Current Lab Members

Prof. Martin Munene Nyaga

Prof. Martin Nyaga is the Head of the University of the Free State-Next Generation Sequencing (UFS-NGS) Unit and the Unit’s Principal Researcher, since its inception in 2016. His academic affiliation is the Division of Medical Virology within the Faculty of Health Sciences. Previously, Prof. Nyaga was a Research Fellow and a visiting Postdoctoral Research Fellow at the J. Craig Venter Institute, Rockville, MD, USA and at the Laboratory of Viral Metagenomics, KU Leuven-University of Leuven, Belgium, respectively. He served at the Medical Research Council-Diarrhoeal Pathogens Research Unit (MRC-DPRU), which is one of the two WHO Regional Reference Laboratories for rotavirus research in Africa, where he coordinated the African rotavirus genomics project and the human Microbiome and Metagenomics studies. He was part of the team that undertook the Phase II and III Rotarix rotavirus vaccine efficacy clinical trials in South Africa and the pre- and post- rotavirus vaccination genomic surveillance studies for the African Rotavirus Surveillance Network (ARSN).

Prof. Nyaga is currently investigating the long-term effects of the introduction of the monovalent RV1 vaccine in five African countries (Cameroon, Ghana, Malawi, Kenya and South Africa), through the African Enteric Viruses Genome Initiative (AEVGI). The AEVGI is a Bill and Melinda Gates Foundation (BMGF) funded consortium of young researchers from Cameroon, Ghana, Malawi, Kenya and South Africa borne out of the ARSN, and which Prof. Nyaga is the Principal Investigator and a co-founder. One of the key goals of the AEVGI is to leverage a genomics and bioinformatics approach to complement the routine work being done by the ARSN. Likewise, the World Health Organization (WHO) designated the UFS-NGS Unit as a Collaborating Centre (CC) for Vaccine Preventable Diseases (VPD) Surveillance and Pathogen Genomics surveillance (2020-2024), of which Prof Nyaga is the Director. This WHO CC is undertaking studies on whole genome sequencing of rotavirus positive samples obtained from pre- and post- Rotarixâ, RotaTeqâ, Rotavacâ and Rotasiilâ rotavirus vaccines, within the ARSN.

Prof. Nyaga is the Team Lead of studies on metagenomics of Gut and Respiratory Virome funded by grants from the South African Medical Research Council (SAMRC), Poliomyelitis Research Foundation (PRF) and the National Research Foundation (NRF). The aim of these studies is to establish the role played by the gut and respiratory virome in young children over time, to effect normal and metabolic disorders that may influence a child’s healthy growth or impact medical conditions such as obesity later in life. He is also an integral member of the Network of Genomic Surveillance, South Africa (NGS-SA), a National consortium formed as a rapid response team to fast track COVID-19 global pandemic solutions, through whole-genome sequencing of SARS-CoV-2 in South Africa.

Most recently, in 2022, Prof. Nyaga was nominated by the Africa Pathogen Genomic Initiative (PGI) of Africa Centres for Disease Control and Prevention (CDC), to strengthen multi-pathogen sequencing and bioinformatics capacity of emerging and re-merging diseases and genomic surveillance of pathogens of public health importance in Africa. The Africa PGI is working with a Focus Group of experts in Vaccine Preventable Disease (VPD) genomic surveillance, which is chaired by Prof Nyaga, to provide technical guidance and support to develop a continental VPD road map and implementation strategy.

Prof. Nyaga is an NRF Rated Researcher who collaborates with numerous local and International Associates. He has published over 40 peer-reviewed articles in International journals, deposited over 50,000 full-length and partial genome sequences at the NCBI GenBank and supervised over 30 postgraduate students. His research profile can be found in the links, herein.

Dr. Peter Nthiga Mwangi

Dr. Peter Nthiga Mwangi obtained his Ph.D. at the University of the Free State – Next Generation Unit (UFS-NGS) and Division of Virology in 2021 through a full scholarship by the African Enteric Viruses Genome Initiative (AEVGI), funded by the Bill and Melinda Gates Foundation (BMGF). His doctoral work investigated molecular epidemiology at the whole-genome level of rotavirus strains collected over a 14 year period in South Africa.

