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

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.

Spatial analysis of COVID-19 clusters and contextual factors in New York City

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Proportion positive tests were positively associated with marginalized statuses.

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Low testing and high positivity were associated with public transportation use.

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We recommend testing and health care resources be directed to eastern Brooklyn.

Identifying areas with low access to testing and high case burden is necessary to understand risk and allocate resources in the COVID-19 pandemic. Using zip code level data for New York City, we analyzed testing rates, positivity rates, and proportion positive. A spatial scan statistic identified clusters of high and low testing rates, high positivity rates, and high proportion positive. Boxplots and Pearson correlations determined associations between outcomes, clusters, and contextual factors. Clusters with less testing and low proportion positive tests had higher income, education, and white population, whereas clusters with high testing rates and high proportion positive tests were disproportionately black and without health insurance. Correlations showed inverse associations of white race, education, and income with proportion positive tests, and positive associations with black race, Hispanic ethnicity, and poverty. We recommend testing and health care resources be directed to eastern Brooklyn, which has low testing and high proportion positives.

The impact of climate and antigenic evolution on seasonal influenza virus epidemics in Australia

Although seasonal influenza viruses circulate globally, prevention and treatment occur at the level of regions, cities, and communities. At these scales, the timing, duration and magnitude of epidemics vary substantially, but the underlying causes of this variation are poorly understood. Here, based on analyses of a 15-year city-level dataset of 18,250 laboratory-confirmed and antigenically-characterised influenza virus infections from Australia, we investigate the effects of previously hypothesised environmental and virological drivers of influenza epidemics. We find that anomalous fluctuations in temperature and humidity do not predict local epidemic onset timings. We also find that virus antigenic change has no consistent effect on epidemic size. In contrast, epidemic onset time and heterosubtypic competition have substantial effects on epidemic size and composition. Our findings suggest that the relationship between influenza population immunity and epidemiology is more complex than previously supposed and that the strong influence of short-term processes may hinder long-term epidemiological forecasts.

The unique spatial ecology of human hunters

Human hunters are described as 'superpredators' with a unique ecology. Chronic wasting disease among cervids and African swine fever among wild boar are emerging wildlife diseases in Europe, with huge economic and cultural repercussions. Understanding hunter movements at broad scales has implications for how to control the spread of these diseases. Here we show, based on analysis of the settlement patterns and movements of hunters of reindeer (n = 9,685), red deer (n = 47,845), moose (n = 60,365) and roe deer (n = 42,530) from across Norway (2001-2017), that hunter density was more closely linked to human density than prey density and that hunters were largely migratory, aggregated with increasing regional prey densities and often used dogs. Hunter movements extended across Europe and to other continents. Our results provide extensive evidence that the broad-scale movements and residency patterns of postindustrial hunters relative to their prey differ from those of large carnivores.

FluSense: A Contactless Syndromic Surveillance Platform for Influenza-Like Illness in Hospital Waiting Areas

We developed a contactless syndromic surveillance platform FluSense that aims to expand the current paradigm of influenza-like illness (ILI) surveillance by capturing crowd-level bio-clinical signals directly related to physical symptoms of ILI from hospital waiting areas in an unobtrusive and privacy-sensitive manner. FluSense consists of a novel edge-computing sensor system, models and data processing pipelines to track crowd behaviors and influenza-related indicators, such as coughs, and to predict daily ILI and laboratory-confirmed influenza caseloads. FluSense uses a microphone array and a thermal camera along with a neural computing engine to passively and continuously characterize speech and cough sounds along with changes in crowd density on the edge in a real-time manner. We conducted an IRB-approved 7 month-long study from December 10, 2018 to July 12, 2019 where we deployed FluSense in four public waiting areas within the hospital of a large university. During this period, the FluSense platform collected and analyzed more than 350,000 waiting room thermal images and 21 million non-speech audio samples from the hospital waiting areas. FluSense can accurately predict daily patient counts with a Pearson correlation coefficient of 0.95. We also compared signals from FluSense with the gold standard laboratory-confirmed influenza case data obtained in the same facility and found that our sensor-based features are strongly correlated with laboratory-confirmed influenza trends.

Spatial and temporal clustering of patients hospitalized with laboratory-confirmed influenza in the United States

BACKGROUND

Timing of influenza spread across the United States is dependent on factors including local and national travel patterns and climate. Local epidemic intensity may be influenced by social, economic and demographic patterns. Data are needed to better explain how local socioeconomic factors influence both the timing and intensity of influenza seasons to result in national patterns.

