Publications

Here is a list of my current publications, ordered from newest to oldest (Updated May 2019):

Longbottom, J., Shearer, F. M., Devine, M., Alcoba, G., Chappuis, F., Weiss, D. J., Ray, S. E., Ray, N., Warrell, D. A., Ruiz De Castañeda, R., Williams, D. J., Hay, S. I. & Pigott, D. M. 2018. Vulnerability to snakebite envenoming: a global mapping of hotspots. The Lancet, 392, 673-684.

Background: Snakebite envenoming is a frequently overlooked cause of mortality and morbidity. Data for snake ecology and existing snakebite interventions are scarce, limiting accurate burden estimation initiatives. Low global awareness stunts new interventions, adequate health resources, and available health care. Therefore, we aimed to synthesise currently available data to identify the most vulnerable populations at risk of snakebite, and where additional data to manage this global problem are needed.

Methods: We assembled a list of snake species using WHO guidelines. Where relevant, we obtained expert opinion range (EOR) maps from WHO or the Clinical Toxinology Resources. We also obtained occurrence data for each snake species from a variety of websites, such as VertNet and iNaturalist, using the spocc R package (version 0.7.0). We removed duplicate occurrence data and categorised snakes into three groups: group A (no available EOR map or species occurrence records), group B (EOR map but <5 species occurrence records), and group C (EOR map and ≥5 species occurrence records). For group C species, we did a multivariate environmental similarity analysis using the 2008 WHO EOR maps and newly available evidence. Using these data and the EOR maps, we produced contemporary range maps for medically important venomous snake species at a 5 × 5 km resolution. We subsequently triangulated these data with three health system metrics (antivenom availability, accessibility to urban centres, and the Healthcare Access and Quality [HAQ] Index) to identify the populations most vulnerable to snakebite morbidity and mortality.

Findings: We provide a map showing the ranges of 278 snake species globally. Although about 6·85 billion people worldwide live within range of areas inhabited by snakes, about 146·70 million live within remote areas lacking quality health-care provisioning. Comparing opposite ends of the HAQ Index, 272·91 million individuals (65·25%) of the population within the lowest decile are at risk of exposure to any snake for which no effective therapy exists compared with 519·46 million individuals (27·79%) within the highest HAQ Index decile, showing a disproportionate coverage in reported antivenom availability. Antivenoms were available for 119 (43%) of 278 snake species evaluated by WHO, while globally 750·19 million (10·95%) of those living within snake ranges live more than 1 h from population centres. In total, we identify about 92·66 million people living within these vulnerable geographies, including many sub-Saharan countries, Indonesia, and other parts of southeast Asia.

Interpretation: Identifying exact populations vulnerable to the most severe outcomes of snakebite envenoming at a subnational level is important for prioritising new data collection and collation, reinforcing envenoming treatment, existing health-care systems, and deploying currently available and future interventions. These maps can guide future research efforts on snakebite envenoming from both ecological and public health perspectives and better target future estimates of the burden of this neglected tropical disease.


Shearer, F. M., Longbottom, J., Browne, A. J., Pigott, D. M., Brady, O. J., Kraemer, M. U. G., Marinho, F., Yactayo, S., De Araújo, V. E. M., Da Nóbrega, A. A., Fullman, N., Ray, S. E., Mosser, J. F., Stanaway, J. D., Lim, S. S., Reiner, R. C., Jr., Moyes, C. L., Hay, S. I. & Golding, N. 2018. Existing and potential infection risk zones of yellow fever worldwide: a modelling analysis. The Lancet Global Health, 6, e270-e278.

Background: Yellow fever cases are under-reported and the exact distribution of the disease is unknown. An effective vaccine is available but more information is needed about which populations within risk zones should be targeted to implement interventions. Substantial outbreaks of yellow fever in Angola, Democratic Republic of the Congo, and Brazil, coupled with the global expansion of the range of its main urban vector, Aedes aegypti, suggest that yellow fever has the propensity to spread further internationally. The aim of this study was to estimate the disease’s contemporary distribution and potential for spread into new areas to help inform optimal control and prevention strategies.