He is currently a post-doctoral fellow/Research Associate at the UFS-NGS Unit, which also serves as a World Health Organization Collaborating Centre (WHO CC) for Vaccine Preventable Diseases (VPD) Surveillance and Pathogen Genomics, under the supervision and mentorship of Prof. Martin Nyaga. He serves in the secretariat for the VPD Focus Group (FG) arm of the Pathogen Genome Initiative (PGI) of the Africa Centers for Disease Control and Prevention (CDC). The key objective of the VPD FG is to develop a roadmap and implementation strategy for pathogen genomics research in the African continent.

His initial research interest was in phytomedicine, in which he attained a M.Sc. in the Department of Biochemistry and Biotechnology, Kenyatta University, Kenya. His study evaluated the therapeutic potential of phytomedicine by performing preliminary drug screening of selected medicinal plants (Harrisonia abysinicca Oliv and Landolphia buchananii (Hallier F.) stapf) using animal (Wistar rats and swiss albino mice) models. Thereafter, he joined the dynamic team at the UFS-NGS Unit to study enteric and respiratory viruses and viral vaccine surveillance.

His assignments at the UFS-NGS Unit involve performing whole-genome surveillance of rotavirus to decipher the impact of rotavirus vaccines’ introduction in Africa. He is also part of the UFS-NGS team working on sequencing of whole-genomes of SARS-CoV-2 in the Free State Province, South Africa, as part of the Network of Genomic Surveillance South Africa (NGS-SA) consortium that contributed to the discovery of the Beta and Omicron variants.

Mr. Milton Tshidiso Mogotsi

Mr. Milton Tshidiso Mogotsi is a Ph.D. candidate in Medical Virology at UFS, under the supervision of Prof. Martin Nyaga. His research seeks to establish the origin of early life virome in the gut of infant cohorts and determine the diversity and dynamics of these viral populations using NGS. He obtained his M.Sc. in Microbiology (Cum Laude) at UFS in 2019, in which he demonstrated the application of viral metagenomics in characterizing viruses that colonize the gastrointestinal tract of infants and described the enteric viral profiles, thereof. He has disseminated his research findings in local and international forums like the 12th African Rotavirus Symposium in Johannesburg, South Africa (2019), and the 13th International dsRNA Virus Symposium in Houffalize, Belgium (2018).

Mr. Mogotsi joined the UFS-NGS Unit in 2016 as an NRF intern, working as a laboratory assistant. Over the years he has gained experience in molecular biology techniques applied for NGS workflows and bioinformatics. He is currently the NGS wet-lab coordinator in the Unit, assisting with planning and performing laboratory experiments, and ensuring proper usage and maintenance of instrumentation. He is also actively involved in keeping the lab in pace with state of the art labs, in terms of protocols, technique optimization and equipment utilization, while also providing on-site orientation and training to arriving students, interns and visiting students.

As a research assistant, Mr. Mogotsi is involved in a wide range of enteric whole genome sequencing, 16S rRNA/ITS metagenomics and more recently COVID-19 sample processing and generating data for whole genome SARS-CoV-2 surveillance in the Free State Province, as part of the Network for Genomic Surveillance in South Africa (NGS-SA).

Mr. Ayodeji Emmanuel Ogunbayo

Mr. Ayodeji Emmanuel Ogunbayo is a Ph.D. NRF grant holder’s fellow at the Next-Generation Sequencing (NGS) Unit and Division of Virology, University of the Free State (UFS), under the mentorship of Prof. Martin Nyaga. He holds BSc Degree in Biochemistry and Microbiology (University of South Africa (UNISA) and BMedSci and M.MedSci (UFS) degrees with specialization in Medical Microbiology and Virology. Previously, he worked on alternative methods for diagnosing Tuberculosis (TB) in children and deciphering mutations in different genes that confers resistance to different classes of antibiotics in TB patients.

