Human mobility and the spatial transmission of influenza in the United States

What Heterogeneities in Individual-level Mobility Are Lost During Aggregation? Leveraging GPS Logger Data to Understand Fine-scale and Aggregated Patterns of Mobility

Human movement drives spatial transmission patterns of infectious diseases. Population-level mobility patterns are often quantified using aggregated data sets, such as census migration surveys or mobile phone data. These data are often unable to quantify individual-level travel patterns and lack the information needed to discern how mobility varies by demographic groups. Individual-level datasets can capture additional, more precise, aspects of mobility that may impact disease risk or transmission patterns and determine how mobility differs across cohorts; however, these data are rare, particularly in locations such as sub-Saharan Africa. Using detailed GPS logger data collected from three sites in southern Africa, we explore metrics of mobility such as percent time spent outside home, number of locations visited, distance of locations, and time spent at locations to determine whether they vary by demographic, geographic, or temporal factors. We further create a composite mobility score to identify how well aggregated summary measures would capture the full extent of mobility patterns. Although sites had significant differences in all mobility metrics, no site had the highest mobility for every metric, a distinction that was not captured by the composite mobility score. Further, the effects of sex, age, and season on mobility were all dependent on site. No factor significantly influenced the number of trips to locations, a common way to aggregate datasets. When collecting and analyzing human mobility data, it is difficult to account for all the nuances; however, these analyses can help determine which metrics are most helpful and what underlying differences may be present.

Fine scale human mobility changes in 26 US cities in 2020 in response to the COVID-19 pandemic were associated with distance and income

Human mobility patterns changed greatly due to the COVID-19 pandemic. Despite many analyses investigating general mobility trends, there has been less work characterising changes in mobility on a fine spatial scale and developing frameworks to model these changes. We analyse zip code-level mobility data from 26 US cities between February 2 â€" August 31, 2020. We use Bayesian models to characterise the initial decrease in mobility and mobility patterns between June - August at this fine spatial scale. There were similar temporal trends across cities but large variations in the magnitude of mobility reductions. Long-distance routes and higher-income subscribers, but not age, were associated with greater mobility reductions. At the city level, mobility rates around early April, when mobility was lowest, and over summer showed little association with non-pharmaceutical interventions or case rates. Changes in mobility patterns lasted until the end of the study period, despite overall numbers of trips recovering to near baseline levels in many cities.

Transmission Patterns of Seasonal Influenza in China between 2010 and 2018

Background Understanding the transmission source, pattern, and mechanism of infectious diseases is essential for targeted prevention and control. Though it has been studied for many years, the detailed transmission patterns and drivers for the seasonal influenza epidemics in China remain elusive. Methods In this study, utilizing a suite of epidemiological and genetic approaches, we analyzed the updated province-level weekly influenza surveillance, sequence, climate, and demographic data between 1 April 2010 and 31 March 2018 from continental China, to characterize detailed transmission patterns and explore the potential initiating region and drivers of the seasonal influenza epidemics in China. Results An annual cycle for influenza A(H1N1)pdm09 and B and a semi-annual cycle for influenza A(H3N2) were confirmed. Overall, the seasonal influenza A(H3N2) virus caused more infection in China and dominated the summer season in the south. The summer season epidemics in southern China were likely initiated in the “Lingnan” region, which includes the three most southern provinces of Hainan, Guangxi, and Guangdong. Additionally, the regions in the south play more important seeding roles in maintaining the circulation of seasonal influenza in China. Though intense human mobility plays a role in the province-level transmission of influenza epidemics on a temporal scale, climate factors drive the spread of influenza epidemics on both the spatial and temporal scales. Conclusion The surveillance of seasonal influenza in the south, especially the “Lingnan” region in the summer, should be strengthened. More broadly, both the socioeconomic and climate factors contribute to the transmission of seasonal influenza in China. The patterns and mechanisms revealed in this study shed light on the precise forecasting, prevention, and control of seasonal influenza in China and worldwide.

Urban mobility patterns and the spatial distribution of infections in Santiago de Chile

The process of a virus spread is inherently spatial. Even though Latin America became the epicenter of the COVID-19 pandemic in May 2020, there is still little evidence of the relationship between urban mobility and virus propagation in the region. This paper combines network analysis of mobility patterns in public transportation with a spatial error correction model for Santiago de Chile. Results indicate that a 10% higher number of daily public transportation trips received by an administrative unit in the city was associated with a 1.3% higher number of confirmed COVID-19 cases per 100,000 inhabitants. Following these findings, we propose an empirical method to identify and classify neighborhoods according to the level and type of risk for COVID-19-like disease propagation, helping policymakers manage mobility during the initial stages of an epidemic outbreak.

Possibility of the COVID-19 third wave in India: mapping from second wave to third wave

After a consistent drop in daily new coronavirus cases during the second wave of COVID-19 in India, there is speculation about the possibility of a future third wave of the virus. The pandemic is returning in different waves; therefore, it is necessary to determine the factors or conditions at the initial stage under which a severe third wave could occur. Therefore, first, we examine the effect of related multi-source data, including social mobility patterns, meteorological indicators, and air pollutants, on the COVID-19 cases during the initial phase of the second wave so as to predict the plausibility of the third wave. Next, based on the multi-source data, we proposed a simple short-term fixed-effect multiple regression model to predict daily confirmed cases. The study area findings suggest that the coronavirus dissemination can be well explained by social mobility. Furthermore, compared with benchmark models, the proposed model improves prediction R 2 by 33.6%, 10.8%, 27.4%, and 19.8% for Maharashtra, Kerala, Karnataka, and Tamil Nadu, respectively. Thus, the simplicity and interpretability of the model are a meaningful contribution to determining the possibility of upcoming waves and direct pandemic prevention and control decisions at a local level in India.

Days of Flooding Associated with Increased Risk of Influenza

Influenza typically causes mild infection but can lead to severe outcomes for those with compromised lung health. Flooding, a seasonal problem in Iowa, can expose many Iowans to molds and allergens shown to alter lung inflammation, leading to asthma attacks and decreased viral clearance. Based on this, the hypothesis for this research was that there would be geographically specific positive associations in locations with flooding with influenza diagnosis. An ecological study was performed using influenza diagnoses and positive influenza polymerase chain reaction tests from a de-identified large private insurance database and Iowa State Hygienic Lab. After adjustment for multiple confounding factors, Poisson regression analysis resulted in a consistent 1% associated increase in influenza diagnoses per day above flood stage (95% confidence interval: 1.00–1.04). This relationship remained after removal of the 2009–2010 influenza pandemic year. There was no associated risk between flooding and influenza-like illness as a nonspecific diagnosis. Associated risks between flooding and increased influenza diagnoses were geographically specific, with the greatest risk in the most densely populated areas. This study indicates that populations who live, work, or volunteer in flooded environments should consider preventative measures to avoid environmental exposures to mitigate illness from influenza in the following year.

