The risk of indoor airborne transmission among co-located individuals is generally non-uniform, which remains a critical challenge for public health modelling. Thus, we present CompARE, an integrated risk assessment framework for indoor airborne disease transmission that reveals a striking bimodal distribution of infection risk driven by airflow dynamics and human behavior. Combining computational fluid dynamics (CFD), machine learning (ML), and agent-based modeling (ABM), our model captures the complex interplay between aerosol transport, human mobility, and environmental context. Based on a prototypical childcare center, our approach quantifies how incorporation of ABM can unveil significantly different infection risk profiles across agents, with more than two-fold change in risk of infection between the individuals with the lowest and highest risks in more than 90% of cases, despite all individuals being in the same overall environment. We found that infection risk distributions can exhibit not only a striking bimodal pattern in certain activities but also exponential decay and fat-tailed behavior in others. Specifically, we identify low-risk modes arising from source containment, as well as high-risk tails from prolonged close contact. Our approach enables near-real-time scenario analysis and provides policy-relevant quantitative insights into how ventilation design, spatial layout, and social distancing policies can mitigate transmission risk. These findings challenge simple distance-based heuristics and support the design of targeted, evidence-based interventions in high-occupancy indoor settings.

We study viral transmission in crowds via the short-ranged airborne pathway using a purely model-based approach. Our goal is two-pronged. Firstly, we illustrate with a concrete and pedagogical case study how to estimate the risks of new viral infections by coupling pedestrian simulations with the transmission algorithm that we recently released as open-source code. The algorithm hinges on pre-computed viral concentration maps derived from computational fluid dynamics (CFD) simulations. Secondly, we investigate to what extent the transmission risk predictions depend on the pedestrian dynamics model in use. For the simple bidirectional flow under consideration, the predictions are found to be surprisingly stable across initial conditions and models, despite the different microscopic arrangements of the simulated crowd, as long as the crowd evolves in a qualitatively similarly way. On the other hand, when major changes are observed in the crowd's behaviour, notably whenever a jam occurs at the centre of the channel, the estimated risks surge drastically.

The node-place model has been widely used to classify and evaluate transit stations, which sheds light on individual travel behaviors and supports urban planning through effectively integrating land use and transportation development. This article adapts this model to investigate whether and how node, place, and mobility would be associated with the transmission risks and presences of the local COVID-19 cases in a city. Similar studies on the model and its relevance to COVID-19, according to our knowledge, have not been undertaken before. Moreover, the unique metric drawn from detailed visit history of the infected, i.e., the COVID-19 footprints, is proposed and exploited. This study then empirically uses the adapted model to examine the station-level factors affecting the local COVID-19 footprints. The model accounts for traditional measures of the node and place as well as actual human mobility patterns associated with the node and place. It finds that stations with high node, place, and human mobility indices normally have more COVID-19 footprints in proximity. A multivariate regression is fitted to see whether and to what degree different indices and indicators can predict the COVID-19 footprints. The results indicate that many of the place, node, and human mobility indicators significantly impact the concentration of COVID-19 footprints. These are useful for policy-makers to predict and monitor hotspots for COVID-19 and other pandemics transmission.

The spread of COVID-19 revealed that transmission risk patterns are not homogenous across different cities and communities, and various heterogeneous features can influence the spread trajectories. Hence, for predictive pandemic monitoring, it is essential to explore latent heterogeneous features in cities and communities that distinguish their specific pandemic spread trajectories. To this end, this study creates a network embedding model capturing cross-county visitation networks, as well as heterogeneous features to uncover clusters of counties in the United States based on their pandemic spread transmission trajectories. We collected and computed location intelligence features from 2,787 counties from March 3 to June 29, 2020 (initial wave). Second, we constructed a human visitation network, which incorporated county features as node attributes, and visits between counties as network edges. Our attributed network embeddings approach integrates both typological characteristics of the cross-county visitation network, as well as heterogeneous features. We conducted clustering analysis on the attributed network embeddings to reveal four archetypes of spread risk trajectories corresponding to four clusters of counties. Subsequently, we identified four features as important features underlying the distinctive transmission risk patterns among the archetypes. The attributed network embedding approach and the findings identify and explain the non-homogenous pandemic risk trajectories across counties for predictive pandemic monitoring. The study also contributes to data-driven and deep learning-based approaches for pandemic analytics to complement the standard epidemiological models for policy analysis in pandemics.

