Modeling geographic vaccination strategies for COVID-19 in Norway.

Vaccination was a key intervention in controlling the COVID-19 pandemic globally. In early 2021, Norway faced significant regional variations in COVID-19 incidence and prevalence, with large differences in population density, necessitating efficient vaccine allocation to reduce infections and severe outcomes. This study explored alternative vaccination strategies to minimize health outcomes (infections, hospitalizations, ICU admissions, deaths) by varying regions prioritized, extra doses prioritized, and implementation start time. Using two models (individual-based and meta-population), we simulated COVID-19 transmission during the primary vaccination period in Norway, covering the first 7 months of 2021. We investigated alternative strategies to allocate more vaccine doses to regions with a higher force of infection. We also examined the robustness of our results and highlighted potential structural differences between the two models. Our findings suggest that early vaccine prioritization could reduce COVID-19 related health outcomes by 8% to 20% compared to a baseline strategy without geographic prioritization. For minimizing infections, hospitalizations, or ICU admissions, the best strategy was to initially allocate all available vaccine doses to fewer high-risk municipalities, comprising approximately one-fourth of the population. For minimizing deaths, a moderate level of geographic prioritization, with approximately one-third of the population receiving doubled doses, gave the best outcomes by balancing the trade-off between vaccinating younger people in high-risk areas and older people in low-risk areas. The actual strategy implemented in Norway was a two-step moderate level aimed at maintaining the balance and ensuring ethical considerations and public trust. However, it did not offer significant advantages over the baseline strategy without geographic prioritization. Earlier implementation of geographic prioritization could have more effectively addressed the main wave of infections, substantially reducing the national burden of the pandemic.

Effects of non-compulsory and mandatory COVID-19 interventions on travel distance and time away from home, Norway, 2021.

BackgroundGiven the societal, economic and health costs of COVID-19 non-pharmaceutical interventions (NPI), it is important to assess their effects. Human mobility serves as a surrogate measure for human contacts and compliance with NPI. In Nordic countries, NPI have mostly been advised and sometimes made mandatory. It is unclear if making NPI mandatory further reduced mobility.AimWe investigated the effect of non-compulsory and follow-up mandatory measures in major cities and rural regions on human mobility in Norway. We identified NPI categories that most affected mobility.MethodsWe used mobile phone mobility data from the largest Norwegian operator. We analysed non-compulsory and mandatory measures with before-after and synthetic difference-in-differences approaches. By regression, we investigated the impact of different NPI on mobility.ResultsNationally and in less populated regions, time travelled, but not distance, decreased after follow-up mandatory measures. In urban areas, however, distance decreased after follow-up mandates, and the reduction exceeded the decrease after initial non-compulsory measures. Stricter metre rules, gyms reopening, and restaurants and shops reopening were significantly associated with changes in mobility.ConclusionOverall, distance travelled from home decreased after non-compulsory measures, and in urban areas, distance further decreased after follow-up mandates. Time travelled reduced more after mandates than after non-compulsory measures for all regions and interventions. Stricter distancing and reopening of gyms, restaurants and shops were associated with changes in mobility.

A real-time regional model for COVID-19: Probabilistic situational awareness and forecasting.

The COVID-19 pandemic is challenging nations with devastating health and economic consequences. The spread of the disease has revealed major geographical heterogeneity because of regionally varying individual behaviour and mobility patterns, unequal meteorological conditions, diverse viral variants, and locally implemented non-pharmaceutical interventions and vaccination roll-out. To support national and regional authorities in surveilling and controlling the pandemic in real-time as it unfolds, we here develop a new regional mathematical and statistical model. The model, which has been in use in Norway during the first two years of the pandemic, is informed by real-time mobility estimates from mobile phone data and laboratory-confirmed case and hospitalisation incidence. To estimate regional and time-varying transmissibility, case detection probabilities, and missed imported cases, we developed a novel sequential Approximate Bayesian Computation method allowing inference in useful time, despite the high parametric dimension. We test our approach on Norway and find that three-week-ahead predictions are precise and well-calibrated, enabling policy-relevant situational awareness at a local scale. By comparing the reproduction numbers before and after lockdowns, we identify spatially heterogeneous patterns in their effect on the transmissibility, with a stronger effect in the most populated regions compared to the national reduction estimated to be 85% (95% CI 78%-89%). Our approach is the first regional changepoint stochastic metapopulation model capable of real time spatially refined surveillance and forecasting during emergencies.

