Quantifying the impact of human mobility on malaria

A Bibliometric Analysis and Network Visualisation of Human Mobility Studies from 1990 to 2020: Emerging Trends and Future Research Directions

Studies on human mobility have a long history with increasingly strong interdisciplinary connections across social science, environmental science, information and technology, computer science, engineering, and health science. However, what is lacking in the current research is a synthesis of the studies to identify the evolutional pathways and future research directions. To address this gap, we conduct a systematic review of human mobility-related studies published from 1990 to 2020. Drawing on the selected publications retrieved from the Web of Science, we provide a bibliometric analysis and network visualisation using CiteSpace and VOSviewer on the number of publications and year published, authors and their countries and afflictions, citations, topics, abstracts, keywords, and journals. Our findings show that human mobility-related studies have become increasingly interdisciplinary and multi-dimensional, which have been strengthened by the use of the so-called ‘big data’ from multiple sources, the development of computer technologies, the innovation of modelling approaches, and the novel applications in various areas. Based on our synthesis of the work by top cited authors we identify four directions for future research relating to data sources, modelling methods, applications, and technologies. We advocate for more in-depth research on human mobility using multi-source big data, improving modelling methods and integrating advanced technologies including artificial intelligence, and machine and deep learning to address real-world problems and contribute to social good.

Comparing metapopulation dynamics of infectious diseases under different models of human movement

Newly available datasets present exciting opportunities to investigate how human population movement contributes to the spread of infectious diseases across large geographical distances. It is now possible to construct realistic models of infectious disease dynamics for the purposes of understanding global-scale epidemics. Nevertheless, a remaining unanswered question is how best to leverage the new data to parameterize models of movement, and whether one's choice of movement model impacts modeled disease outcomes. We adapt three well-studied models of infectious disease dynamics, the susceptible-infected-recovered model, the susceptible-infected-susceptible model, and the Ross-Macdonald model, to incorporate either of two candidate movement models. We describe the effect that the choice of movement model has on each disease model's results, finding that in all cases, there are parameter regimes where choosing one movement model instead of another has a profound impact on epidemiological outcomes. We further demonstrate the importance of choosing an appropriate movement model using the applied case of malaria transmission and importation on Bioko Island, Equatorial Guinea, finding that one model produces intelligible predictions of R ₀, whereas the other produces nonsensical results.

Modeling the Distribution of Human Mobility Metrics with Online Car-Hailing Data—An Empirical Study in Xi’an, China

Modeling the distribution of daily and hourly human mobility metrics is beneficial for studying underlying human travel patterns. In previous studies, some probability distribution functions were employed in order to establish a base for human mobility research. However, the selection of the most suitable distribution is still a challenging task. In this paper, we focus on modeling the distributions of travel distance, travel time, and travel speed. The daily and hourly trip data are fitted with several candidate distributions, and the best one is selected based on the Bayesian information criterion. A case study with online car-hailing data in Xi’an, China, is presented to demonstrate and evaluate the model fit. The results indicate that travel distance and travel time of daily and hourly human mobility tend to follow Gamma distribution, and travel speed can be approximated by Burr distribution. These results can contribute to a better understanding of online car-hailing travel patterns and establish a base for human mobility research.

Ethical machines: The human-centric use of artificial intelligence

Today's increased availability of large amounts of human behavioral data and advances in artificial intelligence (AI) are contributing to a growing reliance on algorithms to make consequential decisions for humans, including those related to access to credit or medical treatments, hiring, etc. Algorithmic decision-making processes might lead to more objective decisions than those made by humans who may be influenced by prejudice, conflicts of interest, or fatigue. However, algorithmic decision-making has been criticized for its potential to lead to privacy invasion, information asymmetry, opacity, and discrimination. In this paper, we describe available technical solutions in three large areas that we consider to be of critical importance to achieve a human-centric AI: (1) privacy and data ownership; (2) accountability and transparency; and (3) fairness. We also highlight the criticality and urgency to engage multi-disciplinary teams of researchers, practitioners, policy makers, and citizens to co-develop and evaluate in the real-world algorithmic decision-making processes designed to maximize fairness, accountability, and transparency while respecting privacy.

The risk of re-identification remains high even in country-scale location datasets

Although anonymous data are not considered personal data, recent research has shown how individuals can often be re-identified. Scholars have argued that previous findings apply only to small-scale datasets and that privacy is preserved in large-scale datasets. Using 3 months of location data, we (1) show the risk of re-identification to decrease slowly with dataset size, (2) approximate this decrease with a simple model taking into account three population-wide marginal distributions, and (3) prove that unicity is convex and obtain a linear lower bound. Our estimates show that 93% of people would be uniquely identified in a dataset of 60M people using four points of auxiliary information, with a lower bound at 22%. This lower bound increases to 87% when five points are available. Taken together, our results show how the privacy of individuals is very unlikely to be preserved even in country-scale location datasets.

Continental-scale dynamics of avian influenza in U.S. waterfowl are driven by demography, migration, and temperature

Emerging diseases of wildlife origin are increasingly spilling over into humans and domestic animals. Surveillance and risk assessments for transmission between these populations are informed by a mechanistic understanding of the pathogens in wildlife reservoirs. For avian influenza viruses (AIV), much observational and experimental work in wildlife has been conducted at local scales, yet fully understanding their spread and distribution requires assessing the mechanisms acting at both local, (e.g., intrinsic epidemic dynamics), and continental scales, (e.g., long-distance migration). Here, we combined a large, continental-scale data set on low pathogenic, Type A AIV in the United States with a novel network-based application of bird banding/recovery data to investigate the migration-based drivers of AIV and their relative importance compared to well-characterized local drivers (e.g., demography, environmental persistence). We compared among regression models reflecting hypothesized ecological processes and evaluated their ability to predict AIV in space and time using within and out-of-sample validation. We found that predictors of AIV were associated with multiple mechanisms at local and continental scales. Hypotheses characterizing local epidemic dynamics were strongly supported, with age, the age-specific aggregation of migratory birds in an area and temperature being the best predictors of infection. Hypotheses defining larger, network-based features of the migration processes, such as clustering or between-cluster mixing explained less variation but were also supported. Therefore, our results support a role for local processes in driving the continental distribution of AIV.

Integrated vaccination and physical distancing interventions to prevent future COVID-19 waves in Chinese cities

The coronavirus disease 2019 (COVID-19) pandemic has posed substantial challenges to the formulation of preventive interventions, particularly since the effects of physical distancing measures and upcoming vaccines on reducing susceptible social contacts and eventually halting transmission remain unclear. Here, using anonymized mobile geolocation data in China, we devise a mobility-associated social contact index to quantify the impact of both physical distancing and vaccination measures in a unified way. Building on this index, our epidemiological model reveals that vaccination combined with physical distancing can contain resurgences without relying on stay-at-home restrictions, whereas a gradual vaccination process alone cannot achieve this. Further, for cities with medium population density, vaccination can reduce the duration of physical distancing by 36% to 78%, whereas for cities with high population density, infection numbers can be well-controlled through moderate physical distancing. These findings improve our understanding of the joint effects of vaccination and physical distancing with respect to a city's population density and social contact patterns.

