Publications by authors named "Simon I Hay"

312 Publications

Global, regional, and national time trends in mortality for congenital heart disease, 1990-2019: An age-period-cohort analysis for the Global Burden of Disease 2019 study.

EClinicalMedicine 2022 Jan 11;43:101249. Epub 2022 Jan 11.

Heart Center and Shanghai Institute of Pediatric Congenital Heart Disease, Shanghai Children's Medical Center, National Children's Medical Center, Shanghai Jiaotong University School of Medicine, Room 7016, Heart centre, Shanghai Children's Medical centre, No. 1678, Dongfang Rd, Pudong District, Shanghai, China.

Background: Congenital heart disease (CHD) is the leading cause of morbidity and mortality from birth defects worldwide. We report an overview of trends in CHD mortality in 204 countries and territories over the past 30 years and associations with age, period, and birth cohort.

Methods: Cause-specific CHD mortality estimates were derived from the Global Burden of Disease 2019 study. We utilised an age-period-cohort model to estimate overall annual percentage changes in mortality (net drifts), annual percentage changes from 0 to 4 to 65-69 years (local drifts), period and cohort relative risks (period/cohort effects) between 1990 and 2019. This approach allows for the examination and differentiation of age, period, and cohort effects in the mortality trends, with the potential to identify disparities and treatment gaps in cardiac care.

Findings: CHD is the leading cause of deaths from non-communicable diseases (NCDs) in those under 20 years. Global CHD deaths in 2019 were 217,000 (95% uncertainty interval 177,000-262,000). There were 129 countries with at least 50 deaths. India, China, Pakistan, and Nigeria had the highest mortality, accounting for 39.7% of deaths globally. Between 1990 and 2019, the net drift of CHD mortality ranged from -2.41% per year (95% confidence interval [CI] -2.55, -2.67) in high Socio-demographic Index (SDI) countries to -0.62% per year (95% CI: -0.82, -0.42) in low-SDI countries. Globally, there was an emerging transition in the age distribution of deaths from paediatric to adult populations, except for an increasing trend of mortality in those aged 10-34 years in Mexico and Pakistan. During the past 30 years, favourable mortality reductions were generally found in most high-SDI countries like South Korea (net drift = -4.0% [95% CI -4.8 to -3.1] per year) and the United States (-2.3% [-2.5 to -2.0]), and also in many middle-SDI countries like Brazil (-2.7% [-3.1 to 2.4]) and South Africa (-2.5% [-3.2 to -1.8]). However, 52 of 129 countries had either increasing trends (net drifts ≥0.0%) or stagnated reductions (≥-0.5%) in mortality. The relative risk of mortality generally showed improving trends over time and in successively younger birth cohorts amongst high- and high-middle-SDI countries, with the exceptions of Saudi Arabia and Kazakhstan. 14 middle-SDI countries such as Ecuador and Mexico, and 16 low-middle-SDI countries including India and 20 low-SDI countries including Pakistan, had unfavourable or worsening risks for recent periods and birth cohorts.

Interpretation: CHD mortality is a useful and accessible indicator of trends in the provision of congenital cardiac care both in early childhood and across later life. Improvements in the treatment of CHD should reduce the risk for successively younger cohorts and shift the risk for all age groups over time. Although there were gains in CHD mortality globally over the past three decades, unfavourable period and cohort effects were found in many countries, raising questions about adequacy of their health care for CHD patients across all age groups. These failings carry significant implications for the likelihood of achieving the Sustainable Development Goal targets for under-5 years and NCD mortality.

Funding: Supported by the National Natural Science Foundation of China (81525002, 31971048, 82073573 to ZZ and HZ), Shanghai Outstanding Medical Academic Leader program (2019LJ22 to HZ), and Collaborative Innovation Program of Shanghai Municipal Health Commission (2020CXJQ01 to HZ), the Bill & Melinda Gates Foundation for the Global Burden of Disease Project (to NJK) and NHMRC fellowship administered through the University of Melbourne (to GCP).
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http://dx.doi.org/10.1016/j.eclinm.2021.101249DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8760503PMC
January 2022

Health trends, inequalities and opportunities in South Africa's provinces, 1990-2019: findings from the Global Burden of Disease 2019 Study.

J Epidemiol Community Health 2022 Jan 19. Epub 2022 Jan 19.

Discipline of Public Health Medicine, University of KwaZulu-Natal, Durban, South Africa.

Background: Over the last 30 years, South Africa has experienced four 'colliding epidemics' of HIV and tuberculosis, chronic illness and mental health, injury and violence, and maternal, neonatal, and child mortality, which have had substantial effects on health and well-being. Using data from the 2019 Global Burden of Diseases, Injuries and Risk Factors Study (GBD 2019), we evaluated national and provincial health trends and progress towards important Sustainable Development Goal targets from 1990 to 2019.

Methods: We analysed GBD 2019 estimates of mortality, non-fatal health loss, summary health measures and risk factor burden, comparing trends over 1990-2007 and 2007-2019. Additionally, we decomposed changes in life expectancy by cause of death and assessed healthcare system performance.

Results: Across the nine provinces, inequalities in mortality and life expectancy increased over 1990-2007, largely due to differences in HIV/AIDS, then decreased over 2007-2019. Demographic change and increases in non-communicable diseases nearly doubled the number of years lived with disability between 1990 and 2019. From 1990 to 2019, risk factor burdens generally shifted from communicable and nutritional disease risks to non-communicable disease and injury risks; unsafe sex remained the top risk factor. Despite widespread improvements in healthcare system performance, the greatest gains were generally in economically advantaged provinces.

Conclusions: Reductions in HIV/AIDS and related conditions have led to improved health since 2007, though most provinces still lag in key areas. To achieve health targets, provincial governments should enhance health investments and exchange of knowledge, resources and best practices alongside populations that have been left behind, especially following the COVID-19 pandemic.
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http://dx.doi.org/10.1136/jech-2021-217480DOI Listing
January 2022

Etiological and epidemiological features of acute meningitis or encephalitis in China: a nationwide active surveillance study.

Lancet Reg Health West Pac 2022 Mar 3;20:100361. Epub 2022 Jan 3.

The Institute for Disease Prevention and Control of PLA, Beijing, China.

Background: Acute meningitis or encephalitis (AME) results from a neurological infection causing high case fatality and severe sequelae. AME lacked comprehensive surveillance in China.

Methods: Nation-wide surveillance of all-age patients with AME syndromes was conducted in 144 sentinel hospitals of 29 provinces in China. Eleven AME-causative viral and bacterial pathogens were tested with multiple diagnostic methods.

Findings: Between 2009 and 2018, 20,454 AME patients were recruited for tests. Based on 9,079 patients with all-four-virus tested, 28.43% (95% CI: 27.50%‒29.36%) of them had at least one virus-positive detection. Enterovirus was the most frequently determined virus in children <18 years, herpes simplex virus and Japanese encephalitis virus were the most frequently determined in 18-59 and ≥60 years age groups, respectively. Based on 6,802 patients with all-seven-bacteria tested, 4.43% (95% CI: 3.94%‒4.91%) had at least one bacteria-positive detection, and were the leading bacterium in children aged <5 years and 5-17 years, respectively. was the most frequently detected in adults aged 18-59 and ≥60 years. The pathogen spectrum also differed statistically significantly between northern and southern China. Joinpoint analysis revealed age-specific positive rates, with enterovirus, herpes simplex virus and mumps virus peaking at 3-6 years old, while Japanese encephalitis virus peaked in the ≥60 years old. As age increased, the positive rate for and statistically significantly decreased, while for and it increased.

