Delineating natural catchment health districts with routinely collected health data from women's travel to give birth in Ghana

Background

Health service areas are essential for planning, policy and managing public health interventions. In this study, we delineate health service areas from routinely collected health data as a robust geographic basis for presenting access to maternal care indicators.

Methods

A zone design algorithm was adapted to delineate health service areas through a cross-sectional, ecological study design. Health sub-districts were merged into health service areas such that patient flows across boundaries were minimised. Delineated zones and existing administrative boundaries were used to provide estimates of access to maternal health services. We analysed secondary data comprising routinely collected health records from 32,921 women attending 27 hospitals to give birth, spatial demographic data, a service provision assessment on the quality of maternal healthcare and health sub-district boundaries from Eastern Region, Ghana.

Results

Clear patterns of cross border movement to give birth emerged from the analysis, but more women originated closer to the hospitals. After merging the 250 sub-districts in 33 districts, 11 health service areas were created. The minimum percent of internal flows of women giving birth within any health service area was 97.4%. Because the newly delineated boundaries are more “natural” and sensitive to observed flow patterns, when we calculated areal indicator estimates, they showed a marked improvement over the existing administrative boundaries, with the inclusion of a hospital in every health service area.

Conclusion

Health planning can be improved by using routine health data to delineate natural catchment health districts. In addition, data-driven geographic boundaries derived from public health events will improve areal health indicator estimates, planning and interventions.

Untangling the changing impact of non-pharmaceutical interventions and vaccination on European COVID-19 trajectories

Non-pharmaceutical interventions (NPIs) and vaccination are two fundamental approaches for mitigating the coronavirus disease 2019 (COVID-19) pandemic. However, the real-world impact of NPIs versus vaccination, or a combination of both, on COVID-19 remains uncertain. To address this, we built a Bayesian inference model to assess the changing effect of NPIs and vaccination on reducing COVID-19 transmission, based on a large-scale dataset including epidemiological parameters, virus variants, vaccines, and climate factors in Europe from August 2020 to October 2021. We found that (1) the combined effect of NPIs and vaccination resulted in a 53% (95% confidence interval: 42–62%) reduction in reproduction number by October 2021, whereas NPIs and vaccination reduced the transmission by 35% and 38%, respectively; (2) compared with vaccination, the change of NPI effect was less sensitive to emerging variants; (3) the relative effect of NPIs declined 12% from May 2021 due to a lower stringency and the introduction of vaccination strategies. Our results demonstrate that NPIs were complementary to vaccination in an effort to reduce COVID-19 transmission, and the relaxation of NPIs might depend on vaccination rates, control targets, and vaccine effectiveness concerning extant and emerging variants.

Non-pharmaceutical interventions (NPIs) and COVID-19 vaccination have been implemented concurrently, making their relative effects difficult to measure. Here, the authors show that effects of NPIs reduced as vaccine coverage increased, but that NPIs could still be important in the context of more transmissible variants.

Multilevel analysis of predictors of multiple indicators of childhood vaccination in Nigeria

Background

Substantial inequalities exist in childhood vaccination coverage levels. To increase vaccine uptake, factors that predict vaccination coverage in children should be identified and addressed.

Methods

Using data from the 2018 Nigeria Demographic and Health Survey and geospatial data sets, we fitted Bayesian multilevel binomial and multinomial logistic regression models to analyse independent predictors of three vaccination outcomes: receipt of the first dose of Pentavalent vaccine (containing diphtheria-tetanus-pertussis, Hemophilus influenzae type B and Hepatitis B vaccines) (PENTA1) (n = 6059) and receipt of the third dose having received the first (PENTA3/1) (n = 3937) in children aged 12–23 months, and receipt of measles vaccine (MV) (n = 11839) among children aged 12–35 months.

Results

Factors associated with vaccination were broadly similar for documented versus recall evidence of vaccination. Based on any evidence of vaccination, we found that health card/document ownership, receipt of vitamin A and maternal educational level were significantly associated with each outcome. Although the coverage of each vaccine dose was higher in urban than rural areas, urban residence was not significant in multivariable analyses that included travel time. Indicators relating to socio-economic status, as well as ethnic group, skilled birth attendance, lower travel time to the nearest health facility and problems seeking health care were significantly associated with both PENTA1 and MV. Maternal religion was related to PENTA1 and PENTA3/1 and maternal age related to MV and PENTA3/1; other significant variables were associated with one outcome each. Substantial residual community level variances in different strata were observed in the fitted models for each outcome.

