NIMR

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    Molecular surveillance of malaria parasite populations and antimalarial drug resistance to support malaria control and elimination in Tanzania

    Investigators

    Deus S. Ishengoma1,2,3, Celine I. Mandara1, Rashid A. Madebe1, Jeffrey Bailey4, Jonathan J. Juliano5,6,7, Eric Rogier8, Udhayakumar Venkatachalam8, Bronwyn MacInnis3,9, Ritha Njau10, Samwel Lazaro11, Sijenunu Mwaikambo11, Frank Chacky11, Daniel Mbwambo11, Issa Garimo11, Abdallah Lusasi11, Fabrizio Molteni12, Ndekya Oriyo1, Paul E. Kazyoba1, Ally Mohamed11

    Principal Institution(s)

    1National Institute for Medical Research, Dar es Salaam, Tanzania.

    2Faculty of Pharmaceutical Sciences, Monash University, Melbourne, Australia.

    3Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA.

    4Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA.

    5Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, USA.

    6Curriculum in Genetics and Molecular Biology, University of North Carolina Chapel Hill, Chapel Hill, NC, USA.

    7Department of Epidemiology, Gillings School of Global Public Health, Chapel Hill, USA.

    8The Centers for Disease Control and Prevention, Center for Global Health, Division of Parasitic Diseases and Malaria, Malaria Branch, Atlanta, GA, United States of America.

    9Broad Institute of Harvard and MIT, Boston, MA, USA.

    10World Health Organization, Country Office, Dar es Salaam, Tanzania

    11National Malaria Control Programme, Dodoma, Tanzania

    12Swiss TPH, Dar es Salaam, Tanzania

    Objectives

    To establish local molecular, genetic, and genomic laboratory and analytic capacity to support malaria surveillance in Tanzania.

    1. Generating genetic/genomic data to support malaria elimination using population genetics metrics for monitoring changes in transmission related to interventions, parasite connectivity and migration.
    2. Mapping and monitoring non-falciparum species, and hrp2/hrp3 gene deletion and their impacts on performance of HRP2-based mRDTs.
    3. Creating a country-wide profile of drug resistance markers as a measure of performance for antimalarial drugs to guide current and future use for effective case management and accelerate ongoing malaria elimination strategies.
    4. Training for capacity building, career development and science leadership for empowering Tanzanian researcher.
    5. Engage the Ministry of Health, Community Development, Gender, Eldery and Children (MoHCDGEC) through NMCP; President’s Office, Regional Administration and Local Governments (PO-RALG) and other stakeholders and undertake a landscape mapping to understand needs and existing gaps; in order to develop use cases and operational plans for implementing molecular surveillance in Tanzania.
    6. Working with government experts to help specify, adopt and user-test the anticipated cloud-based data platform for the storage, management, analysis, and sharing of the genomic data and associated metadata generated in objectives 1-3. 

    Introduction

    Recent developments in genomics and bioinformatics, and their application in public health are playing a key role in the detection, monitoring and control of pandemics, as well as emerging and re-emerging pathogens. However, in developing countries with the highest burden of infectious diseases including malaria, there is a lack of genomics capacity to detect pathogens and perform bioinformatics analysis. In malaria, molecular surveillance can be used to monitor trends of disease burden and impacts of interventions and to determine sources of parasites in eliminating areas. It can also be used to assess the emergence and trends of antimalarial drugs and insecticide resistance, as well as important changes in parasites/vectors such as deletion of histidine rich protein 2/3 genes (hrp2/3, which are the targets of Histidine rich protein 2 – HRP2 based malaria rapid diagnostic tests – mRDTs). This study aims at strengthening genomics and bioinformatics capacity in Tanzania for detection and surveillance of malaria, with an ultimate goal of extending these technologies to other infectious diseases of significant global health impact. Genomic data and next generation sequencing (NGS) will be powerful tools to help Tanzania as it embarks on its plan of eliminating malaria by 2030 and controlling other infectious diseases.

