Rt estimation and evaluation of the efficacy of mitigation measures.