Increased transmissibility of the alpha SARS-CoV-2 variant: evidence from contact tracing data in Oslo, January to February 2021.

BACKGROUND: Information about the contagiousness of new SARS-CoV-2 variants, including the alpha lineage, and how they spread in various locations is essential. Country-specific estimates are needed because local interventions influence transmissibility. METHODS: We analysed contact tracing data from Oslo municipality, reported from January through February 2021, when the alpha lineage became predominant in Norway and estimated the relative transmissibility of the alpha lineage with the use of Poisson regression. RESULTS: Within households, we found an increase in the secondary attack rate by 60% (95% CI 20-114%) among cases infected with the alpha lineage compared to other variants; including all close contacts, the relative increase in the secondary attack rate was 24% (95% CI -6%-43%). There was a significantly higher risk of infecting household members in index cases aged 40-59 years who were infected with the alpha lineage; we found no association between transmission and household size. Overall, including all close contacts, we found that the reproduction number among cases with the alpha lineage was increased by 24% (95% CI 0%-52%), corresponding to an absolute increase of 0.19, compared to the group of index cases infected with other variants. CONCLUSION: Our study suggests that households are the primary locations for rapid transmission of the new lineage alpha.

Low parasite connectivity among three malaria hotspots in Thailand.

Identifying sources and sinks of malaria transmission is critical for designing effective intervention strategies particularly as countries approach elimination. The number of malaria cases in Thailand decreased 90% between 2012 and 2020, yet elimination has remained a major public health challenge with persistent transmission foci and ongoing importation. There are three main hotspots of malaria transmission in Thailand: Ubon Ratchathani and Sisaket in the Northeast; Tak in the West; and Yala in the South. However, the degree to which these hotspots are connected via travel and importation has not been well characterized. Here, we develop a metapopulation model parameterized by mobile phone call detail record data to estimate parasite flow among these regions. We show that parasite connectivity among these regions was limited, and that each of these provinces independently drove the malaria transmission in nearby provinces. Overall, our results suggest that due to the low probability of domestic importation between the transmission hotspots, control and elimination strategies can be considered separately for each region.

Participatory syndromic surveillance as a tool for tracking COVID-19 in Bangladesh.

Limitations in laboratory diagnostic capacity and reporting delays have hampered efforts to mitigate and control the ongoing coronavirus disease 2019 (COVID-19) pandemic globally. To augment traditional lab and hospital-based surveillance, Bangladesh established a participatory surveillance system for the public to self-report symptoms consistent with COVID-19 through multiple channels. Here, we report on the use of this system, which received over 3 million responses within two months, for tracking the COVID-19 outbreak in Bangladesh. Although we observe considerable noise in the data and initial volatility in the use of the different reporting mechanisms, the self-reported syndromic data exhibits a strong association with lab-confirmed cases at a local scale. Moreover, the syndromic data also suggests an earlier spread of the outbreak across Bangladesh than is evident from the confirmed case counts, consistent with predicted spread of the outbreak based on population mobility data. Our results highlight the usefulness of participatory syndromic surveillance for mapping disease burden generally, and particularly during the initial phases of an emerging outbreak.

Reconstructing unseen transmission events to infer dengue dynamics from viral sequences.

For most pathogens, transmission is driven by interactions between the behaviours of infectious individuals, the behaviours of the wider population, the local environment, and immunity. Phylogeographic approaches are currently unable to disentangle the relative effects of these competing factors. We develop a spatiotemporally structured phylogenetic framework that addresses these limitations by considering individual transmission events, reconstructed across spatial scales. We apply it to geocoded dengue virus sequences from Thailand (N = 726 over 18 years). We find infected individuals spend 96% of their time in their home community compared to 76% for the susceptible population (mainly children) and 42% for adults. Dynamic pockets of local immunity make transmission more likely in places with high heterotypic immunity and less likely where high homotypic immunity exists. Age-dependent mixing of individuals and vector distributions are not important in determining spread. This approach provides previously unknown insights into one of the most complex disease systems known and will be applicable to other pathogens.

The impact of mobility network properties on predicted epidemic dynamics in Dhaka and Bangkok.

