Anopheles gambiae genomic surveillance project
Using whole-genome sequencing for enhanced monitoring and surveillance of major malaria vectors in the Anopheles gambiae species complex.
Objectives & Coordination
The Anopheles gambiae genomic surveillance project is a collaborative effort to develop and utilise whole-genome sequencing as an operational tool for surveillance of malaria vector populations in the Anopheles gambiae species complex.
Malaria vector control in Africa is going through a period of major change, as new insecticides are being brought into public health use through new insecticide-treated net (ITN) and indoor residual spray (IRS) products. Enhanced sentinel surveillance of major vector populations is essential during this period of change, to provide early warning of new insecticide resistance adaptations, and to help understand where these new vector control products are most effective.
High-throughput data for genomic epidemiology and surveillance - Our primary goal is to support and complement existing entomological monitoring activities by providing access to high-throughput whole-genome sequencing and genomic data services. We are developing a capability to generate high-quality genomic surveillance data that can operate at the scale and speed needed for malaria vector surveillance, and which is tailored for use with malaria vectors in the Anopheles gambiae species complex.
Accessible data and computing tools - Mosquito whole-genome sequencing generates big data which can be technically challenging to store and analyse. To overcome this, we are using cloud computing to build an open access data repository that can be accessed from anywhere in the world, and which is coupled with advanced computing and software tools to perform the data analyses needed for malaria vector surveillance.
Training and professional development - To ensure that the power to access and analyse these data is in the hands of those who need it most, we are developing educational materials and hands-on training programmes to build skills in genomic surveillance data analysis, and delivering these through online learning courses.
Equitable partnership and collaboration - The project is a collaboration between Africa, Europe and North America. At its heart, the project is a network of African partners who are actively collecting mosquitoes as part of operational research programmes or routine entomological surveillance, and who are collaborating to generate genomic data from mosquitoes sampled regularly from sentinel surveillance sites.
New partners
The project is currently open to new partnerships. If you are a vector biologist studying or monitoring mosquitoes in the An. gambiae complex and are interested in partnering with the project, please email the project contact, or see the information about Applying for a Partner Study.
Sampling locations
Below are all locations to date from which we have generated genomic data on one or more species from the Anopheles gambiae complex.
Data
We routinely release analysis-ready genomic data to project partners. In addition, we periodically release public access datasets. These data are made available via our cloud data repository, and are accompanied by analytical software to simplify data access.
In order to ensure regularly and timely data are available, data from this project will be made available as a series of data releases. Each data release will be given a version identifier (e.g., "Ag3.1") and will be associated with a date of public release.
To find out more about currently available data please visit the Vector Data User Guide.
Terms of use
Although malaria is generally an endemic rather than an epidemic disease, and the focus of this project is on surveillance of disease vectors rather than pathogens, our data terms of use build on MalariaGEN's approach to data sharing, and adopt norms which have been established for rapid sharing of pathogen genomic data during disease outbreaks. The primary rationale for this approach is that malaria remains a public health emergency, where ethically appropriate and rapid sharing of genomic surveillance data can help to detect and respond to biological threats such as new forms of insecticide resistance, and to adapt malaria vector control strategies to different settings and changing circumstances.
Accordingly, data from this project will be made publicly available before journal publication. Data from this project may be accessed and analysed at any time for the purposes of supporting public health programmes to control malaria and for teaching. Unless otherwise stated, analyses of project data are ongoing and publications are in preparation by project partners, and it is not permitted to use project data for publication (including any type of communication with the general public) without prior permission from the project.
Training
We are currently working together with the Pan-African Mosquito Control Association (PAMCA) to develop an online training course in data analysis for genomic surveillance of African malaria vectors. This course is still in development, but lectures and notebooks will be published on the course website as soon as they are available.