Prof Alex Welte, PhD

Research Professor

Research theme: Measuring Infection and Disease

The biggest single issue that has Alex has been engaged with over the last few years is the challenge of defining, and then applying in the field, laboratory based characterizations of 'recent infection'. This idea, and the SACEMA group's work in this area, has attracted a lot of interest in recent years as it offers tremendous potential to improve epidemiological surveillance. Tools arising out of this work are available from the Comprehensive R Archive Network, as a package called inctools.

Alex was director of SACEMA from July 2010 to June 2016. Before that, Alex was in the School of Computational and Applied Mathematics at the University of the Witwatersrand, where he was involved with SACEMA projects since the beginning of the centre's existence. A physicist by training, he is interested in a diverse range of projects involving the mathematical modeling of biological, chemical and population-dynamic processes.

Recent publications

Osman.M., A. Welte, P. Naidoo, M. Loveday, & A.C. Hesseling (2020) Limitations and potential bias in vital registration data and tuberculosis mortality reporting in South Africa. South African Medical Journal 110(17): 607-609 doi: 10.7196/SAMJ.2020.v110i7.14533

Facente S.N., E. Grebe, C.D. Pilcher, M.P. Busch, G. Murphy, & A. Welte (2020) Estimated dates of detectable infection (EDDIs) as an improvement upon Fiebig staging for HIV infection dating. Epidemiology and Infection 148:1-5 doi: 10.1017/S0950268820000503

Desmond, C., P. Labuschagne, L. Cluver, M. Tomlinson, L. Ritcher, X. Hunt, M. Marlow, & A. Welte (2020) Modelling the impact of maternal HIV on uninfected children: correcting current estimates. AIDS care 32 (11): 1406-1414 doi: 10.1080/09540121.2020.1720587

Grebe, E., S.N. Facente, J. Bingham, C.D. Pilcher, A. Powrie, J.Gerber, G. Priede, T. Chibawara, M.P. Busch, G. Murphy, R. Kassanjee, & A. Welte (2019) Interpreting HIV diagnostic histories into infection time estimates: analytical framework and online tool. BMC infectious diseases 19(1):894, doi: 10.1186/s12879-019-4543-9

Mehta, U.C., C. van Schalkwyk, P. Naidoo, A. Ramkissoon, O. Mhlongo, N.R. Maharaj, N. Naidoo, K. Fieggen, M.F. Urban, S. Krog, A. Welte, M. Dheda, Y. Pillay, & N.F. Moran (2019) Birth outcomes following antiretroviral exposure during pregnancy: Initial results from a pregnancy exposure registry in South Africa Southern African Journal of HIV Medicine 20(1):12 doi:10.4102/sajhivmed.v20i1.971

Sempa J.B., A. Welte, M.P. Busch, J. Hall, D. Hampton, S.N. Facente, .S.M Keating, K. Marson, N. Parkin, C. D. Pilcher, G. Murphy, & E. Grebe (2019) Performance comparison of the Maxim and Sedia Limiting Antigen Avidity assays for HIV incidence surveillance. PloS one 14(7):e0220345 doi: /10.1101/572677

Van Schalkwyk, C., J. Moodley, A. Welte, & L.F. Johnson (2019) Estimated impact of human papillomavirus vaccines on infection burden: The effect of structural assumptions. Vaccine 37 (36): 5460-5465 doi: 10.1016/j.vaccine.2019.06.013

Pilcher, C., T.C Porco, S.N. Facente, P.E. Grebe, K.P. Delaney, M. Silvina, R. Kassanjee, M.P. Busch, G. Murphy, S.M. Owen, & A. Welte. (2019) A generalizable method for estimating duration of HIV infections using clinical testing history and HIV test results. AIDS 33(7): 1231-1240. doi: 10.1097/QAD.0000000000002190

Osman, M., A. Welte, R. Dunbar, R. Brown, G. Hoddinott , A.C. Hesseling, & F.M Marx (2019) Morbidity and mortality up to 5 years post tuberculosis treatment in South Africa: A pilot study. International Journal of Infectious Diseases 85:57-63 doi: org/10.1016/j.ijid.2019.05.024

