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Dr Nicholas Bbosa

Post-Doctorial Scientist

United Kingdom

Assistant Professor at the London School of Hygiene and Tropical Medicine (LSHTM). A Molecular Virologist by training and Scientist at the MRC/UVRI & LSHTM Uganda Research Unit. I am the project leader of the viral pathogen surveillance and discovery in Uganda study. I am also an accredited researcher with the Phylogenetics and Networks for Generalized Epidemics in Africa (PANGEA) HIV consortium and a lecturer in Viral Genomics and related Bioinformatics on the Masters/PhD in Bioinformatics BReCA (Bioinformatics Research Capacity in Africa) program at Makerere University, Kampala.

Affiliations

MRC/UVRI and LSHTM Uganda Research Unit

Teaching

1. Faculty and lecturer on the Master of Science and PhD in Bioinformatics program (Bioinformatics Research Capacity in Africa, BReCA), Makerere University Kampala. Courses taught on the program include online bioinformatics & sequence databases, molecular phylogenetics (phylodynamics/phylogeography) and viral genomics. 2019 to present

2. Instructor in viral genomics and bioinformatics on the H3ABionet online Bioinformatics course. 2016 to present

3. Instructor in metagenomic deep sequence data analysis on the Presidential Scientific Initiative on Epidemics (PRESIDE) project whose main goal was to identify unique adenoviruses for the development of an Adeno-Vector COVID-19 vaccine at the Uganda Virus Research Institute (UVRI). Topics covered included: De novo assembly using Spades, reference-based mapping using Bowtie and Tanoti, phylogenetic analysis using iqtree and RAxML. 3rd to 7th May 2021

4. Trainer at the East African Consortium for Clinical Research 3 (EACCR3) HIV Virology training. EACCR3 is part of the European and Developing Countries Clinical Trials Partnership 2 (EDCTP2) programme. Courses taught included HIV Molecular Epidemiology, molecular phylogenetics and pathogen phylodynamics. 21st to 25th March 2021

5. Taught principles of Molecular Epidemiology and Molecular Phylogenetics at the "Epidemiology meets phylogenetics" course, co-organised by PANGEA and SANTHE (Africa Health Research Institute, Durban, South Africa). 2019

Research

My research interests include HIV molecular epidemiology, infectious disease transmission networks and pathogen phylodynamics to inform epidemic response. My past research has focused on understanding the genetic diversity, evolution, drug resistance patterns and transmission dynamics of HIV in key & general population groups. Also currently involved in SARS-CoV-2 genomic studies.
Research Area
Bioinformatics
Molecular epidemiology
Virology
Disease and Health Conditions
HIV/AIDS
Country
Uganda

