Request for Proposals. Strengthening vector surveillance systems and addressing Anopheles mosquito genomic data gaps in Africa

Transcription

1 Request for Proposals Strengthening vector surveillance systems and addressing Anopheles mosquito genomic data gaps in Africa August 2018

2 Introduction to RFP Malaria elimination in Africa requires intelligent use of existing insecticide-based vector control tools, such as LLINs, to mitigate the spread of insecticide resistance, and complementary new tools that can be used alongside existing ones to rapidly reduce malaria vector populations and diminish malaria transmission. New LLIN products and IRS formulations are becoming available, providing new options for insecticide resistance management (IRM). However, new kinds of data are needed in order to tailor IRM to local vector populations, and to gain feedback on the impact and efficacy of different IRM strategies. Genetic approaches to vector control, such as the use of gene-drive mosquitoes for population suppression or replacement offer potential high-impact interventions to achieve malaria elimination. However, successful implementation of such interventions will require improved understanding of the genetic diversity of the common malaria vectors, and gene-flow dynamics across regions. Recent efforts such as the Anopheles gambiae 1000 genome consortium have made key contributions to our understanding of the genetic diversity of this important vector and the evolution of resistance to insecticide-based vector control methods. However, much remains to be elucidated including essential information regarding the genetic diversity, evolution and gene-flow trends among An. coluzzii, An. arabiensis and An. funestus which dominate malaria transmission in Africa as well as several other anopheline vectors which contribute to local transmission across Africa. Though technological advancements already allow for such analysis to be done, there remain limitations on local institutional and human capacity, data supply and access to wild-caught field samples from across Africa. This new partnership will accelerate formation of new networks across Africa to address this gap, by leveraging existing synergies and diversities in expertise across geographies. The Pan African Mosquito Control Association (PAMCA) announces a new partnership with the Bill & Melinda Gates Foundation (BMGF) to support African-led research regarding the genomic epidemiology of African malaria vectors. PAMCA is conducting a Request for Proposals in partnership with the Bill & Melinda Gates Foundation. While PAMCA will be intricately involved in the selection process, each institution that is selected will be considered for funding directly from the Bill & Melinda Gates foundation. In order for the foundation to be able to provide funding, institutions must first be evaluated through an equivalency affidavit process which confirms that charitable intent can be verified.

3 Under United States law, the Foundation must ensure that its funds are used for charitable purposes. The purpose of the affidavit of equivalency is to determine whether institutions qualify as a public charity. African institutions selected by PAMCA will be provided with a Foreign Public Charity Equivalency Affidavit document to complete and submit to the Foundation. It will provide the Gates Foundation with the necessary information so the foundation can determine whether the institution s governing documents and operations are consistent with public charity requirements. Proposals that will be selected for funding will be asked to provide the following information: Your institution s full legal name, as it appears in your governing documents and any official registry. The date you were formed, which is generally found on your governing documents or official registry. If applicable, a copy of the statute pursuant to which you were created or formed. For example, if you were created by the government pursuant to a legislative act, please provide a copy of that legislation. You should also indicate whether you are exempt from taxation under local law, are registered with a charity commission or have other special status. The country or other jurisdiction in which you were formed (e.g. Federal Republic of Nigeria). The date of your fiscal year end. Note that further detailed questions will be provided by the foundation to those institutions selected through PAMCA s Request for Proposals. No institution may receive foundation funds without first being evaluated through the equivalency affidavit process. Aim of RFP This initiative will support local capacities in selected African institutions for collection, curation, analysis and interpretation of essential genomic data on diversity, evolution and gene flow in Anopheles mosquitoes in Africa. The specific objectives of this grant are to: Create, strengthen and improve the entomological surveillance systems of National Malaria Control Programmes

4 Build skills/infrastructure/resources needed in entomological operational research in Africa Consolidate a network of outstanding African entomologists who will provide mentorship for the next generation of leaders in Vector Biology Strengthen Anopheles mosquito genomic research with practical applications for malaria endemic countries in Africa Generate an open-access resource of genomic data from contemporary mosquito populations across major malaria vector species from a variety of geographical locations and ecological and epidemiological contexts These objectives are in line with the overall goal of PAMCA to build entomology capacity in Africa, to promote the study, prevention and control of mosquito-borne diseases and to develop and implement new materials, techniques and tools for mosquito control. The objectives are also in line with the overall goal of WSI and MalariaGEN to build a comprehensive genomic data resource that can accelerate vector research and form the basis of new public health systems for vector population surveillance. Under this scheme, PAMCA would like to request proposals describing new projects to investigate the genetic diversity, evolution and gene flow of malaria vector populations, and how these relate to mosquito ecology and malaria epidemiology, to be led by African institutions. Multidisciplinary and multi-institution projects with a wide coverage of geographic area will be prioritized. This call focuses on low-income African countries, therefore successful projects should also take into account data gap filling on Anopheles mosquitoes in the continent, strengthening of National Malaria Control programmes on disease surveillance and genomics of the vectors. Preliminary data is not required, but proposals should clearly demonstrate how the idea is an innovative leap in progress from current practices with the potential to be transformative at scale. Also essential is for investigators to demonstrate maximum potential for filling the existing gaps with minimal sampling effort. Projects will be undertaken in partnership with Wellcome Sanger Institute (WSI) and the MalariaGEN Vector Observatory, which will provide capacity to perform deep Illumina wholegenome sequencing on at least 500 mosquito specimens from each project, via core sequencing facilities at WSI. Some additional capacity for amplicon sequencing of targeted genomic regions will also be provided, at a scale to be determined. The MalariaGEN Vector Observatory core team will also perform all initial data processing, including sequence read

