GEOFIL: A spatially-explicit agent-based modelling framework for predicting the long-term transmission dynamics of lymphatic filariasis in American Samoa

Heterogeneity in elimination efforts could increase the risk of resurgence of lymphatic filariasis in Madagascar

BACKGROUND

Progress in lymphatic filariasis (LF) elimination is spatially heterogeneous in many endemic countries, which may lead to resurgence in areas that have achieved elimination. Understanding the drivers and consequences of such heterogeneity could help inform strategies to reach global LF elimination goals by 2030. This study assesses whether differences in age-specific compliance with mass drug administration (MDA) could explain LF prevalence patterns in southeastern Madagascar and explores how spatial heterogeneity in prevalence and age-specific MDA compliance may affect the risk of LF resurgence after transmission interruption.

METHODOLOGY

We used LYMFASIM model with parameters in line with the context of southeastern Madagascar and explored a wide range of scenarios with different MDA compliance for adults and children (40-100%) to estimate the proportion of elimination, non-elimination and resurgence events associated with each scenario. Finally, we evaluated the risk of resurgence associated with different levels of migration (2-6%) from surrounding districts combined with varying levels of LF microfilaria (mf) prevalence (0-24%) during that same study period.

RESULTS

Differences in MDA compliance between adults and children better explained the observed heterogeneity in LF prevalence for these age groups than differences in exposure alone. The risk of resurgence associated with differences in MDA compliance scenarios ranged from 0 to 19% and was highest when compliance was high for children (e.g. 90%) and low for adults (e.g. 50%). The risk of resurgence associated with migration was generally higher, exceeding 60% risk for all the migration levels explored (2-6% per year) when mf prevalence in the source districts was between 9% and 20%.

CONCLUSION

Gaps in the implementation of LF elimination programme can increase the risk of resurgence and undermine elimination efforts. In Madagascar, districts that have not attained elimination pose a significant risk for those that have achieved it. More research is needed to help guide LF elimination programme on the optimal strategies for surveillance and control that maximize the chances to sustain elimination and avoid resurgence.

Lymphatic filariasis endgame strategies: Using GEOFIL to model mass drug administration and targeted surveillance and treatment strategies in American Samoa

American Samoa underwent seven rounds of mass drug administration (MDA) for lymphatic filariasis (LF) from 2000-2006, but subsequent surveys found evidence of ongoing transmission. American Samoa has since undergone further rounds of MDA in 2018, 2019, and 2021; however, recent surveys indicate that transmission is still ongoing. GEOFIL, a spatially-explicit agent-based LF model, was used to compare the effectiveness of territory-wide triple-drug MDA (3D-MDA) with targeted surveillance and treatment strategies. Both approaches relied on treatment with ivermectin, diethylcarbamazine, and albendazole. We simulated three levels of whole population coverage for 3D-MDA: 65%, 73%, and 85%, while the targeted strategies relied on surveillance in schools, workplaces, and households, followed by targeted treatment. In the household-based strategies, we simulated 1-5 teams travelling village-to-village and offering antigen (Ag) testing to randomly selected households in each village. If an Ag-positive person was identified, treatment was offered to members of all households within 100m-1km of the positive case. All simulated interventions were finished by 2027 and their effectiveness was judged by their 'control probability'-the proportion of simulations in which microfilariae prevalence decreased between 2030 and 2035. Without future intervention, we predict Ag prevalence will rebound. With 3D-MDA, a 90% control probability required an estimated ≥ 4 further rounds with 65% coverage, ≥ 3 rounds with 73% coverage, or ≥ 2 rounds with 85% coverage. While household-based strategies were substantially more testing-intensive than 3D-MDA, they could offer comparable control probabilities with substantially fewer treatments; e.g. three teams aiming to test 50% of households and offering treatment to a 500m radius had approximately the same control probability as three rounds of 73% 3D-MDA, but used < 40% the number of treatments. School- and workplace-based interventions proved ineffective. Regardless of strategy, reducing Ag prevalence below the 1% target threshold recommended by the World Health Organization was a poor indicator of the interruption of LF transmission, highlighting the need to review blanket elimination targets.

