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Moss S, Jones RT, Pretorius E, da Silva ET, Higgins M, Kristan M, Acford-Palmer H, Collins EL, Rodrigues A, Krishna S, Clark TG, Last A, Campino S. Phenotypic evidence of deltamethrin resistance and identification of selective sweeps in Anopheles mosquitoes on the Bijagós Archipelago, Guinea-Bissau. Sci Rep 2024; 14:22840. [PMID: 39354094 PMCID: PMC11445403 DOI: 10.1038/s41598-024-73996-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 09/23/2024] [Indexed: 10/03/2024] Open
Abstract
Vector control in the Bijagós Archipelago of Guinea-Bissau currently relies on pyrethroid insecticide-treated nets. However, data on insecticide resistance in Guinea-Bissau is limited. This study identified deltamethrin resistance in the Anopheles gambiae sensu lato complex on Bubaque island using WHO tube tests in November 2022. Whole genome sequencing of An. gambiae sensu stricto mosquitoes identified six single nucleotide polymorphisms (SNPs) previously associated with, or putatively associated with, insecticide resistance: T791M, L995F, N1570Y, A1746S and P1874L in the vgsc gene, and L119V in the gste2 gene. Twenty additional non-synonymous SNPs were identified in insecticide-resistance associated genes. Four of these SNPs were present at frequencies over 5% in the population: T154S, I126F and G26S in the vgsc gene and A65S in ace1. Genome wide selection scans using Garud's H12 statistic identified two selective sweeps: one in chromosome X and one in chromosome 2R. Both selective sweeps overlap with metabolic genes previously associated with insecticide resistance, including cyp9k1 and the cyp6aa/cyp6p gene cluster. This study presents the first phenotypic testing for deltamethrin resistance and the first whole genome sequence data for Anophelesgambiae mosquitoes from the Bijagós, contributing data of significance for vector control policy in this region.
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Affiliation(s)
- Sophie Moss
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK.
| | - Robert T Jones
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Elizabeth Pretorius
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Eunice Teixeira da Silva
- Projecto de Saúde Bandim, Bissau, Guinea-Bissau
- Ministério de Saúde Pública, Bissau, Guinea-Bissau
| | - Matthew Higgins
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Mojca Kristan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Holly Acford-Palmer
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Emma L Collins
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Amabelia Rodrigues
- Projecto de Saúde Bandim, Bissau, Guinea-Bissau
- Ministério de Saúde Pública, Bissau, Guinea-Bissau
| | - Sanjeev Krishna
- Clinical Academic Group, Institute for Infection and Immunity, and St, George's University Hospitals NHS Foundation Trust, St. George's University of London, London, UK
- Centre de Recherches Médicales de Lambaréné (CERMEL), Lambaréné, Gabon
- Institut für Tropenmedizin Universitätsklinikum Tübingen, Tübingen, Germany
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Anna Last
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
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2
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Caputo B, De Marco CM, Pichler V, Bottà G, Bennett KL, Amambua-Ngwa A, Assogba SB, Opondo KO, Clarkson CS, Tennessen JA, Weetman D, Miles A, Della Torre A. Population genomic evidence of a putative 'far-west' African cryptic taxon in the Anopheles gambiae complex. Commun Biol 2024; 7:1115. [PMID: 39256556 PMCID: PMC11387608 DOI: 10.1038/s42003-024-06809-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 08/29/2024] [Indexed: 09/12/2024] Open
Abstract
The two main Afrotropical malaria vectors - Anopheles coluzzii and An. gambiae - are genetically distinct and reproductively isolated across West Africa. However, populations at the western extreme of their range are assigned as "intermediate" between the two species by whole genome sequence (WGS) data, and as hybrid forms by conventional molecular diagnostics. By exploiting WGS data from 1190 specimens collected across west Africa via the Anopheles gambiae 1000 Genomes network, we identified a putative taxon in the far-west (provisionally named Bissau molecular form), which did not arise by admixture but rather may have originated at the same time as the split between An. coluzzii and An. gambiae. Intriguingly, this taxon lacks insecticide resistance mechanisms commonly observed in the two main species. These findings lead to a change of perspective on malaria vector species in the far-west region with potential for epidemiological implications, and a new challenge for genetic-based mosquito control approaches.
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Affiliation(s)
- Beniamino Caputo
- Dipartimento di Sanità Pubblica e Malattie Infettive, Istituto Pasteur Italia-Fondazione Cenci-Bolognetti, Università di Roma "Sapienza", Rome, Italy
| | - Carlo M De Marco
- Dipartimento di Sanità Pubblica e Malattie Infettive, Istituto Pasteur Italia-Fondazione Cenci-Bolognetti, Università di Roma "Sapienza", Rome, Italy
| | - Verena Pichler
- Dipartimento di Sanità Pubblica e Malattie Infettive, Istituto Pasteur Italia-Fondazione Cenci-Bolognetti, Università di Roma "Sapienza", Rome, Italy
| | - Giordano Bottà
- Dipartimento di Sanità Pubblica e Malattie Infettive, Istituto Pasteur Italia-Fondazione Cenci-Bolognetti, Università di Roma "Sapienza", Rome, Italy
| | - Kelly L Bennett
- Wellcome Sanger Genomic Surveillance Unit, Wellcome Sanger Institute, Cambridge, UK
| | - Alfred Amambua-Ngwa
- Disease Control and Elimination Theme (DCE), Medical Research Council Unit, The Gambia at the London School of Hygiene and Tropical Medicine (MRCG-LSHTM), Banjul, The Gambia
| | - Sessinou B Assogba
- Disease Control and Elimination Theme (DCE), Medical Research Council Unit, The Gambia at the London School of Hygiene and Tropical Medicine (MRCG-LSHTM), Banjul, The Gambia
| | - Kevin O Opondo
- Disease Control and Elimination Theme (DCE), Medical Research Council Unit, The Gambia at the London School of Hygiene and Tropical Medicine (MRCG-LSHTM), Banjul, The Gambia
| | - Chris S Clarkson
- Wellcome Sanger Genomic Surveillance Unit, Wellcome Sanger Institute, Cambridge, UK
| | - Jacob A Tennessen
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - David Weetman
- Liverpool School of Tropical Medicine, Liverpool, UK
| | - Alistair Miles
- Wellcome Sanger Genomic Surveillance Unit, Wellcome Sanger Institute, Cambridge, UK
| | - Alessandra Della Torre
- Dipartimento di Sanità Pubblica e Malattie Infettive, Istituto Pasteur Italia-Fondazione Cenci-Bolognetti, Università di Roma "Sapienza", Rome, Italy.
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3
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Amaya Romero JE, Chenal C, Ben Chehida Y, Miles A, Clarkson CS, Pedergnana V, Wertheim B, Fontaine MC. Mitochondrial Variation in Anopheles gambiae and Anopheles coluzzii: Phylogeographic Legacy and Mitonuclear Associations With Metabolic Resistance to Pathogens and Insecticides. Genome Biol Evol 2024; 16:evae172. [PMID: 39226386 PMCID: PMC11370803 DOI: 10.1093/gbe/evae172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/22/2024] [Indexed: 09/05/2024] Open
Abstract
Mitochondrial DNA has been a popular marker in phylogeography, phylogeny, and molecular ecology, but its complex evolution is increasingly recognized. Here, we investigated mitochondrial DNA variation in Anopheles gambiae and Anopheles coluzzii, in relation to other species in the Anopheles gambiae complex, by assembling the mitogenomes of 1,219 mosquitoes across Africa. The mitochondrial DNA phylogeny of the Anopheles gambiae complex was consistent with previously reported highly reticulated evolutionary history, revealing important discordances with the species tree. The three most widespread species (An. gambiae, An. coluzzii, and Anopheles arabiensis), known for extensive historical introgression, could not be discriminated based on mitogenomes. Furthermore, a monophyletic clustering of the three saltwater-tolerant species (Anopheles merus, Anopheles melas, and Anopheles bwambae) in the Anopheles gambiae complex also suggested that introgression and possibly selection shaped mitochondrial DNA evolution. Mitochondrial DNA variation in An. gambiae and An. coluzzii across Africa revealed significant partitioning among populations and species. A peculiar mitochondrial DNA lineage found predominantly in An. coluzzii and in the hybrid taxon of the African "far-west" exhibited divergence comparable to the interspecies divergence in the Anopheles gambiae complex, with a geographic distribution matching closely An. coluzzii's geographic range. This phylogeographic relict of the An. coluzzii and An. gambiae split was associated with population and species structure, but not with the rare Wolbachia occurrence. The lineage was significantly associated with single nucleotide polymorphisms in the nuclear genome, particularly in genes associated with pathogen and insecticide resistance. These findings underline potential mitonuclear coevolution history and the role played by mitochondria in shaping metabolic responses to pathogens and insecticides in Anopheles.
