Dataset Information

Genetic surveillance in the Greater Mekong subregion and South Asia to support malaria control and elimination.

ABSTRACT:

Background

National Malaria Control Programmes (NMCPs) currently make limited use of parasite genetic data. We have developed GenRe-Mekong, a platform for genetic surveillance of malaria in the Greater Mekong Subregion (GMS) that enables NMCPs to implement large-scale surveillance projects by integrating simple sample collection procedures in routine public health procedures.

Methods

Samples from symptomatic patients are processed by SpotMalaria, a high-throughput system that produces a comprehensive set of genotypes comprising several drug resistance markers, species markers and a genomic barcode. GenRe-Mekong delivers Genetic Report Cards, a compendium of genotypes and phenotype predictions used to map prevalence of resistance to multiple drugs.

Results

GenRe-Mekong has worked with NMCPs and research projects in eight countries, processing 9623 samples from clinical cases. Monitoring resistance markers has been valuable for tracking the rapid spread of parasites resistant to the dihydroartemisinin-piperaquine combination therapy. In Vietnam and Laos, GenRe-Mekong data have provided novel knowledge about the spread of these resistant strains into previously unaffected provinces, informing decision-making by NMCPs.

Conclusions

GenRe-Mekong provides detailed knowledge about drug resistance at a local level, and facilitates data sharing at a regional level, enabling cross-border resistance monitoring and providing the public health community with valuable insights. The project provides a rich open data resource to benefit the entire malaria community.

Funding

The GenRe-Mekong project is funded by the Bill and Melinda Gates Foundation (OPP11188166, OPP1204268). Genotyping and sequencing were funded by the Wellcome Trust (098051, 206194, 203141, 090770, 204911, 106698/B/14/Z) and Medical Research Council (G0600718). A proportion of samples were collected with the support of the UK Department for International Development (201900, M006212), and Intramural Research Program of the National Institute of Allergy and Infectious Diseases.

SUBMITTER: Jacob CG

PROVIDER: S-EPMC8354633 | biostudies-literature | 2021 Aug

REPOSITORIES: biostudies-literature

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Publications

Genetic surveillance in the Greater Mekong subregion and South Asia to support malaria control and elimination.

Jacob Christopher G CG Thuy-Nhien Nguyen N Mayxay Mayfong M Maude Richard J RJ Quang Huynh Hong HH Hongvanthong Bouasy B Vanisaveth Viengxay V Ngo Duc Thang T Rekol Huy H van der Pluijm Rob R von Seidlein Lorenz L Fairhurst Rick R Nosten François F Hossain Md Amir MA Park Naomi N Goodwin Scott S Ringwald Pascal P Chindavongsa Keobouphaphone K Newton Paul P Ashley Elizabeth E Phalivong Sonexay S Maude Rapeephan R Leang Rithea R Huch Cheah C Dong Le Thanh LT Nguyen Kim-Tuyen KT Nhat Tran Minh TM Hien Tran Tinh TT Nguyen Hoa H Zdrojewski Nicole N Canavati Sara S Sayeed Abdullah Abu AA Uddin Didar D Buckee Caroline C Fanello Caterina I CI Onyamboko Marie M Peto Thomas T Tripura Rupam R Amaratunga Chanaki C Myint Thu Aung A Delmas Gilles G Landier Jordi J Parker Daniel M DM Chau Nguyen Hoang NH Lek Dysoley D Suon Seila S Callery James J Jittamala Podjanee P Hanboonkunupakarn Borimas B Pukrittayakamee Sasithon S Phyo Aung Pyae AP Smithuis Frank F Lin Khin K Thant Myo M Hlaing Tin Maung TM Satpathi Parthasarathi P Satpathi Sanghamitra S Behera Prativa K PK Tripura Amar A Baidya Subrata S Valecha Neena N Anvikar Anupkumar R AR Ul Islam Akhter A Faiz Abul A Kunasol Chanon C Drury Eleanor E Kekre Mihir M Ali Mozam M Love Katie K Rajatileka Shavanthi S Jeffreys Anna E AE Rowlands Kate K Hubbart Christina S CS Dhorda Mehul M Vongpromek Ranitha R Kotanan Namfon N Wongnak Phrutsamon P Almagro Garcia Jacob J Pearson Richard D RD Ariani Cristina V CV Chookajorn Thanat T Malangone Cinzia C Nguyen T T Stalker Jim J Jeffery Ben B Keatley Jonathan J Johnson Kimberly J KJ Muddyman Dawn D Chan Xin Hui S XHS Sillitoe John J Amato Roberto R Simpson Victoria V Gonçalves Sonia S Rockett Kirk K Day Nicholas P NP Dondorp Arjen M AM Kwiatkowski Dominic P DP Miotto Olivo O

