scholarly journals Predicting the effects of COVID-19 related interventions in urban settings by combining activity-based modelling, agent-based simulation, and mobile phone data

Author(s):  
Sebastian A. Müller ◽  
Michael Balmer ◽  
William Charlton ◽  
Ricardo Ewert ◽  
Andreas Neumann ◽  
...  

Epidemiological simulations as a method are used to better understand and predict the spreading of infectious diseases, for example of COVID-19. This paper presents an approach that combines a well-established approach from transportation modelling that uses person-centric data-driven human mobility modelling with a mechanistic infection model and a person-centric disease progression model. The model includes the consequences of different room sizes, air exchange rates, disease import, changed activity participation rates over time (coming from mobility data), masks, indoors vs. outdoors leisure activities, and of contact tracing. The model is validated against the infection dynamics in Berlin (Germany). The model can be used to understand the contributions of different activity types to the infection dynamics over time. The model predicts the effects of contact reductions, school closures/vacations, masks, or the effect of moving leisure activities from outdoors to indoors in fall, and is thus able to quantitatively predict the consequences of interventions. It is shown that these effects are best given as additive changes of the reinfection rate R. The model also explains why contact reductions have decreasing marginal returns, i.e. the first 50% of contact reductions have considerably more effect than the second 50%. Our work shows that is is possible to build detailed epidemiological simulations from microscopic mobility models relatively quickly. They can be used to investigate mechanical aspects of the dynamics, such as the transmission from political decisions via human behavior to infections, consequences of different lockdown measures, or consequences of wearing masks in certain situations. The results can be used to inform political decisions.

2020 ◽  
Author(s):  
Sebastian A Müller ◽  
Michael Balmer ◽  
Billy Charlton ◽  
Ricardo Ewert ◽  
Andreas Neumann ◽  
...  

Abstract Epidemiological simulations as a method are used to better understand and predict the spreading of infectious diseases, for example of COVID-19. This paper presents an approach that combines person-centric data-driven human mobility modelling with a mechanistic infection model and a person-centric disease progression model. Results show that in Berlin (Germany), behavioral changes of the population mostly happened before the government-initiated so-called contact ban came into effect. Also, the model is used to determine differentiated changes to the reinfection rate for different interventions such as reductions in activity participation, the wearing of masks, or contact tracing followed by quarantine-at-home. One important result is that successful contact tracing reduces the reinfection rate by about 30 to 40%, and that if contact tracing becomes overwhelmed then infection rates immediately jump up accordingly, making rather strong lockdown measures necessary to bring the reinfection rate back to below one.


Author(s):  
Sebastian A Müller ◽  
Michael Balmer ◽  
Billy Charlton ◽  
Ricardo Ewert ◽  
Andreas Neumann ◽  
...  

Epidemiological simulations as a method are used to better understand and predict the spreading of infectious diseases, for example of COVID-19. This paper presents an approach that combines person-centric data-driven human mobility modelling with a mechanistic infection model and a person-centric disease progression model. Results show that in Berlin (Germany), behavioral changes of the population mostly happened \textit{before} the government-initiated so-called contact ban came into effect. Also, the model is used to determine differentiated changes to the reinfection rate for different interventions such as reductions in activity participation, the wearing of masks, or contact tracing followed by quarantine-at-home. One important result is that successful contact tracing reduces the reinfection rate by about 30 to 40\%, and that if contact tracing becomes overwhelmed then infection rates immediately jump up accordingly, making rather strong lockdown measures necessary to bring the reinfection rate back to below one.


2017 ◽  
Vol 4 (5) ◽  
pp. 160950 ◽  
Author(s):  
Cecilia Panigutti ◽  
Michele Tizzoni ◽  
Paolo Bajardi ◽  
Zbigniew Smoreda ◽  
Vittoria Colizza

The recent availability of large-scale call detail record data has substantially improved our ability of quantifying human travel patterns with broad applications in epidemiology. Notwithstanding a number of successful case studies, previous works have shown that using different mobility data sources, such as mobile phone data or census surveys, to parametrize infectious disease models can generate divergent outcomes. Thus, it remains unclear to what extent epidemic modelling results may vary when using different proxies for human movements. Here, we systematically compare 658 000 simulated outbreaks generated with a spatially structured epidemic model based on two different human mobility networks: a commuting network of France extracted from mobile phone data and another extracted from a census survey. We compare epidemic patterns originating from all the 329 possible outbreak seed locations and identify the structural network properties of the seeding nodes that best predict spatial and temporal epidemic patterns to be alike. We find that similarity of simulated epidemics is significantly correlated to connectivity, traffic and population size of the seeding nodes, suggesting that the adequacy of mobile phone data for infectious disease models becomes higher when epidemics spread between highly connected and heavily populated locations, such as large urban areas.