Methods: We assembled 1155 geographical records of yellow fever virus infection in people from 1970 to 2016. We used a Poisson point process boosted regression tree model that explicitly incorporated environmental and biological explanatory covariates, vaccination coverage, and spatial variability in disease reporting rates to predict the relative risk of apparent yellow fever virus infection at a 5 × 5 km resolution across all risk zones (47 countries across the Americas and Africa). We also used the fitted model to predict the receptivity of areas outside at-risk zones to the introduction or reintroduction of yellow fever transmission. By use of previously published estimates of annual national case numbers, we used the model to map subnational variation in incidence of yellow fever across at-risk countries and to estimate the number of cases averted by vaccination worldwide.

Findings: Substantial international and subnational spatial variation exists in relative risk and incidence of yellow fever as well as varied success of vaccination in reducing incidence in several high-risk regions, including Brazil, Cameroon, and Togo. Areas with the highest predicted average annual case numbers include large parts of Nigeria, the Democratic Republic of the Congo, and South Sudan, where vaccination coverage in 2016 was estimated to be substantially less than the recommended threshold to prevent outbreaks. Overall, we estimated that vaccination coverage levels achieved by 2016 avert between 94 336 and 118 500 cases of yellow fever annually within risk zones, on the basis of conservative and optimistic vaccination scenarios. The areas outside at-risk regions with predicted high receptivity to yellow fever transmission (eg, parts of Malaysia, Indonesia, and Thailand) were less extensive than the distribution of the main urban vector, A aegypti, with low receptivity to yellow fever transmission in southern China, where A aegypti is known to occur.

Interpretation: Our results provide the evidence base for targeting vaccination campaigns within risk zones, as well as emphasising their high effectiveness. Our study highlights areas where public health authorities should be most vigilant for potential spread or importation events.


Osgood-Zimmerman, A., Millear, A. I., Stubbs, R. W., Shields, C., Pickering, B. V., Earl, L., Graetz, N., Kinyoki, D. K., Ray, S. E., Bhatt, S., Browne, A. J., Burstein, R., Cameron, E., Casey, D. C., Deshpande, A., Fullman, N., Gething, P. W., Gibson, H. S., Henry, N. J., Herrero, M., Krause, L. K., Letourneau, I. D., Levine, A. J., Liu, P. Y., Longbottom, J., Mayala, B. K., Mosser, J. F., Noor, A. M., Pigott, D. M., Piwoz, E. G., Rao, P., Rawat, R., Reiner, R. C., Smith, D. L., Weiss, D. J., Wiens, K. E., Mokdad, A. H., Lim, S. S., Murray, C. J. L., Kassebaum, N. J. & Hay, S. I. 2018. Mapping child growth failure in Africa between 2000 and 2015. Nature, 555, 41.

Insufficient growth during childhood is associated with poor health outcomes and an increased risk of death. Between 2000 and 2015, nearly all African countries demonstrated improvements for children under 5 years old for stunting, wasting, and underweight, the core components of child growth failure. Here we show that striking subnational heterogeneity in levels and trends of child growth remains. If current rates of progress are sustained, many areas of Africa will meet the World Health Organization Global Targets 2025 to improve maternal, infant and young child nutrition, but high levels of growth failure will persist across the Sahel. At these rates, much, if not all of the continent will fail to meet the Sustainable Development Goal target-to end malnutrition by 2030. Geospatial estimates of child growth failure provide a baseline for measuring progress as well as a precision public health platform to target interventions to those populations with the greatest need, in order to reduce health disparities and accelerate progress.