eLife 20210810

<h4>Background</h4>National Malaria Control Programmes (NMCPs) currently make limited use of parasite genetic data. We have developed GenRe-Mekong, a platform for genetic surveillance of malaria in the Greater Mekong Subregion (GMS) that enables NMCPs to implement large-scale surveillance projects by integrating simple sample collection procedures in routine public health procedures.<h4>Methods</h4>Samples from symptomatic patients are processed by SpotMalaria, a high-throughput system that prod ...[more]

PMID: 34372970

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Project description:BackgroundPrivate sector malaria programmes contribute to government-led malaria elimination strategies in Cambodia, Lao PDR, and Myanmar by increasing access to quality malaria services and surveillance data. However, reporting from private sector providers remains suboptimal in many settings. To support surveillance strengthening for elimination, a key programme strategy is to introduce electronic surveillance tools and systems to integrate private sector data with national systems, and enhance the use of data for decision-making. During 2013-2017, an electronic surveillance system based on open source software, District Health Information System 2 (DHIS2), was implemented as part of a private sector malaria case management and surveillance programme. The electronic surveillance system covered 16,000 private providers in Myanmar (electronic reporting conducted by 200 field officers with tablets), 710 in Cambodia (585 providers reporting through mobile app), and 432 in Laos (250 providers reporting through mobile app).MethodsThe purpose of the study was to document the costs of introducing electronic surveillance systems and mobile reporting solutions in Cambodia, Lao PDR, and Myanmar, comparing the cost in different operational settings, the cost of introduction and maintenance over time, and assessing the affordability and financial sustainability of electronic surveillance. The data collection methods included extracting data from PSI's financial and operational records, collecting data on prices and quantities of resources used, and interviewing key informants in each setting. The costing study used an ingredients-based approach and estimated both financial and economic costs.ResultsAnnual economic costs of electronic surveillance systems were $152,805 in Laos, $263,224 in Cambodia, and $1,310,912 in Myanmar. The annual economic cost per private provider surveilled was $82 in Myanmar, $371 in Cambodia, and $354 in Laos. Cost drivers varied depending on operational settings and number of private sector outlets covered in each country; whether purchased or personal mobile devices were used; and whether electronic (mobile) reporting was introduced at provider level or among field officers who support multiple providers for case reporting.ConclusionThe study found that electronic surveillance comprises about 0.5-1.5% of national malaria strategic plan cost and 7-21% of surveillance budgets and deemed to be affordable and financially sustainable.

Project description:BackgroundThe malaria elimination plan of the Greater Mekong Subregion (GMS) is jeopardized by the increasing number of Plasmodium vivax infections and emergence of parasite strains with reduced susceptibility to the frontline drug treatment chloroquine/primaquine. This study aimed to determine the evolution of the P. vivax multidrug resistance 1 (Pvmdr1) gene in P. vivax parasites isolated from the China-Myanmar border area during the major phase of elimination.MethodsClinical isolates were collected from 275 P. vivax patients in 2008, 2012-2013 and 2015 in the China-Myanmar border area and from 55 patients in central China. Comparison was made with parasites from three border regions of Thailand.ResultsOverall, genetic diversity of the Pvmdr1 was relatively high in all border regions, and over the seven years in the China-Myanmar border, though slight temporal fluctuation was observed. Single nucleotide polymorphisms previously implicated in reduced chloroquine sensitivity were detected. In particular, M908L approached fixation in the China-Myanmar border area. The Y976F mutation sharply decreased from 18.5% in 2008 to 1.5% in 2012-2013 and disappeared in 2015, whereas F1076L steadily increased from 33.3% in 2008 to 77.8% in 2015. While neutrality tests suggested the action of purifying selection on the pvmdr1 gene, several likelihood-based algorithms detected positive as well as purifying selections operating on specific amino acids including M908L, T958M and F1076L. Fixation and selection of the nonsynonymous mutations are differently distributed across the three border regions and central China. Comparison with the global P. vivax populations clearly indicated clustering of haplotypes according to geographic locations. It is noteworthy that the temperate-zone parasites from central China were completely separated from the parasites from other parts of the GMS.ConclusionsThis study showed that P. vivax populations in the China-Myanmar border has experienced major changes in the Pvmdr1 residues proposed to be associated with chloroquine resistance, suggesting that drug selection may play an important role in the evolution of this gene in the parasite populations.

