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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>
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: 1
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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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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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
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
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
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, 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.
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
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.
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.
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
<ns7:p><ns7:bold>Introduction: </ns7: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.</ns7:p><ns7:p> <ns7:bold>Methods: </ns7: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.</ns7:p><ns7:p> <ns7:bold>Results: </ns7: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.</ns7:p><ns7:p> <ns7:bold>Discussion: </ns7:bold>Cost-effectiveness studies of LTBI screening/PT for PLWH in lower TB incidence settings are
Prada JM, Stolk WA, Davis EL, et al., 2021, Delays in lymphatic filariasis elimination programmes due to COVID-19, and possible mitigation strategies, TRANSACTIONS OF THE ROYAL SOCIETY OF TROPICAL MEDICINE AND HYGIENE, Vol: 115, Pages: 261-268, ISSN: 0035-9203
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Borlase A, Blumberg S, Callahan EK, et al., 2021, Modelling trachoma post-2020: opportunities for mitigating the impact of COVID-19 and accelerating progress towards elimination, TRANSACTIONS OF THE ROYAL SOCIETY OF TROPICAL MEDICINE AND HYGIENE, Vol: 115, Pages: 213-221, ISSN: 0035-9203
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Blumberg S, Borlase A, Prada JM, et al., 2021, Implications of the COVID-19 pandemic in eliminating trachoma as a public health problem, TRANSACTIONS OF THE ROYAL SOCIETY OF TROPICAL MEDICINE AND HYGIENE, Vol: 115, Pages: 222-228, ISSN: 0035-9203
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- Citations: 2
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
Mabey D, Agler E, Amuasi JH, et al., 2021, Towards a comprehensive research and development plan to support the control, elimination and eradication of neglected tropical diseases, TRANSACTIONS OF THE ROYAL SOCIETY OF TROPICAL MEDICINE AND HYGIENE, Vol: 115, Pages: 196-199, ISSN: 0035-9203
Graham M, Ayabina D, Lucas TCD, et al., 2021, SCHISTOX: An individual based model for the epidemiology and control of schistosomiasis, INFECTIOUS DISEASE MODELLING, Vol: 6, Pages: 438-447
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- Citations: 1
Blumberg S, Prada JM, Tedijanto C, et al., 2020, Forecasting trachoma control and identifying transmission-hotspots
<jats:title>Abstract</jats:title><jats:sec><jats:title>Background</jats:title><jats:p>Tremendous progress towards elimination of trachoma as a public health problem has been made. However, there are areas where the clinical indicator of disease, trachomatous inflammation—follicular (TF), remains prevalent. We quantify the progress that has been made, and forecast how TF prevalence will evolve with current interventions. We also determine the probability that a district is a transmission-hotspot based on its TF prevalence (i.e. reproduction number greater than one).</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>Data on trachoma prevalence comes from the GET2020 global repository organized by the World Health Organization and the International Trachoma Initiative. Forecasts of TF prevalence and the percent of districts achieving local control is achieved by regressing the coefficients of a fitted exponential distribution for the year-by-year distribution of TF prevalence. The probability of a district being a transmission-hotspot is extrapolated from the residuals of the regression.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>Forecasts suggest that with current interventions, 96.5% of surveyed districts will have TF prevalence among children aged 1-9 years <5% by 2030 (95% CI: 86.6-100.0%). Districts with TF prevalence < 20% appear unlikely to be transmission-hotspots. However, a district having TF prevalence of over 28% in 2016-2019 corresponds to at least 50% probability of being a transmission-hotspot.</jats:p></jats:sec><jats:sec><jats:title>Conclusions</jats:title><jats:p>Sustainable control of trachoma appears achievable. However there are transmission-hotspots that are not responding to annual mass drug administration of azithromycin and require enhance
Lucas TCD, Pollington TM, Davis EL, et al., 2020, Responsible modelling: Unit testing for infectious disease epidemiology, Epidemics: the journal of infectious disease dynamics, Vol: 33, ISSN: 1755-4365
Infectious disease epidemiology is increasingly reliant on large-scale computation and inference. Models have guided health policy for epidemics including COVID-19 and Ebola and endemic diseases including malaria and tuberculosis. Yet a coding bug may bias results, yielding incorrect conclusions and actions causing avoidable harm. We are ethically obliged to make our code as free of error as possible. Unit testing is a coding method to avoid such bugs, but it is rarely used in epidemiology. We demonstrate how unit testing can handle the particular quirks of infectious disease models and aim to increase the uptake of this methodology in our field.
