Uganda Virus Research Institute, Uganda








Tell us something interesting about your institution The Uganda Virus Research Institute, UVRI, is a leading research institution in East Africa, with a remit involving a broad role in health research. It was established in the 1930s with funding from the Rockefeller Foundation for Yellow Fever research and has a distinguished history in arbovirology.

What are the main research interests of your institution? The UVRI engages in health research pertaining to human infections and disease processes associated with or linked to viral aetiology and provides expert advice, enables partnerships and communication and serves as a centre for training and education.

Class of 2016


What are the academic backgrounds of the IBT_2016 participants in the UVRI classroom? 8 Biomedical scientists, 3 Medical students and 2 Computer scientists/ Mathematicians

The UVRI team



Jonathan Kayondo

role for IBT_2016: co-trainer (Molecular Evolution and Phylogenetics module) and classroom PI

I am a Senior Research Officer (SRO) at the Uganda Virus Research Institute (UVRI), with a molecular genetic training background. My research encompasses investigations on disease vectors and pathogens with a focus on the genetics of malaria transmitting mosquitoes and HIV drug resistance. I am currently involved in research exploring controlling malaria vectors using engineered endonucleases, and the design of more sensitive assays for detection of HIV-drug resistance minority variants. I also contribute to Bioinformatics capacity development at the institute where various analysis pipelines, e.g. for NGS-based metagenomics and variant calling, are being developed to enhance pathogen detection for research purposes or disease outbreak investigations. The Uganda Virus Research Institute is a reference centre for various viral infections and is involved in investigations on communicable and also non-communicable diseases to generate information that will help initiate new or to improve on existing control and prevention strategies.



Jamirah Nazziwa

role for IBT_2016: teaching assistant

Jamirah works at the Medical Research Council / UVRI Uganda Unit on AIDS as a laboratory technologist and for 5 years, she has acquired experience in the fields of molecular virology, bacteriology, bioinformatics and molecular genomics including DNA sequencing and analysis with focus on HIV-1, influenza, tuberculosis and measles. Jamirah has built a strong technical background and practical experience in the molecular epidemiology and drug resistance of HIV -1 and contributed to publications in that effect. Jamirah received her BSc. In Biomedical laboratory technology from Makerere university and her MSc. in Bioinformatics from Skovde and Lund University.




Joseph Kirangwa

role for IBT_2016: teaching assistant

I am working with the Basic Science Virology MRC Uganda/Uganda Virus Research Institute and have remarkably been involved in various projects to mention but a few HIV-1 drug resistance genotyping, HIV-1 Molecular epidemiology and HIV-1 Superinfection several of which have benefited from bioinformatics based investigations. My research interest is in the development and application of algorithms for the analysis of large-scale datasets from transcriptomic, proteomics, genomics, molecular and signalling pathways and networks. I have developed expertise in analysis techniques for dealing with Next Generation Sequencing (NGS) data, including an introduction to programming for the study of large data sets of HIV, Linux, SNP calling, HIV-1 drug resistance mutation genotyping and population phylogenetics. I am also well versed with some bioinformatics softwares PHYLIP, PAUP*, PHYML, MEGA, BEAST, Simplot, Recall, MrBayes and RegaDB. I recently received funding from the Swedish Institute Scholarships for my masters studies in Sweden Bioinformatics University of Skovde and I will be looking at “The Association between HIV-1 Amino Acid Significant Interaction Network and Drug Resistance Mutation Frequency” .

Deo portrait


Deogratius Ssemwanga

role for IBT_2016: teaching assistant, co-trainer for Multiple Sequence Alignment module

Dr. Ssemwanga received his PhD in Molecular Virology at Makerere University, in 2013 where he studied the prevalence of individuals infected with multiple strains of HIV in Uganda and the effect of these multiple infections on disease progression. He received a Wellcome Trust funded Makerere University/UVRI Infection and Immunity Postdoctoral fellowship to study the virological and immunological correlates of HIV-1 superinfection. This work involves the use of ultra-deep sequencing with phylogenetic analysis to determine HIV-1 superinfection and neutralization assays to determine the development of neutralizing antibodies prior to and after superinfection. In his current position as a Senior Research Scientist with the MRC/UVRI Uganda Research Unit on AIDS he continues to work on HIV-1 superinfection. His other research interests include the use of Molecular Epidemiology approaches to understand the HIV transmission networks in our populations: a key approach necessary to reduce transmissions in the most at risk populations. He is involved in studies on HIV-1 drug resistance in light of the increased access to treatment. He is also involved in H3ABioNet, a network tasked to develop bioinformatics capacity in Africa. He organizes and teaches at the annual Bioinformatics in the Tropics Uganda series.



Nicholas Bbosa

role for IBT_2016: teaching assistant

I am a PhD fellow in Molecular Virology with particular interest in the use of phylogenetics/phylogeography to delineate the molecular basis of viral transmission dynamics among key populations. My research involves utilizing a wide range of bioinformatics tools in analysing molecular sequence data. My interest in bioinformatics dates back in 2009 when I first attended a bioinformatics workshop organised by the REGA institute in collaboration with the Uganda Virus Research Institute that covered aspects of multiple sequence alignment, molecular evolution of viruses and phylogenetic analysis. I have since attended several bioinformatics courses in molecular phylogenetics, network analysis, hypothesis testing and application of programming languages in data editing analysis and analysis. I am currently involved in molecular epidemiology projects at the Medical Research Council involving large sequence data sets.


Read more about all the IBT_2016 classrooms here