Interpretation: The current findings allow enhanced identification of the predominant AME-related pathogen candidates for diagnosis in clinical practice and more targeted application of prevention and control measures in China, and a possible reassessment of vaccination strategy.

Funding: China Mega-Project on Infectious Disease Prevention and the National Natural Science Funds.
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http://dx.doi.org/10.1016/j.lanwpc.2021.100361DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8743210PMC
March 2022

Cancer Incidence, Mortality, Years of Life Lost, Years Lived With Disability, and Disability-Adjusted Life Years for 29 Cancer Groups From 2010 to 2019: A Systematic Analysis for the Global Burden of Disease Study 2019.

JAMA Oncol 2021 Dec 30. Epub 2021 Dec 30.

Department of Computer Science and Engineering, University of Kurdistan Hewler, Erbil, Iraq.

Importance: The Global Burden of Diseases, Injuries, and Risk Factors Study 2019 (GBD 2019) provided systematic estimates of incidence, morbidity, and mortality to inform local and international efforts toward reducing cancer burden.

Objective: To estimate cancer burden and trends globally for 204 countries and territories and by Sociodemographic Index (SDI) quintiles from 2010 to 2019.

Evidence Review: The GBD 2019 estimation methods were used to describe cancer incidence, mortality, years lived with disability, years of life lost, and disability-adjusted life years (DALYs) in 2019 and over the past decade. Estimates are also provided by quintiles of the SDI, a composite measure of educational attainment, income per capita, and total fertility rate for those younger than 25 years. Estimates include 95% uncertainty intervals (UIs).

Findings: In 2019, there were an estimated 23.6 million (95% UI, 22.2-24.9 million) new cancer cases (17.2 million when excluding nonmelanoma skin cancer) and 10.0 million (95% UI, 9.36-10.6 million) cancer deaths globally, with an estimated 250 million (235-264 million) DALYs due to cancer. Since 2010, these represented a 26.3% (95% UI, 20.3%-32.3%) increase in new cases, a 20.9% (95% UI, 14.2%-27.6%) increase in deaths, and a 16.0% (95% UI, 9.3%-22.8%) increase in DALYs. Among 22 groups of diseases and injuries in the GBD 2019 study, cancer was second only to cardiovascular diseases for the number of deaths, years of life lost, and DALYs globally in 2019. Cancer burden differed across SDI quintiles. The proportion of years lived with disability that contributed to DALYs increased with SDI, ranging from 1.4% (1.1%-1.8%) in the low SDI quintile to 5.7% (4.2%-7.1%) in the high SDI quintile. While the high SDI quintile had the highest number of new cases in 2019, the middle SDI quintile had the highest number of cancer deaths and DALYs. From 2010 to 2019, the largest percentage increase in the numbers of cases and deaths occurred in the low and low-middle SDI quintiles.

Conclusions And Relevance: The results of this systematic analysis suggest that the global burden of cancer is substantial and growing, with burden differing by SDI. These results provide comprehensive and comparable estimates that can potentially inform efforts toward equitable cancer control around the world.
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http://dx.doi.org/10.1001/jamaoncol.2021.6987DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8719276PMC
December 2021

Temporal trend and attributable risk factors of stroke burden in China, 1990-2019: an analysis for the Global Burden of Disease Study 2019.

Lancet Public Health 2021 12;6(12):e897-e906

Department of Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, China. Electronic address:

Background: Understanding the temporal trend of the disease burden of stroke and its attributable risk factors in China, especially at provincial levels, is important for effective prevention strategies and improvement. The aim of this analysis from the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) is to investigate the disease burden of stroke and its risk factors at national and provincial levels in China from 1990 to 2019.

Methods: Following the methodology in the GBD 2019, the incidence, prevalence, mortality, and disability-adjusted life-years (DALYs) of stroke cases in the Chinese population were estimated by sex, age, year, stroke subtypes (ischaemic stroke, intracerebral haemorrhage, and subarachnoid haemorrhage), and across 33 provincial administrative units in China from 1990 to 2019. Attributable mortality and DALYs of underlying risk factors were calculated by a comparative risk assessment.

Findings: In 2019, there were 3·94 million (95% uncertainty interval 3·43-4·58) new stroke cases in China. The incidence rate of stroke increased by 86·0% (73·2-99·0) from 1990, reaching 276·7 (241·3-322·0) per 100 000 population in 2019. The age-standardised incidence rate declined by 9·3% (3·3-15·5) from 1990 to 2019. Among 28·76 million (25·60-32·21) prevalent cases of stroke in 2019, 24·18 million (20·80-27·87) were ischaemic stroke, 4·36 million (3·69-5·05) were intracerebral haemorrhage, and 1·58 million (1·32-1·91) were subarachnoid haemorrhage. The prevalence rate increased by 106·0% (93·7-118·8) and age-standardised prevalence rate increased by 13·2% (7·7-19·1) from 1990 to 2019. In 2019, there were 2·19 million (1·89-2·51) deaths and 45·9 million (39·8-52·3) DALYs due to stroke. The mortality rate increased by 32·3% (8·6-59·0) from 1990 to 2019. Over the same period, the age-standardised mortality rate decreased by 39·8% (28·6-50·7) and the DALY rate decreased by 41·6% (30·7-50·9). High systolic blood pressure, ambient particulate matter pollution exposure, smoking, and diet high in sodium were four major risk factors for stroke burden in 2019. Moreover, we found marked differences of stroke burden and attributable risk factors across provinces in China from 1990 to 2019.

Interpretation: The disease burden of stroke is still severe in China, although the age-standardised incidence and mortality rates have decreased since 1990. The stroke burden in China might be reduced through blood pressure management, lifestyle interventions, and air pollution control. Moreover, because substantial heterogeneity of stroke burden existed in different provinces, improved health care is needed in provinces with heavy stroke burden.

Funding: National Key Research and Development Program of China and Taikang Yicai Public Health and Epidemic Control Fund.
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http://dx.doi.org/10.1016/S2468-2667(21)00228-0DOI Listing
December 2021

Changes in notifiable infectious disease incidence in China during the COVID-19 pandemic.

Nat Commun 2021 11 26;12(1):6923. Epub 2021 Nov 26.

State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China.

Nationwide nonpharmaceutical interventions (NPIs) have been effective at mitigating the spread of the novel coronavirus disease (COVID-19), but their broad impact on other diseases remains under-investigated. Here we report an ecological analysis comparing the incidence of 31 major notifiable infectious diseases in China in 2020 to the average level during 2014-2019, controlling for temporal phases defined by NPI intensity levels. Respiratory diseases and gastrointestinal or enteroviral diseases declined more than sexually transmitted or bloodborne diseases and vector-borne or zoonotic diseases. Early pandemic phases with more stringent NPIs were associated with greater reductions in disease incidence. Non-respiratory diseases, such as hand, foot and mouth disease, rebounded substantially towards the end of the year 2020 as the NPIs were relaxed. Statistical modeling analyses confirm that strong NPIs were associated with a broad mitigation effect on communicable diseases, but resurgence of non-respiratory diseases should be expected when the NPIs, especially restrictions of human movement and gathering, become less stringent.
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http://dx.doi.org/10.1038/s41467-021-27292-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8626444PMC
November 2021

Global antibiotic consumption and usage in humans, 2000-18: a spatial modelling study.

Lancet Planet Health 2021 Dec 12;5(12):e893-e904. Epub 2021 Nov 12.

Oxford Centre for Global Health Research, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand. Electronic address:

Background: Antimicrobial resistance (AMR) is a serious threat to global public health. WHO emphasises the need for countries to monitor antibiotic consumption to combat AMR. Many low-income and middle-income countries (LMICs) lack surveillance capacity; we aimed to use multiple data sources and statistical models to estimate global antibiotic consumption.