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Affiliation(s)
- Jorge E Amaya Romero
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen 9747 AG, Netherlands
- MIVEGEC, University of Montpellier, CNRS, IRD, Montpellier, France
| | - Clothilde Chenal
- MIVEGEC, University of Montpellier, CNRS, IRD, Montpellier, France
- Institut des Science de l’Évolution de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Yacine Ben Chehida
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen 9747 AG, Netherlands
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Alistair Miles
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | | | | | - Bregje Wertheim
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen 9747 AG, Netherlands
| | - Michael C Fontaine
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen 9747 AG, Netherlands
- MIVEGEC, University of Montpellier, CNRS, IRD, Montpellier, France
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Dietz L, Mayer C, Stolle E, Eberle J, Misof B, Podsiadlowski L, Niehuis O, Ahrens D. Metazoa-level USCOs as markers in species delimitation and classification. Mol Ecol Resour 2024; 24:e13921. [PMID: 38146909 DOI: 10.1111/1755-0998.13921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 12/06/2023] [Accepted: 12/13/2023] [Indexed: 12/27/2023]
Abstract
Metazoa-level universal single-copy orthologs (mzl-USCOs) are universally applicable markers for DNA taxonomy in animals that can replace or supplement single-gene barcodes. Previously, mzl-USCOs from target enrichment data were shown to reliably distinguish species. Here, we tested whether USCOs are an evenly distributed, representative sample of a given metazoan genome and therefore able to cope with past hybridization events and incomplete lineage sorting. This is relevant for coalescent-based species delimitation approaches, which critically depend on the assumption that the investigated loci do not exhibit autocorrelation due to physical linkage. Based on 239 chromosome-level assembled genomes, we confirmed that mzl-USCOs are genetically unlinked for practical purposes and a representative sample of a genome in terms of reciprocal distances between USCOs on a chromosome and of distribution across chromosomes. We tested the suitability of mzl-USCOs extracted from genomes for species delimitation and phylogeny in four case studies: Anopheles mosquitos, Drosophila fruit flies, Heliconius butterflies and Darwin's finches. In almost all instances, USCOs allowed delineating species and yielded phylogenies that corresponded to those generated from whole genome data. Our phylogenetic analyses demonstrate that USCOs may complement single-gene DNA barcodes and provide more accurate taxonomic inferences. Combining USCOs from sources that used different versions of ortholog reference libraries to infer marker orthology may be challenging and, at times, impact taxonomic conclusions. However, we expect this problem to become less severe as the rapidly growing number of reference genomes provides a better representation of the number and diversity of organismal lineages.
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Affiliation(s)
- Lars Dietz
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
| | - Christoph Mayer
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
| | - Eckart Stolle
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
| | - Jonas Eberle
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
- Paris-Lodron-University, Salzburg, Austria
| | - Bernhard Misof
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
- Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Lars Podsiadlowski
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
| | - Oliver Niehuis
- Abt. Evolutionsbiologie und Ökologie, Institut für Biologie I, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Dirk Ahrens
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
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5
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Caputo B, De Marco C, Pichler V, Bottà G, Bennett K, Clarkson C, Tennessen J, Weetman D, Miles A, Torre AD. Speciation within the Anopheles gambiae complex: high-throughput whole genome sequencing reveals evidence of a putative new cryptic taxon in 'far-west' Africa. RESEARCH SQUARE 2024:rs.3.rs-3914444. [PMID: 38562903 PMCID: PMC10984024 DOI: 10.21203/rs.3.rs-3914444/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The two main Afrotropical malaria vectors - Anopheles coluzzii and An. gambiae - are genetically distinct and reproductively isolated across West Africa. However, populations at the western extreme of their range are assigned as "intermediate" between the two species by whole genome sequence (WGS) data, and as hybrid forms by conventional molecular diagnostics. By exploiting WGS data from 1,190 specimens collected across west Africa via the Anopheles gambiae 1000 Genomes network, we identify a novel putative taxon in the far-west (provisionally named Bissau molecular form), which did not arise by admixture but rather originated at the same time as the split between An. coluzzii and An. gambiae. Intriguingly, these populations lack insecticide resistance mechanisms commonly observed in the two main species. These findings lead to a change of perspective on malaria vector species in the far-west region with potential for epidemiological implications, and a new challenge for genetic-based mosquito control approaches.
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Affiliation(s)
- B. Caputo
- Dipartimento di Sanità Pubblica e Malattie Infettive, Istituto Pasteur Italia-Fondazione Cenci-Bolognetti, Università di Roma “Sapienza”, Rome Italy
| | - C.M. De Marco
- Dipartimento di Sanità Pubblica e Malattie Infettive, Istituto Pasteur Italia-Fondazione Cenci-Bolognetti, Università di Roma “Sapienza”, Rome Italy
| | - V. Pichler
- Dipartimento di Sanità Pubblica e Malattie Infettive, Istituto Pasteur Italia-Fondazione Cenci-Bolognetti, Università di Roma “Sapienza”, Rome Italy
| | - G. Bottà
- Dipartimento di Sanità Pubblica e Malattie Infettive, Istituto Pasteur Italia-Fondazione Cenci-Bolognetti, Università di Roma “Sapienza”, Rome Italy
| | - K.L. Bennett
- Wellcome Sanger Genomic Surveillance Unit, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - C.S. Clarkson
- Wellcome Sanger Genomic Surveillance Unit, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - J.A. Tennessen
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - D. Weetman
- Liverpool School of Tropical Medicine, Liverpool, UK
| | - A. Miles
- Wellcome Sanger Genomic Surveillance Unit, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - A. della Torre
- Dipartimento di Sanità Pubblica e Malattie Infettive, Istituto Pasteur Italia-Fondazione Cenci-Bolognetti, Università di Roma “Sapienza”, Rome Italy
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Moss S, Pretorius E, Ceesay S, Hutchins H, da Silva ET, Ndiath MO, Jones RT, Vasileva H, Phelan J, Acford-Palmer H, Collins E, Rodrigues A, Krishna S, Clark TG, Last A, Campino S. Genomic surveillance of Anopheles mosquitoes on the Bijagós Archipelago using custom targeted amplicon sequencing identifies mutations associated with insecticide resistance. Parasit Vectors 2024; 17:10. [PMID: 38178249 PMCID: PMC10768400 DOI: 10.1186/s13071-023-06085-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 12/06/2023] [Indexed: 01/06/2024] Open
Abstract
BACKGROUND Insecticide resistance is reducing the efficacy of vector control interventions, consequently threatening efforts to control vector-borne diseases, including malaria. Investigating the prevalence of molecular markers of resistance is a useful tool for monitoring the spread of insecticide resistance in disease vectors. The Bijagós Archipelago (Bijagós) in Guinea-Bissau is a region of stable malaria transmission where insecticide-treated nets are the mainstay for malaria control. However, the prevalence of molecular markers of insecticide resistance in malaria vectors is not well understood. METHODS A total of 214 Anopheles mosquitoes were analysed from 13 islands across the Bijagós. These mosquitoes were collected using CDC light traps in November 2019, during the peak malaria transmission season. High-throughput multiplex amplicon sequencing was used to investigate the prevalence of 17 different molecular markers associated with insecticide resistance in four genes: vgsc, rdl, ace1 and gste2. RESULTS Of the 17 screened mutations, four were identified in mosquitoes from the Bijagós: vgsc L995F (12.2%), N1570Y (6.2%) and A1746S (0.7%) and rdl A269G (1.1%). This study is the first to report the L995F knock-down resistance (kdr)-west allele in Anopheles melas on the Archipelago. An additional eight non-synonymous single-nucleotide polymorphisms were identified across the four genes which have not been described previously. The prevalences of the vgsc L995F and N1570Y mutations were higher on Bubaque Island than on the other islands in this study; Bubaque is the most populous island in the archipelago, with the greatest population mobility and connection to continental Guinea-Bissau. CONCLUSIONS This study provides the first surveillance data for genetic markers present in malaria vectors from islands across the Bijagós Archipelago. Overall prevalence of insecticide resistance mutations was found to be low. However, the identification of the vgsc L995F and N1570Y mutations associated with pyrethroid resistance warrants further monitoring. This is particularly important as the mainstay of malaria control on the islands is the use of pyrethroid insecticide-treated nets.
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Affiliation(s)
- Sophie Moss
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK.
| | - Elizabeth Pretorius
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Sainey Ceesay
- Medical Research Council, The Gambia (MRCG), Fajara, Gambia
| | - Harry Hutchins
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Eunice Teixeira da Silva
- Ministério de Saúde Pública, Bissau, Guinea-Bissau
- Projecto de Saúde Bandim, Bissau, Guinea-Bissau
| | | | - Robert T Jones
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Hristina Vasileva
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Jody Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Holly Acford-Palmer
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Emma Collins
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | | | - Sanjeev Krishna
- Clinical Academic Group, Institute for Infection and Immunity, St. George's University Hospitals NHS Foundation Trust-St. George's University of London, London, UK
- Centre de Recherches Médicales de Lambaréné (CERMEL), Lambaréné, Gabon
- Institut Für Tropenmedizin Universitätsklinikum Tübingen, Tübingen, Germany
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Anna Last
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
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Kormos A, Dimopoulos G, Bier E, Lanzaro GC, Marshall JM, James AA. Conceptual risk assessment of mosquito population modification gene-drive systems to control malaria transmission: preliminary hazards list workshops. Front Bioeng Biotechnol 2023; 11:1261123. [PMID: 37965050 PMCID: PMC10641379 DOI: 10.3389/fbioe.2023.1261123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 10/09/2023] [Indexed: 11/16/2023] Open
Abstract
The field-testing and eventual adoption of genetically-engineered mosquitoes (GEMs) to control vector-borne pathogen transmission will require them meeting safety criteria specified by regulatory authorities in regions where the technology is being considered for use and other locales that might be impacted. Preliminary risk considerations by researchers and developers may be useful for planning the baseline data collection and field research used to address the anticipated safety concerns. Part of this process is to identify potential hazards (defined as the inherent ability of an entity to cause harm) and their harms, and then chart the pathways to harm and evaluate their probability as part of a risk assessment. The University of California Malaria Initiative (UCMI) participated in a series of workshops held to identify potential hazards specific to mosquito population modification strains carrying gene-drive systems coupled to anti-parasite effector genes and their use in a hypothetical island field trial. The hazards identified were placed within the broader context of previous efforts discussed in the scientific literature. Five risk areas were considered i) pathogens, infections and diseases, and the impacts of GEMs on human and animal health, ii) invasiveness and persistence of GEMs, and interactions of GEMs with target organisms, iii) interactions of GEMs with non-target organisms including horizontal gene transfer, iv) impacts of techniques used for the management of GEMs and v) evolutionary and stability considerations. A preliminary hazards list (PHL) was developed and is made available here. This PHL is useful for internal project risk evaluation and is available to regulators at prospective field sites. UCMI project scientists affirm that the subsequent processes associated with the comprehensive risk assessment for the application of this technology should be driven by the stakeholders at the proposed field site and areas that could be affected by this intervention strategy.
