Epidemiological modelling of the health and economic effects of COVID-19 control in Australia's second wave.

BACKGROUND: We investigated the public health and economy outcomes of different levels of social distancing to control a 'second wave' outbreak in Australia and identify implications for public health management of COVID-19. METHODS: Individual-based and compartment models were used to simulate the effects of different social distancing and detection strategies on Australian COVID-19 infections and the economy from March to July 2020. These models were used to evaluate the effects of different social distancing levels and the early relaxation of suppression measures, in terms of public health and economy outcomes. RESULTS: The models, fitted to observations up to July 2020, yielded projections consistent with subsequent cases and showed that better public health outcomes and lower economy costs occur when social distancing measures are more stringent, implemented earlier and implemented for a sufficiently long duration. Early relaxation of suppression results in worse public health outcomes and higher economy costs. CONCLUSIONS: Better public health outcomes (reduced COVID-19 fatalities) are positively associated with lower economy costs and higher levels of social distancing; achieving zero community transmission lowers both public health and economy costs compared to allowing community transmission to continue; and early relaxation of social distancing increases both public health and economy costs.

Contact Tracing and Epidemic Intervention via Deep Reinforcement Learning

The recent outbreak of COVID-19 poses a serious threat to people's lives. Epidemic control strategies have also caused damage to the economy by cutting off humans' daily commute. In this article, we develop an Individual-based Reinforcement Learning Epidemic Control Agent (IDRLECA) to search for smart epidemic control strategies that can simultaneously minimize infections and the cost of mobility intervention. IDRLECA first hires an infection probability model to calculate the current infection probability of each individual. Then, the infection probabilities together with individuals' health status and movement information are fed to a novel GNN to estimate the spread of the virus through human contacts. The estimated risks are used to further support an RL agent to select individual-level epidemic-control actions. The training of IDRLECA is guided by a specially designed reward function considering both the cost of mobility intervention and the effectiveness of epidemic control. Moreover, we design a constraint for control-action selection that eases its difficulty and further improve exploring efficiency. Extensive experimental results demonstrate that IDRLECA can suppress infections at a very low level and retain more than 95% of human mobility. © 2023 Copyright held by the owner/author(s). Publication rights licensed to ACM.

Modelling COVID-19 epidemic with confirmed cases-driven contact tracing quarantine.

The pandemic of novel coronavirus disease 2019 (COVID-19) has been a severe threat to public health. The policy of close contract tracing quarantine is an effective strategy in controlling the COVID-19 epidemic outbreak. In this paper, we developed a mathematical model of the COVID-19 epidemic with confirmed case-driven contact tracing quarantine, and applied the model to evaluate the effectiveness of the policy of contact tracing and quarantine. The model is established based on the combination of the compartmental model and individual-based model simulations, which results in a closed-form delay differential equation model. The proposed model includes a novel form of quarantine functions to represent the number of quarantine individuals following the confirmed cases every day and provides analytic expressions to study the effects of changing the quarantine rate. The proposed model can be applied to epidemic dynamics during the period of community spread and when the policy of confirmed cases-driven contact tracing quarantine is efficient. We applied the model to study the effectiveness of contact tracing and quarantine. The proposed delay differential equation model can describe the average epidemic dynamics of the stochastic-individual-based model, however, it is not enough to describe the diverse response due to the stochastic effect. Based on model simulations, we found that the policy of contact tracing and quarantine can obviously reduce the epidemic size, however, may not be enough to achieve zero-infectious in a short time, a combination of close contact quarantine and social contact restriction is required to achieve zero-infectious. Moreover, the effect of reducing epidemic size is insensitive to the period of quarantine, there are no significant changes in the epidemic dynamics when the quarantine days vary from 7 to 21 days.