Urban Scaling of Health Outcomes: a Scoping Review

Urban scaling is a framework that describes how city-level characteristics scale with variations in city size. This scoping review mapped the existing evidence on the urban scaling of health outcomes to identify gaps and inform future research. Using a structured search strategy, we identified and reviewed a total of 102 studies, a majority set in high-income countries using diverse city definitions. We found several historical studies that examined the dynamic relationships between city size and mortality occurring during the nineteenth and early twentieth centuries. In more recent years, we documented heterogeneity in the relation between city size and health. Measles and influenza are influenced by city size in conjunction with other factors like geographic proximity, while STIs, HIV, and dengue tend to occur more frequently in larger cities. NCDs showed a heterogeneous pattern that depends on the specific outcome and context. Homicides and other crimes are more common in larger cities, suicides are more common in smaller cities, and traffic-related injuries show a less clear pattern that differs by context and type of injury. Future research should aim to understand the consequences of urban growth on health outcomes in low- and middle-income countries, capitalize on longitudinal designs, systematically adjust for covariates, and examine the implications of using different city definitions.

Evaluating the effectiveness of Hong Kong's border restriction policy in reducing COVID-19 infections

This study evaluates the effectiveness of Hong Kong's strict border restrictions with mainland China in curbing the transmission of COVID-19. Combining big data from Baidu Population Migration with traditional meteorological data and census data for over 200 Chinese cities, we utilize an advanced quantitative approach, namely synthetic control modeling, to produce a counterfactual "synthetic Hong Kong" without a strict border restriction policy. We then simulate infection trends under the hypothetical scenarios and compare them to actual infection numbers. Our counterfactual synthetic control model demonstrates a lower number of COVID-19 infections than the actual scenario, where strict border restrictions with mainland China were implemented from February 8 to March 6, 2020. Moreover, the second synthetic control model, which assumes a border reopen on 7 May 2020 demonstrates nonpositive effects of extending the border restriction policy on preventing and controlling infections. We conclude that the border restriction policy and its further extension may not be useful in containing the spread of COVID-19 when the virus is already circulating in the local community. Given the substantial economic and social costs, and as precautionary measures against COVID-19 becomes the new normal, countries can consider reopening borders with neighbors who have COVID-19 under control. Governments also need to closely monitor the changing epidemic situations in other countries in order to make prompt and sensible amendments to their border restriction policies.

Revealing Dynamic Spatial Structures of Urban Mobility Networks and the Underlying Evolutionary Patterns

Urban space exhibits rich and diverse organizational structures, which is difficult to characterize and interpret. Modelling urban spatial structures in the context of mobility and revealing their underlying patterns in dynamic networks are key to understanding urban spatial structures and how urban systems work. Most existing methods overlook its temporal dimension and oversimplify its spatial heterogeneity, and it is challenging to address these complex properties using one single method. Therefore, we propose a framework based on temporal networks for modeling dynamic urban mobility structures. First, we cast aggregated traffic flows into a compact and informative temporal network for structure representation. Then, we explore spatial cluster substructures and temporal evolution patterns to acquire evolution regularities. Last, the capability of the proposed framework is examined by an empirical analysis based on taxi mobility networks. The experiment results enable to quantitatively depict urban space dynamics and effectively detect spatiotemporal heterogeneity in mobility networks.

Understanding the heterogeneity of COVID-19 deaths and contagions: The role of air pollution and lockdown decisions

The uneven geographical distribution of the novel coronavirus epidemic (COVID-19) in Italy is a puzzle given the intense flow of movements among the different geographical areas before lockdown decisions. To shed light on it, we test the effect of the quality of air (as measured by particulate matter and nitrogen dioxide) and lockdown restrictions on daily adverse COVID-19 outcomes during the first pandemic wave in the country. We find that air pollution is positively correlated with adverse outcomes of the pandemic, with lockdown being strongly significant and more effective in reducing deceases in more polluted areas. Results are robust to different methods including cross-section, pooled and fixed-effect panel regressions (controlling for spatial correlation), instrumental variable regressions, and difference-in-differences estimates of lockdown decisions through predicted counterfactual trends. They are consistent with the consolidated body of literature in previous medical studies suggesting that poor quality of air creates chronic exposure to adverse outcomes from respiratory diseases. The estimated correlation does not change when accounting for other factors such as temperature, commuting flows, quality of regional health systems, share of public transport users, population density, the presence of Chinese community, and proxies for industry breakdown such as the share of small (artisan) firms. Our findings provide suggestions for investigating uneven geographical distribution patterns in other countries, and have implications for environmental and lockdown policies.

The lockdown, mobility, and spatial health disparities in COVID-19 pandemic: A case study of New York City

The world has adopted unprecedented lockdown as the key method to mitigate COVID-19; yet its effect on pandemic outcomes and health disparities remains largely unknown. Adopting a multilevel conceptual framework, this research investigates how city-level lockdown policy and public transit system shape mobility and thus intra-city health disparities, using New York City as a case study. With a spatial method and multiple sources of data, this research demonstrates the uneven impact of the lockdown policy and public transit system in shaping local pandemic outcomes. Census tracts with people spending more time at home have lower infection and death rates, while those with a higher density of transit stations have higher infection and death rates. Residential profile matters and census tracts with a higher concentration of disadvantaged population, such as Blacks, Hispanics, poor and elderly people, and people with no health insurance, have higher infection and death rates. Spatial analyses identify clusters where the lockdown policy was not effective and census tracts that share similar pandemic characteristics. Through the lens of mobility, this research advances knowledge of health disparities by focusing on institutional causes for health disparities and the role of the government through intervention policy and public transit system.

Insufficient ventilation led to a probable long-range airborne transmission of SARS-CoV-2 on two buses

Uncertainty remains on the threshold of ventilation rate in airborne transmission of SARS-CoV-2. We analyzed a COVID-19 outbreak in January 2020 in Hunan Province, China, involving an infected 24-year-old man, Mr. X, taking two subsequent buses, B1 and B2, in the same afternoon. We investigated the possibility of airborne transmission and the ventilation conditions for its occurrence. The ventilation rates on the buses were measured using a tracer-concentration decay method with the original driver on the original route. We measured and calculated the spread of the exhaled virus-laden droplet tracer from the suspected index case. Ten additional passengers were found to be infected, with seven of them (including one asymptomatic) on B1 and two on B2 when Mr. X was present, and one passenger infected on the subsequent B1 trip. B1 and B2 had time-averaged ventilation rates of approximately 1.7 and 3.2 L/s per person, respectively. The difference in ventilation rates and exposure time could explain why B1 had a higher attack rate than B2. Airborne transmission due to poor ventilation below 3.2 L/s played a role in this two-bus outbreak of COVID-19.