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Affiliation(s)
- Ana Kormos
- Vector Genetics Laboratory, University of California, Davis, Davis, CA, United States
| | - George Dimopoulos
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Malaria Research Institute, Johns Hopkins University, Baltimore, MD, United States
| | - Ethan Bier
- Department of Cell and Developmental Biology, University of California, San Diego, San Diego, CA, United States
| | - Gregory C. Lanzaro
- Vector Genetics Laboratory, University of California, Davis, Davis, CA, United States
| | - John M. Marshall
- Divisions of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, Berkeley, CA, United States
| | - Anthony A. James
- Departments of Microbiology and Molecular Genetics and Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
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8
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Nagi SC, Oruni A, Weetman D, Donnelly MJ. RNA-Seq-Pop: Exploiting the sequence in RNA sequencing-A Snakemake workflow reveals patterns of insecticide resistance in the malaria vector Anopheles gambiae. Mol Ecol Resour 2023; 23:946-961. [PMID: 36695302 PMCID: PMC10568660 DOI: 10.1111/1755-0998.13759] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 11/12/2022] [Accepted: 01/06/2023] [Indexed: 01/26/2023]
Abstract
We provide a reproducible and scalable Snakemake workflow, called RNA-Seq-Pop, which provides end-to-end analysis of RNA sequencing data sets. The workflow allows the user to perform quality control, perform differential expression analyses and call genomic variants. Additional options include the calculation of allele frequencies of variants of interest, summaries of genetic variation and population structure, and genome-wide selection scans, together with clear visualizations. RNA-Seq-Pop is applicable to any organism, and we demonstrate the utility of the workflow by investigating pyrethroid resistance in selected strains of the major malaria mosquito, Anopheles gambiae. The workflow provides additional modules specifically for An. gambiae, including estimating recent ancestry and determining the karyotype of common chromosomal inversions. The Busia laboratory colony used for selections was collected in Busia, Uganda, in November 2018. We performed a comparative analysis of three groups: a parental G24 Busia strain; its deltamethrin-selected G28 offspring; and the susceptible reference strain Kisumu. Measures of genetic diversity reveal patterns consistent with that of laboratory colonization and selection, with the parental Busia strain exhibiting the highest nucleotide diversity, followed by the selected Busia offspring, and finally, Kisumu. Differential expression and variant analyses reveal that the selected Busia colony exhibits a number of distinct mechanisms of pyrethroid resistance, including the Vgsc-995S target-site mutation, upregulation of SAP genes, P450s and a cluster of carboxylesterases. During deltamethrin selections, the 2La chromosomal inversion rose in frequency (from 33% to 86%), supporting a previous link with pyrethroid resistance. RNA-Seq-Pop is hosted at: github.com/sanjaynagi/rna-seq-pop. We anticipate that the workflow will provide a useful tool to facilitate reproducible, transcriptomic studies in An. gambiae and other taxa.
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Affiliation(s)
- Sanjay C. Nagi
- Department of Vector BiologyLiverpool School of Tropical MedicineLiverpoolUK
| | | | - David Weetman
- Department of Vector BiologyLiverpool School of Tropical MedicineLiverpoolUK
| | - Martin J. Donnelly
- Department of Vector BiologyLiverpool School of Tropical MedicineLiverpoolUK
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Ravazi A, de Oliveira J, Madeira FF, Nunes GM, dos Reis YV, de Oliveira ABB, Azevedo LMS, Galvão C, de Azeredo-Oliveira MTV, da Rosa JA, Alevi KCC. Climate and Environmental Changes and Their Potential Effects on the Dynamics of Chagas Disease: Hybridization in Rhodniini (Hemiptera, Triatominae). INSECTS 2023; 14:378. [PMID: 37103193 PMCID: PMC10143345 DOI: 10.3390/insects14040378] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/24/2023] [Accepted: 03/01/2023] [Indexed: 06/19/2023]
Abstract
Chagas disease affects about eight million people. In view of the issues related to the influence of anthropogenic changes in the dynamics of the distribution and reproductive interaction of triatomines, we performed experimental crosses between species of the Rhodniini tribe in order to evaluate interspecific reproductive interactions and hybrid production capacity. Reciprocal crossing experiments were conducted among Rhodnius brethesi × R. pictipes, R. colombiensis × R. ecuadoriensis, R. neivai × R. prolixus, R. robustus × R. prolixus, R. montenegrensis × R. marabaensis; R. montenegrensis × R. robustus, R. prolixus × R. nasutus and R. neglectus × R. milesi. With the exception of crosses between R. pictipes ♀ × R. brethesi ♂, R. ecuadoriensis ♀ × R. colombiensis ♂ and R. prolixus ♀ × R. neivai ♂, all experimental crosses resulted in hybrids. Our results demonstrate that both allopatric and sympatric species produce hybrids, which can generate concern for public health agencies in the face of current anthropogenic events. Thus, we demonstrate that species of the Rhodniini tribe are capable of producing hybrids under laboratory conditions. These results are of great epidemiological importance and raise an important discussion about the influence of climatic and environmental interactions on Chagas disease dynamics.
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Affiliation(s)
- Amanda Ravazi
- Instituto de Biociências de Botucatu, Universidade Estadual Paulista “Júlio de Mesquita Filho” (UNESP), Rua Dr. Antônio Celso Wagner Zanin, 250, Distrito de Rubião Junior, Botucatu 18618-689, SP, Brazil
| | - Jader de Oliveira
- Laboratório de Entomologia em Saúde Pública, Faculdade de Saúde Pública, Universidade de São Paulo (USP), Av. Dr. Arnaldo 715, São Paulo 01246-904, SP, Brazil
| | - Fernanda Fernandez Madeira
- Laboratório de Biologia Celular, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista “Júlio de Mesquita Filho” (UNESP), Rua Cristóvão Colombo 2265, São José do Rio Preto 15054-000, SP, Brazil
| | - Giovana Menezes Nunes
- Laboratório de Biologia Celular, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista “Júlio de Mesquita Filho” (UNESP), Rua Cristóvão Colombo 2265, São José do Rio Preto 15054-000, SP, Brazil
| | - Yago Visinho dos Reis
- Instituto de Biociências de Botucatu, Universidade Estadual Paulista “Júlio de Mesquita Filho” (UNESP), Rua Dr. Antônio Celso Wagner Zanin, 250, Distrito de Rubião Junior, Botucatu 18618-689, SP, Brazil
| | - Ana Beatriz Bortolozo de Oliveira
- Laboratório de Biologia Celular, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista “Júlio de Mesquita Filho” (UNESP), Rua Cristóvão Colombo 2265, São José do Rio Preto 15054-000, SP, Brazil
| | - Luísa Martins Sensato Azevedo
- Laboratório de Biologia Celular, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista “Júlio de Mesquita Filho” (UNESP), Rua Cristóvão Colombo 2265, São José do Rio Preto 15054-000, SP, Brazil
| | - Cleber Galvão
- Laboratório Nacional e Internacional de Referência em Taxonomia de Triatomíneos, Instituto Oswaldo Cruz (FIOCRUZ), Av. Brazil 4365, Pavilhão Rocha Lima, Sala 505, Rio de Janeiro 21040-360, RJ, Brazil
| | - Maria Tercília Vilela de Azeredo-Oliveira
- Laboratório de Biologia Celular, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista “Júlio de Mesquita Filho” (UNESP), Rua Cristóvão Colombo 2265, São José do Rio Preto 15054-000, SP, Brazil
| | - João Aristeu da Rosa
- Laboratório de Parasitologia, Faculdade de Ciências Farmacêuticas, Universidade Estadual Paulista “Júlio de Mesquita Filho” (UNESP), Rodovia Araraquara-Jaú km 1, Araraquara 14801-902, SP, Brazil
| | - Kaio Cesar Chaboli Alevi
- Instituto de Biociências de Botucatu, Universidade Estadual Paulista “Júlio de Mesquita Filho” (UNESP), Rua Dr. Antônio Celso Wagner Zanin, 250, Distrito de Rubião Junior, Botucatu 18618-689, SP, Brazil
- Laboratório de Entomologia em Saúde Pública, Faculdade de Saúde Pública, Universidade de São Paulo (USP), Av. Dr. Arnaldo 715, São Paulo 01246-904, SP, Brazil
- Laboratório Nacional e Internacional de Referência em Taxonomia de Triatomíneos, Instituto Oswaldo Cruz (FIOCRUZ), Av. Brazil 4365, Pavilhão Rocha Lima, Sala 505, Rio de Janeiro 21040-360, RJ, Brazil
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10
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Pollegioni P, Persampieri T, Minuz RL, Bucci A, Trusso A, Martino SD, Leo C, Bruttini M, Ciolfi M, Waldvogel A, Tripet F, Simoni A, Crisanti A, Müller R. Introgression of a synthetic sex ratio distortion transgene into different genetic backgrounds of Anopheles coluzzii. INSECT MOLECULAR BIOLOGY 2023; 32:56-68. [PMID: 36251429 PMCID: PMC10092091 DOI: 10.1111/imb.12813] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
The development of genetically modified mosquitoes (GMM) and their subsequent field release offers innovative approaches for vector control of malaria. A non-gene drive self-limiting male-bias Ag(PMB)1 strain has been developed in a 47-year-old laboratory G3 strain of Anopheles gambiae s.l. When Ag(PMB)1 males are crossed to wild-type females, expression of the endonuclease I-PpoI during spermatogenesis causes the meiotic cleavage of the X chromosome in sperm cells, leading to fertile offspring with a 95% male bias. However, World Health Organization states that the functionality of the transgene could differ when inserted in different genetic backgrounds of Anopheles coluzzii which is currently a predominant species in several West-African countries and thus a likely recipient for a potential release of self-limiting GMMs. In this study, we introgressed the transgene from the donor Ag(PMB)1 by six serial backcrosses into two recipient colonies of An. coluzzii that had been isolated in Mali and Burkina Faso. Scans of informative Single Nucleotide Polymorphism (SNP) markers and whole-genome sequencing analysis revealed a nearly complete introgression of chromosomes 3 and X, but a remarkable genomic divergence in a large region of chromosome 2 between the later backcrossed (BC6) transgenic offspring and the recipient paternal strains. These findings suggested to extend the backcrossing breeding strategy beyond BC6 generation and increasing the introgression efficiency of critical regions that have ecological and epidemiological implications through the targeted selection of specific markers. Disregarding differential introgression efficiency, we concluded that the phenotype of the sex ratio distorter is stable in the BC6 introgressed An. coluzzii strains.