Control and elimination of lymphatic filariasis in Oceania: Prevalence, geographical distribution, mass drug administration, and surveillance in Samoa, 1998-2017

Lymphatic filariasis (LF) is a major public health problem globally and in the Pacific Region. The Global Programme to Eliminate LF has made great progress but LF is persistent and resurgent in some Pacific countries and territories. Samoa remains endemic for LF despite elimination efforts through multiple two-drug mass drug administrations (MDA) since 1965, including renewed elimination efforts started in 1999 under the Pacific Programme for Elimination of LF (PacELF). Despite eight rounds of national and two rounds of subnational MDA under PacELF, Samoa failed transmission assessment surveys (TAS) in all three evaluation units in 2017. In 2018, Samoa was the first to distribute countrywide triple-drug MDA using ivermectin, diethylcarbamazine (DEC), and albendazole. This paper provides a review of MDAs and historical survey results from 1998 to 2017 in Samoa and highlights lessons learnt from LF elimination efforts, including challenges and potential ways to overcome them to successfully achieve elimination.

Evaluating the plausible application of advanced machine learnings in exploring determinant factors of present pandemic: A case for continent specific COVID-19 analysis

Coronavirus disease, a novel severe acute respiratory syndrome (SARS COVID-19), has become a global health concern due to its unpredictable nature and lack of adequate medicines. Machine Learning (ML) models could be effective in identifying the most critical factors which are responsible for the overall fatalities caused by COVID-19. The functional capabilities of ML models in epidemiological research, especially for COVID-19, are not substantially explored. To bridge this gap, this study has adopted two advanced ML models, viz. Random Forest (RF) and Gradient Boosted Machine (GBM), to perform the regression modelling and provide subsequent interpretation. Five successive steps were followed to carry out the analysis: (1) identification of relevant key explanatory variables; (2) application of data dimensionality reduction for eliminating redundant information; (3) utilizing ML models for measuring relative influence (RI) of the explanatory variables; (4) evaluating interconnections between and among the key explanatory variables and COVID-19 case and death counts; (5) time series analysis for examining the rate of incidences of COVID-19 cases and deaths. Among the explanatory variables considered in this study, air pollution, migration, economy, and demographic factor were found to be the most significant controlling factors. Since a very limited research is available to discuss the superiority of ML models for identifying the key determinants of COVID-19, this study could be a reference for future public health research. Additionally, all the models and data used in this study are open source and freely available, thereby, reproducibility and scientific replication will be achievable easily.

Potential strategies for strengthening surveillance of lymphatic filariasis in American Samoa after mass drug administration: Reducing 'number needed to test' by targeting older age groups, hotspots, and household members of infected persons

Under the Global Programme to Eliminate Lymphatic Filariasis (LF), American Samoa conducted mass drug administration (MDA) from 2000-2006. Despite passing Transmission Assessment Surveys (TAS) in 2011/2012 and 2015, American Samoa failed TAS-3 in 2016, with antigen (Ag) prevalence of 0.7% (95%CI 0.3-1.8%) in 6-7 year-olds. A 2016 community survey (Ag prevalence 6.2% (95%CI 4.4-8.5%) in age ≥8 years) confirmed resurgence. Using data from the 2016 survey, this study aims to i) investigate antibody prevalence in TAS-3 and the community survey, ii) identify risk factors associated with being seropositive for Ag and anti-filarial antibodies, and iii) compare the efficiency of different sampling strategies for identifying seropositive persons in the post-MDA setting. Antibody prevalence in TAS-3 (n = 1143) were 1.6% for Bm14 (95%CI 0.9-2.9%), 7.9% for Wb123 (95%CI 6.4-9.6%), and 20.2% for Bm33 (95%CI 16.7-24.3%); and in the community survey (n = 2507), 13.9% for Bm14 (95%CI 11.2-17.2%), 27.9% for Wb123 (95%CI 24.6-31.4%), and 47.3% for Bm33 (95%CI 42.1-52.6%). Multivariable logistic regression was used to identify risk factors for being seropositive for Ag and antibodies. Higher Ag prevalence was found in males (adjusted odds ratio [aOR] 3.01), age ≥18 years (aOR 2.18), residents of Fagali'i (aOR 15.81), and outdoor workers (aOR 2.61). Ag prevalence was 20.7% (95%CI 9.7-53.5%) in households of Ag-positive children identified in TAS-3. We used NNTestav (average number needed to test to identify one positive) to compare the efficiency of the following strategies for identifying persons who were seropositive for Ag and each antibody: i) TAS of 6-7 year-old children, ii) population representative surveys of older age groups, and iii) targeted surveillance of subpopulations at higher risk of being seropositive (older ages, householders of Ag-positive TAS children, and known hotspots). For Ag, NNTestav ranged from 142.5 for TAS, to <5 for households of index children. NNTestav was lower in older ages, and highest for Ag, followed by Bm14, Wb123 and Bm33 antibodies. We propose a multi-stage surveillance strategy, starting with population-representative sampling (e.g. TAS or population representative survey of older ages), followed by strategies that target subpopulations and/or locations with low NNTestav. This approach could potentially improve the efficiency of identifying remaining infected persons and residual hotspots. Surveillance programs should also explore the utility of antibodies as indicators of transmission.

