Publications
202 results found
Bertozzi-Villa A, Bever C, Gerardin J, et al., 2022, An archetypes approach to malaria intervention impact mapping: a new framework and example application
<jats:title>Abstract</jats:title><jats:sec><jats:title>Background</jats:title><jats:p>As both mechanistic and geospatial malaria modeling methods become more integrated into malaria policy decisions, there is increasing demand for strategies that combine these two methods. This paper introduces a novel archetypes-based methodology for generating high-resolution intervention impact maps based on mechanistic model simulations. An example configuration of the framework is described and explored.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>First, dimensionality reduction and clustering techniques were applied to rasterized geospatial environmental and mosquito covariates to find archetypal malaria transmission patterns. Next, mechanistic models were run on a representative site from each archetype to assess intervention impact. Finally, these mechanistic results were reprojected onto each pixel to generate full maps of intervention impact. The example configuration used ERA5 and Malaria Atlas Project covariates, singular value decomposition, k-means clustering, and the Institute for Disease Modeling’s EMOD model to explore a range of three-year malaria interventions primarily focused on vector control and case management.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>Rainfall, temperature, and mosquito abundance layers were clustered into ten transmission archetypes with distinct properties. Example intervention impact curves and maps highlighted archetype-specific variation in efficacy of vector control interventions. A sensitivity analysis showed that the procedure for selecting representative sites to simulate worked well in all but one archetype.</jats:p></jats:sec><jats:sec><jats:title>Conclusion</jats:title><jats:p>This paper introduces a novel methodology which combine
Touloupou P, Retkute R, Hollingsworth TD, et al., 2022, Statistical methods for linking geostatistical maps and transmission models: Application to lymphatic filariasis in East Africa, SPATIAL AND SPATIO-TEMPORAL EPIDEMIOLOGY, Vol: 41, ISSN: 1877-5845
Kumar V, Siddiqui NA, Pollington TM, et al., 2022, Impact of intensified control on visceral leishmaniasis in a highly-endemic district of Bihar, India: an interrupted time series analysis, EPIDEMICS, Vol: 39, ISSN: 1755-4365
Kura K, Ayabina D, Hollingsworth TD, et al., 2022, Determining the optimal strategies to achieve elimination of transmission for Schistosoma mansoni, PARASITES & VECTORS, Vol: 15, ISSN: 1756-3305
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- Citations: 1
Metcalf CJE, Andriamandimby SF, Baker RE, et al., 2021, Challenges in evaluating risks and policy options around endemic establishment or elimination of novel pathogens., Epidemics, Vol: 37
When a novel pathogen emerges there may be opportunities to eliminate transmission - locally or globally - whilst case numbers are low. However, the effort required to push a disease to elimination may come at a vast cost at a time when uncertainty is high. Models currently inform policy discussions on this question, but there are a number of open challenges, particularly given unknown aspects of the pathogen biology, the effectiveness and feasibility of interventions, and the intersecting political, economic, sociological and behavioural complexities for a novel pathogen. In this overview, we detail how models might identify directions for better leveraging or expanding the scope of data available on the pathogen trajectory, for bounding the theoretical context of emergence relative to prospects for elimination, and for framing the larger economic, behavioural and social context that will influence policy decisions and the pathogen's outcome.
Retkute R, Touloupou P, Basanez M-G, et al., 2021, Integrating geostatistical maps and infectious disease transmission models using Adaptive Multiple Importance Sampling, Annals of Applied Statistics, Vol: 15, Pages: 1980-1998, ISSN: 1932-6157
The Adaptive Multiple Importance Sampling algorithm (AMIS)is an iterative technique which recycles samples from all previousiterations in order to improve the efficiency of the proposal distribution. We have formulated a new statistical framework, based onAMIS, to take the output from a geostatistical model of infectiousdisease prevalence, incidence or relative risk, and project it forwardin time under a mathematical model for transmission dynamics. Weadapted the AMIS algorithm so that it can sample from multiple targets simultaneously by changing the focus of the adaptation at eachiteration. By comparing our approach against the standard AMIS algorithm, we showed that these novel adaptations greatly improve theefficiency of the sampling. We tested the performance of our algorithmon four case studies: ascariasis in Ethiopia, onchocerciasis in Togo,human immunodeficiency virus (HIV) in Botswana, and malaria inthe Democratic Republic of the Congo.