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Affiliation(s)
- Paola Pollegioni
- Research Institute on Terrestrial EcosystemsNational Research CouncilTerniItaly
- Genetics and Ecology Research CentrePolo d'Innovazione di Genomica, Genetica e BiologiaTerniItaly
| | - Tania Persampieri
- Genetics and Ecology Research CentrePolo d'Innovazione di Genomica, Genetica e BiologiaTerniItaly
| | - Roxana L. Minuz
- Genetics and Ecology Research CentrePolo d'Innovazione di Genomica, Genetica e BiologiaTerniItaly
| | - Alessandro Bucci
- Genetics and Ecology Research CentrePolo d'Innovazione di Genomica, Genetica e BiologiaTerniItaly
| | - Alessandro Trusso
- Genetics and Ecology Research CentrePolo d'Innovazione di Genomica, Genetica e BiologiaTerniItaly
| | - Salvatore Di Martino
- Genetics and Ecology Research CentrePolo d'Innovazione di Genomica, Genetica e BiologiaTerniItaly
| | - Chiara Leo
- Genetics and Ecology Research CentrePolo d'Innovazione di Genomica, Genetica e BiologiaTerniItaly
| | - Marco Bruttini
- Genetics and Ecology Research CentrePolo d'Innovazione di Genomica, Genetica e BiologiaTerniItaly
- Tuscan Centre of Precision Medicine, Department of Medicine, Surgery and NeurosciencesUniversity of SienaSienaItaly
| | - Marco Ciolfi
- Research Institute on Terrestrial EcosystemsNational Research CouncilTerniItaly
| | | | - Frédéric Tripet
- Centre for Applied Entomology and ParasitologyKeele UniversityNewcastle‐under‐LymeUK
| | - Alekos Simoni
- Genetics and Ecology Research CentrePolo d'Innovazione di Genomica, Genetica e BiologiaTerniItaly
| | - Andrea Crisanti
- Department of Molecular MedicineUniversity of PadovaPadovaItaly
| | - Ruth Müller
- Genetics and Ecology Research CentrePolo d'Innovazione di Genomica, Genetica e BiologiaTerniItaly
- Unit Entomology, Department of Biomedical SciencesInstitute of Tropical MedicineAntwerpBelgium
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11
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Tondossama N, Coulibaly ZI, Traoré I, Ako BA, Zoh DD, Virgillito C, Guindo-Coulibaly N, Serini P, Assouho FK, Dia I, Touré AO, Adja MA, Caputo B, della Torre A, Pichler V. High Levels of Admixture in Anopheles gambiae Populations from Côte d'Ivoire Revealed by Multilocus Genotyping. INSECTS 2022; 13:1090. [PMID: 36555000 PMCID: PMC9782310 DOI: 10.3390/insects13121090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 11/22/2022] [Accepted: 11/23/2022] [Indexed: 06/17/2023]
Abstract
Anopheles coluzzii and An. gambiae-the two most recently radiated species of the An. gambiae complex and the major Afrotropical malaria vector species-are identified by markers in the X-centromeric IGS rDNA region. Putative IGS-hybrids are rarely found in the field, except in restricted areas where genomic studies have led to the hypothesis that the observed IGS-patterns are due to cryptic taxa rather than to hybridization between the two species. We investigated the genome-wide levels of admixture in two villages in Côte d'Ivoire where high levels of IGS-hybrids have been detected, confirming unparalleled high frequencies in the coastal village. Genotyping of 24 Ancestry Informative Markers (AIMs) along the three chromosomes produced discordant results between the IGS-marker and the multilocus genotype obtained for AIMs across the whole genome (29%) as well as AIMs on chromosome-X (considered to be fundamental for species reproductive isolation) only (21%). Results highlight a complicated pattern of admixture that deserves deeper genomic analyses to understand better possible underlying causes (from extensive processes of hybridization to the existence of different cryptic taxa), and stress the need of developing advanced diagnostics for An. coluzzii, An. gambiae and putative new taxa, instrumental for assessing taxon-specific epidemiological characters.
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Affiliation(s)
- Naminata Tondossama
- Laboratoire de Biologie et Santé, UFR Biosciences, Université Félix Houphouet Boigny Cocody, Abidjan 01 BP V34, Côte d’Ivoire
- Entomology and Herpetology Unit, Institut Pasteur de Côte d’Ivoire, Abidjan 01 PB 490, Côte d’Ivoire
| | - Zanakoungo I. Coulibaly
- Entomology and Herpetology Unit, Institut Pasteur de Côte d’Ivoire, Abidjan 01 PB 490, Côte d’Ivoire
| | - Issouf Traoré
- Laboratoire de Biologie et Santé, UFR Biosciences, Université Félix Houphouet Boigny Cocody, Abidjan 01 BP V34, Côte d’Ivoire
- Entomology and Herpetology Unit, Institut Pasteur de Côte d’Ivoire, Abidjan 01 PB 490, Côte d’Ivoire
| | - Bérenger A. Ako
- Malaria Unit, Institut Pasteur de Côte d’Ivoire, Abidjan 01 PB 490, Côte d’Ivoire
| | - Danielle D. Zoh
- Laboratoire de Biologie et Santé, UFR Biosciences, Université Félix Houphouet Boigny Cocody, Abidjan 01 BP V34, Côte d’Ivoire
- Institut Pierre Richet/Institut National de Santé Publique, Bouaké 01 BP 1500, Côte d’Ivoire
| | - Chiara Virgillito
- Dipartimento di Sanità Pubblica e Malattie Infettive, Istituto Pasteur Italia-Fondazione Cenci-Bolognetti, Università di Roma “La Sapienza,” Piazzale Aldo Moro, 5, 00185 Rome, Italy
| | - Négnorogo Guindo-Coulibaly
- Laboratoire de Biologie et Santé, UFR Biosciences, Université Félix Houphouet Boigny Cocody, Abidjan 01 BP V34, Côte d’Ivoire
| | - Paola Serini
- Dipartimento di Sanità Pubblica e Malattie Infettive, Istituto Pasteur Italia-Fondazione Cenci-Bolognetti, Università di Roma “La Sapienza,” Piazzale Aldo Moro, 5, 00185 Rome, Italy
| | - Fabrice K. Assouho
- Institut Pierre Richet/Institut National de Santé Publique, Bouaké 01 BP 1500, Côte d’Ivoire
| | - Ibrahima Dia
- Pôle de Zoologie Médicale, Institut Pasteur de Dakar, 36 Avenue Pasteur, Dakar BP 220, Senegal
| | - Andre O. Touré
- Malaria Unit, Institut Pasteur de Côte d’Ivoire, Abidjan 01 PB 490, Côte d’Ivoire
| | - Maurice A. Adja
- Laboratoire de Biologie et Santé, UFR Biosciences, Université Félix Houphouet Boigny Cocody, Abidjan 01 BP V34, Côte d’Ivoire
- Institut Pierre Richet/Institut National de Santé Publique, Bouaké 01 BP 1500, Côte d’Ivoire
| | - Beniamino Caputo
- Dipartimento di Sanità Pubblica e Malattie Infettive, Istituto Pasteur Italia-Fondazione Cenci-Bolognetti, Università di Roma “La Sapienza,” Piazzale Aldo Moro, 5, 00185 Rome, Italy
| | - Alessandra della Torre
- Dipartimento di Sanità Pubblica e Malattie Infettive, Istituto Pasteur Italia-Fondazione Cenci-Bolognetti, Università di Roma “La Sapienza,” Piazzale Aldo Moro, 5, 00185 Rome, Italy
| | - Verena Pichler
- Dipartimento di Sanità Pubblica e Malattie Infettive, Istituto Pasteur Italia-Fondazione Cenci-Bolognetti, Università di Roma “La Sapienza,” Piazzale Aldo Moro, 5, 00185 Rome, Italy
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12
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Perfect association between spatial swarm segregation and the X-chromosome speciation island in hybridizing Anopheles coluzzii and Anopheles gambiae populations. Sci Rep 2022; 12:10800. [PMID: 35750745 PMCID: PMC9232630 DOI: 10.1038/s41598-022-14865-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 06/14/2022] [Indexed: 11/08/2022] Open
Abstract
The sibling species An. coluzzii and An. gambiae s.s. are major malaria vectors thought to be undergoing sympatric speciation with gene flow. In the absence of intrinsic post-zygotic isolation between the two taxa, speciation is thought possible through the association of assortative mating and genomic regions protected from gene flow by recombination suppression. Such genomic islands of speciation have been described in pericentromeric regions of the X, 2L and 3L chromosomes. Spatial swarm segregation plays a major role in assortative mating between sympatric populations of the two species and, given their importance for speciation, genes responsible for such pre-mating reproductive barriers are expected to be protected within divergence islands. In this study 2063 male and 266 female An. coluzzii and An. gambiae s.s. individuals from natural swarms in Burkina Faso, West Africa were sampled. These were genotyped at 16 speciation island SNPs, and characterized as non-hybrid individuals, F1 hybrids or recombinant F1+n backcrossed individuals. Their genotypes at each speciation island were associated with their participation in An. coluzzii and An. gambiae-like swarms. Despite extensive introgression between the two species, the X-island genotype of non-hybrid individuals (37.6%), F1 hybrids (0.1%) and F1+n recombinants (62.3%) of either sex perfectly associated to each swarm type. Associations between swarm type and the 3L and 2L speciation islands were weakened or broken down by introgression. The functional demonstration of a close association between spatial segregation behaviour and the X speciation island lends further support to sympatric speciation models facilitated by pericentric recombination suppression in this important species complex.