Properties of city-level commuting networks are expected to influence epidemic potential of cities and modify the speed and spatial trajectory of epidemics when they occur. In this study, we use aggregated mobile phone user data to reconstruct commuter mobility networks for Bangkok (Thailand) and Dhaka (Bangladesh), two megacities in Asia with populations of 16 and 21 million people, respectively. We model the dynamics of directly-transmitted infections (such as SARS-CoV-2) propagating on these commuting networks, and find that differences in network structure between the two cities drive divergent predicted epidemic trajectories: the commuting network in Bangkok is composed of geographically-contiguous modular communities and epidemic dispersal is correlated with geographic distance between locations, whereas the network in Dhaka has less distinct geographic structure and epidemic dispersal is less constrained by geographic distance. We also find that the predicted dynamics of epidemics vary depending on the local topology of the network around the origin of the outbreak. Measuring commuter mobility, and understanding how commuting networks shape epidemic dynamics at the city level, can support surveillance and preparedness efforts in large cities at risk for emerging or imported epidemics.

Megacities as drivers of national outbreaks: The 2017 chikungunya outbreak in Dhaka, Bangladesh.

BACKGROUND: Several large outbreaks of chikungunya have been reported in the Indian Ocean region in the last decade. In 2017, an outbreak occurred in Dhaka, Bangladesh, one of the largest and densest megacities in the world. Population mobility and fluctuations in population density are important drivers of epidemics. Measuring population mobility during outbreaks is challenging but is a particularly important goal in the context of rapidly growing and highly connected cities in low- and middle-income countries, which can act to amplify and spread local epidemics nationally and internationally. METHODS: We first describe the epidemiology of the 2017 chikungunya outbreak in Dhaka and estimate incidence using a mechanistic model of chikungunya transmission parametrized with epidemiological data from a household survey. We combine the modeled dynamics of chikungunya in Dhaka, with mobility estimates derived from mobile phone data for over 4 million subscribers, to understand the role of population mobility on the spatial spread of chikungunya within and outside Dhaka during the 2017 outbreak. RESULTS: We estimate a much higher incidence of chikungunya in Dhaka than suggested by official case counts. Vector abundance, local demographics, and population mobility were associated with spatial heterogeneities in incidence in Dhaka. The peak of the outbreak in Dhaka coincided with the annual Eid holidays, during which large numbers of people traveled from Dhaka to other parts of the country. We show that travel during Eid likely resulted in the spread of the infection to the rest of the country. CONCLUSIONS: Our results highlight the impact of large-scale population movements, for example during holidays, on the spread of infectious diseases. These dynamics are difficult to capture using traditional approaches, and we compare our results to a standard diffusion model, to highlight the value of real-time data from mobile phones for outbreak analysis, forecasting, and surveillance.

Incorporating human mobility data improves forecasts of Dengue fever in Thailand.

Over 390 million people worldwide are infected with dengue fever each year. In the absence of an effective vaccine for general use, national control programs must rely on hospital readiness and targeted vector control to prepare for epidemics, so accurate forecasting remains an important goal. Many dengue forecasting approaches have used environmental data linked to mosquito ecology to predict when epidemics will occur, but these have had mixed results. Conversely, human mobility, an important driver in the spatial spread of infection, is often ignored. Here we compare time-series forecasts of dengue fever in Thailand, integrating epidemiological data with mobility models generated from mobile phone data. We show that geographically-distant provinces strongly connected by human travel have more highly correlated dengue incidence than weakly connected provinces of the same distance, and that incorporating mobility data improves traditional time-series forecasting approaches. Notably, no single model or class of model always outperformed others. We propose an adaptive, mosaic forecasting approach for early warning systems.

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

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

Time-aggregated mobile phone mobility data are sufficient for modelling influenza spread: the case of Bangladesh.

Human mobility plays a major role in the spatial dissemination of infectious diseases. We develop a spatio-temporal stochastic model for influenza-like disease spread based on estimates of human mobility. The model is informed by mobile phone mobility data collected in Bangladesh. We compare predictions of models informed by daily mobility data (reference) with that of models informed by time-averaged mobility data, and mobility model approximations. We find that the gravity model overestimates the spatial synchrony, while the radiation model underestimates the spatial synchrony. Using time-averaged mobility resulted in spatial spreading patterns comparable to the daily mobility model. We fit the model to 2014-2017 influenza data from sentinel hospitals in Bangladesh, using a sequential version of approximate Bayesian computation. We find a good agreement between our estimated model and the case data. We estimate transmissibility and regional spread of influenza in Bangladesh, which are useful for policy planning. Time-averaged mobility appears to be a good proxy for human mobility when modelling infectious diseases. This motivates a more general use of the time-averaged mobility, with important implications for future studies and outbreak control. Moreover, time-averaged mobility is subject to less privacy concerns than daily mobility, containing less temporal information on individual movements.