Conclusion

Our analysis has highlighted socio-demographic and health care access factors that affect not only beginning but completing the vaccination series in Nigeria. Other factors not measured by the DHS such as health service quality and community attitudes should also be investigated and addressed to tackle inequities in coverage.

Unmet need for COVID-19 vaccination coverage in Kenya

COVID-19 has impacted the health and livelihoods of billions of people since it emerged in 2019. Vaccination for COVID-19 is a critical intervention that is being rolled out globally to end the pandemic. Understanding the spatial inequalities in vaccination coverage and access to vaccination centres is important for planning this intervention nationally. Here, COVID-19 vaccination data, representing the number of people given at least one dose of vaccine, a list of the approved vaccination sites, population data and ancillary GIS data were used to assess vaccination coverage, using Kenya as an example. Firstly, physical access was modelled using travel time to estimate the proportion of population within 1 hour of a vaccination site. Secondly, a Bayesian conditional autoregressive (CAR) model was used to estimate the COVID-19 vaccination coverage and the same framework used to forecast coverage rates for the first quarter of 2022. Nationally, the average travel time to a designated COVID-19 vaccination site (n = 622) was 75.5 min (Range: 62.9 - 94.5 min) and over 87% of the population >18 years reside within 1 hour to a vaccination site. The COVID-19 vaccination coverage in December 2021 was 16.70% (95% CI: 16.66 - 16.74) - 4.4 million people and was forecasted to be 30.75% (95% CI: 25.04 - 36.96) - 8.1 million people by the end of March 2022. Approximately 21 million adults were still unvaccinated in December 2021 and, in the absence of accelerated vaccine uptake, over 17.2 million adults may not be vaccinated by end March 2022 nationally. Our results highlight geographic inequalities at sub-national level and are important in targeting and improving vaccination coverage in hard-to-reach populations. Similar mapping efforts could help other countries identify and increase vaccination coverage for such populations.

High-resolution population estimation using household survey data and building footprints

The national census is an essential data source to support decision-making in many areas of public interest. However, this data may become outdated during the intercensal period, which can stretch up to several decades. In this study, we develop a Bayesian hierarchical model leveraging recent household surveys and building footprints to produce up-to-date population estimates. We estimate population totals and age and sex breakdowns with associated uncertainty measures within grid cells of approximately 100 m in five provinces of the Democratic Republic of the Congo, a country where the last census was completed in 1984. The model exhibits a very good fit, with an R² value of 0.79 for out-of-sample predictions of population totals at the microcensus-cluster level and 1.00 for age and sex proportions at the province level. This work confirms the benefits of combining household surveys and building footprints for high-resolution population estimation in countries with outdated censuses.

A lack of up-to-date population figures may hamper effective decision-making. Here, the authors develop a Bayesian model to estimate population data at high resolution in five provinces of the Democratic Republic of the Congo.

Understanding factors associated with attending secondary school in Tanzania using household survey data

BACKGROUND

Sustainable Development Goal (SDG) 4 aims to ensure inclusive and equitable access for all by 2030, leaving no one behind. One indicator selected to measure progress towards achievement is the participation rate of youth in education (SDG 4.3.1). Here we aim to understand drivers of school attendance using one country in East Africa as an example.

METHODS

Nationally representative household survey data (2015-16 Tanzania Demographic and Health Survey) were used to explore individual, household and contextual factors associated with secondary school attendance in Tanzania. These included, age, head of household's levels of education, gender, household wealth index and total number of children under five. Contextual factors such as average pupil to qualified teacher ratio and geographic access to school were also tested at cluster level. A two-level random intercept logistic regression model was used in exploring association of these factors with attendance in a multi-level framework.

RESULTS

Age of household head, educational attainments of either of the head of the household or parent, child characteristics such as gender, were important predictors of secondary school attendance. Being in a richer household and with fewer siblings of lower age (under the age of 5) were associated with increased odds of attendance (OR = 0.91, CI 95%: 0.86; 0.96). Contextual factors were less likely to be associated with secondary school attendance.

CONCLUSIONS

Individual and household level factors are likely to impact secondary school attendance rates more compared to contextual factors, suggesting an increased focus of interventions at these levels is needed. Future studies should explore the impact of interventions targeting these levels. Policies should ideally promote gender equality in accessing secondary school as well as support those families where the dependency ratio is high. Strategies to reduce poverty will also increase the likelihood of attending school.

