References
1. Ranson, H. and N. Lissenden, Insecticide resistance in African Anopheles mosquitoes: a worsening situation that needs urgent action to maintain malaria control. . Trends in Parasitology, 2016.32 (3): p. 187-196.
2. WHO, World malaria report 2019 , W.H. Organization, Editor. 2019, World Health Organization: Geneva. p. 232.
3. Kleinschmidt, I., et al., Implications of insecticide resistance for malaria vector control with long-lasting insecticidal nets: a WHO-coordinated, prospective, international, observational cohort study. Lancet Infectious Diseases, 2018. 18 (6): p. 640-649.
4. Staedke, S.G., Gonahasa, S., Dorsey, G, Kamya, M.R., Maiteki-Sebuguzi, C., Lynd, A., Katureebe, A., Kyohere, M., Mutungi, P., Kigozi, S.P., Opigo, J., Hemingway, J., and M.J. Donnelly, Effect of long-lasting insecticidal nets with and without piperonyl butoxide on malaria indicators in Uganda (LLINEUP): a pragmatic, cluster-randomised trial embedded in a national LLIN distribution campaign. Lancet, 2020(395): p. 1292–303.
5. Killeen, G.F. and H. Ranson, Insecticide-resistant malaria vectors must be tackled. Lancet, 2018. 391 (10130): p. 1551-1552.
6. The Anopheles gambiae 1000 Genomes Consortium, Genome variation and population structure among 1142 mosquitoes of the African malaria vector species Anopheles gambiae and Anopheles coluzzii. Genome Research, 2020. 30 (10): p. 1533-1546.
7. Mugenzi, L.M.J., et al., Cis-regulatory CYP6P9b P450 variants associated with loss of insecticide-treated bed net efficacy against Anopheles funestus. Nature Communications, 2019. 10 .
8. Donnelly, M.J., A. Isaacs, and D. Weetman, Identification, validation, and application of molecular diagnostics for insecticide resistance in malaria vectors. Trends in Parasitology, 2016.32 (3): p. 197-206.
9. Mitchell, S.N., et al., Metabolic and Target-Site Mechanisms Combine to Confer Strong DDT Resistance in Anopheles gambiae. PLoS ONE, 2014. 9 (3).
10. Weetman, D., Wilding, C.S., Neafsey, D.E., Muller, P., Ochomo, E., Isaacs, A.T., Steen, K., Rippon, E.J., Morgan, J.C., Mawejee, H.D., Rigden, D.J., Okedi, L.M., Donnelly, M.J. , Candidate-gene based GWAS identifies reproducible DNA markers for metabolic pyrethroid resistance from standing genetic variation in East African Anopheles gambiae. Scientific Reports, 2018. 8 : p. e2920.
11. Weetman, D. and M.J. Donnelly, Evolution of insecticide resistance diagnostics in malaria vectors. Transactions of The Royal Society of Tropical Medicine and Hygiene, 2015. 109 (5): p. 291-293.
12. Bhatt, S., et al., The effect of malaria control on Plasmodium falciparum in Africa between 2000 and 2015. Nature, 2015.526 (7572): p. 207-+.
13. Hancock, P.A., et al., Mapping trends in insecticide resistance phenotypes in African malaria vectors. PLoS Biology, 2020.18 (6): p. e3000633.
14. Clarkson, C.S., et al., The genetic architecture of target-site resistance to pyrethroid insecticides in the African malaria vectors Anopheles gambiae and Anopheles coluzzii. bioRxiv, 2018(https://doi.org/10.1101/323980).
15. Müller, P., et al., Field-caught permethrin-resistant Anopheles gambiae overexpress CYP6P3, a P450 that metabolises pyrethroids. PLoS Genetics, 2008. 4 (11): p. e1000286.
16. Weedall, G.D., et al., A cytochrome P450 allele confers pyrethroid resistance on a major African malaria vector, reducing insecticide-treated bednet efficacy. Science Translational Medicine, 2019. 11 (484).
17. Protopopoff, N., et al., Effectiveness of a long-lasting piperonyl butoxide-treated insecticidal net and indoor residual spray interventions, separately and together, against malaria transmitted by pyrethroid-resistant mosquitoes: a cluster, randomised controlled, two-by-two factorial design trial. Lancet, 2018. 391 (10130): p. 1577-1588.
18. Lynd, A., et al., LLIN Evaluation in Uganda Project (LLINEUP) − A cross-sectional survey of species diversity and insecticide resistance in 48 districts of Uganda. Parasites and Vectors, 2019.12 : p. e94.
19. The Anopheles gambiae 1000 Genomes Consortium, Natural diversity of the malaria vector Anopheles gambiae. Nature (London), 2017. 552 : p. 96-100.
20. Lucas, E., et al., Whole genome sequencing reveals high complexity of copy number variation at insecticide resistance loci in malaria mosquitoes. Genome Research, 2019. https://doi.org/10.1101/399568 (29): p. 1250-1261
21. Ibrahim, S.S., et al., Pyrethroid resistance in the major malaria vector Anopheles funestus is exacerbated by overexpression and overactivity of the P450 CYP6AA1 across Africa. Genes, 2018.9 (3): p. 17.
22. Zhou, D., et al., Genomic analysis of detoxification supergene families in the mosquito Anopheles sinensis. PLoS One, 2015.10 (11): p. e0143387.
