Smart surveillance towards malaria elimination in Mpumalanga: novel approaches for mapping antimalarial resistance

Lead Research Organisation: University of Oxford

Abstract

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Technical Summary

BACKGROUND: Antimalarial drug resistance is one of the biggest threats to the control & eventual elimination of malaria. Resistance is confirmed to all currently available antimalarials. Resistance to the most pivotal antimalarial group, the artemisinins, has spread from Cambodia to, or emerged in, another five neighbouring countries across South-East Asia, nearing the Indian border - from where global spread is considered inevitable. Areas of lowest malaria transmission intensity, like South Africa, are at the highest risk of antimalarial drug resistance. In these very low transmission areas, the incidence of infection is too infrequent for development of the partial malaria immunity needed to compensate for failing treatments, & drug pressure is increased as all cases are symptomatic. Thus, the areas of lowest intensity transmission most need efficient, up to date & effective targeted information system, such as our proposed “Smart Surveillance 4 Elimination”, in order to rapidly detect & respond to emerging drug resistance, before it increases malaria transmission, morbidity & mortality & derails elimination efforts.

GOAL: To develop a draft strategic plan, that can be pilot tested in Mpumalanga Province to improve malaria treatment & surveillance approaches to advance malaria elimination in South Africa & beyond.

MAIN OBJECTIVE: To develop & pilot our “Smart Surveillance 4 Elimination” approach for real-time mapping of antimalarial drug resistance using novel technologies to scale up assays for molecular markers of antimalarial resistance (assayed from positive malaria rapid diagnostic tests) & integrate these data with data from individual malaria case notifications (active & passive detection), in order to identify the foci that require more intensive investigation & additional interventions to further reduce malaria transmission, as well as inform changes to malaria treatment policy & effective targeting of single low dose primaquine treatment for malaria transmission blocking.

IMPORTANCE: New approaches, knowledge & skills sharing are urgently needed to advance malaria elimination in South Africa. The key challenges that need to be overcome include fragmented malaria information systems & health information systems, & very high levels of cross border migration from areas of high intensity malaria transmission, as well as the ever-present threat of antimalarial drug resistance. Developing & evaluating novel technology to consolidate & exp& current surveillance activities will provide the information needed to underst& & address these challenges. Leveraging existing resources to amplify their impact through data integration will be of great value not just for South Africa, but also for other countries working towards malaria elimination, particularly neighbouring countries within southern Africa & regional collaborations such as MOSASWA & the Elimination8. Such smart surveillance approaches could also be applied more broadly to geospatial mapping of antibiotic & other antimicrobial resistance.
 
Description Defining best practise for antimalarial resistance surveillance
Geographic Reach Local/Municipal/Regional 
Policy Influence Type Influenced training of practitioners or researchers
Impact Through the Smart Surveillance for Malaria Elimination (SS4ME) Pilot study in Mpumalanga, South Africa we have established best practice for enhanced surveillance for antimalarial drug resistance in an area advancing towards malaria elimination. Strengths of the SS4ME system include near real-time linked individual case data on molecular markers of resistance, geo-location (health facility, residential and source location) and patient demographics. Together these data will allow for the prompt detection of any emerging antimalarial resistance and enable effective targeting of containment strategies. Much interest has been expressed in expanding this programme in neighbouring provinces and countries. SS4ME has already been launched in northern KwaZulu-Natal Natal province in South Africa, and a protocol for SS4ME has been finalised by the Eswatini (formerly Swaziland) Malaria Programme. Further scale up is planned together with the Malaria Elimination 8 initiative and the Southern African Development Community.
 
Description Global Challenges Research Fund
Amount £50,000 (GBP)
Funding ID GCRF Oxford University C445 
Organisation University of Oxford 
Sector Academic/University
Country United Kingdom
Start 01/2019 
End 07/2019
 