Deriving fine-scale models of human mobility from aggregated origin-destination flow data

The spatial dynamics of epidemics are fundamentally affected by patterns of human mobility. Mobile phone call detail records (CDRs) are a rich source of mobility data, and allow semi-mechanistic models of movement to be parameterised even for resource-poor settings. While the gravity model typically reproduces human movement reasonably well at the administrative level spatial scale, past studies suggest that parameter estimates vary with the level of spatial discretisation at which models are fitted. Given that privacy concerns usually preclude public release of very fine-scale movement data, such variation would be problematic for individual-based simulations of epidemic spread parametrised at a fine spatial scale. We therefore present new methods to fit fine-scale mathematical mobility models (here we implement variants of the gravity and radiation models) to spatially aggregated movement data and investigate how model parameter estimates vary with spatial resolution. We use gridded population data at 1km resolution to derive population counts at different spatial scales (down to ∼ 5km grids) and implement mobility models at each scale. Parameters are estimated from administrative-level flow data between overnight locations in Kenya and Namibia derived from CDRs: where the model spatial resolution exceeds that of the mobility data, we compare the flow data between a particular origin and destination with the sum of all model flows between cells that lie within those particular origin and destination administrative units. Clear evidence of over-dispersion supports the use of negative binomial instead of Poisson likelihood for count data with high values. Radiation models use fewer parameters than the gravity model and better predict trips between overnight locations for both considered countries. Results show that estimates for some parameters change between countries and with spatial resolution and highlight how imperfect flow data and spatial population distribution can influence model fit.

The growing use of large-scale individual-based models calls for reliable modelling of human population movement at ever finer scales. Mobility models have at times been fit to fine-scale movement data, such as travel questionnaires and GPS data. However, the restricted size of such datasets make them suboptimal for parametrising large-scale simulations. Larger datasets, such as census commuting data or mobile phone data, pose a different problem in that such datasets are usually made available at a much coarser spatial resolution than required for individual-based simulations. Here we present a straightforward, if computationally intensive, method to obtain fine-scale movement estimates from coarse-scale movement data. We trial the method on movement data from Kenya and Namibia and implement two of the most common mathematical mobility models, the gravity and the radiation models. Our findings confirm previous research that the parameter estimates for the mobility models differ across spatial scales and countries. We also investigate how population spatial distribution and the characteristics of the flow datasets influence parameter estimates.

Forecasting influenza activity using machine-learned mobility map

Human mobility is a primary driver of infectious disease spread. However, existing data is limited in availability, coverage, granularity, and timeliness. Data-driven forecasts of disease dynamics are crucial for decision-making by health officials and private citizens alike. In this work, we focus on a machine-learned anonymized mobility map (hereon referred to as AMM) aggregated over hundreds of millions of smartphones and evaluate its utility in forecasting epidemics. We factor AMM into a metapopulation model to retrospectively forecast influenza in the USA and Australia. We show that the AMM model performs on-par with those based on commuter surveys, which are sparsely available and expensive. We also compare it with gravity and radiation based models of mobility, and find that the radiation model’s performance is quite similar to AMM and commuter flows. Additionally, we demonstrate our model’s ability to predict disease spread even across state boundaries. Our work contributes towards developing timely infectious disease forecasting at a global scale using human mobility datasets expanding their applications in the area of infectious disease epidemiology.

Human mobility plays a central role in the spread of infectious diseases and can help in forecasting incidence. Here the authors show a comparison of multiple mobility benchmarks in forecasting influenza, and demonstrate the value of a machine-learned mobility map with global coverage at multiple spatial scales.

Attitudes Toward a Proposed GPS-Based Location Tracking Smartphone App for Improving Engagement in HIV Care Among Pregnant and Postpartum Women in South Africa: Focus Group and Interview Study

Background

Peripartum women living with HIV in South Africa are at high risk of dropping out of care and are also a particularly mobile population, which may impact their engagement in HIV care. With the rise in mobile phone use worldwide, there is an opportunity to use smartphones and GPS location software to characterize mobility in real time.

Objective

The aim of this study was to propose a smartphone app that could collect individual GPS locations to improve engagement in HIV care and to assess potential users’ attitudes toward the proposed app.

Methods

We conducted 50 in-depth interviews (IDIs) with pregnant women living with HIV in Cape Town and Johannesburg, South Africa, and 6 focus group discussions (FGDs) with 27 postpartum women living with HIV in Cape Town. Through an open-ended question in the IDIs, we categorized “positive,” “neutral,” or “negative” reactions to the proposed app and identified key quotations. For the FGD data, we grouped the text into themes, then analyzed it for patterns, concepts, and associations and selected illustrative quotations.

Results

In the IDIs, the majority of participants (76%, 38/50) responded favorably to the proposed app. Favorable comments were related to the convenience of facilitated continued care, a sense of helpfulness on the part of the researchers and facilities, and the difficulties of trying to maintain care while traveling. Among the 4/50 participants (8%) who responded negatively, their comments were primarily related to the individual’s responsibility for their own health care. The FGDs revealed four themes: facilitating connection to care, informed choice, disclosure (intentional or unintentional), and trust in researchers.

Conclusions

Women living with HIV were overwhelmingly positive about the idea of a GPS-based smartphone app to improve engagement in HIV care. Participants reported that they would welcome a tool to facilitate connection to care when traveling and expressed trust in researchers and health care facilities. Within the context of the rapid increase of smartphone use in South Africa, these early results warrant further exploration and critical evaluation following real-world experience with the app.

Effects of COVID-19 government travel restrictions on mobility in a rural border area of Northern Thailand: A mobile phone tracking study

BACKGROUND

Thailand is among the top five countries with effective COVID-19 transmission control. This study examines how news of presence of COVID-19 in Thailand, as well as varying levels of government restriction on movement, affected human mobility in a rural Thai population along the border with Myanmar.

METHODS

This study makes use of mobility data collected using a smartphone app. Between November 2019 and June 2020, four major events concerning information dissemination or government intervention give rise to five time intervals of analysis. Radius of gyration is used to analyze movement in each interval, and movement during government-imposed curfew. Human mobility network visualization is used to identify changes in travel patterns between main geographic locations of activity. Cross-border mobility analysis highlights potential for intervillage and intercountry disease transmission.

RESULTS

Inter-village and cross-border movement was common in the pre-COVID-19 period. Radius of gyration and cross-border trips decreased following news of the first imported cases. During the government lockdown period, radius of gyration was reduced by more than 90% and cross-border movement was mostly limited to short-distance trips. Human mobility was nearly back to normal after relaxation of the lockdown.

CONCLUSIONS

This study provides insight into the impact of the government lockdown policy on an area with extremely low socio-economic status, poor healthcare resources, and highly active cross-border movement. The lockdown had a great impact on reducing individual mobility, including cross-border movement. The quick return to normal mobility after relaxation of the lockdown implies that close monitoring of disease should be continued to prevent a second wave.

