A genomic toolkit for surveillance and elimination of the principal malaria vectors in Southeast Asia.

Dennis, T. P. W.; Vantaux, A.; Kobylinski, K. C.; Alam, M. S.; Witkowski, B.; Al-Amin, H. M.; Lobo, N. F.; Wilson, A. J.; Drury, E.; Goncalves, S.; Harding, N. J.; Hernandez-Koutoucheva, A.; Kwiatkowski, D.; Miles, A. J.; Donnelly, M. J.; St Laurent, B.

doi:10.64898/2025.12.04.691712

bioRxiv · 10.64898/2025.12.04.691712

A genomic toolkit for surveillance and elimination of the principal malaria vectors in Southeast Asia.

Dennis, T. P. W.·Vantaux, A.·Kobylinski, K. C.·Alam, M. S.·Witkowski, B.·Al-Amin, H. M.·Lobo, N. F.·Wilson, A. J.·Drury, E.·Goncalves, S.·Harding, N. J.·Hernandez-Koutoucheva, A.·Kwiatkowski, D.·Miles, A. J.·Donnelly, M. J.·St Laurent, B.

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Abstract

While substantial progress has been made toward malaria elimination in Southeast Asia, major challenges remain. The principal mosquito vectors, Anopheles dirus and Anopheles minimus, inhabit diverse ecological niches and exhibit a wide range of behavioural and physiological insecticide resistance phenotypes, complicating vector control efforts. In Africa, genomic surveillance has transformed our understanding of vector evolution and resistance, supported by open-access tools and data. Comparable resources for Southeast Asian vectors remain limited. Here, we release Adir1.0, a curated, analysis-ready catalog of 540 An. dirus whole-genome sequences, accessible for interactive cloud-based analysis via the malariagen-data-python application programming interface (API). Alongside, we provide an updated Amin1.0 API to enhance functionality and usability, enabling integrated analyses across historical and new datasets. We demonstrate these resources by performing the first exploratory population genomic analysis of An. dirus from Bangladesh, Thailand, and Cambodia, revealing population structure, candidate regions of physiological resistance, and genomic structural variation. Together, these resources provide a foundation for genomic surveillance studies to inform vector control and malaria elimination strategies in Southeast Asia.

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Dennis, T. P. W., Vantaux, A., Kobylinski, K. C., Alam, M. S., Witkowski, B., Al-Amin, H. M., Lobo, N. F., Wilson, A. J., Drury, E., Goncalves, S., Harding, N. J., Hernandez-Koutoucheva, A., Kwiatkowski, D., Miles, A. J., Donnelly, M. J., St Laurent, B.. 2025-12-06. A genomic toolkit for surveillance and elimination of the principal malaria vectors in Southeast Asia.. https://doi.org/10.64898/2025.12.04.691712

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