METHODS

To determine the spatial and temporal impacts of socioeconomics on influenza hospitalization burden and timing, we used population-based laboratory-confirmed influenza hospitalization surveillance data from the CDC-sponsored Influenza Hospitalization Surveillance Network (FluSurv-NET) at up to 14 sites from the 2009/2010 through 2013/2014 seasons (n = 35,493 hospitalizations). We used a spatial scan statistic and spatiotemporal wavelet analysis, to compare temporal patterns of influenza spread between counties and across the country.

RESULTS

There were 56 spatial clusters identified in the unadjusted scan statistic analysis using data from the 2010/2011 through the 2013/2014 seasons, with relative risks (RRs) ranging from 0.09 to 4.20. After adjustment for socioeconomic factors, there were five clusters identified with RRs ranging from 0.21 to 1.20. In the wavelet analysis, most sites were in phase synchrony with one another for most years, except for the H1N1 pandemic year (2009-2010), wherein most sites had differential epidemic timing from the referent site in Georgia.

CONCLUSIONS

Socioeconomic factors strongly impact local influenza hospitalization burden. Influenza phase synchrony varies by year and by socioeconomics, but is less influenced by socioeconomics than is disease burden.

Spatiotemporal Analysis of Influenza in China, 2005-2018

Influenza is a major cause of morbidity and mortality worldwide, as well as in China. Knowledge of the spatial and temporal characteristics of influenza is important in evaluating and developing disease control programs. This study aims to describe an accurate spatiotemporal pattern of influenza at the prefecture level and explore the risk factors associated with influenza incidence risk in mainland China from 2005 to 2018. The incidence data of influenza were obtained from the Chinese Notifiable Infectious Disease Reporting System (CNIDRS). The Besag York Mollié (BYM) model was extended to include temporal and space-time interaction terms. The parameters for this extended Bayesian spatiotemporal model were estimated through integrated nested Laplace approximations (INLA) using the package R-INLA in R. A total of 702,226 influenza cases were reported in mainland China in CNIDRS from 2005–2018. The yearly reported incidence rate of influenza increased 15.6 times over the study period, from 3.51 in 2005 to 55.09 in 2008 per 100,000 populations. The temporal term in the spatiotemporal model showed that much of the increase occurred during the last 3 years of the study period. The risk factor analysis showed that the decreased number of influenza vaccines for sale, the new update of the influenza surveillance protocol, the increase in the rate of influenza A (H1N1)pdm09 among all processed specimens from influenza-like illness (ILI) patients, and the increase in the latitude and longitude of geographic location were associated with an increase in the influenza incidence risk. After the adjusting for fixed covariate effects and time random effects, the map of the spatial structured term shows that high-risk areas clustered in the central part of China and the lowest-risk areas in the east and west. Large space-time variations in influenza have been found since 2009. In conclusion, an increasing trend of influenza was observed from 2005 to 2018. The insufficient flu vaccine supplements, the newly emerging influenza A (H1N1)pdm09 and expansion of influenza surveillance efforts might be the major causes of the dramatic changes in outbreak and spatio-temporal epidemic patterns. Clusters of prefectures with high relative risks of influenza were identified in the central part of China. Future research with more risk factors at both national and local levels is necessary to explain the changing spatiotemporal patterns of influenza in China.

Optimizing spatial allocation of seasonal influenza vaccine under temporal constraints

Prophylactic interventions such as vaccine allocation are some of the most effective public health policy planning tools. The supply of vaccines, however, is limited and an important challenge is to optimally allocate the vaccines to minimize epidemic impact. This resource allocation question (which we refer to as VaccIntDesign) has multiple dimensions: when, where, to whom, etc. Most of the existing literature in this topic deals with the latter (to whom), proposing policies that prioritize individuals by age and disease risk. However, since seasonal influenza spread has a typical spatial trend, and due to the temporal constraints enforced by the availability schedule, the when and where problems become equally, if not more, relevant. In this paper, we study the VaccIntDesign problem in the context of seasonal influenza spread in the United States. We develop a national scale metapopulation model for influenza that integrates both short and long distance human mobility, along with realistic data on vaccine uptake. We also design GreedyAlloc, a greedy algorithm for allocating the vaccine supply at the state level under temporal constraints and show that such a strategy improves over the current baseline of pro-rata allocation, and the improvement is more pronounced for higher vaccine efficacy and moderate flu season intensity. Further, the resulting strategy resembles a ring vaccination applied spatiallyacross the US.

Annual vaccination campaigns continue to be one of the prime measures which help alleviate the burden of seasonal influenza. Due to production and logistic constraints, there is a need for prioritization policies associated with vaccine deployment. While there is general consensus on age-based or risk-based prioritization, spatial optimization of vaccine allocation has not yet been explored in sufficient detail. In order to do this, we develop a mechanistic model of influenza spread across the United States, and propose a greedy mechanism for spatial optimization. We test the methodology on different realistic scenarios with temporal constraints on vaccine production.