Genetic epidemiology of lymphatic filariasis in American Samoa after mass drug administration

Over 892 million people in 48 countries are at risk of infection by nematodes that cause lymphatic filariasis. As part of the Global Programme to Eliminate Lymphatic Filariasis, mass drug administration is distributed to communities until surveillance indicates infection rates are below target prevalence thresholds. In some countries, including American Samoa, lymphatic filariasis transmission persists despite years of mass drug administration and/or has resurged after cessation. Nothing is known about the population genetics of Wuchereria bancrofti worms in Polynesia, or whether local transmission is persisting and/or increasing due to inadequate mass drug administration coverage, expansion from residual hotspots, reintroduction from elsewhere, or a combination. We extracted DNA from microfilariae on blood slides collected during prevalence surveys in 2014 and 2016, comprising 31 pools of five microfilariae from 22 persons living in eight villages. We sequenced 1104 bp across three mitochondrial markers (ND4, COI, CYTB). We quantified parasite genetic differentiation using variant calls and estimated haplotypes using principal components analysis, F-statistics, and haplotype networks. Of the variants called, all but eight were shared across the main island of Tutuila, and three of those were from a previously described hotspot village, Fagali'i. Genotypic data did not support population genetic structure among regions or villages in 2016, although differences were observed between worms collected in Fagali'i in 2014 and those from 2016. Because estimated haplotype frequency varied between villages, these statistics suggested genetic differentiation, but were not consistent among villages. Finally, haplotype networks demonstrated American Samoan sequence clusters were related to previously published sequences from Papua New Guinea. These are, to our knowledge, the first reports of W. bancrofti genetic variation in Polynesia. The resurgent parasites circulating on the main island of American Samoa represent a single population. This study is the first step towards investigating how parasite population structure might inform strategies to manage resurgence and elimination of lymphatic filariasis.

Risk factors associated with failing pre-transmission assessment surveys (pre-TAS) in lymphatic filariasis elimination programs: Results of a multi-country analysis

Achieving elimination of lymphatic filariasis (LF) as a public health problem requires a minimum of five effective rounds of mass drug administration (MDA) and demonstrating low prevalence in subsequent assessments. The first assessments recommended by the World Health Organization (WHO) are sentinel and spot-check sites—referred to as pre-transmission assessment surveys (pre-TAS)—in each implementation unit after MDA. If pre-TAS shows that prevalence in each site has been lowered to less than 1% microfilaremia or less than 2% antigenemia, the implementation unit conducts a TAS to determine whether MDA can be stopped. Failure to pass pre-TAS means that further rounds of MDA are required. This study aims to understand factors influencing pre-TAS results using existing programmatic data from 554 implementation units, of which 74 (13%) failed, in 13 countries. Secondary data analysis was completed using existing data from Bangladesh, Benin, Burkina Faso, Cameroon, Ghana, Haiti, Indonesia, Mali, Nepal, Niger, Sierra Leone, Tanzania, and Uganda. Additional covariate data were obtained from spatial raster data sets. Bivariate analysis and multilinear regression were performed to establish potential relationships between variables and the pre-TAS result. Higher baseline prevalence and lower elevation were significant in the regression model. Variables statistically significantly associated with failure (p-value ≤0.05) in the bivariate analyses included baseline prevalence at or above 5% or 10%, use of Filariasis Test Strips (FTS), primary vector of Culex, treatment with diethylcarbamazine-albendazole, higher elevation, higher population density, higher enhanced vegetation index (EVI), higher annual rainfall, and 6 or more rounds of MDA. This paper reports for the first time factors associated with pre-TAS results from a multi-country analysis. This information can help countries more effectively forecast program activities, such as the potential need for more rounds of MDA, and prioritize resources to ensure adequate coverage of all persons in areas at highest risk of failing pre-TAS.