Pan D, Sze S, Martin CA, et al., 2021, Covid-19 and ethnicity: we must seek to understand the drivers of higher transmission, BMJ-BRITISH MEDICAL JOURNAL, Vol: 375, ISSN: 0959-535X
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- Citations: 2
Ayabina DV, Clark J, Bayley H, et al., 2021, Gender-related differences in prevalence, intensity and associated risk factors of Schistosoma infections in Africa: A systematic review and meta-analysis, PLOS NEGLECTED TROPICAL DISEASES, Vol: 15, ISSN: 1935-2735
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- Citations: 2
Anderson RM, Vegvari C, Hollingsworth TD, et al., 2021, The SARS-CoV-2 pandemic: remaining uncertainties in our understanding of the epidemiology and transmission dynamics of the virus, and challenges to be overcome, INTERFACE FOCUS, Vol: 11, ISSN: 2042-8898
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- Citations: 13
Vegvari C, Abbott S, Ball F, et al., 2021, Commentary on the use of the reproduction number R during the COVID-19 pandemic, STATISTICAL METHODS IN MEDICAL RESEARCH, Vol: 31, Pages: 1675-1685, ISSN: 0962-2802
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- Citations: 4
Davis EL, Lucas TCD, Borlase A, et al., 2021, Contact tracing is an imperfect tool for controlling COVID-19 transmission and relies on population adherence, NATURE COMMUNICATIONS, Vol: 12
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- Citations: 5
Spencer SEF, Laeyendecker O, Dyson L, et al., 2021, Estimating HIV, HCV and HSV2 incidence from emergency department serosurvey, Gates Open Research, Vol: 5, Pages: 116-116
<ns3:p><ns3:bold>Background: </ns3:bold>Our understanding of pathogens and disease transmission has improved dramatically over the past 100 years, but coinfection, how different pathogens interact with each other, remains a challenge. Cross-sectional serological studies including multiple pathogens offer a crucial insight into this problem. </ns3:p><ns3:p> <ns3:bold>Methods: </ns3:bold>We use data from three cross-sectional serological surveys (in 2003, 2007 and 2013) in a Baltimore emergency department to predict the prevalence for HIV, hepatitis C virus (HCV) and herpes simplex virus, type 2 (HSV2), in a fourth survey (in 2016). We develop a mathematical model to make this prediction and to estimate the incidence of infection and coinfection in each age and ethnic group in each year.</ns3:p><ns3:p> <ns3:bold>Results: </ns3:bold>Overall we find a much stronger age cohort effect than a time effect, so that, while incidence at a given age may decrease over time, individuals born at similar times experience a more constant force of infection over time.</ns3:p><ns3:p> <ns3:bold>Conclusions: </ns3:bold>These results emphasise the importance of age-cohort counselling and early intervention while people are young. Our approach adds value to data such as these by providing age- and time-specific incidence estimates which could not be obtained any other way, and allows forecasting to enable future public health planning.</ns3:p>
Clark J, Stolk WA, Basáñez M-G, et al., 2021, How modelling can help steer the course set by the World Health Organization 2021-2030 roadmap on neglected tropical diseases, Gates Open Research, Vol: 5, Pages: 112-112
<ns3:p>The World Health Organization recently launched its 2021-2030 roadmap, <ns3:italic>Ending</ns3:italic><ns3:italic> the </ns3:italic><ns3:italic>Neglect</ns3:italic><ns3:italic> to </ns3:italic><ns3:italic>Attain</ns3:italic><ns3:italic> the </ns3:italic><ns3:italic>Sustainable Development Goals</ns3:italic><ns3:italic>,</ns3:italic> an updated call to arms to end the suffering caused by neglected tropical diseases. Modelling and quantitative analyses played a significant role in forming these latest goals. In this collection, we discuss the insights, the resulting recommendations and identified challenges of public health modelling for 13 of the target diseases: Chagas disease, dengue, <ns3:italic>gambiense</ns3:italic> human African trypanosomiasis (gHAT), lymphatic filariasis (LF), onchocerciasis, rabies, scabies, schistosomiasis, soil-transmitted helminthiases (STH), <ns3:italic>Taenia solium</ns3:italic> taeniasis/ cysticercosis, trachoma, visceral leishmaniasis (VL) and yaws. This piece reflects the three cross-cutting themes identified across the collection, regarding the contribution that modelling can make to timelines, programme design, drug development and clinical trials.</ns3:p>
Gog JR, Hollingsworth TD, 2021, Epidemic interventions: insights from classic results, PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, Vol: 376, ISSN: 0962-8436
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- Citations: 4
Lucas TCD, Davis EL, Ayabina D, et al., 2021, Engagement and adherence trade-offs for SARS-CoV-2 contact tracing, PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, Vol: 376, ISSN: 0962-8436