Mapping imported malaria in Bangladesh using parasite genetic and human mobility data.

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

A theoretical single-parameter model for urbanisation to study infectious disease spread and interventions.

The world is continuously urbanising, resulting in clusters of densely populated urban areas and more sparsely populated rural areas. We propose a method for generating spatial fields with controllable levels of clustering of the population. We build a synthetic country, and use this method to generate versions of the country with different clustering levels. Combined with a metapopulation model for infectious disease spread, this allows us to in silico explore how urbanisation affects infectious disease spread. In a baseline scenario with no interventions, the underlying population clustering seems to have little effect on the final size and timing of the epidemic. Under within-country restrictions on non-commuting travel, the final size decreases with increased population clustering. The effect of travel restrictions on reducing the final size is larger with higher clustering. The reduction is larger in the more rural areas. Within-country travel restrictions delay the epidemic, and the delay is largest for lower clustering levels. We implemented three different vaccination strategies-uniform vaccination (in space), preferentially vaccinating urban locations and preferentially vaccinating rural locations. The urban and uniform vaccination strategies were most effective in reducing the final size, while the rural vaccination strategy was clearly inferior. Visual inspection of some European countries shows that many countries already have high population clustering. In the future, they will likely become even more clustered. Hence, according to our model, within-country travel restrictions are likely to be less and less effective in delaying epidemics, while they will be more effective in decreasing final sizes. In addition, to minimise final sizes, it is important not to neglect urban locations when distributing vaccines. To our knowledge, this is the first study to systematically investigate the effect of urbanisation on infectious disease spread and in particular, to examine effectiveness of prevention measures as a function of urbanisation.

Measles outbreak risk in Pakistan: exploring the potential of combining vaccination coverage and incidence data with novel data-streams to strengthen control.

Although measles incidence has reached historic lows in many parts of the world, the disease still causes substantial morbidity globally. Even where control programs have succeeded in driving measles locally extinct, unless vaccination coverage is maintained at extremely high levels, susceptible numbers may increase sufficiently to spark large outbreaks. Human mobility will drive potentially infectious contacts and interact with the landscape of susceptibility to determine the pattern of measles outbreaks. These interactions have proved difficult to characterise empirically. We explore the degree to which new sources of data combined with existing public health data can be used to evaluate the landscape of immunity and the role of spatial movement for measles introductions by retrospectively evaluating our ability to predict measles outbreaks in vaccinated populations. Using inferred spatial patterns of accumulation of susceptible individuals and travel data, we predicted the timing of epidemics in each district of Pakistan during a large measles outbreak in 2012-2013 with over 30 000 reported cases. We combined these data with mobility data extracted from over 40 million mobile phone subscribers during the same time frame in the country to quantify the role of connectivity in the spread of measles. We investigate how different approaches could contribute to targeting vaccination efforts to reach districts before outbreaks started. While some prediction was possible, accuracy was low and we discuss key uncertainties linked to existing data streams that impede such inference and detail what data might be necessary to robustly infer timing of epidemics.

Understanding tie strength in social networks using a local "bow tie" framework.

Understanding factors associated with tie strength in social networks is essential in a wide variety of settings. With the internet and cellular phones providing additional avenues of communication, measuring and inferring tie strength has become much more complex. We introduce the social bow tie framework, which consists of a focal tie and all actors connected to either or both of the two focal nodes on either side of the focal tie. We also define several intuitive and interpretable metrics that quantify properties of the bow tie which enable us to investigate associations between the strength of the "central" tie and properties of the bow tie. We combine the bow tie framework with machine learning to investigate what aspects of the bow tie are most predictive of tie strength in two very different types of social networks, a collection of medium-sized social networks from 75 rural villages in India and a nationwide call network of European mobile phone users. Our results show that tie strength depends not only on the properties of shared friends, but also on non-shared friends, those observable to only one person in the tie, hence introducing a fundamental asymmetry to social interaction.

The peer effect on pain tolerance.

