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1. The V410L knockdown resistance mutation occurs in island and continental populations of Aedes aegypti in West and Central Africa.

Author

Constância F J Ayres, Gonçalo Seixas, Sílvia Borrego, Cátia Marques, Inilça Monteiro, Camila S Marques, Bruna Gouveia, Silvania Leal, Arlete D Troco, Filomeno Fortes, Ricardo Parreira, João Pinto, and Carla A Sousa

Subjects
Arctic medicine. Tropical medicine, RC955-962, Public aspects of medicine, RA1-1270
Abstract

The extensive use of insecticides for vector control has led to the development of insecticide resistance in Aedes aegypti populations on a global scale, which has significantly compromised control actions. Insecticide resistance, and its underlying mechanisms, has been investigated in several countries, mostly in South American and Asian countries. In Africa, however, studies reporting insecticide resistance are rare and data on resistance mechanisms, notably knockdown resistance (kdr) mutations, is scarce. In this study, the recently described V410L kdr mutation is reported for the first time in old world Ae. aegypti populations, namely from Angola and Madeira island. Two additional kdr mutations, V1016I and F1534C, are also reported for the first time in populations from Angola and Cape Verde. Significant associations with the resistance phenotype were found for both V410L and V1016I individually as well as for tri-locus genotypes in the Angolan population. However, no association was found in Madeira island, probably due to the presence of a complex pattern of multiple insecticide resistance mechanisms in the local Ae. aegypti population. These results suggest that populations carrying the same kdr mutations may respond differently to the same insecticide, stressing the need for complementary studies when assessing the impact of kdr resistance mechanisms in the outcome of insecticide-based control strategies.

Published
2020
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2. Genetic diversity of the African malaria vector Anopheles gambiae

Author

Matthew W. Hahn, Alison T. Isaacs, Samantha M. O’Loughlin, Tiago Antao, Austin Burt, Mara K. N. Lawniczak, Dominic P. Kwiatkowski, Christina M. Bergey, Michelle M. Riehle, Giordano Bottà, Boubacar Coulibaly, Martin J. Donnelly, Joao Dinis, Alessandra della Torre, Kirk A. Rockett, Krzysztof Kozak, Andrew D. Kern, Christina Hubbart, Nohal Elissa, Kate Rowlands, Bradley J. White, Eleanor Drury, Rachel Giacomantonio, Craig S. Wilding, Ian J. Wright, Kenneth D. Vernick, Michael C. Fontaine, Diego Ayala, Alistair Miles, Kyanne R. Rohatgi, Daniel Mead, Arlete D. Troco, Philip Bejon, Jim Stalker, Janet Midega, Nicholas J. Harding, Abdoulaye Diabaté, Nora J. Besansky, Henry D. Mawejje, Cinzia Malangone, Daniel R. Schrider, Paul Vauterin, H. Charles J. Godfray, Charles M. Mbogo, Igor V. Sharakhov, Anna E. Jeffreys, Seth Redmond, João Pinto, Dushyanth Jyothi, Chris S Clarkson, Victoria Cornelius, Krzysztof Kluczynski, Carlo Costantini, Lee Hart, Richard D. Pearson, Daniel E. Neafsey, Christa Henrichs, Bronwyn MacInnis, David Weetman, Beniamino Caputo, Ben Jeffery, The Royal Society, Bill & Melinda Gates Foundation, Silicon Valley Community Foundation, Medical Research Council (MRC), Diversity, ecology, evolution & Adaptation of arthropod vectors (MIVEGEC-DEEVA), Evolution des Systèmes Vectoriels (ESV), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Groningen Institute for Evolutionary Life Sciences [Groningen] (GELIFES), University of Groningen [Groningen], and Fontaine lab

Subjects
Male, 0106 biological sciences, 0301 basic medicine, Mosquito Control, POSITIVE SELECTION, Anopheles gambiae, FLOW, Genome, Insect, Web application development, Guinea-Bissau, 01 natural sciences, Genome, Partner working group, Gene flow, Insecticide Resistance, Kenya, Effective population size, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, RA0421, Gabon, Sequencing and data production, ComputingMilieux_MISCELLANEOUS, Multidisciplinary, biology, Uganda, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], INTROGRESSION, genomics, malaria, anopheles gambiae, Anopheles, Project coordination, Crosses, 3. Good health, MOSQUITO, Multidisciplinary Sciences, Mosquito control, QR180, Science & Technology - Other Topics, Female, Burkina Faso, Sample collections—Angola, Gene Flow, X Chromosome, General Science & Technology, Data analysis group, Mosquito Vectors, Polymorphism, Single Nucleotide, 010603 evolutionary biology, Article, QH301, 03 medical and health sciences, CULICIDAE, Cameroon, parasitic diseases, DIVERGENCE, Animals, Anopheles gambiae 1000 Genomes Consortium, POPULATION-STRUCTURE, INCIPIENT SPECIATION, Population Density, Genetic diversity, Science & Technology, Gene Drive Technology, Genetic Variation, Guinea, biology.organism_classification, Malaria, 030104 developmental biology, Evolutionary biology, DROSOPHILA-MELANOGASTER, Africa, Threatened species, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, RESISTANCE
Abstract