Achieving global malaria eradication in changing landscapes

Land use and land cover changes, such as deforestation, agricultural expansion and urbanization, are one of the largest anthropogenic environmental changes globally. Recent initiatives to evaluate the feasibility of malaria eradication have highlighted impacts of landscape changes on malaria transmission and the potential of these changes to undermine malaria control and elimination efforts. Multisectoral approaches are needed to detect and minimize negative impacts of land use and land cover changes on malaria transmission while supporting development aiding malaria control, elimination and ultimately eradication. Pathways through which land use and land cover changes disrupt social and ecological systems to increase or decrease malaria risks are outlined, identifying priorities and opportunities for a global malaria eradication campaign. The impacts of land use and land cover changes on malaria transmission are complex and highly context-specific, with effects changing over time and space. Landscape changes are only one element of a complex development process with wider economic and social dimensions affecting human health and wellbeing. While deforestation and other landscape changes threaten to undermine malaria control efforts and have driven the emergence of zoonotic malaria, most of the malaria elimination successes have been underpinned by agricultural development and land management. Malaria eradication is not feasible without addressing these changing risks while, conversely, consideration of malaria impacts in land management decisions has the potential to significantly accelerate progress towards eradication. Multisectoral cooperation and approaches to linking malaria control and environmental science, such as conducting locally relevant ecological monitoring, integrating landscape data into malaria surveillance systems and designing environmental management strategies to reduce malaria burdens, are essential to achieve malaria eradication.

The association of mode of location activity and mobility with acute coronary syndrome: a nationwide ecological study

BACKGROUND

We aimed to study the effect of social containment mandates on ACS presentation during COVID-19 pandemic using location activity and mobility data from mobile phone map services.

METHODS

We conducted a cross-sectional study using data from the Swedish Coronary Angiography and Angioplasty Registry (SCAAR) including all ACS presentations during the pandemic until 7 May 2020. Using a count regression model, we adjusted for day of the week, daily weather and incidence of COVID-19.

RESULTS

A 10% increase in activity around areas of residence was associated with 38% lower rates of ACS hospitalizations, whereas increased activity relating to retail and recreation, grocery stores and pharmacies, workplaces and mode of mobility was associated with 10-20% higher rates of ACS hospitalizations.

CONCLUSION

Government policy regarding social containment mandates has important public health implications for medical emergencies such as ACS and may explain the decline in ACS presentations observed during COVID-19 pandemic.

Malaria in Southern Venezuela: The hottest hotspot in Latin America

Malaria elimination in Latin America is becoming an elusive goal. Malaria cases reached a historical ~1 million in 2017 and 2018, with Venezuela contributing 53% and 51% of those cases, respectively. Historically, malaria incidence in southern Venezuela has accounted for most of the country's total number of cases. The efficient deployment of disease prevention measures and prediction of disease spread to new regions requires an in-depth understanding of spatial heterogeneity on malaria transmission dynamics. Herein, we characterized the spatial epidemiology of malaria in southern Venezuela from 2007 through 2017 and described the extent to which malaria distribution has changed country-wide over the recent years. We found that disease transmission was focal and more prevalent in the southeast region of southern Venezuela where two persistent hotspots of Plasmodium vivax (76%) and P. falciparum (18%) accounted for ~60% of the total number of cases. Such hotspots are linked to deforestation as a consequence of illegal gold mining activities. Incidence has increased nearly tenfold over the last decade, showing an explosive epidemic growth due to a significant lack of disease control programs. Our findings highlight the importance of spatially oriented interventions to contain the ongoing malaria epidemic in Venezuela. This work also provides baseline epidemiological data to assess cross-border malaria dynamics and advocates for innovative control efforts in the Latin American region.

Satellite images and machine learning can identify remote communities to facilitate access to health services

OBJECTIVE

Community health systems operating in remote areas require accurate information about where people live to efficiently provide services across large regions. We sought to determine whether a machine learning analyses of satellite imagery can be used to map remote communities to facilitate service delivery and planning.

MATERIALS AND METHODS

We developed a method for mapping communities using a deep learning approach that excels at detecting objects within images. We trained an algorithm to detect individual buildings, then examined building clusters to identify groupings suggestive of communities. The approach was validated in southeastern Liberia, by comparing algorithmically generated results with community location data collected manually by enumerators and community health workers.

RESULTS

The deep learning approach achieved 86.47% positive predictive value and 79.49% sensitivity with respect to individual building detection. The approach identified 75.67% (n = 451) of communities registered through the community enumeration process, and identified an additional 167 potential communities not previously registered. Several instances of false positives and false negatives were identified.

DISCUSSION

Analysis of satellite images is a promising solution for mapping remote communities rapidly, and with relatively low costs. Further research is needed to determine whether the communities identified algorithmically, but not registered in the manual enumeration process, are currently inhabited.

CONCLUSIONS

To our knowledge, this study represents the first effort to apply image recognition algorithms to rural healthcare delivery. Results suggest that these methods have the potential to enhance community health worker scale-up efforts in underserved remote communities.

Optimizing respiratory virus surveillance networks using uncertainty propagation

Infectious disease prevention, control and forecasting rely on sentinel observations; however, many locations lack the capacity for routine surveillance. Here we show that, by using data from multiple sites collectively, accurate estimation and forecasting of respiratory diseases for locations without surveillance is feasible. We develop a framework to optimize surveillance sites that suppresses uncertainty propagation in a networked disease transmission model. Using influenza outbreaks from 35 US states, the optimized system generates better near-term predictions than alternate systems designed using population and human mobility. We also find that monitoring regional population centers serves as a reasonable proxy for the optimized network and could direct surveillance for diseases with limited records. The  proxy method is validated using model simulations for 3,108 US counties and historical data for two other respiratory pathogens - human metapneumovirus and seasonal coronavirus - from 35 US states and can be used to guide systemic allocation of surveillance efforts.

Accessing the syndemic of COVID-19 and malaria intervention in Africa

BACKGROUND

The pandemic of the coronavirus disease 2019 (COVID-19) has caused substantial disruptions to health services in the low and middle-income countries with a high burden of other diseases, such as malaria in sub-Saharan Africa. The aim of this study is to assess the impact of COVID-19 pandemic on malaria transmission potential in malaria-endemic countries in Africa.

METHODS

We present a data-driven method to quantify the extent to which the COVID-19 pandemic, as well as various non-pharmaceutical interventions (NPIs), could lead to the change of malaria transmission potential in 2020. First, we adopt a particle Markov Chain Monte Carlo method to estimate epidemiological parameters in each country by fitting the time series of the cumulative number of reported COVID-19 cases. Then, we simulate the epidemic dynamics of COVID-19 under two groups of NPIs: (1) contact restriction and social distancing, and (2) early identification and isolation of cases. Based on the simulated epidemic curves, we quantify the impact of COVID-19 epidemic and NPIs on the distribution of insecticide-treated nets (ITNs). Finally, by treating the total number of ITNs available in each country in 2020, we evaluate the negative effects of COVID-19 pandemic on malaria transmission potential based on the notion of vectorial capacity.

RESULTS

We conduct case studies in four malaria-endemic countries, Ethiopia, Nigeria, Tanzania, and Zambia, in Africa. The epidemiological parameters (i.e., the basic reproduction number [Formula: see text] and the duration of infection [Formula: see text]) of COVID-19 in each country are estimated as follows: Ethiopia ([Formula: see text], [Formula: see text]), Nigeria ([Formula: see text], [Formula: see text]), Tanzania ([Formula: see text], [Formula: see text]), and Zambia ([Formula: see text], [Formula: see text]). Based on the estimated epidemiological parameters, the epidemic curves simulated under various NPIs indicated that the earlier the interventions are implemented, the better the epidemic is controlled. Moreover, the effect of combined NPIs is better than contact restriction and social distancing only. By treating the total number of ITNs available in each country in 2020 as a baseline, our results show that even with stringent NPIs, malaria transmission potential will remain higher than expected in the second half of 2020.