Existing human mobility data sources poorly predicted the spatial spread of SARS-CoV-2 in Madagascar

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.

Socioeconomic and environmental patterns behind H1N1 spreading in Sweden

Identifying the critical factors related to influenza spreading is crucial in predicting and mitigating epidemics. Specifically, uncovering the relationship between epidemic onset and various risk indicators such as socioeconomic, mobility and climate factors can reveal locations and travel patterns that play critical roles in furthering an outbreak. We study the 2009 A(H1N1) influenza outbreaks in Sweden’s municipalities between 2009 and 2015 and use the Generalized Inverse Infection Method (GIIM) to assess the most significant contributing risk factors. GIIM represents an epidemic spreading process on a network: nodes correspond to geographical objects, links indicate travel routes, and transmission probabilities assigned to the links guide the infection process. Our results reinforce existing observations that the influenza outbreaks considered in this study were driven by the country’s largest population centers, while meteorological factors also contributed significantly. Travel and other socioeconomic indicators have a negligible effect. We also demonstrate that by training our model on the 2009 outbreak, we can predict the epidemic onsets in the following five seasons with high accuracy.

Optimal strategic pandemic control: human mobility and travel restriction

This paper presents a model for finding optimal pandemic control policy considering cross-region human mobility. We extend the baseline susceptible-infectious-recovered (SIR) epidemiology model by including the net human mobility from a severely-impacted region to a mildly-affected region. The strategic optimal mitigation policy combining testing and lockdown in each region is then obtained with the goal of minimizing economic cost under the constraint of limited resources. We parametrize the model using the data of the COVID-19 pandemic and show that the optimal response strategy and mitigation outcome greatly rely on the mitigation duration, available resources, and cross-region human mobility. Furthermore, we discuss the economic impact of travel restriction policies through a quantitative analysis.

Welfare costs of travel reductions within the United States due to COVID-19

Using daily county-level travel data within the United States, this paper investigates the welfare costs of travel reductions due to coronavirus disease 2019 (COVID-19) for the period between 20 January and 5 September 2020. Welfare of individuals (related to their travel) is measured by their inter-county and intra-county travel, where travel costs are measured by the corresponding distance measures. Important transport policy implications follow regarding how policymakers can act to mitigate welfare costs of travel reductions without worsening the COVID-19 spread.

Universal risk phenotype of US counties for flu-like transmission to improve county-specific COVID-19 incidence forecasts

The spread of a communicable disease is a complex spatio-temporal process shaped by the specific transmission mechanism, and diverse factors including the behavior, socio-economic and demographic properties of the host population. While the key factors shaping transmission of influenza and COVID-19 are beginning to be broadly understood, making precise forecasts on case count and mortality is still difficult. In this study we introduce the concept of a universal geospatial risk phenotype of individual US counties facilitating flu-like transmission mechanisms. We call this the Universal Influenza-like Transmission (UnIT) score, which is computed as an information-theoretic divergence of the local incidence time series from an high-risk process of epidemic initiation, inferred from almost a decade of flu season incidence data gleaned from the diagnostic history of nearly a third of the US population. Despite being computed from the past seasonal flu incidence records, the UnIT score emerges as the dominant factor explaining incidence trends for the COVID-19 pandemic over putative demographic and socio-economic factors. The predictive ability of the UnIT score is further demonstrated via county-specific weekly case count forecasts which consistently outperform the state of the art models throughout the time-line of the COVID-19 pandemic. This study demonstrates that knowledge of past epidemics may be used to chart the course of future ones, if transmission mechanisms are broadly similar, despite distinct disease processes and causative pathogens.

Accurate case count forecasts in an epidemic is non-trivial, with the spread of infectious diseases being modulated by diverse hard-to-model factors. This study introduces the concept of a universal risk phenotype for US counties that predictably increases the risk of person-to-person transmission of influenza-like illnesses; universal in the sense that it is pathogen-agnostic provided the transmission mechanism is similar to that of seasonal influenza. We call this the Universal Influenza-like Transmission (UnIT) score, which accounts for unmodeled effects by automatically leveraging subtle geospatial patterns underlying the flu epidemics of the past. It is a phenotype of the counties themselves, as it characterizes how the transmission process is differentially impacted in different geospatial contexts. Grounded in information-theory and machine learning, the UnIT score reduces the need to manually identify every factor that impacts the case counts. Applying to the COVID-19 pandemic, we show that incidence patterns from a past epidemic caused by an appropriately-chosen distinct pathogen can substantially inform future projections. Our forecasts consistently outperform the state of the art models throughout the time-line of the COVID-19 pandemic, and thus is an important step to inform policy decisions in current and future pandemics.

Catch Me if You Can: Superspreading of COVID-19

While significant insights have been gained concerning COVID-19, superspreading of coronaviruses remains a mystery. The vast majority of cases have been linked to a relatively small portion of infected individuals. Yet, the genetic sequence of the virus, severity of disease, and underlying host parameters, such as age, sex, and health conditions, are not clearly driving the superspreading phenomenon. In this commentary we discuss what is known and what is not known about coronavirus superspreader transmission and explore whether characteristics of the virion, the donor, or the environment contribute to this phenomenon.

Welfare costs of COVID-19: Evidence from US counties

Using daily US county-level data on consumption, employment, mobility, and the coronavirus disease 2019 (COVID-19) cases, this paper investigates the welfare costs of COVID-19. The investigation is achieved by using implications of a model, where there is a trade-off between consumption and COVID-19 cases that are both determined by the optimal mobility decision of individuals. The empirical results show evidence for about 11% of an average (across days) reduction of welfare during the sample period between February and December 2020 for the average county. There is also evidence for heterogeneous welfare costs across US counties and days, where certain counties have experienced welfare reductions up to 46 % on average across days and up to 97 % in late March 2020 that are further connected to the socioeconomic characteristics of the US counties.

