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• 2017 Publications

  1	Ngomu Akeem Akilimali, Christina C. Chang, Daniel M. Muema, Tarylee Reddy, Mahomed-Yunus S. Moosa, Sharon R. Lewin, Martyn A. French, and Thumbi Ndung’u. Plasma but not Cerebrospinal Fluid IL-7 and IL-5 Levels Pre-antiretroviral Therapy Commencement Predict Cryptococcosis-Associated Immune Reconstitution Inflammatory Syndrome. In press, Clinical Infectious Diseases.
  2	Vanessa L. Naidoo, Jaclyn K. Mann, Christie Noble, Emily Adland, Jonathan M. Carlson, Jake Thomas, Chanson J. Brumme, Christina F. Thobakgale-Tshabalala, Zabrina L. Brumme, Mark A. Brockman, Philip J.R. Goulder, Thumbi Ndung’u. Mother-to-Child HIV Transmission Bottleneck Selects for Consensus Virus with Lower Gag-Protease-driven Replication Capacity. Journal of Virology Jun 21. pii: JVI.00518-17. doi: 10.1128/JVI.00518-17. [Epub ahead of print]. PMID: 28637761.
  3	Colin P. Sharp, William F. Gregory, Louise Hattingh, Amna Malik, Emily Adland, Samantha Daniels, Anriette van Zyl, Jonathan M. Carlson, Susan Wareing, Anthony Ogwu, Roger Shapiro, Lynn Riddell, Fabian Chen, Thumbi Ndung’u, Philip J.R. Goulder, Paul Klenerman, Peter Simmonds, Pieter Jooste, Philippa C. Matthews. PARV4 prevalence, phylogeny, immunology and coinfection with HIV, HBV and HCV in a multicentre African cohort. Wellcome Open Research 2017 Apr 7;2:26. doi: 10.12688/wellcomeopenres.11135.1. PMID: 28497124.
  4	Guinevere Q. Lee, Nina Orlova-Fink, Kevin Einkauf, Fatema Chowdhury, Xiaoming Sun, Sean Harrington, Hsiao-Hsuan Kuo, Stephane Hua, HsiaoRong Chen, Zhengyu Ouyang, Kavidha Reddy, Krista Dong, Thumbi Ndung’u, Bruce D. Walker, Eric S. Rosenberg, Xu G. Yu, Mathias Lichterfeld. Clonal expansion of genome-intact HIV-1 in functionally-polarized Th1 CD4 T cells. Journal of Clinical Investigation 2017 Jun 19. pii: 93289. doi: 10.1172/JCI93289. [Epub ahead of print]. PMID: 28628034.
  5	Marion W. Kiguoya, Jaclyn K. Mann, Denis Chopera, Kamini Gounder, Guinevere Q. Lee, Peter W. Hunt, Jeffrey N. Martin, T. Blake Ball, Joshua Kimani, Zabrina L. Brumme, Mark A. Brockman, Thumbi Ndung’u. Subtype-Specific Differences in Gag-Protease-Driven Replication Capacity are Consistent with Inter-Subtype Differences in HIV-1 Disease Progression. Journal of Virology 2017 Jun 9;91(13). pii: e00253-17. doi: 10.1128/JVI.00253-17. Print 2017 Jul 1. PMID: 28424286.
  6	Christina C Chang, Richard Kangethe, Saleha Omarjee, Keshni Hiramen, Bernadett Gosnell, Katlego Sojane, Mohamed-Yunus S Moosa,  Sharon R Lewin, Martyn A French, Thumbi Ndung’u. Relationship of HIV RNA in CSF and plasma in patients co-infected with cryptococcal meningitis. Open Forum Infectious Diseases 2017 Feb 12;4(2):ofx032. doi: 10.1093/ofid/ofx032. eCollection 2017 Spring. PMID: 28470016.
  7	Christina Gosmann, Melis N. Anahtar, Scott A. Handley, Mara Farcasanu, Galeb Abu-Ali, Brittany A. Bowman, Nikita Padavattan, Chandni Desai, Lindsay Droit, Amber Moodley, Mary Dong, Yuezhou Chen, Nasreen Ismail, Thumbi Ndung’u, Musie S. Ghebremichael, Duane R. Wesemann, Caroline Mitchell, Krista L. Dong, Curtis Huttenhower, Bruce D. Walker, Herbert W. Virgin MD, Douglas S. Kwon. Lactobacillus-Deficient Cervicovaginal Bacterial Communities Are Associated with Increased HIV Acquisition in Young South African Women. Immunity 2017 Jan 17;46(1):29-37. doi: 10.1016/j.immuni.2016.12.013. Epub 2017 Jan 10. PMID: 28087240.
  8	Kamini Gounder, Micah Oyaro, Nagavelli Padayachi, Thando Mbali Zulu, Tulio de Oliveira, John Wylie and Thumbi Ndung’u. Complex subtype diversity of HIV-1 among drug users in major Kenyan cities. AIDS Research and Human Retroviruses 2017 May;33(5):500-510. doi: 10.1089/AID.2016.0321. Epub 2017 Mar 1. PMID: 28068781.
  9	Faatima Laher, Srinika Ranasinghe, Filippos Porichis, Nikoshia Mewalal, Karyn Pretorius, Nasreen Ismail, Søren Buus, Anette Stryhn, Mary Carrington, Bruce D. Walker, Thumbi Ndung'u, and Zaza M. Ndhlovu. HIV controllers exhibit enhanced frequencies of MHC class II tetramer+ Gag-specific CD4+ T cells in chronic clade C HIV-1 infection. Journal of Virology 2017 Mar 13;91(7). pii: e02477-16. doi: 10.1128/JVI.02477-16. Print 2017 Apr 1. PMID: 28077659.
  10	Christina Thobakgale, Kewreshini Naidoo, Lyle R. McKinnon, Lise Werner, Natasha Samsunder, Salim Abdool Karim, Thumbi Ndung’u, Marcus Altfeld and Kogieleum Naidoo. Interleukin 1-beta (IL-1β) production by innate cells following TLR stimulation correlates with TB recurrence in ART-treated HIV infected patients. Journal of Acquired Immune Deficiency Syndromes 2017 Feb 1;74(2):213-220. doi: 10.1097/QAI.0000000000001181. PMID: 27654812.
  11	Emily B. Wong, Thumbi Ndung’u, Victoria O. Kasprowicz. The role of MAIT cells in infectious diseases. Immunology 2017 Jan;150(1):45-54. doi: 10.1111/imm.12673. Review. PMID: 27633333.

• 2016 Publications

  1	Maximilian Muenchhoff, Emily Adland, Owen Karimanzari, Carol Crowther, Matthew Pace, Anna Csala, Ellen Leitman, Angeline Moonsamy, Callum McGregor, Jacob Hurst, Andreas Groll, Masahiko Mori, Smruti Sinmyee, Christina Thobakgale, Gareth Tudor-Williams, Andrew J Prendergast, Henrik Kloverpris, Julia Roider, Alasdair Leslie, Delane Shingadia, Thea Brits, Samantha Daniels, John Frater, Christian B Willberg, Bruce D Walker, Thumbi Ndung’u, Pieter Jooste, Penny L. Moore, Lynn Morris, Philip Goulder. Non-progressing HIV-infected children share fundamental immunological features of non-pathogenic SIV infection in sooty mangabey natural hosts. Science Translational Medicine 2016 Sep 28;8(358):358ra125. doi: 10.1126/scitranslmed.aag1048. PMID: 27683550.
  2	Ming-Han Tsai, Maximilian Muenchhoff, Emily Adland, Anna Carlqvist, Julia Roider, David K. Cole, Andrew K. Sewell, Jonathan Carlson, Thumbi Ndung’u, Philip J. Goulder. Paediatric non-progression following grandmother-to-child HIV transmission. Retrovirology 2016 Sep 8;13(1):65. doi: 10.1186/s12977-016-0300-y. PMID: 27608713.
  3	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. 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 2016 Jul 11;90(15):6818-31. doi: 10.1128/JVI.00276-16. Print 2016 Aug 1. PMID: 27194762.
  4	Kavidha Reddy, Marcel Ooms, Michael Letko, Nigel Garrett, Viviana Simon and Thumbi Ndung’u. Functional characterization of Vif proteins from HIV-1 infected patients with different APOBEC3G haplotypes. AIDS 2016 Jul 17;30(11):1723-9. doi: 10.1097/QAD.0000000000001113. PMID: 27064995.
  5	Paradise Madlala, Ravesh Singh, Ping An, Lise Werner, Koleka Mlisana, Salim S. Abdool Karim, Cheryl A. Winkler, and Thumbi Ndung’u. 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 2016 Aug 15;72(5):465-73. doi: 10.1097/QAI.0000000000001028. PMID: 27088296.
  6	Manjeetha Jaggernath, Rumallen Naicker, Savathree Madurai, Mark A Brockman, Thumbi Ndung’u, Huub C Gelderblom. Diagnostic accuracy of the HemoCue Hb 301, STAT-Site MHgb and URIT-12 point-of-care hemoglobin meters in a central laboratory and a community based clinic in Durban, South Africa. PLoS One 2016 Apr 5;11(4):e0152184. doi: 10.1371/journal.pone.0152184. eCollection 2016. PMID: 27046200.
  7	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. Impact of Pre-adapted HIV Transmission. Nature Medicine 2016 Jun;22(6):606-13. doi: 10.1038/nm.4100. Epub 2016 May 16. PMID: 27183217.
  8	Ellen M. Leitman, Jacob Hurst, Masahiko Mori, James Kublin, Thumbi Ndung’u, Bruce D. Walker, Jonathan Carlson, Glenda E. Gray, Philippa C. Matthews, Nicole Frahm, Philip J.R. Goulder. Lower Viral Loads and Slower CD4 Decline in MRKAd5 HIV-1 Vaccinees Expressing Disease-Susceptible HLA-B*58:02. Journal of Infectious Diseases 2016 Aug 1;214(3):379-89. doi: 10.1093/infdis/jiw093. Epub 2016 Mar 6. PMID: 26951820.
  9	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. Innate Lymphoid Cells Are Depleted Irreversibly during Acute HIV-1 Infection in the Absence of Viral Suppression. Immunity 2016 Feb 1. pii: S1074-7613(16)00030-3. doi: 10.1016/j.immuni.2016.01.006. [Epub ahead of print]. PMID: 26850658.
  10	V. Naranbhai, D. de Assis Rosa, L. Werner, R. Moodley, H. Hong, A. Kharsany, K. Mlisana, S. Sibeko, N. Garrett, D. Chopera, W.H. Carr, Q. Abdool Karim, A.V.S. Hill, S.S. Abdool Karim, M. Altfeld, C.M. Gray, T. Ndung’u. Killer-cell Immunoglobulin-like Receptor (KIR) gene profiles modify HIV disease course, not HIV acquisition in South African women. BMC Infectious Diseases 2016 Jan 25;16(1):27. doi: 10.1186/s12879-016-1361-1. PMID: 26809736.