Background and aims Twin studies have found that approximately half of the variance in pain tolerance can be explained by genetic factors, while shared family environment has a negligible effect. Hence, a large proportion of the variance in pain tolerance is explained by the (non-shared) unique environment. The social environment beyond the family is a potential candidate for explaining some of the variance in pain tolerance. Numerous individual traits have previously shown to be associated with friendship ties. In this study, we investigate whether pain tolerance is associated with friendship ties. Methods We study the friendship effect on pain tolerance by considering data from the Tromsø Study: Fit Futures I, which contains pain tolerance measurements and social network information for adolescents attending first year of upper secondary school in the Tromsø area in Northern Norway. Pain tolerance was measured with the cold-pressor test (primary outcome), contact heat and pressure algometry. We analyse the data by using statistical methods from social network analysis. Specifically, we compute pairwise correlations in pain tolerance among friends. We also fit network autocorrelation models to the data, where the pain tolerance of an individual is explained by (among other factors) the average pain tolerance of the individual's friends. Results We find a significant and positive relationship between the pain tolerance of an individual and the pain tolerance of their friends. The estimated effect is that for every 1 s increase in friends' average cold-pressor tolerance time, the expected cold-pressor pain tolerance of the individual increases by 0.21 s (p-value: 0.0049, sample size n=997). This estimated effect is controlled for sex. The friendship effect remains significant when controlling for potential confounders such as lifestyle factors and test sequence among the students. Further investigating the role of sex on this friendship effect, we only find a significant peer effect of male friends on males, while there is no significant effect of friends' average pain tolerance on females in stratified analyses. Similar, but somewhat lower estimates were obtained for the other pain modalities. Conclusions We find a positive and significant peer effect in pain tolerance. Hence, there is a significant tendency for students to be friends with others with similar pain tolerance. Sex-stratified analyses show that the only significant effect is the effect of male friends on males. Implications Two different processes can explain the friendship effect in pain tolerance, selection and social transmission. Individuals might select friends directly due to similarity in pain tolerance, or indirectly through similarity in other confounding variables that affect pain tolerance. Alternatively, there is an influence effect among friends either directly in pain tolerance, or indirectly through other variables that affect pain tolerance. If there is indeed a social influence effect in pain tolerance, then the social environment can account for some of the unique environmental variance in pain tolerance. If so, it is possible to therapeutically affect pain tolerance through alteration of the social environment.

Product diffusion through on-demand information-seeking behaviour.

Most models of product adoption predict S-shaped adoption curves. Here we report results from two country-scale experiments in which we find linear adoption curves. We show evidence that the observed linear pattern is the result of active information-seeking behaviour: individuals actively pulling information from several central sources facilitated by modern Internet searches. Thus, a constant baseline rate of interest sustains product diffusion, resulting in a linear diffusion process instead of the S-shaped curve of adoption predicted by many diffusion models. The main experiment seeded 70 000 (48 000 in Experiment 2) unique voucher codes for the same product with randomly sampled nodes in a social network of approximately 43 million individuals with about 567 million ties. We find that the experiment reached over 800 000 individuals with 80% of adopters adopting the same product-a winner-take-all dynamic consistent with search engine driven rankings that would not have emerged had the products spread only through a network of social contacts. We provide evidence for (and characterization of) this diffusion process driven by active information-seeking behaviour through analyses investigating (a) patterns of geographical spreading; (b) the branching process; and (c) diffusion heterogeneity. Using data on adopters' geolocation we show that social spreading is highly localized, while on-demand diffusion is geographically independent. We also show that cascades started by individuals who actively pull information from central sources are more effective at spreading the product among their peers.

Multinational patterns of seasonal asymmetry in human movement influence infectious disease dynamics.

Seasonal variation in human mobility is globally ubiquitous and affects the spatial spread of infectious diseases, but the ability to measure seasonality in human movement has been limited by data availability. Here, we use mobile phone data to quantify seasonal travel and directional asymmetries in Kenya, Namibia, and Pakistan, across a spectrum from rural nomadic populations to highly urbanized communities. We then model how the geographic spread of several acute pathogens with varying life histories could depend on country-wide connectivity fluctuations through the year. In all three countries, major national holidays are associated with shifts in the scope of travel. Within this broader pattern, the relative importance of particular routes also fluctuates over the course of the year, with increased travel from rural to urban communities after national holidays, for example. These changes in travel impact how fast communities are likely to be reached by an introduced pathogen.