Mobility in times of pandemics: Evidence on the spread of COVID19 in Italy's labour market areas

We investigate the interplay between the local spread of COVID-19 and patterns of individual mobility within and across self-contained geographical areas. Conceptually, we connect the debate on regional development in the presence of shocks with the literature on spatial labour markets and address some research questions about the role of individual mobility in affecting the spread of the disease. By looking at granular flows of Facebook users moving within and across Italian labour market areas (LMAs), we analyse whether their heterogeneous internal and external mobility has had a significant impact on excess mortality. We also explore how individual mobility plays different roles in LMAs hosting industrial districts - characterised by a thicker local labour market and denser business and social interactions - and with a high presence of "essential sectors" - activities not affected by the COVID-19 containment measures taken by the Italian government at the onset of the crisis.

Exploring the Utility of Google Mobility Data During the COVID-19 Pandemic in India: Digital Epidemiological Analysis

BACKGROUND

Association between human mobility and disease transmission has been established for COVID-19, but quantifying the levels of mobility over large geographical areas is difficult. Google has released Community Mobility Reports (CMRs) containing data about the movement of people, collated from mobile devices.

OBJECTIVE

The aim of this study is to explore the use of CMRs to assess the role of mobility in spreading COVID-19 infection in India.

METHODS

In this ecological study, we analyzed CMRs to determine human mobility between March and October 2020. The data were compared for the phases before the lockdown (between March 14 and 25, 2020), during lockdown (March 25-June 7, 2020), and after the lockdown (June 8-October 15, 2020) with the reference periods (ie, January 3-February 6, 2020). Another data set depicting the burden of COVID-19 as per various disease severity indicators was derived from a crowdsourced API. The relationship between the two data sets was investigated using the Kendall tau correlation to depict the correlation between mobility and disease severity.

RESULTS

At the national level, mobility decreased from -38% to -77% for all areas but residential (which showed an increase of 24.6%) during the lockdown compared to the reference period. At the beginning of the unlock phase, the state of Sikkim (minimum cases: 7) with a -60% reduction in mobility depicted more mobility compared to -82% in Maharashtra (maximum cases: 1.59 million). Residential mobility was negatively correlated (-0.05 to -0.91) with all other measures of mobility. The magnitude of the correlations for intramobility indicators was comparatively low for the lockdown phase (correlation ≥0.5 for 12 indicators) compared to the other phases (correlation ≥0.5 for 45 and 18 indicators in the prelockdown and unlock phases, respectively). A high correlation coefficient between epidemiological and mobility indicators was observed for the lockdown and unlock phases compared to the prelockdown phase.

CONCLUSIONS

Mobile-based open-source mobility data can be used to assess the effectiveness of social distancing in mitigating disease spread. CMR data depicted an association between mobility and disease severity, and we suggest using this technique to supplement future COVID-19 surveillance.

Pollen antigens and atmospheric circulation driven seasonal respiratory viral outbreak and its implication to the Covid-19 pandemic

The patterns of respiratory virus illness are expressed differently between temperate and tropical climates. Tropical outbreaks often peak in wet seasons. Temperate outbreaks typically peak during the winter. The prevailing causal hypotheses focus on sunlight, temperature and humidity variations. Yet no consistent factors have been identified to sufficiently explain seasonal virus emergence and decline at any latitude. Here we demonstrate close connections among global-scale atmospheric circulations, IgE antibody enhancement through seasonal pollen inhalation, and respiratory virus patterns at any populated latitude, with a focus on the US. Pollens emerge each Spring, and the renewed IgE titers in the population are argued to terminate each winter peak of respiratory illness. Globally circulated airborne viruses are postulated to subsequently deposit across the Southern US during lower zonal geostrophic winds each late Summer. This seasonally refreshed viral load is postulated to trigger a new influenza outbreak, once the existing IgE antibodies diminish to a critical value each Fall. Our study offers a new and consistent explanation for the seasonal diminishment of respiratory viral illnesses in temperate climates, the subdued seasonal signature in the tropics, the annually circulated virus phenotypes, and the northerly migration of influenza across the US every year. Our integrated geospatial and IgE hypothesis provides a new perspective for prediction, mitigation and prevention of the outbreak and spread of seasonal respiratory viruses including Covid-19 pandemic.

Airline transportation and arrival time of international disease spread: A case study of Covid-19

In this era of globalization, airline transportation has greatly increased international trade and travel within the World Airport Network (WAN). Unfortunately, this convenience has expanded the scope of infectious disease spread from a local to a worldwide occurrence. Thus, scholars have proposed several methods to measure the distances between airports and define the relationship between the distances and arrival times of infectious diseases in various countries. However, such studies suffer from the following limitations. (1) Only traditional statistical methods or graphical representations were utilized to show that the effective distance performed better than the geographical distance technique. Researchers seldom use the survival model to quantify the actual differences among arrival times via various distance methods. (2) Although scholars have found that most diseases tend to spread via the random walk rather than the shortest path method, this hypothesis may no longer be true because the network has been severally altered due to recent COVID-related travel reductions. Therefore, we used 2017 IATA (International Air Transport Association) to establish an airline network via various chosen path strategies (random walk and shortest path). Then, we employed these two networks to quantify each model's predictive performance in order to estimate the importation probability function of COVID-19 into various countries. The effective distance model was found to more accurately predict arrival dates of COVID-19 than the geographical distance model. However, if pre-Covid airline data is included, the path of disease spread might not follow the random walk theory due to recent flight suspensions and travel restrictions during the epidemic. Lastly, when testing effective distance, the inverse distance survival model and the Cox model yielded very similar importation risk estimates. The results can help authorities design more effective international epidemic prevention and control strategies.

Trip duration drives shift in travel network structure with implications for the predictability of spatial disease spread

Human travel is one of the primary drivers of infectious disease spread. Models of travel are often used that assume the amount of travel to a specific destination decreases as cost of travel increases with higher travel volumes to more populated destinations. Trip duration, the length of time spent in a destination, can also impact travel patterns. We investigated the spatial patterns of travel conditioned on trip duration and find distinct differences between short and long duration trips. In short-trip duration travel networks, trips are skewed towards urban destinations, compared with long-trip duration networks where travel is more evenly spread among locations. Using gravity models to inform connectivity patterns in simulations of disease transmission, we show that pathogens with shorter generation times exhibit initial patterns of spatial propagation that are more predictable among urban locations. Further, pathogens with a longer generation time have more diffusive patterns of spatial spread reflecting more unpredictable disease dynamics.

During an epidemic of an infectious pathogen, cases of disease can be imported to new locations when people travel. The amount of time that an infected person spends in a destination (trip duration) determines how likely they are to infect others while travelling. In this study, we analyzed travel data and found specific spatial patterns in trip duration, where short-duration trips are more common between urban destinations and long-duration trips are evenly spread out among locations. To show how this spatial pattern impacts the spread of infectious diseases, we used data-driven models and simulations to show that pathogens with shorter generation times have patterns of spatial spread that are more predictable among urban locations. However, pathogens with longer generation times tend to spread along the long-duration travel networks that are more evenly distributed among locations giving them more unpredictable disease dynamics.