• 2015 Publications

  1	Azure Tariro Makadzange, Molly Higgins-Biddle, Benjamin Chimukangara, Rutendo Birri, Michelle Gordon, Tatenda Mahlanza, Grace McHugh, Janneke van Dyjk, Mutsa Bwakura Dangarembizi, Thumbi Ndung'u, Collen Masimirembwa, Benjamin Phelps, Anouk Amzel, Bisola Ojikutu, Bruce Walker, Chiratidzo Ellen Ndhlovu. Clinical, virologic, immunologic outcomes and emerging HIV drug resistance patterns in children and adolescents in public ART care in Zimbabwe. PLoS One 2015 Dec 14;10(12):e0144057. doi: 10.1371/journal.pone.0144057. eCollection 2015. PMID: 26658814.
  2	Philippa C. Matthews, Jonathan M. Carlson, Apostolos Beloukas, Amna Malik, Pieter Jooste, Anthony Ogwu, Roger Shapiro, Lynn Riddell, Fabian Chen, Graz Luzzi, Gerald Jesuthasan, Katie Jeffery, Nebojsa Jojic, Thumbi Ndung’u, Mary Carrington, Philip J. R. Goulder, Anna Maria Geretti, Paul Klenerman. HLA-A is a Predictor of Hepatitis B e-Antigen Status in HIV-positive African Adults. Journal of Infectious Diseases 2016 Apr 15;213(8):1248-52. doi: 10.1093/infdis/jiv592. Epub 2015 Dec 9. PMID: 26655301.
  3	Elizabeth H. Byrne, Melis N. Anahtar, Kathleen E. Doherty, Amber Moodley, Nikita Padavattan, Nasreen Ismail, Brittany A. Bowman, Gregory S. Olson, Amanda Mabhula, Alasdair Leslie, Thumbi Ndung'u, Bruce D. Walker, Musie S. Ghebremichael, Krista L. Dong, Douglas S. Kwon. Association between progestin-only injectable contraceptives with HIV acquisition and HIV target cell frequency in the female genital tract in South African women: a prospective cohort study. Lancet Infectious Diseases 2016 Apr;16(4):441-8. doi: 10.1016/S1473-3099(15)00429-6. Epub 2015 Dec 24. PMID: 26723758.
  4	Jaclyn K. Mann, Saleha Omarjee, Phumzile Khumalo, Thumbi Ndung’u. Genetic determinants of Nef-mediated CD4 and HLA class I down-regulation differences between HIV-1 subtypes B and C. Virology Journal 2015 Nov 25;12(1):200. PMID: 26607225.
  5	Angelique Hölzemer, Christina F. Thobakgale, Camilo A. Jimenez Cruz, Wilfredo F. Garcia-Beltran, Jonathan M. Carlson, Nienke H. van Teijlingen, Jaclyn K. Mann, Manjeetha Jaggernath, Seung-gu Kang, Christian Körner, Amy Chung, Jamie L. Schafer, David T. Evans, Galit Alter, Bruce D. Walker, Philip J. Goulder, Mary Carrington, Pia Hartmann, Thomas Pertel, Ruhong Zhou, Thumbi Ndung’u, Marcus Altfeld. Selection of an HLA-C*03:04-restricted HIV-1 p24 Gag Sequence Variant is Associated with Viral Escape from KIR2DL3+ NK Cells: Data from an Observational Cohort in South Africa. PLoS Medicine 2015 Nov 17;12(11):e1001900. doi: 10.1371/journal.pmed.1001900. eCollection 2015. PMID: 26575988.
  6	Sivapragashini Danaviah, Tulio de Oliveira, Michelle Gordon, Shunmugam Govender, Paul Chelule, Sureshnee Pillay, Thajasvarie Naicker, Sharon Cassol, Thumbi Ndung’u. Analysis of dominant HIV quasispecies suggests independent viral evolution within spinal granulomas co-infected with Mycobacterium tuberculosis and HIV-1 subtype C. AIDS Research and Human Retroviruses 2016 Mar;32(3):262-270. Epub 2015 Dec 17. PMID: 26564424.
  7	Victoria O Kasprowicz, Tan-Yun Cheng, Thumbi Ndung’u, Henry Sunpath, D Branch Moody and Anne G Kasmar. HIV disrupts human T cells that target mycobacterial glycolipids. Journal of Infectious Diseases 2016 Feb 15;213(4):628-33. doi: 10.1093/infdis/jiv455. Epub 2015 Sep 15. PMID: 26374910.
  8	Zaza M. Ndhlovu, Philomena Kamya, Nikoshia Mewalal, Henrik N. Kløverpris, Thandeka Nkosi, Karyn Pretorius, Faatima Laher, Funsho Ogunshola, Denis Chopera, Karthik Shekhar, Musie Ghebremichael, Nasreen Ismail, Amber Moodley, Amna Malik, Alasdair Leslie, Philip J.R. Goulder, Søren Buus, Arup Chakraborty, Krista Dong, Thumbi Ndung’u and Bruce D. Walker. Magnitude and kinetics of CD8+ T cell activation during hyperacute HIV infection impact viral set point. Immunity 2015 Sep 5. pii: S1074-7613(15)00344-1. doi: 10.1016/j.immuni.2015.08.012. [Epub ahead of print]. PMID: 26362266.
  9	German G. Gornalusse, Srinivas Mummidi, Alvaro A. Gaitan, Fabio Jimenez, Veron Ramsuran, Anabela Picton, Kristen Rogers, Muthu Saravanan Manoharan, Nymisha Avadhanam, Krishna K. Murthy, Hernan Martinez, Angela Molano Murillo, Zoya A. Chykarenko, Richard Hutt, Demetre Daskalakis, Ludmila Shostakovich-Koretskaya, Salim Abdool Karim, Jeffrey N. Martin, Steven G. Deeks, Frederick Hecht, Elizabeth Sinclair, Robert A. Clark, Jason Okulicz, Fred T. Valentine, Neil Martinson, Caroline T. Tiemessen, Thumbi Ndung’u, Peter W. Hunt, Weijing He, Sunil K. Ahuja. Epigenetic mechanisms, T-cell activation, and CCR5 genetics interact to regulate T-cell expression of CCR5, the major HIV-1 coreceptor. Proceedings of the National Academy of Sciences of the United States of America. 2015 Aug 25;112(34):E4762-71. doi: 10.1073/pnas.1423228112. Epub 2015 Aug 11. PMID: 26307764.
  10	Philippa C Matthews, Apostolos Beloukas, Amna Malik, Jonathan M. Carlson, Pieter Jooste, Anthony Ogwu, Roger Shapiro, Lynn Riddell, Fabien Chen, Graz Luzzi, Manjeetha Jaggernath, Gerald Jesuthasan, Katie Jeffery, Thumbi Ndung’u, Philip J. Goulder, Anna Maria Geretti, Paul Klenerman. Prevalence and Characteristics of Hepatitis B Virus (HBV) Coinfection among HIV-Positive Women in South Africa and Botswana. PLoS One 2015 Jul 28;10(7):e0134037. doi: 10.1371/journal.pone.0134037. eCollection 2015. PMID: 26218239.
  11	Masahiko Mori, Emily Adland, Paolo Paioni, Alice Swordy, Luisa Mori, Leana Laker,Maximillian Muenchhoff, Philippa C. Matthews, Gareth Tudor-Williams, Nora Lavandier, Anriette van Zyl, Jacob Hurst, Bruce D. Walker, Thumbi Ndung'u, Andrew Prendergast, Philip Goulder, Pieter Jooste. Sex Differences in Antiretroviral Therapy Initiation in Pediatric HIV Infection. PLoS One 2015 Jul 7;10(7):e0131591. doi: 10.1371/journal.pone.0131591. eCollection 2015. PMID: 26151555.
  12	William Kilembe, Kristin M. Wall, Mammekwa Mokgoro, Annie Mwaanga, Elisabeth Dissen, Miriam Kamusoko, Hilda Phiri, Jean Sakulanda, Jonathan Davitte, Tarylee Reddy, Mark Brockman, Thumbi Ndung’u, Susan Allen. Implementation of Couples’ Voluntary HIV Counseling and Testing Services in Durban, South Africa. BMC Public Health 2015 Jul 2;15(1):601. PMID: 26136116.
  13	Emily Adland, Paolo Paioni, Christina Thobakgale, Leana Laker, Luisa Mori, Maximilian Muenchhoff, Anna Csala, Margaret Clapson, Jacquie Flynn, Vas Novelli, Jacob Hurst, Vanessa Naidoo, Roger Shapiro, Kuan-Hsiang Gary Huang, John Frater, Andrew Prendergast, Julia G Prado, Thumbi Ndung’u, Bruce D Walker, Mary Carrington, Pieter Jooste, Philip Goulder. Discordant Impact of HLA on Viral Replicative Capacity and Disease Progression in Pediatric and Adult HIV Infection. PLoS Pathogens 2015 Jun 15;11(6):e1004954. doi: 10.1371/journal.ppat.1004954. eCollection 2015 Jun. PMID: 26076345.
  14	George J. Xu, Tomasz Kula, Qikai Xu, Mamie Z. Li, Suzanne D. Vernon, Thumbi Ndung’u, Kiat Ruxrungtham, Jorge Sanchez, Christian Brander, Raymond Chung, Kevin C. O’Connor, Bruce Walker, H. Benjamin Larman, Stephen J. Elledge. Comprehensive serological profiling of human populations using a synthetic human virome. Science 2015 Jun 5;348(6239):aaa0698. doi: 10.1126/science.aaa0698. PMID: 26045439.
  15	Shih-Jung Pan, Asa Tapley, John Adamson, Tessa Little, Michael Urbanowski, Keira Cohen, Alexander Pym, Deepak Almeida, Afton Dorasamy, Jacques Grosset, Emily Layre, David C. Young, Ravesh Singh, Vinod B Patel, Kristina Wallengren, Thumbi Ndung'u, Douglas Wilson, D. Branch Moody, William Bishai. Biomarkers for tuberculosis based on secreted, species-specific, bacterial small molecules. Journal of Infectious Diseases 2015 May 26. pii: jiv312. [Epub ahead of print]. PMID: 26014799.
  16	Melis N. Anahtar, Elizabeth H. Byrne, Kathleen E. Doherty, Brittany A. Bowman, Hidemi S. Yamamoto, Magali Soumillon, Nikita Padavattan, Nasreen Ismail, Amber Moodley, Mary E. Sabatini, Musie S. Ghebremichael, Chad Nusbaum, Curtis Huttenhower, Herbert W. Virgin, Thumbi Ndung’u, Krista L. Dong, Bruce D. Walker, Raina N. Fichorova and Douglas S. Kwon. Cervicovaginal Bacteria Are a Major Modulator of Host Inflammatory Responses in the Female Genital Tract. Immunity 2015 May 19;42(5):965-976. doi: 10.1016/j.immuni.2015.04.019. PMID: 25992865.
  17	Henrik N. Kløverpris, Reuben McGregor, James McLaren, Kristin Ladell, Mikkel Harndahl, Anette Stryhn, Jonathan Carlson, Catherine Koofhethile, Can Kesmir, Fabian Chen, Lynn Riddell, Luzzi Graziano, Alasdair Leslie, Bruce D. Walker, Thumbi Ndung’u, Søren Buus, David Price and Philip Goulder. CD8+ T-cell receptor bias and immunodominance in HIV-1 infection. Journal of Immunology 2015 Jun 1;194(11):5329-45. doi: 10.4049/jimmunol.1400854. Epub 2015 Apr 24. PMID: 25911754.
  18	William Kilembe, Kristin M. Wall, Mammekwa Mokgoro, Annie Mwaanga, Elisabeth Dissen, Miriam Kamusoko, Hilda Phiri, Jean Sakulanda, Jonathan Davitte, Tarylee Reddy, Mark Brockman, Thumbi Ndung'u, Susan Allen.  Knowledge of HIV Serodiscordance, Transmission and Prevention among Couples in Durban, South Africa. PLoS One 2015 Apr 20;10(4):e0124548. doi: 10.1371/journal.pone.0124548. eCollection 2015. PMID: 25894583.
  19	Prabhat K. Sharma, Emily B. Wong, Ruth J. Napier, William R. Bishai, Thumbi Ndung’u, Victoria O. Kasprowicz, Deborah A. Lewinsohn, David M. Lewinsohn, Marielle C. Gold. High Expression of CD26 Accurately Identifies Human Bacterial-Reactive MR1-restricted MAIT cells. Immunology 2015 Mar 5. doi: 10.1111/imm.12461. [Epub ahead of print]. PMID: 25752900.
  20	Zuri A. Sullivan, Emily B. Wong, Thumbi Ndung’u, Victoria O. Kasprowicz, William R. Bishai. Latent and Active TB Infection Increase Immune Activation in Individuals Co-Infected with HIV. EBioMedicine 2015 Apr 1;2(4):334-340. PMID: 26114158.
  21	Kamini Gounder, Nagavelli Padayachi, Jaclyn K. Mann, Mopo Radebe, Mammekwa Mokgoro, Mary van der Stok, Lungile Mkhize, Zenele Mncube, Manjeetha Jaggernath, Tarylee Reddy, Bruce D. Walker and Thumbi Ndung’u. High frequency of transmitted HIV-1 Gag HLA class I-driven immune escape variants but minimal immune selection over the first year of clade C infection. PLoS One 2015 Mar 17;10(3):e0119886. doi: 10.1371/journal.pone.0119886. eCollection 2015. PMID: 25781986.
  22	Shivan Chetty, Pamla Govender, Jennifer Zupkosky, Mona Pillay, Musie Ghebremichael, Mahomed-Yunus S Moosa, Thumbi Ndung’u, Filippos Porichis, Victoria O. Kasprowicz. Co-infection with Mycobacterium tuberculosis impairs HIV-specific CD8+ and CD4+ T cell functionality. PLoS One 2015 Mar 17;10(3):e0118654. doi: 10.1371/journal.pone.0118654. eCollection 2015. PMID: 25781898.
  23	Jaclyn K. Mann and Thumbi Ndung’u. HIV-1 vaccine immunogen design strategies. Virology Journal 2015 Jan 24;12(1):3. [Epub ahead of print]. PMID: 25616599.
  24	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. AIDS 2015 Jan 2;29(1):23-33. doi: 10.1097/QAD.0000000000000508. PMID: 25387316.