Impacts of worldwide individual non-pharmaceutical interventions on COVID-19 transmission across waves and space

Governments worldwide have rapidly deployed non-pharmaceutical interventions (NPIs) to mitigate the COVID-19 pandemic. However, the effect of these individual NPI measures across space and time has yet to be sufficiently assessed, especially with the increase of policy fatigue and the urge for NPI relaxation in the vaccination era. Using the decay ratio in the suppression of COVID-19 infections and multi-source big data, we investigated the changing performance of different NPIs across waves from global and regional levels (in 133 countries) to national and subnational (in the United States of America [USA]) scales before the implementation of mass vaccination. The synergistic effectiveness of all NPIs for reducing COVID-19 infections declined along waves, from 95.4% in the first wave to 56.0% in the third wave recently at the global level and similarly from 83.3% to 58.7% at the USA national level, while it had fluctuating performance across waves on regional and subnational scales. Regardless of geographical scale, gathering restrictions and facial coverings played significant roles in epidemic mitigation before the vaccine rollout. Our findings have important implications for continued tailoring and implementation of NPI strategies, together with vaccination, to mitigate future COVID-19 waves, caused by new variants, and other emerging respiratory infectious diseases.

Global holiday datasets for understanding seasonal human mobility and population dynamics

Public and school holidays have important impacts on population mobility and dynamics across multiple spatial and temporal scales, subsequently affecting the transmission dynamics of infectious diseases and many socioeconomic activities. However, worldwide data on public and school holidays for understanding their changes across regions and years have not been assembled into a single, open-source and multitemporal dataset. To address this gap, an open access archive of data on public and school holidays in 2010-2019 across the globe at daily, weekly, and monthly timescales was constructed. Airline passenger volumes across 90 countries from 2010 to 2018 were also assembled to illustrate the usage of the holiday data for understanding the changing spatiotemporal patterns of population movements.

Assessing the characteristics of un- and under-vaccinated children in low- and middle-income countries: A multi-level cross-sectional study

Achieving equity in vaccination coverage has been a critical priority within the global health community. Despite increased efforts recently, certain populations still have a high proportion of un- and under-vaccinated children in many low- and middle-income countries (LMICs). These populations are often assumed to reside in remote-rural areas, urban slums and conflict-affected areas. Here, we investigate the effects of these key community-level factors, alongside a wide range of other individual, household and community level factors, on vaccination coverage. Using geospatial datasets, including cross-sectional data from the most recent Demographic and Health Surveys conducted between 2008 and 2018 in nine LMICs, we fitted Bayesian multi-level binary logistic regression models to determine key community-level and other factors significantly associated with non- and under-vaccination. We analyzed the odds of receipt of the first doses of diphtheria-tetanus-pertussis (DTP1) vaccine and measles-containing vaccine (MCV1), and receipt of all three recommended DTP doses (DTP3) independently, in children aged 12-23 months. In bivariate analyses, we found that remoteness increased the odds of non- and under-vaccination in nearly all the study countries. We also found evidence that living in conflict and urban slum areas reduced the odds of vaccination, but not in most cases as expected. However, the odds of vaccination were more likely to be lower in urban slums than formal urban areas. Our multivariate analyses revealed that the key community variables-remoteness, conflict and urban slum-were sometimes associated with non- and under-vaccination, but they were not frequently predictors of these outcomes after controlling for other factors. Individual and household factors such as maternal utilization of health services, maternal education and ethnicity, were more common predictors of vaccination. Reaching the Immunisation Agenda 2030 target of reducing the number of zero-dose children by 50% by 2030 will require country tailored analyses and strategies to identify and reach missed communities with reliable immunisation services.

