A simulation study of disaggregation regression for spatial disease mapping.

Disaggregation regression has become an important tool in spatial disease mapping for making fine-scale predictions of disease risk from aggregated response data. By including high resolution covariate information and modeling the data generating process on a fine scale, it is hoped that these models can accurately learn the relationships between covariates and response at a fine spatial scale. However, validating these high resolution predictions can be a challenge, as often there is no data observed at this spatial scale. In this study, disaggregation regression was performed on simulated data in various settings and the resulting fine-scale predictions are compared to the simulated ground truth. Performance was investigated with varying numbers of data points, sizes of aggregated areas and levels of model misspecification. The effectiveness of cross validation on the aggregate level as a measure of fine-scale predictive performance was also investigated. Predictive performance improved as the number of observations increased and as the size of the aggregated areas decreased. When the model was well-specified, fine-scale predictions were accurate even with small numbers of observations and large aggregated areas. Under model misspecification predictive performance was significantly worse for large aggregated areas but remained high when response data was aggregated over smaller regions. Cross-validation correlation on the aggregate level was a moderately good predictor of fine-scale predictive performance. While these simulations are unlikely to capture the nuances of real-life response data, this study gives insight into the effectiveness of disaggregation regression in different contexts.

Mapping malaria seasonality in Madagascar using health facility data.

BACKGROUND: Many malaria-endemic areas experience seasonal fluctuations in case incidence as Anopheles mosquito and Plasmodium parasite life cycles respond to changing environmental conditions. Identifying location-specific seasonality characteristics is useful for planning interventions. While most existing maps of malaria seasonality use fixed thresholds of rainfall, temperature, and/or vegetation indices to identify suitable transmission months, we construct a statistical modelling framework for characterising the seasonal patterns derived directly from monthly health facility data. METHODS: With data from 2669 of the 3247 health facilities in Madagascar, a spatiotemporal regression model was used to estimate seasonal patterns across the island. In the absence of catchment population estimates or the ability to aggregate to the district level, this focused on the monthly proportions of total annual cases by health facility level. The model was informed by dynamic environmental covariates known to directly influence seasonal malaria trends. To identify operationally relevant characteristics such as the transmission start months and associated uncertainty measures, an algorithm was developed and applied to model realisations. A seasonality index was used to incorporate burden information from household prevalence surveys and summarise 'how seasonal' locations are relative to their surroundings. RESULTS: Positive associations were detected between monthly case proportions and temporally lagged covariates of rainfall and temperature suitability. Consistent with the existing literature, model estimates indicate that while most parts of Madagascar experience peaks in malaria transmission near March-April, the eastern coast experiences an earlier peak around February. Transmission was estimated to start in southeast districts before southwest districts, suggesting that indoor residual spraying should be completed in the same order. In regions where the data suggested conflicting seasonal signals or two transmission seasons, estimates of seasonal features had larger deviations and therefore less certainty. CONCLUSIONS: Monthly health facility data can be used to establish seasonal patterns in malaria burden and augment the information provided by household prevalence surveys. The proposed modelling framework allows for evidence-based and cohesive inferences on location-specific seasonal characteristics. As health surveillance systems continue to improve, it is hoped that more of such data will be available to improve our understanding and planning of intervention strategies.

Global estimation of anti-malarial drug effectiveness for the treatment of uncomplicated Plasmodium falciparum malaria 1991-2019.