5 alignment, variant calling, haplotype phasing, data quality filtering and annotation, and will provide analysis-ready genome variation data to project partners. MalariaGEN will also provide a cloud-based computing environment which partners can use to remotely analyse data, thus projects will not require any special computing facilities or hardware. The grant is administered by PAMCA with funds generously provided by the Bill & Melinda Gates Foundation. Project Scope To be considered, proposals must closely align with the goals of PAMCA and MalariaGEN. As such, we are looking for proposals that: Build on to malaria vector surveillance Offer potential for linkages to National Control Programmes either by creating, strengthening and or improving vector borne disease surveillance Be amenable to building and strengthening a base for PAMCA in Country chapters Have potential of building capacity in human resource and infrastructure Convey a clear potential for achieving broad geographic scale Focus on gap filling especially in countries with missing genomic data for malaria vectors We will not consider funding for: Ideas that are not directly relevant to malaria vectors in African countries; Proposals that focus solely on one-directional extension services to demonstrate or advertise existing technologies without data collection; Proposals that focus solely on modeling of existing data The application process PAMCA invites organisations to apply for grants through a three stage open competitive process. Stage 1 Concept note submission using the online application form Stage 2 Shortlisted applicants who have successfully passed first round selection will be invited to attend a 3-day grant writing bootcamp (location TBD) to further develop their concept note into a full proposal. The boot camp will be facilitated by PAMCA and partners including WSI and Ifakara Health Institute, Tanzania Stage 3 Applicants submit a full proposal and supporting information to PAMCA for review

6 Eligibility Low- and middle-income countries are eligible for this call for proposals. The principal investigator must be from a public health institution in Africa and private institutions are not eligible to apply as principal investigators. Only applicants from African institutions will be considered for the grant award. Funding should not be used to pay for additional staff within the program, policy or system. Funding may be used to cover the costs of researchers time, data collection and analysis and other related research activities. Applicants must submit an official letter of support from the public institution sponsoring their project. Budget We anticipate awarding grants of up to $ (United States Dollars) per project/institution for a period of 12 months. A no-cost extension of up to six months might be considered. Applicants should ensure their budgets are commensurate to the planned activities. Evaluation Criteria Concept notes should be submitted HERE Submissions received by the deadline will be evaluated using the following criteria: Evidence of a strong technical understanding of the proposed subject matter; Clear illustration of methods, including appropriate sampling plans to achieve the overall goal of this program. In-country experience in conducting entomological survey design and implementation, preferably in Africa. Solid analytical skills and ability to synthesize information from multiple sources, and advanced knowledge of analytical methods and tools for entomological surveillance Evidence of sustainability of the project outputs and willingness to use the results in improving the policies, programs or systems Support and readiness of the institution(s) to ensure successful implementation of the project; Demonstrated partnership with local malaria control program and other in-country institutions.

7 Clear approach for capacity building of in-country institutions, including Ministry of Health and sustainability of technical support provided. Commitment to data sharing and to full analyses of the data to achieve overall goals of the program The decision to award any contract as a result of this RFP process will be based on the applicant s responses to this RFP, demonstrated capacity to deliver, quality of recommended expert resources and any subsequent negotiations or discussions. Conflict of interest Any conflict of interest, or potential conflict of interest, should be declared to PAMCA when prospective grantees are applying. If a conflict of interest, or potential conflict of interest, arises after that point, the prospective grantee must clearly declare this in their application. Partnership for strengthening vector surveillance systems and addressing Anopheles mosquito genomic data gaps in Africa PAMCA The Pan-African Mosquito Control Association (PAMCA) is a professional body that brings together players in the field of mosquito and mosquito-borne disease control. PAMCA s mission is to provide a platform for capacity building, knowledge sharing, strengthening partnerships and collaboration, and to advocate for coordinated governance structures for concerted vector control initiatives in Africa. PAMCA s overarching goal is to bring together African-based scientists and other partner institutions, to work together and adopt common approaches to tackling the burden of mosquito-borne diseases across the continent. For more information please visit BMGF Bill & Melinda Gates Foundation will deliver to the programme general and specific support that will accelerate the strengthening of the vector surveillance systems and Anopheles mosquito genomic research across the continent. The Foundation will mobilize support for this programme and bring to the table partners who can synergistically work to achieve the programme objectives. IHI Ifakara Health Institute (IHI) is a registered Tanzanian Trust, and one of the leading health research organizations in Africa. The mission of IHI is to contribute to improvements in people s health and wellbeing by generating new knowledge and information for public health policy and action. IHI has a strong track record in developing, testing and validating

