Mopo Radebe, Kamini Gounder, Mammekwa Mokgoro, Zaza M. Ndhlovu, Zenele Mncube, Lungile Mkhize, Mary van der Stok, Manjeetha Jaggernath, Bruce D. Walker, Thumbi Ndung’u. Broad and persistent Gag-specific CD8+ T-cell responses are associated with viral control but rarely drive viral escape during primary HIV-1 infection. In press, AIDS.

Y. Mahabeer, C.C. Chang, D. Naidu, A.A. Dorasamy, S.R. Lewin, T. Ndung’u, M-Y. S. Moosa, M.A. French, K.P. Mlisana, Y.M. Coovadia. Comparison of Etests and Vitek 2® to Broth Microdilution for the Susceptibility Testing of Cryptococcus neoformans. Diagnostic Microbiology and Infectious Disease 2014 Sep 16. pii: S0732-8893(14)00368-X. doi: 10.1016/j.diagmicrobio.2014.09.006. [Epub ahead of print]. PMID: 25277745.

Jonas Demeulemeester, Sofie Vets, Rik Schrijvers, Paradise Madlala, Marc De Maeyer, Jan De Rijck, Thumbi Ndung’u, Zeger Debyser, Rik Gijsbers. HIV-1 integrase variants retarget viral integration and are associated with disease progression in a chronic infection cohort. In press, Cell Host and Microbe.

Jaclyn K. Mann, Denis R. Chopera, Saleha Omarjee, Xiaomei T. Kuang, Anh Q. Le, Gursev Anmole, Ryan Danroth, Philip Mwimanzi, Tarylee Reddy, Jonathan Carlson, Mopo Radebe, Philip J.R. Goulder, Bruce D. Walker, Salim Abdool Karim, Vladimir Novitsky, Carolyn Williamson, Mark A. Brockman, Zabrina L. Brumme, Thumbi Ndung’u. Nef-mediated down-regulation of CD4 and HLA class I in HIV-1 subtype C infection: association with disease progression and influence of immune pressure. In press, Virology. Virology. 2014 Sep 2;468-470C:214-225. doi: 10.1016/j.virol.2014.08.009. [Epub ahead of print]. PMID: 25193656.

Shivan Chetty, Filippos Porichis, Pamla Govender, Jennifer Zupkosky, Musie Ghebremichael, Mona Pillay, Bruce D. Walker, Thumbi Ndung’u, Daniel E. Kaufmann, Victoria O. Kasprowicz. Tuberculosis distorts the inhibitory impact of IL-10 in HIV infection. AIDS 2014 Sep 10. [Epub ahead of print]. PMID: 25211438.

Maximilian Muenchhoff, Savathee Madurai, Allison J Hempenstall, Emily Adland, Anna Carlqvist, Angeline Moonsamy, Manjeetha Jaggernath, Busisiwe Mlotshwa, Emma Siboto, Thumbi Ndung’u, Philip JR Goulder. Evaluation of the NucliSens EasyQ v2.0 Assay in Comparison with the Roche Amplicor v1.5 and the Roche CAP/CTM HIV-1 Test v2.0 in Quantification of C-Clade HIV-1 in Plasma. PLoS One 2014 Aug 26;9(8):e103983. doi: 10.1371/journal.pone.0103983. eCollection 2014. PMID: 25157919.

Vinod B. Patel, Cathy Connolly, Ravesh Singh, Laura Lenders, Brian Matinyenya, Grant Theron, Thumbi Ndung'u, Keertan Dheda. Comparison of Amplicor and GeneXpert MTB/RIF for Diagnosis of Tuberculous Meningitis. Journal of Clinical Microbiology 2014 Oct;52(10):3777-80. doi: 10.1128/JCM.01235-14. Epub 2014 Jul 23. PMID: 2505632.

Jaclyn K. Mann, John P. Barton, Andrew L. Ferguson, Saleha Omarjee, Bruce D. Walker, Arup Chakraborty, Thumbi Ndung’u. The Fitness Landscape of HIV-1 Gag: Advanced Modeling Approaches and Validation of Model Predictions by In Vitro Testing. PLoS Computational Biology 2014 Aug 7;10(8):e1003776. doi: 10.1371/journal.pcbi.1003776. eCollection 2014. PMID: 25102049