Van Schalkwyk, C., J. Maritz, G.U. Van Zyl, W. Preiser, & A. Welte (2019) Pooled PCR testing of dried blood spots for infant HIV diagnosis is cost efficient and accurate. BMC Infectious Diseases 19:136 doi: 10.1186/s12879-019-3767-z

Facente, S.N., M.P. Busch, E. Grebe, C.E. Pilcher, A. Welte, B. Rice, & G. Murphy (2019) Challenges to the performance of current HIV diagnostic assays and the need for centralized specimen archives: a review of the Consortium for the Evaluation and Performance of HIV Incidence Assays (CEPHIA) repository [version 1; peer review: 3 approved, 1 approved with reservations]. Gates Open Research, 3:1511 doi: 10.12688/gatesopenres.13048.1

Vermeulen, M., N. Lelie, C. Coleman, N. Sykes, G. Jacobs, R. Swanevelder, M. Busch, G. van Zyl, E. Grebe, A. Welte, & R. Reddy (2019) Assessment of HIV transfusion transmission risk in South Africa: a 10-year analysis following implementation of individual donation nucleic acid amplification technology testing and donor demographics eligibility changes. Transfusion, 59(1): 267-276 doi: 10.1111/trf.14959

Grebe, P.E., A. Welte, L.F. Johnson, G. Van Cutsem, A. Puren, T. Ellman, J. Etard, & H. Huerga. (2018) Population-level HIV incidence estimates using a combination of synthetic cohort and recency biomarker approaches in KwaZulu-Natal, South Africa. PLOS ONE 13(9):1-16. doi: 10.1371/journal.pone.0203638

Van Schalkwyk, C., J. Moodley, A. Welte, & L.F. Johnson (2018) Are associations between HIV and human papillomavirus transmission due to behavioural confounding or biological effects? Sexualy Transmitted Infections 95(2):122-128. doi: 10.1136/sextrans-2018-053558

Nascimento, E.J.M., J.W. Huleatt, M.T. Cordeiro, P.M.S Castanha, J.K. George, P.E. Grebe, A. Welte, M. Brown, D.S. Burke, & E.T.A. Marques. (2018) Development of antibody biomarkers of long term and recent dengue virus infections. Journal of Virological Methods 257:62-68. doi: 10.1016/j.jviromet.2018.04.009

Geffen, N., & A. Welte (2018) Modelling the human immunodeficiency virus (HIV) epidemic: A review of the substance and role of models in South Africa. Southern African Journal of HIV Medicine 19(1). doi: 10.4102/sajhivmed.v19i1.756

Grebe, P.E., A. Welte, J. Hall, S.M. Keating, S.N. Facente, K. Marson, J.N. Martin, S. J. Little , M.A. Price, E.G. Kallas, M.P. Busch, C.D. Pilcher, & G. Murphy. (2017) Infection Staging and Incidence Surveillance Applications of High Dynamic Range Diagnostic Immuno-Assay Platforms. Journal of Acquired Immune Deficiency Syndromes 76(5):547-555. doi: 10.1097/QAI.0000000000001537

Keating, S.M., C.D. Pilcher, V. Jain, M. Lebedeva, D. Hampton, M. Abdel-Mohsen, X. Deng, G. Murphy, A. Welte, S.N. Facente, F. Hecht, S.G. Deeks, S.K. Pillai, & M.P. Busch (2017) HIV antibody level as a marker of HIV persistence and low-level viral replication. The Journal of Infectious Diseases 216 (1), 72-81. doi: 10.1093/infdis/jix225

Murphy, G., C.D. Pilcher, S.M. Keating, R. Kassanjee, S.N. Facente, A. Welte, E. Grebe, K. Marson, M.P. Busch, P. Dailey, N. Parkin, J. Osborn, S. Ongarello, K. Marsh, & J.M. Garcia-Calleja (2017) Moving towards a reliable HIV incidence test-current status, resources available, future directions and challenges ahead. Epidemiology & Infection 145 (5), 925-941 doi: 10.1017/S0950268816002910