Project description:BackgroundThe aim of this paper is to review multi-country evidence of private sector adherence to national regulations, guidelines, and quality-assurance standards for malaria case management and to document current coverage of private sector engagement and support through ACTwatch outlet surveys implemented in 2015 and 2016.ResultsOver 76,168 outlets were screened, and approximately 6500 interviews were conducted (Cambodia, N = 1303; the Lao People's Democratic Republic (PDR), N = 724; Myanmar, N = 4395; and Thailand, N = 74). There was diversity in the types of private sector outlets providing malaria treatment across countries, and the extent to which they were authorized to test and treat for malaria differed. Among outlets stocking at least one anti-malarial, public sector availability of the first-line treatment for uncomplicated Plasmodium falciparum or Plasmodium vivax malaria was >75%. In the anti-malarial stocking private sector, first-line treatment availability was variable (Cambodia, 70.9%; the Lao PDR, 40.8%; Myanmar P. falciparum = 42.7%, P. vivax = 19.6%; Thailand P. falciparum = 19.6%, P. vivax = 73.3%), as was availability of second-line treatment (the Lao PDR, 74.9%; Thailand, 39.1%; Myanmar, 19.8%; and Cambodia, 0.7%). Treatment not in the National Treatment Guidelines (NTGs) was most common in Myanmar (35.8%) and Cambodia (34.0%), and was typically stocked by the informal sector. The majority of anti-malarials distributed in Cambodia and Myanmar were first-line P. falciparum or P. vivax treatments (90.3% and 77.1%, respectively), however, 8.8% of the market share in Cambodia was treatment not in the NTGs (namely chloroquine) and 17.6% in Myanmar (namely oral artemisinin monotherapy). In the Lao PDR, approximately 9 in 10 anti-malarials distributed in the private sector were second-line treatments-typically locally manufactured chloroquine. In Cambodia, 90% of anti-malarials were distributed through outlets that had confirmatory testing available. Over half of all anti-malarial distribution was by outlets that did not have confirmatory testing available in the Lao PDR (54%) and Myanmar (59%). Availability of quality-assured rapid diagnostic tests (RDT) amongst the RDT-stocking public sector ranged from 99.3% in the Lao PDR to 80.1% in Cambodia. In Cambodia, the Lao PDR, and Myanmar, less than 50% of the private sector reportedly received engagement (access to subsidized commodities, supervision, training or caseload reporting), which was most common among private health facilities and pharmacies.ConclusionsFindings from this multi-country study suggest that Cambodia, the Lao PDR, Myanmar, and Thailand are generally in alignment with national regulations, treatment guidelines, and quality-assurance standards. However, important gaps persist in the private sector which pose a threat to national malaria control and elimination goals. Several options are discussed to help align the private sector anti-malarial market with national elimination strategies.

Project description:BackgroundMalaria reactive case detection is the testing and, if positive, treatment of close contacts of index cases. It is included in national malaria control programmes of countries in the Greater Mekong Subregion to accelerate malaria elimination. Yet the value of reactive case detection in the control and elimination of malaria remains controversial because of the low yield, limited evidence for impact, and high demands on resources.MethodsData from the epidemiological assessments of large mass drug administration (MDA) studies in Myanmar, Vietnam, Cambodia and Laos were analysed to explore malaria infection clustering in households. The proportion of malaria positive cases among contacts screened in a hypothetical reactive case detection programme was then determined. The parasite density thresholds for rapid diagnostic test (RDT) detection was assumed to be > 50/µL (50,000/mL), for dried-blood-spot (DBS) based PCR > 5/µL (5000/mL), and for ultrasensitive PCR (uPCR) with a validated limit of detection at 0.0022/µL (22/mL).ResultsAt baseline, before MDA, 1223 Plasmodium infections were detected by uPCR in 693 households. There was clustering of Plasmodium infections. In 637 households with asymptomatic infections 44% (278/637) had more than one member with Plasmodium infections. In the 132 households with symptomatic infections, 65% (86/132) had more than one member with Plasmodium infections. At baseline 4% of households had more than one Plasmodium falciparum infection, but three months after MDA no household had more than one P. falciparum infected member. Reactive case detection using DBS PCR would have detected ten additional cases in six households, and an RDT screen would have detected five additional cases in three households among the 169 households with at least one RDT positive case. This translates to 19 and 9 additional cases identified per 1000 people screened, respectively. Overall, assuming all febrile RDT positive patients would seek treatment and provoke reactive case detection using RDTs, then 1047 of 1052 (99.5%) Plasmodium infections in these communities would have remained undetected.ConclusionReactive case detection in the Greater Mekong subregion is predicted to have a negligible impact on the malaria burden, but it has substantial costs in terms of human and financial resources.