Graetz, N., Friedman, J., Osgood-Zimmerman, A., Burstein, R., Biehl, M. H., Shields, C., Mosser, J. F., Casey, D. C., Deshpande, A., Earl, L., Reiner, R. C., Ray, S. E., Fullman, N., Levine, A. J., Stubbs, R. W., Mayala, B. K., Longbottom, J., Browne, A. J., Bhatt, S., Weiss, D. J., Gething, P. W., Mokdad, A. H., Lim, S. S., Murray, C. J. L., Gakidou, E. & Hay, S. I. 2018. Mapping local variation in educational attainment across Africa. Nature, 555, 48.

Educational attainment for women of reproductive age is linked to reduced child and maternal mortality, lower fertility and improved reproductive health. Comparable analyses of attainment exist only at the national level, potentially obscuring patterns in subnational inequality. Evidence suggests that wide disparities between urban and rural populations exist, raising questions about where the majority of progress towards the education targets of the Sustainable Development Goals is occurring in African countries. Here we explore within-country inequalities by predicting years of schooling across five by five kilometre grids, generating estimates of average educational attainment by age and sex at subnational levels. Despite marked progress in attainment from 2000 to 2015 across Africa, substantial differences persist between locations and sexes. These differences have widened in many countries, particularly across the Sahel. These high-resolution, comparable estimates improve the ability of decision-makers to plan the precisely targeted interventions that will be necessary to deliver progress during the era of the Sustainable Development Goals.


Golding, N., Burstein, R., Longbottom, J., Browne, A. J., Fullman, N., Osgood-Zimmerman, A., Earl, L., Bhatt, S., Cameron, E., Casey, D. C., Dwyer-Lindgren, L., Farag, T. H., Flaxman, A. D., Fraser, M. S., Gething, P. W., Gibson, H. S., Graetz, N., Krause, L. K., Kulikoff, X. R., Lim, S. S., Mappin, B., Morozoff, C., Reiner, R. C., Jr., Sligar, A., Smith, D. L., Wang, H., Weiss, D. J., Murray, C. J. L., Moyes, C. L. & Hay, S. I. 2017. Mapping under-5 and neonatal mortality in Africa, 2000-2015: a baseline analysis for the Sustainable Development Goals. The Lancet, 390, 2171-2182.

Background: During the Millennium Development Goal (MDG) era, many countries in Africa achieved marked reductions in under-5 and neonatal mortality. Yet the pace of progress toward these goals substantially varied at the national level, demonstrating an essential need for tracking even more local trends in child mortality. With the adoption of the Sustainable Development Goals (SDGs) in 2015, which established ambitious targets for improving child survival by 2030, optimal intervention planning and targeting will require understanding of trends and rates of progress at a higher spatial resolution. In this study, we aimed to generate high-resolution estimates of under-5 and neonatal all-cause mortality across 46 countries in Africa.

Methods: We assembled 235 geographically resolved household survey and census data sources on child deaths to produce estimates of under-5 and neonatal mortality at a resolution of 5 × 5 km grid cells across 46 African countries for 2000, 2005, 2010, and 2015. We used a Bayesian geostatistical analytical framework to generate these estimates, and implemented predictive validity tests. In addition to reporting 5 × 5 km estimates, we also aggregated results obtained from these estimates into three different levels-national, and subnational administrative levels 1 and 2-to provide the full range of geospatial resolution that local, national, and global decision makers might require.

Findings: Amid improving child survival in Africa, there was substantial heterogeneity in absolute levels of under-5 and neonatal mortality in 2015, as well as the annualised rates of decline achieved from 2000 to 2015. Subnational areas in countries such as Botswana, Rwanda, and Ethiopia recorded some of the largest decreases in child mortality rates since 2000, positioning them well to achieve SDG targets by 2030 or earlier. Yet these places were the exception for Africa, since many areas, particularly in central and western Africa, must reduce under-5 mortality rates by at least 8·8% per year, between 2015 and 2030, to achieve the SDG 3.2 target for under-5 mortality by 2030.