Jonathan M. Carlson, Malinda Schaefer, Daniela Monaco, Rebecca Batorsky, Daniel T. Claiborne, Jessica Prince, Martin J. Deymier, Zachary S. Ende, Nichole R. Klatt, Charles E. DeZiel, Tien-Ho Lin, Jian Peng, Aaron Seese, Roger Shapiro, John Frater, Thumbi Ndung’u, Jianming Tang, Paul Goepfert, Jill Gilmour, Matt A. Price, William Kilembe, David Heckerman, Philip J.R. Goulder, Todd M. Allen, Susan Allen and Eric Hunter. Selection bias at the heterosexual HIV-1 transmission bottleneck. Science 2014 Jul 11;345(6193):1254031. doi: 10.1126/science.1254031. Epub 2014 Jul 10. PMID: 25013080

Elisabeth Kleppa, Veron Ramsuran, Sipho Zulu, Gunn Hege Karlsen, Alfred Bere, Jo-Ann Passmore, Patricia Ndhlovu, Kristine Lillebø, Sigve D. Holmen, Mathias Onsrud, Svein Gunnar Gundersen, Myra Taylor, Eyrun F. Kjetland and Thumbi Ndung’u. Effect of Female Genital Schistosomiasis and Anti-Schistosomal Treatment on Monocytes, CD4+ T-Cells and CCR5 in the Female Genital Tract. PLoS One 2014 Jun 4;9(6):e98593. doi: 10.1371/journal.pone.0098593. eCollection 2014. PMID 24896815.

Rebecca Payne, Songee Branch, Henrik Kloverpris, Philippa Matthews, Catherine Koofhethile, Tom Strong, Emily Adland, Ellen Leitman, Alexander John Frater, Thumbi Ndung’u, Eric Hunter, Richard Haubrich, Beatriz Mothe, Anne Edwards, Lynn Riddell, Fabian Chen, Richard Harrigan, Zabrina Brumme, Simon Mallal, Mina John, Pieter Jooste, Roger Shapiro, Steven Deeks, Bruce Walker, Christian Brander, Clive Landis, Jonathan Carlson, Julia Prado, and Philip Goulder. Differential escape patterns within the dominant HLA-B*57:03-restricted HIV Gag epitope reflect distinct clade-specific functional constraints. Journal of Virology 2014 May;88(9):4668-78. doi: 10.1128/JVI.03303-13. Epub 2014 Feb 5. PMID: 24501417.

Ravesh Singh, Vinod Patel, Marianne W. Mureithi, Vivek Naranbhai, Duran Ramsuran, Sahil Tulsi, Keshni Hiramen, Lise Werner, Koleka Mlisana, Marcus Altfeld, Jeremy Luban, Victoria Kasprowicz, Keertan Dheda, Salim S. Abdool Karim, Thumbi Ndung’u. TRIM5α and TRIM22 are differentially regulated according to HIV-1 infection phase and compartment. Journal of Virology 2014 Apr;88(8):4291-303. doi: 10.1128/JVI.03603-13. Epub 2014 Jan 29. PMID: 24478420.

Vivek Naranbhai, Christina C. Chang, Raveshni Durgiah, Saleha Omarjee, Andrew Lim, Mahomed-Yunus S. Moosa, Julian H. Elliot, Thumbi Ndung’u, Sharon R. Lewin, Martyn A. French, William H. Carr. Compartmentalisation of innate immune responses in the central nervous system during cryptococcal meningitis/HIV co-infection. AIDS 2014 Mar 13;28(5):657-666. PMID: 24451162.

Mathieu Angin, Paul L. Klarenbeek, Melanie King, Eshia S. Moodley, Ashley Rezai, Alicja Piechocka-Trocha, Ildiko Toth, Philip Goulder, Thumbi Ndung’u, Douglas S. Kwon, Marylyn M. Addo. Regulatory T cells expanded from HIV-1-infected individuals maintain phenotype, TCR repertoire and suppressive capacity. PLoS One 2014 Feb 3;9(2):e86920. doi: 10.1371/journal.pone.0086920. eCollection 2014. PMID: 24498287.

Emily Wong, Ngomu Akeem Akilimali , Pamla Govender, Zuri Sullivan, Cormac Cosgrove, Mona Pillay, David M. Lewinsohn, William R. Bishai, Bruce D. Walker, Thumbi Ndung’u, Paul Klenerman, Victoria O. Kasprowicz. Low levels of peripheral CD161++CD8+ Mucosal Associated Invariant T (MAIT) cells are found in HIV and HIV/TB co-infection. PLoS One 2013 Dec 31;8(12):e83474. doi: 10.1371/journal.pone.0083474. PMID: 24391773.

Christina F Thobakgale and Thumbi Ndung’u. Neutrophil Counts in Persons of African Origins. Current Opinion in Hematology 2014 Jan;21(1):50-7. doi: 10.1097/MOH.0000000000000007. PMID: 24257098.