• 2014 Publications

  1	Rebecca Payne, Maximilian Muenchhoff, Jaclyn Mann, Hannah E. Roberts, Philippa Matthews, Emily Adland, Allison Hempenstall, Kuan-Hsiang Huang, Mark Brockman, Zabrina Brumme, Marc Sinclair, Toshiyuki Miura, John Frater, Myron Essex, Roger Shapiro, Bruce D. Walker, Thumbi Ndung’u, Angela R. McLean, Jonathan M Carlson, Philip J.R. Goulder. Impact of HLA-driven HIV adaptation on virulence in populations of high HIV seroprevalence. Proceedings of the National Academy of Sciences USA 2014 Dec 16;111(50):E5393-400. doi: 10.1073/pnas.1413339111. Epub 2014 Dec 1. PMID: 25453107.
  2	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 Dec;80(4):294-8. doi: 10.1016/j.diagmicrobio.2014.09.006. Epub 2014 Sep 16. PMID: 25277745.
  3	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. Cell Host & Microbe 2014 Nov 12;16(5):651-662. doi: 10.1016/j.chom.2014.09.016. Epub 2014 Nov 12. PMID: 25525795.
  4	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. Virology 2014 Sep 2;468-470C:214-225. doi: 10.1016/j.virol.2014.08.009. [Epub ahead of print]. PMID: 25193656.
  5	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 Nov 28;28(18):2671-6. doi: 10.1097/QAD.0000000000000437. PMID: 25211438.
  6	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.
  7	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.
  8	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.
  9	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.
  10	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.
  11	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. In press, Journal of Virology.
  12	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 Jan 29. [Epub ahead of print]. PMID: 24478420.
  13	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 Jan 21. [Epub ahead of print]. PMID: 24451162.
  14	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. In press, PLoS One.
  15	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.

• 2013 Publications

  1	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.
  2	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):1717-23. doi: 10.1097/QAD.0b013e32836146cd. PMID: 23525031.
  3	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 2013 Sep;208(6):898-906. doi: 10.1093/infdis/jit271. Epub 2013 Jun 12. PMID: 23766525.
  4	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. PMID: 23521886.
  5	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):294-8. doi: 10.1097/QAI.0b013e31828e604b. PMID: 23481666.
  6	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]. PMID: 23541388.
  7	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.
  8	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. PMID: 23687292.
  9	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.
  10	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.
  11	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.
  12	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.
  13	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.
  14	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.
  15	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 Sep 16;10:100. doi: 10.1186/1742-4690-10-100. PMID: 24041011.
  16	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.

