Thumbi Ndung’u
Professor Thumbi Ndung’u is interested in understanding antiviral immune mechanisms and viral adaptation in HIV-1 subtype C infection as a pathway to vaccine development. His work has focussed on understudied populations and viral strains in resource-limited, high burden settings where knowledge of the role of antiviral immune responses, viral strains and associated genetic factors is likely to yield the greatest impact in terms of biomedical interventions like vaccines. Thumbi’s early work addressed the lack of biological tools for HIV vaccine and pathogenesis research on HIV-1 subtype C, the predominant subtype globally and in southern Africa. He generated and characterised the first infectious molecular of HIV-1 subtype C from primary isolates, and constructed the first infectious subtype C envelope-derived simian-human immunodeficiency virus able to replicate in rhesus macaque peripheral blood mononuclear cells. These tools were deposited in the NIH AIDS reagent program and remain available to researchers. The tools have facilitated in vitro and animal model studies of HIV-1 subtype C biology and vaccine development research.
Thumbi also actively participates in the training of graduate and postdoctoral researchers and has a special interest in capacity building for biomedical research in Africa. He is director for basic and translational science at AHRI, and a member of AHRI faculty. He is an investigator and Max Planck Institute for Infection Biology Research group leader. He is also a University of KwaZulu-Natal (UKZN) professor and Victor Daitz Chair in HIV/TB Research, adjunct professor at the Harvard School of Public Health, the scientific director at UKZN’s HIV Pathogenesis Programme, the programme director for the Sub-Saharan African Network for TB/HIV Research Excellence (SANTHE) and is the South African research chair in systems biology of HIV/Aids.
Get in touch with Thumbi via thumbi.ndungu@ahri.org
Click here for a full list of publications.
Ndung’u Group
The Ndung’u research group’s overarching goal is discovery and translational research to understand how HIV, TB, and SARS-CoV-2 persist and replicate in the face of a hostile host immune system. Ultimately, the group hopes to use this knowledge to aid the design of effective vaccines or immune-based therapies.
The group focuses on understanding how interactions between the host immune system and the pathogen affect clinical outcomes following exposure or infection. The group is also interested in pathogen diversity and its consequences for the spread of disease. The group works with samples from donors with heterogeneous immune control of HIV, TB, or SARS-CoV-2, both in the absence or presence of treatment. The lab’s approach is to understand how innate and adaptive immune responses may prevent people from getting infected or lead to durable viral control in those already infected. The lab also interrogates the mechanisms that ultimately lead to loss of immune control and disease progression, particularly pathogen adaptation to or evasion of host immune responses.
The Ndung’u Group researchers use techniques in virology, immunology, molecular biology, and genetics to understand the complex interaction between the host and pathogen. The Ndung’u Group places emphasis on basic and translational scientific research excellence and the building of the next generation of African scientific research leaders. Some of the work from the group is already being translated into prophylactic or curative strategies.
Meet the Team
Kavidha Reddy
Research associate
Kavidha Reddy earned her PhD at the University of KwaZulu-Natal studying host restriction factors in HIV-1 infection and viral adaptation. Her current research focuses on the persistent latent HIV reservoir, the main barrier to a cure, by characterising reservoirs with novel technologies and investigating factors driving their establishment and persistence. Centered on women and children disproportionately affected by HIV, her work aims to inform cure strategies for non-subtype B infections in African populations.
Omolara Baiyegunhi
Research associate
Omolara Baiyegunhi received her PhD in Immunology from UKZN. Her project characterised T follicular helper cells in hyperacute HIV-1 infection and defined the dynamics of HIV-1 persistence in early-treated individuals, with a particular focus on HIV persistence in lymph nodes. Lymph nodes are sanctuary sites where the virus hides away from the immune system. Her current research investigates the characteristics of transmitted/founder viruses and aims to define the immune responses induced during very early stages of acute HIV-1 infection.
Judie Magura
Postdoctoral fellow
Judie Magura holds a PhD in physiology from the University of KwaZulu-Natal. Her previous research investigated the effects of flavonoids on apoptotic factors and microRNA expression in breast cancer cells. As a postdoctoral research fellow at the Africa Health Research Institute, she now focuses on characterising B-cell immunity. Her work involves using advanced techniques like the 10X Genomics scRNA-seq platform, which she helped establish, to perform single-cell analysis and deep immune profiling of B cells for HIV vaccine research. Her research aims to understand bulk B-cell repertoires and class-specific B-cell precursors to inform the design of effective vaccines.
Daniel Muli Muema
Postdoctoral fellow
Daniel Muli Muema completed his PhD training at Open University UK in collaboration with University of Liverpool and KEMRI-Wellcome Trust Research Programme. Having previously described the defects of B cells in HIV-infected children, Daniel is now investigating the causes of such defects. Since B cells produce antibodies that are the focus of current HIV vaccine research, understanding the mechanisms of B-cell defects in HIV will enable the design of vaccines that can elicit effective antibody responses against the virus.
