Population biology, genetic diversity, and insecticide resistance profile of malaria vector Anopheles funestus in Tanzania

Odero, Joel Ouma (2024) Population biology, genetic diversity, and insecticide resistance profile of malaria vector Anopheles funestus in Tanzania. PhD thesis, University of Glasgow.

Abstract

Anopheles mosquitoes present a major public health challenge in sub Saharan Africa, notably as vectors of malaria killing over 600,000 people annually. In parts of the east and southern Africa regions, one species in the Anopheles funestus group, An. funestus has established itself as an exceptionally dominant vector in some areas and is currently responsible for 9 out of every 10 malaria transmission events. Despite this apparent public health importance, research on this vector has historically lagged behind those of other malaria vectors in the An. gambiae complex, leaving many aspects of its population biology uncertain. For instance, the genetic diversity of this vector across its ecological range in Africa is poorly understood making it difficult to decipher true population structure, patterns of gene flow, and signatures of selection. These are crucial for understanding the distribution of insecticide resistance genes, how vector populations are structured in space for targeted interventions and devising sustainable insecticide-based vector control approaches. Additionally, information on this vector's resistance status and behavioural data is very limited across Africa, partly due to difficulties with laboratory colonization and the unresolved aspects of its aquatic ecology. Attempts at controlling this vector require deliberate efforts to understand these aspects that might impact their response to vector control interventions.

This thesis presents the first large-scale genomic survey and population biology study in An. funestus populations in Tanzania. My overarching aim was to provide a comprehensive understanding of the population biology, insecticide resistance, and population genetic structure of the major malaria vector An. funestus in mainland Tanzania. To achieve this, I began by conducting a wide-scale population sampling in 11 locations in Tanzania, purposively selected to encompass variations in vector ecology and climatic conditions. These samples were individually whole genome sequenced and analysed to elucidate the population genetic diversity and gene flow patterns of An. funestus across Tanzania. This analysis demonstrated the existence of two genetically differentiated An. funestus populations; the inland high-altitude populations, and coastal low-altitude populations, potentially separated by an area of unsuitable climatic conditions, geographically coincident with the eastern arm of the Great Rift Valley. These genetic populations showed demographic differences and divergence, likely due to differentiation at insecticide resistance genes reflecting diverse historical and contemporary dynamics. The genomic analysis also serendipitously led to the first discovery of knockdown resistance (kdr) in An. funestus mosquitoes. The kdr mutations were found at high frequency only in one location, the Morogoro region. One of the mutations, kdr L976F was strongly associated with survivorship to exposure to DDT insecticide, while no clear association was noted with a pyrethroid insecticide (deltamethrin). An urgent follow-up study is required to monitor the evolution of kdr and determine whether kdr confers resistance phenotypes to other widely used pyrethroids, such as permethrin, and alpha-cypermethrin, as well as other insecticide families.

Alongside this genomic survey, I characterised the different Tanzanian An. funestus populations by measuring their behaviour, ecology and level of resistance to insecticides. This analysis revealed widespread pyrethroid resistance, but susceptibility was restored with PBO preexposure. The insecticide resistance genotype patterns indicated a north-south gene flow restriction. Additionally, while the biting behaviour of An. funestus, level of anthropophily, and age structure were similar across the genetic populations, differences were noted in the prevalence of Plasmodium infections, mosquito sizes, and fecundity between the inland and coastal genetic populations. Further research is needed to determine whether these phenotypic and demographic differences are a consequence of, or contribute to, the observed genetic separation between the inland and coastal populations of An. funestus.

Taken together, this thesis provides a deeper understanding of the population biology and genetic diversity of An. funestus in Tanzania. The whole genome sequence dataset developed in this thesis, publicly available at the European Nucleotide Archive (study number PRJEB2141), represents the largest data on a disease vector in Tanzania to date and provides a crucial resource in the continued monitoring of the vector. The population diversity disconnectedness revealed here should be considered when implementing insecticide resistance management and the future rollout of novel genetic-based vector control approaches. It is important for future research to examine the epidemiological relevance of this discontinuity in gene flow and whether these populations have different malaria transmission abilities.

• Item Type: Thesis (PhD)
• Qualification Level: Masters
• Additional Information: Supported by funding from the Bill and Melinda Gates Foundation.
• Subjects: Q Science > QH Natural history > QH301 Biology; Q Science > QR Microbiology
• Colleges/Schools: College of Medical Veterinary and Life Sciences > School of Biodiversity, One Health & Veterinary Medicine
• Funder's Name: Bill and Melinda Gates Foundation
• Supervisor's Name: Baldini, Dr. Francesco, Okumu, Professor Fredros and Ferguson, Professor Heather
• Date of Award: 2024
• Depositing User: Theses Team
• Unique ID: glathesis:2024-84671
• Copyright: Copyright of this thesis is held by the author.
• Date Deposited: 08 Nov 2024 12:12
• Last Modified: 08 Nov 2024 14:28
• Thesis DOI: 10.5525/gla.thesis.84671
• URI: https://theses.gla.ac.uk/id/eprint/84671