• 2012 Publications

  1	Philippa C. Matthews, Jennifer Listgarten, Jonathan M. Carlson, Rebecca Payne, Kuan-Hsiang Gary Huang, John Frater, Dominique Goedhals, Dewald Steyn, Cloete van Vuuren, Paolo Paioni, Pieter Jooste, Anthony Ogwu, Roger Shapiro, Zenele Mncube, Thumbi Ndung’u, Bruce D. Walker, David Heckerman, Philip J.R. Goulder. Co-operative Additive Effects between HLA Alleles in Control of HIV-1. PLoS One 2012; 7(10):e47799. doi: 10.1371/journal.pone.0047799. Epub 2012 Oct 19.
  2	Denis R. Chopera, Laura A. Cotton,  Alexander Zawaira, Jaclyn K. Mann, Nobubelo Ngandu, Roman Ntale, Jonathan M. Carlson, Koleka Mlisana, Zenda Woodman, Debra de Assis Rosa,  Eric Martin, Toshiyuki Miura, Florencia Pereyra, Bruce D. Walker, Clive M. Gray, Darren P. Martin, Thumbi Ndung’u, Mark A. Brockman, Salim Abdool Karim, Zabrina L. Brumme, Carolyn Williamson and the CAPRISA 002 Study Team. Intersubtype differences in the effect of a rare p24 Gag mutation on HIV-1 replicative fitness. Journal of Virology 2012 Dec; 86(24):13423-13433. Epub 2012 Sep 26.
  3	Philippa Matthews, Madoka Koyanagi, Henrik Kloverpris, Mikkel Harndahl, Anette Stryhn, Tomohiro Akahoshi, Hiroyuki Gatanaga, Shinichi Oka, Claudia Molina, Humberto Ponce, Santiago Rios, David Cole, Jonathan Carlson, Rebecca Payne, Anthony Ogwu, Alfred Bere, Thumbi Ndung'u, Kamini Gounder, Fabian Chen, Lynn Riddell, Graz Luzzi, Roger Shapiro, Christian Brander, Bruce Walker, Andrew Sewell, Gustavo Teran, David Heckerman, Eric Hunter, Søren Buus, Masafumi Takiguchi, and Philip Goulder. Differential clade-specific HLA-B*3501 association with HIV-1 disease outcome is linked to immunogenicity of a single Gag epitope. Journal of Virology 2012 Dec;86(23):12643-54. doi: 10.1128/JVI.01381-12. Epub 2012 Sep 12.
  4	Derseree Archary, Rong Rong, Michelle L Gordon, Saikat Boliar,  Maphuti Madiga, Elin S Gray, Anne-Sophie Dugast, Tandile Hermanus, Philip JR Goulder, Hoosen M Coovadia, Lise Werner, Lynn Morris, Galit Alter, Cynthia A Derdeyn and Thumbi Ndung’u. Characterization of anti-HIV-1 neutralizing and binding antibodies in chronic HIV-1 subtype C infection. Virology 2012 Nov 25;433(2):410-20. doi: 10.1016/j.virol.2012.08.033. Epub 2012 Sep 18.
  5	Henrik Kloverpris, Mikkel Harndahl, Alasdair Leslie, Jonathan Carlson, Nasreen Ismail, Mary van der Stok, Gary Huang, Fabian Chen, Lynn Riddell, Dewald Steyn, Dominique Goedhals, Cloete van Vuuren, John Frater, Bruce Walker, Mary Carrington, Thumbi Ndung'u, Søren Buus, and Philip Goulder. HIV control through a single nucleotide on the HLA-B locus. Journal of Virology 2012 Nov;86(21):11493-500. doi: 10.1128/JVI.01020-12. Epub 2012 Aug 15.
  6	Vivek Naranbhai, Marcus Altfeld, Quarraisha Abdool Karim, Thumbi Ndung’u, Salim S Abdool Karim and William H Carr on behalf of the CAPRISA 004 TRAPS Team. Natural Killer cell function in women at high risk for HIV acquisition: Insights from the CAPRISA 004 microbicide trial. AIDS 2012 Sep 10;26(14):1745-1753.
  7	Thumbi Ndung’u and Robin A Weiss. On HIV Diversity. AIDS 2012 Jun 19;26(10):1255-60.
  8	Jessica E. Mitchell, Shivan Chetty, Pamla Govender, Mona Pillay, Manjeetha Jaggernath, Anne Kasmar, Thumbi Ndung'u, Paul Klenerman P, Bruce D. Walker, Victoria O. Kasprowicz.  Prospective monitoring reveals dynamic levels of T cell immunity to Mycobacterium tuberculosis in HIV infected individuals. PLoS One 2012;7(6):e37920. Epub 2012 Jun 7.
  9	Christina F. Thobakgale, Lena Fadda, Kimberly Lane, Ildiko Toth, Florencia Pereyra, Suzane Bazner, Thumbi Ndung’u, Bruce D. Walker, Eric Rosenberg, Galit Alter, Mary Carrington, Todd Allen and Marcus Altfeld. Frequent and Strong Antibody-Mediated Natural Killer Cell Activation to HIV-1 Env in Individuals with Chronic HIV-1 Infection. Journal of Virology 2012 Jun;86(12):6986-93. Epub 2012 Apr 11.
  10	Jonathan M. Carlson, Jennifer Listgarten, Nico Pfeifer, Vincent Tan, Carl Kadie, Bruce D. Walker, Thumbi Ndung'u, Roger Shapiro, John Frater, Zabrina L. Brumme, Philip J. R. Goulder, David Heckerman. Widespread Impact of HLA Restriction on Immune Control and Escape Pathways in HIV-1. Journal of Virology 2012 May;86(9):5230-43. Epub 2012 Feb 29.
  11	Marianne Mureithi, Danielle Poole, Vivek Naranbhai, Shabashini Reddy, Nompumelelo Mkhwanazi, Sengeziwe Sibeko, Quarraisha Abdool Karim, Salim Abdool Karim, Thumbi Ndung'u, Marcus Altfeld. Preservation HIV-1-specific CD4+ T IFN-γ cell responses in breakthrough infections following exposure to Tenofovir Gel in the CAPRISA 004 microbicide trial. Journal of Acquired Immune Deficiency Syndromes 2012 Jun 1;60(2):124-127.
  12	Jaclyn K. Wright, Vanessa L. Naidoo, Zabrina L. Brumme, Jessica L. Prince, Daniel T. Claiborne, Philip J.R. Goulder, Mark A. Brockman, Eric Hunter, Thumbi Ndung’u. The impact of HLA-B*81-associated mutations in HIV-1 Gag on viral replication capacity. Journal of Virology 2012 Mar;86(6):3193-9. Epub 2012 Jan 11.
  13	Raabya Rossenkhan, Vladimir Novitsky, Teresa K Sebunya, Jean Leidner, Jose E Hagan, Sikhulile Moyo, Laura Smeaton, Shahin Lockman, Rosemary Musonda, Thumbi Ndung’u, Simani Gaseitsiwe, Ibou Thior, Mompati Mmalane, Joseph Makhema, M. Essex, and Roger Shapiro. Infant Feeding Practices Were Not Associated with Breast Milk HIV-1 RNA Levels in a Randomized Clinical Trial in Botswana. AIDS and Behavior 2012 Jul;16(5):1260-4.