A Short-Term Prediction Model at the Early Stage of the COVID-19 Pandemic Based on Multisource Urban Data

The ongoing coronavirus disease 2019 (COVID-19) pandemic spread throughout China and worldwide since it was reported in Wuhan city, China in December 2019. 4 589 526 confirmed cases have been caused by the pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), by May 18, 2020. At the early stage of the pandemic, the large-scale mobility of humans accelerated the spread of the pandemic. Rapidly and accurately tracking the population inflow from Wuhan and other cities in Hubei province is especially critical to assess the potential for sustained pandemic transmission in new areas. In this study, we first analyze the impact of related multisource urban data (such as local temperature, relative humidity, air quality, and inflow rate from Hubei province) on daily new confirmed cases at the early stage of the local pandemic transmission. The results show that the early trend of COVID-19 can be explained well by human mobility from Hubei province around the Chinese Lunar New Year. Different from the commonly-used pandemic models based on transmission dynamics, we propose a simple but effective short-term prediction model for COVID-19 cases, considering the human mobility from Hubei province to the target cities. The performance of our proposed model is validated by several major cities in Guangdong province. For cities like Shenzhen and Guangzhou with frequent population flow per day, the values of [Formula: see text] of daily prediction achieve 0.988 and 0.985. The proposed model has provided a reference for decision support of pandemic prevention and control in Shenzhen.

Practical geospatial and sociodemographic predictors of human mobility

Understanding seasonal human mobility at subnational scales has important implications across sciences, from urban planning efforts to disease modelling and control. Assessing how, when, and where populations move over the course of the year, however, requires spatially and temporally resolved datasets spanning large periods of time, which can be rare, contain sensitive information, or may be proprietary. Here, we aim to explore how a set of broadly available covariates can describe typical seasonal subnational mobility in Kenya pre-COVID-19, therefore enabling better modelling of seasonal mobility across low- and middle-income country (LMIC) settings in non-pandemic settings. To do this, we used the Google Aggregated Mobility Research Dataset, containing anonymized mobility flows aggregated over users who have turned on the Location History setting, which is off by default. We combined this with socioeconomic and geospatial covariates from 2018 to 2019 to quantify seasonal changes in domestic and international mobility patterns across years. We undertook a spatiotemporal analysis within a Bayesian framework to identify relevant geospatial and socioeconomic covariates explaining human movement patterns, while accounting for spatial and temporal autocorrelations. Typical pre-pandemic mobility patterns in Kenya mostly consisted of shorter, within-county trips, followed by longer domestic travel between counties and international travel, which is important in establishing how mobility patterns changed post-pandemic. Mobility peaked in August and December, closely corresponding to school holiday seasons, which was found to be an important predictor in our model. We further found that socioeconomic variables including urbanicity, poverty, and female education strongly explained mobility patterns, in addition to geospatial covariates such as accessibility to major population centres and temperature. These findings derived from novel data sources elucidate broad spatiotemporal patterns of how populations move within and beyond Kenya, and can be easily generalized to other LMIC settings before the COVID-19 pandemic. Understanding such pre-pandemic mobility patterns provides a crucial baseline to interpret both how these patterns have changed as a result of the pandemic, as well as whether human mobility patterns have been permanently altered once the pandemic subsides. Our findings outline key correlates of mobility using broadly available covariates, alleviating the data bottlenecks of highly sensitive and proprietary mobile phone datasets, which many researchers do not have access to. These results further provide novel insight on monitoring mobility proxies in the context of disease surveillance and control efforts through LMIC settings.

Using Mobile Phone Data to Estimate the Relationship between Population Flow and Influenza Infection Pathways

This study aimed to analyze population flow using global positioning system (GPS) location data and evaluate influenza infection pathways by determining the relationship between population flow and the number of drugs sold at pharmacies. Neural collective graphical models (NCGMs; Iwata and Shimizu 2019) were applied for 25 cell areas, each measuring 10 × 10 km², in Osaka, Kyoto, Nara, and Hyogo prefectures to estimate population flow. An NCGM uses a neural network to incorporate the spatiotemporal dependency issue and reduce the estimated parameters. The prescription peaks between several cells with high population flow showed a high correlation with a delay of one to two days or with a seven-day time-lag. It was observed that not much population flows from one cell to the outside area on weekdays. This observation may have been due to geographical features and undeveloped transportation networks. The number of prescriptions for anti-influenza drugs in that cell remained low during the observation period. The present results indicate that influenza did not spread to areas with undeveloped traffic networks, and the peak number of drug prescriptions arrived with a time lag of several days in areas with a high amount of area-to-area movement due to commuting.

Spatial and temporal invasion dynamics of the 2014-2017 Zika and chikungunya epidemics in Colombia

Zika virus (ZIKV) and chikungunya virus (CHIKV) were recently introduced into the Americas resulting in significant disease burdens. Understanding their spatial and temporal dynamics at the subnational level is key to informing surveillance and preparedness for future epidemics. We analyzed anonymized line list data on approximately 105,000 Zika virus disease and 412,000 chikungunya fever suspected and laboratory-confirmed cases during the 2014–2017 epidemics. We first determined the week of invasion in each city. Out of 1,122, 288 cities met criteria for epidemic invasion by ZIKV and 338 cities by CHIKV. We analyzed risk factors for invasion using linear and logistic regression models. We also estimated that the geographic origin of both epidemics was located in Barranquilla, north Colombia. We assessed the spatial and temporal invasion dynamics of both viruses to analyze transmission between cities using a suite of (i) gravity models, (ii) Stouffer’s rank models, and (iii) radiation models with two types of distance metrics, geographic distance and travel time between cities. Invasion risk was best captured by a gravity model when accounting for geographic distance and intermediate levels of density dependence; Stouffer’s rank model with geographic distance performed similarly well. Although a few long-distance invasion events occurred at the beginning of the epidemics, an estimated distance power of 1.7 (95% CrI: 1.5–2.0) from the gravity models suggests that spatial spread was primarily driven by short-distance transmission. Similarities between the epidemics were highlighted by jointly fitted models, which were preferred over individual models when the transmission intensity was allowed to vary across arboviruses. However, ZIKV spread considerably faster than CHIKV.

