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Grand Challenges is a family of initiatives fostering innovation to solve key global health and development problems. Each initiative is an experiment in the use of challenges to focus innovation on making an impact. Individual challenges address some of the same problems, but from differing perspectives.


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Challenges: Malaria Surveillance
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Molecular Surveillance of P. falciparum Histidine Rich Protein 2/3 (pfhrp2/3) Deletions in the Context of Transmission Intensity

Elly Munde, Hospital and Health Administration Services (Diani, Kenya)
Jun 7, 2021

Elly Munde of the Hospital and Health Administration Services in Kenya will integrate a multiplex PCR assay into an existing malaria molecular surveillance program to detect a specific variant in the causative malaria parasite Plasmodium falciparum, which is undetectable by most rapid diagnostic tests and is threatening successful disease control. The specific haplotype of concern has a deletion of the genes encoding for histidine-rich proteins 2 and 3 (hrp2/3). Individuals infected with this haplotype produce a false negative result on most diagnostic tests. They will integrate the PCR assay into an ongoing cohort study, and develop statistical analyses to genotype the samples and decision support tools for guiding future intervention strategies. They will also evaluate the emergence and spread of these new haplotypes by genotyping existing samples to determine the effect of previously deployed diagnostic policies on disease control. If successful, they will scale their approach up nationwide.

Integrating Molecular Surveillance into the Malaria Control Program in Papua New Guinea

Moses Laman, Papua New Guinea Institute of Medical Research (Madang, Papua New Guinea)
May 16, 2021

Moses Laman of the Papua New Guinea Institute of Medical Research will extend the national malaria surveillance platform, which maps infections across Papua New Guinea, to incorporate valuable genomic data of the malaria-causing parasites that can be used to better guide control and elimination efforts. They will enable the molecular data from the parasites generated by a central laboratory to be overlaid onto the clinical case data, so that transmission dynamics and parasite population diversity can be displayed on a web-based dashboard for easy access by program managers and health authorities. They will also provide training to relevant staff so they can use the new genomics data to inform their decisions on intervention strategies and outbreak containment.

Implementation of an Integrated Approach of a SNP-Based Molecular Barcode

Issiaka Soulama, Groupe de Recherche Action en Santé (Ouagadougou, Burkina Faso)
May 8, 2021

Issiaka Soulama of Groupe de Recherche Action en Santé in Burkina Faso will build a molecular surveillance platform for monitoring the emergence and spread of different strains of the malaria-causing parasite, Plasmodium falciparum, including drug-resistant ones, to support the National Malaria Control Program and improve the control of malaria. They will develop a web-based platform so that when a person tests positive at one of the existing monitoring sites, they can quickly and easily record the location of the infection. If given consent, they will also take a blood sample for genotyping the parasite at a central laboratory, and analyze them for potential drug resistant mutations. These data will be used for modelling near real-time transmission dynamics to inform future control policies and practices. The data will be shared with program managers who will be trained on how to interpret them to identify effective intervention strategies.

Genomic Epidemiology of Malaria in a Gold Mining Area in Pará, Brazil

Silvia Maria Di Santi, Disease Control Coordination, São Paulo State Department of Health (São Paulo, São Paulo, Brazil)
May 1, 2021

Silvia Maria Di Santi at the São Paulo State Department of Health in Brazil will integrate genomics techniques into their routine malaria surveillance program to genetically characterize the parasite populations and monitor transmission dynamics in gold mining regions. Gold mining is associated with deforestation, which expands breeding sites for malaria-transmitting mosquitoes, poor housing conditions, and illegal activities, which makes eliminating malaria in these regions more difficult. They propose to use advanced sequencing technologies to better monitor the emergence of drug-resistant malaria-causing parasites and insecticide-resistant malaria vectors in a gold mining area in Pará, Brazil. They will collect samples from existing treatment and diagnosis sites and by recruiting miners, and collect Anopheles mosquitoes in different seasons. These will be subjected to whole genome and targeted amplicon sequencing, which will be implemented in a reference laboratory. They will also develop an interactive web browsing tool to visualize the raw sequencing data and reveal patterns of drug and insecticide resistance for informing interventions targeted to this region.

Integrating Molecular Surveillance for P. falciparum Elimination in Brazil

Martha Cecilia Suárez-Mutis, Fiocruz (Rio de Janeiro, Rio de Janeiro, Brazil)
May 1, 2021

Martha Cecilia Suárez-Mutis of Fiocruz in Brazil will develop a molecular surveillance tool with genome sequencing to monitor the entry and subsequent spread of drug-resistant Plasmodium falciparum, the malaria-causing parasite, from across the country’s borders. Elimination of malaria requires close monitoring of the parasite population to track the emergence and spread of new genetic variants, particularly those resistant to the commonly used anti-malarial drugs, which will severely restrict elimination efforts. They will train local teams in five health posts close to selected country borders to collect blood samples from malaria patients, which will be sequenced in an established research laboratory to identify any known resistance mutations. They will also develop an analysis pipeline, tools, and an interactive web platform to translate the sequencing data into a user-friendly interface to assist decision-making by local and national managers.

Identifying Imported and Local Malaria Cases in Eliminating Districts Using Genomic Surveillance

Jaishree Raman, National Institute for Communicable Diseases (NICD) - South Africa (Johannesburg, South Africa)
Mar 29, 2021

Jaishree Raman of the National Institute for Communicable Diseases in South Africa will integrate a genomic surveillance platform with the existing routine malaria surveillance program to better identify the source of infections and monitor parasite spread within South and southern Africa. Eliminating malaria requires knowing whether new infections are imported from other countries or are caused by local outbreaks, because they require different intervention strategies. Distinguishing between these sources is difficult, particularly in countries with a high proportion of migrants whose movements are largely undocumented. Leveraging the recent advances in sequencing technology they will genotype samples collected routinely from patients, and translate the data into a usable format for uploading to the existing malaria information system. The data can then be integrated with the relevant epidemiological data, and utilized by managers of the national control program to track the movement of specific strains and better guide interventions.

Integrated System for pfhrp2/3 Molecular Surveillance Capabilities in Uganda

Agaba Bosco, Infectious Diseases Research Collaboration (Kampala, Uganda)
Mar 21, 2021

Agaba Bosco from the Infectious Diseases Research Collaboration in Uganda will integrate a molecular surveillance system into their National Malaria Control Program to diagnose a currently under-detected variant of the causative parasite Plasmodium falciparum and better track spread. Most rapid diagnostic tests for malaria detect a specific parasite protein, however a new variant has emerged that has a deletion of the corresponding pfhrp2/3 gene, leading to a false negative test result. As these infections fail to be diagnosed, people aren’t being properly treated, and the disease continues to spread. They will upgrade the testing capabilities at the malaria reference laboratory to detect this deletion variant, and select 10 facilities spread across the country from which they will periodically sample 37 malaria patients to track the spread. They will also incorporate information systems for data capture and visualization dashboards to inform program managers and guide their decision-making.

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The Bill & Melinda Gates Foundation is part of the Grand Challenges partnership network. Visit www.grandchallenges.org to view the map of awarded grants across this network and grant opportunities from partners.