Epidemic forecasting is the key to effective control of epidemic transmission and helps the world mitigate the crisis that threatens public health. To better understand the transmission and evolution of epidemics, we propose EpiGNN, a graph neural network-based model for epidemic forecasting. Specifically, we design a transmission risk encoding module to characterize local and global spatial effects of regions in epidemic processes and incorporate them into the model. Meanwhile, we develop a Region-Aware Graph Learner (RAGL) that takes transmission risk, geographical dependencies, and temporal information into account to better explore spatial-temporal dependencies and makes regions aware of related regions' epidemic situations. The RAGL can also combine with external resources, such as human mobility, to further improve prediction performance. Comprehensive experiments on five real-world epidemic-related datasets (including influenza and COVID-19) demonstrate the effectiveness of our proposed method and show that EpiGNN outperforms state-of-the-art baselines by 9.48% in RMSE.

How can the resurgent epidemics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during 2020 be explained? Are they a result of students going back to school? To address this question, Monod et al. created a contact matrix for infection based on data collected in Europe and China and extended it to the United States. Early in the pandemic, before interventions were widely implemented, contacts concentrated among individuals of similar age were the highest among school-aged children, between children and their parents, and between middle-aged adults and the elderly. However, with the advent of nonpharmaceutical interventions, these contact patterns changed substantially. By mid-August 2020, although schools reopening facilitated transmission, the resurgence in the United States was largely driven by adults 20 to 49 years of age. Thus, working adults who need to support themselves and their families have fueled the resurging epidemics in the United States. Science , this issue p. [eabe8372][1] ### INTRODUCTION After initial declines, in mid-2020, a sustained resurgence in the transmission of novel coronavirus disease (COVID-19) occurred in the United States. Throughout the US epidemic, considerable heterogeneity existed among states, both in terms of overall mortality and infection, but also in the types and stringency of nonpharmaceutical interventions. Despite these stark differences among states, little is known about the relationship between interventions, contact patterns, and infections, or how this varies by age and demographics. A useful tool for studying these dynamics is individual, age-specific mobility data. In this study, we use detailed mobile-phone data from more than 10 million individuals and establish a mechanistic relationship between individual contact patterns and COVID-19 mortality data. ### RATIONALE As the pandemic progresses, disease control responses are becoming increasingly nuanced and targeted. Understanding fine-scale patterns of how individuals interact with each other is essential to mounting an efficient public health control program. For example, the choice of closing workplaces, closing schools, limiting hospitality sectors, or prioritizing vaccination to certain population groups should be informed by the demographics currently driving and sustaining transmission. To develop the tools to answer such questions, we introduce a new framework that links mobility to mortality through age-specific contact patterns and then use this rich relationship to reconstruct accurate transmission dynamics (see figure panel A). ### RESULTS We find that as of 29 October 2020, adults aged 20 to 34 and 35 to 49 are the only age groups that have sustained SARS-CoV-2 transmission with reproduction numbers (transmission rates) consistently above one. The high reproduction numbers from adults are linked both to rebounding mobility over the summer and elevated transmission risks per venue visit among adults aged 20 to 49. Before school reopening, we estimate that 75 of 100 COVID-19 infections originated from adults aged 20 to 49, and the share of young adults aged 20 to 34 among COVID-19 infections was highly variable geographically. After school reopening, we reconstruct relatively modest shifts in the age-specific sources of resurgent COVID-19 toward younger individuals, with less than 5% of SARS-CoV-2 transmissions attributable to children aged 0 to 9 and less than 10% attributable to early adolescents and teenagers aged 10 to 19. Thus, adults aged 20 to 49 continue to be the only age groups that contribute disproportionately to COVID-19 spread relative to their size in the population (see figure panel B). However, because children and teenagers seed infections among adults who are more transmission efficient, we estimate that overall, school opening is indirectly associated with a 26% increase in SARS-CoV-2 transmission. ### CONCLUSION We show that considering transmission through the lens of contact patterns is fundamental to understanding which population groups are driving disease transmission. Over time, the share of age groups among reported deaths has been markedly constant, and the data provide no evidence that transmission shifted to younger age groups before school reopening, and no evidence that young adults aged 20 to 34 were the primary source of resurgent epidemics since the summer of 2020. Our key conclusion is that in locations where novel, highly transmissible SARS-CoV-2 lineages have not yet become established, additional interventions among adults aged 20 to 49, such as mass vaccination with transmission-blocking vaccines, could bring resurgent COVID-19 epidemics under control and avert deaths. ![Figure][2] Model developed to estimate the contribution of age groups to resurgent COVID-19 epidemics in the United States. ( A ) Model overview. ( B ) Estimated contribution of age groups to SARS-CoV-2 transmission in October. After initial declines, in mid-2020 a resurgence in transmission of novel coronavirus disease (COVID-19) occurred in the United States and Europe. As efforts to control COVID-19 disease are reintensified, understanding the age demographics driving transmission and how these affect the loosening of interventions is crucial. We analyze aggregated, age-specific mobility trends from more than 10 million individuals in the United States and link these mechanistically to age-specific COVID-19 mortality data. We estimate that as of October 2020, individuals aged 20 to 49 are the only age groups sustaining resurgent SARS-CoV-2 transmission with reproduction numbers well above one and that at least 65 of 100 COVID-19 infections originate from individuals aged 20 to 49 in the United States. Targeting interventions—including transmission-blocking vaccines—to adults aged 20 to 49 is an important consideration in halting resurgent epidemics and preventing COVID-19–attributable deaths. [1]: /lookup/doi/10.1126/science.abe8372 [2]: pending:yes