BACKGROUND: Anti-malarial drugs play a critical role in reducing malaria morbidity and mortality, but their role is mediated by their effectiveness. Effectiveness is defined as the probability that an anti-malarial drug will successfully treat an individual infected with malaria parasites under routine health care delivery system. Anti-malarial drug effectiveness (AmE) is influenced by drug resistance, drug quality, health system quality, and patient adherence to drug use; its influence on malaria burden varies through space and time. METHODS: This study uses data from 232 efficacy trials comprised of 86,776 infected individuals to estimate the artemisinin-based and non-artemisinin-based AmE for treating falciparum malaria between 1991 and 2019. Bayesian spatiotemporal models were fitted and used to predict effectiveness at the pixel-level (5 km × 5 km). The median and interquartile ranges (IQR) of AmE are presented for all malaria-endemic countries. RESULTS: The global effectiveness of artemisinin-based drugs was 67.4% (IQR: 33.3-75.8), 70.1% (43.6-76.0) and 71.8% (46.9-76.4) for the 1991-2000, 2006-2010, and 2016-2019 periods, respectively. Countries in central Africa, a few in South America, and in the Asian region faced the challenge of lower effectiveness of artemisinin-based anti-malarials. However, improvements were seen after 2016, leaving only a few hotspots in Southeast Asia where resistance to artemisinin and partner drugs is currently problematic and in the central Africa where socio-demographic challenges limit effectiveness. The use of artemisinin-based combination therapy (ACT) with a competent partner drug and having multiple ACT as first-line treatment choice sustained high levels of effectiveness. High levels of access to healthcare, human resource capacity, education, and proximity to cities were associated with increased effectiveness. Effectiveness of non-artemisinin-based drugs was much lower than that of artemisinin-based with no improvement over time: 52.3% (17.9-74.9) for 1991-2000 and 55.5% (27.1-73.4) for 2011-2015. Overall, AmE for artemisinin-based and non-artemisinin-based drugs were, respectively, 29.6 and 36% below clinical efficacy as measured in anti-malarial drug trials. CONCLUSIONS: This study provides evidence that health system performance, drug quality and patient adherence influence the effectiveness of anti-malarials used in treating uncomplicated falciparum malaria. These results provide guidance to countries' treatment practises and are critical inputs for malaria prevalence and incidence models used to estimate national level malaria burden.

The contribution of non-malarial febrile illness co-infections to Plasmodium falciparum case counts in health facilities in sub-Saharan Africa.

BACKGROUND: The disease burden of Plasmodium falciparum malaria illness is generally estimated using one of two distinct approaches: either by transforming P. falciparum infection prevalence estimates into incidence estimates using conversion formulae; or through adjustment of counts of recorded P. falciparum-positive fever cases from clinics. Whilst both ostensibly seek to evaluate P. falciparum disease burden, there is an implicit and problematic difference in the metric being estimated. The first enumerates only symptomatic malaria cases, while the second enumerates all febrile episodes coincident with a P. falciparum infection, regardless of the fever's underlying cause. METHODS: Here, a novel approach was used to triangulate community-based data sources capturing P. falciparum infection, fever, and care-seeking to estimate the fraction of P. falciparum-positive fevers amongst children under 5 years of age presenting at health facilities that are attributable to P. falciparum infection versus other non-malarial causes. A Bayesian hierarchical model was used to assign probabilities of malaria-attributable fever (MAF) and non-malarial febrile illness (NMFI) to children under five from a dataset of 41 surveys from 21 countries in sub-Saharan Africa conducted between 2006 and 2016. Using subsequent treatment-seeking outcomes, the proportion of MAF and NMFI amongst P. falciparum-positive febrile children presenting at public clinics was estimated. RESULTS: Across all surveyed malaria-positive febrile children who sought care at public clinics across 41 country-years in sub-Saharan Africa, P. falciparum infection was estimated to be the underlying cause of only 37.7% (31.1-45.4, 95% CrI) of P. falciparum-positive fevers, with significant geographical and temporal heterogeneity between surveys. CONCLUSIONS: These findings highlight the complex nature of the P. falciparum burden amongst children under 5 years of age and indicate that for many children presenting at health clinics, a positive P. falciparum diagnosis and a fever does not necessarily mean P. falciparum is the underlying cause of the child's symptoms, and thus other causes of illness should always be investigated, in addition to prescribing an effective anti-malarial medication. In addition to providing new large-scale estimates of malaria-attributable fever prevalence, the results presented here improve comparability between different methods for calculating P. falciparum disease burden, with significant implications for national and global estimation of malaria burden.

How long do rapid diagnostic tests remain positive after anti-malarial treatment?