Title Tools developed for surveillance for near real time surveillance for antimalarial resistance 
Description Following a three month assessment of maximising blood volume collected for DNA analysis by managing bleeding from the finger-prick site using a filter-paper strip (as opposed to a webcol swab), we concluded that a) the parasite DNA yield from the filter paper sample + RDT was far superior to the DNA yield from the RDT alone and that b) the collection of bar-coded / labelled filter-paper samples was a feasible option in rural remote health facilities. This innovative sample collection method combined with enhanced surveillance has been expanded in Mpumalanga and KwaZulu-Natal Natal, with elements rolled out nationally in South Africa and Eswatini. In addition the pooled analysis of RDT negative samples has proved to be both cost-effective and time efficient, and therefore has become our standard operating procedure for analysing RDT negative samples as part of smart surveillance. We have completed our cost-effectiveness assessment of a new malaria species differentiation qualitative PCR assay. While the assay proved to be sensitive, implementing it as routine assay is currently not possible due to the high cost of the specialised kits. The possibility of using these kits will be re-visited should the price drop substantially. The option of establishing a MassArray system to facilitate rapid generation and curation of data was also explored. Unfortunately, it is not a cost effective option at this stage due to the lack of essential infrastructure, specialised equipment and human resources at the NICD. It was hoped that funding to cover the equipment and human resources costs would be leveraged from other funders. However, these funding applications have not been successful to date. While the MassARRAY option has been put on hold, the development of a parasite genotyping screening assay using a targeted amplicon sequencing platform in collaboration with colleagues from the Universities of Pretoria and California-San Francisco is progressing well. Samples from South Africa have been analysed at the University of California-San Francisco using an amplicon panel that establishes relatedness of parasites as well as assesses the prevalence of drug resistance markers. The panel is currently undergoing optimization at the University of California-San Francisco and once optimized for low transmission setting, the amplicon sequencing platform will be trialled at the NICD. If successful, the rapid genotyping of parasites for both population genetic and resistance marker studies will be possible in a single assay. This type of genotyping tool is off great interest to the SADC region, as it is hypothesised that the fine scale differentiation of parasite origin will help accelerate the SADC region towards malaria elimination by identifying areas where control/elimination interventions should be targeted. Given the potential impact of having this technology readily available in the region, the NICD and University of California-San Francisco are involved in preliminary discussion with potential funders to establish a regional genotyping Hub at the NICD. By working with the malaria programme, we identified and co-developed some training manuals that would empower malaria case investigators to achieve better data collection including geolocating malaria cases at an accuracy of <15m radius. This was complemented by training focused on sharing basic knowledge for getting a correct location, useful field skills on ways to utilise landmarks and important identifiers for telling location, GPS device setting configurations and mobile phone applications usage. Finally plotting these coordinates in Google Maps for visualising the coordinates as an empowerment exercise, quality assurance and for evaluating the training goals. The following draft tools have been shared with provincial malaria programmes and disseminated through the WWARN tools and resources portal: WWARN SS4ME_GPS training manual for trainers__Draft08Nov2019; WWARN SS4ME_SOP GPS essentials installation and data collection guide_ver1.2_Draft08Nov2019 and WWARN SS4ME_SOP GPS location eTrex10 data collection_ver 1.2_Draft08Nov2019. Currently we are also working on opening a GitHub open-source platform to share the coding and processes for curating GPS data to solve some formatting and transcription errors identified by malaria programme data managers. 
Type Of Material Improvements to research infrastructure 
Year Produced 2018 
Provided To Others? Yes  
Impact Improved methods for collecting and recording antimalarial resistance data associated with the smart surveillance for malaria elimination project included: - DNA yield from routine malaria rapid diagnostic tests has increased to over 70% (compared with 40% reported historically) - Samples now routinely assayed for all 25 polymorphisms confirmed or suspected to be associated with artemisinin resistance / delayed parasite clearance in South-East Asia by 2018, and increased to 27 with thee 2 new polymorphisms identified (G625R and N672S) in 2019; fortunately to date none of the samples assayed were found to have any markers associated with artemisinin resistance. - Near real-time linkage of data on molecular markers of antimalarial resistance with individual malaria case notification data will enable prompt effective targeting of investigation and containment efforts should any artemisinin (or partner drug) resistance be identified. This work has been strengthened by comparisons with molecular marker data available since 2001. - Before and after implementing the above listed training & tools, coverage of malaria case investigations with household GPS coordinates has increased from 59% to 85% and their accuracy has increased from 82% to 98%. - These methods have proven to be feasible and sustainable within the normal context of routine malaria surveillance, and their generalisability is now being tested in neighbouring provinces / countries. 
 
Title Database development for the smart surveillance project 
Description Data specifications have been developed for the merging of demographic data from malaria case notifications and the resistance data from the NICD to ensure that each reported malaria case can be linked to its specific antimalarial resistance profile. The merging of the datasets was trialled on a small sample set. Based on this initial testing a structured approach to the labelling using triplicate barcoding of rapid diagnostic tests, filter papers and case notification forms was developed and implemented to ensure linking between the demographic and resistance datasets. The study team has developed a range of mapping methods to display individual malaria cases and geo-temporal trends in the collated resistance data. These are being evaluated by a range of stakeholders in a formal survey, and using in depth interviews and focus group discussion. Once this process has been refined, the generated prevalence maps will be used to support mathematical modelling of the smart surveillance maps. These models are needed to inform targeting of interventions, such as further investigation in areas of emerging antimalarial resistance or where data is lacking, and evaluating the impact and cost-effectiveness of strategies to contain / manage antimalarial resistance. 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? Yes  
Impact Some data on molecular markers of resistance generated using samples collected during the 2017/2018 malaria season has published as part of long-term drug resistance surveillance study in Mpumalanga (Raman et al Absence of kelch13 artemisinin resistance markers but strong selection for lumefantrine-tolerance molecular markers following 18 years of artemisinin-based combination therapy use in Mpumalanga Province, South Africa (2001-2018). Malaria Journal 2019;18:280) Anonymised individual patient data on antimalarial resistance markers from the study areas have been shared with the WorldWide Antimalarial Resistance Network (WWARN), and are available through their Independent Data Access Committee hosted by WHO TDR. 
URL https://www.wwarn.org/about-us/governance-people/data-access-committee
 