Understanding the spread of infectious diseases across space and time is critical for preparedness, designing interventions, and elucidating mechanisms underlying transmission. We analyzed human case data from over 500,000 reported cases to investigate the spread of the recent Zika virus (ZIKV) and chikungunya virus (CHIKV) epidemics in Colombia. Both viruses were introduced into northern Colombia. We found that gravity models and Stouffer’s rank models best described transmission and that transmission mainly occurred over short distances. Our results highlight similarities and key differences between the ZIKV and CHIKV epidemics in Colombia, which can be used to anticipate future epidemic waves and prioritize cities for active surveillance and targeted interventions.

Does city lockdown prevent the spread of COVID-19? New evidence from the synthetic control method

BACKGROUND

At 10 a.m. on January 23, 2020 Wuhan, China imposed a 76-day travel lockdown on its 11 million residents in order to stop the spread of COVID-19. This lockdown represented the largest quarantine in the history of public health and provides us with an opportunity to critically examine the relationship between a city lockdown on human mobility and controlling the spread of a viral epidemic, in this case COVID-19. This study aims to assess the causal impact of the Wuhan lockdown on population movement and the increase of newly confirmed COVID-19 cases.

METHODS

Based on the daily panel data from 279 Chinese cities, our research is the first to apply the synthetic control approach to empirically analyze the causal relationship between the Wuhan lockdown of its population mobility and the progression of newly confirmed COVID-19 cases. By using a weighted average of available control cities to reproduce the counterfactual outcome trajectory that the treated city would have experienced in the absence of the lockdown, the synthetic control approach overcomes the sample selection bias and policy endogeneity problems that can arise from previous empirical methods in selecting control units.

RESULTS

In our example, the lockdown of Wuhan reduced mobility inflow by approximately 60 % and outflow by about 50 %. A significant reduction of new cases was observed within four days of the lockdown. The increase in new cases declined by around 50% during this period. However, the suppression effect became less discernible after this initial period of time. A 2.25-fold surge was found for the increase in new cases on the fifth day following the lockdown, after which it died down rapidly.

CONCLUSIONS

Our study provided urgently needed and reliable causal evidence that city lockdown can be an effective short-term tool in containing and delaying the spread of a viral epidemic. Further, the city lockdown strategy can buy time during which countries can mobilize an effective response in order to better prepare. Therefore, in spite of initial widespread skepticism, lockdowns are likely to be added to the response toolkit used for any future pandemic outbreak.

Community factors associated with local epidemic timing of respiratory syncytial virus: A spatiotemporal modeling study

Respiratory syncytial virus (RSV) causes a large burden of morbidity in young children and the elderly. Spatial variability in the timing of RSV epidemics provides an opportunity to probe the factors driving its transmission, including factors that influence epidemic seeding and growth rates. Using hospitalization data from Connecticut, New Jersey, and New York, we estimated epidemic timing at the ZIP code level using harmonic regression and then used a Bayesian meta-regression model to evaluate correlates of epidemic timing. Earlier epidemics were associated with larger household size and greater population density. Nearby localities had similar epidemic timing. Our results suggest that RSV epidemics grow faster in areas with more local contact opportunities, and that epidemic spread follows a spatial diffusion process based on geographic proximity. Our findings can inform the timing of delivery of RSV extended half-life prophylaxis and maternal vaccines and guide future studies on the transmission dynamics of RSV.

Toward the use of neural networks for influenza prediction at multiple spatial resolutions

Mitigating the effects of disease outbreaks with timely and effective interventions requires accurate real-time surveillance and forecasting of disease activity, but traditional health care-based surveillance systems are limited by inherent reporting delays. Machine learning methods have the potential to fill this temporal "data gap," but work to date in this area has focused on relatively simple methods and coarse geographic resolutions (state level and above). We evaluate the predictive performance of a gated recurrent unit neural network approach in comparison with baseline machine learning methods for estimating influenza activity in the United States at the state and city levels and experiment with the inclusion of real-time Internet search data. We find that the neural network approach improves upon baseline models for long time horizons of prediction but is not improved by real-time internet search data. We conduct a thorough analysis of feature importances in all considered models for interpretability purposes.

Mitigation policies, community mobility, and COVID-19 case counts in Australia, Japan, Hong Kong, and Singapore

OBJECTIVES

The objective of the study was to characterize the timing and trends of select mitigation policies, changes in community mobility, and coronavirus disease 2019 (COVID-19) epidemiology in Australia, Japan, Hong Kong, and Singapore.

STUDY DESIGN

Prospective abstraction of publicly available mitigation policies obtained from media reports and government websites.

METHODS

Data analyzed include seven kinds of mitigation policies (mass gathering restrictions, international travel restrictions, passenger screening, traveler isolation/quarantine, school closures, business closures, and domestic movement restrictions) implemented between January 1 and April 26, 2020, changes in selected measures of community mobility assessed by Google Community Mobility Reports data, and COVID-19 epidemiology in Australia, Japan, Hong Kong, and Singapore.

RESULTS

During the study period, community mobility decreased in Australia, Japan, and Singapore; there was little change in Hong Kong. The largest declines in mobility were seen in places that enforced mitigation policies. Across settings, transit-associated mobility declined the most and workplace-associated mobility the least. Singapore experienced an increase in cases despite the presence of stay-at-home orders, as migrant workers living in dormitories faced challenges to safely quarantine.

CONCLUSIONS

Public policies may have different impacts on mobility and transmission of severe acute respiratory coronavirus-2 transmission. When enacting mitigation policies, decision makers should consider the possible impact of enforcement measures, the influence on transmission of factors other than movement restrictions, and the differential impact of mitigation policies on subpopulations.

Could Air Quality Get Better during Epidemic Prevention and Control in China? An Analysis Based on Regression Discontinuity Design

Though many scholars and practitioners are paying more attention to the health and life of the public after the COVID-19 outbreak, extant literature has so far failed to explore the variation of ambient air quality during this pandemic. The current study attempts to fill the gap by disentangling the causal effects of epidemic prevention on air quality in China, measured by the individual pollutant dimensionless index, from other confounding factors. Using the fixed effects model, this article finds that five air indicators, PM2.5, PM10, CO, NO2, and SO2, significantly improved during the shutdown period, with NO2 showing the most improvement. On the contrary, O3 shows an inverse pattern, that is, O3 gets worse unexpectedly. The positive impact of epidemic prevention on air quality, especially in terms of PM2.5, PM10, and NO2, become manifest five days after the resumption of labor, indicated by the result of a regression discontinuity design. These findings are still robust and consistent after the dataset of 2019 as a counterfactual sample is utilized. The findings of this paper make contributions to both environmental governance and pandemic prevention, with relevant guidelines regarding the health and life of the public and governmental behavioral management strategies discussed.