Individual-based epidemiological model of COVID19 using location data

Because human movement spreads infection, and mobility is a good proxy for other social distancing measures, human mobility has been an important factor in the COVID19 epidemic. Therefore, the control of human mobility is one of the countermeasures used to suppress an epidemic.As a notable feature, COVID19 has had multiple waves (subepidemics). Understanding the causes of the start and end of each wave has important implications for a policy evaluation and the timely implementation of countermeasures. Some of the waves have been correlated with the changes in mobility, and some can be attributed to the emergence of new variants. However, the start and end of some of the waves are difficult to explain through known factors.To evaluate the effect of human mobility, we built a stochastic model incorporating individual movements of 500,000 people obtained from anonymized, user-approved location data of smartphones throughout Japan. Instead of using aggregate values of human mobility, our model tracks the movements of individuals and predicts the infection of all persons within the entire country. Although the model only has a single static parameter, it successfully reproduced the occurrence of three waves of the number of confirmed cases within the study period of March 01 to December 31, 2020 in Japan. It was previously difficult to explain the end of the second wave and the start of the third wave in the study period by human mobility alone. Our results suggest the importance of tracking individual movements instead of relaying the aggregate values of human mobility. © 2022 IEEE.

Italians and smart working: A technical study on the effects of smart working on the society

Due to the COVID-19 pandemic, "smart working” (hereafter SW) has become the norm for millions of workers around the world. A new way of working for most workers and in particular in Italy, a country where the use of SW was extremely rare before the pandemic. The aim of this paper, was to highlights whether smart working, adopted to face and survive global crises, could be really a suitable tool to generate benefits for companies, society, reduce environmental impacts and guarantee autonomy and flexibility for workers as well as a balance between private life. The analysis was conducted on a sample of 2753 individuals based in Italy during the period January and February 2021 using PLS-SEM model. The contribution of this study to research is identified in clarifying the potential of SW to create sustainable Smart Cities. © 2022 Elsevier Inc.

Assessment of Modified BAT Algorithm for MOOC Learner Influence Maximization

Identification of a small group of individuals based on their maximal influence cascade is influence maximization. During the COVID-19 pandemic, discussion forums on the Massive Open Online Course (MOOC) platform have become a paramount interaction medium among learners, and the identification of influential learners evolved as a substantial research issue. In this research paper, an optimization function based on an independent cascade is established for the discussion forum influence maximization problem. A modified version of the BAT algorithm is proposed which memorizes the bad experience of the BAT. The proposed Modified algorithm helps the BAT to remember the worst location that has already been traversed for a reliable estimation in an optimized manner while exploring the best solution. Further, the performance of BAT and Modified BAT for influence maximization on the discussion forum network of a MOOC platform is evaluated which shows the excellent performance of modified BAT. Convergence graph for different populations on deviating probability depicts the effective performance of modified BAT over generic BAT algorithm. © 2022 ACM.

Individual-based modeling of COVID-19 transmission in college communities.

The ongoing COVID-19 pandemic has created major public health and socio-economic challenges across the United States. Among them are challenges to the educational system where college administrators are struggling with the questions of how to mitigate the risk and spread of diseases on their college campus. To help address this challenge, we developed a flexible computational framework to model the spread and control of COVID-19 on a residential college campus. The modeling framework accounts for heterogeneity in social interactions, activities, environmental and behavioral risk factors, disease progression, and control interventions. The contribution of mitigation strategies to disease transmission was explored without and with interventions such as vaccination, quarantine of symptomatic cases, and testing. We show that even with high vaccination coverage (90%) college campuses may still experience sizable outbreaks. The size of the outbreaks varies with the underlying environmental and socio-behavioral risk factors. Complementing vaccination with quarantine and mass testing was shown to be paramount for preventing or mitigating outbreaks. Though our quantitative results are likely provisional on our model assumptions, sensitivity analysis confirms the robustness of their qualitative nature.

Effective Social Network-Based Allocation of COVID-19 Vaccines

We study allocation of COVID-19 vaccines to individuals based on the structural properties of their underlying social contact network. Using a realistic representation of a social contact network for the Commonwealth of Virginia, we study how a limited number of vaccine doses can be strategically distributed to individuals to reduce the overall burden of the pandemic. We show that allocation of vaccines based on individuals' degree (number of social contacts) and total social proximity time is significantly more effective than the usually used age-based allocation strategy in reducing the number of infections, hospitalizations and deaths. The overall strategy is robust even: (i) if the social contacts are not estimated correctly;(ii) if the vaccine efficacy is lower than expected or only a single dose is given;(iii) if there is a delay in vaccine production and deployment;and (iv) whether or not non-pharmaceutical interventions continue as vaccines are deployed. For reasons of implementability, we have used degree, which is a simple structural measure and can be easily estimated using several methods, including the digital technology available today. These results are significant, especially for resource-poor countries, where vaccines are less available, have lower efficacy, and are more slowly distributed. © 2022 Owner/Author.