Description Smart Surveillance for malaria elimination in Mpumalanga: novel approaches for mapping antimalarial resistance 
Organisation Government of South Africa
Department Department of Health
Country South Africa 
Sector Public 
PI Contribution Prof Karen Barnes and the co-PI, Dr Jaishree Raman held numerous consultative meetings with national and regional stakeholders including the National Institute for Communicable Disease (NICD), the South African Medical Research Council (SAMRC), the South African Malaria Elimination Committee (SAMEC), the South African national and provincial Malaria Elimination Programmes, the Swaziland Malaria Elimination Programme, the case management technical working group of the Elimination 8 regional network and the World Health Organization African Regional Office (WHO AFRO) in order to gauge support for the proposed smart surveillance initiative. All the stakeholders strongly supported this initiative which is paving the way for the establishment of a Southern African Network for evaluating antimalarial efficacy and monitoring antimalarial drug resistance. These meetings were informed by formative in-depth interviews with national stakeholders, the South African WHO representative and a Clinton Health Action Initiative (CHAI) malaria point person as well as focus group discussions with health workers and malaria elimination programme staff from Mpumalanga, have been conducted. Based on the preliminary findings of the in-depth interviews, and at the request of the Mpumalanga malaria control program, the study data manager, Mrs Lesley Workman, facilitated a workshop on the REDCap on-line application for the Mpumalanga malaria programme data managers and analysts in January 2018. This training was based on a training workshop that the South African PI, UK PI and study data manager facilitated in Kenya in January 2018, which was attended by 40 clinical research professionals from 20 countries. As the aim of these skills sharing workshops is to develop the relevant capacity within the provincial malaria control programmes, the workshop will be offered on a needs basis. In August 2018 a summary of the project thus far was presented at the Southern African Malaria Conference, with a more detailed feedback of both strategic and operational issues discussed at a stakeholders' meeting with representatives from the South African Department of Health Malaria Elimination Programme (national), the Provincial Malaria Elimination Programmes of Mpumalanga, Kwa Zulu Natal and Limpopo, the Swaziland Malaria Programme, and the Clinton Health Action Initiative (CHAI). It was felt important to keep neighbouring areas updated to ensure the success of subsequent roll out. All parties were enthusiastic about the progress thus far and brain-stormed ways to overcome any ongoing challenges. The rollout of Smart Surveillance for Malaria Elimination in the areas of northern KwaZulu Natal that carry the highest malaria burden was launched in February 2019. The malaria programme in Eswatini (formerly Swaziland) has worked with the research team to finalise a protocol to launch Smart Surveillance for Malaria Elimination in the current Malaria Season. The research team secured additional GCRF funding to support the launch if a regional network to enhance surveillance on antimalarial efficacy, which will serve as a platform for reviewing and refining Smart Surveillance for Malaria Elimination across the SADC region in future. Addressing the threat of antimalarial resistance was highlighted as a priority in the Elimination 8 Strategy: Acceleration Plan 2018 - 2020. The Elimination 8 initiative has allocated half of the agenda of the annual meeting of Malaria Control / Elimination Programme Directors and their Case Management Working Group to focus on enhancing regional surveillance of antimalarial efficacy.
Collaborator Contribution In addition, a supportive and active UK - South Africa collaboration with expertise in geo-spatial mapping and mathematical modelling to identify resistance to standard of care treatment for malaria in South Africa, has been developed with Oxford University and its Mahidol Oxford Tropical Medicine Research Unit (MORU). Interactions have included a face to face meeting and weekly teleconferences.
Impact To guide and strengthen specific antimalarial resistance mapping and modelling skills in South Africa, a technical working group comprising researchers from UCT, SAMRC and members of National and Provincial Malaria Elimination Programmes has been established. This collaboration is multidisciplinary and involves disease experts, data managers, malaria control program officers, and spatial epidemiologists. These partners have developed their capacity for improved surveillance of malaria cases, more accurate GPS coordinates of the household location for each case and assessing the prevalence of molecular markers of antimalarial resistance in near real-time.
Start Year 2017
 