A minority of people infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmit most infections. How does this happen? Sun et al. reconstructed transmission in Hunan, China, up to April 2020. Such detailed data can be used to separate out the relative contribution of transmission control measures aimed at isolating individuals relative to population-level distancing measures. The authors found that most of the secondary transmissions could be traced back to a minority of infected individuals, and well over half of transmission occurred in the presymptomatic phase. Furthermore, the duration of exposure to an infected person combined with closeness and number of household contacts constituted the greatest risks for transmission, particularly when lockdown conditions prevailed. These findings could help in the design of infection control policies that have the potential to minimize both virus transmission and economic strain. Science , this issue p. [eabe2424][1] ### INTRODUCTION The role of transmission heterogeneities in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) dynamics remains unclear, particularly those heterogeneities driven by demography, behavior, and interventions. To understand individual heterogeneities and their effect on disease control, we analyze detailed contact-tracing data from Hunan, a province in China adjacent to Hubei and one of the first regions to experience a SARS-CoV-2 outbreak in January to March 2020. The Hunan outbreak was swiftly brought under control by March 2020 through a combination of nonpharmaceutical interventions including population-level mobility restriction (i.e., lockdown), traveler screening, case isolation, contact tracing, and quarantine. In parallel, highly detailed epidemiological information on SARS-CoV-2–infected individuals and their close contacts was collected by the Hunan Provincial Center for Disease Control and Prevention. ### RATIONALE Contact-tracing data provide information to reconstruct transmission chains and understand outbreak dynamics. These data can in turn generate valuable intelligence on key epidemiological parameters and risk factors for transmission, which paves the way for more-targeted and cost-effective interventions. ### RESULTS On the basis of epidemiological information and exposure diaries on 1178 SARS-CoV-2–infected individuals and their 15,648 close contacts, we developed a series of statistical and computational models to stochastically reconstruct transmission chains, identify risk factors for transmission, and infer the infectiousness profile over the course of a typical infection. We observe overdispersion in the distribution of secondary infections, with 80% of secondary cases traced back to 15% of infections, which indicates substantial transmission heterogeneities. We find that SARS-CoV-2 transmission risk scales positively with the duration of exposure and the closeness of social interactions, with the highest per-contact risk estimated in the household. Lockdown interventions increase transmission risk in families and households, whereas the timely isolation of infected individuals reduces risk across all types of contacts. There is a gradient of increasing susceptibility with age but no significant difference in infectivity by age or clinical severity. Early isolation of SARS-CoV-2–infected individuals drastically alters transmission kinetics, leading to shorter generation and serial intervals and a higher fraction of presymptomatic transmission. After adjusting for the censoring effects of isolation, we find that the infectiousness profile of a typical SARS-CoV-2 patient peaks just before symptom onset, with 53% of transmission occurring in the presymptomatic phase in an uncontrolled setting. We then use these results to evaluate the effectiveness of individual-based strategies (case isolation and contact quarantine) both alone and in combination with population-level contact reductions. We find that a plausible parameter space for SARS-CoV-2 control is restricted to scenarios where interventions are synergistically combined, owing to the particular transmission kinetics of this virus. ### CONCLUSION