Methods: In this spatial modelling study, we used individual-level data from household surveys to inform a Bayesian geostatistical model of antibiotic usage in children (aged <5 years) with lower respiratory tract infections in LMICs. Antibiotic consumption data were obtained from multiple sources, including IQVIA, WHO, and the European Surveillance of Antimicrobial Consumption Network (ESAC-Net). The estimates of the antibiotic usage model were used alongside sociodemographic and health covariates to inform a model of total antibiotic consumption in LMICs. This was combined with a single model of antibiotic consumption in high-income countries to produce estimates of antibiotic consumption covering 204 countries and 19 years.

Findings: We analysed 209 surveys done between 2000 and 2018, covering 284 045 children with lower respiratory tract infections. We identified large national and subnational variations of antibiotic usage in LMICs, with the lowest levels estimated in sub-Saharan Africa and the highest in eastern Europe and central Asia. We estimated a global antibiotic consumption rate of 14·3 (95% uncertainty interval 13·2-15·6) defined daily doses (DDD) per 1000 population per day in 2018 (40·2 [37·2-43·7] billion DDD), an increase of 46% from 9·8 (9·2-10·5) DDD per 1000 per day in 2000. We identified large spatial disparities, with antibiotic consumption rates varying from 5·0 (4·8-5·3) DDD per 1000 per day in the Philippines to 45·9 DDD per 1000 per day in Greece in 2018. Additionally, we present trends in consumption of different classes of antibiotics for selected Global Burden of Disease study regions using the IQVIA, WHO, and ESAC-net input data. We identified large increases in the consumption of fluoroquinolones and third-generation cephalosporins in North Africa and Middle East, and south Asia.

Interpretation: To our knowledge, this is the first study that incorporates antibiotic usage and consumption data and uses geostatistical modelling techniques to estimate antibiotic consumption for 204 countries from 2000 to 2018. Our analysis identifies both high rates of antibiotic consumption and a lack of access to antibiotics, providing a benchmark for future interventions.

Funding: Fleming Fund, UK Department of Health and Social Care; Wellcome Trust; and Bill & Melinda Gates Foundation.
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http://dx.doi.org/10.1016/S2542-5196(21)00280-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8654683PMC
December 2021

Anemia prevalence in women of reproductive age in low- and middle-income countries between 2000 and 2018.

Nat Med 2021 10 12;27(10):1761-1782. Epub 2021 Oct 12.

Institute for Health Metrics and Evaluation, University of Washington, Seattle, WA, USA.

Anemia is a globally widespread condition in women and is associated with reduced economic productivity and increased mortality worldwide. Here we map annual 2000-2018 geospatial estimates of anemia prevalence in women of reproductive age (15-49 years) across 82 low- and middle-income countries (LMICs), stratify anemia by severity and aggregate results to policy-relevant administrative and national levels. Additionally, we provide subnational disparity analyses to provide a comprehensive overview of anemia prevalence inequalities within these countries and predict progress toward the World Health Organization's Global Nutrition Target (WHO GNT) to reduce anemia by half by 2030. Our results demonstrate widespread moderate improvements in overall anemia prevalence but identify only three LMICs with a high probability of achieving the WHO GNT by 2030 at a national scale, and no LMIC is expected to achieve the target in all their subnational administrative units. Our maps show where large within-country disparities occur, as well as areas likely to fall short of the WHO GNT, offering precision public health tools so that adequate resource allocation and subsequent interventions can be targeted to the most vulnerable populations.
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http://dx.doi.org/10.1038/s41591-021-01498-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8516651PMC
October 2021

The changing pattern of enteric pathogen infections in China during the COVID-19 pandemic: a nation-wide observational study.

Lancet Reg Health West Pac 2021 Nov 20;16:100268. Epub 2021 Sep 20.

Chinese Centre for Disease Control and Prevention, Beijing, China.

Background: Non pharmaceutical interventions (NPI) including hand washing directives were implemented in China and worldwide to combat the COVID-19 pandemic, which are likely to have had impacted a broad spectrum of enteric pathogen infections.

Methods: Etiologically diagnostic data from 45 937 and 67 395 patients with acute diarrhea between 2012 and 2020, who were tested for seven viral pathogens and 13 bacteria respectively, were analyzed to assess the changes of enteric pathogen infections in China during the first COVID-19 pandemic year compared to pre-pandemic years.

Findings: Test positive rates of all enteric viruses decreased during 2020, compared to the average levels during 2012-2019, with a relative decrease of 71•75% for adenovirus, 58•76% for norovirus, 53•50% for rotavirus A, and 72•07% for the combination of other four uncommon viruses. In general, a larger reduction of positive rate in viruses was seen among adults than pediatric patients. A rebound of rotavirus A was seen after September 2020 in North China rather than South China. Test positive rates of bacteria decreased during 2020, compared to the average levels during 2012-2019, excepting for nontyphoidal and with 66•53% and 90•48% increase respectively. This increase was larger for pediatric patients than for adult patients.

Interpretation: The activity of enteric pathogens changed profoundly alongside the NPIs implemented during the COVID-19 pandemic in China. Greater reductions of the test positive rates were found for almost all enteric viruses than for bacteria among acute diarrhea patients, with further large differences by age and geography. Lifting of NPIs will lead to resurgence of enteric pathogen infections, particularly in children whose immunity may not have been developed and/or waned.

Funding: China Mega-Project on Infectious Disease Prevention; National Natural Science Funds.
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http://dx.doi.org/10.1016/j.lanwpc.2021.100268DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8450280PMC
November 2021

Measuring the accuracy of gridded human population density surfaces: A case study in Bioko Island, Equatorial Guinea.

PLoS One 2021 1;16(9):e0248646. Epub 2021 Sep 1.

Institute for Health Metrics and Evaluation, University of Washington, Seattle, WA, United States of America.

Background: Geospatial datasets of population are becoming more common in models used for health policy. Publicly-available maps of human population make a consistent picture from inconsistent census data, and the techniques they use to impute data makes each population map unique. Each mapping model explains its methods, but it can be difficult to know which map is appropriate for which policy work. High quality census datasets, where available, are a unique opportunity to characterize maps by comparing them with truth.

Methods: We use census data from a bed-net mass-distribution campaign on Bioko Island, Equatorial Guinea, conducted by the Bioko Island Malaria Elimination Program as a gold standard to evaluate LandScan (LS), WorldPop Constrained (WP-C) and WorldPop Unconstrained (WP-U), Gridded Population of the World (GPW), and the High-Resolution Settlement Layer (HRSL). Each layer is compared to the gold-standard using statistical measures to evaluate distribution, error, and bias. We investigated how map choice affects burden estimates from a malaria prevalence model.

Results: Specific population layers were able to match the gold-standard distribution at different population densities. LandScan was able to most accurately capture highly urban distribution, HRSL and WP-C matched best at all other lower population densities. GPW and WP-U performed poorly everywhere. Correctly capturing empty pixels is key, and smaller pixel sizes (100 m vs 1 km) improve this. Normalizing areas based on known district populations increased performance. The use of differing population layers in a malaria model showed a disparity in results around transition points between endemicity levels.

Discussion: The metrics in this paper, some of them novel in this context, characterize how these population maps differ from the gold standard census and from each other. We show that the metrics help understand the performance of a population map within a malaria model. The closest match to the census data would combine LandScan within urban areas and the HRSL for rural areas. Researchers should prefer particular maps if health calculations have a strong dependency on knowing where people are not, or if it is important to categorize variation in density within a city.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0248646PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8409626PMC
November 2021

Estimating the cause-specific relative risks of non-optimal temperature on daily mortality: a two-part modelling approach applied to the Global Burden of Disease Study.