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- Citations: 4
Crellen T, Pi L, Davis EL, et al., 2021, Dynamics of SARS-CoV-2 with waning immunity in the UK population, PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, Vol: 376, ISSN: 0962-8436
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- Citations: 9
Fearon E, Buchan IE, Das R, et al., 2021, SARS-CoV-2 antigen testing: weighing the false positives against the costs of failing to control transmission., Lancet Respir Med, Vol: 9, Pages: 685-687
Hatherell H-A, Simpson H, Baggaley RF, et al., 2021, Sustainable Surveillance of Neglected Tropical Diseases for the Post-Elimination Era, CLINICAL INFECTIOUS DISEASES, Vol: 72, Pages: S210-S216, ISSN: 1058-4838
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- Citations: 3
Ayabina D, Kura K, Toor J, et al., 2021, Maintaining low prevalence of Schistosoma mansoni: modelling the effect of less frequent treatment, Clinical Infectious Diseases, Vol: 72, Pages: S140-S145, ISSN: 1058-4838
BACKGROUND: The World Health Organization (WHO) previously set goals of controlling morbidity due to schistosomiasis by 2020 and attaining elimination as a public health problem (EPHP) by 2025 (now adjusted to 2030 in the new neglected tropical diseases roadmap). As these milestones are reached, it is important that programs reassess their treatment strategies to either maintain these goals or progress from morbidity control to EPHP and ultimately to interruption of transmission. In this study, we consider different mass drug administration (MDA) strategies to maintain the goals. METHODS: We use two independently developed individual-based stochastic models of schistosomiasis transmission to assess the optimal treatment strategy of a multi-year program to maintain the morbidity control and the EPHP goals. RESULTS: We find that in moderate prevalence settings, once the morbidity control and EPHP goals are reached, it may be possible to maintain the goals using less frequent MDAs than those that are required to achieve the goals. On the other hand, in some high transmission settings, if control efforts are reduced after achieving the goals, particularly the morbidity control goal, there is a high chance of recrudescence. CONCLUSIONS: To reduce the risk of recrudescence after the goals are achieved, programs have to re-evaluate their strategies and decide to either maintain these goals with reduced efforts where feasible or continue with at least the same efforts required to reach the goals.
Blumberg S, Prada JM, Tedijanto C, et al., 2021, Forecasting Trachoma Control and Identifying Transmission-Hotspots, CLINICAL INFECTIOUS DISEASES, Vol: 72, Pages: S134-S139, ISSN: 1058-4838
Davis EL, Prada J, Reimer LJ, et al., 2021, Modelling the Impact of Vector Control on Lymphatic Filariasis Programs: Current Approaches and Limitations, CLINICAL INFECTIOUS DISEASES, Vol: 72, Pages: S152-S157, ISSN: 1058-4838
Minter A, Pellis L, Medley GF, et al., 2021, What Can Modeling Tell Us About Sustainable End Points for Neglected Tropical Diseases?, CLINICAL INFECTIOUS DISEASES, Vol: 72, Pages: S129-S133, ISSN: 1058-4838
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- Citations: 1
Bertozzi-Villa A, Bever CA, Koenker H, et al., 2021, Maps and metrics of insecticide-treated net access, use, and nets-per-capita in Africa from 2000-2020, NATURE COMMUNICATIONS, Vol: 12, ISSN: 2041-1723
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- Citations: 9
Toor J, Hamley JID, Fronterre C, et al., 2021, Strengthening data collection for neglected tropical diseases: What data are needed for models to better inform tailored intervention programmes?, PLOS NEGLECTED TROPICAL DISEASES, Vol: 15, ISSN: 1935-2735
Toor J, Adams ER, Aliee M, et al., 2021, Predicted impact of COVID-19 on neglected tropical disease programs and the opportunity for innovation, Clinical Infectious Diseases, Vol: 72, Pages: 1463-1466, ISSN: 1058-4838
Due to the COVID-19 pandemic, many key neglected tropical disease (NTD) activities have been postponed. This hindrance comes at a time when the NTDs are progressing towards their ambitious goals for 2030. Mathematical modelling on several NTDs, namely gambiense sleeping sickness, lymphatic filariasis, onchocerciasis, schistosomiasis, soil-transmitted helminthiases (STH), trachoma, and visceral leishmaniasis, shows that the impact of this disruption will vary across the diseases. Programs face a risk of resurgence, which will be fastest in high-transmission areas. Furthermore, of the mass drug administration diseases, schistosomiasis, STH, and trachoma are likely to encounter faster resurgence. The case-finding diseases (gambiense sleeping sickness and visceral leishmaniasis) are likely to have fewer cases being detected but may face an increasing underlying rate of new infections. However, once programs are able to resume, there are ways to mitigate the impact and accelerate progress towards the 2030 goals.