Description Smart Surveillance for malaria elimination in Mpumalanga: novel approaches for mapping antimalarial resistance 
Organisation Government of South Africa
Department Department of Health
Country South Africa 
Sector Public 
PI Contribution Prof Karen Barnes and the co-PI, Dr Jaishree Raman held numerous consultative meetings with national and regional stakeholders including the National Institute for Communicable Disease (NICD), the South African Medical Research Council (SAMRC), the South African Malaria Elimination Committee (SAMEC), the South African national and provincial Malaria Elimination Programmes, the Swaziland Malaria Elimination Programme, the case management technical working group of the Elimination 8 regional network and the World Health Organization African Regional Office (WHO AFRO) in order to gauge support for the proposed smart surveillance initiative. All the stakeholders strongly supported this initiative which is paving the way for the establishment of a Southern African Network for evaluating antimalarial efficacy and monitoring antimalarial drug resistance. These meetings were informed by formative in-depth interviews with national stakeholders, the South African WHO representative and a Clinton Health Action Initiative (CHAI) malaria point person as well as focus group discussions with health workers and malaria elimination programme staff from Mpumalanga, have been conducted. Based on the preliminary findings of the in-depth interviews, and at the request of the Mpumalanga malaria control program, the study data manager, Mrs Lesley Workman, facilitated a workshop on the REDCap on-line application for the Mpumalanga malaria programme data managers and analysts in January 2018. This training was based on a training workshop that the South African PI, UK PI and study data manager facilitated in Kenya in January 2018, which was attended by 40 clinical research professionals from 20 countries. As the aim of these skills sharing workshops is to develop the relevant capacity within the provincial malaria control programmes, the workshop will be offered on a needs basis. In August 2018 a summary of the project thus far was presented at the Southern African Malaria Conference, with a more detailed feedback of both strategic and operational issues discussed at a stakeholders' meeting with representatives from the South African Department of Health Malaria Elimination Programme (national), the Provincial Malaria Elimination Programmes of Mpumalanga, Kwa Zulu Natal and Limpopo, the Swaziland Malaria Programme, and the Clinton Health Action Initiative (CHAI). It was felt important to keep neighbouring areas updated to ensure the success of subsequent roll out. All parties were enthusiastic about the progress thus far and brain-stormed ways to overcome any ongoing challenges. The rollout of Smart Surveillance for Malaria Elimination in the areas of northern KwaZulu Natal that carry the highest malaria burden was launched in February 2019. The malaria programme in Eswatini (formerly Swaziland) has worked with the research team to finalise a protocol to launch Smart Surveillance for Malaria Elimination in the current Malaria Season. The research team secured additional GCRF funding to support the launch if a regional network to enhance surveillance on antimalarial efficacy, which will serve as a platform for reviewing and refining Smart Surveillance for Malaria Elimination across the SADC region in future. Addressing the threat of antimalarial resistance was highlighted as a priority in the Elimination 8 Strategy: Acceleration Plan 2018 - 2020. The Elimination 8 initiative has allocated half of the agenda of the annual meeting of Malaria Control / Elimination Programme Directors and their Case Management Working Group to focus on enhancing regional surveillance of antimalarial efficacy.
Collaborator Contribution In addition, a supportive and active UK - South Africa collaboration with expertise in geo-spatial mapping and mathematical modelling to identify resistance to standard of care treatment for malaria in South Africa, has been developed with Oxford University and its Mahidol Oxford Tropical Medicine Research Unit (MORU). Interactions have included a face to face meeting and weekly teleconferences.
Impact To guide and strengthen specific antimalarial resistance mapping and modelling skills in South Africa, a technical working group comprising researchers from UCT, SAMRC and members of National and Provincial Malaria Elimination Programmes has been established. This collaboration is multidisciplinary and involves disease experts, data managers, malaria control program officers, and spatial epidemiologists. These partners have developed their capacity for improved surveillance of malaria cases, more accurate GPS coordinates of the household location for each case and assessing the prevalence of molecular markers of antimalarial resistance in near real-time.
Start Year 2017
 