• 2011 Publications

  1	Jaclyn K. Wright, Zabrina L. Brumme, Boris Julg, Mary van der Stok, Zenele Mncube, Xiaojiang Gao, Jonathan M. Carlson,  Philip J.R. Goulder, Bruce D. Walker, Mark A. Brockman, Thumbi Ndung’u. Lack of association between HLA class II alleles and in vitro replication capacities of recombinant viruses encoding HIV-1 subtype C Gag-protease from chronically infected individuals. Journal of Virology 2012 Jan;86(2):1273-6. Epub 2011 Nov 16.
  2	Henrik N. Kloverpris, Anette Stryhn, Mikkel Harndahl, Mary van der Stok, Rebecca P. Payne, Philippa C. Matthews, Fabian Chen, Lynn Riddell, Bruce D. Walker, Thumbi Ndung’u, Søren Buus and Philip Goulder. HLA-B*57 micropolymorphism shapes HLA allele-specific epitope immunogenicity, selection pressure and HIV immune control. Journal of Virology 2012 Jan;86(2):919-29. Epub 2011 Nov 16.
  3	Ndlovu BG, Danaviah S, Moodley E, Ghebremichael M, Bland R, Viljoen J, Newell M-L, Ndung’u T, and Carr WH. Use of dried blood spots for the determination of genetic variation of IL-10, Killer immunoglobulin-like receptor and HLA class I genes. Tissue Antigens 2012 Feb;79(2):114-22. doi: 10.1111/j.1399-0039.2011.01807.x. Epub 2011 Nov 22.
  4	Vanessa B. Kerry, Thumbi Ndung’u, Rochelle P. Walensky, Patrick T. Lee, V. Frederick I. B. Kayanja, and David R. Bangsberg. Managing the Demand for Global Health Education. PLoS Medicine Nov;8(11):e1001118. Epub 2011 Nov 8.
  5	Dshanta D. Naicker, Bingxia Wang, Elena Losina, Jennifer Zupkosky, Susan Bryan, Shabashini Reddy, Manjeetha Jaggernath, Mammekwa Mokgoro, Philip J.R. Goulder, Daniel E. Kaufmann, Thumbi Ndung’u. Association of IL-10 Promoter Genetic Variants with the Rate of CD4 T-cell Loss, IL-10 Plasma Levels and Breadth of Cytotoxic T-Cell Lymphocyte Response during Chronic HIV-1 Infection. Clinical Infectious Diseases 2012 Jan;54(2):294-302. Epub 2011 Nov 18.
  6	Vinod B Patel, Ravesh Singh, Cathy Connolly, Victoria Kasprowicz, Thumbi Ndung’u, Keertan Dheda. Comparative utility of cytokine levels and quantitative RD-1-specific T cell responses for the rapid immunodiagnosis of TB meningitis. Journal of Clinical Microbiology 2011 Nov;49(11):3971-6. Epub 2011 Aug 31.
  7	Thumbi Ndung’u. TRIM E3 ligases in HIV-1 infection: can these intrinsic immunity factors be harnessed for novel antiviral strategies? Virulence 2011 Jul-Aug;2(4):360-6. Epub 2011 Jul 1. Review.
  8	Taryn N. Green, Mohendran Archary, Michelle L. Gordon, Nagavelli Padayachi, Yolanda Lie, Elizabeth D. Anton, Jacqueline D. Reeves, Anneke Grobler, Raziya Bobat, Hoosen Coovadia and Thumbi Ndung'u. Drug Resistance and Coreceptor Usage in HIV-1 Subtype C Infected Children Initiating or Failing HAART in South Africa. AIDS Research and Human Retroviruses 2012 Apr;28(4):324-32. Epub 2011 Aug 5.
  9	Victoria O Kasprowicz, Jessica E Mitchell, Shivan Chetty, Pamla Govender, Kuan-Hsiang Gary Huang, Helen A Fletcher, Daniel P Webster, Sebastian Brown, Anne Kasmar, Cheryl L Day, Nompumelelo Mkhwanazi, Cheryl McClurg, Fundisiwe Chonco, Ajit Lalvani, Bruce D Walker, Thumbi Ndung'u, Paul Klenerman. A molecular assay for sensitive detection of pathogen-specific T-cells. PLoS One 2011;6(8):e20606. Epub 2011 Aug 11.
  10	Paradise Madlala, Rik Gijsbers, Frauke Christ, Anneleen Hombrouck, Lise Werner, Koleka Mlisana, Ping An, Salim S. Abdool Karim, Cheryl A. Winkler, Zeger Debyser and Thumbi Ndung’u. Association of Polymorphisms in the LEDGF/p75 Gene (PSIP1) with Susceptibility to HIV-1 Infection and Disease Progression. AIDS 2011 Sep 10;25(14):1711-9.
  11	Ashika Singh, Henry Sunpath, Taryn N. Green, Nagavelli Padayachi, Keshni Hiramen, Yolanda Lie, Elizabeth D. Anton, Richard Murphy, Jacqueline D. Reeves, Daniel R. Kuritzkes, Thumbi Ndung’u. Drug Resistance and Viral Tropism in HIV-1 Subtype C-Infected Patients in KwaZulu-Natal, South Africa: Implications for Future Treatment Options. Journal of Acquired Immune Deficiency Syndromes 2011 Nov 1;58(3):233-240.
  12	Mopo Radebe, Kriebashnie Nair, Fundisiwe Chonco, Karen Bishop, Jaclyn K. Wright, Mary van der Stok, Ingrid V. Bassett, Zenele Mncube, Marcus Altfeld, Bruce D. Walker and Thumbi Ndung’u. Limited immunogenicity of HIV CD8+ T-cell epitopes in acute clade C virus infection. Journal of Infectious Diseases 2011 Sep; 204 (5):768-78.
  13	Zaza M. Ndhlovu, Alicja Piechocka-Trocha, Seanna Vine, Ashley McMullen, Koofthethile C. Kegakilwe, Phillip J. Goulder, Thumbi Ndung’u, Dan H. Barouch and Bruce D. Walker. Mosaic HIV-1 Gag Antigens Can Be Processed and Presented to Human HIV-Specific CD8+ T Cells. Journal of Immunology 2011 Jun 15;186(12):6914-24. Epub 2011 May 16.
  14	Hannah O. Ajoge, Michelle L. Gordon, Sani Ibrahim, Oladapo S. Shittu, Thumbi Ndung’u, Stephen O. Olonitola. Drug resistance pattern of HIV-1 isolates sampled in 2007 from therapy-naive pregnant women in North-Central Nigeria. AIDS Research and Human Retroviruses 2012 Jan;28(1):115-8. Epub 2011 Jun 17.
  15	W.D. Francois Venter, Thumbi Ndung’u, and Quarraisha Abdool Karim. Case 15-2011: A 19-Year-Old South African Woman with Headache, Fatigue, and Vaginal Discharge. New England Journal of Medicine 2011 May 19;364(20):1956-64.
  16	Kuan-Hsiang Gary Huang, Dominique Goedhals, Jonathan M. Carlson, Mark Brockman, Swati Mishra, Zabrina Brumme, Stephen Hickling, Christopher Tang, Chris Seebregts, David Heckerman, Thumbi Ndung’u, Bruce Walker, Paul Klenerman, Dewald Steyn, Philip Goulder, Rodney Phillips, Cloete van Vuuren, Bloemfontein-Oxford Collaborative Group, John Frater. Progression to AIDS in South Africa is associated with both reverting and compensatory viral mutations. PLoS One 2011 Apr 22;6(4):e19018.
  17	Philippa C. Matthews, Emily Adland, Jennifer Listgarten, Alastair Leslie, Nompumelelo Mkhwanazi, Mikkel Harndahl, Rebecca Payne, Kuan-Hsiang Gary Huang, John Frater, Paolo Paioni, Henrik Kloverpris, Jonathan Carlson, Pieter Jooste, Lynn Riddell, Fabian Chen, Graziano Luzzi, Thambiah Balachandran, Thumbi Ndung’u, Søren Buus, Mary Carrington, Roger Shapiro, David Heckerman, Philip J.R. Goulder. HLA-A*7401-mediated control of HIV viremia is independent of its linkage disequilibrium with HLA-B*5703. The Journal of Immunology  2011 May 15;186(10):5675-86. Epub 2011 Apr 15.
  18	Vladimir Novitsky, Thumbi Ndung’u, Rui Wang, Hermann Bussmann, Fundisiwe Chonco, Joseph Makhema, Victor DeGruttola, Bruce D. Walker and Max Essex. Extended High Viremics: A Substantial Fraction of Individuals Maintain High Plasma Viral RNA Levels after Acute HIV-1 Subtype C Infection.  AIDS 2011 Jul 31;25(12):1515-22.
  19	Hannah O. Ajoge, Michelle L. Gordon, Tulio de Oliveira, Taryn N. Green, Sani Ibrahim, Oladapo S. Shittu, Stephen O. Olonitola, Aliyu A. Ahmad, Thumbi Ndung'u. Genetic characteristics, coreceptor usage potential and evolution of Nigerian HIV-1 subtype G and CRF02_AG isolates. PLoS One 2011 Mar 14;6(3):e17865.
  20	Christina F. Thobakgale, Hendrik Streeck, Nompumelelo Mkhwanazi, Zenele Mncube,  Lungile Maphumulo, Fundisiwe Chonco, Andrew Prendergast, Gareth Tudor-Williams, Bruce D. Walker, Philip J. R. Goulder, Marcus  Altfeld, and Thumbi Ndung’u. CD8+ T Cell Polyfunctionality Profiles in Progressive and Non-progressive Paediatric HIV-1 Infection. AIDS Research and Human Retroviruses 2011 Sep;27(9):1005-12. Epub 2011 Mar 21.
  21	Veron Ramsuran, Hemant Kulkarni, Weijing He, Koleka Mlisana, Edwina Wright, Lise Werner, John Castiblanco-Quinche, Rahul Dhanda, Tuan Le, Matthew Dolan, Weihua Guan, Robin Weiss, Robert Clark, Salim Abdool Karim, Sunil K. Ahuja, Thumbi Ndung'u. Duffy-Null-Associated Low Neutrophil Counts Influence HIV-1 Susceptibility in High-Risk South African Black Women. Clinical Infectious Diseases 2011 May;52(10):1248-56.
  22	Jaclyn K. Wright, Vladimir Novitsky, Mark A. Brockman, Zabrina L. Brumme, Chanson J. Brumme, Jonathan M. Carlson, David Heckerman, Bingxia Wang, Elena Losina, Mopo Leshwedi, Mary van der Stok, Lungile Maphumulo, Nompumelelo Mkhwanazi, Fundisiwe Chonco, Philip J.R. Goulder, Max Essex, Bruce D. Walker, Thumbi Ndung’u. Influence of Gag-Protease-Mediated Replication Capacity on Disease Progression in Individuals Recently Infected with HIV-1 Subtype C. Journal of Virology 2011 Apr;85(8):3996-4006. Epub 2011 Feb 2.
  23	Vivek Naranbhai, Pat Bartman, Dudu Ndlovu, Pamela Ramkalawon, Thumbi Ndung’u, Douglas Wilson, Marcus Altfeld, William H Carr. Impact of blood processing variations on Natural Killer cell frequency, activation, chemokine receptor expression and function. Journal of Immunological Methods 2011 Mar 7;366(1-2):28-35. Epub 2011 Jan.
  24	Manju Mamtani, Srinivas Mummidi, Veron Ramsuran, Minh-Hieu T. Pham, Robert Maldonado, Kazi Begum, Maria Soledad Valera, Racquel Sanchez, John Castiblanco, Hemant Kulkarni, Thumbi Ndung'u, Weijing He, Juan Manuel Anaya, Sunil K Ahuja. Influence of Variations in CCL3L1 and CCR5 on Tuberculosis in a Northwestern Colombian population. Journal of Infectious Diseases 2011 Jun;203(11):1590-4.
  25	Vinod B Patel, Ravesh Singh, Cathy Connolly, Victoria Kasprowicz, Allimudin Zumla, Thumbi Ndung’u, Keertan Dheda. Comparison of a clinical prediction rule and a LAM antigen-detection assay for the rapid diagnosis of TBM in a high HIV prevalence setting. PLoS One 2010 Dec 22;5(12):e15664.
  26	Hayley Crawford, Philippa C. Matthews, Malinda Schaefer, Jonathan M. Carlson, Alasdair Leslie, William Kilembe, Susan Allen, Thumbi Ndung’u, David Heckerman, Eric Hunter, Philip J.R. Goulder. The hypervariable HIV‑1 capsid protein residues comprise HLA‑driven CD8+ T‑cell escape mutations and covarying HLA‑independent polymorphisms. Journal of Virology 2011 Feb;85(3):1384-90. Epub 2010 Nov 24.
  27	Boris Julg, Eshia S. Moodley, Ying Qi, Danni Ramduth, Shabashini Reddy, Zenele Mncube, Xiaojiang Gao, Philip Goulder, Roger Detels, Thumbi Ndung’u, Bruce D. Walker and Mary Carrington. Possession of HLA class II DRB1*1303 associates with reduced viral loads in chronic HIV-1 clade C and B infection. Journal of Infectious Diseases 2011 Mar;203(6):803-9. Epub 2011 Jan 21.

