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Anopheles gambiae genomic surveillance project

Started 2021

Mosquito
 

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

17 Nov 2023 Ag3.8: Anopheles gambiae data resource

2261 whole genome sequences from mosquito samples collected in Burkina Faso, Gabon, Nigeria, and Uganda.

17 Nov 2023 Ag3.7: Anopheles gambiae data resource
Species: A. gambiae sensu lato

2546 whole genome sequences from mosquito samples collected in Benin, Burkino Faso, Cameroon, Gabon, Ghana, Guinea, and Tanzania between 2007 – 2021.

17 Nov 2023 Ag3.6: Anopheles gambiae data resource
Species: A. gambiae sensu lato

1404 whole genome sequences from mosquito samples collected across Cote d’Ivôire, South Africa, Uganda and Zambia.

17 Nov 2023 Ag3.5: Anopheles gambiae data resource
Species: A. gambiae sensu lato

1140 whole genome sequences from mosquito samples collected from 36 different locations across DRC, The Gambia and Ethiopia.

17 Nov 2023 Ag3.4: Anopheles gambiae data resource
Species: A. gambiae sensu lato

1817 whole genome sequences from mosquito samples collected from 11 locations in Ghana, and single locations in both Burkina Faso and Mali.

17 Nov 2023 Ag3.3: Anopheles gambiae data resource
Species: A. gambiae sensu lato

1002 whole genome sequences from mosquito samples collected from five locations in Ghana, Kenya and Uganda

17 Nov 2023 Ag3.2: Anopheles gambiae data resource
Species: A. gambiae sensu lato

1138 whole genome sequences from mosquito samples collected in ten locations in Benin, Côte d’Ivoire, Ghana, Mali and Togo.

17 Nov 2023 Ag3.1: Anopheles gambiae data resource
Species: A. gambiae sensu lato

647 whole genome sequences from mosquito samples collected in two locations in Mali.

4 Nov 2021 Ag3.0 (Ag1000G phase 3): Anopheles gambiae data resource

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.

Anopheles infectivity study, Uganda (1178-VO-UG-LAWNICZAK)

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…

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Anopheles gambiae vector surveillance in Ethiopia (1324-VO-ET-GOLASSA)

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…

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Anopheles gambiae vector surveillance in Nigeria (1338-VO-NG-ADEDAPO)

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…

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Anopheles gambiae vector surveillance in Uganda (1297-VO-UG-KAYONDO)

Contributor: Jonathan Kayondo: Uganda Virus Research Institute, Uganda

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26 Oct 2023 Anopheles gambiae vector surveillance in The Gambia (1323-VO-GM-NGWA)

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…

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Anopheles gambiae vector surveillance in Guinea (1330-VO-GN-LAMA)

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…

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Anopheles gambiae vector surveillance in Senegal (1188-VO-SN-NIANG)

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…

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Anopheles gambiae vector surveillance in Uganda (1284-VO-UG-NTEGE)

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…

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11 Sep 2023 ANOSPP screening of Anopheles species and Plasmodium presence in malaria vectors in Burkina Faso (1314-VO-BF-KIENTEGA)

Collaborator Mahamadi Kientega Institut de Recherches en Sciences de la Santé (IRSS), Burkina Faso

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11 Sep 2023 ANOSPP screening of Anopheles species and Plasmodium presence in malaria vectors in Nigeria (1315-VO-NG-OMITOLA)

Contributor: Olaitan Omitola Federal University of Agriculture Abeokuta, Nigeria

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11 Sep 2023 ANOSPP screening of Anopheles species and Plasmodium presence in malaria vectors in Uganda (1326-VO-UG-KAYONDO)

Contributor: Jonathan Kayondo Uganda Virus Research Institute, Uganda

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11 Sep 2023 ANOSPP screening of Anopheles species and Plasmodium presence in malaria vectors in West-Central Africa (1230-VO-MULTI-AYALA)

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…

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3 Apr 2023 Aestivation and migration of An. coluzzii, An. gambiae, and An. arabiensis in the Malian Sahel (1177-VO-ML-LEHMANN)

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…

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Evaluation of the susceptibility of malaria vectors to insecticides in Guinea-Bissau (1352-VO-GW-OSORIO)

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…

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11 Sep 2023 Genome-based diagnostics for monitoring and evaluation of insecticide resistance in Anopheles gambiae in Tanzania (1246-VO-TZ-KABULA)

Contributors: Bilali Kabula, National Institute of Medical Research, Tanzania

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24 Aug 2023 Genomics for African Anopheles Resistance Diagnostics/GAARDian (1237-VO-BJ-DJOGBENOU/1244-VO-GH-YAWSON/1245-VO-CI-CONSTANT/1253-VO-TG-DJOGBENOU)

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…

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IMPAVES: Integration of malaria parasite and vector surveillance in Ghana (1339-VO-GH-AMENGA-ETEGO)

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…

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11 Sep 2023 LLIN Evaluation in Uganda Project (LLINEUP) (1288-VO-UG-DONNELLY)

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…

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26 Oct 2023 PAMCA Anopheles genomics programme - Anopheles gambiae and Anopheles arabiensis genetic diversity and association with insecticide resistance in Kenya (1274-VO-KE-KAMAU)

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…

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26 Oct 2023 PAMCA Anopheles genomics programme - Anopheles gambiae vector surveillance in Gabon (1329-VO-GA-CHRISTOPHE)

Contributor: Antonio-Nkondjio Christophe Organisation de Coordination pour la Lutte contre les Endémies en Afrique Centrale (OCEAC), Cameroon

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7 Sep 2023 PAMCA Anopheles genomics programme - First investigation of genetic diversity in malaria vectors in the Democratic Republic of Congo and the implications for the spread of insecticide resistance (1264-VO-CD-WATSENGA)

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,…

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8 Sep 2023 PAMCA Anopheles genomics programme - Genetic structuring in the major malaria vector Anopheles arabiensis and implication on vector control in South Africa (1280-VO-ZA-MUNHENGA)

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…

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11 Sep 2023 PAMCA Anopheles genomics programme - Malaria vector surveillance, population genetics and insecticide resistance characterization in four eco-epidemiological settings in Cameroon (1281-VO-CM-CHRISTOPHE)

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…

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8 Sep 2023 PAMCA Anopheles genomics programme - Seasonality and impact of vector control interventions on population genetics of Anopheles funestus and Anopheles gambiae malaria vectors in Zambia (1273-VO-ZM-MULEBA)

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…

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8 Sep 2023 PAMCA Anopheles genomics programme - Strengthening malaria vector surveillance in Cote d’Ivoire: An investigation into genetic diversity and gene flow data gap in insecticide resistant Anopheles gambiae (1279-VO-CI-KOFFI)

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…

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7 Sep 2023 PAMCA Anopheles genomics programme - Understanding genomic diversity and heterogeneity of insecticide resistance phenotypes in Anopheles gambiae s.l. in The Gambia (1272-VO-GM-OPONDO)

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…

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7 Sep 2023 Pan-African Malaria Genetic Epidemiology Network (PAMGEN) Anopheles gambiae samples (1270-VO-MULTI-PAMGEN)

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…

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29 Aug 2023 Population genetics, parasite diversity and ecology of the major malaria vectors in the Kassena-Nankana Districts of Ghana (1190-VO-GH-AMENGA-ETEGO)

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…

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29 Aug 2023 Target Malaria (1191-VO-MULTI-OLOUGHLIN)

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…

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User guide

15,036 specimens

from

26 countries

Project contact