Lancet 2021 08;398(10301):685-697

Institute for Health Metrics and Evaluation, University of Washington, Seattle, WA, USA; Department of Health Metrics Sciences, School of Medicine, University of Washington, Seattle, WA, USA.

Background: Associations between high and low temperatures and increases in mortality and morbidity have been previously reported, yet no comprehensive assessment of disease burden has been done. Therefore, we aimed to estimate the global and regional burden due to non-optimal temperature exposure.

Methods: In part 1 of this study, we linked deaths to daily temperature estimates from the ERA5 reanalysis dataset. We modelled the cause-specific relative risks for 176 individual causes of death along daily temperature and 23 mean temperature zones using a two-dimensional spline within a Bayesian meta-regression framework. We then calculated the cause-specific and total temperature-attributable burden for the countries for which daily mortality data were available. In part 2, we applied cause-specific relative risks from part 1 to all locations globally. We combined exposure-response curves with daily gridded temperature and calculated the cause-specific burden based on the underlying burden of disease from the Global Burden of Diseases, Injuries, and Risk Factors Study, for the years 1990-2019. Uncertainty from all components of the modelling chain, including risks, temperature exposure, and theoretical minimum risk exposure levels, defined as the temperature of minimum mortality across all included causes, was propagated using posterior simulation of 1000 draws.

Findings: We included 64·9 million individual International Classification of Diseases-coded deaths from nine different countries, occurring between Jan 1, 1980, and Dec 31, 2016. 17 causes of death met the inclusion criteria. Ischaemic heart disease, stroke, cardiomyopathy and myocarditis, hypertensive heart disease, diabetes, chronic kidney disease, lower respiratory infection, and chronic obstructive pulmonary disease showed J-shaped relationships with daily temperature, whereas the risk of external causes (eg, homicide, suicide, drowning, and related to disasters, mechanical, transport, and other unintentional injuries) increased monotonically with temperature. The theoretical minimum risk exposure levels varied by location and year as a function of the underlying cause of death composition. Estimates for non-optimal temperature ranged from 7·98 deaths (95% uncertainty interval 7·10-8·85) per 100 000 and a population attributable fraction (PAF) of 1·2% (1·1-1·4) in Brazil to 35·1 deaths (29·9-40·3) per 100 000 and a PAF of 4·7% (4·3-5·1) in China. In 2019, the average cold-attributable mortality exceeded heat-attributable mortality in all countries for which data were available. Cold effects were most pronounced in China with PAFs of 4·3% (3·9-4·7) and attributable rates of 32·0 deaths (27·2-36·8) per 100 000 and in New Zealand with 3·4% (2·9-3·9) and 26·4 deaths (22·1-30·2). Heat effects were most pronounced in China with PAFs of 0·4% (0·3-0·6) and attributable rates of 3·25 deaths (2·39-4·24) per 100 000 and in Brazil with 0·4% (0·3-0·5) and 2·71 deaths (2·15-3·37). When applying our framework to all countries globally, we estimated that 1·69 million (1·52-1·83) deaths were attributable to non-optimal temperature globally in 2019. The highest heat-attributable burdens were observed in south and southeast Asia, sub-Saharan Africa, and North Africa and the Middle East, and the highest cold-attributable burdens in eastern and central Europe, and central Asia.

Interpretation: Acute heat and cold exposure can increase or decrease the risk of mortality for a diverse set of causes of death. Although in most regions cold effects dominate, locations with high prevailing temperatures can exhibit substantial heat effects far exceeding cold-attributable burden. Particularly, a high burden of external causes of death contributed to strong heat impacts, but cardiorespiratory diseases and metabolic diseases could also be substantial contributors. Changes in both exposures and the composition of causes of death drove changes in risk over time. Steady increases in exposure to the risk of high temperature are of increasing concern for health.

Funding: Bill & Melinda Gates Foundation.
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http://dx.doi.org/10.1016/S0140-6736(21)01700-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8387975PMC
August 2021

Etiological and epidemiological features of acute respiratory infections in China.

Nat Commun 2021 08 18;12(1):5026. Epub 2021 Aug 18.

Division of Infectious Disease, Key Laboratory of Surveillance and Early-warning on Infectious Disease, Chinese Center for Disease Control and Prevention, Beijing, China.

Nationwide prospective surveillance of all-age patients with acute respiratory infections was conducted in China between 2009‒2019. Here we report the etiological and epidemiological features of the 231,107 eligible patients enrolled in this analysis. Children <5 years old and school-age children have the highest viral positivity rate (46.9%) and bacterial positivity rate (30.9%). Influenza virus, respiratory syncytial virus and human rhinovirus are the three leading viral pathogens with proportions of 28.5%, 16.8% and 16.7%, and Streptococcus pneumoniae, Mycoplasma pneumoniae and Klebsiella pneumoniae are the three leading bacterial pathogens (29.9%, 18.6% and 15.8%). Negative interactions between viruses and positive interactions between viral and bacterial pathogens are common. A Join-Point analysis reveals the age-specific positivity rate and how this varied for individual pathogens. These data indicate that differential priorities for diagnosis, prevention and control should be highlighted in terms of acute respiratory tract infection patients' demography, geographic locations and season of illness in China.
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http://dx.doi.org/10.1038/s41467-021-25120-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8373954PMC
August 2021

Clonorchis sinensis re-infection rate and the determinants: a prospective cohort study in Hengxian County, Guangxi, China.

J Infect Dis 2021 Aug 10. Epub 2021 Aug 10.

National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Center for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai, China.

Background: To understand Clonorchis sinensis re-infection and the determinants in endemic areas is important in establishment of control measures.

Methods: A prospective cohort study was implemented in Hengxian County, Guangxi, China. Individuals with C. sinensis infection were completely treated, and those cured were enrolled as study subjects and followed up for 3, 6 and 12 months. The re-infection frequency and incidence were calculated, and a multivariable Cox proportional hazard model was constructed to capture re-infection determinants.

Results: Among 635 enrolled subjects, 436 (68.7%) completed follow-up. Of these, 177 (40.6%) were re-infected; 133 (75.1%) were re-infected once, 41 (23.2%) twice and 3 (1.7%) three times. The incidence of re-infection was 64.0 per 100 person-years. Males (aHR: 1.67, 95% CI: 1.14-2.44), those with underlying diseases (aHR: 1.41, 95% CI: 1.02-1.95), and those with moderate- and heavy-intensity infections (aHR: 1.45, 95% CI: 1.14-1.85) had increasing re-infection probabilities.

Conclusions: C. sinensis re-infection is high in endemic areas. Males and high-intensity infection are important determinants of re-infection. Repeated chemotherapy is necessary to control re-infection and its associated morbidities, especially in high-risk individuals. In addition, behavioural education is advised to decrease overall re-infection in endemic areas.
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http://dx.doi.org/10.1093/infdis/jiab403DOI Listing
August 2021

Predicting the environmental suitability for onchocerciasis in Africa as an aid to elimination planning.

PLoS Negl Trop Dis 2021 07 28;15(7):e0008824. Epub 2021 Jul 28.

Department of Health Policy Planning and Management, University of Health and Allied Sciences, Ho, Ghana.