CONCLUSIONS

By quantifying the impact of various NPI response to the COVID-19 pandemic on malaria transmission potential, this study provides a way to jointly address the syndemic between COVID-19 and malaria in malaria-endemic countries in Africa. The results suggest that the early intervention of COVID-19 can effectively reduce the scale of the epidemic and mitigate its impact on malaria transmission potential.

Modelling Representative Population Mobility for COVID-19 Spatial Transmission in South Africa

The COVID-19 pandemic starting in the first half of 2020 has changed the lives of everyone across the world. Reduced mobility was essential due to it being the largest impact possible against the spread of the little understood SARS-CoV-2 virus. To understand the spread, a comprehension of human mobility patterns is needed. The use of mobility data in modelling is thus essential to capture the intrinsic spread through the population. It is necessary to determine to what extent mobility data sources convey the same message of mobility within a region. This paper compares different mobility data sources by constructing spatial weight matrices at a variety of spatial resolutions and further compares the results through hierarchical clustering. We consider four methods for constructing spatial weight matrices representing mobility between spatial units, taking into account distance between spatial units as well as spatial covariates. This provides insight for the user into which data provides what type of information and in what situations a particular data source is most useful.

Disparate patterns of movements and visits to points of interest located in urban hotspots across US metropolitan cities during COVID-19

We examined the effect of social distancing on changes in visits to urban hotspot points of interest. In a pandemic situation, urban hotspots could be potential superspreader areas as visits to urban hotspots can increase the risk of contact and transmission of a disease among a population. We mapped census-block-group to point-of-interest (POI) movement networks in 16 cities in the United States. We adopted a modified coarse-grain approach to examine patterns of visits to POIs among hotspots and non-hotspots from January to May 2020. Also, we conducted chi-square tests to identify POIs with significant flux-in changes during the analysis period. The results showed disparate patterns across cities in terms of reduction in hotspot POI visitors. Sixteen cities were divided into two categories using a time series clustering method. In one category, which includes the cities of San Francisco, Seattle and Chicago, we observed a considerable decrease in hotspot POI visitors, while in another category, including the cities of Austin, Houston and San Diego, the visitors to hotspots did not greatly decrease. While all the cities exhibited overall decreased visitors to POIs, one category maintained the proportion of visitors to hotspot POIs. The proportion of visitors to some POIs (e.g. restaurants) remained stable during the social distancing period, while some POIs had an increased proportion of visitors (e.g. grocery stores). We also identified POIs with significant flux-in changes, indicating that related businesses were greatly affected by social distancing. The study was limited to 16 metropolitan cities in the United States. The proposed methodology could be applied to digital trace data in other cities and countries to study the patterns of movements to POIs during the COVID-19 pandemic.

Monitoring the Spatial Spread of COVID-19 and Effectiveness of Control Measures Through Human Movement Data: Proposal for a Predictive Model Using Big Data Analytics

BACKGROUND

Human movement is one of the forces that drive the spatial spread of infectious diseases. To date, reducing and tracking human movement during the COVID-19 pandemic has proven effective in limiting the spread of the virus. Existing methods for monitoring and modeling the spatial spread of infectious diseases rely on various data sources as proxies of human movement, such as airline travel data, mobile phone data, and banknote tracking. However, intrinsic limitations of these data sources prevent us from systematic monitoring and analyses of human movement on different spatial scales (from local to global).

OBJECTIVE

Big data from social media such as geotagged tweets have been widely used in human mobility studies, yet more research is needed to validate the capabilities and limitations of using such data for studying human movement at different geographic scales (eg, from local to global) in the context of global infectious disease transmission. This study aims to develop a novel data-driven public health approach using big data from Twitter coupled with other human mobility data sources and artificial intelligence to monitor and analyze human movement at different spatial scales (from global to regional to local).

METHODS

We will first develop a database with optimized spatiotemporal indexing to store and manage the multisource data sets collected in this project. This database will be connected to our in-house Hadoop computing cluster for efficient big data computing and analytics. We will then develop innovative data models, predictive models, and computing algorithms to effectively extract and analyze human movement patterns using geotagged big data from Twitter and other human mobility data sources, with the goal of enhancing situational awareness and risk prediction in public health emergency response and disease surveillance systems.

RESULTS

This project was funded as of May 2020. We have started the data collection, processing, and analysis for the project.

CONCLUSIONS

Research findings can help government officials, public health managers, emergency responders, and researchers answer critical questions during the pandemic regarding the current and future infectious risk of a state, county, or community and the effectiveness of social/physical distancing practices in curtailing the spread of the virus.

INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID)

DERR1-10.2196/24432.

Malaria Exposure in Ann Township, Myanmar, as a Function of Land Cover and Land Use: Combining Satellite Earth Observations and Field Surveys

Despite progress toward malaria elimination in the Greater Mekong Subregion, challenges remain owing to the emergence of drug resistance and the persistence of focal transmission reservoirs. Malaria transmission foci in Myanmar are heterogeneous and complex, and many remaining infections are clinically silent, rendering them invisible to routine monitoring. The goal of this research is to define criteria for easy-to-implement methodologies, not reliant on routine monitoring, that can increase the efficiency of targeted malaria elimination strategies. Studies have shown relationships between malaria risk and land cover and land use (LCLU), which can be mapped using remote sensing methodologies. Here we aim to explain malaria risk as a function of LCLU for five rural villages in Myanmar's Rakhine State. Malaria prevalence and incidence data were analyzed through logistic regression with a land use survey of ~1,000 participants and a 30-m land cover map. Malaria prevalence per village ranged from 5% to 20% with the overwhelming majority of cases being subclinical. Villages with high forest cover were associated with increased risk of malaria, even for villagers who did not report visits to forests. Villagers living near croplands experienced decreased malaria risk unless they were directly engaged in farm work. Finally, land cover change (specifically, natural forest loss) appeared to be a substantial contributor to malaria risk in the region, although this was not confirmed through sensitivity analyses. Overall, this study demonstrates that remotely sensed data contextualized with field survey data can be used to inform critical targeting strategies in support of malaria elimination.

Describing the current status of Plasmodium falciparum population structure and drug resistance within mainland Tanzania using molecular inversion probes

High-throughput Plasmodium genomic data is increasingly useful in assessing prevalence of clinically important mutations and malaria transmission patterns. Understanding parasite diversity is important for identification of specific human or parasite populations that can be targeted by control programmes, and to monitor the spread of mutations associated with drug resistance. An up-to-date understanding of regional parasite population dynamics is also critical to monitor the impact of control efforts. However, this data is largely absent from high-burden nations in Africa, and to date, no such analysis has been conducted for malaria parasites in Tanzania countrywide. To this end, over 1,000 P. falciparum clinical isolates were collected in 2017 from 13 sites in seven administrative regions across Tanzania, and parasites were genotyped at 1,800 variable positions genome-wide using molecular inversion probes. Population structure was detectable among Tanzanian P. falciparum parasites, approximately separating parasites from the northern and southern districts and identifying genetically admixed populations in the north. Isolates from nearby districts were more likely to be genetically related compared to parasites sampled from more distant districts. Known drug resistance mutations were seen at increased frequency in northern districts (including two infections carrying pfk13-R561H), and additional variants with undetermined significance for antimalarial resistance also varied by geography. Malaria Indicator Survey (2017) data corresponded with genetic findings, including average region-level complexity-of-infection and malaria prevalence estimates. The parasite populations identified here provide important information on extant spatial patterns of genetic diversity of Tanzanian parasites, to which future surveys of genetic relatedness can be compared.