Is annual vaccination best? A modelling study of influenza vaccination strategies in children.

INTRODUCTION: Annual vaccination of children against influenza is a key component of vaccination programs in many countries. However, past infection and vaccination may affect an individual's susceptibility to infection. Little research has evaluated whether annual vaccination is the best strategy. Using the United Kingdom as our motivating example, we developed a framework to assess the impact of different childhood vaccination strategies, specifically annual and biennial (every other year), on attack rate and expected number of infections. METHODS AND FINDINGS: We present a multi-annual, individual-based, stochastic, force of infection model that accounts for individual exposure histories and disease/vaccine dynamics influencing susceptibility. We simulate birth cohorts that experience yearly influenza epidemics and follow them until age 18 to determine attack rates and the number of infections during childhood. We perform simulations under baseline conditions, with an assumed vaccination coverage of 44%, to compare annual vaccination to no and biennial vaccination. We relax our baseline assumptions to explore how our model assumptions impact vaccination program performance. At baseline, we observed less than half the number of infections between the ages 2 and 10 under annual vaccination in children who had been vaccinated at least half the time compared to no vaccination. When averaged over all ages 0-18, the number of infections under annual vaccination was 2.07 (2.06, 2.08) compared to 2.63 (2.62, 2.64) under no vaccination, and 2.38 (2.37, 2.40) under biennial vaccination. When we introduced a penalty for repeated exposures, we observed a decrease in the difference in infections between the vaccination strategies. Specifically, the difference in childhood infections under biennial compared to annual vaccination decreased from 0.31 to 0.04 as exposure penalty increased. CONCLUSION: Our results indicate that while annual vaccination averts more childhood infections than biennial vaccination, this difference is small. Our work confirms the value of annual vaccination in children, even with modest vaccination coverage, but also shows that similar benefits of vaccination may be obtained by implementing a biennial vaccination program. AUTHOR SUMMARY: Many countries include annual vaccination of children against influenza in their vaccination programs. In the United Kingdom (UK), annual vaccination of children aged of 2 to 10 against influenza is recommended. However, little research has evaluated whether annual vaccination is the best strategy, while accounting for how past infection and vaccination may affect an individual's susceptibility to infection in the current influenza season. Prior work has suggested that there may be a negative effect of repeated vaccination. In this work we developed a stochastic, individual-based model to assess the impact of repeated vaccination strategies on childhood infections. Specifically, we first compare annual vaccination to no vaccination and then annual vaccination to biennial (every other year) vaccination. We use the UK as our motivating example. We found that an annual vaccination strategy resulted in the fewest childhood infections, followed by biennial vaccination. The difference in number of childhood infections between the different vaccination strategies decreased when we introduced a penalty for repeated exposures. Our work confirms the value of annual vaccination in children, but also shows that similar benefits of vaccination can be obtained by implementing a biennial vaccination program, particularly when there is a negative effect of repeated vaccinations.

Social Distancing Crowd Segmentation, Estimation and Visualisation

This research shows a modern crowd counting solution which alters typical prediction solutions into a segmentation of individuals based on a distance threshold, allowing for better visualisation and results. The study proposes using YOLOv4-normal and YOLOv4-tiny models, which have shown great results throughout calibration with an MAE of 14 and 36 respectively. However it did present some issues of accuracy degradation when trained on head annotations at any level of crowd density. As for visualisation, perspective transformation was used which directly helped in providing the distance calculation that was absent from standard transformation. If any variants of YOLOv4 are to be used, the main argument is the choice between speed over accuracy while relying on native implementations. In the case of distance regulation, any transformation that maps itself onto the region of interest, such as perspective transformation should be used to precisely determine distances from a camera to the region of interest itself. © 2021 IEEE.

Estimating the effect of non-pharmaceutical interventions to mitigate COVID-19 spread in Saudi Arabia.

