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Evaluation of Nanopore sequencing for interrogating mosquito pools from surveillance systems

Nascimento, Cátia Lagartinho do


Cátia Lagartinho do Nascimento


Daniel Tonge

Frederic Tripet


Vector-borne diseases are responsible for 17% of all infectious diseases worldwide and contribute to more than 700 000 deaths annually, mainly in sub-Saharan countries. Vector surveillance is a crucial element of vector control programmes to assure they remain effective. Genomic surveillance provides valuable information on species identification but is often neglected due to the associated costs and training demands. This thesis focused on the use of the MinION sequencer for interrogating mixed pools from surveillance systems, with minimal bioinformatic analysis requirements to empower African labs and push towards routine genomic analysis. Mosquito pools were designed using different species that act as vectors for main diseases, mimicking possible content of field traps. Some pools included DNA from pathogens carried by these vectors responsible for malaria and filariasis. It was observed that a targeted approach was preferable to whole genome sequencing in estimating species abundance, allowing for cost reduction and detection of target site mutations as well. Different bioinformatic pipelines were tested to verify the accuracy of multiple tools and the training level requirements. The use of the Minimap2 software coupled with Samtools provided the best results and it is suitable to deploy in low-income areas. The MinION device was shown to be effective for interrogating mosquito pools, offering a solution for challenges in vector surveillance in sub-Saharan Africa. Future studies should be done with field-collected mosquitoes and sequencing performed locally to evaluate feasibility. More species of mosquitoes and pathogens should be included as well as the use of RNA sequencing for viral detection.


Nascimento, C. L. D. (2024). Evaluation of Nanopore sequencing for interrogating mosquito pools from surveillance systems. (Thesis). Keele University. Retrieved from

Thesis Type Thesis
Deposit Date Jun 20, 2024
Public URL
Additional Information Embargo on access until 30 April 2027 - The thesis is due for publication, or the author is actively seeking to publish this material.
Award Date 2024-06

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