Quantifying human mobility behaviour changes during the COVID-19 outbreak in the United States

Since the first case of the novel coronavirus disease (COVID-19) was confirmed in Wuhan, China, social distancing has been promoted worldwide, including in the United States, as a major community mitigation strategy. However, our understanding remains limited in how people would react to such control measures, as well as how people would resume their normal behaviours when those orders were relaxed. We utilize an integrated dataset of real-time mobile device location data involving 100 million devices in the contiguous United States (plus Alaska and Hawaii) from February 2, 2020 to May 30, 2020. Built upon the common human mobility metrics, we construct a Social Distancing Index (SDI) to evaluate people's mobility pattern changes along with the spread of COVID-19 at different geographic levels. We find that both government orders and local outbreak severity significantly contribute to the strength of social distancing. As people tend to practice less social distancing immediately after they observe a sign of local mitigation, we identify several states and counties with higher risks of continuous community transmission and a second outbreak. Our proposed index could help policymakers and researchers monitor people's real-time mobility behaviours, understand the influence of government orders, and evaluate the risk of local outbreaks.

Community movement and COVID-19: a global study using Google's Community Mobility Reports

Google's 'Community Mobility Reports' (CMR) detail changes in activity and mobility occurring in response to COVID-19. They thus offer the unique opportunity to examine the relationship between mobility and disease incidence. The objective was to examine whether an association between COVID-19-confirmed case numbers and levels of mobility was apparent, and if so then to examine whether such data enhance disease modelling and prediction. CMR data for countries worldwide were cross-correlated with corresponding COVID-19-confirmed case numbers. Models were fitted to explain case numbers of each country's epidemic. Models using numerical date, contemporaneous and distributed lag CMR data were contrasted using Bayesian Information Criteria. Noticeable were negative correlations between CMR data and case incidence for prominent industrialised countries of Western Europe and the North Americas. Continent-wide examination found a negative correlation for all continents with the exception of South America. When modelling, CMR-expanded models proved superior to the model without CMR. The predictions made with the distributed lag model significantly outperformed all other models. The observed relationship between CMR data and case incidence, and its ability to enhance model quality and prediction suggests data related to community mobility could prove of use in future COVID-19 modelling.

Measuring the contribution of human mobility to malaria persistence

BACKGROUND

To achieve malaria elimination, it is important to determine the role of human mobility in parasite transmission maintenance. The Alto Juruá basin (Brazil) exhibits one of the largest vivax and falciparum malaria prevalence in the Amazon. The goal of this study was to estimate the contribution of human commutes to malaria persistence in this region, using data from an origin-destination survey.

METHODS

Data from an origin-destination survey were used to describe the intensity and motivation for commutations between rural and urban areas in two Alto Juruá basin (Brazil) municipalities, Mâncio Lima and Rodrigues Alves. The relative time-person spent in each locality per household was estimated. A logistic model was developed to estimate the effect of commuting on the probability of contracting malaria for a certain residence zone inhabitant commuting to another zone.

RESULTS

The main results suggest that the assessed population is not very mobile. A total of [Formula: see text] households reported spending over [Formula: see text] of their annual person-hour in areas within the same residence zone. Study and work were the most prevalent commuting motivations, calculated at [Formula: see text] and [Formula: see text] respectively. Spending person-hours in urban Rodrigues Alves conferred relative protection to urban Mâncio Lima residents. The opposite effect was observed for those spending time in rural areas of both municipalities.

CONCLUSION

Residence area is a stronger determinant for contracting malaria than commuting zones in the Alto Juruá region. As these municipalities are a hotspot for Plasmodium transmission, understanding the main local human fluxes is essential for planning control strategies, since the probability of contracting malaria is dependent on the transmission intensity of both the origin and the displacement area. The natural conditions for the circulation of certain pathogens, such as Plasmodium spp., combined with the Amazon human mobility pattern indicate the need for disease control perspective changes. Therefore, intersectoral public policies should become the basis for health mitigation actions.

Better coverage, better outcomes? Mapping mobile network data to official statistics using satellite imagery and radio propagation modelling

Mobile sensing data has become a popular data source for geo-spatial analysis, however, mapping it accurately to other sources of information such as statistical data remains a challenge. Popular mapping approaches such as point allocation or voronoi tessellation provide only crude approximations of the mobile network coverage as they do not consider holes, overlaps and within-cell heterogeneity. More elaborate mapping schemes often require additional proprietary data operators are highly reluctant to share. In this paper, I use human settlement information extracted from publicly available satellite imagery in combination with stochastic radio propagation modelling techniques to account for that. I show in a simulation study and a real-world application on unemployment estimates in Senegal that better coverage approximations do not necessarily lead to better outcome predictions.

Twitter reveals human mobility dynamics during the COVID-19 pandemic

The current COVID-19 pandemic raises concerns worldwide, leading to serious health, economic, and social challenges. The rapid spread of the virus at a global scale highlights the need for a more harmonized, less privacy-concerning, easily accessible approach to monitoring the human mobility that has proven to be associated with viral transmission. In this study, we analyzed over 580 million tweets worldwide to see how global collaborative efforts in reducing human mobility are reflected from the user-generated information at the global, country, and U.S. state scale. Considering the multifaceted nature of mobility, we propose two types of distance: the single-day distance and the cross-day distance. To quantify the responsiveness in certain geographic regions, we further propose a mobility-based responsive index (MRI) that captures the overall degree of mobility changes within a time window. The results suggest that mobility patterns obtained from Twitter data are amenable to quantitatively reflect the mobility dynamics. Globally, the proposed two distances had greatly deviated from their baselines after March 11, 2020, when WHO declared COVID-19 as a pandemic. The considerably less periodicity after the declaration suggests that the protection measures have obviously affected people’s travel routines. The country scale comparisons reveal the discrepancies in responsiveness, evidenced by the contrasting mobility patterns in different epidemic phases. We find that the triggers of mobility changes correspond well with the national announcements of mitigation measures, proving that Twitter-based mobility implies the effectiveness of those measures. In the U.S., the influence of the COVID-19 pandemic on mobility is distinct. However, the impacts vary substantially among states.

Recent Travel History and Plasmodium falciparum Malaria Infection in a Region of Heterogenous Transmission in Southern Province, Zambia

As Zambia continues to reduce its malaria incidence and target elimination in Southern Province, there is a need to identify factors that can reintroduce parasites and sustain malaria transmission. To examine the relative contributions of types of human mobility on malaria prevalence, this analysis quantifies the proportion of the population having recently traveled during both peak and nonpeak transmission seasons over the course of 2 years and assesses the relationship between short-term travel and malaria infection status. Among all residents targeted by mass drug administration in the Lake Kariba region of Southern Province, 602,620 rapid diagnostic tests and recent travel histories were collected during four campaign rounds occurring between December 2014 and February 2016. Rates of short-term travel in the previous 2 weeks fluctuated seasonally from 0.3% to 1.2%. Travel was significantly associated with prevalent malaria infection both seasonally and overall (adjusted odds ratio [AOR]: 2.55; 95% CI: 2.28-2.85). The strength of association between travel and malaria infection varied by travelers' origin and destination, with those recently traveling to high-prevalence areas from low-prevalence areas experiencing the highest odds of malaria infection (AOR: 7.38). Long-lasting insecticidal net usage while traveling was associated with a relative reduction in infections (AOR: 0.74) compared with travelers not using a net. Although travel was directly associated with only a small fraction of infections, importation of malaria via human movement may play an increasingly important role in this elimination setting as transmission rates continue to decline.