Author(s):  
Sebastian Alexander Müller ◽  
Michael Balmer ◽  
Andreas Neumann ◽  
Kai Nagel

1Executive summaryWe use human mobility models, for which we are experts, and attach a virus infection dynamics to it, for which we are not experts but have taken it from the literature, including recent publications. This results in a virus spreading dynamics model. The results should be verified, but because of the current time pressure, we publish them in their current state. Recommendations for improvement are welcome. We come to the following conclusions:Complete lockdown works. About 10 days after lockdown, the infection dynamics dies down. This assumes that lockdown is complete, which can be guaranteed in the simulation, but not in reality. Still, it gives strong support to the argument that it is never too late for complete lockdown.As a rule of thumb, we would suggest complete lockdown no later than once 10% of hospital capacities available for COVID-19 are in use, and possibly much earlier. This is based on the following insights:Even after lockdown, the infection dynamics continues at home, leading to another tripling of the cases before the dynamics is slowed.There will be many critical cases coming from people who were infected before lockdown. Because of the exponential growth dynamics, their number will be large.Researchers with more detailed disease progression models should improve upon these statements.Our simulations say that complete removal of infections at child care, primary schools, workplaces and during leisure activities will not be enough to sufficiently slow down the infection dynamics. It would have been better, but still not sufficient, if initiated earlier.Infections in public transport play an important role. In the simulations shown later, removing infections in the public transport system reduces the infection speed and the height of the peak by approximately 20%. Evidently, this depends on the infection parameters, which are not well known. – This does not point to reducing public transport capacities as a reaction to the reduced demand, but rather use it for lower densities of passengers and thus reduced infection rates.In our simulations, removal of infections at child care, primary schools, workplaces, leisure activities, and in public transport may barely have been sufficient to control the infection dynamics if implemented early on. Now according to our simulations it is too late for this, and (even) harsher measures will have to be initiated until possibly a return to such a restrictive, but still somewhat functional regime will again be possible.Evidently, all of these results have to be taken with care. They are based on preliminary infection parameters taken from the literature, used inside a model that has more transport/movement details than all others that we are aware of but still not enough to describe all aspects of reality, and suffer from having to write computer code under time pressure. Optimally, they should be confirmed independently. Short of that, given current knowledge we believe that they provide justification for “complete lockdown” at the latest when about 10% of available hospital capacities for COVID-19 are in use (and possibly earlier; we are no experts of hospital capabilities).1What was not investigated in detail in our simulations was contact tracing, i.e. tracking down the infection chains and moving all people along infection chains into quarantine. The case of Singapore has so far shown that this may be successful. Preliminary simulation of that tactic shows that it is difficult to implement for COVID-19, since the incubation time is rather long, people are contagious before they feel sick, or maybe never feel sufficiently sick at all. We will investigate in future work if and how contact tracing can be used together with a restrictive, but not totally locked down regime.When opening up after lockdown, it would be important to know the true fraction of people who are already immune, since that would slow down the infection dynamics by itself. For Wuhan, the currently available numbers report that only about 0.1% of the population was infected, which would be very far away from “herd immunity”. However, there have been and still may be many unknown infections (Frankfurter Allgemeine Zeitung GmbH 2020).


eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Sofonias Tessema ◽  
Amy Wesolowski ◽  
Anna Chen ◽  
Maxwell Murphy ◽  
Jordan Wilheim ◽  
...  

Local and cross-border importation remain major challenges to malaria elimination and are difficult to measure using traditional surveillance data. To address this challenge, we systematically collected parasite genetic data and travel history from thousands of malaria cases across northeastern Namibia and estimated human mobility from mobile phone data. We observed strong fine-scale spatial structure in local parasite populations, providing positive evidence that the majority of cases were due to local transmission. This result was largely consistent with estimates from mobile phone and travel history data. However, genetic data identified more detailed and extensive evidence of parasite connectivity over hundreds of kilometers than the other data, within Namibia and across the Angolan and Zambian borders. Our results provide a framework for incorporating genetic data into malaria surveillance and provide evidence that both strengthening of local interventions and regional coordination are likely necessary to eliminate malaria in this region of Southern Africa.


eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Hsiao-Han Chang ◽  
Amy Wesolowski ◽  
Ipsita Sinha ◽  
Christopher G Jacob ◽  
Ayesha Mahmud ◽  
...  