Project description:BackgroundDespite decreases in incidence and related mortality, malaria remains a major public health challenge in the Greater Mekong Sub-region (GMS). The emergence of artemisinin resistance threatens these gains and has prompted efforts to accelerate elimination in the region. In the GMS, transmission now clusters in hotspots along international borders and among high-risk populations, including forest-goers. To eliminate malaria in the region, interventions must target such hard-to-reach populations. This review provides a comprehensive overview of the qualitative research on behaviours and perceptions that influence uptake of and adherence to malaria interventions among forest-goers in the GMS.MethodsA systematic search strategy was used to identify relevant sources, including database (OVID SP, PubMed, ISI Web of Knowledge) and bibliographic searches. Relevant findings from qualitative research methods were extracted and thematic analysis undertaken.ResultsOf 268 sources retrieved in searches twenty-two were reviewed. Most reported studies were conducted in Cambodia (n = 10), and were published after 2014 (n = 16). Four major themes emerged that are particularly relevant to the design of intervention packages targeted at forest-goers: (1) understanding of malaria and perceived risk; (2) preventive measures used when visiting the forest; (3) behaviours that put forest-goers at risk of infection; and, (4) malaria-related treatment seeking. There were notable differences across the reviewed articles that suggest the need for a locally tailored approach.ConclusionA more detailed characterization of forest activities is needed but research on this topic raises methodological challenges. Current vector control measures have limitations, with use of insecticidal-treated nets, hammocks and repellents influenced by the type of forest activities and the characteristics of these measures. In contrast, anti-malarial drugs, for example, as chemoprophylaxis, hold promise but require further evaluation.

Project description:BackgroundSample size calculations for cluster randomized trials are a recognized methodological challenge for malaria research in pre-elimination settings. Positively correlated responses from the participants in the same cluster are a key feature in the estimated sample size required for a cluster randomized trial. The degree of correlation is measured by the intracluster correlation coefficient (ICC) where a higher coefficient suggests a closer correlation hence less heterogeneity within clusters but more heterogeneity between clusters.MethodsData on uPCR-detected Plasmodium falciparum and Plasmodium vivax infections from a recent cluster randomized trial which aimed at interrupting malaria transmission through mass drug administrations were used to calculate the ICCs for prevalence and incidence of Plasmodium infections. The trial was conducted in four countries in the Greater Mekong Subregion, Laos, Myanmar, Vietnam and Cambodia. Exact and simulation approaches were used to estimate ICC values for both the prevalence and the incidence of parasitaemia. In addition, the latent variable approach to estimate ICCs for the prevalence was utilized.ResultsThe ICCs for prevalence ranged between 0.001 and 0.082 for all countries. The ICC from the combined 16 villages in the Greater Mekong Subregion were 0.26 and 0.21 for P. falciparum and P. vivax respectively. The ICCs for incidence of parasitaemia ranged between 0.002 and 0.075 for Myanmar, Cambodia and Vietnam. There were very high ICCs for incidence in the range of 0.701 to 0.806 in Laos during follow-up.ConclusionICC estimates can help researchers when designing malaria cluster randomized trials. A high variability in ICCs and hence sample size requirements between study sites was observed. Realistic sample size estimates for cluster randomized malaria trials in the Greater Mekong Subregion have to assume high between cluster heterogeneity and ICCs. This work focused on uPCR-detected infections; there remains a need to develop more ICC references for trials designed around prevalence and incidence of clinical outcomes. Adequately powered trials are critical to estimate the benefit of interventions to malaria in a reliable and reproducible fashion.Trial registrationClinicalTrials.govNCT01872702. Registered 7 June 2013. Retrospectively registered. https://clinicaltrials.gov/ct2/show/NCT01872702.