Kassanjee, K., D. De Angelis, M. Farah, D. Hanson, J.P.L. Labuschagne, O. Laeyendecker, S. Le Vu, B. Tom, R. Wang, & A. Welte (2017) Cross-sectional HIV incidence surveillance: a benchmarking of approaches for estimating the 'mean duration of recent infection'. Statistical Communications in Infectious Diseases 9 (1):1-12. doi: 10.1515/scid-2016-0002

Schlusser, K.E., C.D. Pilcher, E.G. Kallas, B.R. Santos, S.G. Deeks, S. Facente, S.M. Keating, M.P. Busch, G. Murphy, A. Welte, T. Quinn, S.H. Eshleman, & O. Laeyendecker. (2017) Comparison of cross-sectional HIV incidence assay results from dried blood spots and plasma. PLOS ONE 12(2), e0172283. doi: 10.1371/journal.pone.0172283

Murphy, G., C.D. Pilcher, S.M. Keating, R. Kassanjee, S.N. Facente, A. Welte, E. Grebe, K. Marson, M.P. Busch, P. Dailey, N. Parkin, J. Osborn, S. Ongarello, K. Marsh, & J.M. Garcia-Calleja (2016) Moving towards a reliable HIV incidence test - current status, resources available, future directions and challenges ahead. Epidemiology and Infection 145(5):925-941. doi: 10.1017/S0950268816002910

Kharsany. A.B., C. Cawood, D. Khanyile, A. Grobler, L.R. Mckinnon, N. Samsunder, J.A. Frohlich, A, Q.A. Karim, A. Puren, A Welte, G. George, K. Govender, C. Toledo, Z. Chipeta, L. Zembe, M.T Glenshaw, L. Madurai, V.M Deyde & A. Bere (2015) Strengthening HIV surveillance in the antiretroviral therapy era: rationale and design of a longitudinal study to monitor HIV prevalence and incidence in the uMgungundlovu District, KwaZulu-Natal, South Africa. BMC Public Health 15:1149. doi: 10.1186/s12889-015-2179-2.

Yen T. Duong, Reshma Kassanjee, Alex Welte, Meade Morgan, Anindya De, Trudy Dobbs, Erin Rottinghaus, John Nkengasong, Marcel E. Curlin, Chonticha Kittinunvorakoon, Boonyos Raengsakulrach, Michael Martin, Kachit Choopanya, Suphak Vanichseni, Yan Jiang, Maofeng Qiu, Haiying Yu, Yan Hao, Neha Shah, Linh-Vi Le, Andrea A. Kim, Tuan Anh Nguyen, William Ampofo, Bharat S. Parekh (2015) Recalibration of the Limiting Antigen Avidity EIA to Determine Mean Duration of Recent Infection in Divergent HIV-1 Subtypes. Plos One 10(2). doi.org/10.1371/journal.pone.0114947.

Kassanjee R, Pilcher C. D, Keating S. M, Facente S. N, McKinney E, Price M. A, Martin J. N, Little S, Hecht F. M, Kallas E. G, Welte A, Busch M. P, Murphy G. (2014) Independent assessment of candidate HIV incidence assays on specimens in the CEPHIA repository. AIDS. 28(16). doi: 10.1097/QAD.0000000000000429.

Keertan Dheda, Grant Theron, Alex Welte. (2014) Cost-effectiveness of Xpert MTB/RIF and investing in health care in Africa. Lancet Global Health 2(10). doi.org/10.1016/S2214-109X(14)70305-5.

Desmond C, Bruce F, Tomlinson M, Marlow MB, Aber J. L, Ouifki R, Welte A. (2014) Modelling the long-term impacts on affected children of adult HIV: benefits, challenges and a possible approach. AIDS. 28 (Suppl 3). doi: 10.1097/QAD.0000000000000329.

Van Schalkwyk C, Variava E, Shapiro A. E, Rakgokong M, Masonoke K, Lebina L, Welte A, Martinson N. (2014) Incidence of TB and HIV in prospectively followed household contacts of TB index patients in South Africa. PLoS One. 9(4). doi: 10.1371/journal.pone.0095372.