8 innovations for health within our core strategic mandate for research, training and services. Their work now spans a wide spectrum, covering biomedical and ecological sciences, intervention studies, health-systems research and policy translation. IHI will contribute in building the technical capacity of the applicants and subsequently to the awardees through jointly workshops and site visits organized by PAMCA. WSI and MalariaGEN The Wellcome Sanger Institute (WSI) is a world-leading centre for genome research and its applications to human, pathogen and vector biology, located in the UK. The WSI initiated a programme of population-scale malaria vector genome sequencing in 2013, to accelerate the development of new approaches to vector control, and to develop new technologies for genomic surveillance of vector populations. This work has been undertaken in collaboration with an international community of researchers and public health professionals, mediated by the Malaria Genomic Epidemiology Network (MalariaGEN; Between 2013 and 2018 this work focused on the Anopheles gambiae species complex, and has been carried out within the framework of the MalariaGEN Anopheles gambiae 1000 Genomes Project (Ag1000G; From 2018 onwards, the scope of this work is expanding to increase the scale of mosquito genome sequencing to allow for temporal surveillance over a greater number of mosquito populations, and to include other malaria vector species in Africa and elsewhere, and is being carried out within the framework of a new initiative called the MalariaGEN Vector Observatory.

9 Project activities & timelines Activity Responsible Party Timelines Launch RFP PAMCA 31 August 2018 Q&A submitted Potential Applicants 31 August-26 September 2018 Project briefing session at PAMCA Conference PAMCA 26 September 2018 Concept note submitted Applicants 3 October 2018 Review Concept notes PAMCA, WSI & external 15 October 2018 experts First round selection PAMCA & WSI 30 October 2018 Bootcamp proposal writing BMGF, PAMCA, IHI, WSI November 2018 workshop for shortlisted applicants &Potential Shortlisted Applicants Full proposals submitted Shortlisted Applicants 30 November 2018 Review full Proposals PAMCA, External Experts, & 1-15 December 2018 WSI Second round selection PAMCA & WSI 30 December 2018 Notification of awards PAMCA 4 January 2019 Sign Agreements BMGF, PAMCA & Grantees 15 February 2019 Project implementation initiation How to Apply Grantees 1 March 2019 Interested candidates must apply HERE. Only applications submitted through this portal will be considered. Applications and submission enquiries should be sent directly to PAMCA at communications@pamca.org. RFP published: 31 st August 2018 Applications deadline: 12pm GMT, 3 rd October 2018 Anticipated award and project start date: 01 March 2019

10 Technical Notes As mentioned above, each project will be able to submit approximately 500 mosquito specimens to the MalariaGEN Vector Observatory for whole genome sequencing. When designing the project and planning mosquito collections, bear in mind that at least 30 specimens are required for each sampling unit in order to obtain sufficient statistical power for population genomic analyses and robust comparison of mosquitoes between different sampling units. A sampling unit will usually comprise specimens of a single species, collected from the same location at the same time, and also subject to the same experimental treatment or variable. E.g., if insecticide resistance bioassays are being performed, specimens that were alive following the treatment should be considered a separate sampling unit from those which were dead. The spatial scale at which mosquitoes can be grouped together in the same sampling unit will depend on local heterogeneities in the environment, and may vary between projects, however in general it should be reasonable to group all specimens from the same ~5x5km region into the same sampling unit. The temporal scale at which mosquitoes can be grouped into a single sampling unit will depend on changes in seasonality and other relevant events such as the beginning or ending of a vector control campaign, however, all else being equal, it should be reasonable to group all specimens collected within the same calendar month into the same sampling unit. For example, in planning collection of mosquitoes for whole-genome analyses, a project could aim to collect mosquitoes of a single species from 5 locations at 3 time points. Also bear in mind that some capacity for amplicon sequencing will also be provided by MalariaGEN. Amplicon sequencing does not provide the same resolution as whole-genome sequencing; however, it can provide some valuable diagnostics regarding species composition, population structure, and insecticide resistance variants and haplotypes. Therefore, your sampling scheme can also include sampling units which you will submit for amplicon sequencing but not for whole genome sequencing. Again, for analysis of amplicon sequencing data, at least 30 specimens are required per sampling unit. Whole specimens can be shipped directly to WSI where the MalariaGEN lab team will perform DNA extraction and prepare samples for sequencing assays. There is no need to account for DNA extraction or any molecular diagnostics within the project plan, unless you

11 want to investigate more mosquitoes beyond the capacity for sequencing provided by MalariaGEN. Finally, bear in mind that sequencing reactions do not always work and other issues can arise which prevent data being generated for some specimens, therefore it is generally wise to aim to actually collect at least twice as many specimens as are required for each sampling unit, i.e., at least 60 specimens.