Investigating malaria mosquito vector and Plasmodium parasite genetic diversity in and around Lake Victoria, Kenya

Title of PhD project

Investigating malaria mosquito vector and Plasmodium parasite genetic diversity in and around Lake Victoria, Kenya

Supervisory team


Lead: Prof. Taane Clark (ITD, lead;,  

Prof. Susana Campino (ITD;  

Nagasaki University 

Prof. Kiyoshi Kita (TMGH;

Professor Akira Kaneko (ITM;

Brief description of project

Malaria, a mosquito-borne disease caused by Plasmodium parasites, is an important public health problem causing an estimated >200 million cases and >400,000 deaths annually. Most malaria cases and deaths occur in sub-Saharan Africa, including in Kenya. To assist the task of malaria elimination, it is crucial to improve our understanding of the genetic diversity of female Anopheles mosquito vectors and Plasmodium parasites. For example, it is important to identify insecticide resistance genotypes in mosquitos and drug resistance mutations in P. falciparum. In this project we will collect blood samples from severe and asymptomatic individuals around Lake Victoria, and characterise the genomes of the parasites, including identifying drug resistance mutations and loci under selection [1,2]. In parallel, we will collect and sequence mosquitos from the same communities, characterising Anopheles genomes, as well as gut microbiomes which may include P. falciparum parasites. The population structure of both mosquitos and parasites will be inferred [1,2], and a genome-to-genome analysis performed to identify vector-pathogen genetic interactions. This work could provide insights into the biology underlying malaria infections and transmission; such insights could inform the process of drug/insecticide discovery, the development of tools for rapid diagnosis, surveillance, and evaluation of malaria control interventions. The outputs of this work will inform malaria control measures and policy in Kenya.

[1] Ravenhall M, …, Campino S, Clark TG. An analysis of large structural variation in global Plasmodium falciparum isolates identifies a novel duplication of the chloroquine resistance associated gene. Sci Rep. 2019 Jun 4;9(1):8287.  

[2] Osborne A, Manko E, Takeda M, …, Clark TG. Characterizing the genomic variation and population dynamics of Plasmodium falciparum malaria parasites in and around Lake Victoria, Kenya. Sci Rep 2021;11(1):19809.

The role of LSHTM and NU in this collaborative project

NU runs field studies around Lake Victoria, and routinely collects mosquito and clinical samples for genomic characterisation. The LSHTM has expertise in high throughput DNA genotyping and sequencing, and data analysis (e.g., GWAS). NU has expertise in functional studies to follow-up any interesting biological insights. 

Particular prior educational requirements for a student undertaking this project

A background in molecular biology, entomology, parasitology, or another related area; an interest in genomics and sequence data analysis. 

Skills we expect a student to develop/acquire whilst pursuing this project

Bioinformatics, population genetics, whole genome sequencing, advanced molecular biology skills, and genomic epidemiology, GWAS.