Interpretation: In the absence of unprecedented political commitment, financial support, and medical advances, the viability of SDG 3.2 achievement in Africa is precarious at best. By producing under-5 and neonatal mortality rates at multiple levels of geospatial resolution over time, this study provides key information for decision makers to target interventions at populations in the greatest need. In an era when precision public health increasingly has the potential to transform the design, implementation, and impact of health programmes, our 5 × 5 km estimates of child mortality in Africa provide a baseline against which local, national, and global stakeholders can map the pathways for ending preventable child deaths by 2030.


Shearer, F. M., Moyes, C. L., Pigott, D. M., Brady, O. J., Marinho, F., Deshpande, A., Longbottom, J., Browne, A. J., Kraemer, M. U. G., O’reilly, K. M., Hombach, J., Yactayo, S., De Araujo, V. E. M., Da Nobrega, A. A., Mosser, J. F., Stanaway, J. D., Lim, S. S., Hay, S. I., Golding, N. & Reiner, R. C., Jr. 2017. Global yellow fever vaccination coverage from 1970 to 2016: an adjusted retrospective analysis. The Lancet Infectious Diseases, 17, 1209-1217.

Background: Substantial outbreaks of yellow fever in Angola and Brazil in the past 2 years, combined with global shortages in vaccine stockpiles, highlight a pressing need to assess present control strategies. The aims of this study were to estimate global yellow fever vaccination coverage from 1970 through to 2016 at high spatial resolution and to calculate the number of individuals still requiring vaccination to reach population coverage thresholds for outbreak prevention.

Methods: For this adjusted retrospective analysis, we compiled data from a range of sources (eg, WHO reports and health-service-provider registeries) reporting on yellow fever vaccination activities between May 1, 1939, and Oct 29, 2016. To account for uncertainty in how vaccine campaigns were targeted, we calculated three population coverage values to encompass alternative scenarios. We combined these data with demographic information and tracked vaccination coverage through time to estimate the proportion of the population who had ever received a yellow fever vaccine for each second level administrative division across countries at risk of yellow fever virus transmission from 1970 to 2016.

Findings: Overall, substantial increases in vaccine coverage have occurred since 1970, but notable gaps still exist in contemporary coverage within yellow fever risk zones. We estimate that between 393·7 million and 472·9 million people still require vaccination in areas at risk of yellow fever virus transmission to achieve the 80% population coverage threshold recommended by WHO; this represents between 43% and 52% of the population within yellow fever risk zones, compared with between 66% and 76% of the population who would have required vaccination in 1970.

Interpretation: Our results highlight important gaps in yellow fever vaccination coverage, can contribute to improved quantification of outbreak risk, and help to guide planning of future vaccination efforts and emergency stockpiling.


Longbottom, J., Browne, A. J., Pigott, D. M., Sinka, M. E., Golding, N., Hay, S. I., Moyes, C. L. & Shearer, F. M. 2017. Mapping the spatial distribution of the Japanese encephalitis vector, Culex tritaeniorhynchus Giles, 1901 (Diptera: Culicidae) within areas of Japanese encephalitis risk. Parasites & Vectors, 10, 148.

Background: Japanese encephalitis (JE) is one of the most significant aetiological agents of viral encephalitis in Asia. This medically important arbovirus is primarily spread from vertebrate hosts to humans by the mosquito vector Culex tritaeniorhynchus. Knowledge of the contemporary distribution of this vector species is lacking, and efforts to define areas of disease risk greatly depend on a thorough understanding of the variation in this mosquito’s geographical distribution.

Results: We assembled a contemporary database of Cx. tritaeniorhynchus presence records within Japanese encephalitis risk areas from formal literature and other relevant resources, resulting in 1,045 geo-referenced, spatially and temporally unique presence records spanning from 1928 to 2014 (71.9% of records obtained between 2001 and 2014). These presence data were combined with a background dataset capturing sample bias in our presence dataset, along with environmental and socio-economic covariates, to inform a boosted regression tree model predicting environmental suitability for Cx. tritaeniorhynchus at each 5 × 5 km gridded cell within areas of JE risk. The resulting fine-scale map highlights areas of high environmental suitability for this species across India, Nepal and China that coincide with areas of high JE incidence, emphasising the role of this vector in disease transmission and the utility of the map generated.