Measuring mobility to monitor travel and physical distancing interventions: a common framework for mobile phone data analysis

A surge of interest has been noted in the use of mobility data from mobile phones to monitor physical distancing and model the spread of severe acute respiratory syndrome coronavirus 2, the virus that causes COVID-19. Despite several years of research in this area, standard frameworks for aggregating and making use of different data streams from mobile phones are scarce and difficult to generalise across data providers. Here, we examine aggregation principles and procedures for different mobile phone data streams and describe a common syntax for how aggregated data are used in research and policy. We argue that the principles of privacy and data protection are vital in assessing more technical aspects of aggregation and should be an important central feature to guide partnerships with governments who make use of research products.

Managing the spread of disease with mobile phone data

While human mobility has important benefits for economic growth, it can generate negative externalities. This paper studies the effect of mobility on the spread of disease in a low-incidence setting when people do not internalize their risks to others. Using malaria as a case study and 15 billion mobile phone records across nine million SIM cards, this paper quantifies the relationship between travel and the spread of disease. The estimates indicate that an infected traveler contributes to 1.66 additional cases reported in the health facility at the traveler's destination. This paper develops a simulation-based policy tool that uses mobile phone data to inform strategic targeting of travelers based on their origins and destinations. The simulations suggest that targeting informed by mobile phone data could reduce the caseload by 50 percent more than current strategies that rely only on previous incidence.

Interactive Analysis of Epidemic Situations Based on a Spatiotemporal Information Knowledge Graph of COVID-19

In view of the lack of data association in spatiotemporal information analysis and the lack of spatiotemporal situation analysis in knowledge graphs, this article combines the semantic web of the geographic knowledge graph with the visual analysis model of spatial information and puts forward the comprehensive utilization of the related technologies of the geographic knowledge graph and big data visual analysis. Then, it realizes the situational analysis of COVID-19 (Coronavirus Disease 2019) and the exploration of patient relationships through interactive collaborative analysis. The main contributions of the paper are as follows. (1) Based on the characteristics of the geographic knowledge graph, a patient entity model and an entity relationship type and knowledge representation method are proposed, and a knowledge graph of the spatiotemporal information of COVID-19 is constructed. (2) To analyse the COVID-19 patients' situations and explore their relationships, an analytical framework is designed. The framework, combining the semantic web of the geographic knowledge graph and the visual analysis model of geographic information, allows one to analyse the semantic web by using the node attribute similarity calculation, key stage mining, community prediction and other methods. (3)An efficient epidemic prevention and anti-epidemic method is proposed which is of referential significance. It is based on experiments and the collaborative analysis of the semantic web and spatial information, allowing for real-time situational understanding, the discovery of patients' relationships, the analysis of the spatiotemporal distribution of patients, super spreader mining, key node analysis, and the prevention and control of high-risk groups.

Non-compulsory measures sufficiently reduced human mobility in Tokyo during the COVID-19 epidemic

While large scale mobility data has become a popular tool to monitor the mobility patterns during the COVID-19 pandemic, the impacts of non-compulsory measures in Tokyo, Japan on human mobility patterns has been under-studied. Here, we analyze the temporal changes in human mobility behavior, social contact rates, and their correlations with the transmissibility of COVID-19, using mobility data collected from more than 200K anonymized mobile phone users in Tokyo. The analysis concludes that by April 15th (1 week into state of emergency), human mobility behavior decreased by around 50%, resulting in a 70% reduction of social contacts in Tokyo, showing the strong relationships with non-compulsory measures. Furthermore, the reduction in data-driven human mobility metrics showed correlation with the decrease in estimated effective reproduction number of COVID-19 in Tokyo. Such empirical insights could inform policy makers on deciding sufficient levels of mobility reduction to contain the disease.

A general approach to detecting migration events in digital trace data

Empirical research on migration has historically been fraught with measurement challenges. Recently, the increasing ubiquity of digital trace data-from mobile phones, social media, and related sources of 'big data'-has created new opportunities for the quantitative analysis of migration. However, most existing work relies on relatively ad hoc methods for inferring migration. Here, we develop and validate a novel and general approach to detecting migration events in trace data. We benchmark this method using two different trace datasets: four years of mobile phone metadata from a single country's monopoly operator, and three years of geo-tagged Twitter data. The novel measures more accurately reflect human understanding and evaluation of migration events, and further provide more granular insight into migration spells and types than what are captured in standard survey instruments.

The use of mobile phone data to inform analysis of COVID-19 pandemic epidemiology

The ongoing coronavirus disease 2019 (COVID-19) pandemic has heightened discussion of the use of mobile phone data in outbreak response. Mobile phone data have been proposed to monitor effectiveness of non-pharmaceutical interventions, to assess potential drivers of spatiotemporal spread, and to support contact tracing efforts. While these data may be an important part of COVID-19 response, their use must be considered alongside a careful understanding of the behaviors and populations they capture. Here, we review the different applications for mobile phone data in guiding and evaluating COVID-19 response, the relevance of these applications for infectious disease transmission and control, and potential sources and implications of selection bias in mobile phone data. We also discuss best practices and potential pitfalls for directly integrating the collection, analysis, and interpretation of these data into public health decision making.

The duration of travel impacts the spatial dynamics of infectious diseases

Humans can impact the spatial transmission dynamics of infectious diseases by introducing pathogens into susceptible environments. The rate at which this occurs depends in part on human-mobility patterns. Increasingly, mobile-phone usage data are used to quantify human mobility and investigate the impact on disease dynamics. Although the number of trips between locations and the duration of those trips could both affect infectious-disease dynamics, there has been limited work to quantify and model the duration of travel in the context of disease transmission. Using mobility data inferred from mobile-phone calling records in Namibia, we calculated both the number of trips between districts and the duration of these trips from 2010 to 2014. We fit hierarchical Bayesian models to these data to describe both the mean trip number and duration. Results indicate that trip duration is positively related to trip distance, but negatively related to the destination population density. The highest volume of trips and shortest trip durations were among high-density districts, whereas trips among low-density districts had lower volume with longer duration. We also analyzed the impact of including trip duration in spatial-transmission models for a range of pathogens and introduction locations. We found that inclusion of trip duration generally delays the rate of introduction, regardless of pathogen, and that the variance and uncertainty around spatial spread increases proportionally with pathogen-generation time. These results enhance our understanding of disease-dispersal dynamics driven by human mobility, which has potential to elucidate optimal spatial and temporal scales for epidemic interventions.