Human mobility and poverty as key drivers of COVID-19 transmission and control

BACKGROUND

Applying heavy nationwide restrictions is a powerful method to curtail COVID-19 transmission but poses a significant humanitarian and economic crisis. Thus, it is essential to improve our understanding of COVID-19 transmission, and develop more focused and effective strategies. As human mobility drives transmission, data from cellphone devices can be utilized to achieve these goals.

METHODS

We analyzed aggregated and anonymized mobility data from the cell phone devices of> 3 million users between February 1, 2020, to May 16, 2020 - in which several movement restrictions were applied and lifted in Israel. We integrated these mobility patterns into age-, risk- and region-structured transmission model. Calibrated to coronavirus incidence in 250 regions covering Israel, we evaluated the efficacy and effectiveness in decreasing morbidity and mortality of applying localized and temporal lockdowns (stay-at-home order).

RESULTS

Poorer regions exhibited lower and slower compliance with the restrictions. Our transmission model further indicated that individuals from impoverished areas were associated with high transmission rates. Considering a horizon of 1-3 years, we found that to reduce COVID-19 mortality, school closure has an adverse effect, while interventions focusing on the elderly are the most efficient. We also found that applying localized and temporal lockdowns during regional outbreaks reduces the overall mortality and morbidity compared to nationwide lockdowns. These trends were consistent across vast ranges of epidemiological parameters, and potential seasonal forcing.

CONCLUSIONS

More resources should be devoted to helping impoverished regions. Utilizing cellphone data despite being anonymized and aggregated can help policymakers worldwide identify hotspots and apply designated strategies against future COVID-19 outbreaks.

Scaling of contact networks for epidemic spreading in urban transit systems

Improved mobility not only contributes to more intensive human activities but also facilitates the spread of communicable disease, thus constituting a major threat to billions of urban commuters. In this study, we present a multi-city investigation of communicable diseases percolating among metro travelers. We use smart card data from three megacities in China to construct individual-level contact networks, based on which the spread of disease is modeled and studied. We observe that, though differing in urban forms, network layouts, and mobility patterns, the metro systems of the three cities share similar contact network structures. This motivates us to develop a universal generation model that captures the distributions of the number of contacts as well as the contact duration among individual travelers. This model explains how the structural properties of the metro contact network are associated with the risk level of communicable diseases. Our results highlight the vulnerability of urban mass transit systems during disease outbreaks and suggest important planning and operation strategies for mitigating the risk of communicable diseases.

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.

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.

Top-Down and Bottom-Up Lockdown: Evidence from COVID-19 Prevention and Control in China

Utilizing national migration data regarding the outbreak of the novel coronavirus (2019-nCoV), this paper employs a difference-in-differences approach to empirically analyze the relationship between human mobility and the transmission of infectious diseases in China. We show that national human mobility restrictions ascribed to the first-level public health emergency response policy effectively reduce both intercity and intracity migration intensities, thus leading to a declining scale of human mobility, which improves the effectiveness in controlling the epidemic. Human mobility restrictions have greater influences on cities with better economic development, denser populations, or larger passenger volumes. Moreover, mobility restriction measures are found to be better implemented in regions with increased public awareness, or with provincial leaders who have healthcare crisis management experience, local administrative experience, or the opportunity to serve a consecutive term.

Intracity Pandemic Risk Evaluation Using Mobile Phone Data: The Case of Shanghai during COVID-19

The coronavirus disease 2019 (COVID-19) pandemic has provided an opportunity to rethink the development of a sustainable and resilient city. A framework for comprehensive intracity pandemic risk evaluation using mobile phone data is proposed in this study. Four steps were included in the framework: identification of high-risk groups, calculation of dynamic population flow and construction of a human mobility network, exposure and transmission risk assessment, and pandemic prevention guidelines. First, high-risk groups were extracted from mobile phone data based on multi-day activity chains. Second, daily human mobility networks were created by aggregating population and origin-destination (OD) flows. Third, clustering analysis, time series analysis, and network analysis were employed to evaluate pandemic risk. Finally, several solutions are proposed to control the pandemic. The outbreak period of COVID-19 in Shanghai was used to verify the proposed framework and methodology. The results show that the evaluation method is able to reflect the different spatiotemporal patterns of pandemic risk. The proposed framework and methodology may help prevent future public health emergencies and localized epidemics from evolving into global pandemics.

The role of "spillover" in antibiotic resistance

Antibiotic use is a key driver of antibiotic resistance. Understanding the quantitative association between antibiotic use and resulting resistance is important for predicting future rates of antibiotic resistance and for designing antibiotic stewardship policy. However, the use-resistance association is complicated by "spillover," in which one population's level of antibiotic use affects another population's level of resistance via the transmission of bacteria between those populations. Spillover is known to have effects at the level of families and hospitals, but it is unclear if spillover is relevant at larger scales. We used mathematical modeling and analysis of observational data to address this question. First, we used dynamical models of antibiotic resistance to predict the effects of spillover. Whereas populations completely isolated from one another do not experience any spillover, we found that if even 1% of interactions are between populations, then spillover may have large consequences: The effect of a change in antibiotic use in one population on antibiotic resistance in that population could be reduced by as much as 50%. Then, we quantified spillover in observational antibiotic use and resistance data from US states and European countries for three pathogen-antibiotic combinations, finding that increased interactions between populations were associated with smaller differences in antibiotic resistance between those populations. Thus, spillover may have an important impact at the level of states and countries, which has ramifications for predicting the future of antibiotic resistance, designing antibiotic resistance stewardship policy, and interpreting stewardship interventions.

Human mobility restrictions and the spread of the Novel Coronavirus (2019-nCoV) in China

We quantify the causal impact of human mobility restrictions, particularly the lockdown of Wuhan on January 23, 2020, on the containment and delay of the spread of the Novel Coronavirus (2019-nCoV). We employ difference-in-differences (DID) estimations to disentangle the lockdown effect on human mobility reductions from other confounding effects including panic effect, virus effect, and the Spring Festival effect. The lockdown of Wuhan reduced inflows to Wuhan by 76.98%, outflows from Wuhan by 56.31%, and within-Wuhan movements by 55.91%. We also estimate the dynamic effects of up to 22 lagged population inflows from Wuhan and other Hubei cities - the epicenter of the 2019-nCoV outbreak - on the destination cities' new infection cases. We also provide evidence that the enhanced social distancing policies in the 98 Chinese cities outside Hubei province were effective in reducing the impact of the population inflows from the epicenter cities in Hubei province on the spread of 2019-nCoV in the destination cities. We find that in the counterfactual world in which Wuhan were not locked down on January 23, 2020, the COVID-19 cases would be 105.27% higher in the 347 Chinese cities outside Hubei province. Our findings are relevant in the global efforts in pandemic containment.