Increased infection severity in downstream cities in infectious disease transmission and tourists surveillance analysis

Infectious disease severely threatens human life. Human mobility and travel patterns influence the spread of infection between cities and countries. We find that the infection severity in downstream cities during outbreaks is related to transmission rate, recovery rate, travel rate, travel duration and the average number of person-to-person contacts per day. The peak value of the infected population in downstream cities is slightly higher than that in source cities. However, as the number of cities increases, the severity increase percentage during outbreaks between end and source cities is constant. The surveillance of important nodes connecting cities, such as airports and train stations, can help delay the occurrence time of infection outbreaks. The city-entry surveillance of hub cities is not only useful to these cities, but also to cities that are strongly connected (i.e., have a high travel rate) to them. The city-exit surveillance of hub cities contributes to other downstream cities, but only slightly to itself. Surveillance conducted in hub cities is highly efficient in controlling infection transmission. Only strengthening the individual immunity of frequent travellers is not efficient for infection control. However, reducing the number of person-to-person contacts per day effectively limits the spread of infection.

What can urban mobility data reveal about the spatial distribution of infection in a single city?

Background

Infectious diseases spread through inherently spatial processes. Road and air traffic data have been used to model these processes at national and global scales. At metropolitan scales, however, mobility patterns are fundamentally different and less directly observable. Estimating the spatial distribution of infection has public health utility, but few studies have investigated this at an urban scale. In this study we address the question of whether the use of urban-scale mobility data can improve the prediction of spatial patterns of influenza infection. We compare the use of different sources of urban-scale mobility data, and investigate the impact of other factors relevant to modelling mobility, including mixing within and between regions, and the influence of hub and spoke commuting patterns.

Methods

We used journey-to-work (JTW) data from the Australian 2011 Census, and GPS journey data from the Sygic GPS Navigation & Maps mobile app, to characterise population mixing patterns in a spatially-explicit SEIR (susceptible, exposed, infectious, recovered) meta-population model.

Results

Using the JTW data to train the model leads to an increase in the proportion of infections that arise in central Melbourne, which is indicative of the city’s spoke-and-hub road and public transport networks, and of the commuting patterns reflected in these data. Using the GPS data increased the infections in central Melbourne to a lesser extent than the JTW data, and produced a greater heterogeneity in the middle and outer regions. Despite the limitations of both mobility data sets, the model reproduced some of the characteristics observed in the spatial distribution of reported influenza cases.

Conclusions

Urban mobility data sets can be used to support models that capture spatial heterogeneity in the transmission of infectious diseases at a metropolitan scale. These data should be adjusted to account for relevant urban features, such as highly-connected hubs where the resident population is likely to experience a much lower force of infection that the transient population. In contrast to national and international scales, the relationship between mobility and infection at an urban level is much less apparent, and requires a richer characterisation of population mobility and contact.

Electronic supplementary material

The online version of this article (10.1186/s12889-019-6968-x) contains supplementary material, which is available to authorized users.

Seasonal characteristics of influenza vary regionally across US

Given substantial regional differences in absolute humidity across the US and our understanding of the relationship between absolute humidity and influenza, we may expect important differences in regional seasonal influenza activity. Here, we assessed cross-seasonal influenza activity by comparing counts of positive influenza A and B rapid test results during the influenza season versus summer baseline periods for the 2016/2017 and 2017/2018 influenza years. Our analysis indicates significant regional patterns in cross-seasonal influenza activity, with relatively fewer influenza cases during the influenza season compared to summertime baseline periods in humid areas of the US, particularly in Florida and Hawaii. The cross-seasonal ratios vary from year-to-year and influenza type, but the geographic patterning of the ratios is relatively consistent. Mixed-effects regression models indicated absolute humidity during the influenza season was the strongest predictor of cross-seasonal influenza activity, suggesting a relationship between absolute humidity and cross-seasonal influenza activity. There was also evidence that absolute humidity during the summer plays a role, as well. This analysis suggests that spatial variation in seasonal absolute humidity levels may generate important regional differences in seasonal influenza activity and dynamics in the US.