Mobility in China, 2020: a tale of four phases

2020 was an unprecedented year, with rapid and drastic changes in human mobility due to the COVID-19 pandemic. To understand the variation in commuting patterns among the Chinese population across stable and unstable periods, we used nationwide mobility data from 318 million mobile phone users in China to examine the extreme fluctuations of population movements in 2020, ranging from the Lunar New Year travel season (chunyun), to the exceptional calm of COVID-19 lockdown, and then to the recovery period. We observed that cross-city movements, which increased substantially in chunyun and then dropped sharply during the lockdown, are primarily dependent on travel distance and the socio-economic development of cities. Following the Lunar New Year holiday, national mobility remained low until mid-February, and COVID-19 interventions delayed more than 72.89 million people returning to large cities. Mobility network analysis revealed clusters of highly connected cities, conforming to the social-economic division of urban agglomerations in China. While the mass migration back to large cities was delayed, smaller cities connected more densely to form new clusters. During the recovery period after travel restrictions were lifted, the netflows of over 55% city pairs reversed in direction compared to before the lockdown. These findings offer the most comprehensive picture of Chinese mobility at fine resolution across various scenarios in China and are of critical importance for decision making regarding future public-health-emergency response, transportation planning and regional economic development, among others.

Domestic and international mobility trends in the United Kingdom during the COVID-19 pandemic: an analysis of facebook data

BACKGROUND

Since early March 2020, the COVID-19 epidemic across the United Kingdom has led to a range of social distancing policies, which resulted in changes to mobility across different regions. An understanding of how these policies impacted travel patterns over time and at different spatial scales is important for designing effective strategies, future pandemic planning and in providing broader insights on the population geography of the country. Crowd level data on mobile phone usage can be used as a proxy for population mobility patterns and provide a way of quantifying in near-real time the impact of social distancing measures on changes in mobility.

METHODS

Here we explore patterns of change in densities, domestic and international flows and co-location of Facebook users in the UK from March 2020 to March 2021.

RESULTS

We find substantial heterogeneities across time and region, with large changes observed compared to pre-pademic patterns. The impacts of periods of lockdown on distances travelled and flow volumes are evident, with each showing variations, but some significant reductions in co-location rates. Clear differences in multiple metrics of mobility are seen in central London compared to the rest of the UK, with each of Scotland, Wales and Northern Ireland showing significant deviations from England at times. Moreover, the impacts of rapid changes in rules on international travel to and from the UK are seen in substantial fluctuations in traveller volumes by destination.

CONCLUSIONS

While questions remain about the representativeness of the Facebook data, previous studies have shown strong correspondence with census-based data and alternative mobility measures, suggesting that findings here are valuable for guiding strategies.

Key opportunities and challenges for the use of big data in migration research and policy

Migration is one of the defining issues of the 21st century. Better data is required to improve understanding about how and why people are moving, target interventions and support evidence-based migration policy. Big data, defined as large, complex data from diverse sources, is regularly proposed as a solution to help address current gaps in knowledge. The authors participated in a workshop held in London, UK, in July 2019, that brought together experts from the United Nations (UN), humanitarian non-governmental organisations (NGOs), policy and academia to develop a better understanding of how big data could be used for migration research and policy. We identified six key areas regarding the application of big data in migration research and policy: accessing and utilising data; integrating data sources and knowledge; understanding environmental drivers of migration; improving healthcare access for migrant populations; ethical and security concerns around the use of big data; and addressing political narratives. We advocate the need for careful consideration of the challenges faced by the use of big data, as well as increased cross-disciplinary collaborations to advance the use of big data in migration research whilst safeguarding vulnerable migrant communities.

Risk of SARS-CoV-2 Transmission among Air Passengers in China

BACKGROUND

Modern transportation plays a key role in the spread of SARS-CoV-2 and new variants. However, little is known about the exact transmission risk of the virus on airplanes.

METHODS

Using the itinerary and epidemiological data of COVID-19 cases and close contacts on domestic airplanes departing from Wuhan city in China before the lockdown on January 23, 2020, we estimated the upper and lower bounds of overall transmission risk of COVID-19 among travellers.

RESULTS

175 index cases were identified among 5797 passengers on 177 airplanes. The upper and lower attack rates (ARs) of a seat were 0.60% (34/5622, 95%CI 0.43%-0.84%) and 0.33% (18/5400, 95%CI 0.21%-0.53%), respectively. In the upper- and lower-bound risk estimates, each index case infected 0.19 (SD 0.45) and 0.10 (SD 0.32) cases respectively. The seats immediately adjacent to the index cases had an AR of 9.2% (95%CI 5.7%-14.4%), with a relative risk 27.8 (95%CI 14.4-53.7) compared to other seats in the upper limit estimation. The middle seat had the highest AR (0.7%, 95%CI 0.4%-1.2%). The upper-bound AR increased from 0.7% (95%CI 0.5%-1.0%) to 1.2% (95%CI 0.4%-3.3%) when the co-travel time increased from 2.0 hours to 3.3 hours.