Recent evidence suggests that, in some foci, elimination of onchocerciasis from Africa may be feasible with mass drug administration (MDA) of ivermectin. To achieve continental elimination of transmission, mapping surveys will need to be conducted across all implementation units (IUs) for which endemicity status is currently unknown. Using boosted regression tree models with optimised hyperparameter selection, we estimated environmental suitability for onchocerciasis at the 5 × 5-km resolution across Africa. In order to classify IUs that include locations that are environmentally suitable, we used receiver operating characteristic (ROC) analysis to identify an optimal threshold for suitability concordant with locations where onchocerciasis has been previously detected. This threshold value was then used to classify IUs (more suitable or less suitable) based on the location within the IU with the largest mean prediction. Mean estimates of environmental suitability suggest large areas across West and Central Africa, as well as focal areas of East Africa, are suitable for onchocerciasis transmission, consistent with the presence of current control and elimination of transmission efforts. The ROC analysis identified a mean environmental suitability index of 0·71 as a threshold to classify based on the location with the largest mean prediction within the IU. Of the IUs considered for mapping surveys, 50·2% exceed this threshold for suitability in at least one 5 × 5-km location. The formidable scale of data collection required to map onchocerciasis endemicity across the African continent presents an opportunity to use spatial data to identify areas likely to be suitable for onchocerciasis transmission. National onchocerciasis elimination programmes may wish to consider prioritising these IUs for mapping surveys as human resources, laboratory capacity, and programmatic schedules may constrain survey implementation, and possibly delaying MDA initiation in areas that would ultimately qualify.
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http://dx.doi.org/10.1371/journal.pntd.0008824DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8318275PMC
July 2021

Estimating global and regional disruptions to routine childhood vaccine coverage during the COVID-19 pandemic in 2020: a modelling study.

Lancet 2021 08 17;398(10299):522-534. Epub 2021 Jul 17.

Institute for Health Metrics and Evaluation, University of Washington, Seattle, WA, USA; Department of Health Metrics Sciences, School of Medicine, University of Washington, Seattle, WA, USA; Pediatric Infectious Diseases, Seattle Children's Hospital, Seattle, WA, USA. Electronic address:

Background: The COVID-19 pandemic and efforts to reduce SARS-CoV-2 transmission substantially affected health services worldwide. To better understand the impact of the pandemic on childhood routine immunisation, we estimated disruptions in vaccine coverage associated with the pandemic in 2020, globally and by Global Burden of Disease (GBD) super-region.

Methods: For this analysis we used a two-step hierarchical random spline modelling approach to estimate global and regional disruptions to routine immunisation using administrative data and reports from electronic immunisation systems, with mobility data as a model input. Paired with estimates of vaccine coverage expected in the absence of COVID-19, which were derived from vaccine coverage models from GBD 2020, Release 1 (GBD 2020 R1), we estimated the number of children who missed routinely delivered doses of the third-dose diphtheria-tetanus-pertussis (DTP3) vaccine and first-dose measles-containing vaccine (MCV1) in 2020.

Findings: Globally, in 2020, estimated vaccine coverage was 76·7% (95% uncertainty interval 74·3-78·6) for DTP3 and 78·9% (74·8-81·9) for MCV1, representing relative reductions of 7·7% (6·0-10·1) for DTP3 and 7·9% (5·2-11·7) for MCV1, compared to expected doses delivered in the absence of the COVID-19 pandemic. From January to December, 2020, we estimated that 30·0 million (27·6-33·1) children missed doses of DTP3 and 27·2 million (23·4-32·5) children missed MCV1 doses. Compared to expected gaps in coverage for eligible children in 2020, these estimates represented an additional 8·5 million (6·5-11·6) children not routinely vaccinated with DTP3 and an additional 8·9 million (5·7-13·7) children not routinely vaccinated with MCV1 attributable to the COVID-19 pandemic. Globally, monthly disruptions were highest in April, 2020, across all GBD super-regions, with 4·6 million (4·0-5·4) children missing doses of DTP3 and 4·4 million (3·7-5·2) children missing doses of MCV1. Every GBD super-region saw reductions in vaccine coverage in March and April, with the most severe annual impacts in north Africa and the Middle East, south Asia, and Latin America and the Caribbean. We estimated the lowest annual reductions in vaccine delivery in sub-Saharan Africa, where disruptions remained minimal throughout the year. For some super-regions, including southeast Asia, east Asia, and Oceania for both DTP3 and MCV1, the high-income super-region for DTP3, and south Asia for MCV1, estimates suggest that monthly doses were delivered at or above expected levels during the second half of 2020.

Interpretation: Routine immunisation services faced stark challenges in 2020, with the COVID-19 pandemic causing the most widespread and largest global disruption in recent history. Although the latest coverage trajectories point towards recovery in some regions, a combination of lagging catch-up immunisation services, continued SARS-CoV-2 transmission, and persistent gaps in vaccine coverage before the pandemic still left millions of children under-vaccinated or unvaccinated against preventable diseases at the end of 2020, and these gaps are likely to extend throughout 2021. Strengthening routine immunisation data systems and efforts to target resources and outreach will be essential to minimise the risk of vaccine-preventable disease outbreaks, reach children who missed routine vaccine doses during the pandemic, and accelerate progress towards higher and more equitable vaccination coverage over the next decade.

Funding: Bill & Melinda Gates Foundation.
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http://dx.doi.org/10.1016/S0140-6736(21)01337-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8285122PMC
August 2021

Mapping inequalities in exclusive breastfeeding in low- and middle-income countries, 2000-2018.

Nat Hum Behav 2021 08 3;5(8):1027-1045. Epub 2021 Jun 3.

Institute for Health Metrics and Evaluation, University of Washington, Seattle, WA, USA.

Exclusive breastfeeding (EBF)-giving infants only breast-milk for the first 6 months of life-is a component of optimal breastfeeding practices effective in preventing child morbidity and mortality. EBF practices are known to vary by population and comparable subnational estimates of prevalence and progress across low- and middle-income countries (LMICs) are required for planning policy and interventions. Here we present a geospatial analysis of EBF prevalence estimates from 2000 to 2018 across 94 LMICs mapped to policy-relevant administrative units (for example, districts), quantify subnational inequalities and their changes over time, and estimate probabilities of meeting the World Health Organization's Global Nutrition Target (WHO GNT) of ≥70% EBF prevalence by 2030. While six LMICs are projected to meet the WHO GNT of ≥70% EBF prevalence at a national scale, only three are predicted to meet the target in all their district-level units by 2030.
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http://dx.doi.org/10.1038/s41562-021-01108-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8373614PMC
August 2021

Spatial, temporal, and demographic patterns in prevalence of smoking tobacco use and initiation among young people in 204 countries and territories, 1990-2019.

Lancet Public Health 2021 07 28;6(7):e472-e481. Epub 2021 May 28.

Institute for Health Metrics and Evaluation, Department of Health Metrics Sciences, University of Washington, Seattle, WA, USA. Electronic address:

Background: Universally, smoking cessation rates among established smokers are poor. Preventing young people from starting use of and becoming addicted to tobacco products remains a key strategy to end the tobacco epidemic. Previous country-specific studies have found that initiation of smoking tobacco use occurs predominantly among young people and have found mixed progress in reducing the prevalence of smoking tobacco use among young people. Current and comparable estimates for all countries are needed to inform targeted interventions and policies.

Methods: We modelled two indicators: prevalence of current smoking tobacco use among young adults aged 15-24 years, and the age at which current smokers aged 20-54 years in 2019 began smoking regularly. We synthesised data from 3625 nationally representative surveys on prevalence of smoking and 254 on age at initiation. We used spatiotemporal Gaussian process regression to produce estimates of the prevalence of smoking and age of initiation by sex, for 204 countries and territories for each year between 1990 and 2019.

Findings: Globally in 2019, an estimated 155 million (95% uncertainty interval 150-160) individuals aged 15-24 years were tobacco smokers, with a prevalence of 20·1% (19·4-20·8) among males and 4·95% (4·64-5·29) among females. We estimated that 82·6% (82·1-83·1) of current smokers initiated between ages 14 and 25 years, and that 18·5% (17·7-19·3) of smokers began smoking regularly by age 15 years. Although some countries have made substantial progress in reducing the prevalence of smoking tobacco use among young people, prevalence in 2019 still exceeds 20% among males aged 15-24 years in 120 countries and among females aged 15-24 years in 43 countries.

