Introduction
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.
Locations
Below are all locations to date from which we have generated genomic data on one or more species from the Anopheles gambiae complex.
Sampling locations
Benin, Burkina Faso, Cameroon, Congo, Ethiopia, Gabon, The Gambia, Ghana, Guinea, Ivory Coast, Kenya, Mali, Nigeria, South Africa, Tanzania, Togo, Uganda, Zambia.
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.
Current
420 whole genome sequences from mosquito samples collected in Ethiopia.
This data is subject to
Anopheles gambiae Genomic Surveillance Project Terms of Use
720 whole genome sequences from mosquito samples collected in Nigeria.
This data is subject to
Anopheles gambiae Genomic Surveillance Project Terms of Use
755 whole genome sequences from mosquito samples collected in Burkina Faso and South Sudan.
This data is subject to
Anopheles gambiae Genomic Surveillance Project Terms of Use
1164 whole genome sequences from mosquito samples collected in Burkina Faso, Cameroon, Guinea, Kenya, Mali, Senegal, South Africa, Tanzania and Zimbabwe.
This data is subject to
Anopheles gambiae Genomic Surveillance Project Terms of Use
3639 whole genome sequences from mosquito samples collected in Angola, Benin, Burkina Faso, Cameroon, Equatorial Guinea, Ethiopia, Gabon, Guinea Bissau, Kenya, Madagascar, Mali, Sao Tome and Principe, South Africa, Tanzania, The Gambia, The Union of the Comoros, Uganda, Zambia and Zimbabwe.
This data is subject to
Anopheles gambiae Genomic Surveillance Project Terms of Use
2261 whole genome sequences from mosquito samples collected in Burkina Faso, Gabon, Nigeria, and Uganda.
This data is subject to
Anopheles gambiae Genomic Surveillance Project Terms of Use
2546 whole genome sequences from mosquito samples collected in Benin, Burkino Faso, Cameroon, Gabon, Ghana, Guinea, and Tanzania between 2007 – 2021.
This data is subject to
Anopheles gambiae Genomic Surveillance Project Terms of Use
1404 whole genome sequences from mosquito samples collected across Cote d’Ivôire, South Africa, Uganda and Zambia.
This data is subject to
Anopheles gambiae Genomic Surveillance Project Terms of Use
1140 whole genome sequences from mosquito samples collected from 36 different locations across DRC, The Gambia and Ethiopia.
This data is subject to
Anopheles gambiae Genomic Surveillance Project Terms of Use
1817 whole genome sequences from mosquito samples collected from 11 locations in Ghana, and single locations in both Burkina Faso and Mali.
This data is subject to
Anopheles gambiae Genomic Surveillance Project Terms of Use
1002 whole genome sequences from mosquito samples collected from five locations in Ghana, Kenya and Uganda
This data is subject to
Anopheles gambiae Genomic Surveillance Project Terms of Use
1138 whole genome sequences from mosquito samples collected in ten locations in Benin, Côte d’Ivoire, Ghana, Mali and Togo.
This data is subject to
Anopheles gambiae Genomic Surveillance Project Terms of Use
647 whole genome sequences from mosquito samples collected in two locations in Mali.
This data is subject to
Anopheles gambiae Genomic Surveillance Project Terms of Use
Sample set: 2,784 wild-caught specimens from 19 countries and 297 specimens comprising parents and progeny of 15 crosses.
This data is subject to
Ag1000G Terms of Use
Training
We are currently working together with the Pan-African Mosquito Control Association (PAMCA) to deliver the second edition of the online training course in data analysis for genomic surveillance of African malaria vectors. This free course will run for 8 weeks with whole-day workshops every Wednesday from June 7th to July 26th, 2023.
Partner studies
We work with a number of researchers undertaking independent studies to address unique questions about malaria biology and disease in malaria endemic areas. Each study is different, but they all involve a genomic component whereby they partner with us to sequence parasite samples and share the population genetic data. Click a link below to learn more about their work.