• 2010 Publications

  1	Malene Erup Larsen, Henrik Kløverpris, Anette Stryhn, Catherine K. Koofhethile, Stuart Sims, Thumbi Ndung’u, Philip Goulder, Søren Buus, Morten Nielsen. HLArestrictor – a tool for patient-specific prediction of HLA restriction and optimal epitopes within peptides or proteins. Immunogenetics 2011 Jan;63(1):43-55. Epub 2010 Nov 16.
  2	Ravesh Singh, Gaurav Gaiha, Lise Werner, Kevin McKim, Koleka Mlisana, Jeremy Luban, Bruce D. Walker, Salim S. Abdool Karim, Abraham L. Brass, Thumbi Ndung’u, and the CAPRISA Acute Infection Study Team. Association of TRIM22 with the Type 1 Interferon Response and Viral Control during Primary HIV-1 Infection. Journal of Virology 2011 Jan;85(1):208-16. Epub 2010 Oct 27.
  3	Derseree Archary, Michelle L. Gordon, Taryn N. Green, Hoosen M. Coovadia, Philip J.R. Goulder and Thumbi Ndung'u. HIV‑1 subtype C envelope characteristics associated with divergent rates of chronic disease progression. Retrovirology 2010 Nov 4;7(1):92.
  4	Marianne W. Mureithi, Kristen Cohen, Ramona Moodley, Danielle Poole, Zenele Mncube, Anne Kasmar, D. Branch Moody, Philip Goulder, Bruce D. Walker, Marcus Altfeld and  Thumbi Ndung’u. Impairment of CD1d-restricted Natural Killer T cells in chronic HIV-1 clade C infection. AIDS Research and Human Retroviruses 2011 May; 27(5):501-9. Epub 2010 Dec 13.
  5	Morgane Rolland, Jonathan M. Carlson, Siriphan Manocheewa, J. Victor Swain, Erinn Lanxon-Cookson, Wenjie Deng, Christine M. Rousseau, Dana N. Raugi, Gerald H. Learn, Brandon S. Maust, Hoosen Coovadia, Thumbi Ndung'u, Philip J.R. Goulder, Bruce D. Walker, Christian Brander, David E. Heckerman and James I. Mullins. Amino-acid co-variation in HIV-1 gag subtype C: HLA-mediated selection pressure and compensatory dynamics. PLoS One. 2010 Sep 1;5(9). pii: e12463.
  6	Tammy M. Meyers and Thumbi Ndung'u. Case 18-2010. A 7-year-old boy with elevated HIV RNA levels despite antiretroviral medications. New England Journal of Medicine 2010 Jun 17; 362(24):2305-12.
  7	Dan H. Barouch*, Thumbi Ndung’u*, Galit Alter, Timothy Cardozo, Bhavna Chohan, Jacques Fellay, Nicole Frahm, Jonathan Fuchs, Al Leslie, Yong Liu, Penny Moore, Raul Rabadan. Young and Early Career Investigators: Report from a Global HIV Vaccine Enterprise Working Group. Nature Precedings: doi:10.1038/npre.2010.4800.2: Posted 7 Sep 2010. *Working Group Chairs
  8	Isobella Honeyborne, Francisco Codoñer, Alasdair Leslie,  Gareth Tudor-Williams, Graz Luzzi, Thumbi Ndung’u, Bruce D. Walker, Philip J.R. Goulder and Julia G. Prado. HLA-Cw*03-restricted CD8+ T-cell responses targeting the HIV-1 Gag Major Homology Region drive virus immune escape and fitness constraints compensated by intra-codon variation. Journal of Virology 2010 Nov; 84(21):11279-88. Epub 2010 Aug 25.
  9	Jaclyn K. Wright, Zabrina L. Brumme, Jonathan M. Carlson, David Heckerman, Carl M. Kadie, Chanson J. Brumme, Bingxia Wang, Elena Losina, Toshiyuki Miura, Fundisiwe Chonco, Mary van der Stok, Zenele Mncube, Karen Bishop, Philip J.R. Goulder, Bruce D. Walker, Mark A. Brockman, Thumbi Ndung’u. Gag-Protease-Mediated Replication Capacity in HIV-1 Subtype C Chronic Infection: Associations with HLA Type and Clinical Parameters. Journal of Virology 2010 Oct;84(20):10820-31. Epub 2010 Aug 11.
  10	Morgane Rolland, Jonathan M. Carlson, Siriphan Manocheewa, J. Victor Swain, Erinn Lanxon-Cookson, Wenjie Deng, Christine M. Rousseau, Dana N. Raugi, Gerald H. Learn, Brandon S. Maust, Hoosen Coovadia, Thumbi Ndung'u, Philip J.R. Goulder, Bruce D. Walker, Christian Brander, David E. Heckerman and James I. Mullins. Amino-acid co-variation in HIV-1 gag subtype C: HLA-mediated selection pressure and compensatory dynamics. PLoS One. 2010 Sep 1;5(9). pii: e12463.
  11	Alasdair Leslie, Phillipa C Matthews, Jennifer Listgarten, Jonathan Carslon, Carl Kadie, Thumbi Ndung’u, Christian Brander, Hoosen Coovadia, Bruce D Walker, David Heckerman and Philip J R Goulder. Additive contribution of HLA class I alleles in the immune control of HIV-1 infection. Journal of Virology 2010 Oct;84(19):9879-88. Epub 2010 Jul 21.
  12	Marianne W. Mureithi, J. Judy Chang, Jeffrey D. Lifson, Thumbi Ndung’u, Marcus Altfeld. Exposure to HIV-1 encoded TLR8 ligands enhances monocytes response to microbial encoded TLR2/4 ligands. AIDS 2010 Jul 31;42(12):1841-8.
  13	Nompumelelo Mkhwanazi, Christina F. Thobakgale, Mary van der Stok, Shabashini Reddy, Zenele Mncube,  Fundisiwe Chonco, Bruce D. Walker, Marcus Altfeld, Philip J.R. Goulder, Thumbi Ndung’u. Immunodominant HIV-1-Specific HLA-B- and HLA-C-Restricted CD8+ T-cells do not differ in Polyfunctionality. Virology 2010 Sep 30;405(2):483-91. Epub 2010 Jul 17.
  14	Julg B, Williams KL, Reddy S, Bishop K, Qi Y, Carrington M, Goulder PJ, Ndung’u T, Walker BD. Enhanced anti-HIV functional activity associated with Gag-specific CD8 T-cell responses. Journal of Virology 2010 Jun; 84 (11):5540-9. Epub 2010 Mar 24.
  15	Vinod B Patel, Ravesh Singh, Cathy Connolly, Yacoob Coovadia, Abdool KC Peer, Priyashini Parag, Victoria Kasprowicz, Alimuddin Zumla, Thumbi Ndung’u, Keertan Dheda. Cerebrospinal T cell responses aid the diagnosis of tuberculous meningitis in a HIV and TB endemic population. American Journal of Respiratory and Critical Care Medicine 2010 Aug 15;182(4):569-77. Epub 2010 May 4.
  16	Gelderblom HC, Beld MG. Transient reappearance of serum hepatitis C virus RNA observed by real-time PCR during antiviral therapy with peginterferon and ribavirin: Reappearance of references published in 2005-2009.Journal of Clinical Virology 2010 Jun; 48(2):150-1.
  17	Anju Bansal, Jonathan Carlson, Jiyu Yan, Olusimidele T. Akinsiku, Malinda Schaefer, Steffanie Sabbaj, Anne Bet, David Levy, Sonya Heath, Jianming Tang, Richard A. Kaslow, Bruce D. Walker, Thumbi Ndung’u, Philip J. Goulder, David Heckerman, Eric Hunter, and Paul A. Goepfert. CD8 T cell and evolutionary pressure to HIV-1 cryptic epitopes derived from antisense transcription. Journal of Experimental Medicine 2010; 207 (1): 51-9, S1-3.
  18	Ambrose H.W. Wong, Katie Williams, Sharon Reddy, Douglas Wilson, Janet Giddy, Galit Alter, Musie Ghebremichael, Mary N. Carrington, Thumbi Ndung’u, Bruce D. Walker, Marcus Altfeld, and William H. Carr. Alterations in natural killer cell receptor profiles during HIV-1 disease progression among chronically infected South African adults. AIDS Research and Human Retroviruses. 2010; 26 (4):459-69.
  19	Kavidha Reddy, Cheryl A. Winkler, Lise Werner, Koleka Mlisana, Salim S. Abdool Karim, Thumbi Ndung’u, and the CAPRISA Acute Infection Study Team. APOBEC3G Expression is Dysregulated in Primary HIV-1 Infection and Polymorphic Variants Influence CD4+ T Cell Counts and Plasma Viral Load. AIDS 2010; 24 (2):195-204.
  20	Julia G. Prado, Andrew Prendergast, Christina Thobakgale, Claudia Molina, Gareth Tudor-Williams, Thumbi Ndung’u, Bruce D. Walker and Philip Goulder. Replicative Capacity of Mother-to-child transmitted virus is associated with paediatric HIV-1 disease progression. Journal of Virology 2010; 84 (1):492-502.