Interpretation: The fact that most smokers start smoking regularly before age 20 years highlights the unique window of opportunity to target prevention efforts among young people and save millions of lives and avert health-care costs in the future. Countries can substantially improve the health of their populations by implementing and enforcing evidence-based tobacco control policies that prevent the next generation from initiating smoking.

Funding: Bloomberg Philanthropies.
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http://dx.doi.org/10.1016/S2468-2667(21)00102-XDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8251503PMC
July 2021

Predictive performance of international COVID-19 mortality forecasting models.

Nat Commun 2021 05 10;12(1):2609. Epub 2021 May 10.

Institute for Health Metrics and Evaluation, University of Washington, Seattle, WA, USA.

Forecasts and alternative scenarios of COVID-19 mortality have been critical inputs for pandemic response efforts, and decision-makers need information about predictive performance. We screen n = 386 public COVID-19 forecasting models, identifying n = 7 that are global in scope and provide public, date-versioned forecasts. We examine their predictive performance for mortality by weeks of extrapolation, world region, and estimation month. We additionally assess prediction of the timing of peak daily mortality. Globally, models released in October show a median absolute percent error (MAPE) of 7 to 13% at six weeks, reflecting surprisingly good performance despite the complexities of modelling human behavioural responses and government interventions. Median absolute error for peak timing increased from 8 days at one week of forecasting to 29 days at eight weeks and is similar for first and subsequent peaks. The framework and public codebase ( https://github.com/pyliu47/covidcompare ) can be used to compare predictions and evaluate predictive performance going forward.
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http://dx.doi.org/10.1038/s41467-021-22457-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8110547PMC
May 2021

Etiological, epidemiological, and clinical features of acute diarrhea in China.

Nat Commun 2021 04 29;12(1):2464. Epub 2021 Apr 29.

The Institute for Disease Prevention and Control of PLA, Beijing, China.

National-based prospective surveillance of all-age patients with acute diarrhea was conducted in China between 2009‒2018. Here we report the etiological, epidemiological, and clinical features of the 152,792 eligible patients enrolled in this analysis. Rotavirus A and norovirus are the two leading viral pathogens detected in the patients, followed by adenovirus and astrovirus. Diarrheagenic Escherichia coli and nontyphoidal Salmonella are the two leading bacterial pathogens, followed by Shigella and Vibrio parahaemolyticus. Patients aged <5 years had higher overall positive rate of viral pathogens, while bacterial pathogens were more common in patients aged 18‒45 years. A joinpoint analysis revealed the age-specific positivity rate and how this varied for individual pathogens. Our findings fill crucial gaps of how the distributions of enteropathogens change across China in patients with diarrhea. This allows enhanced identification of the predominant diarrheal pathogen candidates for diagnosis in clinical practice and more targeted application of prevention and control measures.
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http://dx.doi.org/10.1038/s41467-021-22551-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8085116PMC
April 2021

Oral rehydration therapies in Senegal, Mali, and Sierra Leone: a spatial analysis of changes over time and implications for policy.

BMC Med 2020 12 21;18(1):405. Epub 2020 Dec 21.

Demographic Change and Aging Research Area, Federal Institute for Population Research, Wiesbaden, Germany.

Background: Oral rehydration solution (ORS) is a simple intervention that can prevent childhood deaths from severe diarrhea and dehydration. In a previous study, we mapped the use of ORS treatment subnationally and found that ORS coverage increased over time, while the use of home-made alternatives or recommended home fluids (RHF) decreased, in many countries. These patterns were particularly striking within Senegal, Mali, and Sierra Leone. It was unclear, however, whether ORS replaced RHF in these locations or if children were left untreated, and if these patterns were associated with health policy changes.

Methods: We used a Bayesian geostatistical model and data from household surveys to map the percentage of children with diarrhea that received (1) any ORS, (2) only RHF, or (3) no oral rehydration treatment between 2000 and 2018. This approach allowed examination of whether RHF was replaced with ORS before and after interventions, policies, and external events that may have impacted healthcare access.

Results: We found that RHF was replaced with ORS in most Sierra Leone districts, except those most impacted by the Ebola outbreak. In addition, RHF was replaced in northern but not in southern Mali, and RHF was not replaced anywhere in Senegal. In Senegal, there was no statistical evidence that a national policy promoting ORS use was associated with increases in coverage. In Sierra Leone, ORS coverage increased following a national policy change that abolished health costs for children.

Conclusions: Children in parts of Mali and Senegal have been left behind during ORS scale-up. Improved messaging on effective diarrhea treatment and/or increased ORS access such as through reducing treatment costs may be needed to prevent child deaths in these areas.
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http://dx.doi.org/10.1186/s12916-020-01857-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7750121PMC
December 2020

Prevalence and intensity of soil-transmitted helminth infections of children in sub-Saharan Africa, 2000-18: a geospatial analysis.

Lancet Glob Health 2021 01;9(1):e52-e60

Department of Disease Control, London School of Hygiene and Tropical Medicine, London, UK.

Background: Driven by global targets to eliminate soil-transmitted helminths as a public health problem, governments have rapidly rolled out control programmes using school and community-based platforms. To justify and target ongoing investment, quantification of impact and identification of remaining high-risk areas are needed. We aimed to assess regional progress towards these targets.

Methods: We did a continental-scale ecological analysis using a Bayesian space-time hierarchical model to estimate the effects of known environmental, socioeconomic, and control-related factors on the prevalence of soil-transmitted helminths, and we mapped the probability that implementation units had achieved moderate-to-heavy intensity infection prevalence of less than 2% among children aged 5-14 years between Jan 1, 2000, and Dec 31, 2018.

Findings: We incorporated data from 26 304 georeferenced surveys, spanning 3096 (60%) of the 5183 programmatic implementation units. Our findings suggest a reduction in the prevalence of soil-transmitted helminths in children aged 5-14 years in sub-Saharan Africa, from 44% in 2000 to 13% in 2018, driven by sustained delivery of preventive chemotherapy, improved sanitation, and economic development. Nevertheless, 1301 (25%) of 5183 implementation units still had an estimated prevalence of moderate-to-heavy intensity infection exceeding the 2% target threshold in 2018, largely concentrated in nine countries (in 1026 [79%] of 1301 implementation units): Nigeria, Democratic Republic of the Congo, Ethiopia, Cameroon, Angola, Mozambique, Madagascar, Equatorial Guinea, and Gabon.

Interpretation: Our estimates highlight the areas to target and strengthen interventions, and the areas where data gaps remain. If elimination of soil-transmitted helminths as a public health problem is to be achieved in sub-Saharan Africa by 2030, continued investment in treatment and prevention activities are essential to ensure that no areas are left behind.

Funding: Bill & Melinda Gates Foundation.
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http://dx.doi.org/10.1016/S2214-109X(20)30398-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7786448PMC
January 2021

Risk mapping of scrub typhus infections in Qingdao city, China.

PLoS Negl Trop Dis 2020 12 2;14(12):e0008757. Epub 2020 Dec 2.

Key Laboratory of Surveillance and Early Warning on Infectious Disease, Division of Infectious Disease, Chinese Center for Disease Control and Prevention, Beijing, China.

Background: The emergence and re-emergence of scrub typhus has been reported in the past decade in many global regions. In this study, we aim to identify potential scrub typhus infection risk zones with high spatial resolution in Qingdao city, in which scrub typhus is endemic, to guide local prevention and control strategies.