23. Kwiatkowska, R.M., et al., Dissecting the mechanisms responsible for the multiple insecticide resistance phenotype in Anopheles gambiae s.s., M form, from Vallee du Kou, Burkina Faso. Gene, 2013. 519 (1): p. 98-106.
24. Mitchell, S., et al., Identification and validation of a gene causing cross-resistance between insecticide classes in Anopheles gambiae from Ghana. Proceedings of the National Academy of Sciences of the United States of America, 2012. 109 : p. 6147-6152
25. Edi, C.V., et al., CYP6 P450 enzymes and ACE-1 duplication produce extreme and multiple insecticide resistance in the malaria mosquito Anopheles gambiae. PLoS Genetics, 2014. 10 (3): p. e1004236-e1004236.
26. Vontas, J., et al., Rapid selection of a pyrethroid metabolic enzyme CYP9K1 by operational malaria control activities. Proceedings of the National Academy of Sciences of the United States of America, 2018.115 (18): p. 4619-4624.
27. Miles, A., et al., cggh/scikit-allel . 2019, Zenodo.
28. Garud, N.R., et al., Recent selective sweeps in North American Drosophila melanogaster show signatures of soft Sweeps. PLOS Genetics, 2015. 11 (2): p. e1005004.
29. Wat’senga, F., et al., Intensity of pyrethroid resistance in Anopheles gambiae before and after a mass distribution of insecticide-treated nets in Kinshasa and in 11 provinces of the Democratic Republic of Congo. Malaria Journal, 2020. 19 (1): p. e169.
30. Lynd, A., et al., Insecticide resistance in Anopheles gambiae from the northern Democratic Republic of Congo, with extreme knockdown resistance (kdr) mutation frequencies revealed by a new diagnostic assay. Malaria Journal, 2018. 17 .
31. Lynd, A., Weetman, D., Barbosa, S., Yawson, A.E., Mitchell, S., Pinto, J., Hastings, I. and Donnelly, M.J., Field, genetic and modelling approaches show strong positive selection acting upon an insecticide resistance mutation in Anopheles gambiae s.s. Molecular Biology and Evolution, 2010. 27 : p. 1117-1125.
32. Yunta, C., et al., Cross-resistance profiles of malaria mosquito P450s associated with pyrethroid resistance against WHO insecticides. Pesticide Biochemistry and Physiology, 2019.161 : p. 61-67.
33. Yeka, A., et al., Malaria in Uganda: Challenges to control on the long road to elimination I. Epidemiology and current control efforts. Acta Tropica, 2012. 121 (3): p. 184-195.
34. Ministry of Health, R.o.K., Insecticide Resistance Management Plan, Kenya 2020 – 2024 . 2019, Ministry of Health, Republic of Kenya.
35. Ruiz, J.L., L.C. Ranford-Cartwright, and E. Gómez-Díaz, The regulatory genome of the malaria vector Anopheles gambiae: integrating chromatin accessibility and gene expression. bioRxiv, 2020: p. 2020.06.22.164228.
36. Liu, B., et al., iEnhancer-2L: a two-layer predictor for identifying enhancers and their strength by pseudo k-tuple nucleotide composition. Bioinformatics, 2015. 32 (3): p. 362-369.
37. Liu, B., et al., iEnhancer-EL: identifying enhancers and their strength with ensemble learning approach. Bioinformatics, 2018.34 (22): p. 3835-3842.
38. Schmidt, J.M., et al., Copy number variation and transposable elements feature in recent, ongoing adaptation at the Cyp6g1 locus.PLoS Genetics, 2010. 6 (6): p. e1000998.
39. Jones, C., et al., Footprints of positive selection associated with a novel mutation (N1575Y) in the voltage gated sodium channel of Anopheles gambiae. Proceedings of the National Academy of Sciences of the United States of America, 2012. 109 : p. 6614-6619.
40. Djogbenou, L., et al., Ace-I duplication in Anopheles gambiae: a challenge for malaria control. Malaria Journal, 2009. 8 .
41. Boakye, D.A., et al., Patterns of household insecticide use and pyrethroid resistance in Anopheles gambiae sensu stricto (Diptera: Culicidae) within the Accra metropolis of Ghana. African Entomology, 2009. 17 (2): p. 125-130.
42. Grau-Bové, X., et al., Evolution of the insecticide target Rdl in African Anopheles is driven by interspecific and interkaryotypic introgression. bioRxiv, 2020: p. 2019.12.17.879775.
43. Neafsey, D.E., et al., Highly evolvable malaria vectors: The genomes of 16 Anopheles mosquitoes. Science, 2015. 347 (6217): p. 43-+.
44. Nene, V., et al., Genome sequence of Aedes aegypti, a major arbovirus vector. Science, 2007. 316 (5832): p. 1718-1723.
45. Buss, D.S. and A. Callaghan, Molecular comparisons of the Culex pipiens (L.) complex esterase gene amplicons. Insect Biochemistry and Molecular Biology, 2004. 34 (5): p. 433-441.
46. Rugnao, S., et al., LLIN Evaluation in Uganda Project (LLINEUP): factors associated with childhood parasitaemia and anaemia 3years after a national long-lasting insecticidal net distribution campaign: a cross-sectional survey. Malaria Journal, 2019. 18 : p. e207.
47. Newcombe, R.G., Two-sided confidence intervals for the single proportion: comparison of seven methods. Statistics in Medicine, 1998.17 : p. 857-872.