Conclusions: Our map contributes towards efforts determining the spatial heterogeneity in Cx. tritaeniorhynchus distribution within the limits of JE transmission. Specifically, this map can be used to inform vector control programs and can be used to identify key areas where the prevention of Cx. tritaeniorhynchus establishment should be a priority.


Wiebe, A., Longbottom, J., Gleave, K., Shearer, F. M., Sinka, M. E., Massey, N. C., Cameron, E., Bhatt, S., Gething, P. W., Hemingway, J., Smith, D. L., Coleman, M. & Moyes, C. L. 2017. Geographical distributions of African malaria vector sibling species and evidence for insecticide resistance. Malaria Journal, 16, 85.

Background: Many of the mosquito species responsible for malaria transmission belong to a sibling complex; a taxonomic group of morphologically identical, closely related species. Sibling species often differ in several important factors that have the potential to impact malaria control, including their geographical distribution, resistance to insecticides, biting and resting locations, and host preference. The aim of this study was to define the geographical distributions of dominant malaria vector sibling species in Africa so these distributions can be coupled with data on key factors such as insecticide resistance to aid more focussed, species-selective vector control.

Results: Within the Anopheles gambiae species complex and the Anopheles funestus subgroup, predicted geographical distributions for Anopheles coluzzii, An. gambiae (as now defined) and An. funestus (distinct from the subgroup) have been produced for the first time. Improved predicted geographical distributions for Anopheles arabiensis, Anopheles melas and Anopheles merus have been generated based on records that were confirmed using molecular identification methods and a model that addresses issues of sampling bias and past changes to the environment. The data available for insecticide resistance has been evaluated and differences between sibling species are apparent although further analysis is required to elucidate trends in resistance.

Conclusions: Sibling species display important variability in their geographical distributions and the most important malaria vector sibling species in Africa have been mapped here for the first time. This will allow geographical occurrence data to be coupled with species-specific data on important factors for vector control including insecticide resistance. Species-specific data on insecticide resistance is available for the most important malaria vectors in Africa, namely An. arabiensis, An. coluzzii, An. gambiae and An. funestus. Future work to combine these data with the geographical distributions mapped here will allow more focussed and resource-efficient vector control and provide information to greatly improve and inform existing malaria transmission models.


Ishak, I. H., Riveron, J. M., Ibrahim, S. S., Stott, R., Longbottom, J., Irving, H. & Wondji, C. S. 2016. The Cytochrome P450 gene CYP6P12 confers pyrethroid resistance in kdr-free Malaysian populations of the dengue vector Aedes albopictus. Scientific Reports, 6, 24707.

Control of Aedes albopictus, major dengue and chikungunya vector, is threatened by growing cases of insecticide resistance. The mechanisms driving this resistance remain poorly characterised. This study investigated the molecular basis of insecticide resistance in Malaysian populations of Ae. albopictus. Microarray-based transcription profiling revealed that metabolic resistance (cytochrome P450 up-regulation) and possibly a reduced penetration mechanism (consistent over-expression of cuticular protein genes) were associated with pyrethroid resistance. CYP6P12 over-expression was strongly associated with pyrethroid resistance whereas CYP6N3 was rather consistently over-expressed across carbamate and DDT resistant populations. Other detoxification genes also up-regulated in permethrin resistant mosquitoes included a glucuronosyltransferase (AAEL014279-RA) and the glutathione-S transferases GSTS1 and GSTT3. Functional analyses further supported that CYP6P12 contributes to pyrethroid resistance in Ae. albopictus as transgenic expression of CYP6P12 in Drosophila was sufficient to confer pyrethroid resistance in these flies. Furthermore, molecular docking simulations predicted CYP6P12 possessing enzymatic activity towards pyrethroids. Patterns of polymorphism suggested early sign of selection acting on CYP6P12 but not on CYP6N3. The major role played by P450 in the absence of kdr mutations suggests that addition of the synergist PBO to pyrethroids could improve the efficacy of this insecticide class and overcome resistance in field populations of Ae. albopictus.