COVID-19 spread and inter-county travel: Daily evidence from the U.S

Daily data at the U.S. county level suggest that coronavirus disease 2019 (COVID-19) cases and deaths are lower in counties where a higher share of people have stayed in the same county (or travelled less to other counties). This observation is tested formally by using a difference-in-difference design controlling for county-fixed effects and time-fixed effects, where weekly changes in COVID-19 cases or deaths are regressed on weekly changes in the share of people who have stayed in the same county during the previous 14 days. A counterfactual analysis based on the formal estimation results suggests that staying in the same county has the potential of reducing total weekly COVID-19 cases and deaths in the U.S. as much as by 139,503 and by 23,445, respectively.

Human mobility restrictions and the spread of the Novel Coronavirus (2019-nCoV) in China

We quantify the causal impact of human mobility restrictions, particularly the lockdown of Wuhan on January 23, 2020, on the containment and delay of the spread of the Novel Coronavirus (2019-nCoV). We employ difference-in-differences (DID) estimations to disentangle the lockdown effect on human mobility reductions from other confounding effects including panic effect, virus effect, and the Spring Festival effect. The lockdown of Wuhan reduced inflows to Wuhan by 76.98%, outflows from Wuhan by 56.31%, and within-Wuhan movements by 55.91%. We also estimate the dynamic effects of up to 22 lagged population inflows from Wuhan and other Hubei cities - the epicenter of the 2019-nCoV outbreak - on the destination cities' new infection cases. We also provide evidence that the enhanced social distancing policies in the 98 Chinese cities outside Hubei province were effective in reducing the impact of the population inflows from the epicenter cities in Hubei province on the spread of 2019-nCoV in the destination cities. We find that in the counterfactual world in which Wuhan were not locked down on January 23, 2020, the COVID-19 cases would be 105.27% higher in the 347 Chinese cities outside Hubei province. Our findings are relevant in the global efforts in pandemic containment.

The Epidemiological Framework for Biological Invasions (EFBI): an interdisciplinary foundation for the assessment of biosecurity threats

Emerging microparasite (e.g. viruses, bacteria, protozoa and fungi) epidemics and the introduction of non-native pests and weeds are major biosecurity threats worldwide. The likelihood of these threats is often estimated from probabilities of their entry, establishment, spread and ease of prevention. If ecosystems are considered equivalent to hosts, then compartment disease models should provide a useful framework for understanding the processes that underpin non-native species invasions. To enable greater cross-fertilisation between these two disciplines, the Epidemiological Framework for Biological Invasions (EFBI) is developed that classifies ecosystems in relation to their invasion status: Susceptible, Exposed, Infectious and Resistant. These states are linked by transitions relating to transmission, latency and recovery. This viewpoint differs markedly from the species-centric approaches often applied to non-native species. It allows generalisations from epidemiology, such as the force of infection, the basic reproductive ratio R0, super-spreaders, herd immunity, cordon sanitaire and ring vaccination, to be discussed in the novel context of non-native species and helps identify important gaps in the study of biological invasions. The EFBI approach highlights several limitations inherent in current approaches to the study of biological invasions including: (i) the variance in non-native abundance across ecosystems is rarely reported; (ii) field data rarely (if ever) distinguish source from sink ecosystems; (iii) estimates of the susceptibility of ecosystems to invasion seldom account for differences in exposure to non-native species; and (iv) assessments of ecosystem susceptibility often confuse the processes that underpin patterns of spread within -and between- ecosystems. Using the invasion of lakes as a model, the EFBI approach is shown to present a new biosecurity perspective that takes account of ecosystem status and complements demographic models to deliver clearer insights into the dynamics of biological invasions at the landscape scale. It will help to identify whether management of the susceptibility of ecosystems, of the number of vectors, or of the diversity of pathways (for movement between ecosystems) is the best way of limiting or reversing the population growth of a non-native species. The framework can be adapted to incorporate increasing levels of complexity and realism and to provide insights into how to monitor, map and manage biological invasions more effectively.

A Mutation Network Method for Transmission Analysis of Human Influenza H3N2

Characterizing the spatial transmission pattern is critical for better surveillance and control of human influenza. Here, we propose a mutation network framework that utilizes network theory to study the transmission of human influenza H3N2. On the basis of the mutation network, the transmission analysis captured the circulation pattern from a global simulation of human influenza H3N2. Furthermore, this method was applied to explore, in detail, the transmission patterns within Europe, the United States, and China, revealing the regional spread of human influenza H3N2. The mutation network framework proposed here could facilitate the understanding, surveillance, and control of other infectious diseases.

Differences in epidemic spread patterns of norovirus and influenza seasons of Germany: an application of optical flow analysis in epidemiology

This analysis presents data from a new perspective offering key insights into the spread patterns of norovirus and influenza epidemic events. We utilize optic flow analysis to gain an informed overview of a wealth of statistical epidemiological data and identify trends in movement of influenza waves throughout Germany on the NUTS 3 level (413 locations) which maps municipalities on European level. We show that Influenza and norovirus seasonal outbreak events have a highly distinct pattern. We investigate the quantitative statistical properties of the epidemic patterns and find a shifted distribution in the time between influenza and norovirus seasonal peaks of reported infections over one decade. These findings align with key biological features of both pathogens as shown in the course of this analysis.

How the individual human mobility spatio-temporally shapes the disease transmission dynamics

Human mobility plays a crucial role in the temporal and spatial spreading of infectious diseases. During the past few decades, researchers have been extensively investigating how human mobility affects the propagation of diseases. However, the mechanism of human mobility shaping the spread of epidemics is still elusive. Here we examined the impact of human mobility on the infectious disease spread by developing the individual-based SEIR model that incorporates a model of human mobility. We considered the spread of human influenza in two contrasting countries, namely, Belgium and Martinique, as case studies, to assess the specific roles of human mobility on infection propagation. We found that our model can provide a geo-temporal spreading pattern of the epidemics that cannot be captured by a traditional homogenous epidemic model. The disease has a tendency to jump to high populated urban areas before spreading to more rural areas and then subsequently spread to all neighboring locations. This heterogeneous spread of the infection can be captured by the time of the first arrival of the infection \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$(T_{fi} )$$\end{document}(Tfi), which relates to the landscape of the human mobility characterized by the relative attractiveness. These findings can provide insights to better understand and forecast the disease spreading.