Description Smart Surveillance for malaria elimination in Mpumalanga: novel approaches for mapping antimalarial resistance 
Organisation Medical Research Council of South Africa (MRC)
Country South Africa 
Sector Public 
PI Contribution Prof Karen Barnes and the co-PI, Dr Jaishree Raman held numerous consultative meetings with national and regional stakeholders including the National Institute for Communicable Disease (NICD), the South African Medical Research Council (SAMRC), the South African Malaria Elimination Committee (SAMEC), the South African national and provincial Malaria Elimination Programmes, the Swaziland Malaria Elimination Programme, the case management technical working group of the Elimination 8 regional network and the World Health Organization African Regional Office (WHO AFRO) in order to gauge support for the proposed smart surveillance initiative. All the stakeholders strongly supported this initiative which is paving the way for the establishment of a Southern African Network for evaluating antimalarial efficacy and monitoring antimalarial drug resistance. These meetings were informed by formative in-depth interviews with national stakeholders, the South African WHO representative and a Clinton Health Action Initiative (CHAI) malaria point person as well as focus group discussions with health workers and malaria elimination programme staff from Mpumalanga, have been conducted. Based on the preliminary findings of the in-depth interviews, and at the request of the Mpumalanga malaria control program, the study data manager, Mrs Lesley Workman, facilitated a workshop on the REDCap on-line application for the Mpumalanga malaria programme data managers and analysts in January 2018. This training was based on a training workshop that the South African PI, UK PI and study data manager facilitated in Kenya in January 2018, which was attended by 40 clinical research professionals from 20 countries. As the aim of these skills sharing workshops is to develop the relevant capacity within the provincial malaria control programmes, the workshop will be offered on a needs basis. In August 2018 a summary of the project thus far was presented at the Southern African Malaria Conference, with a more detailed feedback of both strategic and operational issues discussed at a stakeholders' meeting with representatives from the South African Department of Health Malaria Elimination Programme (national), the Provincial Malaria Elimination Programmes of Mpumalanga, Kwa Zulu Natal and Limpopo, the Swaziland Malaria Programme, and the Clinton Health Action Initiative (CHAI). It was felt important to keep neighbouring areas updated to ensure the success of subsequent roll out. All parties were enthusiastic about the progress thus far and brain-stormed ways to overcome any ongoing challenges. The rollout of Smart Surveillance for Malaria Elimination in the areas of northern KwaZulu Natal that carry the highest malaria burden was launched in February 2019. The malaria programme in Eswatini (formerly Swaziland) has worked with the research team to finalise a protocol to launch Smart Surveillance for Malaria Elimination in the current Malaria Season. The research team secured additional GCRF funding to support the launch if a regional network to enhance surveillance on antimalarial efficacy, which will serve as a platform for reviewing and refining Smart Surveillance for Malaria Elimination across the SADC region in future. Addressing the threat of antimalarial resistance was highlighted as a priority in the Elimination 8 Strategy: Acceleration Plan 2018 - 2020. The Elimination 8 initiative has allocated half of the agenda of the annual meeting of Malaria Control / Elimination Programme Directors and their Case Management Working Group to focus on enhancing regional surveillance of antimalarial efficacy.
Collaborator Contribution In addition, a supportive and active UK - South Africa collaboration with expertise in geo-spatial mapping and mathematical modelling to identify resistance to standard of care treatment for malaria in South Africa, has been developed with Oxford University and its Mahidol Oxford Tropical Medicine Research Unit (MORU). Interactions have included a face to face meeting and weekly teleconferences.
Impact To guide and strengthen specific antimalarial resistance mapping and modelling skills in South Africa, a technical working group comprising researchers from UCT, SAMRC and members of National and Provincial Malaria Elimination Programmes has been established. This collaboration is multidisciplinary and involves disease experts, data managers, malaria control program officers, and spatial epidemiologists. These partners have developed their capacity for improved surveillance of malaria cases, more accurate GPS coordinates of the household location for each case and assessing the prevalence of molecular markers of antimalarial resistance in near real-time.
Start Year 2017
 