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13
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Hancock PA, Lynd A, Wiebe A, Devine M, Essandoh J, Wat'senga F, Manzambi EZ, Agossa F, Donnelly MJ, Weetman D, Moyes CL. Modelling spatiotemporal trends in the frequency of genetic mutations conferring insecticide target-site resistance in African mosquito malaria vector species. BMC Biol 2022; 20:46. [PMID: 35164747 PMCID: PMC8845222 DOI: 10.1186/s12915-022-01242-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 01/28/2022] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Resistance in malaria vectors to pyrethroids, the most widely used class of insecticides for malaria vector control, threatens the continued efficacy of vector control tools. Target-site resistance is an important genetic resistance mechanism caused by mutations in the voltage-gated sodium channel (Vgsc) gene that encodes the pyrethroid target-site. Understanding the geographic distribution of target-site resistance, and temporal trends across different vector species, can inform strategic deployment of vector control tools. RESULTS We develop a Bayesian statistical spatiotemporal model to interpret species-specific trends in the frequency of the most common resistance mutations, Vgsc-995S and Vgsc-995F, in three major malaria vector species Anopheles gambiae, An. coluzzii, and An. arabiensis over the period 2005-2017. The models are informed by 2418 observations of the frequency of each mutation in field sampled mosquitoes collected from 27 countries spanning western and eastern regions of Africa. For nine selected countries, we develop annual predictive maps which reveal geographically structured patterns of spread of each mutation at regional and continental scales. The results show associations, as well as stark differences, in spread dynamics of the two mutations across the three vector species. The coverage of ITNs was an influential predictor of Vgsc allele frequencies, with modelled relationships between ITN coverage and allele frequencies varying across species and geographic regions. We found that our mapped Vgsc allele frequencies are a significant partial predictor of phenotypic resistance to the pyrethroid deltamethrin in An. gambiae complex populations. CONCLUSIONS Our predictive maps show how spatiotemporal trends in insecticide target-site resistance mechanisms in African An. gambiae vary across individual vector species and geographic regions. Molecular surveillance of resistance mechanisms will help to predict resistance phenotypes and track their spread.
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Affiliation(s)
| | - Amy Lynd
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, L35QA, UK
| | | | - Maria Devine
- Big Data Institute, University of Oxford, Oxford, OX3 7LF, UK
| | - John Essandoh
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, L35QA, UK
| | - Francis Wat'senga
- Institut National de Recherche Biomédicale, PO Box 1192, Kinshasa, Democratic Republic of Congo
| | - Emile Z Manzambi
- Institut National de Recherche Biomédicale, PO Box 1192, Kinshasa, Democratic Republic of Congo
| | - Fiacre Agossa
- USAID President's Malaria Initiative, VectorLink Project, Abt Associates, 6130 Executive Blvd 16, Rockville, MD, 20852, USA
| | - Martin J Donnelly
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, L35QA, UK
| | - David Weetman
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, L35QA, UK
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14
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Ngom EHM, Virgillito C, Manica M, Rosà R, Pichler V, Sarleti N, Kassé I, Diallo M, della Torre A, Dia I, Caputo B. Entomological Survey Confirms Changes in Mosquito Composition and Abundance in Senegal and Reveals Discrepancies among Results by Different Host-Seeking Female Traps. INSECTS 2021; 12:692. [PMID: 34442258 PMCID: PMC8396443 DOI: 10.3390/insects12080692] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/26/2021] [Accepted: 07/28/2021] [Indexed: 11/16/2022]
Abstract
Mosquitoes-borne diseases are major public health issues particularly in Africa. Vector control interventions and human-made environmental/climatic changes significantly affect the distribution and abundance of vector species. We carried out an entomological survey targeting host-seeking mosquitos in two different ecological contexts-coastal and inland-in Senegal, by CDC-light and BG-sentinel traps. Results show high predominance of Culex quinquefasciatus (90%) and of Anopheles arabiensis within malaria vectors (46%), with mean numbers of females/trap/nights =8 and <1, respectively, reinforcing previous evidence of changes in species composition and abundance, highlighting thus increasing risk of transmission of filariasis and emerging arboviruses in the Senegambia region. From the methodological perspective, results show a higher specificity of BG traps for Cx. quinquefasciatus and of CDC traps for An. gambiae s.l. and highlight that, despite both traps target the host-seeking fraction of the population, they provide different patterns of species abundance, temporal dynamics and host-seeking activity, leading to possible misinterpretation of the species bionomics. This draws attention to the need of taking into account trapping performance, in order to provide realistic quantification of the number of mosquitoes per units of space and time, the crucial parameter for evaluating vector-human contact, and estimating risk of pathogen transmission.
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Affiliation(s)
- El Hadji Malick Ngom
- Medical Zoology Pole, Institut Pasteur de Dakar, Dakar 12500, Senegal; (E.H.M.N.); (I.K.); (M.D.)
| | - Chiara Virgillito
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Rome, Italy; (C.V.); (V.P.); (N.S.); (A.d.T.)
- Department of Biodiversity and Molecular Ecology, Edmund Mach Foundation, 38098 San Michele all’Adige, Italy; (M.M.); (R.R.)
| | - Mattia Manica
- Department of Biodiversity and Molecular Ecology, Edmund Mach Foundation, 38098 San Michele all’Adige, Italy; (M.M.); (R.R.)
- Center for Health Emergencies, Bruno Kessler Foundation, 380123 Trento, Italy
| | - Roberto Rosà
- Department of Biodiversity and Molecular Ecology, Edmund Mach Foundation, 38098 San Michele all’Adige, Italy; (M.M.); (R.R.)
- Center Agriculture Food Environment, University of Trento, 38098 San Michele all’Adige, Italy
| | - Verena Pichler
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Rome, Italy; (C.V.); (V.P.); (N.S.); (A.d.T.)
| | - Noemi Sarleti
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Rome, Italy; (C.V.); (V.P.); (N.S.); (A.d.T.)
| | - Isseu Kassé
- Medical Zoology Pole, Institut Pasteur de Dakar, Dakar 12500, Senegal; (E.H.M.N.); (I.K.); (M.D.)
| | - Mawlouth Diallo
- Medical Zoology Pole, Institut Pasteur de Dakar, Dakar 12500, Senegal; (E.H.M.N.); (I.K.); (M.D.)
| | - Alessandra della Torre
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Rome, Italy; (C.V.); (V.P.); (N.S.); (A.d.T.)
| | - Ibrahima Dia
- Medical Zoology Pole, Institut Pasteur de Dakar, Dakar 12500, Senegal; (E.H.M.N.); (I.K.); (M.D.)
| | - Beniamino Caputo
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Rome, Italy; (C.V.); (V.P.); (N.S.); (A.d.T.)