The sustainability of malaria control in Africa is threatened by the rise of insecticide resistance in Anopheles mosquitoes, which transmit the disease(1). To gain a deeper understanding of how mosquito populations are evolving, here we sequenced the genomes of 765 specimens of Anopheles gambiae and Anopheles coluzzii sampled from 15 locations across Africa, and identified over 50 million single nucleotide polymorphisms within the accessible genome. These data revealed complex population structure and patterns of gene flow, with evidence of ancient expansions, recent bottlenecks, and local variation in effective population size. Strong signals of recent selection were observed in insecticide-resistance genes, with several sweeps spreading over large geographical distances and between species. The design of new tools for mosquito control using gene-drive systems will need to take account of high levels of genetic diversity in natural mosquito populations.

Published
2017

3. Population structure of a vector of human diseases: Aedes aegypti in its ancestral range, Africa

Author

Basile Kamgang, Carla A. Sousa, Martin N. Mayanja, Gilbert Le Goff, Panayiota Kotsakiozi, Arlete D. Troco, João Pinto, Athanase Badolo, Andrea Gloria-Soria, Christophe Paupy, Julius J. Lutwama, Diego Ayala, Benjamin R. Evans, Jeffrey R. Powell, Yale University [New Haven], Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), International Network for the Sequencing of resPIRratory vIrusEs (INSPIRE), Diversity, ecology, evolution & Adaptation of arthropod vectors (MIVEGEC-DEEVA), Evolution des Systèmes Vectoriels (ESV), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Centre International de Recherches Médicales de Franceville (CIRMF), Université Joseph Ki-Zerbo [Ouagadougou] (UJZK), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA), Centre international de recherches médicales de Franceville (CIRMF), Organisation Mondiale de la Santé (OMS), Université de Ouagadougou, Universidade Nova de Lisboa (NOVA), and Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)

Subjects
0301 basic medicine, Range (biology), SNP-chip, Aedes aegypti, medicine.disease_cause, migration, Dengue fever, 03 medical and health sciences, lcsh:QH540-549.5, parasitic diseases, medicine, genetics, Chikungunya, Ecology, Evolution, Behavior and Systematics, Nature and Landscape Conservation, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Ecology, biology, Phylogenetic tree, Yellow fever, population structure, SNP‐chip, biology.organism_classification, medicine.disease, 3. Good health, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, 030104 developmental biology, Geography, Vector (epidemiology), Genetic structure, Africa, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, lcsh:Ecology
Abstract

International audience; Aedes aegypti, the major vector of dengue, yellow fever, chikungunya, and Zika viruses , remains of great medical and public health concern. There is little doubt that the ancestral home of the species is Africa. This mosquito invaded the New World 400-500 years ago and later, Asia. However, little is known about the genetic structure and history of Ae. aegypti across Africa, as well as the possible origin(s) of the New World invasion. Here, we use ~17,000 genome-wide single nucleotide polymor-phisms (SNPs) to characterize a heretofore undocumented complex picture of this mosquito across its ancestral range in Africa. We find signatures of human-assisted migrations, connectivity across long distances in sylvan populations, and of local ad-mixture between domestic and sylvan populations. Finally, through a phylogenetic analysis combined with the genetic structure analyses, we suggest West Africa and especially Angola as the source of the New World's invasion, a scenario that fits well with the historic record of 16th-century slave trade between Africa and Americas.

Published
2018

4. Genome variation and population structure among 1142 mosquitoes of the African malaria vector species Anopheles gambiae and Anopheles coluzzii

Author

Matthew W. Hahn, Alison T. Isaacs, Edi Constant, Jim Stalker, Boubacar Coulibaly, Michelle M. Riehle, Alistair Miles, Austin Burt, Chris S Clarkson, Charles Mbogo, Alessandra della Torre, Michael C Fontaine, Nora J. Besansky, Eric R. Lucas, Victoria Simpson, Daniel R. Schrider, Samantha M. O’Loughlin, Kirk A. Rockett, Henry D. Mawejje, Bradley J. White, Arlete D. Troco, Andrew D. Kern, Jorge Edouardo Amaya-Romero, Abdoulaye Diabaté, Jorge Cano, Beniamino Caputo, H. Charles J. Godfray, Nicholas J. Harding, Kyanne R. Rohatgi, Igor V. Sharakhov, Christa Henrichs, Martin J. Donnelly, C. J. Battey, Cinzia Malangone, Anna E. Jeffreys, João Pinto, Nohal Elissa, Kate Rowlands, Maryam Kamali, Davis Nwakanma, Kenneth D. Vernick, Carlo Costantini, Janet Midega, John Essandoh, Diego Ayala, Musa Jawara, Eleanor Drury, Daniel Mead, Vincent Robert, Mara K. N. Lawniczak, Dushyanth Jyothi, Joao Dinis, Gilbert Le Goff, Christina Hubbart, Dominic P. Kwiatkowski, Van Doorn group, Fontaine lab, Centre Muraz [Bobo-Dioulasso, Burkina Faso], Diversity, ecology, evolution & Adaptation of arthropod vectors (MIVEGEC-DEEVA), Evolution des Systèmes Vectoriels (ESV), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Unité d'Entomologie Médicale [Antananarivo, Madagascar] (IPM), Institut Pasteur de Madagascar, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), The Wellcome Trust Sanger Institute [Cambridge], The Wellcome Trust Centre for Human Genetics [Oxford], University of Oxford [Oxford], Laboratorio Pasteur [Istituto Pasteur-Fondazione Cenci Bolognetti, Rome], Institut Pasteur, Fondation Cenci Bolognetti - Istituto Pasteur Italia, Fondazione Cenci Bolognetti, Groningen Institute for Evolutionary Life Sciences [Groningen] (GELIFES), University of Groningen [Groningen], Computer Science Departement [Indiana], Indiana University [Bloomington], Indiana University System-Indiana University System, Virginia Tech [Blacksburg], and University of Oxford