     

    The National Institute for Medical Research (NIMR) secured funding from the Bill and Melinda Gates Foundation in May 2020 to conduct a project on Molecular Surveillance of Malaria in Tanzania (MSMT). This project is being implemented by NIMR in collaboration with the National Malaria Control Program (NMCP) both under the Ministry of Health (MoH) and the President’s Office, Regional Administration and Local Government (PO-RALG). The project covered 13 regions in 2021 and 2022, now extended to cover all the 26 regions of mainland Tanzania with different malaria transmission intensities according to the most recent NMCP reports. The regions include Dar es Salaam, Dodoma, Kagera, Kigoma, Kilimanjaro, Manyara, Mara, Mtwara, Njombe, Ruvuma, Songwe, Tabora, Geita, Mwanza, Simiyu, Singida, Pwani, Morogoro, Arusha, Iringa, Katavi, Lindi, Mbeya, Rukwa, Shinyanga, and Tanga.

     

    The fourth period was implemented for 12 months from 01st November 2022 and completed on 31st October 2023. This marked the final period of the MSMT project implementation for the first phase. The project received a no cost extension period of six months from 01st November 2023 to 30th April 2024. The main activities which were planned and implemented included procurement of supplies for sample collection and laboratory analyses, field collection of samples and data, dissemination of the findings of field studies done in 2022, finalizing procurement of laboratory equipment, and training of researchers and students. The team continued to do laboratory analysis in the country with assistance from our partners in the USA. Results obtained from 2021 and 2022 surveys were shared with regional and district authorities during initiation of the third round of surveys.

     

    The MSMT project aims to establish a sustainable, self-supported genomics laboratory capacity at NIMR over a 42-month period that can operate independently, performing malaria genomic surveillance and bioinformatics analysis. It will also support the training of Tanzanian researchers in genomics and bioinformatics, and NMCP in the ongoing malaria elimination. The project has been undertaken for 42 months and this report provides a summary of the progress of the project activities over a period of 12 months from November 2022 to December 2023

    Aim/Objective

    Main Objective

    To undertake studies on the population genetics of malaria parasites, drug resistance markers and surveillance of histidine-rich protein 2/3 (hrp2/3) gene deletions.

    Specific Objectives

    1. Undertaking population studies of malaria parasites to establish genomic-based metrics for assessing and monitoring the trends of malaria transmission as well as the impacts of current  and future interventions.
    2. To conduct studies to map and generate profiles of drug resistance markers in Tanzania.
    3. To establish the current status and monitor the trends of hrp2/3 gene deletions which are believed to affect the performance of malaria rapid diagnostic tests (mRDTs).
    4. To undertake training of Tanzania researchers for capacity building, career development and science leadership. The project will empower Tanzanian researchers to run the genomics laboratory and attract research funds for sustainability.
    5. To engage with NMCP and undertake a landscape mapping to understand their needs and existing gaps; in order to develop use cases and operational plans for implementing malaria molecular surveillance (MMS) and real-time utilization of the data for policy and decision making to support malaria elimination in Tanzania.
    6. Working with BMGF and the Malaria Cloud Data Platform development team in USA to help specify, adopt, and user-test the anticipated cloud-based data platform for the storage, management, analysis, and sharing of genomic data and associated metadata to be generated by the project.

    Methods

    Study Sites

    In the first and second rounds (2021 and 2022) the study covered      13 regions with different malaria transmission intensities (high, moderate, low, and very low transmission) in Mainland Tanzania. Data and samples were collected from 100 health facilities in 10 regions (Kagera, Mara, Tabora, Dar es Salaam, Dodoma, Kilimanjaro, Manyara, Mtwara, Njombe and Songwe) that were selected based on the World Health Organization’s (WHO) recommendations for the surveillance of hrp2/3 gene deletions (1). The 10 regions in Mainland Tanzania were selected based on the malaria indicator survey of 2017 (2) and 10 HFs were selected in each region to cover facilities of all levels as recommended by the WHO. For the genomics analysis, 30 HFs were selected (three from each region) among the 100 facilities for intensive sampling to increase the sample size to adequately address aims 1 & 2 of the project (defining population structure and monitoring markers of antimalarial resistance). In addition, three villages from the three regions of Kigoma, Ruvuma and Tanga were selected based on the availability of data from previous studies for collection of data and samples from both symptomatic and asymptomatic individuals in the communities.

     

    The third round (2023) covered      all the 26 regions of Mainland Tanzania. The study regions included Kagera, Kigoma, Mtwara, Ruvuma, Katavi, Lindi and Geita, (high), Mara, Tabora, Mwanza, Shinyanga, Simiyu, Morogoro, Pwani, Rukwa, Mbeya and Tanga (moderate), Dar es Salaam, Dodoma, Singida and Songwe (low) and Kilimanjaro, Manyara, Arusha, Iringa, and Njombe (very low malaria transmission).      Data and samples were collected from 86 health facilities (HFs) in the 26 regions and delivered to the NIMR Genomics Laboratory for processing and analysis.