BACKGROUND: Rapid diagnostic tests (RDTs) are increasingly becoming a paradigm for both clinical diagnosis of malaria infections and for estimating community parasite prevalence in household malaria indicator surveys in malaria-endemic countries. The antigens detected by RDTs are known to persist in the blood after treatment with anti-malarials, but reports on the duration of persistence (and the effect this has on RDT positivity) of these antigens post-treatment have been variable. METHODS: In this review, published studies on the persistence of positivity of RDTs post-treatment are collated, and a bespoke Bayesian survival model is fit to estimate the number of days RDTs remain positive after treatment. RESULTS: Half of RDTs that detect the antigen histidine-rich protein II (HRP2) are still positive 15 (5-32) days post-treatment, 13 days longer than RDTs that detect the antigen Plasmodium lactate dehydrogenase, and that 5% of HRP2 RDTs are still positive 36 (21-61) days after treatment. The duration of persistent positivity for combination RDTs that detect both antigens falls between that for HRP2- or pLDH-only RDTs, with half of RDTs remaining positive at 7 (2-20) days post-treatment. This study shows that children display persistent RDT positivity for longer after treatment than adults, and that persistent positivity is more common when an individual is treated with artemisinin combination therapy than when treated with other anti-malarials. CONCLUSIONS: RDTs remain positive for a highly variable amount of time after treatment with anti-malarials, and the duration of positivity is highly dependent on the type of RDT used for diagnosis. Additionally, age and treatment both impact the duration of persistence of RDT positivity. The results presented here suggest that caution should be taken when using RDT-derived diagnostic outcomes from cross-sectional data where individuals have had a recent history of anti-malarial treatment.

Geography versus sociodemographics as predictors of changes in daily mobility across the USA during the COVID-19 pandemic: a two-stage regression analysis across 26 metropolitan areas.

OBJECTIVE: We investigated whether a zip code's location or demographics are most predictive of changes in daily mobility throughout the course of the COVID-19 pandemic. DESIGN: We used a population-level study to examine the predictability of daily mobility during the COVID-19 pandemic using a two-stage regression approach, where generalised additive models (GAM) predicted mobility trends over time at a large spatial level, then the residuals were used to determine which factors (location, zip code-level features or number of non-pharmaceutical interventions (NPIs) in place) best predict the difference between a zip code's measured mobility and the average trend on a given date. SETTING: We analyse zip code-level mobile phone records from 26 metropolitan areas in the USA on 15 March-31 September 2020, relative to October 2020. RESULTS: While relative mobility had a general trend, a zip code's city-level location significantly helped to predict its daily mobility patterns. This effect was time-dependent, with a city's deviation from general mobility trends differing in both direction and magnitude throughout the course of 2020. The characteristics of a zip code further increased predictive power, with the densest zip codes closest to a city centre tended to have the largest decrease in mobility. However, the effect on mobility change varied by city and became less important over the course of the pandemic. CONCLUSIONS: The location and characteristics of a zip code are important for determining changes in daily mobility patterns throughout the course of the COVID-19 pandemic. These results can determine the efficacy of NPI implementation on multiple spatial scales and inform policy makers on whether certain NPIs should be implemented or lifted during the ongoing COVID-19 pandemic and when preparing for future public health emergencies.

Exploring how space, time, and sampling impact our ability to measure genetic structure across Plasmodium falciparum populations.

A primary use of malaria parasite genomics is identifying highly related infections to quantify epidemiological, spatial, or temporal factors associated with patterns of transmission. For example, spatial clustering of highly related parasites can indicate foci of transmission and temporal differences in relatedness can serve as evidence for changes in transmission over time. However, for infections in settings of moderate to high endemicity, understanding patterns of relatedness is compromised by complex infections, overall high forces of infection, and a highly diverse parasite population. It is not clear how much these factors limit the utility of using genomic data to better understand transmission in these settings. In particular, further investigation is required to determine which patterns of relatedness we expect to see with high quality, densely sampled genomic data in a high transmission setting and how these observations change under different study designs, missingness, and biases in sample collection. Here we investigate two identity-by-state measures of relatedness and apply them to amplicon deep sequencing data collected as part of a longitudinal cohort in Western Kenya that has previously been analysed to identify individual-factors associated with sharing parasites with infected mosquitoes. With these data we use permutation tests, to evaluate several hypotheses about spatiotemporal patterns of relatedness compared to a null distribution. We observe evidence of temporal structure, but not of fine-scale spatial structure in the cohort data. To explore factors associated with the lack of spatial structure in these data, we construct a series of simplified simulation scenarios using an agent based model calibrated to entomological, epidemiological and genomic data from this cohort study to investigate whether the lack of spatial structure observed in the cohort could be due to inherent power limitations of this analytical method. We further investigate how our hypothesis testing behaves under different sampling schemes, levels of completely random and systematic missingness, and different transmission intensities.