Jaclyn K Mann, Helen Byakwaga, Xiaomei T Kuang, Anh Q Le, Chanson J Brumme, Philip Mwimanzi, Saleha Omarjee, Eric Martin, Guinevere Q Lee, Bemuluyigza Baraki, Ryan Danroth, Rosemary McCloskey, Conrad Muzoora, David R Bangsberg, Peter W Hunt, Philip JR Goulder, Bruce D Walker, P Richard Harrigan, Jeff N Martin, Thumbi Ndung’u, Mark A Brockman and Zabrina L Brumme. Ability of HIV-1 Nef to downregulate CD4 and HLA class I differs among viral subtypes. Retrovirology 2013 16;10:100. doi: 10.1186/1742-4690-10-100. PMID: 24041011.

Henrik N. Kløverpris, Emily Adland, Madoka Koyanagi, Anette Stryhn, Mikkel Harndahl, Philippa C. Matthews, Fabian Chen, Lynn Riddell, Bruce D. Walker, Thumbi Ndung’u, Roger Shapiro, Christian Brander, Masafumi Takiguchi, Søren Buus and Philip Goulder. HIV subtype influences HLA-B*07:02-associated HIV disease outcome. AIDS Research and Human Retroviruses 2013 Sep 6. [Epub ahead of print]. PMID: 24010680.

Vinod B Patel, Grant Theron, Laura Lenders, Brian Matinyena, Cathy Connolly, Ravesh Singh, Yacoob Coovadia, Thumbi Ndung’u, Keertan Dheda. Quantitative PCR (GeneXpert MTB/RIF) for the diagnosis of tuberculous meningitis in HIV-infected patients from a high burden setting: a prospective study. PLoS Medicine 2013 Oct;10(10):e1001536. doi: 10.1371/journal.pmed.1001536. Epub 2013 Oct 22. PMID: 24167451.

Emily Adland, Jonathan Carlson, Paolo Paioni, Henrik Kløverpris, Roger Shapiro, Anthony Ogwu, Lynn Riddell, Graz Luzzi, Fabian Chen, Thambiah Balachandran, David Heckerman, Anette Stryhn, Anne Edwards, Thumbi Ndung’u, Bruce D. Walker, Soren Buus, Philip Goulder, Philippa C Matthews. Nef-Specific CD8+ T Cell Responses Contribute to HIV-1 Immune Control. PLoS One 2013 Sep 2;8(9):e73117. doi: 10.1371/journal.pone.0073117. PMID: 24023819.

Henrik Kloverpris, Anette Stryhn, Mikkel Harndahl, Rebecca Payne, Greg Towers, Fabian Chen, Lynn Riddell, Bruce Walker, Thumbi Ndung’u, Alasdair Leslie, Søren Buus, and Philip Goulder. HLA-specific intracellular epitope processing shapes an immunodominance pattern for HLA-B*57 that is distinct from HLA-B*58:01. Journal of Virology 2013 Oct;87(19):10889-94. doi: 10.1128/JVI.01122-13. Epub 2013 Jul 17. PMID: 23864640.

Denis R. Chopera, Jaclyn K. Mann, Philip Mwimanzi, Saleha Omarjee, Xiaomei T. Kuang, Nonkululeko Ndabambi, Sarah Goodier, Eric Martin, Vivek Naranbhai, Salim Abdool Karim, Quarraisha Abdool Karim, Zabrina L. Brumme, Thumbi Ndung’u, Carolyn Williamson, Mark A. Brockman and the CAPRISA 004 TRAPS Team. No evidence for selection of HIV-1 with enhanced Gag-Protease or Nef function among breakthrough infections in the CAPRISA 004 tenofovir microbicide trial. PLoS One 2013 Aug 28;8(8):e71758. PMID: 24015191.

Christina C Chang, Saleha Omarjee, Andrew Lim, Tim Spelman, Bernadett I Gosnell, William H Carr, Julian H Elliott, Mohamed-Yunus S Moosa, Thumbi Ndung’u, Martyn A French, Sharon R Lewin. Chemokine levels and chemokine receptor expression in blood and the CSF of HIV-infected patients with cryptococcal meningitis and C-IRIS. Journal of Infectious Diseases 2013 Nov 15;208(10):1604-12. doi: 10.1093/infdis/jit388. Epub 2013 Aug 1. PMID: 23908492.

Christina C Chang, Afton A Dorasamy, Bernadett I Gosnell, Julian H Elliott, Tim Spelman, Saleha Omarjee, Vivek Naranbhai, Yacoob Coovadia, Thumbi Ndung’u, Mohamed-Yunus S Moosa, Sharon R Lewin, Martyn A French. Clinical and mycological predictors of Cryptococcosis-associated Immune reconstitution inflammatory syndrome (C-IRIS). AIDS 2013 Aug 24;27(13):2089-99. doi: 10.1097/QAD.0b013e3283614a8d. PMID: 23525034.

