Current Lab Members

Prof. Martin Munene Nyaga

Prof. Martin Nyaga, a B-Rated NRF Researcher, is the Head of the University of the Free State-Next Generation Sequencing (UFS-NGS) Unit, within the School of Biomedical Sciences and is 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‘s research investigates the long-term effects of the introduction of the monovalent RV-1 vaccine in five African countries (Cameroon, Ghana, Malawi, Kenya and South Africa), through the African Enteric Viruses Genome Initiative (AEVGI) and the Sequencing of the Antigenic Cartography of Enteric Viruses (SACEV) . The AEVGI and SACEV are 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 and SACEVare 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, 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- Rotarix, RotaTeq, Rotavac and Rotasiil 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 South African 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 in 2020 as a rapid response team to fast track COVID-19 global pandemic solutions, through whole-genome sequencing of SARS-CoV-2 in South Africa.

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 collaborates with numerous local and International Associates. He has published over 70 peer-reviewed articles in International journals, deposited over 50,000 full-length and partial genome sequences at the NCBI GenBank and supervised over 40 postgraduate students.

Dr. Ayodeji Emmanuel Ogunbayo

Dr Ayodeji Emmanuel Ogunbayo completed his Ph.D as an 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 a BSc Degree (UNISA), a B.MedSc. Honours (UFS), M.MedSci. (UFS) degrees with specialization in Medical Microbiology and Virology.

Previously, Dr Ogunbayo worked on alternative methods for diagnosing tuberculosis in children and deciphering mutations in different genes that confers resistance to different classes of antibiotics in tuberculosis patients.

His doctoral research made an immense contribution to the applicability of metagenomics next-generation sequencing (mNGS) in deciphering the respiratory virome and in diagnosing severe acute respiratory infection (SARI) in children under five years of age. The findings from this study included a validated and robust workflow to recover respiratory RNA viruses from clinical samples. The established workflow was adapted to decipher children’s respiratory virome composition in health and disease, while simultaneously establishing the clinical diagnostic applicability of mNGS and, more importantly, the increased utility of dual-triple mNGS analysis tools in robust detection of viral pathogens in SARI. His research further established the interference and enormous impact of COVID-19 pandemic and the adopted non-pharmaceutical intervention on the transmission dynamics of other respiratory viruses. Four research articles from this study with pioneering data in Africa were published in high-impact international journals.

He is currently a post-doctoral fellow/research associate at the UFS-NGS Unit. His research interests/activities include viral metagenomics for surveillance and diagnostics in respiratory cases, paediatric infectious diseases, tuberculosis diagnostics, and viral epidemiological studies.

Dr. Milton Tshidiso Mogotsi

Dr. Milton Tshidiso Mogotsi holds an M.Sc. degree in Microbiology (Cum Laude), and a Ph.D. in Medical Virology obtained in 2024, from University of the Free State, Bloemfontein, South Africa, supervised by Prof. Martin Nyaga.

With research experience spanning over seven years, he has been an integral member of the UFS-NGS Unit, joining as an Intern Laboratory Assistant in 2016, and currently serving as a Wet-Lab Coordinator. His roles include management of daily laboratory operations, coordinating the execution of research projects and genomic services for internal and external clients, and collaborative projects mainly funded by organizations such as the World Health Organisation, Poliomyelitis Research Foundation and Bill and Melinda Gates Foundation. He is also responsible for training junior staff members, students and visiting researchers on advanced lab techniques including next generation sequencing.

In addition to the above role, Dr. Mogotsi has undertaken a Postdoctoral Research Fellowship under Prof. Nyaga, conducting ground-breaking research on genomic characterization of enteric virome in paediatric populations in South Africa, using viral metagenomics. His other primary roles include facilitating coordination between collaborators on related research projects currently ongoing at the UFS-NGS Unit, postgraduate project supervision and funding acquisition.