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

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

Changes in mobility patterns during the COVID-19 pandemic in Zambia: Implications for the effectiveness of NPIs in Sub-Saharan Africa.

The COVID-19 pandemic has impacted many facets of human behavior, including human mobility partially driven by the implementation of non-pharmaceutical interventions (NPIs) such as stay at home orders, travel restrictions, and workplace and school closures. Given the importance of human mobility in the transmission of SARS-CoV-2, there have been an increase in analyses of mobility data to understand the COVID-19 pandemic to date. However, despite an abundance of these analyses, few have focused on Sub-Saharan Africa (SSA). Here, we use mobile phone calling data to provide a spatially refined analysis of sub-national human mobility patterns during the COVID-19 pandemic from March 2020-July 2021 in Zambia using transmission and mobility models. Overall, among highly trafficked intra-province routes, mobility decreased up to 52% during the time of the strictest NPIs (March-May 2020) compared to baseline. However, despite dips in mobility during the first wave of COVID-19 cases, mobility returned to baseline levels and did not drop again suggesting COVID-19 cases did not influence mobility in subsequent waves.

Using text and charts to provide social norm feedback to general practices with high overall and high broad-spectrum antibiotic prescribing: a series of national randomised controlled trials.

BACKGROUND: Sending a social norms feedback letter to general practitioners who are high prescribers of antibiotics has been shown to reduce antibiotic prescribing. The 2017-9 Quality Premium for primary care in England sets a target for broad-spectrum prescribing, which should be at or below 10% of total antibiotic prescribing. We tested a social norm feedback letter that targeted broad-spectrum prescribing and the addition of a chart to a text-only letter that targeted overall prescribing. METHODS: We conducted three 2-armed randomised controlled trials, on different groups of practices: Trial A compared a broad-spectrum message and chart to the standard-practice overall prescribing letter (practices whose percentage of broad-spectrum prescribing was above 10% and who had relatively high overall prescribing). Trial C compared a broad-spectrum message and a chart to a no-letter control (practices whose percentage of broad-spectrum prescribing was above 10% and who had relatively moderate overall prescribing). Trial B compared an overall-prescribing message with a chart to the standard practice overall letter (practices whose percentage of broad-spectrum prescribing was below 10% but who had relatively high overall prescribing). Letters were posted to general practitioners, timed to be received on 1 November 2018. The primary outcomes were practices' percentage of broad-spectrum prescribing (trials A and C) and overall antibiotic prescribing (trial B) each month from November 2018 to April 2019 (all weighted by the number and characteristics of patients registered in the practice). RESULTS: We randomly assigned 1909 practices; 58 closed or merged during the trial, leaving 1851 practices: 385 in trial A, 674 in trial C, and 792 in trial B. AR(1) models showed that there were no statistically significant differences in our primary outcome measures: trial A ß = - .199, p = .13; trial C ß = .006, p = .95; trial B ß = - .0021, p = .81. In all three trials, there were statistically significant time trends, showing that overall antibiotic prescribing and total broad-spectrum prescribing were decreasing. CONCLUSION: Our broad-spectrum feedback letters had no effect on broad-spectrum prescribing; adding a bar chart to a text-only letter had no effect on overall antibiotic prescribing. Broad-spectrum and overall prescribing were both decreasing over time. TRIAL REGISTRATION: ClinicalTrials.gov NCT03862794. March 5, 2019.

Encouraging healthier grocery purchases online: A randomised controlled trial and lessons learned.

