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.