BACKGROUND: The Kingdom of Saudi Arabia (KSA) quickly controlled the spread of SARS-CoV-2 by implementing several non-pharmaceutical interventions (NPIs), including suspension of international and national travel, local curfews, closing public spaces (i.e., schools and universities, malls and shops), and limiting religious gatherings. The KSA also mandated all citizens to respect physical distancing and to wear face masks. However, after relaxing some restrictions during June 2020, the KSA is now planning a strategy that could allow resuming in-person education and international travel. The aim of our study was to evaluate the effect of NPIs on the spread of the COVID-19 and test strategies to open schools and resume international travel. METHODS: We built a spatial-explicit individual-based model to represent the whole KSA population (IBM-KSA). The IBM-KSA was parameterized using country demographic, remote sensing, and epidemiological data. A social network was created to represent contact heterogeneity and interaction among age groups of the population. The IBM-KSA also simulated the movement of people across the country based on a gravity model. We used the IBM-KSA to evaluate the effect of different NPIs adopted by the KSA (physical distancing, mask-wearing, and contact tracing) and to forecast the impact of strategies to open schools and resume international travels. RESULTS: The IBM-KSA results scenarios showed the high effectiveness of mask-wearing, physical distancing, and contact tracing in controlling the spread of the disease. Without NPIs, the KSA could have reported 4,824,065 (95% CI: 3,673,775-6,335,423) cases by June 2021. The IBM-KSA showed that mandatory mask-wearing and physical distancing saved 39,452 lives (95% CI: 26,641-44,494). In-person education without personal protection during teaching would have resulted in a high surge of COVID-19 cases. Compared to scenarios with no personal protection, enforcing mask-wearing and physical distancing in schools reduced cases, hospitalizations, and deaths by 25% and 50%, when adherence to these NPIs was set to 50% and 70%, respectively. The IBM-KSA also showed that a quarantine imposed on international travelers reduced the probability of outbreaks in the country. CONCLUSIONS: This study showed that the interventions adopted by the KSA were able to control the spread of SARS-CoV-2 in the absence of a vaccine. In-person education should be resumed only if NPIs could be applied in schools and universities. International travel can be resumed but with strict quarantine rules. The KSA needs to keep strict NPIs in place until a high fraction of the population is vaccinated in order to reduce hospitalizations and deaths.

Integrating Human Mobility into the Epidemiological Models of COVID-19: Progress and Challenges

The spread of infectious diseases is usually a highly nonlinear space-time diffusion process. Epidemiological models can not only be used to predict the epidemic trend, but also be used to systematically and scientifically study the transmission mechanism of the complex processes under different hypothetical intervention scenarios, which provide crucial analytical and planning tools for public health studies and policy-making. Since host behavior is one of the critical driven factors for the dynamics of infectious diseases, it is important to effectively integrate human spatiotemporal behavior into the epidemiological models for human-hosted infectious diseases. Due to the rapid development of human mobility research and applications aided by big trajectory data, many of the epidemiological models for Coronavirus Disease 2019 (COVID-19) have already coupled human mobility. By incorporating real trajectory data such as mobile phone location data at an individual or aggregated level, researchers are working towards the direction of accurately depicting the real world, so as to improve the effectiveness of the model in guiding actual epidemic prevention and control. The epidemic trend prediction, Non-pharmaceutical Interventions (NPIs) evaluation, vaccination strategy design, and transmission driven factors have been studied by the epidemiological models coupled with human mobility, which provides scientific decision-making aid for controlling epidemic in different countries and regions. In order to systematically understand this important progress of epidemiological models, this study collected and summarized relevant literatures. First, the interactions between the COVID-19 epidemic and human mobility were analyzed, which demonstrated the necessity of integrating the complex spatiotemporal behavior, such as population-based or individual-based mobility, activity, and contact interaction, into the epidemiological models. Then, according to the modeling purpose and mechanism, the models integrated with human mobility were discussed by two types: short-term epidemic prediction models and process simulation models. Among them, based on the coupling methods of human mobility, short-term epidemic prediction models can further be divided into models coupled with first-order and second-order human mobility, while process simulation models can be divided into models coupled with population-based mobility and individual-based mobility. Finally, we concluded that epidemiological models integrating human mobility should be developed towards more complex human spatiotemporal behaviors with a fine spatial granularity. Besides, it is in urgent need to improve the model capability to better understand the disease spread processes over space and time, break through the bottleneck of the huge computational cost of fine-grained models, cooperate cutting-edge artificial intelligence approaches, and develop more universal and accessible modeling data sets and tools for general users. 2021, Science Press. All right reserved.