Online supermarket platforms present an opportunity for encouraging healthier consumer purchases. A parallel, double-blind randomised controlled trial tested whether promoting healthier products (e.g. lower fat and lower calorie) on the Sainsbury's online supermarket platform would increase purchases of those products. Participants were Nectar loyalty membership scheme cardholders who shopped online with Sainsbury's between 20th September and 10th October 2017. Intervention arm customers saw advertisement banners and recipe ingredient lists containing healthier versions of the products presented in control arm banners and ingredient lists. The primary outcome measure was purchases of healthier products. Additional outcome measures were banner clicks, purchases of standard products, overall purchases and energy (kcal) purchased. Sample sizes were small due to customers navigating the website differently than expected. The intervention encouraged purchases of some promoted healthier products (spaghetti [B = 2.10, p < 0.001], spaghetti sauce [B = 2.06, p < 0.001], spaghetti cheese [B = 2.45, p = 0.001], sour cream [B = 2.52, p < 0.001], fajita wraps [B = 2.10, p < 0.001], fajita cheese [B = 1.19, p < 0.001], bakery aisle products (B = 3.05, p = 0.003) and cola aisle products [B = 0.97, p < 0.002]) but not others (spaghetti mince, or products in the yogurt and ice cream aisles). There was little evidence of effects on banner clicks and energy purchased. Small sample sizes may affect the robustness of these findings. We discuss the benefits of collaborating to share expertise and implement a trial in a live commercial environment, alongside key learnings for future collaborative research in similar contexts.

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

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

Improving disaggregation models of malaria incidence by ensembling non-linear models of prevalence.

Maps of disease burden are a core tool needed for the control and elimination of malaria. Reliable routine surveillance data of malaria incidence, typically aggregated to administrative units, is becoming more widely available. Disaggregation regression is an important model framework for estimating high resolution risk maps from aggregated data. However, the aggregation of incidence over large, heterogeneous areas means that these data are underpowered for estimating complex, non-linear models. In contrast, prevalence point-surveys are directly linked to local environmental conditions but are not common in many areas of the world. Here, we train multiple non-linear, machine learning models on Plasmodium falciparum prevalence point-surveys. We then ensemble the predictions from these machine learning models with a disaggregation regression model that uses aggregated malaria incidences as response data. We find that using a disaggregation regression model to combine predictions from machine learning models improves model accuracy relative to a baseline model.

Predicting non-state terrorism worldwide.

Several thousand people die every year worldwide because of terrorist attacks perpetrated by non-state actors. In this context, reliable and accurate short-term predictions of non-state terrorism at the local level are key for policy makers to target preventative measures. Using only publicly available data, we show that predictive models that include structural and procedural predictors can accurately predict the occurrence of non-state terrorism locally and a week ahead in regions affected by a relatively high prevalence of terrorism. In these regions, theoretically informed models systematically outperform models using predictors built on past terrorist events only. We further identify and interpret the local effects of major global and regional terrorism drivers. Our study demonstrates the potential of theoretically informed models to predict and explain complex forms of political violence at policy-relevant scales.

Using geospatial models to map zero-dose children: factors associated with zero-dose vaccination status before and after a mass measles and rubella vaccination campaign in Southern province, Zambia.

INTRODUCTION: Despite gains in global coverage of childhood vaccines, many children remain undervaccinated. Although mass vaccination campaigns are commonly conducted to reach these children their effectiveness is unclear. We evaluated the effectiveness of a mass vaccination campaign in reaching zero-dose children. METHODS: We conducted a prospective study in 10 health centre catchment areas in Southern province, Zambia in November 2020. About 2 months before a national mass measles and rubella vaccination campaign conducted by the Ministry of Health, we used aerial satellite maps to identify built structures. These structures were visited and diphtheria-tetanus-pertussis (DTP) and measles zero-dose children were identified (children who had not received any DTP or measles-containing vaccines, respectively). After the campaign, households where measles zero-dose children were previously identified were targeted for mop-up vaccination and to assess if these children were vaccinated during the campaign. A Bayesian geospatial model was used to identify factors associated with zero-dose status and measles zero-dose children being reached during the campaign. We also produced fine-scale zero-dose prevalence maps and identified optimal locations for additional vaccination sites. RESULTS: Before the vaccination campaign, 17.3% of children under 9 months were DTP zero-dose and 4.3% of children 9-60 months were measles zero-dose. Of the 461 measles zero-dose children identified before the vaccination campaign, 338 (73.3%) were vaccinated during the campaign and 118 (25.6%) were reached by a targeted mop-up activity. The presence of other children in the household, younger age, greater travel time to health facilities and living between health facility catchment areas were associated with zero-dose status. Mapping zero-dose prevalence revealed substantial heterogeneity within and between catchment areas. Several potential locations were identified for additional vaccination sites. CONCLUSION: Fine-scale variation in zero-dose prevalence and the impact of accessibility to healthcare facilities on vaccination coverage were identified. Geospatial modelling can aid targeted vaccination activities.