For countries aiming for malaria elimination, travel of infected individuals between endemic areas undermines local interventions. Quantifying parasite importation has therefore become a priority for national control programs. We analyzed epidemiological surveillance data, travel surveys, parasite genetic data, and anonymized mobile phone data to measure the spatial spread of malaria parasites in southeast Bangladesh. We developed a genetic mixing index to estimate the likelihood of samples being local or imported from parasite genetic data and inferred the direction and intensity of parasite flow between locations using an epidemiological model integrating the travel survey and mobile phone calling data. Our approach indicates that, contrary to dogma, frequent mixing occurs in low transmission regions in the southwest, and elimination will require interventions in addition to reducing imported infections from forested regions. Unlike risk maps generated from clinical case counts alone, therefore, our approach distinguishes areas of frequent importation as well as high transmission.


2019 ◽  
Vol 4 (1) ◽  
Author(s):  
Takahiro Yabe ◽  
Satish V. Ukkusuri ◽  
P. Suresh C. Rao

Abstract Recent disasters have shown the existence of large variance in recovery trajectories across cities that have experienced similar damage levels. Case studies of such events reveal the high complexity of the recovery process of cities, where inter-city dependencies and intra-city coupling of social and physical systems may affect the outcomes in unforeseen ways. Despite the large implications of understanding the recovery processes of cities after disasters for many domains including critical services, disaster management, and public health, little work have been performed to unravel this complexity. Rather, works are limited to analyzing and modeling cities as independent entities, and have largely neglected the effect that inter-city connectivity may have on the recovery of each city. Large scale mobility data (e.g. mobile phone data, social media data) have enabled us to observe human mobility patterns within and across cities with high spatial and temporal granularity. In this paper, we investigate how inter-city dependencies in both physical as well as social forms contribute to the recovery performances of cities after disasters, through a case study of the population recovery patterns of 78 Puerto Rican counties after Hurricane Maria using mobile phone location data. Various network metrics are used to quantify the types of inter-city dependencies that play an important role for effective post-disaster recovery. We find that inter-city social connectivity, which is measured by pre-disaster mobility patterns, is crucial for quicker recovery after Hurricane Maria. More specifically, counties that had more influx and outflux of people prior to the hurricane, were able to recover faster. Our findings highlight the importance of fostering the social connectivity between cities to prepare effectively for future disasters. This paper introduces a new perspective in the community resilience literature, where we take into account the inter-city dependencies in the recovery process rather than analyzing each community as independent entities.


2019 ◽  
Vol 8 (1) ◽  
Author(s):  
Guangshuo Chen ◽  
Aline Carneiro Viana ◽  
Marco Fiore ◽  
Carlos Sarraute

Abstract Mobile phone data are a popular source of positioning information in many recent studies that have largely improved our understanding of human mobility. These data consist of time-stamped and geo-referenced communication events recorded by network operators, on a per-subscriber basis. They allow for unprecedented tracking of populations of millions of individuals over long periods that span months. Nevertheless, due to the uneven processes that govern mobile communications, the sampling of user locations provided by mobile phone data tends to be sparse and irregular in time, leading to substantial gaps in the resulting trajectory information. In this paper, we illustrate the severity of the problem through an empirical study of a large-scale Call Detail Records (CDR) dataset. We then propose Context-enhanced Trajectory Reconstruction, a new technique that hinges on tensor factorization as a core method to complete individual CDR-based trajectories. The proposed solution infers missing locations with a median displacement within two network cells from the actual position of the user, on an hourly basis and even when as little as 1% of her original mobility is known. Our approach lets us revisit seminal works in the light of complete mobility data, unveiling potential biases that incomplete trajectories obtained from legacy CDR induce on key results about human mobility laws, trajectory uniqueness, and movement predictability.