CONCLUSIONS

The ARs among travellers varied by seat distance from the index case and joint travel time, but the variation was not significant between the types of aircraft. The overall risk of SARS-CoV-2 transmission during domestic travel on planes was relatively low. These findings can improve our understanding of COVID-19 spread during travel and inform response efforts in the pandemic.

Characterizing human mobility patterns in rural settings of sub-Saharan Africa

Human mobility is a core component of human behavior and its quantification is critical for understanding its impact on infectious disease transmission, traffic forecasting, access to resources and care, intervention strategies, and migratory flows. When mobility data are limited, spatial interaction models have been widely used to estimate human travel, but have not been extensively validated in low- and middle-income settings. Geographic, sociodemographic, and infrastructure differences may impact the ability for models to capture these patterns, particularly in rural settings. Here, we analyzed mobility patterns inferred from mobile phone data in four Sub-Saharan African countries to investigate the ability for variants on gravity and radiation models to estimate travel. Adjusting the gravity model such that parameters were fit to different trip types, including travel between more or less populated areas and/or different regions, improved model fit in all four countries. This suggests that alternative models may be more useful in these settings and better able to capture the range of mobility patterns observed.

A review of geospatial methods for population estimation and their use in constructing reproductive, maternal, newborn, child and adolescent health service indicators

Background

Household survey data are frequently used to measure reproductive, maternal, newborn, child and adolescent health (RMNCAH) service utilisation in low and middle income countries. However, these surveys are typically only undertaken every 5 years and tend to be representative of larger geographical administrative units. Investments in district health management information systems (DHMIS) have increased the capability of countries to collect continuous information on the provision of RMNCAH services at health facilities. However, reliable and recent data on population distributions and demographics at subnational levels necessary to construct RMNCAH coverage indicators are often missing. One solution is to use spatially disaggregated gridded datasets containing modelled estimates of population counts. Here, we provide an overview of various approaches to the production of gridded demographic datasets and outline their potential and their limitations. Further, we show how gridded population estimates can be used as alternative denominators to produce RMNCAH coverage metrics in combination with data from DHMIS, using childhood vaccination as examples.

Methods

We constructed indicators on the percentage of children one year old for diphtheria, pertussis and tetanus vaccine dose 3 (DTP3) and measles vaccine dose (MCV1) in Zambia and Nigeria at district levels. For the numerators, information on vaccines doses was obtained from each country’s respective DHMIS. For the denominators, the number of children was obtained from 3 different sources including national population projections and aggregated gridded estimates derived using top-down and bottom-up geospatial methods.

Results

In Zambia, vaccination estimates utilising the bottom-up approach to population estimation substantially reduced the number of districts with > 100% coverage of DTP3 and MCV1 compared to estimates using population projection and the top-down method. In Nigeria, results were mixed with bottom-up estimates having a higher number of districts > 100% and estimates using population projections performing better particularly in the South.

Conclusions

Gridded demographic data utilising traditional and novel data sources obtained from remote sensing offer new potential in the absence of up to date census information in the estimation of RMNCAH indicators. However, the usefulness of gridded demographic data is dependent on several factors including the availability and detail of input data.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12913-021-06370-y.

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.

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.

Untangling introductions and persistence in COVID-19 resurgence in Europe

After the first wave of SARS-CoV-2 infections in spring 2020, Europe experienced a resurgence of the virus starting in late summer 2020 that was deadlier and more difficult to contain1. Relaxed intervention measures and summer travel have been implicated as drivers of the second wave2. Here we build a phylogeographical model to evaluate how newly introduced lineages, as opposed to the rekindling of persistent lineages, contributed to the resurgence of COVID-19 in Europe. We inform this model using genomic, mobility and epidemiological data from 10 European countries and estimate that in many countries more than half of the lineages circulating in late summer resulted from new introductions since 15 June 2020. The success in onward transmission of newly introduced lineages was negatively associated with the local incidence of COVID-19 during this period. The pervasive spread of variants in summer 2020 highlights the threat of viral dissemination when restrictions are lifted, and this needs to be carefully considered in strategies to control the current spread of variants that are more transmissible and/or evade immunity. Our findings indicate that more effective and coordinated measures are required to contain the spread through cross-border travel even as vaccination is reducing disease burden.