• 2009 Publications

  1	Raabya Rossenkhan, Thumbi Ndung’u, Teresa K. Sebunya, Jose E. Hagan, Roger Shapiro, Vladimir Novitsky, Sikhulile M. Moyo, Ibou Thior, Shahin Lockman, Rebecca Mitchell, Soyeon Kim, Rosemary Musonda, Erik van Widenfelt, Joseph Makhema, and M. Essex. Temporal Reduction of HIV-1 Viral Load in Breast Milk by Single-Dose Nevirapine during Prevention of MTCT. AIDS Research and Human Retroviruses 2009; 25 (12): 1261-1264.
  2	Vinod B. Patel, Ahmed I. Bhigjee, Hoosain F. Paruk, Ravesh Singh, Richard Meldau, Cathy Connolly, Thumbi Ndung’u, Keertan Dheda. Utility of a novel lipoarabinomannan assay for the diagnosis of tuberculous meningitis in a resource-poor high HIV prevalence setting. Cerebrospinal Fluid Research. 2009 Nov 2; 6 (1):13 [Epub ahead of print].
  3	Nesri Padayatchi, Ellen Stiefvater,  Kogieleum Naidoo, Kasavan Naidoo, Thumbi Ndung’u, Quarraisha Abdool Karim. Expanding HIV surveillance to include tuberculosis patients, in resource-limited settings with a generalized epidemic. The International Journal of Tuberculosis and Lung Disease. 2009; 13 (12): 1447-1449.
  4	Ashika Singh, Taryn Page, Penny L. Moore, Rachel L. Allgaier, Keshni Hiramen, Hoosen M. Coovadia, Bruce D. Walker, Lynn Morris, Thumbi Ndung’u. Functional and Genetic Analysis of Coreceptor Usage by Dualtropic HIV-1 Subtype C Isolates. Virology 2009; 392 (1): 56-67.
  5	Christina F Thobakgale, Andrew Prendergast, Hayley Crawford, Nompumelelo  Mkhwanazi, Danni Ramduth,  Sharon Reddy, Claudia Molina,  Zenele Mncube, Alasdair Leslie, Julia Prado, Fundi Chonco, Wendy Mphatshwe, Gareth Tudor-Williams, Prakash Jeena, Natasha Blanckenberg, Krista Dong, Photini Kiepiela, Hoosen Coovadia, Thumbi Ndung’u, Bruce D Walker, and Philip J R Goulder.Impact of HLA in Mother and Child on Paediatric HIV-1 Disease Progression. Journal of Virology 2009; 83 (19): 10234-44.
  6	Zabrina Brumme, Bingxia Wang, Kriebashne Nair, Chanson Brumme, Chantal de Pierres, Shabashini Reddy, Boris Julg, Eshia Moodley, Christina Thobakgale, Zhigang Lu, Mary van der Stok, Karen Bishop, Zenele Mncube, Fundisiwe Chonco, Yuko Yuki, Nicole Frahm, Christian Brander, Mary Carrington, Kenneth Freedberg, Photini Kiepiela, Philip Goulder, Bruce Walker, Thumbi Ndung’u, Elena Losina. Impact of select immunologic and virologic biomarkers on CD4 decline in chronic HIV-1 subtype C infection: Results from Sinikithemba longitudinal population-based cohort, Durban, South Africa. Clinical Infectious Diseases 2009; 49: 956-64.
  7	Dshanta D. Naicker, Lise Werner, Emil Kormuth, Jo-Ann Passmore, Koleka Mlisana, Salim Abdool Karim, Thumbi Ndung’u, and the CAPRISA Acute Infection Study Team. Interleukin-10 Promoter Polymorphisms Influence HIV-1 Susceptibility and Primary HIV-1 Pathogenesis. Journal of Infectious Diseases 2009; 200 (3): 448-452.
  8	Shamman Sewram, Ravesh Singh, Emil Kormuth, Lise Werner, Koleka Mlisana, SS Abdool Karim, Thumbi Ndung’u, and the CAPRISA Acute Infection Study Team. Human TRIM5α Expression Levels and Reduced Susceptibility to Human Immunodeficiency Virus Type 1 Infection. Journal of Infectious Diseases 2009; 199 (11): 1657-1663.
  9	Boris Julg, Shabashini Reddy, Mary van der Stok, Smita Kulkarni, Ying Qi, Sara Bass, Bert Gold, Michael A. Nalls, George W. Nelson, Bruce D. Walker, Mary Carrington, Thumbi Ndung’u. Lack of Duffy Antigen Receptor for Chemokines: No Influence on HIV Disease Progression in an African Treatment-Naïve Population. Cell Host and Microbe 2009; 5 (5): 413-5.
  10	Ramduth D, Day CL, Thobakgale CF, Mkhwanazi NP, de Pierres C, Reddy S, van der Stok M, Mncube Z, Nair K, Moodley ES, Kaufmann DE, Streeck H, Coovadia HM, Kiepiela P, Goulder PJ, Walker BD. Immunodominant HIV-1 CD4+ T cell epitopes in chronic untreated clade C HIV-1 infection. PLoS ONE. 2009; 4(4) e5013.
  11	Philippa C Matthews, Alasdair J Leslie, Aris Katzourakis, Hayley Crawford, Rebecca Payne, Andrew  Prendergast, Karen Power, Anthony D Kelleher, Paul Klenerman, Jonathan Carlson, David Heckerman,   Thumbi Ndung’u, Bruce D Walker, Todd M Allen, Oliver G Pybus, Philip J R Goulder. HLA Footprints on HIV-1 are associated with Inter-Clade Polymorphisms and Intra-Clade Phylogenetic Clustering. Journal of Virology 2009; 83 (9): 4605-15.
  12	Hayley Crawford, Wendy Lumm, Alasdair Leslie, Malinda Schaefer, Debrah Boeras, Julia G Prado, Jainming Tang, Paul Farmer, Thumbi Ndung’u, Shabir Lakhi, Jill Gillmour, Paul Goepfert,  Bruce D Walker, Richard Kaslow,  Joseph Mulenga, Susan Allen, Philip J R Goulder, Eric Hunter. Evolution of HLA-B*5703 HIV-1 Escape Mutations in HLA-B*5703-Positive Individuals and their Transmission Recipients. Journal of Experimental Medicine 2009; 206 (4): 909-21.
  13	Yuka Kawashima, Katja Pfafferott, John Frater, Philippa Matthews, Rebecca Payne, Marylyn Addo, Hiroyuki Gatanaga, Mamoru Fujiwara, Atsuko Hachiya, Hirokazu Koizumi, Nozomi Kuse, Shinichi Oka, Anna Duda, Andrew Prendergast, Hayley Crawford, Alasdair Leslie, Zabrina Brumme, Chanson Brumme, Todd Allen, Christian Brander, Richard Kaslow, James Tang, Eric Hunter, Susan Allen, Joseph Mulenga, Songee Branch, Tim Roach, Mina John, Simon Mallal,  Anthony Ogwu,  Roger Shapiro, Julia G. Prado, Sarah Fidler, Jonathan Weber, Oliver G. Pybus, Paul Klenerman, Thumbi Ndung’u, Rodney Phillips, David Heckerman, P. Richard Harrigan, Bruce D. Walker, Masafumi Takiguchi, Philip Goulder. Adaptation of HIV-1 to Human Leukocyte Antigen Class I. Nature 2009; 458 (7238): 641-5.
  14	Christine M. Rousseau, David W. Lockhart, Jennifer Listgarten, Carl Kadie, Gerald H. Learn, David C. Nickle, David E. Heckerman, Wenjie Deng, Christian Brander, Thumbi Ndung'u, Hoosen Coovadia, Philip J. R. Goulder, Bette T. Korber, Bruce D. Walker, James I. Mullins. Rare HLA Alleles Drive Additional HIV-1 Viral Evolution. AIDS Research and Human Retroviruses 2009; 25 (3): 297-303.

• 2008 Publications

  1	Philippa C. Matthews, Andrew Prendergast, Alasdair Leslie, Hayley Crawford, Rebecca Payne, Christine Rousseau, Morgane Rolland, Isobella Honeyborne, Jonathan Carlson, Carl Kadie, Christian Brander, Karen Bishop, Nonkululeko Mlotshwa, James I. Mullins, Hoosen Coovadia, Thumbi Ndung'u, Bruce D. Walker, David Heckerman, and Philip J. R. Goulder. Central Role of Reverting Mutations in HLA Associations with Human Immunodeficiency Virus Set Point. Journal of Virology 2008; 82 (17): 8548-8559.
  2	Christine M. Rousseau, Marcus G. Daniels, Jonathan Carlson, Carl Kadie, Hayley Crawford, Andrew Prendergast, Philippa Matthews, Rebecca Payne, Morgane Rolland, Dana N. Raugi, Brandon S. Maust, Gerald H. Learn, David C. Nickle, Hoosen Coovadia, Thumbi Ndung'u, Nicole Frahm, Christian Brander, Bruce D. Walker, Philip J. R. Goulder, Tanmoy Bhattacharya, David E. Heckerman, Bette T. Korber, and James I. Mullins. HLA Class-I Driven Evolution of HIV-1 Subtype C Proteome: Immune Escape and Viral Load. Journal of Virology 2008; 82 (13): 6434-6446.
  3	Kholiswa C. Ngumbela,  Day CL, Mncube Z, Nair K, Ramduth D, Thobakgale C, Moodley E, Reddy S, de Pierres C, Mkhwanazi N, Bishop K, van der Stok M, Ismail N, Honeyborne I, Crawford H, Kavanagh DG, Rousseau C, Nickle D, Mullins J, Heckerman D, Korber B, Coovadia H,  Goulder PJR and  Walker BD: Targeting of a CD8 T cell Env epitope presented by HLA-B*5802 is associated with markers of HIV disease progression and lack of selection pressure.   AIDS Research and Human Retroviruses. 2008 24(1) 72-82.
  4	Prendergast A, Mphatshwe W, Tudor-Williams G, Rakgotho M, Pillay V, Thobakgale C, McCarthy N, Morris L, Walker BD, Goulder P. Early Virological Suppression with Three-Class Antiretroviral Therapy in HIV-Infected African Infants. AIDS. 2008; 22(11) 1333-43.
  5	Day CL, Mkhwanazi N, Reddy S, Mncube Z, van der Stok M, Klenerman P, Walker BD. Detection of Polyfunctional Mycobacterium Tuberculosis-Specific T-cells and Association with Viral Load in HIV-1 Infected Persons. Journal of Infectious Diseases. 2008 April 197 (7) 990-999.
  6	Day CL, Mkhwanazi N, Reddy S, Mncube Z, van der Stok M, Klenerman P, Walker BD. Detection of HIV Type Gag-Specific CD4 (+) T cell Responses in Acutely Infected Infants. AIDS Research and Human Retroviruses. 2008 February; 24(2) 265-270.

• 2007 Publications

  1	Day CL, Kiepiela P, Leslie AJ, van der Stok M, Nair K, Ismail N, Honeyborne I, Crawford H, Coovadia HM, Goulder PJR, Walker BD, Klenerman P. Proliferative capacity of epitope-specific CD8 T cell responses is inversely related to viral load in chronic HIV-1 infection. Journal of Virology 2007; 81(1):434-8.
  2	Daisuke Watanabe, Mark A Brockman, Thumbi Ndung'u, Lydia Mathews, William Lucas, Cynthia G Murphy, Barbara K Felber, George N Pavlakis, Neal A Deluca, and David M Knipe. Properties of a Herpes Simplex Virus Multiple Immediate-Early Gene-Deleted Recombinant as a Vaccine Vector. Virology 2007; 357 (2): 186-198.
  3	Christina F. Thobakgale, Dhanwanthie Ramduth, Sharon Reddy, Nompumelelo Mkhwanazi, Chantal de Pierres, Eshia Moodley, Wendy Mphatswe, Natasha Blanckenberg, Ayanda Cengimbo, Andrew Prendergast, Gareth Tudor-Williams, Krista Dong, Prakash Jeena, Gupreet Kindra, Raziya Bobat, Hoosen Coovadia, Photini Kiepiela, Bruce D. Walker, and Philip J. R. Goulder. Human Immunodeficiency Virus-Specific CD8 T cell Activity is Detectable from birth in the majority of In Utero-Infected Infants. Journal of Virology. 2007; 81(23) 12775–12784.
  4	Isobella Honeyborne, Andrew Prendergast, Florencia Pereyra, Alasdair Leslie, Hayley Crawford, Rebecca Payne, Shabashini Reddy, Karen Bishop, Eshia Moodley, Kriebashnie Nair, Mary van der Stok, Noel McCarthy, Christine M Rousseau, Marylyn Addo, James I Mullins, Christian Brander, Photini Kiepiela, Bruce D Walker, and Philip J.R. Goulder. Control of HIV-1 is associated with HLA-B*13 and targeting of multiple GAG-specific CD8+ T cell epitopes. Journal of Virology. 2007; 81(7): 3667–3672.
  5	Photini Kiepiela, Kholiswa Ngumbela, Christina Thobakgale, Dhanwanthie Ramduth, Isobella Honeyborne, Eshia Moodley, Shabashini Reddy, Chantal de Pierres, Zenele Mncube, Nompumelelo Mkhwanazi, Karen Bishop, Mary van der Stok, Kriebashnie Nair, Nasreen Khan, Hayley Crawford, Rebecca Payne, Alasdair Leslie, Julia Prado, Andrew Prendergast, John Frater, Noel McCarthy, Christian Brander, Gerald H Learn, David Nickle, Christine Rousseau, Hoosen Coovadia, James I Mullins, David Heckerman, Bruce D Walker and Philip Goulder. CD8+ T cell responses to different HIV proteins have discordant associations with viral load. Nature Medicine 2007; 13(1):46-53.
  6	Olson DP, Day CL, Magula NP, Sahid F, Moosa M-Y S. Cutaneous Extensively Drug-Resistant Tuberculosis. American Journal of Tropical Medicine and Hygiene 2007; 77:551-554.
  7	Day CL, Mkhwanazi N, Reddy S, Mncube Z, van der Stok M, Klenerman P, Walker BD. Detection of polyfunctional Mycobacterium tuberculosis-specific T cells and relation to viral load in HIV-1 infected persons. Journal of Infectious Diseases 2007; 197: 990-9.
  8	Christine M. Rousseau, Gerald H. Learn,  Tanmoy Bhattacharya,  David C. Nickle, David Heckerman, Senica Chetty,  Christian Brander,  Philip J.R. Goulder; Bruce D. Walker, Photini Kiepiela,  Bette T. Korber,  James I. Mullins. Extensive Intra-subtype Recombination in South African HIV-1 Subtype C Infections.  Journal of Virology 2007; 81(9): 4492–4500