As a recent Ph.D. graduate, throughout his postgraduate studies Dr. Mogotsi has consistently demonstrated outstanding research skills, intellectual curiosity, and a strong work ethic. His research in the field of virology has been both innovative and impactful, contributing significantly to the field through publications in peer-reviewed international journals. Beyond his technical expertise, he possesses excellent communication skills, effectively disseminating his research findings at national and international conferences (Africa, Europe, and Asia). His ability to convey complex scientific concepts in a clear and concise manner has won him several awards including the National 3-Minute Thesis competition 2023 and the Dr. Lehlohonolo Mathengtheng Trophy for best Ph.D. presentation at the UFS Faculty of Health Sciences Research Forum 2023.

As a passionate and enthusiastic emerging researcher who is eager to make a meaningful contribution towards genomic research in Africa, Dr. Mogotsi believes that the UFS-NGS Unit’s reputation for cutting-edge research and commitment to innovation aligns perfectly with his career goals.

Ms. Sesiyanda Maseko

Ms. Sesiyanda Maseko, holds a B.Sc. in Microbiology and Biochemistry and B.Sc. Honours in Biochemistry (University of the Free State). She joined the UFS-NGS Unit in 2024 as an intern under the Enteric Viruses Research Group.

She was motivated to pursue an internship fellowship at the UFS-NGS unit to build on the role genomics played in the success of her honours project titled “An Escherichia coli-based heterologous expression system for the Hepatitis B-virus polymerase to produce soluble protein for structural studies” and is eager to delve deeper into genomics and bioinformatics beyond the scope of her honours year.

With a strong determination to pursue a career in clinical research, Sesiyanda expresses gratitude for this opportunity, viewing it as a stepping stone towards making a Nobel-worthy contributions in the field. She is committed to seizing every moment and maximizing every learning opportunity to continually improve and enhance her skills.

Ms. Somila Nazo

Ms. Somila Nazo is a M.MedSc candidate at the University of the Free State Next Generation Sequencing (UFS-NGS) Unit, and registered under the Division of Virology. She holds a B.Sc Medical Bioscience degree (University of Western Cape) and recently obtained her B.MedSc. Honors degree with specialization in Medical Microbiology and Virology (University of the Free State), where she investigated Tigecycline resistance determinants among Acinetobacter baumannii complex clinical isolates.

Her current research under the supervision of Prof. Martin Nyaga and Co-supervision of Dr. Ayodeji Ogunbayo focuses on Integrated Metagenomic Insights into Microbial Communities and Resistome Profile Analysis of Intensive Care Unit and Wastewater of Major Hospitals in the Free State Province. This study is funded by the National Research Foundation, the Poliomyelitis Research foundation, and the Bill and Melinda Gates Foundation.

Ms. Somila expresses great enthusiasm for her involvement with the UFS-NGS team and is eager to acquire proficiency in NGS techniques, anticipating substantial personal and professional growth within the genomic-medical research field.

Miss Hlengiwe Sondlane

Ms. Hlengiwe holds an Honours degree in Microbiology from the University of Venda and a M.MedSc Virology (Cum Laude) from the University of the Free State. Her Master’s project titled genomic analysis of Respiratory Syncytial Virus (RSV) circulating in the Free State during the COVID-19 pandemic contributed significantly to scientific knowledge on the impact of pandemic such as COVID-19 on the transmission of respiratory viruses.

Ms. Sondlane during her M.MedSc study supervised by Prof. Martin Nyaga acquired knowledge spanning across viral metagenomics, whole genome sequencing of respiratory pathogens as well as targeted sequencing such as 16S and ITS. She has considerable experience in genomic data analysis frow raw data processing to data interpretation. Her proficiency in the use of data analysis tools was honed through several specialised bioinformatics training workshops hosted by the UFS-NGS unit.

Ms. Sondlane is currently an intern within the respiratory niche under the mentorship of Prof. Martin Nyaga and Dr. Ayodeji Ogunbayo at the UFS-NGS Unit. She believes this position will further enhance her capacity to build on her existing genomic knowledge while gaining professional and work experience needed for the rapidly evolving genomic market.

Ms. Eyong Manyi Marcelle

Ms. Eyong Manyi Marcelle is a Ph.D. Candidate at the UFS-NGS Unit, Division of Virology, under the supervision of Prof. Martin Nyaga. She holds a B.Sc. in Microbiology from the University of Buea in Cameroon and an M.Sc. in Medical Microbiology from the University of Yaoundé in Cameroon. Her master’s dissertation was defended on the ‟Molecular Characterization of Porcine Group A Rotavirus Strains in Farm Pigs in the Towns of Kumba and Mamfe, South-West Region of Cameroon” in 2019.