Exploring the Local Determinants of SARS-CoV-2 Transmission and Control via an Exposure-Based Model.

A simulation model was developed aimed at assisting local public health authorities in exploring strategies for the suppression of SARS-CoV-2 transmission. A mechanistic modeling framework is utilized based on the daily airborne exposure of individuals defined in terms of inhaled viruses. Comparison of model outputs and observed data confirms that the model can generate realistic patterns of secondary cases. In the example investigated, the highest risk of being newly infected was among young adults, males, and people living in large households. Among risky occupations are food preparation and serving, personal care and service, sales, and production-related occupations. Results also show a pattern consistent with superspreading with 70% of initial cases who do not transmit at all while 13.4% of primary cases contribute 80% of secondary cases. The impacts of school closure and masking on the synthetic population are very small, but for students, school closure resulted in more time at home and increased secondary cases among them by over 25%. Requiring masks at schools decreased the case count by 80%. We conclude that the simulator can be useful in exploring local intervention scenarios and provides output useful in assessing the confidence that might be placed on its predictions.

A runtime alterable epidemic model with genetic drift, waning immunity and vaccinations.

We present methods for building a Java Runtime-Alterable-Model Platform (RAMP) of complex dynamical systems. We illustrate our methods by building a multivariant SEIR (epidemic) RAMP. Underlying our RAMP is an individual-based model that includes adaptive contact rates, pathogen genetic drift, waning and cross-immunity. Besides allowing parameter values, process descriptions and scriptable runtime drivers to be easily modified during simulations, our RAMP can used within R-Studio and other computational platforms. Process descriptions that can be runtime altered within our SEIR RAMP include pathogen variant-dependent host shedding, environmental persistence, host transmission and within-host pathogen mutation and replication. They also include adaptive social distancing and adaptive application of vaccination rates and variant-valency of vaccines. We present simulation results using parameter values and process descriptions relevant to the current COVID-19 pandemic. Our results suggest that if waning immunity outpaces vaccination rates, then vaccination rollouts may fail to contain the most transmissible variants, particularly if vaccine valencies are not adapted to deal with escape mutations. Our SEIR RAMP is designed for easy use by others. More generally, our RAMP concept facilitates construction of highly flexible complex systems models of all types, which can then be easily shared as stand-alone application programs.

June: open-source individual-based epidemiology simulation.

We introduce June, an open-source framework for the detailed simulation of epidemics on the basis of social interactions in a virtual population constructed from geographically granular census data, reflecting age, sex, ethnicity and socio-economic indicators. Interactions between individuals are modelled in groups of various sizes and properties, such as households, schools and workplaces, and other social activities using social mixing matrices. June provides a suite of flexible parametrizations that describe infectious diseases, how they are transmitted and affect contaminated individuals. In this paper, we apply June to the specific case of modelling the spread of COVID-19 in England. We discuss the quality of initial model outputs which reproduce reported hospital admission and mortality statistics at national and regional levels as well as by age strata.

Effectiveness of non-pharmaceutical interventions against local transmission of COVID-19: An individual-based modelling study.

The outbreak of the novel coronavirus disease 2019 (COVID-19), caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has caused global transmission, and been spread all over the world. For those regions that are currently free of infected cases, it is an urgent issue to prevent and control the local outbreak of COVID-19 when there are sporadic cases. To evaluate the effects of non-pharmaceutical interventions against local transmission of COVID-19, and to forecast the epidemic dynamics after local outbreak of diseases under different control measures, we developed an individual-based model (IBM) to simulate the transmission dynamics of COVID-19 from a microscopic perspective of individual-to-individual contacts to heterogenous among individuals. Based on the model, we simulated the effects of different levels of non-pharmaceutical interventions in controlling disease transmission after the appearance of sporadic cases. Simulations shown that isolation of infected cases and quarantine of close contacts alone would not eliminate the local transmission of COVID-19, and there is a risk of a second wave epidemics. Quarantine the second-layer close contacts can obviously reduce the size of outbreak. Moreover, to effectively eliminate the daily new infections in a short time, it is necessary to reduce the individual-to-individual contacts. IBM provides a numerical representation for the local transmission of infectious diseases, and extends the compartmental models to include individual heterogeneity and the close contacts network. Our study suggests that combinations of self-isolation, quarantine of close contacts, and social distancing would be necessary to block the local transmission of COVID-19.

