Pyrethroid-treated bed nets are the main malaria vector control tool in East Africa, and Anopheles gambiae around Lake Victoria is highly resistant to pyrethroids. In this course you work as an analyst on a study with three questions:
Which genes are involved in pyrethroid resistance in this population?
Are those genes under selection in wild mosquitoes?
Can we build cheap assays to monitor them, and do they predict whether mosquitoes survive?
All of the data is public.
The data¶
| Data | Source | Used on |
|---|---|---|
| RNA-seq of a colony from Busia, Uganda (collected 2018): a deltamethrin-selected line, its unselected parent line, and the susceptible Kisumu strain | Nagi et al. (2023) Mol Ecol Resour, ENA PRJNA748581 | Days 1–2 |
| Expression meta-analysis across many resistance studies in An. gambiae s.l. and An. funestus | AnoExpress | Day 2 |
| Whole genomes of wild mosquitoes from Uganda and Kenya, including Busia in 2016 | MalariaGEN Ag3 | Day 3 |
Selection signals for the Busia 2016 cohort (UG-E_Busia_gamb_2016_Q2) and its neighbours | Malaria vector selection atlas | Day 3 |
| Amplicon sequencing (Ag-vampIR panel) of mosquitoes from Siaya, Kenya that were exposed to deltamethrin nets and scored dead or alive | Nagi et al. (2025) bioRxiv, SRA PRJNA1207724 | Day 4 |
Busia and Siaya lie about 50 km apart, on either side of the Uganda–Kenya border.
The worked example: CYP6AA1¶
Every module first demonstrates its method on one gene, the cytochrome P450 CYP6AA1 (AGAP002862). It is upregulated in many pyrethroid-resistant populations, and in Uganda and Kenya it is duplicated on a rapidly spreading “triple mutant” haplotype that also carries the Cyp6p4-I236M mutation and a transposable element insertion (Njoroge et al. 2022, Mol Ecol, Njoroge et al. (2022)). You will follow it from expression, to copy number, to a selective sweep, to an assay, to the field.
Your task¶
On Day 2 you are given two or three candidate genes from the Busia RNA-seq results. For each gene, build a gene dossier as you go:
Expression: how strongly is it differentially expressed in Busia?
Replication: is it overexpressed in other studies?
Genomic variation: do CNVs or amino acid changes in wild populations explain the expression?
Selection: is it inside a selective sweep?
Assay: primers and probes to measure its expression or genotype it.
Field evidence: is it (or a linked marker) associated with surviving deltamethrin in Siaya?
On Day 5, present your dossier and give a verdict: how strong is the case that this gene contributes to resistance, and what should be done next? Use the dossier template.
- Njoroge, H., van’t Hof, A., Oruni, A., Pipini, D., Nagi, S. C., Lynd, A., Lucas, E. R., Tomlinson, S., Grau‐Bove, X., McDermott, D., Wat’senga, F. T., Manzambi, E. Z., Agossa, F. R., Mokuba, A., Irish, S., Kabula, B., Mbogo, C., Bargul, J., Paine, M. J. I., … Donnelly, M. J. (2022). Identification of a rapidly‐spreading triple mutant for high‐level metabolic insecticide resistance in Anopheles gambiae provides a real‐time molecular diagnostic for antimalarial intervention deployment. Molecular Ecology, 31(16), 4307–4318. 10.1111/mec.16591