Genomic surveillance of malaria intervention programmes in East Africa

Malaria is a major cause of mortality and morbidity in Sub-Saharan Africa (SSA) and one of the biggest impediments to the economic development. The major method for controlling these malaria-transmitting mosquitoes is through the use of chemical insecticides but resistance has emerged and is a major threat to the recent reductions in both deaths and malaria infections.

A major challenge facing malaria control programme managers is knowing to what extent insecticide resistance is impacting control and when to take action eg by switching to a new intervention. The PhD student will work within two large vector control trials in East Africa. Using genomic sequencing approaches they will investigate the key genetic drivers of insecticide resistance and then then using insecticide resistance models, quantify the impact of resistance on intervention efficacy on epidemiological indicators.

Work will be conducted at LSTM and with partners in Kenya.

Where does the project lie on the Translational Pathway?

T1 – Basic Research, T2 – Clinical Research, T3 – Evidence into Practice, T4 – Practice to Policy/Population

Expected Outputs

The project will produce high quality REF returnable 3*/4* publications and will provide the evidence base for large scale research council and industry funding. Research costs will be partially underwritten by recent awards from BMGF and NIAID. Recent PhD graduates from our labs have published extensively in the general science journals (Nature, PNAS, Nature Communications). This is a key strategic area for LSTM and brings together research groups from across the Biological and Clinical Sciences faculty

Training Opportunities

The student will gain skills in field entomology; molecular biology; experimental design; statistical analysis; genomics; epidemiology

Skills Required


Key Publications associated with this project

Staedke, S.G. et al (2020) 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, 395, 1292-1303

Abong’o et al (2020) Impact of indoor residual spraying with pirimiphos methyl (Actellic 300CS®) on entomological indicators of transmission and malaria case burden in Migori County, western Kenya. Scientific Reports, 10, e4518

Njoroge  et al (2021) Identification of a rapidly-spreading triple mutant for high-level metabolic insecticide resistance in Anopheles gambiae provides a real-time molecular diagnostic for anti-malarial intervention deployment. BioRxiv,

Clarkson et al (2021) The genetic architecture of target-site resistance to pyrethroid insecticides in the African malaria vectors Anopheles gambiae and Anopheles coluzzii. Molecular Ecology (in press)

The Anopheles gambiae 1000 Genomes Consortium (2020) Genome variation and population structure among 1,142 mosquitoes of the African malaria vector species Anopheles gambiae and Anopheles coluzzii Genome Research, 10, 1533-1546

Now Accepting Applications 

CLOSING DATE FOR APPLICATIONS: Application Portal closes: Wednesday 9th February 2022 (12:00 noon UK time)

Shortlisting complete by: End Feb/early March 2022

Interviews by: Late March/early April 2022

For more information on Eligibility, funding and how to apply please visit the MRC DTP/CASE pages