Assessing the Effect of Global Travel and Contact Restrictions on Mitigating the COVID-19 Pandemic

Travel restrictions and physical distancing have been implemented across the world to mitigate the coronavirus disease 2019 (COVID-19) pandemic, but studies are needed to understand their effectiveness across regions and time. Based on the population mobility metrics derived from mobile phone geolocation data across 135 countries or territories during the first wave of the pandemic in 2020, we built a metapopulation epidemiological model to measure the effect of travel and contact restrictions on containing COVID-19 outbreaks across regions. We found that if these interventions had not been deployed, the cumulative number of cases could have shown a 97-fold (interquartile range 79-116) increase, as of May 31, 2020. However, their effectiveness depended upon the timing, duration, and intensity of the interventions, with variations in case severity seen across populations, regions, and seasons. Additionally, before effective vaccines are widely available and herd immunity is achieved, our results emphasize that a certain degree of physical distancing at the relaxation of the intervention stage will likely be needed to avoid rapid resurgences and subsequent lockdowns.

Geographical distribution of fertility rates in 70 low-income, lower-middle-income, and upper-middle-income countries, 2010-16: a subnational analysis of cross-sectional surveys

BACKGROUND

Understanding subnational variation in age-specific fertility rates (ASFRs) and total fertility rates (TFRs), and geographical clustering of high fertility and its determinants in low-income and middle-income countries, is increasingly needed for geographical targeting and prioritising of policy. We aimed to identify variation in fertility rates, to describe patterns of key selected fertility determinants in areas of high fertility.

METHODS

We did a subnational analysis of ASFRs and TFRs from the most recent publicly available and nationally representative cross-sectional Demographic and Health Surveys and Multiple Indicator Cluster Surveys collected between 2010 and 2016 for 70 low-income, lower-middle-income, and upper-middle-income countries, across 932 administrative units. We assessed the degree of global spatial autocorrelation by using Moran's I statistic and did a spatial cluster analysis using the Getis-Ord Gi* local statistic to examine the geographical clustering of fertility and key selected fertility determinants. Descriptive analysis was used to investigate the distribution of ASFRs and of selected determinants in each cluster.

FINDINGS

TFR varied from below replacement (2·1 children per women) in 36 of the 932 subnational regions (mainly located in India, Myanmar, Colombia, and Armenia), to rates of 8 and higher in 14 subnational regions, located in sub-Saharan Africa and Afghanistan. Areas with high-fertility clusters were mostly associated with areas of low prevalence of women with secondary or higher education, low use of contraception, and high unmet needs for family planning, although exceptions existed.

INTERPRETATION

Substantial within-country variation in the distribution of fertility rates highlights the need for tailored programmes and strategies in high-fertility cluster areas to increase the use of contraception and access to secondary education, and to reduce unmet need for family planning.

FUNDING

Wellcome Trust, the UK Foreign, Commonwealth and Development Office, and the Bill & Melinda Gates Foundation.

Variation in SARS-CoV-2 outbreaks across sub-Saharan Africa

A surprising feature of the SARS-CoV-2 pandemic to date is the low burdens reported in sub-Saharan Africa (SSA) countries relative to other global regions. Potential explanations (for example, warmer environments1, younger populations2-4) have yet to be framed within a comprehensive analysis. We synthesized factors hypothesized to drive the pace and burden of this pandemic in SSA during the period from 25 February to 20 December 2020, encompassing demographic, comorbidity, climatic, healthcare capacity, intervention efforts and human mobility dimensions. Large diversity in the probable drivers indicates a need for caution in interpreting analyses that aggregate data across low- and middle-income settings. Our simulation shows that climatic variation between SSA population centers has little effect on early outbreak trajectories; however, heterogeneity in connectivity, although rarely considered, is likely an important contributor to variance in the pace of viral spread across SSA. Our synthesis points to the potential benefits of context-specific adaptation of surveillance systems during the ongoing pandemic. In particular, characterizing patterns of severity over age will be a priority in settings with high comorbidity burdens and poor access to care. Understanding the spatial extent of outbreaks warrants emphasis in settings where low connectivity could drive prolonged, asynchronous outbreaks resulting in extended stress to health systems.