Project description:BackgroundNovel vector control methods that can directly target outdoor malaria transmission are urgently needed in the Greater Mekong Subregion (GMS) to accelerate malaria elimination and artemisinin resistance containment efforts. Ivermectin mass drug administration (MDA) to humans has been shown to effectively kill wild Anopheles and suppress malaria transmission in West Africa. Preliminary laboratory investigations were performed to determine ivermectin susceptibility and sporontocidal effect in GMS Anopheles malaria vectors coupled with pharmacokinetic models of ivermectin at escalating doses.MethodsA population-based pharmacokinetic model of ivermectin was developed using pre-existing data from a clinical trial conducted in Thai volunteers at the 200 µg/kg dose. To assess ivermectin susceptibility, various concentrations of ivermectin compound were mixed in human blood meals and blood-fed to Anopheles dirus, Anopheles minimus, Anopheles sawadwongporni, and Anopheles campestris. Mosquito survival was monitored daily for 7 days and a non-linear mixed effects model with probit analyses was used to calculate concentrations of ivermectin that killed 50% (LC50) of mosquitoes for each species. Blood samples were collected from Plasmodium vivax positive patients and offered to mosquitoes with or without ivermectin at the ivermectin LC25 or LC5 for An. dirus and An. minimus.ResultsThe GMS Anopheles displayed a range of susceptibility to ivermectin with species listed from most to least susceptible being An. minimus (LC50 = 16.3 ng/ml) > An. campestris (LC50 = 26.4 ng/ml) = An. sawadwongporni (LC50 = 26.9 ng/ml) > An. dirus (LC50 = 55.6 ng/ml). Mosquito survivorship results, the pharmacokinetic model, and extensive safety data indicated that ivermectin 400 µg/kg is the ideal minimal dose for MDA in the GMS for malaria parasite transmission control. Ivermectin compound was sporontocidal to P. vivax in both An. dirus and An. minimus at the LC25 and LC5 concentrations.ConclusionsIvermectin is lethal to dominant GMS Anopheles malaria vectors and inhibits sporogony of P. vivax at safe human relevant concentrations. The data suggest that ivermectin MDA has potential in the GMS as a vector and transmission blocking control tool to aid malaria elimination efforts.

Project description:BACKGROUND:As malaria elimination becomes a goal in malaria-endemic nations, questions of feasibility become critical. This article explores the potential challenges associated with this goal and future strategies for malaria elimination in the Greater Mekong Sub-region. METHODS:Thirty-two semi-structured interviews were conducted with policy makers (n?=?17) and principal investigators (n?=?15) selected based on their involvement in malaria prevention, control and elimination in the GMS. Interviews were audio-recorded and transcribed for qualitative content (thematic) analysis using QSR NVivo. RESULTS:All respondents described current malaria control and elimination strategies, such as case detection and management, prevention and strengthening of surveillance systems as critical and of equal priority. Aware of the emergence of multi-drug resistance in the GMS, researchers and policy makers outlined the need for additional elimination tools. As opposed to a centralized strategy, more targeted and tailored approaches to elimination were recommended. These included targeting endemic areas, consideration for local epidemiology and malaria species, and strengthening the peripheral health system. A decline in malaria transmission could lead to complacency amongst funders and policy makers resulting in a reduction or discontinuation of support for malaria elimination. Strong commitment of policymakers combined with strict monitoring and supervision by funders were considered pivotal to successful elimination programmes. CONCLUSION:Against a backdrop of increasing anti-malarial resistance and decreasing choices of anti-malarial regimens, policy makers and researchers stressed the urgency of finding new malaria elimination strategies. There was consensus that multi-pronged strategies and approaches are needed, that no single potential tool/strategy can be appropriate to all settings. Hence there is a need to customize malaria control and elimination strategies based on the better surveillance data.

Dataset Information

Genetic surveillance in the Greater Mekong subregion and South Asia to support malaria control and elimination.

Background

Methods

Results

Conclusions

Funding

Publications

Genetic surveillance in the Greater Mekong subregion and South Asia to support malaria control and elimination.

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