Currently, his research focuses on deciphering the composition and diversity of respiratory virome in children, while simultaneously evaluating the utility and applicability of using metagenomics next generation sequencing technique for the diagnosis and characterization of severe acute respiratory infection in children in clinical settings. His research interests includes paediatric infectious diseases, TB diagnostics, epidemiological studies, viral metagenomics, and vaccine preventable diseases.

Mr. Teboho Mooko

Mr. T Mooko is a Doctoral fellow at the Department of Internal Medicine, University of the Free State (UFS). He is also affiliated with the Next Generation Sequencing (UFS-NGS) Unit and Division of Virology, UFS. His PhD study is funded by the Council of Scientific and Industrial Research (CSIR).

His PhD research is seeking to address possible factors contributing to HIV-1 shedding into peritoneal dialysis effluent in end-stage kidney failure patients. It is an open-label non-randomised clinical trial study, which is intends to help improve current antiretroviral therapy dosing guidelines and clinical practices to prioritise high-risk patients, improve care and reduce treatment costs in this study group.

He was previously a National Research Foundation (NRF) Intern at the UFS-NGS Unit (2019-2020). His Master’s research involved in-vitro and pre-clinical studies on the mechanisms of cannabinoids in the treatment of Alzheimer’s disease. Part of his Master’s objectives were completed at the School of Natural Product Studies, Jadavpur University, Kolkata, India. It was funded by the collaboration between the Department of Science and Innovation (DSI), South Africa and the Ministry of Science and Technology, India.

Miss Robyn-Lee Potgieter

Miss Robyn-Lee Potgieter is currently a first year M.MedSc. candidate at the Next-Generation Sequencing (NGS) Unit and Division of Virology, University of the Free State (UFS), under the supervision of Prof. Martin Nyaga. Her research involves performing whole genome sequencing and analysis on rotavirus strains pre- and post-RotaTeq® vaccine introduction, particularly on Rwandan genotype G9P[8] rotavirus strains.

Miss Potgieter attained her Honours degree (Cum laude) at the Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria where she characterised circulating non-invasive strains of Klebsiella pneumoniae in the Gauteng region. In 2020, she completed her undergraduate degree at the Department of Natural Sciences, UFS and attained her B.Sc. degree, majoring in Genetics and Microbiology.

Miss Hlengiwe Sondlane

Miss. Hlengiwe Sondlane is a M.MedSc. student at the UFS-NGS Unit and Division of Virology, University of the Free State under the supervision of Prof. Martin Nyaga. Her research focuses on genetic analysis of Respiratory Syncytial Virus (RSV) circulating in the Free State, in paediatric patients during the COVID-19 pandemic. The study is funded by National Research Foundation (NRF) and Poliomyelitis Research Foundation (PRF).

She attained her Honours degree at the Department of Microbiology, University of Venda, under the HIV/AIDS and Global Health Research Programme, where she investigated the genetic diversity of HIV-1 integrase in drug naïve and experienced individuals. The goal of the study was to examine for naturally occurring mutations/ variability of the integrase gene to determine if integrase inhibitors introduced as a salvage therapy, would be beneficial for individuals who fail first-line and second-line combination antiretroviral therapy/regimens.

Teaching and Training

Prof. Martin Munene Nyaga

Dr. Peter Nthiga Mwangi

Mr. Milton Tshidiso Mogotsi

Mr. Ayodeji Emmanuel Ogunbayo

Mr. Teboho Mooko

Miss Robyn-Lee Potgieter

Miss Hlengiwe Sondlane

Prof. Martin Munene Nyaga

Dr. Peter Nthiga Mwangi

Mr. Milton Tshidiso Mogotsi​

Mr. Ayodeji Emmanuel Ogunbayo

Mr. Teboho Mooko

Miss Robyn-Lee Potgieter

Miss Hlengiwe Sondlane

Mr. Milton Tshidiso Mogotsi