Description Smart Surveillance for malaria elimination in Mpumalanga: novel approaches for mapping antimalarial resistance 
Organisation National Institute for Communicable Diseases
Country South Africa 
Sector Charity/Non Profit 
PI Contribution Prof Karen Barnes and the co-PI, Dr Jaishree Raman held numerous consultative meetings with national and regional stakeholders including the National Institute for Communicable Disease (NICD), the South African Medical Research Council (SAMRC), the South African Malaria Elimination Committee (SAMEC), the South African national and provincial Malaria Elimination Programmes, the Swaziland Malaria Elimination Programme, the case management technical working group of the Elimination 8 regional network and the World Health Organization African Regional Office (WHO AFRO) in order to gauge support for the proposed smart surveillance initiative. All the stakeholders strongly supported this initiative which is paving the way for the establishment of a Southern African Network for evaluating antimalarial efficacy and monitoring antimalarial drug resistance. These meetings were informed by formative in-depth interviews with national stakeholders, the South African WHO representative and a Clinton Health Action Initiative (CHAI) malaria point person as well as focus group discussions with health workers and malaria elimination programme staff from Mpumalanga, have been conducted. Based on the preliminary findings of the in-depth interviews, and at the request of the Mpumalanga malaria control program, the study data manager, Mrs Lesley Workman, facilitated a workshop on the REDCap on-line application for the Mpumalanga malaria programme data managers and analysts in January 2018. This training was based on a training workshop that the South African PI, UK PI and study data manager facilitated in Kenya in January 2018, which was attended by 40 clinical research professionals from 20 countries. As the aim of these skills sharing workshops is to develop the relevant capacity within the provincial malaria control programmes, the workshop will be offered on a needs basis. In August 2018 a summary of the project thus far was presented at the Southern African Malaria Conference, with a more detailed feedback of both strategic and operational issues discussed at a stakeholders' meeting with representatives from the South African Department of Health Malaria Elimination Programme (national), the Provincial Malaria Elimination Programmes of Mpumalanga, Kwa Zulu Natal and Limpopo, the Swaziland Malaria Programme, and the Clinton Health Action Initiative (CHAI). It was felt important to keep neighbouring areas updated to ensure the success of subsequent roll out. All parties were enthusiastic about the progress thus far and brain-stormed ways to overcome any ongoing challenges. The rollout of Smart Surveillance for Malaria Elimination in the areas of northern KwaZulu Natal that carry the highest malaria burden was launched in February 2019. The malaria programme in Eswatini (formerly Swaziland) has worked with the research team to finalise a protocol to launch Smart Surveillance for Malaria Elimination in the current Malaria Season. The research team secured additional GCRF funding to support the launch if a regional network to enhance surveillance on antimalarial efficacy, which will serve as a platform for reviewing and refining Smart Surveillance for Malaria Elimination across the SADC region in future. Addressing the threat of antimalarial resistance was highlighted as a priority in the Elimination 8 Strategy: Acceleration Plan 2018 - 2020. The Elimination 8 initiative has allocated half of the agenda of the annual meeting of Malaria Control / Elimination Programme Directors and their Case Management Working Group to focus on enhancing regional surveillance of antimalarial efficacy.
Collaborator Contribution In addition, a supportive and active UK - South Africa collaboration with expertise in geo-spatial mapping and mathematical modelling to identify resistance to standard of care treatment for malaria in South Africa, has been developed with Oxford University and its Mahidol Oxford Tropical Medicine Research Unit (MORU). Interactions have included a face to face meeting and weekly teleconferences.
Impact To guide and strengthen specific antimalarial resistance mapping and modelling skills in South Africa, a technical working group comprising researchers from UCT, SAMRC and members of National and Provincial Malaria Elimination Programmes has been established. This collaboration is multidisciplinary and involves disease experts, data managers, malaria control program officers, and spatial epidemiologists. These partners have developed their capacity for improved surveillance of malaria cases, more accurate GPS coordinates of the household location for each case and assessing the prevalence of molecular markers of antimalarial resistance in near real-time.
Start Year 2017
 
Description Smart Surveillance for malaria elimination in Mpumalanga: novel approaches for mapping antimalarial resistance 
Organisation Wellcome Trust
Department Mahidol University-Oxford Tropical Medicine Research Programme
Country United Kingdom 
Sector Academic/University 
PI Contribution Prof Karen Barnes and the co-PI, Dr Jaishree Raman held numerous consultative meetings with national and regional stakeholders including the National Institute for Communicable Disease (NICD), the South African Medical Research Council (SAMRC), the South African Malaria Elimination Committee (SAMEC), the South African national and provincial Malaria Elimination Programmes, the Swaziland Malaria Elimination Programme, the case management technical working group of the Elimination 8 regional network and the World Health Organization African Regional Office (WHO AFRO) in order to gauge support for the proposed smart surveillance initiative. All the stakeholders strongly supported this initiative which is paving the way for the establishment of a Southern African Network for evaluating antimalarial efficacy and monitoring antimalarial drug resistance. These meetings were informed by formative in-depth interviews with national stakeholders, the South African WHO representative and a Clinton Health Action Initiative (CHAI) malaria point person as well as focus group discussions with health workers and malaria elimination programme staff from Mpumalanga, have been conducted. Based on the preliminary findings of the in-depth interviews, and at the request of the Mpumalanga malaria control program, the study data manager, Mrs Lesley Workman, facilitated a workshop on the REDCap on-line application for the Mpumalanga malaria programme data managers and analysts in January 2018. This training was based on a training workshop that the South African PI, UK PI and study data manager facilitated in Kenya in January 2018, which was attended by 40 clinical research professionals from 20 countries. As the aim of these skills sharing workshops is to develop the relevant capacity within the provincial malaria control programmes, the workshop will be offered on a needs basis. In August 2018 a summary of the project thus far was presented at the Southern African Malaria Conference, with a more detailed feedback of both strategic and operational issues discussed at a stakeholders' meeting with representatives from the South African Department of Health Malaria Elimination Programme (national), the Provincial Malaria Elimination Programmes of Mpumalanga, Kwa Zulu Natal and Limpopo, the Swaziland Malaria Programme, and the Clinton Health Action Initiative (CHAI). It was felt important to keep neighbouring areas updated to ensure the success of subsequent roll out. All parties were enthusiastic about the progress thus far and brain-stormed ways to overcome any ongoing challenges. The rollout of Smart Surveillance for Malaria Elimination in the areas of northern KwaZulu Natal that carry the highest malaria burden was launched in February 2019. The malaria programme in Eswatini (formerly Swaziland) has worked with the research team to finalise a protocol to launch Smart Surveillance for Malaria Elimination in the current Malaria Season. The research team secured additional GCRF funding to support the launch if a regional network to enhance surveillance on antimalarial efficacy, which will serve as a platform for reviewing and refining Smart Surveillance for Malaria Elimination across the SADC region in future. Addressing the threat of antimalarial resistance was highlighted as a priority in the Elimination 8 Strategy: Acceleration Plan 2018 - 2020. The Elimination 8 initiative has allocated half of the agenda of the annual meeting of Malaria Control / Elimination Programme Directors and their Case Management Working Group to focus on enhancing regional surveillance of antimalarial efficacy.
Collaborator Contribution In addition, a supportive and active UK - South Africa collaboration with expertise in geo-spatial mapping and mathematical modelling to identify resistance to standard of care treatment for malaria in South Africa, has been developed with Oxford University and its Mahidol Oxford Tropical Medicine Research Unit (MORU). Interactions have included a face to face meeting and weekly teleconferences.
Impact To guide and strengthen specific antimalarial resistance mapping and modelling skills in South Africa, a technical working group comprising researchers from UCT, SAMRC and members of National and Provincial Malaria Elimination Programmes has been established. This collaboration is multidisciplinary and involves disease experts, data managers, malaria control program officers, and spatial epidemiologists. These partners have developed their capacity for improved surveillance of malaria cases, more accurate GPS coordinates of the household location for each case and assessing the prevalence of molecular markers of antimalarial resistance in near real-time.
Start Year 2017
 