Subjects
Insecticides, [SDV]Life Sciences [q-bio], Anopheles gambiae, Genome, Insect, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Population genomics, 0302 clinical medicine, CRISPR-Associated Protein 9, Pyrethrins, Copy-number variation, Genetics (clinical), 0303 health sciences, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], INTROGRESSION, KDR MUTATION, 3. Good health, Mosquito control, Resource, mosquito, anopheles, genome, MOLECULAR-FORMS, DNA Copy Number Variations, 030231 tropical medicine, Mosquito Vectors, Biology, Polymorphism, Single Nucleotide, MECHANISMS, 03 medical and health sciences, QH301, Genetic variation, Anopheles, parasitic diseases, Genetics, medicine, Animals, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, GENE DRIVE, QH426, 030304 developmental biology, Isolation by distance, Genetic diversity, COMPLEX, IDENTIFICATION, Whole Genome Sequencing, QH, Genetic Variation, AMPLIFICATION, Gene drive, 15. Life on land, medicine.disease, biology.organism_classification, EVOLUTION, Haplotypes, Evolutionary biology, INSECTICIDE RESISTANCE, 030217 neurology & neurosurgery, Malaria
Abstract

Mosquito control remains a central pillar of efforts to reduce malaria burden in sub-Saharan Africa. However, insecticide resistance is entrenched in malaria vector populations, and countries with a high malaria burden face a daunting challenge to sustain malaria control with a limited set of surveillance and intervention tools. Here we report on the second phase of a project to build an open resource of high-quality data on genome variation among natural populations of the major African malaria vector species Anopheles gambiae and Anopheles coluzzii. We analyzed whole genomes of 1142 individual mosquitoes sampled from the wild in 13 African countries, as well as a further 234 individuals comprising parents and progeny of 11 laboratory crosses. The data resource includes high-confidence single-nucleotide polymorphism (SNP) calls at 57 million variable sites, genome-wide copy number variation (CNV) calls, and haplotypes phased at biallelic SNPs. We use these data to analyze genetic population structure and characterize genetic diversity within and between populations. We illustrate the utility of these data by investigating species differences in isolation by distance, genetic variation within proposed gene drive target sequences, and patterns of resistance to pyrethroid insecticides. This data resource provides a foundation for developing new operational systems for molecular surveillance and for accelerating research and development of new vector control tools. It also provides a unique resource for the study of population genomics and evolutionary biology in eukaryotic species with high levels of genetic diversity under strong anthropogenic evolutionary pressures.

5. Population structure of a vector of human diseases: Aedes aegypti in its ancestral range, Africa

Author

Panayiota Kotsakiozi, Benjamin R. Evans, Andrea Gloria‐Soria, Basile Kamgang, Martin Mayanja, Julius Lutwama, Gilbert Le Goff, Diego Ayala, Christophe Paupy, Athanase Badolo, Joao Pinto, Carla A. Sousa, Arlete D. Troco, and Jeffrey R. Powell

Subjects
Aedes aegypti, Africa, genetics, migration, population structure, SNP‐chip, Ecology, QH540-549.5
Abstract

Abstract Aedes aegypti, the major vector of dengue, yellow fever, chikungunya, and Zika viruses, remains of great medical and public health concern. There is little doubt that the ancestral home of the species is Africa. This mosquito invaded the New World 400‐500 years ago and later, Asia. However, little is known about the genetic structure and history of Ae. aegypti across Africa, as well as the possible origin(s) of the New World invasion. Here, we use ~17,000 genome‐wide single nucleotide polymorphisms (SNPs) to characterize a heretofore undocumented complex picture of this mosquito across its ancestral range in Africa. We find signatures of human‐assisted migrations, connectivity across long distances in sylvan populations, and of local admixture between domestic and sylvan populations. Finally, through a phylogenetic analysis combined with the genetic structure analyses, we suggest West Africa and especially Angola as the source of the New World's invasion, a scenario that fits well with the historic record of 16th‐century slave trade between Africa and Americas.

Published
2018
Full Text
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