Nicole Reddy
PhD student
Nicole Reddy holds an Honours degree in Medical Microbiology from the Nelson R Mandela School of Medicine. For Nicole’s Master’s project, she characterised the anti-APOBEC3 activity of founder vif variants and longitudinally assessing vif sequences and functional changes over the course of one year of HIV infection, under the mentorship of Postdoctoral Fellow Kavidha Reddy.
Qondubuhle Dube
Masters student
Qondubuhle obtained his bachelor of health sciences and honours (Virology) degree from the University of the Witwatersrand, with distinction. As a master's student at AHRI, his work focuses on investigating the association between transmitted/founder HIV and their reservoir dynamics in a cohort undergoing antiretroviral therapy for a year and a half in Durban.
Sam Rasehlo
Laboratory technician
Sam Rasehlo completed his MSc at the University of Pretoria . His MSc work focused on determining the effects of cigarette smoke on antimycobacterial activity of anti-tuberculosis drugs on Mycobacterium tuberculosis biofilm. Sam is currently working with Dr Daniel Muema to determine the causes of B cell defects in HIV.
Selected Recent Publications
Catherine K. Koofhethile, Zaza M. Ndhlovu, Christina Thobakgale-Tshabalala, Julia G. Prado, Nasreen Ismail, Zenele Mncube, Lungile Mkhize, Mary van der Stok, Nonhlanhla Yende, Bruce D. Walker, Philip J.R. Goulder and Thumbi Ndung’u. (2016). CD8+ T cell breadth and ex vivo virus inhibition capacity distinguish between viremic controllers with and without protective HLA class I alleles. Journal of Virology, Jul 11;90(15):6818-31. doi: 10.1128/JVI.00276-16. Print 2016 Aug 1. PMID: 27194762.
Kavidha Reddy, Marcel Ooms, Michael Letko, Nigel Garrett, Viviana Simon and Thumbi Ndung’u. (2016). Functional characterization of Vif proteins from HIV-1 infected patients with different APOBEC3G haplotypes. AIDS, Jul 17;30(11):1723-9. doi: 10.1097/QAD.0000000000001113. PMID: 27064995.
Paradise Madlala, Ravesh Singh, Ping An, Lise Werner, Koleka Mlisana, Salim S. Abdool Karim, Cheryl A. Winkler, and Thumbi Ndung’u. (2016). Association of polymorphisms in the regulatory region of the cyclophilin A gene (PPIA) with gene expression and HIV/AIDS disease progression. Journal of Acquired Immune Deficiency Syndromes, Aug 15;72(5):465-73. doi: 10.1097/QAI.0000000000001028. PMID: 27088296.
Jonathan M. Carlson, Victor Y. Du, Nico Pfeifer, Anju Bansal, Vincent Y.F. Tan, Karen Power, Chanson J. Brumme, Anat Kreimer, Charles E. DeZiel, Nicolo Fusi, Malinda Schaefer, Mark A. Brockman, Jill Gilmour, Matt A. Price, William Kilembe, Richard Haubrich, Mina John, Simon Mallal, Roger Shapiro, John Frater, P. Richard Harrigan, Thumbi Ndung’u, Susan Allen, David Heckerman, John Sidney, Todd M. Allen, Philip J.R. Goulder, Zabrina L. Brumme, Eric Hunter, Paul A. Goepfert. (2016). Impact of Pre-adapted HIV Transmission. Nature Medicine, Jun;22(6):606-13. doi: 10.1038/nm.4100. Epub, May 16. PMID: 27183217.
Henrik N. Kløverpris, Samuel W. Kazer, Jenny Mjösberg, Jenniffer M. Mabuka, Amanda Wellmann, Zaza Ndhlovu, Marisa C. Yadon, Shepherd Nhamoyebonde, Maximilian Muenchhoff, Yannick Simoni, Frank Andersson, Warren Kuhn, Nigel Garrett, Wendy A. Burgers, Philomena Kamya, Karyn Pretorius, Krista Dong, Amber Moodley, Evan W. Newell, Victoria Kasprowicz, Salim S. Abdool Karim, Philip Goulder, Alex K. Shalek, Bruce D. Walker, Thumbi Ndung’u, Alasdair Leslie. (2016). Innate Lymphoid Cells Are Depleted Irreversibly during Acute HIV-1 Infection in the Absence of Viral Suppression. Immunity, Feb 1. pii: S1074-7613(16)00030-3. doi: 10.1016/j.immuni.2016.01.006. [Epub ahead of print]. PMID: 26850658.