Cambridge-Africa

Dr Samuel Kojo Kwofie

Dr Samuel Kwofie (University of Ghana)

Research title: Genomics and Bioinformatics of Infectious Pathogens

Research project: The use of High Performance Computing (HPC) to undertake research in bioinformatics, phylogenetics and genomics of infectious pathogens, including Hepatitis A, B, C, D and E viruses. Hepatitis viruses sampled from infected patients from across the middle belt, northern and southern regions of Ghana will be characterized using Next-generation sequencing (NGS) analysis. The NGS analysis will allow the study of the mutational landscape of genetic variants with the aim to gain insight into the transmission dynamics, molecular clock analysis, molecular epidemiology of host-pathogen interactions, geospatial approaches to the design of targeted hepatitis virus prevention strategies, immune escape and drugresistance. The techniques to be used involve virus RNA extraction, PCR, sequencing on Roche 454 and Illumina sequencing platforms, genome assembly and phylogenetics. Additionally, network and population analysis will be integrated with NGS to understand the evolutionary dynamics. Finally, whole-genome deep sequencing and de novo assembly will be applied to elucidate entire hepatitis virus genomes. Aims:
1. Use NGS methods to generate entire genomes from hepatitis viruses.
2. Elucidate phylogeography patterns of hepatitis virus transmission and drug resistance mechanisms
3. NGS analysis of host and viral genomes to understand disease pathogenesis and epidemiology
4. Develop robust bioinformatics pipelines integrating algorithms which facilitate easy and efficient assembly of viral genomes

Collaborator: Dr Simon Frost, Department of Veterinary Medicine, Cambridge Veterinary School, University of Cambridge

Contact: skkwofie@ug.edu.gh

Watch a video of Samuel talking about his work here