Description Smart Surveillance for malaria elimination in Mpumalanga: novel approaches for mapping antimalarial resistance 
Organisation Worldwide Antimalarial Resistance Network
Country Global 
Sector Charity/Non Profit 
PI Contribution Prof Karen Barnes and the co-PI, Dr Jaishree Raman held numerous consultative meetings with national and regional stakeholders including the National Institute for Communicable Disease (NICD), the South African Medical Research Council (SAMRC), the South African Malaria Elimination Committee (SAMEC), the South African national and provincial Malaria Elimination Programmes, the Swaziland Malaria Elimination Programme, the case management technical working group of the Elimination 8 regional network and the World Health Organization African Regional Office (WHO AFRO) in order to gauge support for the proposed smart surveillance initiative. All the stakeholders strongly supported this initiative which is paving the way for the establishment of a Southern African Network for evaluating antimalarial efficacy and monitoring antimalarial drug resistance. These meetings were informed by formative in-depth interviews with national stakeholders, the South African WHO representative and a Clinton Health Action Initiative (CHAI) malaria point person as well as focus group discussions with health workers and malaria elimination programme staff from Mpumalanga, have been conducted. Based on the preliminary findings of the in-depth interviews, and at the request of the Mpumalanga malaria control program, the study data manager, Mrs Lesley Workman, facilitated a workshop on the REDCap on-line application for the Mpumalanga malaria programme data managers and analysts in January 2018. This training was based on a training workshop that the South African PI, UK PI and study data manager facilitated in Kenya in January 2018, which was attended by 40 clinical research professionals from 20 countries. As the aim of these skills sharing workshops is to develop the relevant capacity within the provincial malaria control programmes, the workshop will be offered on a needs basis. In August 2018 a summary of the project thus far was presented at the Southern African Malaria Conference, with a more detailed feedback of both strategic and operational issues discussed at a stakeholders' meeting with representatives from the South African Department of Health Malaria Elimination Programme (national), the Provincial Malaria Elimination Programmes of Mpumalanga, Kwa Zulu Natal and Limpopo, the Swaziland Malaria Programme, and the Clinton Health Action Initiative (CHAI). It was felt important to keep neighbouring areas updated to ensure the success of subsequent roll out. All parties were enthusiastic about the progress thus far and brain-stormed ways to overcome any ongoing challenges. The rollout of Smart Surveillance for Malaria Elimination in the areas of northern KwaZulu Natal that carry the highest malaria burden was launched in February 2019. The malaria programme in Eswatini (formerly Swaziland) has worked with the research team to finalise a protocol to launch Smart Surveillance for Malaria Elimination in the current Malaria Season. The research team secured additional GCRF funding to support the launch if a regional network to enhance surveillance on antimalarial efficacy, which will serve as a platform for reviewing and refining Smart Surveillance for Malaria Elimination across the SADC region in future. Addressing the threat of antimalarial resistance was highlighted as a priority in the Elimination 8 Strategy: Acceleration Plan 2018 - 2020. The Elimination 8 initiative has allocated half of the agenda of the annual meeting of Malaria Control / Elimination Programme Directors and their Case Management Working Group to focus on enhancing regional surveillance of antimalarial efficacy.
Collaborator Contribution In addition, a supportive and active UK - South Africa collaboration with expertise in geo-spatial mapping and mathematical modelling to identify resistance to standard of care treatment for malaria in South Africa, has been developed with Oxford University and its Mahidol Oxford Tropical Medicine Research Unit (MORU). Interactions have included a face to face meeting and weekly teleconferences.
Impact To guide and strengthen specific antimalarial resistance mapping and modelling skills in South Africa, a technical working group comprising researchers from UCT, SAMRC and members of National and Provincial Malaria Elimination Programmes has been established. This collaboration is multidisciplinary and involves disease experts, data managers, malaria control program officers, and spatial epidemiologists. These partners have developed their capacity for improved surveillance of malaria cases, more accurate GPS coordinates of the household location for each case and assessing the prevalence of molecular markers of antimalarial resistance in near real-time.
Start Year 2017
 