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15
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Genotyping of Ascaris spp. infecting humans and pigs in Italy, Slovakia and Colombia. INFECTION GENETICS AND EVOLUTION 2021; 94:104997. [PMID: 34252615 DOI: 10.1016/j.meegid.2021.104997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 07/05/2021] [Accepted: 07/07/2021] [Indexed: 11/20/2022]
Abstract
BACKGROUND The systematics and taxonomy of Ascaris lumbricoides and Ascaris suum, two of the world's most widespread nematodes, still represent a highly debated scientific issue. Two different transmission scenarios have been described according to endemicity: separated host-specific transmission cycles in endemic regions, and a single pool of infection shared by humans and pigs in non-endemic regions. The swine roundworm A. suum is now recognized as an important cause of human ascariasis also in endemic areas such as China, where cross-infections and hybridization have also been reported, as well as in non-endemic regions like Italy. This study aimed to investigate the molecular epidemiology of human and pig ascariasis in three countries representing different epidemiological scenarios: Italy as a non-endemic country, Colombia as an endemic country, and Slovakia as a non-endemic country, but with a poor socio-economic context linked to some focal populations of Roma settlements. MATERIALS AND METHODS A total of 237 nematodes were analysed: 46 from Colombia (13 from humans, 33 from pigs), 114 from Slovakia (20 from humans, 94 from pigs) and 77 from Italy (17 from humans and 60 from pigs). Genotyping by PCR-RFLP of nuclear (ITS) and sequencing of mitochondrial (cox1) target regions were performed. ITS genotypes were used to estimate the Hardy-Weinberg (HW) equilibrium according to hosts and country of origin. The partial cox1 sequences were used to analyse genetic polymorphisms according to hosts and country of origin, as well as to infer the network of haplotypes, their evolutionary relationships and geographical distribution. RESULTS 110 quality cox1 sequences were obtained. Haplotype network revealed three main groups corresponding to clade A, B and C. Clade C included most of the human cases from Italy, while those from Slovakia and Colombia were grouped in clade B. Ascaris from Italian and Colombian pigs showed HW equilibrium at the ITS marker, while disequilibrium was found in A. lumbricoides from Slovak pigs, which suggest a high unexpected amount of roundworms of human origin circulating also in pigs. CONCLUSIONS This study updates and extends the current understanding of Ascaris species and genotypes circulating in different epidemiological scenarios, with particular attention to the inclusion of human-derived Ascaris in the phylogenetic cluster C. Despite the evidence of HW equilibrium in the ITS in pig-derived Italian samples, the amount of genetic variation seems to support the existence of two closely related species.
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16
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Campos M, Rona LDP, Willis K, Christophides GK, MacCallum RM. Unravelling population structure heterogeneity within the genome of the malaria vector Anopheles gambiae. BMC Genomics 2021; 22:422. [PMID: 34103015 PMCID: PMC8185951 DOI: 10.1186/s12864-021-07722-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 05/18/2021] [Indexed: 12/26/2022] Open
Abstract
Background Whole genome re-sequencing provides powerful data for population genomic studies, allowing robust inferences of population structure, gene flow and evolutionary history. For the major malaria vector in Africa, Anopheles gambiae, other genetic aspects such as selection and adaptation are also important. In the present study, we explore population genetic variation from genome-wide sequencing of 765 An. gambiae and An. coluzzii specimens collected from across Africa. We used t-SNE, a recently popularized dimensionality reduction method, to create a 2D-map of An. gambiae and An. coluzzii genes that reflect their population structure similarities. Results The map allows intuitive navigation among genes distributed throughout the so-called “mainland” and numerous surrounding “island-like” gene clusters. These gene clusters of various sizes correspond predominantly to low recombination genomic regions such as inversions and centromeres, and also to recent selective sweeps. Because this mosquito species complex has been studied extensively, we were able to support our interpretations with previously published findings. Several novel observations and hypotheses are also made, including selective sweeps and a multi-locus selection event in Guinea-Bissau, a known intense hybridization zone between An. gambiae and An. coluzzii. Conclusions Our results present a rich dataset that could be utilized in functional investigations aiming to shed light onto An. gambiae s.l genome evolution and eventual speciation. In addition, the methodology presented here can be used to further characterize other species not so well studied as An. gambiae, shortening the time required to progress from field sampling to the identification of genes and genomic regions under unique evolutionary processes. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07722-y.
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Affiliation(s)
- Melina Campos
- Department of Life Sciences, Imperial College London, London, UK
| | - Luisa D P Rona
- Department of Life Sciences, Imperial College London, London, UK.,Department of Cell Biology, Embryology and Genetics, Federal University of Santa Catarina (UFSC), Florianópolis, Brazil.,National Institute of Science and Technology in Molecular Entomology, National Council for Scientific and Technological Development (INCT-EM, CNPq), Rio de Janeiro, Brazil
| | - Katie Willis
- Department of Life Sciences, Imperial College London, London, UK
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17
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Jeffries CL, Cansado-Utrilla C, Beavogui AH, Stica C, Lama EK, Kristan M, Irish SR, Walker T. Evidence for natural hybridization and novel Wolbachia strain superinfections in the Anopheles gambiae complex from Guinea. ROYAL SOCIETY OPEN SCIENCE 2021; 8:202032. [PMID: 33868697 PMCID: PMC8025300 DOI: 10.1098/rsos.202032] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 03/15/2021] [Indexed: 05/05/2023]
Abstract
Wolbachia, a widespread bacterium which can influence mosquito-borne pathogen transmission, has recently been detected within Anopheles (An.) species that are malaria vectors in Sub-Saharan Africa. Although studies have reported Wolbachia strains in the An. gambiae complex, apparent low density and prevalence rates require confirmation. In this study, wild Anopheles mosquitoes collected from two regions of Guinea were investigated. In contrast with previous studies, RNA was extracted from adult females (n = 516) to increase the chances for the detection of actively expressed Wolbachia genes, determine Wolbachia prevalence rates and estimate relative strain densities. Molecular confirmation of mosquito species and Wolbachia multilocus sequence typing (MLST) were carried out to analyse phylogenetic relationships of mosquito hosts and newly discovered Wolbachia strains. Strains were detected in An. melas (prevalence rate of 11.6%-16/138) and hybrids between An. melas and An. gambiae sensu stricto (prevalence rate of 40.0%-6/15) from Senguelen in the Maferinyah region. Furthermore, a novel high-density strain, termed wAnsX, was found in an unclassified Anopheles species. The discovery of novel Wolbachia strains (particularly in members, and hybrids, of the An. gambiae complex) provides further candidate strains that could be used for future Wolbachia-based malaria biocontrol strategies.
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Affiliation(s)
- Claire L. Jeffries
- Department of Disease Control, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Cintia Cansado-Utrilla
- Department of Disease Control, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Abdoul H. Beavogui
- Centre National de Formation et de Recherche en Santé Rurale de Mafèrinyah B.P. 2649, Conakry, Guinea
| | - Caleb Stica
- Department of Disease Control, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Eugene K. Lama
- Programme National de Lutte contre le Paludisme, Guinée, B.P. 6339 Conakry, Guinea
| | - Mojca Kristan
- Department of Disease Control, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Seth R. Irish
- The US President's Malaria Initiative and Entomology Branch, Centers for Disease Control and Prevention, Atlanta, GA 30329-4027, USA
| | - Thomas Walker
- Department of Disease Control, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
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18
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Caputo B, Pichler V, Bottà G, De Marco C, Hubbart C, Perugini E, Pinto J, Rockett KA, Miles A, Della Torre A. Novel genotyping approaches to easily detect genomic admixture between the major Afrotropical malaria vector species, Anopheles coluzzii and An. gambiae. Mol Ecol Resour 2021; 21:1504-1516. [PMID: 33590707 PMCID: PMC8252489 DOI: 10.1111/1755-0998.13359] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 02/05/2021] [Accepted: 02/11/2021] [Indexed: 11/28/2022]
Abstract
The two most efficient and most recently radiated Afrotropical vectors of human malaria - Anopheles coluzzii and An. gambiae - are identified by single-locus diagnostic PCR assays based on species-specific markers in a 4 Mb region on chromosome-X centromere. Inherently, these diagnostic assays cannot detect interspecific autosomal admixture shown to be extensive at the westernmost and easternmost extremes of the species range. The main aim of this study was to develop novel, easy-to-implement tools for genotyping An. coluzzii and An. gambiae-specific ancestral informative markers (AIMs) identified from the Anopheles gambiae 1000 genomes (Ag1000G) project. First, we took advantage of this large set of data in order to develop a multilocus approach to genotype 26 AIMs on all chromosome arms valid across the species range. Second, we tested the multilocus assay on samples from Guinea Bissau, The Gambia and Senegal, three countries spanning the westernmost hybridization zone, where conventional species diagnostic is problematic due to the putative presence of a novel "hybrid form". The multilocus assay was able to capture patterns of admixture reflecting those revealed by the whole set of AIMs and provided new original data on interspecific admixture in the region. Third, we developed an easy-to-use, cost-effective PCR approach for genotyping two AIMs on chromosome-3 among those included in the multilocus approach, opening the possibility for advanced identification of species and of admixed specimens during routine large scale entomological surveys, particularly, but not exclusively, at the extremes of the range, where WGS data highlighted unexpected autosomal admixture.