Achieving elimination of lymphatic filariasis (LF) as a public health problem requires a minimum of five rounds of mass drug administration (MDA) and being able to demonstrate low prevalence in several subsequent assessments. LF elimination programs implement sentinel and spot-check site assessments, called pre-TAS, to determine whether districts are eligible to implement more rigorous population-based surveys to determine whether MDA can be stopped or if further rounds are required. Reasons for failing pre-TAS are not well understood and have not previously been examined with data compiled from multiple countries. For this analysis, we analyzed data from routine USAID and WHO reports from Bangladesh, Benin, Burkina Faso, Cameroon, Ghana, Haiti, Indonesia, Mali, Nepal, Niger, Sierra Leone, Tanzania, and Uganda. In a model that included multiple variables, high baseline prevalence and lower elevation were significant. In models comparing only one variable to the outcome, the following were statistically significantly associated with failure: higher baseline prevalence at or above 5% or 10%, use of the FTS, primary vector of Culex, treatment with diethylcarbamazine-albendazole, lower elevation, higher population density, higher Enhanced Vegetation Index, higher annual rainfall, and six or more rounds of mass drug administration. These results can help national programs plan MDA more effectively, e.g., by focusing resources on areas with higher baseline prevalence and/or lower elevation.

Low transmission of Wuchereria bancrofti in cross-border districts of Côte d'Ivoire: A great step towards lymphatic filariasis elimination in West Africa

BACKGROUND

Lymphatic filariasis (LF) is widely endemic in Côte d'Ivoire, and elimination as public health problem (EPHP) is based on annual mass drug administration (MDA) using ivermectin and albendazole. To guide EPHP efforts, we evaluated Wuchereria bancrofti infection indices among humans, and mosquito vectors after four rounds of MDA in four cross-border health districts of Côte d'Ivoire.

METHODOLOGY

We monitored people and mosquitoes for W. bancrofti infections in the cross-border health districts of Aboisso, Bloléquin, Odienné and Ouangolodougou, Côte d'Ivoire. W. bancrofti circulating filarial antigen (CFA) was identified using filariasis test strips, and antigen-positive individuals were screened for microfilaremia. Moreover, filarial mosquito vectors were sampled using window exit traps and pyrethrum sprays, and identified morphologically at species level. Anopheles gambiae s.l. and Culex quinquefasciatus females were analyzed for W. bancrofti infection using polymerase chain reaction (PCR) technique.

PRINCIPAL FINDINGS

Overall, we found a substantial decline in W. bancrofti infection indices after four rounds of MDA compared to pre-MDA baseline data. CFA prevalence fell from 3.38-5.50% during pre-MDA to 0.00-1.53% after MDA interventions. No subjects had detectable levels of CFA in Ouangolodougou. Moreover, post-MDA CFA prevalence was very low, and below the 1% elimination threshold in Aboisso (0.19%) and Odienné (0.49%). Conversely, CFA prevalence remained above 1% in Bloléquin (1.53%). W. bancrofti microfilariae (Mf) were not found in Aboisso, Bloléquin, and Ouangolodougou, except for Odienné with low prevalence (0.16%; n = 613) and microfilaremia of 32.0 Mf/mL. No An. gambiae s.l. and Cx. quinquefasciatus pools were infected with W. bancrofti in Bloléquin and Ouangolodougou, while they exhibited low infection rates in Aboisso (1% and 0.07%), and Odienné (0.08% and 0.08%), respectively.

CONCLUSIONS

In cross-border areas of Côte d'Ivoire, LF infection indices in humans and mosquito vectors substantially declined after four rounds of MDA. CFA prevalence fell under the World Health Organization (WHO)-established threshold (1%) in Aboisso, Ouangolodougou and Odienné. Moreover, W. bancrofti prevalence in mosquitoes was lower than WHO-established threshold (2%) in all areas. This might suggest the interruption of W. bancrofti transmission, and possible MDA cessation. However, a formal transmission assessment survey (TAS) and molecular xenomonitoring in mosquito vectors should be implemented before eventual MDA cessation. However, MDA should pursue in Bloléquin where W. bancrofti infection prevalence remained above 1%. Our results provided important ramifications for LF control efforts towards EPHP in Côte d'Ivoire.

Demographic, socioeconomic and disease knowledge factors, but not population mobility, associated with lymphatic filariasis infection in adult workers in American Samoa in 2014

Background

Prevalence of lymphatic filariasis (LF) antigen in American Samoa was 16.5% in 1999. Seven rounds of mass drug administration (MDA) programmes between 2000 and 2006 reduced antigen prevalence to 2.3%. The most efficient methods of surveillance after MDA are not clear, but testing specific at-risk groups such as adults may provide earlier warning of resurgence. The role of migration from LF endemic countries in maintaining transmission also needs investigation. Few studies have investigated knowledge about LF and how that relates to infection risk. This study aims to investigate associations between socio-demographics, population mobility, disease knowledge and LF infection risk.

Methods

In 2014, we surveyed 670 adults aged 16–68 years (62% female) at two worksites in American Samoa. Sera were tested for LF antigen and antibodies (Bm14 and Wb123) by rapid test and/or ELISA. Multivariate logistic regression was used to assess association between seromarkers and demographic factors, household socioeconomic status (SES), residence, travel history, and knowledge of LF.