Methodology/principal Findings: Scrub typhus cases in Qingdao city during 2006-2018 were retrieved from the Chinese National Infectious Diseases Reporting System. We divided Qingdao city into 1,101 gridded squares and classified them into two categories: areas with and without recorded scrub typhus cases. A boosted regression tree model was used to explore environmental and socioeconomic covariates associated with scrub typhus occurrence and predict the risk of scrub typhus infection across the whole area of Qingdao city. A total of 989 scrub typhus cases were reported in Qingdao from 2006-2018, with most cases located in rural and suburban areas. The predicted risk map generated by the boosted regression tree models indicated that the highest infection risk areas were mainly concentrated in the mid-east and northeast regions of Qingdao, with gross domestic product (20.9%±1.8% standard error) and annual cumulative precipitation (20.3%±1.1%) contributing the most to the variation in the models. By using a threshold environmental suitability value of 0.26, we identified 757 squares (68.7% of the total) with a favourable environment for scrub typhus infection; 66.2% (501/757) of the squares had not yet recorded cases. It is estimated that 6.32 million people (72.5% of the total population) reside in areas with a high risk of scrub typhus infection.

Conclusions/significance: Many locations in Qingdao city with no recorded scrub typhus cases were identified as being at risk for scrub typhus occurrence. In these at-risk areas, awareness and capacity for case diagnosis and treatment should be enhanced in the local medical service institutes.
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http://dx.doi.org/10.1371/journal.pntd.0008757DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7735632PMC
December 2020

Predictive performance of international COVID-19 mortality forecasting models.

medRxiv 2020 Nov 19. Epub 2020 Nov 19.

Forecasts and alternative scenarios of COVID-19 mortality have been critical inputs into a range of policies and decision-makers need information about predictive performance. We identified n=386 public COVID-19 forecasting models and included n=8 that were global in scope and provided public, date-versioned forecasts. For each, we examined the median absolute percent error (MAPE) compared to subsequently observed mortality trends, stratified by weeks of extrapolation, world region, and month of model estimation. Models were also assessed for ability to predict the timing of peak daily mortality. The MAPE among models released in July rose from 1.8% at one week of extrapolation to 24.6% at twelve weeks. The MAPE at six weeks were the highest in Sub-Saharan Africa (34.8%), and the lowest in high-income countries (6.3%). At the global level, several models had about 10% MAPE at six weeks, showing surprisingly good performance despite the complexities of modelling human behavioural responses and government interventions. The framework and publicly available codebase presented here ( https://github.com/pyliu47/covidcompare ) can be routinely used to compare predictions and evaluate predictive performance in an ongoing fashion.
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http://dx.doi.org/10.1101/2020.07.13.20151233DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7685335PMC
November 2020

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

Lancet Infect Dis 2021 01 21;21(1):59-69. Epub 2020 Sep 21.

Telethon Kids Institute, Perth Children's Hospital, Perth, WA, Australia; Curtin University, Perth, WA, Australia. Electronic address:

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.
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http://dx.doi.org/10.1016/S1473-3099(20)30700-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7505634PMC
January 2021

Predicting the environmental suitability and population at risk of podoconiosis in Africa.

PLoS Negl Trop Dis 2020 08 27;14(8):e0008616. Epub 2020 Aug 27.

Department of Disease Control, London School of Hygiene & Tropical Medicine, London, United Kingdom.

Podoconiosis is a type of tropical lymphedema that causes massive swelling of the lower limbs. The disease is associated with both economic insecurity, due to long-term morbidity-related loss of productivity, and intense social stigma. The geographical distribution and burden of podoconiosis in Africa are uncertain. We applied statistical modelling to the most comprehensive database compiled to date to predict the environmental suitability of podoconiosis in the African continent. By combining climate and environmental data and overlaying population figures, we predicted the environmental suitability and human population at risk of podoconiosis in Africa. Environmental suitability for podoconiosis was predicted in 29 African countries. In the year 2020, the total population in areas suitable for podoconiosis is estimated at 114.5 million people, (95% uncertainty interval: 109.4-123.9) with 16.9 million in areas suitable for both lymphatic filariasis and podoconiosis. Of the total 5,712 implementation units (typically second administrative-level units, such as districts) defined by the World Health Organization in Africa, 1,655 (29.0%) were found to be environmentally suitable for podoconiosis. The majority of implementation units with high environmental suitability are located in Angola (80, 4.8%), Cameroon (170, 10.3%), the DRC (244, 14.7%), Ethiopia (495, 29.9%), Kenya (217, 13.1%), Uganda (116, 7.0%) and Tanzania (112, 6.8%). Of the 1,655 environmentally suitable implementation units, 960 (58.0%) require more detailed community-level mapping. Our estimates provide key evidence of the population at risk and geographical extent of podoconiosis in Africa, which will help decision-makers to better plan more integrated intervention programmes.
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http://dx.doi.org/10.1371/journal.pntd.0008616DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7480865PMC
August 2020

Estimating global injuries morbidity and mortality: methods and data used in the Global Burden of Disease 2017 study.

Inj Prev 2020 10 24;26(Supp 1):i125-i153. Epub 2020 Aug 24.

Department of Pharmacy, Adigrat University, Adigrat, Ethiopia.

Background: While there is a long history of measuring death and disability from injuries, modern research methods must account for the wide spectrum of disability that can occur in an injury, and must provide estimates with sufficient demographic, geographical and temporal detail to be useful for policy makers. The Global Burden of Disease (GBD) 2017 study used methods to provide highly detailed estimates of global injury burden that meet these criteria.

Methods: In this study, we report and discuss the methods used in GBD 2017 for injury morbidity and mortality burden estimation. In summary, these methods included estimating cause-specific mortality for every cause of injury, and then estimating incidence for every cause of injury. Non-fatal disability for each cause is then calculated based on the probabilities of suffering from different types of bodily injury experienced.

Results: GBD 2017 produced morbidity and mortality estimates for 38 causes of injury. Estimates were produced in terms of incidence, prevalence, years lived with disability, cause-specific mortality, years of life lost and disability-adjusted life-years for a 28-year period for 22 age groups, 195 countries and both sexes.

Conclusions: GBD 2017 demonstrated a complex and sophisticated series of analytical steps using the largest known database of morbidity and mortality data on injuries. GBD 2017 results should be used to help inform injury prevention policy making and resource allocation. We also identify important avenues for improving injury burden estimation in the future.
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http://dx.doi.org/10.1136/injuryprev-2019-043531DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7571362PMC
October 2020

Informing Rift Valley Fever preparedness by mapping seasonally varying environmental suitability.

Int J Infect Dis 2020 Oct 30;99:362-372. Epub 2020 Jul 30.

Institute for Health Metrics and Evaluation, University of Washington, Seattle, WA, USA; Department of Health Metrics Sciences, School of Medicine, University of Washington, Seattle, WA, USA. Electronic address:

Background: Rift Valley Fever (RVF) poses a threat to human and animal health throughout much of Africa and the Middle East and has been recognized as a global health security priority and a key preparedness target.

Methods: We combined RVF occurrence data from a systematic literature review with animal notification data from an online database. Using boosted regression trees, we made monthly environmental suitability predictions from January 1995 to December 2016 at a 5 × 5-km resolution throughout regions of Africa, Europe, and the Middle East. We calculated the average number of months per year suitable for transmission, the mean suitability for each calendar month, and the "spillover potential," a measure incorporating suitability with human and livestock populations.

Results: Several countries where cases have not yet been reported are suitable for RVF. Areas across the region of interest are suitable for transmission at different times of the year, and some areas are suitable for multiple seasons each year. Spillover potential results show areas within countries where high populations of humans and livestock are at risk for much of the year.