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Affiliation(s)
- Beniamino Caputo
- Dipartimento di Sanità Pubblica e Malattie Infettive, Istituto Pasteur Italia-Fondazione Cenci-Bolognetti, Università di Roma "Sapienza", Rome, Italy
| | - Verena Pichler
- Dipartimento di Sanità Pubblica e Malattie Infettive, Istituto Pasteur Italia-Fondazione Cenci-Bolognetti, Università di Roma "Sapienza", Rome, Italy
| | - Giordano Bottà
- Dipartimento di Sanità Pubblica e Malattie Infettive, Istituto Pasteur Italia-Fondazione Cenci-Bolognetti, Università di Roma "Sapienza", Rome, Italy.,Wellcome Centre for Human Genetics, University of Oxford, Headington, Oxford, UK
| | - Carlo De Marco
- Dipartimento di Sanità Pubblica e Malattie Infettive, Istituto Pasteur Italia-Fondazione Cenci-Bolognetti, Università di Roma "Sapienza", Rome, Italy
| | - Christina Hubbart
- Wellcome Centre for Human Genetics, University of Oxford, Headington, Oxford, UK
| | - Eleonora Perugini
- Dipartimento di Sanità Pubblica e Malattie Infettive, Istituto Pasteur Italia-Fondazione Cenci-Bolognetti, Università di Roma "Sapienza", Rome, Italy
| | - Joao Pinto
- Global Health & Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Kirk A Rockett
- Wellcome Centre for Human Genetics, University of Oxford, Headington, Oxford, UK
| | - Alistair Miles
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.,MRC Centre for Genomics and Global Health, University of Oxford, Oxford, UK
| | - Alessandra Della Torre
- Dipartimento di Sanità Pubblica e Malattie Infettive, Istituto Pasteur Italia-Fondazione Cenci-Bolognetti, Università di Roma "Sapienza", Rome, Italy
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19
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Grau-Bové X, Tomlinson S, O’Reilly AO, Harding NJ, Miles A, Kwiatkowski D, Donnelly MJ, Weetman D. Evolution of the Insecticide Target Rdl in African Anopheles Is Driven by Interspecific and Interkaryotypic Introgression. Mol Biol Evol 2020; 37:2900-2917. [PMID: 32449755 PMCID: PMC7530614 DOI: 10.1093/molbev/msaa128] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The evolution of insecticide resistance mechanisms in natural populations of Anopheles malaria vectors is a major public health concern across Africa. Using genome sequence data, we study the evolution of resistance mutations in the resistance to dieldrin locus (Rdl), a GABA receptor targeted by several insecticides, but most notably by the long-discontinued cyclodiene, dieldrin. The two Rdl resistance mutations (296G and 296S) spread across West and Central African Anopheles via two independent hard selective sweeps that included likely compensatory nearby mutations, and were followed by a rare combination of introgression across species (from A. gambiae and A. arabiensis to A. coluzzii) and across nonconcordant karyotypes of the 2La chromosomal inversion. Rdl resistance evolved in the 1950s as the first known adaptation to a large-scale insecticide-based intervention, but the evolutionary lessons from this system highlight contemporary and future dangers for management strategies designed to combat development of resistance in malaria vectors.
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Affiliation(s)
- Xavier Grau-Bové
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Sean Tomlinson
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Centre for Health Informatics, Computing and Statistics, Lancaster University, Lancaster, United Kingdom
| | - Andrias O O’Reilly
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, United Kingdom
| | - Nicholas J Harding
- Big Data Institute, University of Oxford, Li Ka Shing Centre for Health Information and Discovery, Oxford, United Kingdom
| | - Alistair Miles
- Big Data Institute, University of Oxford, Li Ka Shing Centre for Health Information and Discovery, Oxford, United Kingdom
- Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Dominic Kwiatkowski
- Big Data Institute, University of Oxford, Li Ka Shing Centre for Health Information and Discovery, Oxford, United Kingdom
- Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Martin J Donnelly
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Wellcome Sanger Institute, Hinxton, United Kingdom
| | - David Weetman
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
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20
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Hancock PA, Hendriks CJM, Tangena JA, Gibson H, Hemingway J, Coleman M, Gething PW, Cameron E, Bhatt S, Moyes CL. Mapping trends in insecticide resistance phenotypes in African malaria vectors. PLoS Biol 2020; 18:e3000633. [PMID: 32584814 PMCID: PMC7316233 DOI: 10.1371/journal.pbio.3000633] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 05/11/2020] [Indexed: 11/25/2022] Open
Abstract
Mitigating the threat of insecticide resistance in African malaria vector populations requires comprehensive information about where resistance occurs, to what degree, and how this has changed over time. Estimating these trends is complicated by the sparse, heterogeneous distribution of observations of resistance phenotypes in field populations. We use 6,423 observations of the prevalence of resistance to the most important vector control insecticides to inform a Bayesian geostatistical ensemble modelling approach, generating fine-scale predictive maps of resistance phenotypes in mosquitoes from the Anopheles gambiae complex across Africa. Our models are informed by a suite of 111 predictor variables describing potential drivers of selection for resistance. Our maps show alarming increases in the prevalence of resistance to pyrethroids and DDT across sub-Saharan Africa from 2005 to 2017, with mean mortality following insecticide exposure declining from almost 100% to less than 30% in some areas, as well as substantial spatial variation in resistance trends.
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Affiliation(s)
| | | | - Julie-Anne Tangena
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Harry Gibson
- Big Data Institute, University of Oxford, Oxford, United Kingdom
| | - Janet Hemingway
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Michael Coleman
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Peter W. Gething
- Telethon Kids Institute, Perth Children's Hospital, Perth, Australia
- Curtin University, Bentley, Perth, Australia
| | - Ewan Cameron
- Big Data Institute, University of Oxford, Oxford, United Kingdom
| | - Samir Bhatt
- Department of Infectious Disease Epidemiology, Imperial College, St Mary’s Hospital, London, United Kingdom
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21
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Monitoring and molecular profiling of contemporary insecticide resistance status of malaria vectors in Guinea-Bissau. Acta Trop 2020; 206:105440. [PMID: 32156617 DOI: 10.1016/j.actatropica.2020.105440] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 03/06/2020] [Accepted: 03/06/2020] [Indexed: 01/23/2023]
Abstract
Despite reduction in the prevalence of malaria, Guinea-Bissau (GB) is still widely affected by the disease that is primarily vectored by Anopheles gambiae s.l. mosquitoes. Monitoring mosquito susceptibility and investigating the insecticide resistance status is an integral part of malaria control actions. Here, mosquito populations from five regions of GB: Bafatá, Bissau, Buba, Cacheu and Gabu were monitored for species ID and insecticide resistance, using diagnostic and intensity WHO bioassays, as well as molecular assays. Phenotypic and molecular identification of species showed the presence of An. gambiae s.s. (S form), An. coluzzii (M form) and An. arabiensis, as well as rare An. arabiensis/ An. gambiae hybrids. Resistance to permethrin and deltamethrin was found in all Anopheles populations assayed, with the intensity of resistance for permethrin being moderate to high, as confirmed by bioassays performed at concentration intensities of 5X and 10X. Consistent to these findings, molecular analysis showed a higher frequency of knock-down resistance (kdr) mutations (L1014F, L1014S, reaching > 90% in some areas) compared to previous studies in the same region, as well as detected for the first time the presence of the super kdr mutation (N1575Y) in GB. The "iAche" (G119S) resistance mutation was also found in GB in low frequencies (up to 12.41%). Additionally, the synergistic PBO-permethrin bioassays suggested partial involvement of non target (metabolic and/or reduced penetration) resistance mechanism. Expression analysis of known pyrethroid metabolisers indicated the slight overexpression and possible association of the cytochrome P450s CYP6Z1, CYP4G16 with the pyrethroid resistance phenotype. The findings should guide future evidence-based resistance management strategies in GB.
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22
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Lee Y, Schmidt H, Collier TC, Conner WR, Hanemaaijer MJ, Slatkin M, Marshall JM, Chiu JC, Smartt CT, Lanzaro GC, Mulligan FS, Cornel AJ. Genome-wide divergence among invasive populations of Aedes aegypti in California. BMC Genomics 2019; 20:204. [PMID: 30866822 PMCID: PMC6417271 DOI: 10.1186/s12864-019-5586-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 03/05/2019] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND In the summer of 2013, Aedes aegypti Linnaeus was first detected in three cities in central California (Clovis, Madera and Menlo Park). It has now been detected in multiple locations in central and southern CA as far south as San Diego and Imperial Counties. A number of published reports suggest that CA populations have been established from multiple independent introductions. RESULTS Here we report the first population genomics analyses of Ae. aegypti based on individual, field collected whole genome sequences. We analyzed 46 Ae. aegypti genomes to establish genetic relationships among populations from sites in California, Florida and South Africa. Based on 4.65 million high quality biallelic SNPs, we identified 3 major genetic clusters within California; one that includes all sample sites in the southern part of the state (South of Tehachapi mountain range) plus the town of Exeter in central California and two additional clusters in central California. CONCLUSIONS A lack of concordance between mitochondrial and nuclear genealogies suggests that the three founding populations were polymorphic for two main mitochondrial haplotypes prior to being introduced to California. One of these has been lost in the Clovis populations, possibly by a founder effect. Genome-wide comparisons indicate extensive differentiation between genetic clusters. Our observations support recent introductions of Ae. aegypti into California from multiple, genetically diverged source populations. Our data reveal signs of hybridization among diverged populations within CA. Genetic markers identified in this study will be of great value in pursuing classical population genetic studies which require larger sample sizes.