• 2006 Publications

  1	I Honeyborne, A Rathod, R Buchli, D Ramduth, E Moodley, P Rathnavalu, S Chetty, C Day, C. Brander, W. Hilderbrand, BD Walker, P. Kiepiela, PJ Goulder. Motif inference reveals optimal CTL epitopes presented by HLA class I alleles highly prevalent in Southern Africa. Journal of Immunology, 2006, 176(8):4699-4705.
  2	CM Rousseau, B.A Birditt, AR McKay, JN Stoddard, TC Lee, S McLaughlin, SW Moore, N Shindo, G H Learn, BT Korber, C Brander, PJ Goulder, P Kiepiela, BD Walker, and JI Mullins. Large-scale amplification, cloning and sequencing of near full-length HIV-1 subtype C genomes. Journal of Virological Methods 2006, 136:118-25.
  3	A Leslie, DA Price, P. Mkhize, K.Bishop, A.Rathod, H.Crawford, I.Honeyborne, TE Asher, G Luzzi, A Edwards, CM Rousseau, JI Mullins, G Tudor-Williams, V Novelli, C Brander, DC Douek, P Kiepiela, BD Walker, PJ Goulder. Differential selection pressure exerted on HIV by CTL targeting identical epitopes but restricted by distinct HLA alleles from the same HLA supertype. Journal of Immunology 2006, 177(7):4699-4708.
  4	J Martinez-Picado, JG Prado, EE Fry, K Pfafferott, A Leslie, S Chetty, C Thobakgale, I Honeyborne, H Crawford, P Mathews, T Pillay, C Roouseau, JI Mullins, C Brander, BD Walker, DI Stuart, P Kiepiela, P Goulder.Fitness cost of escape mutations in p24 Gag in association with control of human immunodeficiency virus type 1. Journal of Virology 2006; 80(7): 3617-3623.
  5	CL Day, DE Kaufmann, P Kiepiela, JA Brown, ES Moodley, S Reddy, EW Mackey, JD Miller, AJ Leslie, C DePierres, Z. Mncube, J Duraiswamy, B Zhu, Q Eichbaum, M Altfeld, EJ Wherry, HM Coovadia, PJ Goulder, P Klenerman, R Ahmed, GJ Freeman, BD Walker. PD-1 expression on HIV-specific T cells is associated with T-cell exhaustion and disease progression. Nature 2006, 443: 350-354.
  6	P Kiepiela, K Ngumbela, C Thobakgale, D Ramduth, I Honeyborne, E Moodley, S Reddy, C de Pierres, Z Mncube, N Mkhwanazi, K Bishop, M van der Stok, K Nair, N Khan, H Crawford, R Payne, A Leslie, J Frater, N McCarthy, C Brander, GH Learn, D Nickle, C Rousseau, H Coovadia, JI Mullins, D Heckerman, BD Walker, P Goulder. Discordant protein-specific associations of anti-HIV CD8+ T-cell responses with control of viremia. Nature Medicine 2006; 13, 46 – 53.
  7	Xu. Yu, M Lichterfeld, S Chetty, KL. Williams, SK. Mui, T Miura, N Frahm, ME. Feeney, Y Tang, F Pereyra, MX LaBute, K Pfafferott, A Leslie, H Crawford,R Allgaier, W Hildebrand, R Kaslow, C Brander, TM.Allen, ES Rosenberg, P Kiepiela, M Vajpayee, PA. Goepfert, M Altfeld, PJR Goulder, BD Walker. Mutually exclusive T cell receptor induction and differential susceptibility to HIV-1 mutational escape associated with a two amino acid difference between HLA class I subtypes.  Journal of Virology, 2006 [Epub ahead of print].
  8	Wherry EJ, Day CL, Draenert R, Miller JD, Kiepiela P, Woodberry T, Brander C, Addo M, Klenerman P, Ahmed R, Walker BD. HIV-specific CD8 T cells express low levels of IL-7Ra: Implications for HIV-specific T cell memory. Virology 2006; 353(2):366-73.
  9	Nicole Frahm, Photini Kiepiela, Sharon Adams, Caitlyn H Linde, Hannah S Hewitt, Kaori Sango, Margaret E Feeney, Marylyn M Addo, Mathias Lichterfeld, Matthew P Lahaie, Eunice Pae, Alysse G Wurcel, Timothy Roach, M Anne St John, Marcus Altfeld, Francesco M Marincola, Corey Moore, Simon Mallal, Mary Carrington, David Heckerman, Todd M Allen, James I Mullins, Bette T Korber, Philip J R Goulder, Bruce D Walker, Christian Brander. Control of human immunodeficiency virus replication by cytotoxic T lymphocytes targeting subdominant epitopes.   Nature immunology. 2006 (2):173-8.

• 2005 Publications

  1

  Alasdair Leslie, Daniel Kavanagh,  Isobella Honeyborne,  Katja Pfafferott,  Charles Edwards,  Tilly Pillay, Louise Hilton,  Christina Thobakgale,  Danni Ramduth,  Rika Draenert,  Sylvie Le Gall,  Graz Luzzi,  Anne Edwards,  Christian Brander,  Andrew K. Sewell,  Sarah Moore,  James Mullins,  Corey Moore,  Simon Mallal,  Nina Bhardwaj,  Karina Yusim,  Rodney Phillips,  Paul Klenerman,  Bette Korber, Photini Kiepiela,  Bruce Walker,  and Philip Goulder. Transmission and accumulation of CTL escape variants drive negative associations between HIV polymorphisms and HLA. Journal of Experimental Medicine 2005 March 21; 201(6): 891–902.

  2

  Nicole Frahm, Sharon Adams, Photini Kiepiela, Caitlyn H. Linde, Hannah S. Hewitt, Mathias Lichterfeld, Kaori Sango, Nancy V. Brown, Eunice Pae, Alysse G. Wurcel, Marcus Altfeld, Margaret E. Feeney, Todd M. Allen, Timothy Roach, M. Anne St. John, Eric S. Daar, Eric Rosenberg, Bette Korber, Francesco Marincola, Bruce D. Walker, Philip J. R. Goulder, and Christian Brander. HLA-B63 Presents HLA-B57/B58-Restricted Cytotoxic T-Lymphocyte Epitopes and Is Associated with Low Human Immunodeficiency Virus Load. Journal of virology, Aug 2005; 79: 10218 - 10225

• 2004 Publications

  1	Kiepiela P, Leslie AJ, Honeyborne I, Ramduth D, Thobakgale C, Chetty S, Rathnavalu P, Moore C, Pfafferott KJ, Hilton L, Zimbwa P, Moore S, Allen T, Brander C, Addo MM,  Altfeld M, James I, Mallal S, Bunce M, Barber LD, Szinger J, Day C, Klenerman P, Mullins J, Korber B, Coovadia HM, Walker BD, Goulder PJR. Dominant influence of HLA-B in mediating the potential co-evolution of HIV and HLA. Nature 2004; 432(7018):769-75.
  2	AJ Leslie, K J Pfafferott, P Chetty, R Draenert, MM Addo, M Feeney, Y Tang, E C Holmes, T Allen, J G Prado, M Altfeld, C Brander, C Dixon, D Ramduth, P Jeena, S A Thomas, A St John, T A Roach, B Kupfer, G Luzzi, A Edwards, G Taylor, H Lyall, G Tudor-Williams, V Novelli, J Martinez-Picado, P Kiepiela, B D Walker & P J R Goulder.  HIV evolution: CTL escape mutation and reversion after transmission.  Nature Medicine, 2004 10, 282 – 289.
  3	Rika Draenert, Sylvie Le Gall, Katja J Pfafferott, Alasdair J Leslie, Polan Chetty, Christian Brander, Edward C Holmes, Shih-Chung Chang, Margaret E Feeney, Marylyn M Addo, Lidia Ruiz, Danni Ramduth, Prakash Jeena, Marcus Altfeld, Stephanie Thomas, Yanhua Tang, Cori L Verrill, Catherine Dixon, Julia G Prado, Photini Kiepiela, Javier Martinez-Picado, Bruce D Walker, Philip J R Goulder.Immune selection for altered antigen processing leads to cytotoxic T lymphocyte escape in chronic HIV-1 infection. Journal of experimental medicine. 2004;199 (7):905-15.