Keebler D, Revill P, Braithwaite S, Phillips A, Blaser N, Borquez A, Cambiano V4, Ciaranello A, Estill J, Gray R, Hill A, Keiser O, Kessler J, Menzies N. A, Nucifora K. A, Vizcaya L. S, Walker S, Welte A, Easterbrook P, Doherty M, Hirnschall G, Hallett T. B. (2014) Cost-effectiveness of different strategies to monitor adults on antiretroviral treatment: a combined analysis of three mathematical models. Lancet Global Health 2(1). doi: 10.1016/S2214-109X(13)70048-2.

Kassanjee R, McWalter T. A, Welte A. (2014) Short Communication: Defining optimality of a test for recent infection for HIV incidence surveillance. AIDS Research And Human Retroviruses 30(1). doi: 10.1089/AID.2013.0113.

Delva W, Meng F, Beauclair R, Deprez N, Temmerman M, Welte A, Hens N. (2013) Coital frequency and condom use in monogamous and concurrent sexual relationships in Cape Town, South Africa. J Int AIDS Soc. 2013 Apr 24;16:18034. doi: 10.7448/IAS.16.1.18034.

Keebler D, Walwyn D, Welte A. (2013) Biology as population dynamics: heuristics for transmission risk. American Journal Of Reproductive Immunology 69(Suppl 1). doi: 10.1111/aji.12040.

Roxanne Beauclair, Fei Meng, Nele Deprez, Marleen Temmerman, Alex Welte, Niel Hens and Wim Delva (2013) Evaluating audio computer assisted self-interviews in urban south African communities: evidence for good suitability and reduced social desirability bias of a cross-sectional survey on sexual behaviour. BMC Medical Research Methodology 13(11). DOI: 10.1186/1471-2288-13-11.

Kassanjee R., T. A. McWalter, T. Bärnighausen & A. Welte (2012) A New General Biomarker-Based Incidence Estimator. Epidemiology. 23(5): doi: 10.1097/EDE.0b013e3182576c07.

Guy Severin Mahiane , Rachid Ouifki, Hilmarie Brand, Wim Delva, Alex Welte. (2012) A General HIV Incidence Inference Scheme Based on Likelihood of Individual Level Data and a Population Renewal Equation. PLoS One. 7(9): e44377. doi:10.1371/journal.pone.0044377.

Rustomjee R, Mcleod R, Hanekom W, Steel G, Mahomed H, Hawkridge A, Welte A, Sinanovic E, Loots G, Grobler A, Mvusi L, Gray G, Hesseling A, Ginsberg A, Lienhardt C, Shea J, Tong X, Lockhart S, Churchyard G. J. (2012) Key issues in the clinical development and implementation of TB vaccines in South Africa. Tuberculosis 92(5). doi: 10.1016/j.tube.2012.05.001.

Delva W, Wilson D. P, Abu-Raddad L, Gorgens M, Wilson D, Hallett T. B, Welte A. (2012) HIV treatment as prevention: principles of good HIV epidemiology modelling for public health decision-making in all modes of prevention and evaluation. PLoS Medicin 9(7). doi: 10.1371/journal.pmed.1001239.

Usha K. Sharma, Marco Schito, Alex Welte, Christine Rousseau, Joseph Fitzgibbon, Brandon Keele, Stuart Shapiro, Andrew McMichael, and David N. Burns (2012) Workshop Summary: Novel Biomarkers for HIV Incidence Assay Development Aids Research And Human Retroviruses 28(6). doi: 10.1089/aid.2011.0332.

Cari van Schalkwyk, Madeleine Cule, Alex Welte, Paul van Helden, Gian van der Spuy, and Pieter Uys. (2012) Towards Eliminating Bias in Cluster Analysis of TB Genotyped Data. PLoS One 7(3). doi: 10.1371/journal.pone.0034109.

Beauclair R, Kassanjee R, Temmerman M, Welte A, Delva W. (2012) Age-disparate relationships and implications for STI transmission among young adults in Cape Town, South Africa. The European Journal Of Contraception and Reproductive Health Care 17(1). doi: 10.3109/13625187.2011.644841.

Venkatesh K. K, de Bruyn G, Lurie M. N, Modisenyane T, Triche E. W, Gray G. E, Welte A, Martinson N. A. (2012) Sexual risk behaviors among HIV-infected South African men and women with their partners in a primary care program: implications for couples-based prevention. AIDS Behavior. 2012 Jan;16(1):139-50. doi: 10.1007/s10461-011-9941-y.