2021 ◽  
Author(s):  
Alberto Hernando ◽  
David Mateo ◽  
Jordi Bayer ◽  
Ignacio Barrios

AbstractTotal and perimetral lockdowns were the strongest nonpharmaceutical interventions to fight against Covid-19, as well as the with the strongest socioeconomic collateral effects. Lacking a metric to predict the effect of lockdowns in the spreading of COVID-19, authorities and decision-makers opted for preventive measures that showed either too strong or not strong enough after a period of two to three weeks, once data about hospitalizations and deaths was available. We present here the radius of gyration as a candidate predictor of the trend in deaths by COVID-19 with an offset of three weeks. Indeed, the radius of gyration aggregates the most relevant microscopic aspects of human mobility into a macroscopic value, very sensitive to temporary trends and local effects, such as lockdowns and mobility restrictions. We use mobile phone data of more than 13 million users in Spain during a period of one year (from January 6th 2020 to January 10th 2021) to compute the users’ daily radius of gyration and compare the median value of the population with the evolution of COVID-19 deaths: we find that for all weeks where the radius of gyration is above a critical value (70% of its pre-pandemic score) the number of weekly deaths increases three weeks after. The reverse also stands: for all weeks where the radius of gyration is below the critical value, the number of weekly deaths decreased after three weeks. This observation leads to two conclusions: i) the radius of gyration can be used as a predictor of COVID-19-related deaths; and ii) partial mobility restrictions are as effective as a total lockdown as far the radius of gyration is below this critical value.BackgroundAuthorities around the World have used lockdowns and partial mobility restrictions as major nonpharmaceutical interventions to control the expansion of COVID-19. While effective, the efficiency of these measures on the number of COVID-19 cases and deaths is difficult to quantify, severely limiting the feedback that can be used to tune the intensity of these measures. In addition, collateral socioeconomic effects challenge the overall effectiveness of lockdowns in the long term, and the degree by which they are followed can be difficult to estimate. It is desirable to find both a metric to accurately monitor the mobility restrictions and a predictor of their effectiveness.MethodsWe correlate the median of the daily radius of gyration of more than 13M users in Spain during all of 2020 with the evolution of COVID-19 deaths for the same period. Mobility data is obtained from mobile phone metadata from one of the major operators in the country.ResultsThe radius of gyration is a predictor of the trend in the number of COVID-19 deaths with 3 weeks offset. When the radius is above/below a critical threshold (70% of the pre-pandemic score), the number of deaths increases/decreases three weeks later.ConclusionsThe radius of gyration can be used to monitor in real time the effectiveness of the mobility restrictions. The existence of a critical threshold suggest that partial lockdowns can be as efficient as total lockdowns, while reducing their socioeconomic impact. The mechanism behind the critical value is still unknow, and more research is needed.


2021 ◽  
Author(s):  
Tanjona Ramiadantsoa ◽  
C. Jessica E. Metcalf ◽  
Antso Hasina Raherinandrasana ◽  
Santatra Randrianarisoa ◽  
Benjamin L. Rice ◽  
...  

For emerging epidemics such as the COVID-19 pandemic, quantifying travel is a key component of developing accurate predictive models of disease spread to inform public health planning. However, in many LMICs, traditional data sets on travel such as commuting surveys as well as non-traditional sources such as mobile phone data are lacking, or, where available, have only rarely been leveraged by the public health community. Evaluating the accuracy of available data to measure transmission-relevant travel may be further hampered by limited reporting of suspected and laboratory confirmed infections. Here, we leverage case data collected as part of a COVID-19 dashboard collated via daily reports from the Malagasy authorities on reported cases of SARS-CoV-2 across the 22 regions of Madagascar. We compare the order of the timing of when cases were reported with predictions from a SARS-CoV-2 metapopulation model of Madagascar informed using various measures of connectivity including a gravity model based on different measures of distance, Internal Migration Flow data, and mobile phone data. Overall, the models based on mobile phone connectivity and the gravity-based on Euclidean distance best predicted the observed spread. The ranks of the regions most remote from the capital were more difficult to predict but interestingly, regions where the mobile phone connectivity model was more accurate differed from those where the gravity model was most accurate. This suggests that there may be additional features of mobility or connectivity that were consistently underestimated using all approaches, but are epidemiologically relevant. This work highlights the importance of data availability and strengthening collaboration among different institutions with access to critical data - models are only as good as the data that they use, so building towards effective data-sharing pipelines is essential.


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