Results

Overall, 1.8% of participants were positive for antigen, 11.8% for Bm14, 11.3% for Wb123 and 17.3% for at least one antibody. Recent travel outside American Samoa was not associated with positivity for any seromarker. Men had higher seroprevalence than women for all outcomes (any antibody: adjusted odds ratio (aOR) = 3.49 (95% CI: 2.21–5.49). Those aged over 35 years (compared to 15–24 years) had higher prevalence of Bm14 antibody (aOR = 3.75, 3.76 and 4.17 for ages 35–44, 45–54 and ≥ 55 years, respectively, P < 0.05). Lower SES was associated with seropositivity (antigen: aOR = 2.89, 95% CI: 1.09–7.69; either antibody: aOR = 1.51, 95% CI: 1.12–2.05). Those who knew that mosquitoes transmitted LF had lower Wb123 antibody prevalence (aOR = 0.55, 95% CI: 0.32–0.95).

Conclusions

Opportunistic sampling of adults at worksites provided an efficient and representative way to assess prevalence and risk factors for LF in American Samoa and in hindsight, foreshadowed the resurgence of transmission. Risk of LF infection, detected by one or more serological markers, was not related to recent travel history, but was strongly associated with male gender, older age, lower SES, and lack of knowledge about mosquito transmission. These results could guide future efforts to increase MDA participation.

Genomic Epidemiology in Filarial Nematodes: Transforming the Basis for Elimination Program Decisions

Onchocerciasis and lymphatic filariasis are targeted for elimination, primarily using mass drug administration at the country and community levels. Elimination of transmission is the onchocerciasis target and global elimination as a public health problem is the end point for lymphatic filariasis. Where program duration, treatment coverage, and compliance are sufficiently high, elimination is achievable for both parasites within defined geographic areas. However, transmission has re-emerged after apparent elimination in some areas, and in others has continued despite years of mass drug treatment. A critical question is whether this re-emergence and/or persistence of transmission is due to persistence of local parasites-i.e., the result of insufficient duration or drug coverage, poor parasite response to the drugs, or inadequate methods of assessment and/or criteria for determining when to stop treatment-or due to re-introduction of parasites via human or vector movement from another endemic area. We review recent genetics-based research exploring these questions in Onchocerca volvulus, the filarial nematode that causes onchocerciasis, and Wuchereria bancrofti, the major pathogen for lymphatic filariasis. We focus in particular on the combination of genomic epidemiology and genome-wide associations to delineate transmission zones and distinguish between local and introduced parasites as the source of resurgence or continuing transmission, and to identify genetic markers associated with parasite response to chemotherapy. Our ultimate goal is to assist elimination efforts by developing easy-to-use tools that incorporate genetic information about transmission and drug response for more effective mass drug distribution, surveillance strategies, and decisions on when to stop interventions to improve sustainability of elimination.

The roadmap towards elimination of lymphatic filariasis by 2030: insights from quantitative and mathematical modelling

The Global Programme to Eliminate Lymphatic Filariasis was launched in 2000 to eliminate lymphatic filariasis (LF) as a public health problem by 1) interrupting transmission through mass drug administration (MDA) and 2) offering basic care to those suffering from lymphoedema or hydrocele due to the infection. Although impressive progress has been made, the initial target year of 2020 will not be met everywhere. The World Health Organization recently proposed 2030 as the new target year for elimination of lymphatic filariasis (LF) as a public health problem. In this letter, LF modelers of the Neglected Tropical Diseases (NTDs) Modelling Consortium reflect on the proposed targets for 2030 from a quantitative perspective. While elimination as a public health problem seems technically and operationally feasible, it is uncertain whether this will eventually also lead to complete elimination of transmission. The risk of resurgence needs to be mitigated by strong surveillance after stopping interventions and sometimes perhaps additional interventions.

Evaluating the Evidence for Lymphatic Filariasis Elimination

In the global drive for elimination of lymphatic filariasis (LF), 15 countries have achieved validation of elimination as a public health problem (EPHP). Recent empirical evidence has demonstrated that EPHP does not always lead to elimination of transmission (EOT). Here we show how the probability of elimination explicitly depends on key biological parameters, many of which have been poorly characterized, leading to a poor evidence base for the elimination threshold. As more countries progress towards EPHP it is essential that this process is well-informed, as prematurely halting treatment and surveillance programs could pose a serious threat to global progress. We highlight that refinement of the weak empirical evidence base is vital to understand drivers of elimination and inform long-term policy.