Howes, R. E., Reiner Jr, R. C., Battle, K. E., Longbottom, J., Mappin, B., Ordanovich, D., Tatem, A. J., Drakeley, C., Gething, P. W., Zimmerman, P. A., Smith, D. L. & Hay, S. I. 2015. Plasmodium vivax Transmission in Africa. PLOS Neglected Tropical Diseases, 9, e0004222.

Malaria in sub-Saharan Africa has historically been almost exclusively attributed to Plasmodium falciparum (Pf). Current diagnostic and surveillance systems in much of sub-Saharan Africa are not designed to identify or report non-Pf human malaria infections accurately, resulting in a dearth of routine epidemiological data about their significance. The high prevalence of Duffy negativity provided a rationale for excluding the possibility of Plasmodium vivax (Pv) transmission. However, review of varied evidence sources including traveller infections, community prevalence surveys, local clinical case reports, entomological and serological studies contradicts this viewpoint. Here, these data reports are weighted in a unified framework to reflect the strength of evidence of indigenous Pv transmission in terms of diagnostic specificity, size of individual reports and corroboration between evidence sources. Direct evidence was reported from 21 of the 47 malaria-endemic countries studied, while 42 countries were attributed with infections of visiting travellers. Overall, moderate to conclusive evidence of transmission was available from 18 countries, distributed across all parts of the continent. Approximately 86.6 million Duffy positive hosts were at risk of infection in Africa in 2015. Analysis of the mechanisms sustaining Pv transmission across this continent of low frequency of susceptible hosts found that reports of Pv prevalence were consistent with transmission being potentially limited to Duffy positive populations. Finally, reports of apparent Duffy-independent transmission are discussed. While Pv is evidently not a major malaria parasite across most of sub-Saharan Africa, the evidence presented here highlights its widespread low-level endemicity. An increased awareness of Pv as a potential malaria parasite, coupled with policy shifts towards species-specific diagnostics and reporting, will allow a robust assessment of the public health significance of Pv, as well as the other neglected non-Pf parasites, which are currently invisible to most public health authorities in Africa, but which can cause severe clinical illness and require specific control interventions.


Mylne, A. Q., Pigott, D. M., Longbottom, J., Shearer, F., Duda, K. A., Messina, J. P., Weiss, D. J., Moyes, C. L., Golding, N. & Hay, S. I. 2015. Mapping the zoonotic niche of Lassa fever in Africa. Transactions of the Royal Society of Tropical Medicine and Hygiene, 109, 483-92.

Background: Lassa fever is a viral haemorrhagic illness responsible for disease outbreaks across West Africa. It is a zoonosis, with the primary reservoir species identified as the Natal multimammate mouse, Mastomys natalensis. The host is distributed across sub-Saharan Africa while the virus’ range appears to be restricted to West Africa. The majority of infections result from interactions between the animal reservoir and human populations, although secondary transmission between humans can occur, particularly in hospital settings.

Methods: Using a species distribution model, the locations of confirmed human and animal infections with Lassa virus (LASV) were used to generate a probabilistic surface of zoonotic transmission potential across sub-Saharan Africa.

Results: Our results predict that 37.7 million people in 14 countries, across much of West Africa, live in areas where conditions are suitable for zoonotic transmission of LASV. Four of these countries, where at-risk populations are predicted, have yet to report any cases of Lassa fever.

Conclusions: These maps act as a spatial guide for future surveillance activities to better characterise the geographical distribution of the disease and understand the anthropological, virological and zoological interactions necessary for viral transmission. Combining this zoonotic niche map with detailed patient travel histories can aid differential diagnoses of febrile illnesses, enabling a more rapid response in providing care and reducing the risk of onward transmission.