Title Innovative method for enhancing sufficient blood got DNA extraction from an RDT 
Description An innovative way to maximise the amount of blood collected for DNA extraction is being tested in this project. Once the RDT has been administered, bleeding from the finger prick site will be managed using a filter paper strip (as opposed to a webcol swab), which will be labelled and sent with the positive RDT to the NICD as a possible additional source of parasite DNA. A pooled PCR method is being tested to fast track the assessment of RDT negative samples. In addition, a parasite genotype barcoding screening process is being developed. It is hoped that this barcoding method would be sensitive enough to detect molecular markers of antimalarial drug resistance as well as parasite clone type, thereby enabling the fine scale differentiation of parasites from different regions in Southern Africa. 
Type Support Tool - For Fundamental Research
Current Stage Of Development Initial development
Year Development Stage Completed 2018
Development Status Under active development/distribution
Impact The impact of this intervention has increased the DNA yield from routine malaria rapid diagnostic tests from 40% historically to over 70%. It has been shown to be feasible within routine malaria surveillance. 
 
Description Establishing a Southern and Central African Network for Monitoring Antimalarial Therapeutic Efficacy (SCAN-MATE) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Policymakers/politicians
Results and Impact Effective antimalarials are key for the control and elimination of malaria. Resistance to all currently available antimalarials has been confirmed in at least seven countries in South-East Asia. Southern and Central Africa and South-East Asia share the malaria epidemiology suitable for antimalarial resistance emerging and spreading. A Southern and Central African Network for Monitoring Antimalarial Therapeutic Efficacy (SCAN-MATE) is being established to address the significant political, technical and resource gaps in the monitoring of antimalarial efficacy and mitigate the public health risks of multi-drug resistance. This workshop brought together representatives of the malaria control and elimination programmes in ten southern and Central African countries, together with their partner organisations, the Elimination 8 and WHO-AFRO to agree on the Terms of Reference for the SCAN-MATE network, that will be tabled for ratification at then next WHO-AFRO meeting of Ministers of Health.
Year(s) Of Engagement Activity 2019
 
Description Formative research including in-depth interviews and focus group discussions, followed by a series of on site training and supervision visits. 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Policymakers/politicians
Results and Impact In-depth interviews and focus group discussions with key stakeholders in the national department of health (including the Director Malaria and Other Vector-Borne Diseases at National Department of Health), members of the provincial department of health (including the CDC Director and Deputy-director of Surveillance), malaria control program staff (including Malaria Elimination Programme director, malaria case-investigators and medical staff responsible testing, treating and notifying new cases of malaria), took place in 2017 and are currently being repeated in 2020 together with an end line survey with clinic staff. Further face-to-face meetings with the malaria control program data managers and analysts have been completed to establish a safe and secure system for data transfer.

Frequent site visits over the past 18 months to provide technical support, training and empowering the provincial malaria elimination programme. These included training on rapid diagnostic test administration and interpretation as well as three trainings conducted by a geospatial mapping expert for relevant malaria control / elimination programme partners (provincial programme director, information officers, case investigators. These activities identified a number of system failures in recording accurate GPS coordinates, including technical problems (incorrect settings, incorrect units), transcription errors and data capture errors that resulted in geo-locations being out by up to 20 - 70 km. These were identified as a major risk for incorrect targeting of malaria interventions, and the national and provincial malaria programmes are working with the research team to address these system failures and share lessons learnt with malaria programmes in neighbouring provinces / countries.

A collaboration between the NICD, University of Pretoria, South Africa and the University of California-San Francisco, USA has been established to refined methods for fine-scale parasite genotyping to assist with more accurate intervention selection and targeting.
Year(s) Of Engagement Activity 2017,2018,2019,2020