Patterns of seasonal influenza activity in U.S. core-based statistical areas, described using prescriptions of oseltamivir in Medicare claims data

Using Medicare claims data on prescriptions of oseltamivir dispensed to people 65 years old and older, we present a descriptive analysis of patterns of influenza activity in the United States for 579 core-based statistical areas (CBSAs) from the 2010-2011 through the 2015-2016 influenza seasons. During this time, 1,010,819 beneficiaries received a prescription of oseltamivir, ranging from 45,888 in 2011-2012 to 380,745 in 2014-2015. For each season, the peak weekly number of prescriptions correlated with the total number of prescriptions (Pearson's r ≥ 0.88). The variance in peak timing decreased with increasing severity (p < 0.0001). Among these 579 CBSAs, neither peak timing, nor relative timing, nor severity of influenza seasons showed evidence of spatial autocorrelation (0.02 ≤ Moran's I ≤ 0.23). After aggregating data to the state level, agreement between the seasonal severity at the CBSA level and the state level was fair (median Cohen's weighted κ = 0.32, interquartile range = 0.26-0.39). Based on seasonal severity, relative timing, and geographic place, we used hierarchical agglomerative clustering to join CBSAs into influenza zones for each season. Seasonal maps of influenza zones showed no obvious patterns that might assist in predicting influenza zones for future seasons. Because of the large number of prescriptions, these data may be especially useful for characterizing influenza activity and geographic distribution during low severity seasons, when other data sources measuring influenza activity are likely to be sparse.

Fogarty International Center collaborative networks in infectious disease modeling: Lessons learnt in research and capacity building

Due to a combination of ecological, political, and demographic factors, the emergence of novel pathogens has been increasingly observed in animals and humans in recent decades. Enhancing global capacity to study and interpret infectious disease surveillance data, and to develop data-driven computational models to guide policy, represents one of the most cost-effective, and yet overlooked, ways to prepare for the next pandemic. Epidemiological and behavioral data from recent pandemics and historic scourges have provided rich opportunities for validation of computational models, while new sequencing technologies and the 'big data' revolution present new tools for studying the epidemiology of outbreaks in real time. For the past two decades, the Division of International Epidemiology and Population Studies (DIEPS) of the NIH Fogarty International Center has spearheaded two synergistic programs to better understand and devise control strategies for global infectious disease threats. The Multinational Influenza Seasonal Mortality Study (MISMS) has strengthened global capacity to study the epidemiology and evolutionary dynamics of influenza viruses in 80 countries by organizing international research activities and training workshops. The Research and Policy in Infectious Disease Dynamics (RAPIDD) program and its precursor activities has established a network of global experts in infectious disease modeling operating at the research-policy interface, with collaborators in 78 countries. These activities have provided evidence-based recommendations for disease control, including during large-scale outbreaks of pandemic influenza, Ebola and Zika virus. Together, these programs have coordinated international collaborative networks to advance the study of emerging disease threats and the field of computational epidemic modeling. A global community of researchers and policy-makers have used the tools and trainings developed by these programs to interpret infectious disease patterns in their countries, understand modeling concepts, and inform control policies. Here we reflect on the scientific achievements and lessons learnt from these programs (h-index = 106 for RAPIDD and 79 for MISMS), including the identification of outstanding researchers and fellows; funding flexibility for timely research workshops and working groups (particularly relative to more traditional investigator-based grant programs); emphasis on group activities such as large-scale modeling reviews, model comparisons, forecasting challenges and special journal issues; strong quality control with a light touch on outputs; and prominence of training, data-sharing, and joint publications.

A maximum curvature method for estimating epidemic onset of seasonal influenza in Japan

BACKGROUND

Detecting the onset of influenza epidemic is important for epidemiological surveillance and for investigating the factors driving spatiotemporal transmission patterns. Most approaches define the epidemic onset based on thresholds, which use subjective criteria and are specific to individual surveillance systems.

METHODS

We applied the empirical threshold method (ETM), together with two non-thresholding methods, including the maximum curvature method (MCM) that we proposed and the segmented regression method (SRM), to determine onsets of influenza epidemics in each prefecture of Japan, using sentinel surveillance data of influenza-like illness (ILI) from 2012/2013 through 2017/2018. Performance of the MCM and SRM was evaluated, in terms of epidemic onset, end, and duration, with those derived from the ETM using the nationwide epidemic onset indicator of 1.0 ILI case per sentinel per week.

RESULTS

The MCM and SRM yielded complete estimates for each of Japan's 47 prefectures. In contrast, ETM estimates for Kagoshima during 2012/2013 and for Okinawa during all six influenza seasons, except 2013/2014, were invalid. The MCM showed better agreement in all estimates with the ETM than the SRM (R2 = 0.82, p < 0.001 vs. R2 = 0.34, p < 0.001 for epidemic onset; R2 = 0.18, p < 0.001 vs. R2 = 0.05, p < 0.001 for epidemic end; R2 = 0.28, p < 0.001 vs. R2 < 0.01, p = 0.35 for epidemic duration). Prefecture-specific thresholds for epidemic onset and end were established using the MCM.

CONCLUSIONS

The Japanese national epidemic onset threshold is not applicable to all prefectures, particularly Okinawa. The MCM could be used to establish prefecture-specific epidemic thresholds that faithfully characterize influenza activity, serving as useful complements to the influenza surveillance system in Japan.