Effect of alcohol label designs with different pictorial representations of alcohol content and health warnings on knowledge and understanding of low-risk drinking guidelines: a randomized controlled trial.

BACKGROUND AND AIMS: The UK low-risk drinking guidelines (LRDG) recommend not regularly drinking more than 14 units of alcohol per week. We tested the effect of different pictorial representations of alcohol content, some with a health warning, on knowledge of the LRDG and understanding of how many drinks it equates to. DESIGN: Parallel randomized controlled trial. SETTING: On-line, 25 January-1 February 2019. PARTICIPANTS: Participants (n = 7516) were English, aged over 18 years and drink alcohol. INTERVENTIONS: The control group saw existing industry-standard labels; six intervention groups saw designs based on: food labels (serving or serving and container), pictographs (servings or containers), pie charts (servings) or risk gradients. A total of 500 participants (~70 per condition) saw a health warning under the design. MEASUREMENTS: Primary outcomes: (i) knowledge: proportion who answered that the LRDG is 14 units; and (ii) understanding: how many servings/containers of beverages one can drink before reaching 14 units (10 questions, average distance from correct answer). FINDINGS: In the control group, 21.5% knew the LRDG; proportions were higher in intervention groups (all P < 0.001). The three best-performing designs had the LRDG in a separate statement, beneath the pictograph container: 51.1% [adjusted odds ratio (aOR) = 3.74, 95% confidence interval (CI) = 3.08-4.54], pictograph serving 48.8% (aOR = 4.11, 95% CI = 3.39-4.99) and pie-chart serving, 47.5% (aOR = 3.57, 95% CI = 2.93-4.34). Participants underestimated how many servings they could drink: control mean = -4.64, standard deviation (SD) = 3.43; intervention groups were more accurate (all P < 0.001), best performing was pictograph serving (mean = -0.93, SD = 3.43). Participants overestimated how many containers they could drink: control mean = 0.09, SD = 1.02; intervention groups overestimated even more (all P < 0.007), worst-performing was food label serving (mean = 1.10, SD = 1.27). Participants judged the alcohol content of beers more accurately than wine or spirits. The inclusion of a health warning had no statistically significant effect on any measure. CONCLUSIONS: Labels with enhanced pictorial representations of alcohol content improved knowledge and understanding of the UK's low-risk drinking guidelines compared with industry-standard labels; health warnings did not improve knowledge or understanding of low-risk drinking guidelines. Designs that improved knowledge most had the low-risk drinking guidelines in a separate statement located beneath the graphics.

Maps and metrics of insecticide-treated net access, use, and nets-per-capita in Africa from 2000-2020.

Insecticide-treated nets (ITNs) are one of the most widespread and impactful malaria interventions in Africa, yet a spatially-resolved time series of ITN coverage has never been published. Using data from multiple sources, we generate high-resolution maps of ITN access, use, and nets-per-capita annually from 2000 to 2020 across the 40 highest-burden African countries. Our findings support several existing hypotheses: that use is high among those with access, that nets are discarded more quickly than official policy presumes, and that effectively distributing nets grows more difficult as coverage increases. The primary driving factors behind these findings are most likely strong cultural and social messaging around the importance of net use, low physical net durability, and a mixture of inherent commodity distribution challenges and less-than-optimal net allocation policies, respectively. These results can inform both policy decisions and downstream malaria analyses.

Indirect effects of the COVID-19 pandemic on malaria intervention coverage, morbidity, and mortality in Africa: a geospatial modelling analysis.