    Study Design

    This study includes HFs and community-based cross-sectional sampling, where samples and data were collected in the first two years (2021 and 2022) from 13 regions and in 2023 from all the 26 regions in mainland Tanzania. From June 2022, HF follow-up surveys have been initiated to obtain data from the facilities serving community members living in the three villages covered by community surveys of the MSMT project in Kigoma, Ruvuma and Tanga. In 2023, the longitudinal HF follow-up surveys were extended to cover 5 regions (Kigoma, Ruvuma, Tanga, Kagera and Njombe), cross sectional and entomological surveys were also conducted in the 5 regions

    Sample Collection

    In the reporting period, four types of samples and data were collected;  cross sectional HF collections in 26 regions, HF longitudinal surveys, cross sectional community surveys and entomological surveys in 5 regions.

    Progress of the Project

    Field collection of clinical data and samples

    Training and Engagement

    The third round of data and samples collection was successfully done in all 26 regions of mainland Tanzania as planned. The surveys were initiated in Kagera region on 23rd January and finalised in Kigoma on 09th June 2023. The surveys covered were done in 86 health facilities (HFs) in the 26 regions (3 out of the 10 facilities per region except for the Kagera region where 10HFs were involved). In regions with low transmission and few malaria cases, the number of HFs covered was either less or more than three (in Arusha, 5 HFs were covered while only one HF was covered in the Iringa region). Community cross-sectional (CSS) and longitudinal health facility follow-up surveys (HF-follow up) were done in five regions of Kagera, Kigoma, Njombe, Ruvuma and Tanga. The HF follow-up surveys were launched in three regions of Kigoma, Ruvuma and Tanga in June 2022 and two new regions of Kagera and Njombe were included from March 2023. Before the initiation of HF follow-up surveys in Kagera, a baseline demographic survey was done and communities were fully characterised to support the ongoing studies. During this round, entomological surveys were also implemented as part of integrated MMS and covered the regions of Kagera, Kigoma, Njombe, Ruvuma and Tanga which are under the community component of the study. 

    All the students recruited are progressing well with their studies at various levels. The two MSc students have finalized their training program and submitted their thesis to the University of Nairobi. Currently waiting for comments from their supervisors and are expected to defend early this year. The three PhD students, post-doctoral fellows and  other project staff are progressing well with ongoing laboratory activities, planning for next round of surveys in February/March 2024, developing manuscripts for publication and other activities

    Planned activities for a period of 6 months of no-cost extension (01st November 2023 to 30th April 2024)

    The project has been given a no-cost extension for a period of six months from 1st November 2023 to 30th April 2024. The project team is planning to finalize all pending laboratory analysis of samples, training, report writing together with accomplishing milestones that were not accomplished during period four, with special attention on finalizing procurement of equipment and reagents and equipping the laboratory with furniture, fixtures and doing minor repairs. The main activities which are planned will be implemented as shown in the revised work plan. This work plan will be continuously monitored and will be appropriately reviewed to ensure the project’s milestones are attained within the specified timelines.

    Conclusion

    The third period of the MSMT project covered 12 months, from 01st November 2022 to 31st October 2023 and most of the planned activities were successfully implemented and accomplished by over 90%. During this period, laboratory analysis of samples that were collected in 2022 and 2023 was done in-country with the support of our partners from Brown University, the UNC and CDC Foundation. The findings emanated from these surveys were disseminated through various platforms, including the feedback meetings that were held in 10 regions from January to March 2023 and other meetings with different stakeholders. Manuscripts have been prepared and submitted for preprint and publication in peer-reviewed journals. Most of the activities planned for 2023 have been adequately implemented, except for a few milestones, such as meetings of different committees and some laboratory set-up. These have been prioritized to be accomplished in the no-cost extension period of six months. Training and capacity building have been successfully implemented as planned, despite the loss of two of our post-doctoral fellows who terminated their contracts for various reasons. However, one post-doctoral fellow from Brown University replaced the post and continued with the ongoing MSMT activities. Technology transfer has continued to be implemented to make sure that the team does most of the genomic analyses in-country. We are continuing to work with our partners to finalize technology transfer to Tanzania to increase our capacity to generate the data in-country while shortening the turn-around time.