Anopheles diversity monitor...

Beschreibung

As part of an ongoing Anopheles diversity monitoring project in Madagascar, we aim to provide a fine-scale understanding of species composition, population structure and Plasmodium transmission rates from targeted sequencing of 50,000 individual mosquitoes.

The primary aim of the project is to improve our understanding of Anopheles species diversity, population structure, and malaria transmission across Africa. In collaboration with partners working in malaria endemic countries, 500,000 mosquitoes will be sequenced using a targeted amplicon panel known as ANOSPP.

ANOSPP is a multi-locus amplicon sequencing panel, targeting 62 short nuclear loci in the generic Anopheles genome, as well as 2 mitochondrial loci in the generic Plasmodium genome. The panel uses a highly multiplexed two-step PCR that first amplifies target sequences and then adds unique barcodes, making it possible to pool amplicons from hundreds of mosquitoes into a single Illumina MiSeq sequencing run (Makunin et al. 2022). Sequences are de-multiplexed using these barcodes and analysed using k-mer approaches to assign a species identity for each individual (Boddé et al. 2022). The sequencing data that results from each individual mosquito reveals its species, population structure, and whether Plasmodium parasites are present – key information for vector control endeavours.

In Madagascar, mosquitoes are collected from more than 120 locations across the country, in collaboration with the National Malaria Control Program and other partners such as President Malaria Initiative EVOLVE programme, allowing for comparison of species composition, population structure and transmission intensity in space and across habitats. For a limited number of sites, samples are collected multiple times, allowing to study temporal variation and population continuity through the seasons. All collected samples will be accompanied by rich metadata, such as collection method, insecticide resistance status, etc, as outlined in the ANOSPP manifest.

This valuable dataset will be used to develop standardised analyses from ANOSPP sequencing data that can be used to inform national and international authorities concerned with vector control. Moreover, we will explore in which ways ANOSPP sequencing data can be used for population genetic analyses, like inversion genotyping, estimating genetic diversity and estimating spatial and temporal connectedness.

The ANOSPP results will also be used to select individuals from major and minor vector species for short-read whole genome sequencing to study their population structure and emerging and existing insecticide resistance in more detail.

This project is led by Diego Ayala from Institut Pasteur de Madagascar and Mara Lawniczak from the Wellcome Sanger Institute in the UK. Marilou Boddé (LIB and IPM) is responsible for data analysis. The project is funded by the Bill and Melinda Gates foundation.

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