Cambridge-Africa

Dr Joseph Humphrey Kofi Bonney

Dr Joseph Humphrey Kofi Bonney (University of Ghana)

Research title: Using advanced genomic analysis to identify viral pathogens in residual diagnostic specimens after routine laboratory
testing for haemorrhagic fever causative agents

Research project: Since the turn of the year 2014, the most widespread epidemic of Ebola virus disease (EVD) in history wreaked havoc mainly in three West African countries. It caused substantial mortality, with a reported total of 11,261 deaths. Ghana, by virtue of its geographic position and ease of passenger flow with the countries affected was ranked topmost of EVD importation risk. However no case was confirmed after laboratory investigations of 153 clinical specimens from suspected EVD patients across the country tested negative by RT-PCR. In this project we apply metagenomics with the use of the next generation sequencing (NGS) approach on these RT-PCR negative specimens to detect pathogen genomic material. A stratified random sampling of 10% is selected for analysis. Total nucleic acid is extracted from the clinical specimens which were found negative by RT-PCR for Ebola, Marburg, Yellow fever, Lassa, Dengue and West Nile virus. This is then subjected to ultra-high throughput Illumina sequencing with NGS synthesis technology. Output is further analyzed to determine the genomic origin of each sequence read. We expect to demonstrate the utility of the metagenomics approach with NGS to identify aetiological agents to enhance rapid and appropriate response to minimize or avert future outbreaks.

Collaborator Dr Simon Frost, Department of Veterinary Medicine