Kura K, Hardwick RJ, Truscott JE, et al., 2020, The impact of mass drug administration on Schistosoma haematobium infection: what is required to achieve morbidity control and elimination?, Parasites and Vectors, Vol: 13, Pages: 1-10, ISSN: 1756-3305
BACKGROUND: Schistosomiasis remains an endemic parasitic disease causing much morbidity and, in some cases, mortality. The World Health Organization (WHO) has outlined strategies and goals to combat the burden of disease caused by schistosomiasis. The first goal is morbidity control, which is defined by achieving less than 5% prevalence of heavy intensity infection in school-aged children (SAC). The second goal is elimination as a public health problem (EPHP), achieved when the prevalence of heavy intensity infection in SAC is reduced to less than 1%. Mass drug administration (MDA) of praziquantel is the main strategy for control. However, there is limited availability of praziquantel, particularly in Africa where there is high prevalence of infection. It is therefore important to explore whether the WHO goals can be achieved using the current guidelines for treatment based on targeting SAC and, in some cases, adults. Previous modelling work has largely focused on Schistosoma mansoni, which in advance cases can cause liver and spleen enlargement. There has been much less modelling of the transmission of Schistosoma haematobium, which in severe cases can cause kidney damage and bladder cancer. This lack of modelling has largely been driven by limited data availability and challenges in interpreting these data. RESULTS: In this paper, using an individual-based stochastic model and age-intensity profiles of S. haematobium from two different communities, we calculate the probability of achieving the morbidity and EPHP goals within 15 years of treatment under the current WHO treatment guidelines. We find that targeting SAC only can achieve the morbidity goal for all transmission settings, regardless of the burden of infection in adults. The EPHP goal can be achieved in low transmission settings, but in some moderate to high settings community-wide treatment is needed. CONCLUSIONS: We show that the key determinants of achieving the WHO goals are the precise form of the ag
Prada JM, Stolk WA, Davis EL, et al., 2020, Predicting the impact of disruptions in lymphatic filariasis elimination programmes due to the outbreak of coronavirus disease (COVID-19) and possible mitigation strategies
<jats:title>Abstract</jats:title><jats:sec><jats:title>Background</jats:title><jats:p>In view of the current global COVID-19 pandemic, mass drug administration interventions for neglected tropical diseases, including lymphatic filariasis, have been halted. We used mathematical modelling to estimate the impact of delaying or cancelling treatment rounds and explore possible mitigation strategies.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>We used three established lymphatic filariasis transmission models to simulate infection trends in settings with annual treatment rounds and programme delays in 2020 of 6, 12, 18 or 24 months. We then evaluated the impact of various mitigation strategies upon resuming activities.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>The delay in achieving the elimination goals is on average similar to the number of years the treatment rounds are missed. Enhanced interventions implemented for as little as one year can allow catch-up on the progress lost, and if maintained throughout the programme can lead to acceleration of up to 3 years.</jats:p></jats:sec><jats:sec><jats:title>Conclusions</jats:title><jats:p>In general, a short delay in the programme does not cause major delay in achieving the goals. Impact is strongest in high endemicity areas. Mitigation strategies such as biannual treatment or increased coverage are key to minimizing the impact of the disruption once the programme resumes; and lead to potential acceleration, should these enhanced strategies be maintained.</jats:p></jats:sec>
Borlase A, Blumberg S, Callahan EK, et al., 2020, Modelling trachoma post 2020: Opportunities for mitigating the impact of COVID-19 and accelerating progress towards elimination
<jats:title>Abstract</jats:title><jats:sec><jats:title>Background</jats:title><jats:p>The COVID-19 pandemic has disrupted planned annual antibiotic mass drug administration (MDA) activities which have formed the cornerstone of the largely successful global efforts to eliminate trachoma as a public health problem.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>Using a mathematical model we investigate the impact of interruption to MDA in trachoma-endemic settings. We evaluate potential measures to mitigate this impact and consider alternative strategies for accelerating progress in those areas where the trachoma elimination targets may not be achievable otherwise.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>We demonstrate that for districts which were hyperendemic at baseline, or where the trachoma elimination thresholds have not already been achieved after 3 rounds of MDA, the interruption to planned MDA could lead to a delay greater than the duration of interruption. We also show that an additional round of MDA in the year following MDA resumption could effectively mitigate this delay. For districts where probability of elimination under annual MDA was already very low, we demonstrate that more intensive MDA schedules are needed to achieve agreed targets.</jats:p></jats:sec><jats:sec><jats:title>Conclusion</jats:title><jats:p>Through appropriate use of additional MDA, the impact of COVID-19 in terms of delay to reaching trachoma elimination targets can be effectively mitigated. Additionally, more frequent MDA may accelerate progress towards 2030 goals.</jats:p></jats:sec>
Kura K, Ayabina D, Toor J, et al., 2020, Disruptions to schistosomiasis programmes due to COVID-19: an analysis of potential impact and mitigation strategies, Publisher: Cold Spring Harbor Laboratory
<jats:title>Abstract</jats:title><jats:sec><jats:title>Background</jats:title><jats:p>The 2030 goal for schistosomiasis is elimination as a public health problem (EPHP), with mass drug administration (MDA) of praziquantel to school-aged children (SAC) a central pillar of the strategy. However, due to COVID-19, many mass treatment campaigns for schistosomiasis have been halted with uncertain implications for the programmes.</jats:p></jats:sec><jats:sec><jats:title>Method</jats:title><jats:p>We use mathematical modelling to explore how postponement of MDA and various mitigation strategies affect achievement of the EPHP goal for <jats:italic>Schistosoma mansoni</jats:italic> and <jats:italic>S. haematobium</jats:italic>.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>In moderate and some high prevalence settings, the disruption may delay the goal by up to two years. 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.</jats:p><jats:p>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 stage of the programme.</jats:p></jats:sec><jats:sec><jats:title>Conclusions</jats:title><jats:p>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.</jats:p></jats:sec>
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