Her Ph.D. Postgraduate project is on Metagenomics analysis of RNA Viruses in Stool Specimens from Children below five years old with Gastroenteritis in Durban, South African. This study aims to characterize the genetic profile of viruses responsible for gastroenteritis in both nourished and malnourished children who are hospitalized in King Edward III Hospital, which is a referral hospital in Durban, Kwa Zulu Natal, South Africa and will also enrich the already available data on metagenomics analysis of viral gastroenteritis in South Africa and globally.

She is very enthusiastic and willing to undertake this journey with the collaborative endeavors of the UFS-NGS Unit team where she will gain experience in more advanced molecular and bioinformatic techniques.

Miss Nkosazana Shange

Miss Nkosazana Shange is a new M.MedSc. student at the University of the Free State-Next Generation Sequencing (UFS-NGS) Unit, under the supervision of Prof. Martin Nyaga and Dr. Nigel Makoah. In 2020, she obtained her undergraduate BSc degree majoring in Biochemistry and Human Anatomy & Physiology from the University of Cape Town (UCT). Thereafter, in 2021, she undertook her Honours degree (Infectious Diseases and Immunology) from the Faculty of Health Sciences, UCT. Miss Shange is a passionate and driven M.MedSci student, who is thrilled to join this trailblazing team at the UFS-NGS Unit and looking forward to contributing to the critical work of improving the health of those affected by viral induced enteric diseases in Africa.

She is eager to learn NGS techniques, with particular focus and link on the Sequencing and Antigenic Cartography of Enteric Viruses (SACEV). With the guidance of Prof. Nyaga, she is confident of growing exponentially in this field. Miss Shange is upfront to appreciate the reception and warm welcome from her new colleagues/peers at the UFS-NGS Unit and is positive that they have a conducive environment that would support her research development to attain her full potential as an emerging young African scholar and researcher. She is looking forward to this incredible journey with a lot of optimism and hopes to push the boundaries of what’s possible in genomic surveillance and working together with the team at the UFS-NGS Unit in this incredible journey.

Ms. Angela Mbele

Ms. Angela Mbele is a first year M.MedSc student at the University of the Free State Next generation sequencing (UFS-NGS) Unit and registered within the Division of Virology under the supervision of Prof. Martin Nyaga and co-supervised by Dr. Emmanuel Ogunbayo. Her current research project is on clinical metagenomics in respiratory cases of unestablished aetiologies from the national reference laboratory in the Free State province, South Africa.

Ms. Mbele attained her B.Sc Biomedical science undergraduate degree (University of South Africa) in 2020 and a B.Sc Hons degree (Sefako Makgatho Health science University) in 2023. Her research was based on the Investigation of Mycoplasma genitalium in Men (MSM) having sex with men in Ga Rankuwa, Pretoria.

Ms. Mamello Maku

Ms. Mamello Maku, B.Sc. in Forensic Science (University of the Free State (UFS), 2022), joined the UFS-NGS Unit on 01st June 2024 as a Scientific Administrative Intern under the Provident Software Solutions Program.

Mamello is excited to support the team with day-to-day tasks, learn the ropes, and contribute to the success of the UFS-NGS unit. She is eager to apply her skills and knowledge in a real-world setting. With strong organizational and communication skills, she’s looking forward to assisting with projects, data entry, and general administrative duties.

Ms. Maku is a quick learner, a team player, and enthusiastic about her growth in this facility under the supervision of Prof. Martin M. Nyaga.

This will enable her to gain new knowledge and enhance her skills in the NGS field. She is ready to pick up skills that can develop her abilities through sustained laboratory time.

Ms. Suprise Baloyi

Ms. Suprise Baloyi, a 2025 intern at the University of the Free State Next Generation Sequencing (UFS-NGS) Unit holds a BSc Microbiology honours degree (University of Pretoria) and recently completed her MSc in Medical Virology (Sefako Makgatho Health Sciences University).