City-Scale Dark Fiber DAS Measurements of Infrastructure Use During the COVID-19 Pandemic

Throughout the recent COVID-19 pandemic, real-time measurements about shifting use of roads, hospitals, grocery stores, and other public infrastructure became vital for government decision makers. Mobile phone locations are increasingly assimilated for this purpose, but an alternative, unexplored, natively anonymous, absolute method would be to use geophysical sensing to directly measure public infrastructure usage. In this paper, we demonstrate how fiber-optic distributed acoustic sensing (DAS) connected to a telecommunication cable beneath Palo Alto, CA, successfully monitored traffic over a 2-month period, including major reductions associated with COVID-19 response. Continuous DAS recordings of over 450,000 individual vehicles were analyzed using an automatic template-matching detection algorithm based on roadbed strain. In one commuter sector, we found a 50% decrease in vehicles immediately following the order, but near Stanford Hospital, the traffic persisted. The DAS measurements correlate with mobile phone locations and urban seismic noise levels, suggesting geophysics would complement future digital city sensing systems.

Feasibility study of mitigation and suppression strategies for controlling COVID-19 outbreaks in London and Wuhan

Recent outbreaks of coronavirus disease 2019 (COVID-19) has led a global pandemic cross the world. Most countries took two main interventions: suppression like immediate lockdown cities at epicenter or mitigation that slows down but not stopping epidemic for reducing peak healthcare demand. Both strategies have their apparent merits and limitations; it becomes extremely hard to conduct one intervention as the most feasible way to all countries. Targeting at this problem, this paper conducted a feasibility study by defining a mathematical model named SEMCR, it extended traditional SEIR (Susceptible-Exposed-Infectious-Recovered) model by adding two key features: a direct connection between Exposed and Recovered populations, and separating infections into mild and critical cases. It defined parameters to classify two stages of COVID-19 control: active contain by isolation of cases and contacts, passive contain by suppression or mitigation. The model was fitted and evaluated with public dataset containing daily number of confirmed active cases including Wuhan and London during January 2020 and March 2020. The simulated results showed that 1) Immediate suppression taken in Wuhan significantly reduced the total exposed and infectious populations, but it has to be consistently maintained at least 90 days (by the middle of April 2020). Without taking this intervention, we predict the number of infections would have been 73 folders higher by the middle of April 2020. Its success requires efficient government initiatives and effective collaborative governance for mobilizing of corporate resources to provide essential goods. This mode may be not suitable to other countries without efficient collaborative governance and sufficient health resources. 2) In London, it is possible to take a hybrid intervention of suppression and mitigation for every 2 or 3 weeks over a longer period to balance the total infections and economic loss. While the total infectious populations in this scenario would be possibly 2 times than the one taking suppression, economic loss and recovery of London would be less affected. 3) Both in Wuhan and London cases, one important issue of fitting practical data was that there were a portion (probably 62.9% in Wuhan) of self-recovered populations that were asymptomatic or mild symptomatic. This finding has been recently confirmed by other studies that the seroprevalence in Wuhan varied between 3.2% and 3.8% in different sub-regions. It highlights that the epidemic is far from coming to an end by means of herd immunity. Early release of intervention intensity potentially increased a risk of the second outbreak.

Effects of human mobility restrictions on the spread of COVID-19 in Shenzhen, China: a modelling study using mobile phone data

Background

Restricting human mobility is an effective strategy used to control disease spread. However, whether mobility restriction is a proportional response to control the ongoing COVID-19 pandemic is unclear. We aimed to develop a model that can quantify the potential effects of various intracity mobility restrictions on the spread of COVID-19.

Methods

In this modelling study, we used anonymous and aggregated mobile phone sightings data to build a susceptible-exposed-infectious-recovered transmission model for COVID-19 based on the city of Shenzhen, China. We simulated how disease spread changed when we varied the type and magnitude of mobility restrictions in different transmission scenarios, with variables such as the basic reproductive number (R 0), length of infectious period, and the number of initial cases.

Findings

331 COVID-19 cases distributed across the ten regions of Shenzhen were reported on Feb 7, 2020. In our basic scenario (R 0 of 2·68), mobility reduction of 20-60% within the city had a notable effect on controlling COVID-19 spread: a flattening of the peak number of cases by 33% (95% UI 21-42) and delay to the peak number by 2 weeks with a 20% restriction, 66% (48-75) reduction and 4 week delay with a 40% restriction, and 91% (79-95) reduction and 14 week delay with a 60% restriction. The effects of mobility restriction were increased when combined with reductions of 25% or 50% in transmissibility of the virus. In specific analyses of mobility restrictions for individuals with symptomatic infections and for high-risk regions, these measures also had substantial effects on reducing the spread of COVID-19. For example, the peak of the epidemic was delayed by 2 weeks if the proportion of individuals with symptomatic infections who could move freely was maintained at 20%, and by 4 weeks if two high-risk regions were locked down. The simulation results were also affected by various transmission parameters.

Interpretation

Our model shows the effects of various types and magnitudes of mobility restrictions on controlling COVID-19 outbreaks at the city level in Shenzhen, China. The model could help policy makers to establish the optimal combinations of mobility restrictions during the COVID-19 pandemic, especially to assess the potential positive effects of mobility restriction on public health in view of the potential negative economic and societal effects.

Funding

Guangdong Medical Science Fund, and National Natural Science Foundation of China.

Health services uptake among nomadic pastoralist populations in Africa: A systematic review of the literature

The estimated 50 million nomadic pastoralists in Africa are among the most "hard-to-reach" populations for health-service delivery. While data are limited, some studies have identified these communities as potential disease reservoirs relevant to neglected tropical disease programs, particularly those slated for elimination and eradication. Although previous literature has emphasized the role of these populations' mobility, the full range of factors influencing health service utilization has not been examined systematically. We systematically reviewed empirical literature on health services uptake among African nomadic pastoralists from seven online journal databases. Papers meeting inclusion criteria were reviewed using STROBE- and PRISMA-derived guidelines. Study characteristics were summarized quantitatively, and 10 key themes were identified through inductive qualitative coding. One-hundred two papers published between 1974-2019 presenting data from 16 African countries met our inclusion criteria. Among the indicators of study-reporting quality, limitations (37%) and data analysis were most frequently omitted (18%). We identified supply- and demand-side influences on health services uptake that related to geographic access (79%); service quality (90%); disease-specific knowledge and awareness of health services (59%); patient costs (35%); contextual tailoring of interventions (75%); social structure and gender (50%); subjects' beliefs, behaviors, and attitudes (43%); political will (14%); social, political, and armed conflict (30%); and community agency (10%). A range of context-specific factors beyond distance to facilities or population mobility affects health service uptake. Approaches tailored to the nomadic pastoralist lifeway, e.g., that integrated human and veterinary health service delivery (a.k.a., "One Health") and initiatives that engaged communities in program design to address social structures were especially promising. Better causal theorization, transdisciplinary and participatory research methods, clearer operational definitions and improved measurement of nomadic pastoralism, and key factors influencing uptake, will improve our understanding of how to increase accessibility, acceptability, quality and equity of health services to nomadic pastoralist populations.

Inference and prediction of malaria transmission dynamics using time series data

BACKGROUND

Disease surveillance systems are essential for effective disease intervention and control by monitoring disease prevalence as time series. To evaluate the severity of an epidemic, statistical methods are widely used to forecast the trend, seasonality, and the possible number of infections of a disease. However, most statistical methods are limited in revealing the underlying dynamics of disease transmission, which may be affected by various impact factors, such as environmental, meteorological, and physiological factors. In this study, we focus on investigating malaria transmission dynamics based on time series data.