Henrik N. Kløverpris, Anette Stryhn, Mikkel Harndahl, Jonathan M. Carlson, Alasdair J Leslie, Fabian Chen, Lynn Riddell, Joseph Mulenga, Bruce D. Walker, Thumbi Ndung’u, Søren Buus and Philip Goulder. Gag-specific CD8+ T cell responses restricted by HLA-A*68:02 can drive selection pressure on HIV but are subdominant and ineffective in natural HIV infection. AIDS 2013 Jul 17;27(11):1717-1723.

Christina C Chang, Andrew Lim, Saleha Omarjee, Stuart M Levitz, Bernadett I Gosnell, Tim Spelman, Julian H Elliott, William H Carr, Mohamed-Yunus S Moosa, Thumbi Ndung’u, Sharon R Lewin, Martyn A French. Cryptococcosis-IRIS is associated with lower Cryptococcus-specific IFN-gamma responses before antiretroviral therapy but not higher T-cell responses during therapy. Journal of Infectious Diseases Jun 12. [Epub ahead of print].

Andrew Ferguson, Jaclyn K Mann, Saleha Omarjee, Thumbi Ndung’u, Bruce Walker, Arup Chakraborty.  Translating HIV sequences into quantitative fitness landscapes predicts viral vulnerabilities for rational immunogen design. Immunity 2013 Mar 21;38(3):606-17. doi: 10.1016/j.immuni.2012.11.022.

Michele W. Tang, Soo-Yon Rhee, Silvia Bertagnolio, Nathan Ford, Susan Holmes, Kim C. Sigaloff, Raph L. Hamers, Tobias F. Rinke de Wit, Herve J. Fleury, Phyllis J. Kanki, Kiat Ruxrungtham, Claudia A. Hawkins, Carole L. Wallis, Wendy Stevens, Gert U. van Zyl, Weerawat Manosuthi, Mina C. Hosseinipour, Nicole Ngo-Giang-Huong, Laurent Belec, Martine Peeters, Avelin Aghokeng, Torsak Bunupuradah, Sherri Burda, Patricia Cane, Giulia Cappelli, Charlotte Charpentier, Anoumou Y. Dagnra, Alaka K. Deshpande, Ziad El-Katib, Susan H. Eshleman, Joseph Fokam, Jean-Chrysostome Gody, David Katzenstein, Donato D. Koyalta, Johnstone J. Kumwenda, Marc Lallemant, Lutgarde Lynen, Vincent C. Marconi, Nicolas A. Margot, Sandrine Moussa, Thumbi Ndung’u, Phillipe N. Nyambi, Catherine Orrell, Jonathan M. Schapiro, Rob Schuurman, Sunee Sirivichayakul, Davey Smith, Maria Zolfo, Michael R. Jordan and Robert W. Shafer.  Nucleoside Reverse Transcriptase Inhibitor Resistance Mutations Associated with First-Line Stavudine-Containing Antiretroviral Therapy: Programmatic Implications for Countries Phasing Out Stavudine. Journal of Infectious Diseases 2013 Jun;207 Suppl 2:S70-7. doi: 10.1093/infdis/jit114.

Vivek Naranbhai, Natasha Samsunder, Netanya G. Sandler, Annalys Roque, Quarraisha Abdool Karim, Thumbi Ndung’u, William H. Carr, Marcus Altfeld, Daniel C. Douek, Salim S. Abdool Karim and the CAPRISA004 Trial Team. Neither microbial translocation nor TLR responsiveness are likely explanations for pre-existing immune activation in women who subsequently acquired HIV in CAPRISA004. Journal of Acquired Immune Deficiency Syndromes 2013 Jul 1;63(3):294-298.

Danaviah S, Sacks JA, Kumar KPS, Taylor L, Fallows DA, Naicker T, Ndung’u T, Govender S, Kaplan G. Immunohistological characterization of spinal TB granulomas from HIV-negative and -positive patients. Tuberculosis (Edinb). 2013 Mar 27. doi:pii: S1472-9792(13)00017-6. 10.1016/j.tube.2013.02.009. [Epub ahead of print]

Vivek Naranbhai, Marcus Altfeld, Salim S Abdool Karim ,Thumbi Ndung’u, Quarraisha Abdool Karim, and William H Carr. Changes in Natural Killer cell activation and function during primary HIV-1 infection. PLoS One 2013;8(1):e53251. doi: 10.1371/journal.pone.0053251. Epub 2013 Jan 9.