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Affiliation(s)
- Yoosook Lee
- Vector Genetics Laboratory, Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California Davis, Davis, CA 95616 USA
| | - Hanno Schmidt
- Vector Genetics Laboratory, Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California Davis, Davis, CA 95616 USA
| | - Travis C. Collier
- Daniel K. Inouye US Pacific Basin Agricultural Research Center (PBARC), United States Department of Agriculture, Agricultural Research Service, Hilo, Hawaii USA
| | - William R. Conner
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California - Davis, Davis, CA 95616 USA
| | - Mark J. Hanemaaijer
- Vector Genetics Laboratory, Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California Davis, Davis, CA 95616 USA
| | - Montgomery Slatkin
- Department of Integrative Biology, University of California - Berkeley, Berkeley, CA 94720 USA
| | - John M. Marshall
- School of Public Health, University of California - Berkeley, Berkeley, CA 94720 USA
| | - Joanna C. Chiu
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California - Davis, Davis, CA 95616 USA
| | - Chelsea T. Smartt
- Florida Medical Entomology Laboratory, Institute of Food and Agricultural Sciences, University of Florida, Vero Beach, FL 32962 USA
| | - Gregory C. Lanzaro
- Vector Genetics Laboratory, Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California Davis, Davis, CA 95616 USA
| | | | - Anthony J. Cornel
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California - Davis, Davis, CA 95616 USA
- Mosquito Control Research Laboratory, Kearney Agricultural Center, Department of Entomology and Nematology, University of California -, Davis, CA 95616 USA
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23
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Duffy CW, Amambua-Ngwa A, Ahouidi AD, Diakite M, Awandare GA, Ba H, Tarr SJ, Murray L, Stewart LB, D'Alessandro U, Otto TD, Kwiatkowski DP, Conway DJ. Multi-population genomic analysis of malaria parasites indicates local selection and differentiation at the gdv1 locus regulating sexual development. Sci Rep 2018; 8:15763. [PMID: 30361631 PMCID: PMC6202401 DOI: 10.1038/s41598-018-34078-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 10/11/2018] [Indexed: 02/08/2023] Open
Abstract
Parasites infect hosts in widely varying environments, encountering diverse challenges for adaptation. To identify malaria parasite genes under locally divergent selection across a large endemic region with a wide spectrum of transmission intensity, genome sequences were obtained from 284 clinical Plasmodium falciparum infections from four newly sampled locations in Senegal, The Gambia, Mali and Guinea. Combining these with previous data from seven other sites in West Africa enabled a multi-population analysis to identify discrete loci under varying local selection. A genome-wide scan showed the most exceptional geographical divergence to be at the early gametocyte gene locus gdv1 which is essential for parasite sexual development and transmission. We identified a major structural dimorphism with alternative 1.5 kb and 1.0 kb sequence deletions at different positions of the 3'-intergenic region, in tight linkage disequilibrium with the most highly differentiated single nucleotide polymorphism, one of the alleles being very frequent in Senegal and The Gambia but rare in the other locations. Long non-coding RNA transcripts were previously shown to include the entire antisense of the gdv1 coding sequence and the portion of the intergenic region with allelic deletions, suggesting adaptive regulation of parasite sexual development and transmission in response to local conditions.
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Affiliation(s)
- Craig W Duffy
- Pathogen Molecular Biology Department, London School of Hygiene and Tropical Medicine, Keppel St, London, UK
| | | | | | - Mahamadou Diakite
- Malaria Research and Training Center, University of Bamako, Bamako, Mali
| | - Gordon A Awandare
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP) and Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Legon, Ghana
| | - Hampate Ba
- Institut National de Recherches en Santé Publique (INRSP), Nouakchott, Mauritania
| | - Sarah J Tarr
- Pathogen Molecular Biology Department, London School of Hygiene and Tropical Medicine, Keppel St, London, UK
| | - Lee Murray
- Pathogen Molecular Biology Department, London School of Hygiene and Tropical Medicine, Keppel St, London, UK
| | - Lindsay B Stewart
- Pathogen Molecular Biology Department, London School of Hygiene and Tropical Medicine, Keppel St, London, UK
| | - Umberto D'Alessandro
- MRC Gambia Unit, Fajara, The Gambia
- Disease Control Department, London School of Hygiene and Tropical Medicine, Keppel St, London, UK
| | - Thomas D Otto
- Malaria Programme, Wellcome Trust Sanger Institute, Cambridge, UK
| | | | - David J Conway
- Pathogen Molecular Biology Department, London School of Hygiene and Tropical Medicine, Keppel St, London, UK.
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24
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Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017; 552:96-100. [PMID: 29186111 DOI: 10.1038/nature24995] [Citation(s) in RCA: 221] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 11/01/2017] [Indexed: 12/20/2022]
Abstract
The sustainability of malaria control in Africa is threatened by the rise of insecticide resistance in Anopheles mosquitoes, which transmit the disease. 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.
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25
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Pombi M, Kengne P, Gimonneau G, Tene-Fossog B, Ayala D, Kamdem C, Santolamazza F, Guelbeogo WM, Sagnon N, Petrarca V, Fontenille D, Besansky NJ, Antonio-Nkondjio C, Dabiré RK, Della Torre A, Simard F, Costantini C. Dissecting functional components of reproductive isolation among closely related sympatric species of the Anopheles gambiae complex. Evol Appl 2017; 10:1102-1120. [PMID: 29151864 PMCID: PMC5680640 DOI: 10.1111/eva.12517] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 07/10/2017] [Indexed: 01/10/2023] Open
Abstract
Explaining how and why reproductive isolation evolves and determining which forms of reproductive isolation have the largest impact on the process of population divergence are major goals in the study of speciation. By studying recent adaptive radiations in incompletely isolated taxa, it is possible to identify barriers involved at early divergence before other confounding barriers emerge after speciation is complete. Sibling species of the Anopheles gambiae complex offer opportunities to provide insights into speciation mechanisms. Here, we studied patterns of reproductive isolation among three taxa, Anopheles coluzzii, An. gambiae s.s. and Anopheles arabiensis, to compare its strength at different spatial scales, to dissect the relative contribution of pre‐ versus postmating isolation, and to infer the involvement of ecological divergence on hybridization. Because F1 hybrids are viable, fertile and not uncommon, understanding the dynamics of hybridization in this trio of major malaria vectors has important implications for how adaptations arise and spread across the group, and in planning studies of the safety and efficacy of gene drive as a means of malaria control. We first performed a systematic review and meta‐analysis of published surveys reporting on hybrid prevalence, showing strong reproductive isolation at a continental scale despite geographically restricted exceptions. Second, we exploited our own extensive field data sets collected at a regional scale in two contrasting environmental settings, to assess: (i) levels of premating isolation; (ii) spatio/temporal and frequency‐dependent dynamics of hybridization, (iii) relationship between reproductive isolation and ecological divergence and (iv) hybrid viability penalty. Results are in accordance with ecological speciation theory predicting a positive association between the strength of reproductive isolation and degree of ecological divergence, and indicate that postmating isolation does contribute to reproductive isolation among these species. Specifically, only postmating isolation was positively associated with ecological divergence, whereas premating isolation was correlated with phylogenetic distance.
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Affiliation(s)
- Marco Pombi
- Dipartimento di Sanità Pubblica e Malattie InfettiveUniversità di Roma "Sapienza"RomeItaly.,Istituto Pasteur Italia-Fondazione Cenci-Bolognetti Rome Italy
| | - Pierre Kengne
- Institut de Recherche pour le Développement (IRD) UMR MIVEGEC (University of Montpellier, CNRS 5290 IRD 224) Centre IRD de Montpellier Montpellier France.,Organisation de Coordination pour la lutte contre les Endemies en Afrique Centrale (OCEAC) Yaoundé Cameroon
| | | | - Billy Tene-Fossog
- Institut de Recherche pour le Développement (IRD) UMR MIVEGEC (University of Montpellier, CNRS 5290 IRD 224) Centre IRD de Montpellier Montpellier France.,Organisation de Coordination pour la lutte contre les Endemies en Afrique Centrale (OCEAC) Yaoundé Cameroon
| | - Diego Ayala
- Institut de Recherche pour le Développement (IRD) UMR MIVEGEC (University of Montpellier, CNRS 5290 IRD 224) Centre IRD de Montpellier Montpellier France.,Centre International de Recherches Médicales de Franceville Franceville Gabon
| | - Colince Kamdem
- Department of Entomology University of California Riverside CA USA
| | - Federica Santolamazza
- Dipartimento di Sanità Pubblica e Malattie InfettiveUniversità di Roma "Sapienza"RomeItaly.,Istituto Pasteur Italia-Fondazione Cenci-Bolognetti Rome Italy
| | | | - N'Falé Sagnon
- Centre National de Recherche et Formation sur le Paludisme (CNRFP) Ouagadougou Burkina Faso
| | - Vincenzo Petrarca
- Dipartimento di Sanità Pubblica e Malattie InfettiveUniversità di Roma "Sapienza"RomeItaly.,Istituto Pasteur Italia-Fondazione Cenci-Bolognetti Rome Italy
| | - Didier Fontenille
- Institut de Recherche pour le Développement (IRD) UMR MIVEGEC (University of Montpellier, CNRS 5290 IRD 224) Centre IRD de Montpellier Montpellier France.,Institut Pasteur du Cambodge Phnom Penh Cambodia
| | - Nora J Besansky
- Eck Institute for Global Health & Department of Biological Sciences University of Notre Dame Notre Dame IN USA
| | | | - Roch Kounbobr Dabiré
- Institut de Recherche en Sciences de la Santé (IRSS) Bobo-Dioulasso Burkina Faso
| | - Alessandra Della Torre
- Dipartimento di Sanità Pubblica e Malattie InfettiveUniversità di Roma "Sapienza"RomeItaly.,Istituto Pasteur Italia-Fondazione Cenci-Bolognetti Rome Italy
| | - Frédéric Simard
- Institut de Recherche pour le Développement (IRD) UMR MIVEGEC (University of Montpellier, CNRS 5290 IRD 224) Centre IRD de Montpellier Montpellier France.,Organisation de Coordination pour la lutte contre les Endemies en Afrique Centrale (OCEAC) Yaoundé Cameroon.,Institut de Recherche en Sciences de la Santé (IRSS) Bobo-Dioulasso Burkina Faso
| | - Carlo Costantini
- Institut de Recherche pour le Développement (IRD) UMR MIVEGEC (University of Montpellier, CNRS 5290 IRD 224) Centre IRD de Montpellier Montpellier France.,Organisation de Coordination pour la lutte contre les Endemies en Afrique Centrale (OCEAC) Yaoundé Cameroon.,Institut de Recherche en Sciences de la Santé (IRSS) Bobo-Dioulasso Burkina Faso
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