Her research in Hepatitis B virus (HBV) mutations and their impact on occult HBV status, sparked her interest in NGS and applications of bioinformatics including protein modelling and molecular docking and in creating innovative solutions for infectious diseases.

She joins the UFS-NGS unit in 2025 as a DIPLOMICS-SA supported intern and expresses her enthusiasm to further learn and upskill herself in this transformative field through the mentorship of Prof. Martin Nyaga.

Ms. Siphe Thabisa Mpaxa

Ms. Siphe Thabisa Mpaxa holds a Bachelor of Science (BSc) degree in Genetics and Microbiology from the University of South Africa and a Bachelor of Medical Science (BMedSc) Honours degree (Cum Laude), from the University of the Free State (UFS). Her academic excellence was recognized with the prestigious Van Rensburg/Lancet Pathology Laboratory Prize, awarded to the BMedSc (Hons) student with the highest research component mark in Pathology, underscoring her outstanding research capabilities and dedication to scientific advancement in 2024.

Currently, Ms. Mpaxa is pursuing a Master of Medical Science (M.MedSc.) degree in Virology at UFS in the Division of Virology and the UFS-NGS Unit. Her current research, titled “Unveiling the Molecular Epidemiology, Genetic Diversity, and Clinical Impact of Human Metapneumovirus (HMPV) in Respiratory Infections in South Africa,” is supervised by Prof. Martin Nyaga and co-supervised by Dr. Emmanuel Ogunbayo. This work aims to deepen the understanding of HMPV infections, contributing valuable insights to molecular virology and public health.

Driven by a passion for genomics and infectious disease research, Ms. Mpaxa is committed to advancing viral diagnostics, precision medicine, and global health initiatives. Her journey at the UFS-NGS Unit continues to shape her expertise, fostering her growth as a researcher at the forefront of molecular innovation. With a keen interest in genomic technology, she aspires to make impactful contributions to the evolving landscape of medical science.

Ms. Mbali Ncube

Ms. Mbali Ncube, a 2025 intern at the University of the Free State Next Generation Sequencing (UFS-NGS) Unit holds a Bachelor of Science (BSc) degree in Genetics and Developmental Biology, as well as Biochemistry and Cell Biology, from the University of the Witwatersrand. She further pursued a Bachelor of Health Sciences (B.HSc.) Honours in Human Genetics at the same institution. Her honours research focused on identifying and analysing genetic variants associated with Xeroderma Pigmentosum using a targeted Next-Generation Sequencing (NGS) panel. This project ignited her passion for integrating both wet lab and computational approaches to tackle complex biological questions.

Ms. Mbali, one of the two 2025 DIPLOMICS-SA supported interns under the mentorship of Prof. Martin Nyaga at the UFS-NGS Unit, eludes strong interest in genomic research, is dedicated to understanding intricate biological systems and leveraging genomics to address pressing challenges in health and disease. Her internship serves as a pivotal step in her career, providing hands-on experience in viral metagenomics, bioinformatics, and NGS-based research. By acquiring advanced technical and analytical skills, she aspires to contribute to cutting-edge genomic studies that enhance disease surveillance and diagnostics across Africa.

Current Lab Members

Teaching and Training

Prof. Martin Munene Nyaga

Dr. Ayodeji Emmanuel Ogunbayo

Dr. Milton Tshidiso Mogotsi

Ms. Sesiyanda Maseko

Ms. Somila Nazo

Ms. Hlengiwe Sondlane

Ms. Eyong Manyi Marcelle

Ms. Nkosazana Shange

Ms. Angela Mbele

Ms. Mamello Maku

Ms. Suprise Baloyi

Ms. Siphe Thabisa Mpaxa

Ms. Mbali Ncube

Prof. Martin Munene Nyaga

Dr. Ayodeji Emmanuel Ogunbayo

Dr. Milton Tshidiso Mogotsi

Ms. Sesiyanda Maseko

Ms. Somila Nazo

Miss Hlengiwe Sondlane

Ms. Eyong Manyi Marcelle

Miss Nkosazana Shange

Ms. Angela Mbele

Ms. Mamello Maku

Ms. Suprise Baloyi

Ms. Siphe Thabisa Mpaxa

Ms. Mbali Ncube