METHODS

A data-driven nonlinear stochastic model is proposed to infer and predict the dynamics of malaria transmission based on the time series of prevalence data. Specifically, the dynamics of malaria transmission is modeled based on the notion of vectorial capacity (VCAP) and entomological inoculation rate (EIR). A particle Markov chain Monte Carlo (PMCMC) method is employed to estimate the model parameters. Accordingly, a one-step-ahead prediction method is proposed to project the number of future malaria infections. Finally, two case studies are carried out on the inference and prediction of Plasmodium vivax transmission in Tengchong and Longling, Yunnan province, China.

RESULTS

The results show that the trained data-driven stochastic model can well fit the historical time series of P. vivax prevalence data in both counties from 2007 to 2010. Moreover, with well-trained model parameters, the proposed one-step-ahead prediction method can achieve better performances than that of the seasonal autoregressive integrated moving average model with respect to predicting the number of future malaria infections.

CONCLUSIONS

By involving dynamically changing impact factors, the proposed data-driven model together with the PMCMC method can successfully (i) depict the dynamics of malaria transmission, and (ii) achieve accurate one-step-ahead prediction about malaria infections. Such a data-driven method has the potential to investigate malaria transmission dynamics in other malaria-endemic countries/regions.

Impact of Intermittent Mass Testing and Treatment on Incidence of Malaria Infection in a High Transmission Area of Western Kenya

Progress with malaria control in western Kenya has stagnated since 2007. Additional interventions to reduce the high burden of malaria in this region are urgently needed. We conducted a two-arm, community-based, cluster-randomized, controlled trial of active case detection and treatment of malaria infections in all residents mass testing and treatment (MTaT) of 10 village clusters (intervention clusters) for two consecutive years to measure differences in the incidence of clinical malaria disease and malaria infections compared with 20 control clusters where MTaT was not implemented. All residents of intervention clusters, irrespective of history of fever or other malaria-related symptoms, were tested three times per year before the peak malaria season using malaria rapid diagnostic tests. All positive cases were treated with dihydroartemisinin-piperaquine. The incidence of clinical malaria was measured through passive surveillance, whereas the cumulative incidence of malaria infection was measured using active surveillance in a cohort comprising randomly selected residents. The incidence of clinical malaria was 0.19 cases/person-year (p-y, 95% CI: 0.13-0.28) in the intervention arm and 0.24 cases/p-y (95% CI: 0.15-0.39) in the control arm (incidence rate ratio [IRR] 0.79, 95% CI: 0.61-1.02). The cumulative incidence of malaria infections was similar between the intervention (2.08 infections/p-y, 95% CI: 1.93-2.26) and control arms (2.19 infections/p-y, 95% CI: 2.02-2.37) with a crude IRR of 0.95 (95% CI: 0.87-1.04). Six rounds of MTaT over 2 years did not have a significant impact on the incidence of clinical malaria or the cumulative incidence of malaria infection in this area of high malaria transmission.

Population structure across scales facilitates coexistence and spatial heterogeneity of antibiotic-resistant infections

Antibiotic-resistant infections are a growing threat to human health, but basic features of the eco-evolutionary dynamics remain unexplained. Most prominently, there is no clear mechanism for the long-term coexistence of both drug-sensitive and resistant strains at intermediate levels, a ubiquitous pattern seen in surveillance data. Here we show that accounting for structured or spatially-heterogeneous host populations and variability in antibiotic consumption can lead to persistent coexistence over a wide range of treatment coverages, drug efficacies, costs of resistance, and mixing patterns. Moreover, this mechanism can explain other puzzling spatiotemporal features of drug-resistance epidemiology that have received less attention, such as large differences in the prevalence of resistance between geographical regions with similar antibiotic consumption or that neighbor one another. We find that the same amount of antibiotic use can lead to very different levels of resistance depending on how treatment is distributed in a transmission network. We also identify parameter regimes in which population structure alone cannot support coexistence, suggesting the need for other mechanisms to explain the epidemiology of antibiotic resistance. Our analysis identifies key features of host population structure that can be used to assess resistance risk and highlights the need to include spatial or demographic heterogeneity in models to guide resistance management.

COVID-19 is spatial: Ensuring that mobile Big Data is used for social good

The mobility restrictions related to COVID-19 pandemic have resulted in the biggest disruption to individual mobilities in modern times. The crisis is clearly spatial in nature, and examining the geographical aspect is important in understanding the broad implications of the pandemic. The avalanche of mobile Big Data makes it possible to study the spatial effects of the crisis with spatiotemporal detail at the national and global scales. However, the current crisis also highlights serious limitations in the readiness to take the advantage of mobile Big Data for social good, both within and beyond the interests of health sector. We propose two strategical pathways for the future use of mobile Big Data for societal impact assessment, addressing access to both raw mobile Big Data as well as aggregated data products. Both pathways require careful considerations of privacy issues, harmonized and transparent methodologies, and attention to the representativeness, reliability and continuity of data. The goal is to be better prepared to use mobile Big Data in future crises.

Rapid Multi-Dimensional Impact Assessment of Floods

Natural disasters affect hundreds of millions of people worldwide every year. The impact assessment of a disaster is key to improve the response and mitigate how a natural hazard turns into a social disaster. An actionable quantification of impact must be integratively multi-dimensional. We propose a rapid impact assessment framework that comprises detailed geographical and temporal landmarks as well as the potential socio-economic magnitude of the disaster based on heterogeneous data sources: Environment sensor data, social media, remote sensing, digital topography, and mobile phone data. As dynamics of floods greatly vary depending on their causes, the framework may support different phases of decision-making during the disaster management cycle. To evaluate its usability and scope, we explored four flooding cases with variable conditions. The results show that social media proxies provide a robust identification with daily granularity even when rainfall detectors fail. The detection also provides information of the magnitude of the flood, which is potentially useful for planning. Network analysis was applied to the social media to extract patterns of social effects after the flood. This analysis showed significant variability in the obtained proxies, which encourages the scaling of schemes to comparatively characterize patterns across many floods with different contexts and cultural factors. This framework is presented as a module of a larger data-driven system designed to be the basis for responsive and more resilient systems in urban and rural areas. The impact-driven approach presented may facilitate public–private collaboration and data sharing by providing real-time evidence with aggregated data to support the requests of private data with higher granularity, which is the current most important limitation in implementing fully data-driven systems for disaster response from both local and international actors.

An investigation of transmission control measures during the first 50 days of the COVID-19 epidemic in China

Responding to an outbreak of a novel coronavirus [agent of coronavirus disease 2019 (COVID-19)] in December 2019, China banned travel to and from Wuhan city on 23 January 2020 and implemented a national emergency response. We investigated the spread and control of COVID-19 using a data set that included case reports, human movement, and public health interventions. The Wuhan shutdown was associated with the delayed arrival of COVID-19 in other cities by 2.91 days. Cities that implemented control measures preemptively reported fewer cases on average (13.0) in the first week of their outbreaks compared with cities that started control later (20.6). Suspending intracity public transport, closing entertainment venues, and banning public gatherings were associated with reductions in case incidence. The national emergency response appears to have delayed the growth and limited the size of the COVID-19 epidemic in China, averting hundreds of thousands of cases by 19 February (day 50).