Tools for mapping multi-scale settlement patterns of building footprints: An introduction to the R package foot

Spatial datasets of building footprint polygons are becoming more widely available and accessible for many areas in the world. These datasets are important inputs for a range of different analyses, such as understanding the development of cities, identifying areas at risk of disasters, and mapping the distribution of populations. The growth of high spatial resolution imagery and computing power is enabling automated procedures to extract and map building footprints for whole countries. These advances are enabling coverage of building footprint datasets for low and middle income countries which might lack other data on urban land uses. While spatially detailed, many building footprints lack information on structure type, local zoning, or land use, limiting their application. However, morphology metrics can be used to describe characteristics of size, shape, spacing, orientation and patterns of the structures and extract additional information which can be correlated with different structure and settlement types or neighbourhoods. We introduce the foot package, a new set of open-source tools in a flexible R package for calculating morphology metrics for building footprints and summarising them in different spatial scales and spatial representations. In particular our tools can create gridded (or raster) representations of morphology summary metrics which have not been widely supported previously. We demonstrate the tools by creating gridded morphology metrics from all building footprints in England, Scotland and Wales, and then use those layers in an unsupervised cluster analysis to derive a pattern-based settlement typology. We compare our mapped settlement types with two existing settlement classifications. The results suggest that building patterns can help distinguish different urban and rural types. However, intra-urban differences were not well-predicted by building morphology alone. More broadly, though, this case study demonstrates the potential of mapping settlement patterns in the absence of a housing census or other urban planning data.

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

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

Risk of Coronavirus Disease 2019 Transmission in Train Passengers: an Epidemiological and Modeling Study

BACKGROUND

Train travel is a common mode of public transport across the globe; however, the risk of coronavirus disease 2019 (COVID-19) transmission among individual train passengers remains unclear.

METHODS

We quantified the transmission risk of COVID-19 on high-speed train passengers using data from 2334 index patients and 72 093 close contacts who had co-travel times of 0-8 hours from 19 December 2019 through 6 March 2020 in China. We analyzed the spatial and temporal distribution of COVID-19 transmission among train passengers to elucidate the associations between infection, spatial distance, and co-travel time.

RESULTS

The attack rate in train passengers on seats within a distance of 3 rows and 5 columns of the index patient varied from 0 to 10.3% (95% confidence interval [CI], 5.3%-19.0%), with a mean of 0.32% (95% CI, .29%-.37%). Passengers in seats on the same row (including the adjacent passengers to the index patient) as the index patient had an average attack rate of 1.5% (95% CI, 1.3%-1.8%), higher than that in other rows (0.14% [95% CI, .11%-.17%]), with a relative risk (RR) of 11.2 (95% CI, 8.6-14.6). Travelers adjacent to the index patient had the highest attack rate (3.5% [95% CI, 2.9%-4.3%]) of COVID-19 infection (RR, 18.0 [95% CI, 13.9-23.4]) among all seats. The attack rate decreased with increasing distance, but increased with increasing co-travel time. The attack rate increased on average by 0.15% (P = .005) per hour of co-travel; for passengers in adjacent seats, this increase was 1.3% (P = .008), the highest among all seats considered.

CONCLUSIONS

COVID-19 has a high transmission risk among train passengers, but this risk shows significant differences with co-travel time and seat location. During disease outbreaks, when traveling on public transportation in confined spaces such as trains, measures should be taken to reduce the risk of transmission, including increasing seat distance, reducing passenger density, and use of personal hygiene protection.

SARS-CoV-2 European resurgence foretold: interplay of introductions and persistence by leveraging genomic and mobility data

Following the first wave of SARS-CoV-2 infections in spring 2020, Europe experienced a resurgence of the virus starting late summer that was deadlier and more difficult to contain. Relaxed intervention measures and summer travel have been implicated as drivers of the second wave. Here, we build a phylogeographic model to evaluate how newly introduced lineages, as opposed to the rekindling of persistent lineages, contributed to the COVID-19 resurgence in Europe. We inform this model using genomic, mobility and epidemiological data from 10 West European countries and estimate that in many countries more than 50% of the lineages circulating in late summer resulted from new introductions since June 15th. The success in onwards transmission of these lineages is predicted by SARS-CoV-2 incidence during this period. Relatively early introductions from Spain into the United Kingdom contributed to the successful spread of the 20A.EU1/B.1.177 variant. The pervasive spread of variants that have not been associated with an advantage in transmissibility highlights the threat of novel variants of concern that emerged more recently and have been disseminated by holiday travel. Our findings indicate that more effective and coordinated measures are required to contain spread through cross-border travel.