Crellen T, Sithithaworn P, Pitaksakulrat O, et al., 2021, Towards Evidence-based Control of Opisthorchis viverrini, TRENDS IN PARASITOLOGY, Vol: 37, Pages: 370-380, ISSN: 1471-4922
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- Citations: 5
Pollington TM, Tildesley MJ, Hollingsworth TD, et al., 2021, Developments in statistical inference when assessing spatiotemporal disease clustering with the tau statistic, Spatial Statistics, Vol: 42, Pages: 1-15, ISSN: 2211-6753
The tau statistic uses geolocation and, usually, symptom onset time to assess global spatiotemporal clustering from epidemiological data. We test different methods that could bias the clustering range estimate based on the statistic or affect its apparent precision, by comparison with a baseline analysis of an open access measles dataset.From re-analysing this data we find evidence against no clustering and no inhibition, (global envelope test). We develop a tau-specific modification of the Loh & Stein spatial bootstrap sampling method, which gives bootstrap tau estimates with 24% lower sampling error and a 110% higher estimated clustering endpoint than previously published (61⋅0 m vs. 29 m) and an equivalent increase in the clustering area of elevated disease odds by 342%. These differences could have important consequences for control efforts.Correct practice of graphical hypothesis testing of no clustering and clustering range estimation of the tau statistic are illustrated in the online Graphical abstract. We advocate proper implementation of this useful statistic, ultimately to reduce inaccuracies in control policy decisions made during disease clustering analysis.
Kura K, Ayabina D, Toor J, et al., 2021, Disruptions to schistosomiasis programmes due to COVID-19: an analysis of potential impact and mitigation strategies., Transactions of the Royal Society of Tropical Medicine and Hygiene, Vol: 115, Pages: 236-244, ISSN: 0035-9203
BACKGROUND: The 2030 goal for schistosomiasis is elimination as a public health problem (EPHP), with mass drug administration (MDA) of praziquantel to school-age children (SAC) as a central pillar of the strategy. However, due to coronavirus disease 2019, many mass treatment campaigns for schistosomiasis have been halted, with uncertain implications for the programmes. METHODS: We use mathematical modelling to explore how postponement of MDA and various mitigation strategies affect achievement of the EPHP goal for Schistosoma mansoni and S. haematobium. RESULTS: For both S. mansoni and S. haematobium in moderate- and some high-prevalence settings, the disruption may delay the goal by up to 2 y. In some high-prevalence settings, EPHP is not achievable with current strategies and so the disruption will not impact this. Here, increasing SAC coverage and treating adults can achieve the goal. The impact of MDA disruption and the appropriate mitigation strategy varies according to the baseline prevalence prior to treatment, the burden of infection in adults and the stage of the programme. CONCLUSIONS: Schistosomiasis MDA programmes in medium- and high-prevalence areas should restart as soon as is feasible and mitigation strategies may be required in some settings.
Hollingsworth TD, Mwinzi P, Vasconcelos A, et al., 2021, Evaluating the potential impact of interruptions to neglected tropical disease programmes due to COVID-19, TRANSACTIONS OF THE ROYAL SOCIETY OF TROPICAL MEDICINE AND HYGIENE, Vol: 115, Pages: 201-204, ISSN: 0035-9203
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- Citations: 8
Baggaley RF, Vegvari C, Dimala CA, et al., 2021, Health economic analyses of latent tuberculosis infection screening and preventive treatment among people living with HIV in lower tuberculosis incidence settings: a systematic review, Wellcome Open Research, Vol: 6, Pages: 51-51
<ns4:p><ns4:bold>Introduction: </ns4:bold>In lower tuberculosis (TB) incidence countries (<100 cases/100,000/year), screening and preventive treatment (PT) for latent TB infection (LTBI) among people living with HIV (PLWH) is often recommended, yet guidelines advising which groups to prioritise for screening can be contradictory and implementation patchy. Evidence of LTBI screening cost-effectiveness may improve uptake and health outcomes at reasonable cost.</ns4:p><ns4:p> <ns4:bold>Methods: </ns4:bold>Our systematic review assessed cost-effectiveness estimates of LTBI screening/PT strategies among PLWH in lower TB incidence countries to identify model-driving inputs and methodological differences. Databases were searched 1980-2020. Studies including health economic evaluation of LTBI screening of PLWH in lower TB incidence countries (<100 cases/100,000/year) were included. Study quality was assessed using the CHEERS checklist.</ns4:p><ns4:p> <ns4:bold>Results: </ns4:bold>Of 2,644 articles screened, nine studies were included. Cost-effectiveness estimates of LTBI screening/PT for PLWH varied widely, with universal screening/PT found highly cost-effective by some studies, while only targeting to high-risk groups (such as those from mid/high TB incidence countries) deemed cost-effective by others. Cost-effectiveness of strategies screening all PLWH from studies published in the past five years varied from US$2828 to US$144,929/quality-adjusted life-year gained (2018 prices). Study quality varied, with inconsistent reporting of methods and results limiting comparability of studies. Cost-effectiveness varied markedly by screening guideline, with British HIV Association guidelines more cost-effective than NICE guidelines in the UK.</ns4:p><ns4:p> <ns4:bold>Discussion: </ns4:bold>Cost-effectiveness studies of LTBI screening/PT for PLWH in lower TB incidence settings are
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