Selected Publications

Global and regional molecular epidemiology of HIV-1 during 1990-2024: systematic review, global survey, and analysis of prevalence.
Khalid, A; Gettins, L; Scullion, L; Liu, X; Lin Wei, LL; Masai, AN; Guerin, PJ; Allel, K; Hemelaar, J; Global HIV Molecular Epidemiology Collaboration,;
2026
The Lancet. Infectious diseases
Pathways, outputs and impact of NIH-supported bioinformatics and genomics graduate trainees in Africa.
Jjingo, D; Walakira, A; Hashim, S; Cheickna, C; Galiwango, R; Kibet, C; Kivunike, FN; Mboowa, G; Kakembo, FE; Ayodele, B; Entfellner, J-BD; De Villiers, S; Wambui, K; FATUMO, S; Chikowore, T; Mukisa, J; Ssekagiri, A; BBOSA, N; Mulindwa, J; Kyobe, S; Nsubuga, M; Kebirungi, G; Katagirya, E; Mwesigwa, S; Lujumba, I; ... H3Africa Consortium,
2026
Briefings in bioinformatics
teamNGS Balances Sensitivity for Viruses with Comprehensive Microbial Detection in Clinical Specimens.
Yamaguchi, J; Orf, GS; Malinauskas, J; Mata, M; Weiss, SL; Forberg, K; Meyer, TV; Wiebe, PO; Mowerman, I; Piotrowski, SJ; Glownia, D; Rodgers, MA; Hackett, J; Suputtamongkol, Y; Phoompoung, P; Gomathi, S; Pradeep, A; Solomon, SS; BBOSA, N; KALEEBU, P; Ahouidi, AD; Mboup, S; Sequeira, AF; Tojo, A; Cloherty, GA; ... Berg, MG.
2025
Microorganisms
Diagnostic Accuracy of Next-Generation Sequencing: Prevalence of HIV-1 Drug Resistance and Associated Factors Among Adults on Integrase Inhibitors with Virologic Failure.
Lunkuse, S; Kiiza, R; Ssekagiri, A; Nannyonjo, M; Ntenkaire, N; Nassolo, F; Namagembe, HS; Kiberu, F; Kabuuka, D; Andia, I; Kalyango, JN; Kibwika, PB; BBOSA, N; KALEEBU, P; Ssemwanga, D;
2025
Viruses
A novel post-mortem pathogen discovery program detects an outbreak of Echovirus E7: Uganda, 2022-2023.
Weiss, SL; BBOSA, N; Orf, GS; Berg, MG; Ssemwanga, D; Kalungi, S; Balinandi, S; Mata, M; Bosa, HK; Nabirye, SE; Buule, J; Lutalo, T; Havron, A; Downing, R; Rodgers, MA; Averhoff, F; Cloherty, GA; KALEEBU, P;
2025
Frontiers in microbiology
BonoboFlow: viral genome assembly and haplotype reconstruction from nanopore reads.
Ndekezi, C; Byamukama, D; KATO, F; Omara, D; Nakyanzi, A; Natwijuka, F; Mugaba, S; Ssekagiri, A; BBOSA, N; Sande, OJ; Kimuda, MP; Byarugaba, DK; KAPAATA, A; Sutar, J; Bhattacharya, J; KALEEBU, P; BALINDA, SN;
2025
Bioinformatics advances
Identification of Anthrax as the Cause of a Cluster of Unexplained Deaths, Uganda, 2023: The Role of Metagenomic Next-Generation Sequencing and Postmortem Specimens.
BBOSA, N; Ssemwanga, D; Weiss, SL; Kalungi, S; Mawanda, A; Ssentudde, R; Ssekyeru, E; Ssekagiri, A; Kiiza, R; Rwankindo, C; Buule, J; Namagembe, HS; Nabirye, S; Nassolo, JP; Downing, R; Lutwama, J; Lutalo, T; Kyobe Bosa, H; Berg, MG; Rodgers, MA; Averhoff, F; Cloherty, GA; KALEEBU, P;
2025
The American journal of tropical medicine and hygiene
Case Reports of Human Monkeypox Virus Infections, Uganda, 2024.
BBOSA, N; Nabirye, SE; Namagembe, HS; Kiiza, R; Ssekagiri, A; Munyagwa, M; Bwambale, A; Bagonza, S; Bosa, HK; Downing, R; Lutwama, J; KALEEBU, P; Ssemwanga, D;
2024
Emerging infectious diseases
Emerging SARS-CoV-2 Variants in Uganda in the Era of COVID-19 Vaccination.
BBOSA, N; Kiiza, R; Ssekagiri, A; Namagembe, HS; Nabirye, SE; Kabuuka, D; Rwankindo, C; Kisakye, A; Woldemariam, YT; KUSEMERERWA, S; Ongaria, TA; KAKANDE, A; ABAASA, A; Kimbugwe, G; Bosa, HK; Driwale, A; Mwenda, JM; Worwui, AK; Humphreys, J; Cohuet, S; ELLIOTT, AM; RUZAGIRA, E; KALEEBU, P; Ssemwanga, D;
2024
Viruses
Next-Generation Sequencing Reveals a High Frequency of HIV-1 Minority Variants and an Expanded Drug Resistance Profile among Individuals on First-Line ART.
Nannyonjo, M; Omooja, J; Bugembe, DL; BBOSA, N; Lunkuse, S; Nabirye, SE; Nassolo, F; Namagembe, H; ABAASA, A; Kazibwe, A; KALEEBU, P; Ssemwanga, D;
2024
Viruses
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