These specimens are being collected as part of an ongoing project to carry out field infections on F1s from wild caught specimens. Contributors: Mara Lawniczak, Wellcome Sanger Institute, UK Charles Mulamba, Wellcome Sanger…
Contributors Abdoulaye Diabate: Institut de Recherche en Sciences de la Santé (IRSS), Burkina Faso
Our general aim is to systematically collect Anopheles gambiae samples across the different ecological areas of Ethiopia and to analyze the dynamics of genes associated with insecticides resistance, determine genetic diversity and population…
The overall objective of this and associated studies is to perform vector genomic surveillance of at least 4000 Anopheles specimens from West Africa (The Gambia, Guinea and Nigeria) to improve understanding of spatial…
Contributor: Jonathan Kayondo: Uganda Virus Research Institute, Uganda
This study is part of the Genomic Surveillance Hubs in West Africa/NIHR Global Health Research Group project. By better understanding the genomic landscape of malaria parasites and vectors in this region, National Malaria…
By conducting sampling in 24 different districts in Uganda, this study aims to monitor population densities and insecticide resistance across the Anopheles genus. Contributors: Charles Ntege: National Malaria Control Division, Ministry of Health, Uganda…
Previously archived samples of Anopheles have been collected as part of the Senegalese PMI Project, providing data on spatial and temporal changes in the vector populations’ dynamics, susceptibility to insecticide, P. falciparum infection…
The overall objective of this and associated studies is to perform vector genomic surveillance of at least 4000 Anopheles specimens from West Africa (The Gambia, Guinea and Nigeria) to improve understanding of spatial…
Collaborator Mahamadi Kientega Institut de Recherches en Sciences de la Santé (IRSS), Burkina Faso
Contributor: Olaitan Omitola Federal University of Agriculture Abeokuta, Nigeria
Contributor: Jonathan Kayondo Uganda Virus Research Institute, Uganda
Contributors: Diego Ayala MIVEGEC, IRD, CNRS, Univ. Montpellier, Montpellier, France Sandrine Nsango Centre Pasteur du Cameroun, Cameroon Jean Akiana Laboratoire National de santé Publique, Democratic Republic of Congo Claire Sangba-Kembi Institut Pasteur de…
As part of an ongoing project on seasonal transmission of malaria in the Sahel, mosquitoes were collected in several villages in the Mali Sahel from 2012 to 2015, along two transects centred on…
These samples will be used to study the genetic structure of vector populations within the Anopheles gambiae complex in Guinea-Bissau, with two main aims. Firstly, the genomic data generated will be used to…
Contributors: Bilali Kabula, National Institute of Medical Research, Tanzania
In Unity State, Bentiu Protection of Civilian camp (PoC) provides shelter to over 100,000 people who are at high risk of malaria especially during the rainy season when rates can triple. Entomological surveillance…
The unifying theme of this project is to exploit the power of whole genome sequencing to identify genes/regulatory regions that are associated with insecticide resistance. We will use a combination of approaches including…
Recent efforts by the Ghana National Malaria Elimination Programme (NMEP) have resulted in decreasing malaria transmission. However, in five northern regions of the country, despite interventions such as indoor residual spraying, long lasting…
LLINEUP trial is a large-scale trial of next generation PBO bed-nets covering 104 health sub-districts in Uganda – approximately half of the area of the country. The primary outcome of the trial is…
Malaria remains an important public health concern in Kenya. Vector control employing mainly insecticide use is a key component of the malaria control strategy but the continued efficacy of this approach is threatened…
Contributor: Antonio-Nkondjio Christophe Organisation de Coordination pour la Lutte contre les Endémies en Afrique Centrale (OCEAC), Cameroon
The study sites for this project (Haut Katanga in Kapolowe, Kongo Central in Kimpese and Kasai Central in Mikalayi) are across ecological zones and land use of the Democtracic Republic of Congo. Historically,…
Specimens were collected as part of the specific objective to understand genetic structuring in the major malaria vector Anopheles arabiensis and implication on vector control in South Africa. Contributors: Givemore Munhenga The National…
The collected mosquitos are part of entomological monitoring and are to assess the evolution of insecticide resistance in vector populations. Collaborators: Antonio Nkondjio Christophe Organisation de Coordination pour la Lutte contre les Endémies…
We seek to address a scientific question on effects of season and vector control interventions on population genetics of Anopheles funestus and Anopheles gambiae malaria vectors in Zambia. Specimens will be collected from…
Malaria vector species of Cote d’Ivoire are mainly An. gambiae, An. coluzzii, An. funestus and An. nili. For the current project, An. gambiae and An. coluzzii are the targeted species. The timeline of…
This study includes whole mosquitoes collected in upper river region (URR) of The Gambia where Ivermectin was used. Samples were collected before, during and after ivermectin use. These samples are collected as part…
The Anopheles gambiae samples due to be collected from seven countries (The Gambia, Ghana, Mali, Cameroon, Ethiopia, Tanzania and Madagascar) will contribute to the Pan-African Malaria Genetic Epidemiology Network (PAMGEN) project. The aim…
We are carrying out a 2-year survey in four different villages in the upper-East region of Ghana (Naaga, Kayoro, Kandiga and Bonia). Samples of An. gambiae sensu lato and An. funestus will be…
Target Malaria is carrying out extensive sampling of Anopheles mosquitoes in three locations in sub-Saharan Africa; the Bobo-Dioulasso region of Burkina Faso, Bamako region of Mali, and Lake Victoria islands in Uganda. Ongoing…
Publications
- The Anopheles coluzzii range extends into Kenya: detection, insecticide resistance profiles and population genetic structure in relation to conspecific populations in West and Central Africa
Kamau et al.Malaria Journal, 2024;- Cryptic population structure and insecticide resistance in Anopheles gambiae from the southern Democratic Republic of Congo
Dennis et al.bioRxiv, 2024;- Copy number variants underlie the major selective sweeps in insecticide resistance genes in Anopheles arabiensis from Tanzania
Lucas et al.bioRxiv, 2024;- Whole-genome sequencing of major malaria vectors revealed an evolution of new insecticide resistance variants in a longitudinal study in Burkina Faso
Kientega et al.bioRxiv, 2023;- Genome-wide association studies reveal novel loci associated with pyrethroid and organophosphate resistance in Anopheles gambiae and Anopheles coluzzii
Lucas et al.Nature Communications, 2023; 14 4946
21,690 specimens
from
32 countries
Project contact
Project news
News
Over 100 African researchers begin MalariaGEN-PAMCA training course
For 11 weeks, participants from across Africa will join virtual workshops to learn how to analyse genomic surveillance data of malaria mosquitoes.