Conclusions: The widespread environmental suitability of RVF highlights the need for increased preparedness, even in countries that have not previously experienced cases. These maps can aid in prioritizing long-term RVF preparedness activities and determining optimal times for recurring preparedness activities. Given an outbreak, our results can highlight areas often at risk for subsequent transmission that month, enabling decision-makers to target responses effectively.
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http://dx.doi.org/10.1016/j.ijid.2020.07.043DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7562817PMC
October 2020

Fertility, mortality, migration, and population scenarios for 195 countries and territories from 2017 to 2100: a forecasting analysis for the Global Burden of Disease Study.

Lancet 2020 10 14;396(10258):1285-1306. Epub 2020 Jul 14.

Institute for Health Metrics and Evaluation, University of Washington, Seattle, WA, USA; Department of Health Metrics Sciences, School of Medicine, University of Washington, Seattle, WA, USA. Electronic address:

Background: Understanding potential patterns in future population levels is crucial for anticipating and planning for changing age structures, resource and health-care needs, and environmental and economic landscapes. Future fertility patterns are a key input to estimation of future population size, but they are surrounded by substantial uncertainty and diverging methodologies of estimation and forecasting, leading to important differences in global population projections. Changing population size and age structure might have profound economic, social, and geopolitical impacts in many countries. In this study, we developed novel methods for forecasting mortality, fertility, migration, and population. We also assessed potential economic and geopolitical effects of future demographic shifts.

Methods: We modelled future population in reference and alternative scenarios as a function of fertility, migration, and mortality rates. We developed statistical models for completed cohort fertility at age 50 years (CCF50). Completed cohort fertility is much more stable over time than the period measure of the total fertility rate (TFR). We modelled CCF50 as a time-series random walk function of educational attainment and contraceptive met need. Age-specific fertility rates were modelled as a function of CCF50 and covariates. We modelled age-specific mortality to 2100 using underlying mortality, a risk factor scalar, and an autoregressive integrated moving average (ARIMA) model. Net migration was modelled as a function of the Socio-demographic Index, crude population growth rate, and deaths from war and natural disasters; and use of an ARIMA model. The model framework was used to develop a reference scenario and alternative scenarios based on the pace of change in educational attainment and contraceptive met need. We estimated the size of gross domestic product for each country and territory in the reference scenario. Forecast uncertainty intervals (UIs) incorporated uncertainty propagated from past data inputs, model estimation, and forecast data distributions.

Findings: The global TFR in the reference scenario was forecasted to be 1·66 (95% UI 1·33-2·08) in 2100. In the reference scenario, the global population was projected to peak in 2064 at 9·73 billion (8·84-10·9) people and decline to 8·79 billion (6·83-11·8) in 2100. The reference projections for the five largest countries in 2100 were India (1·09 billion [0·72-1·71], Nigeria (791 million [594-1056]), China (732 million [456-1499]), the USA (336 million [248-456]), and Pakistan (248 million [151-427]). Findings also suggest a shifting age structure in many parts of the world, with 2·37 billion (1·91-2·87) individuals older than 65 years and 1·70 billion (1·11-2·81) individuals younger than 20 years, forecasted globally in 2100. By 2050, 151 countries were forecasted to have a TFR lower than the replacement level (TFR <2·1), and 183 were forecasted to have a TFR lower than replacement by 2100. 23 countries in the reference scenario, including Japan, Thailand, and Spain, were forecasted to have population declines greater than 50% from 2017 to 2100; China's population was forecasted to decline by 48·0% (-6·1 to 68·4). China was forecasted to become the largest economy by 2035 but in the reference scenario, the USA was forecasted to once again become the largest economy in 2098. Our alternative scenarios suggest that meeting the Sustainable Development Goals targets for education and contraceptive met need would result in a global population of 6·29 billion (4·82-8·73) in 2100 and a population of 6·88 billion (5·27-9·51) when assuming 99th percentile rates of change in these drivers.

Interpretation: Our findings suggest that continued trends in female educational attainment and access to contraception will hasten declines in fertility and slow population growth. A sustained TFR lower than the replacement level in many countries, including China and India, would have economic, social, environmental, and geopolitical consequences. Policy options to adapt to continued low fertility, while sustaining and enhancing female reproductive health, will be crucial in the years to come.

Funding: Bill & Melinda Gates Foundation.
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http://dx.doi.org/10.1016/S0140-6736(20)30677-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7561721PMC
October 2020

Mapping male circumcision for HIV prevention efforts in sub-Saharan Africa.

BMC Med 2020 07 7;18(1):189. Epub 2020 Jul 7.

Institute for Health Metrics and Evaluation, University of Washington, Seattle, WA, USA.

Background: HIV remains the largest cause of disease burden among men and women of reproductive age in sub-Saharan Africa. Voluntary medical male circumcision (VMMC) reduces the risk of female-to-male transmission of HIV by 50-60%. The World Health Organization (WHO) and Joint United Nations Programme on HIV/AIDS (UNAIDS) identified 14 priority countries for VMMC campaigns and set a coverage goal of 80% for men ages 15-49. From 2008 to 2017, over 18 million VMMCs were reported in priority countries. Nonetheless, relatively little is known about local variation in male circumcision (MC) prevalence.

Methods: We analyzed geo-located MC prevalence data from 109 household surveys using a Bayesian geostatistical modeling framework to estimate adult MC prevalence and the number of circumcised and uncircumcised men aged 15-49 in 38 countries in sub-Saharan Africa at a 5 × 5-km resolution and among first administrative level (typically provinces or states) and second administrative level (typically districts or counties) units.

Results: We found striking within-country and between-country variation in MC prevalence; most (12 of 14) priority countries had more than a twofold difference between their first administrative level units with the highest and lowest estimated prevalence in 2017. Although estimated national MC prevalence increased in all priority countries with the onset of VMMC campaigns, seven priority countries contained both subnational areas where estimated MC prevalence increased and areas where estimated MC prevalence decreased after the initiation of VMMC campaigns. In 2017, only three priority countries (Ethiopia, Kenya, and Tanzania) were likely to have reached the MC coverage target of 80% at the national level, and no priority country was likely to have reached this goal in all subnational areas.

Conclusions: Despite MC prevalence increases in all priority countries since the onset of VMMC campaigns in 2008, MC prevalence remains below the 80% coverage target in most subnational areas and is highly variable. These mapped results provide an actionable tool for understanding local needs and informing VMMC interventions for maximum impact in the continued effort towards ending the HIV epidemic in sub-Saharan Africa.
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http://dx.doi.org/10.1186/s12916-020-01635-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7339571PMC
July 2020

Epidemiologic Changes of Scrub Typhus in China, 1952-2016.

Emerg Infect Dis 2020 06;26(6):1091-1101

Scrub typhus, a miteborne rickettsiosis, has emerged in many areas globally. We analyzed the incidence and spatial-temporal distribution of scrub typhus in China during 1952-1989 and 2006-2016 using national disease surveillance data. A total of 133,623 cases and 174 deaths were recorded. The average annual incidence was 0.13 cases/100,000 population during 1952-1989; incidence increased sharply from 0.09/100,000 population in 2006 to 1.60/100,000 population in 2016. The disease, historically endemic to southern China, has expanded to all the provinces across both rural and urban areas. We identified 3 distinct seasonal patterns nationwide; infections peaked in summer in the southwest, summer-autumn in the southeast, and autumn in the middle-east. Persons >40 years of age and in nonfarming occupations had a higher risk for death. The changing epidemiology of scrub typhus in China warrants an enhanced disease control and prevention program.
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http://dx.doi.org/10.3201/eid2606.191168DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7258452PMC
June 2020
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