BACKGROUND: Substantial progress has been made in reducing the burden of malaria in Africa since 2000, but those gains could be jeopardised if the COVID-19 pandemic affects the availability of key malaria control interventions. The aim of this study was to evaluate plausible effects on malaria incidence and mortality under different levels of disruption to malaria control. METHODS: Using an established set of spatiotemporal Bayesian geostatistical models, we generated geospatial estimates across malaria-endemic African countries of the clinical case incidence and mortality of malaria, incorporating an updated database of parasite rate surveys, insecticide-treated net (ITN) coverage, and effective treatment rates. We established a baseline estimate for the anticipated malaria burden in Africa in the absence of COVID-19-related disruptions, and repeated the analysis for nine hypothetical scenarios in which effective treatment with an antimalarial drug and distribution of ITNs (both through routine channels and mass campaigns) were reduced to varying extents. FINDINGS: We estimated 215·2 (95% uncertainty interval 143·7-311·6) million cases and 386·4 (307·8-497·8) thousand deaths across malaria-endemic African countries in 2020 in our baseline scenario of undisrupted intervention coverage. With greater reductions in access to effective antimalarial drug treatment, our model predicted increasing numbers of cases and deaths: 224·1 (148·7-326·8) million cases and 487·9 (385·3-634·6) thousand deaths with a 25% reduction in antimalarial drug coverage; 233·1 (153·7-342·5) million cases and 597·4 (468·0-784·4) thousand deaths with a 50% reduction; and 242·3 (158·7-358·8) million cases and 715·2 (556·4-947·9) thousand deaths with a 75% reduction. Halting planned 2020 ITN mass distribution campaigns and reducing routine ITN distributions by 25%-75% also increased malaria burden to a total of 230·5 (151·6-343·3) million cases and 411·7 (322·8-545·5) thousand deaths with a 25% reduction; 232·8 (152·3-345·9) million cases and 415·5 (324·3-549·4) thousand deaths with a 50% reduction; and 234·0 (152·9-348·4) million cases and 417·6 (325·5-553·1) thousand deaths with a 75% reduction. When ITN coverage and antimalarial drug coverage were synchronously reduced, malaria burden increased to 240·5 (156·5-358·2) million cases and 520·9 (404·1-691·9) thousand deaths with a 25% reduction; 251·0 (162·2-377·0) million cases and 640·2 (492·0-856·7) thousand deaths with a 50% reduction; and 261·6 (167·7-396·8) million cases and 768·6 (586·1-1038·7) thousand deaths with a 75% reduction. INTERPRETATION: Under pessimistic scenarios, COVID-19-related disruption to malaria control in Africa could almost double malaria mortality in 2020, and potentially lead to even greater increases in subsequent years. To avoid a reversal of two decades of progress against malaria, averting this public health disaster must remain an integrated priority alongside the response to COVID-19. FUNDING: Bill and Melinda Gates Foundation; Channel 7 Telethon Trust, Western Australia.

Spatiotemporal mapping of malaria prevalence in Madagascar using routine surveillance and health survey data.

Malaria transmission in Madagascar is highly heterogeneous, exhibiting spatial, seasonal and long-term trends. Previous efforts to map malaria risk in Madagascar used prevalence data from Malaria Indicator Surveys. These cross-sectional surveys, conducted during the high transmission season most recently in 2013 and 2016, provide nationally representative prevalence data but cover relatively short time frames. Conversely, monthly case data are collected at health facilities but suffer from biases, including incomplete reporting and low rates of treatment seeking. We combined survey and case data to make monthly maps of prevalence between 2013 and 2016. Health facility catchment populations were estimated to produce incidence rates from the case data. Smoothed incidence surfaces, environmental and socioeconomic covariates, and survey data informed a Bayesian prevalence model, in which a flexible incidence-to-prevalence relationship was learned. Modelled spatial trends were consistent over time, with highest prevalence in the coastal regions and low prevalence in the highlands and desert south. Prevalence was lowest in 2014 and peaked in 2015 and seasonality was widely observed, including in some lower transmission regions. These trends highlight the utility of monthly prevalence estimates over the four year period. By combining survey and case data using this two-step modelling approach, we were able to take advantage of the relative strengths of each metric while accounting for potential bias in the case data. Similar modelling approaches combining large datasets of different malaria metrics may be applicable across sub-Saharan Africa.