'Accidents waiting to happen'-Insights from a simple model on the emergence of infectious agents in new hosts.

This study evaluates through modelling the possible individual and combined effect of three populational parameters of pathogens (reproduction rate; rate of novelty emergence; and propagule size) on the colonization of new host species-putatively the most fundamental process leading to the emergence of new infectious diseases. The results are analysed under the theoretical framework of the Stockholm Paradigm using IBM simulations to better understand the evolutionary dynamics of the pathogen population and the possible role of Ecological Fitting. The simulations suggest that all three parameters positively influence the success of colonization of new hosts by a novel parasite population, but contrary to the prevailing belief, the rate of novelty emergence (e.g. mutations) is the least important factor. Maximization of all parameters results in a synergetic facilitation of the colonization and emulates the expected scenario for pathogenic microorganisms. The simulations also provide theoretical support for the retention of the capacity of fast-evolving lineages to retro-colonize their previous host species/lineage by ecological fitting. Capacity is, thus, much larger than we can anticipate. Hence, the results support the empirical observations that opportunity of encounter (i.e. the breakdown in mechanisms for ecological isolation) is a fundamental determinant to the emergence of new associations-especially Emergent Infectious Diseases-and the dynamics of host exploration, as observed in SARS-CoV-2. Insights on the dynamics of Emergent Infectious Diseases derived from the simulations and from the Stockholm Paradigm are discussed.

SARS-CoV-2 transmission and control in a hospital setting: an individual-based modelling study.

Development of strategies for mitigating the severity of COVID-19 is now a top public health priority. We sought to assess strategies for mitigating the COVID-19 outbreak in a hospital setting via the use of non-pharmaceutical interventions. We developed an individual-based model for COVID-19 transmission in a hospital setting. We calibrated the model using data of a COVID-19 outbreak in a hospital unit in Wuhan. The calibrated model was used to simulate different intervention scenarios and estimate the impact of different interventions on outbreak size and workday loss. The use of high-efficacy facial masks was shown to be able to reduce infection cases and workday loss by 80% (90% credible interval (CrI): 73.1-85.7%) and 87% (CrI: 80.0-92.5%), respectively. The use of social distancing alone, through reduced contacts between healthcare workers, had a marginal impact on the outbreak. Our results also indicated that a quarantine policy should be coupled with other interventions to achieve its effect. The effectiveness of all these interventions was shown to increase with their early implementation. Our analysis shows that a COVID-19 outbreak in a hospital's non-COVID-19 unit can be controlled or mitigated by the use of existing non-pharmaceutical measures.

Managing Coronavirus Disease 2019 Spread With Voluntary Public Health Measures: Sweden as a Case Study for Pandemic Control.

BACKGROUND: The coronavirus disease 19 (COVID-19) pandemic has spread globally, causing extensive illness and mortality. In advance of effective antiviral therapies, countries have applied different public health strategies to control spread and manage healthcare need. Sweden has taken a unique approach of not implementing strict closures, instead urging personal responsibility. We analyze the results of this and other potential strategies for pandemic control in Sweden. METHODS: We implemented individual-based modeling of COVID-19 spread in Sweden using population, employment, and household data. Epidemiological parameters for COVID-19 were validated on a limited date range; where substantial uncertainties remained, multiple parameters were tested. The effects of different public health strategies were tested over a 160-day period, analyzed for their effects on intensive care unit (ICU) demand and death rate, and compared with Swedish data for April 2020. RESULTS: Swedish mortality rates are intermediate between rates for European countries that quickly imposed stringent public health controls and those for countries that acted later. Models most closely reproducing reported mortality data suggest that large portions of the population voluntarily self-isolate. Swedish ICU use rates remained lower than predicted, but a large fraction of deaths occurred in non-ICU patients. This suggests that patient prognosis was considered in ICU admission, reducing healthcare load at a cost of decreased survival in patients not admitted. CONCLUSIONS: The Swedish COVID-19 strategy has thus far yielded a striking result: mild mandates overlaid with voluntary measures can achieve results highly similar to late-onset stringent mandates. However, this policy causes more healthcare demand and more deaths than early stringent control and depends on continued public will.