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bioRxiv · 10.1101/2024.02.06.579110

A rapid, cost-effective, colorimetric LAMP assay (CLASS) for detecting invasive malaria vector, Anopheles stephensi

Rafferty, C.·Raise, G.·Scaife, J.·Abongo, B.·Omondi, S.·Milanoi, S.·Muchoki, M.·Onyango, B.·Ochomo, E.·Zohdy, S.
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Abstract

Anopheles stephensi, an invasive malaria vector in Africa, has the potential to impact the landscape of malaria on the continent, threatening to put an additional 126 million people per year at risk of malaria, largely in peri-urban/urban areas. To accelerate the early detection and rapid response to An. stephensi and ensure no gains made in malaria control and elimination are lost, it is critical to confirm the presence of the species and the geographic extent of its spread to inform control. However, morphological identification may be misinterpreted if specimens are damaged and existing molecular species confirmation assays require specialized laboratory equipment and training and may be challenging to interpret, requiring additional sequencing confirmation. A colorimetric rapid loop-mediated isothermal amplification (LAMP) assay for molecular An. stephensi species identification was developed and optimized. The colorimetric assay requires only a heat source and reagents and can be used with or without DNA extraction resulting in positive color change in 30-35 minutes. To determine analytical sensitivity, a 1:10 dilution series of the DNA extract was conducted showing 100% assay sensitivity down to 0.003 nanograms. To determine specificity, three different An. stephensi laboratory strains (STE2, SDA 500, UCI), 8 other Anopheles mosquito species, and Aedes aegypti were compared, and the results indicated 100% specificity across these species. To determine use without the need for DNA extraction, samples evaluated included a single mosquito leg, whole adult or larval mosquitoes, and pooled DNA extract from several mosquito species. A total of 1687 individual reactions were tested during optimization and all LAMP assay results were compared against the conventional PCR assay and confirmed through Sanger sequencing. To validate the optimized assay on wild caught specimens, DNA extracted from 12 wild caught, sequence-confirmed An. stephensi from Marsabit, Kenya, were tested and the colorimetric assay was accurate in identifying all of the specimens as An. stephensi. The assay described presents an opportunity to accelerate An. stephensi molecular identification in new and existing locations in Africa, within its endemic range, and globally. These findings present a simple, rapid, unique alternative to existing PCR and sequencing-based An. stephensi species identification and confirmation strategies. With additional field validation studies, molecular screening tools like the colorimetric LAMP-based An. stephensi species identification (CLASS) assay fill an important gap of rapid confirmation of this invasive vector and presents an ideal opportunity to better understand the spread of the species in Africa and other recently invaded areas, thus accelerating a response to mitigate its long-term impacts on malaria on the continent.

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Rafferty, C., Raise, G., Scaife, J., Abongo, B., Omondi, S., Milanoi, S., Muchoki, M., Onyango, B., Ochomo, E., Zohdy, S.. 2024-02-07. A rapid, cost-effective, colorimetric LAMP assay (CLASS) for detecting invasive malaria vector, Anopheles stephensi. https://doi.org/10.1101/2024.02.06.579110

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