There is considerable heterogeneity in SARS-CoV-2 transmission owing to individual differences in biology and contacts that is modulated by the effects of interventions. We estimate that about half of secondary transmission events occur in the presymptomatic phase of a primary case in uncontrolled outbreaks. Achieving epidemic control requires that isolation and contact-tracing interventions are layered with population-level approaches, such as mask wearing, increased teleworking, and restrictions on large gatherings. Our study also demonstrates the value of conducting high-quality contact-tracing investigations to advance our understanding of the transmission dynamics of an emerging pathogen. ![Figure][2] Transmission chains, contact patterns, and transmission kinetics of SARS-CoV-2 in Hunan, China, based on case and contact-tracing data from Hunan, China. (Top left) One realization of the reconstructed transmission chains, with a histogram representing overdispersion in the distribution of secondary infections. (Top right) Contact matrices of community, social, extended family, and household contacts reveal distinct age profiles. (Bottom) Earlier isolation of primary infections shortens the generation and serial intervals while increasing the relative contribution of transmission in the presymptomatic phase. A long-standing question in infectious disease dynamics concerns the role of transmission heterogeneities, which are driven by demography, behavior, and interventions. On the basis of detailed patient and contact-tracing data in Hunan, China, we find that 80% of secondary infections traced back to 15% of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) primary infections, which indicates substantial transmission heterogeneities. Transmission risk scales positively with the duration of exposure and the closeness of social interactions and is modulated by demographic and clinical factors. The lockdown period increases transmission risk in the family and households, whereas isolation and quarantine reduce risks across all types of contacts. The reconstructed infectiousness profile of a typical SARS-CoV-2 patient peaks just before symptom presentation. Modeling indicates that SARS-CoV-2 control requires the synergistic efforts of case isolation, contact quarantine, and population-level interventions because of the specific transmission kinetics of this virus. [1]: /lookup/doi/10.1126/science.abe2424 [2]: pending:yes

Mathematical modeling of epidemic spreading has been widely adopted to estimate the threats of epidemic diseases (i.e., the COVID-19 pandemic) as well as to evaluate epidemic control interventions. The indoor place is considered to be a significant epidemic spreading risk origin, but existing widely-used epidemic spreading models are usually limited for indoor places since the dynamic physical distance changes between people are ignored, and the empirical features of the essential and non-essential travel are not differentiated. In this paper, we introduce a pedestrian-based epidemic spreading model that is capable of modeling indoor transmission risks of diseases during people's social activities. Taking advantage of the before-and-after mobility data from the University of Maryland COVID-19 Impact Analysis Platform, it's found that people tend to spend more time in grocery stores once their travel frequencies are restricted to a low level. In other words, an increase in dwell time could balance the decrease in travel frequencies and satisfy people's demand. Based on the pedestrian-based model and the empirical evidence, combined non-pharmaceutical interventions from different operational levels are evaluated. Numerical simulations show that restrictions on people's travel frequency and open-hours of indoor places may not be universally effective in reducing average infection risks for each pedestrian who visit the place. Entry limitations can be a widely effective alternative, whereas the decision-maker needs to balance the decrease in risky contacts and the increase in queue length outside the place that may impede people from fulfilling their travel needs.