Johnstone-Robertson S, Lawn S. D, Welte A, Bekker L. G, Wood R. (2011) Tuberculosis in a South African prison - a transmission modelling analysis. South African Medical Journal 101(11). PMID: 22272961.

Wim Delva, Roxanne Beauclair, Alex Welte, Stijn Vansteelandt, Niel Hens, Marc Aerts, Elizabeth du Toit, Nulda Beyers and Marleen Temmerman. (2011) Age-disparity, sexual connectedness and HIV infection in disadvantaged communities around Cape Town, South Africa: a study protocol. BMC Public Health 11. DOI: 10.1186/1471-2458-11-616.

Delva W, Verguet S, Hargrove J, Williams B, Sheneberger R, Stander T, Welte A. (2011) Treatment-centred prevention: an integrated biomedical and social approach to HIV prevention. AIDS 25(11). doi: 10.1097/QAD.0b013e3283488503.

Williams B. G, Wood R, Dukay V, Delva W, Ginsburg D, Hargrove J, Stander M, Sheneberger R, Montaner J, Welte A. (2011) Treatment as prevention: preparing the way. Journal of the International Aids Society 14(1). doi: 10.1186/1758-2652-14-S1-S6.

Alex Welte, John Hargrove, Wim Delva, Brian Williams, Tienie Stander (2011) How different are the costs and consequences of delayed versus immediate HIV treatment? South African Medical Journal 101(6).

Reshma Kassanjee, Alex Welte, Thomas A. McWalter, Sheila M. Keating, Marion Vermeulen, Susan L. Stramer, Michael P. Busch. (2011) Seroconverting Blood Donors as a Resource for Characterising and Optimising Recent Infection Testing Algorithms for Incidence Estimation. PLoS ONE 6(6): e20027. doi:10.1371/journal.pone.0020027.

Biccard B.M., Welte A, Kassanjee R. (2011) Is it possible to decrease the incidence of peri-operative stroke associated with acute peri-operative beta-blocker administration? Anaesthesia 66(2). doi:10.1111/j.1365-2044.2010.06617.x.

Bärnighausen T., T. A. McWalter, Z. Rosner, M. L. Newell & A. Welte (2010) HIV incidence estimation using the BED capture enzyme immunoassay: systematic review and sensitivity analysis. Epidemiology. 21(5):685-97. doi: 10.1097/EDE.0b013e3181e9e978.

B?rnighausen T, McWalter T. A, Rosner Z, Newell M. L, Welte A. (2010) HIV incidence estimation using the BED capture enzyme immunoassay: systematic review and sensitivity analysis. Epidemiology 21(5). doi: 10.1097/EDE.0b013e3181e9e978.

A Welte, T A McWalter, O Laeyendecker, T B Hallett (2010) Using tests for recent infection to estimate incidence: problems and prospects for HIV Euro Surveill. 15(24):pii=19589.

McWalter TA, Welte A. (2010) Relating recent infection prevalence to incidence with a sub-population of assay non-progressors. Math Biol. 60(5):687-710. doi:10.1007/s00285-009-0282-7.

Marinda ET, Hargrove J, Preiser W, Slabbert H, van Zyl G, Levin J, Moulton LH, Welte A and Humphrey J. (2010) Significantly Diminished Long-Term Specificity of the BED Capture Enzyme Immunoassay Among Patients With HIV-1 With Very Low CD4 Counts and Those on Antiretroviral Therapy J Acquir Immune Defic Syndr. 53(4). PMID: 20306555.

Timothy D. Mastro, Andrea A. Kim, Timothy Hallett, Thomas Rehle, Alex Welte, Oliver Laeyendecker, Tom Oluoch, and Jesus M. Garcia-Calleja. (2010) Estimating HIV Incidence in Populations Using Tests for Recent Infection: Issues, Challenges and the Way Forward. Journal of HIV/AIDS Surveillance and Epidemiology 2(1).

Thomas A. McWalter, and Alex Welte (2009) A Comparison of Biomarker Based Incidence Estimators PLoS ONE 4(10): e7368. doi:10.1371/journal.pone.0007368

Brian G. Williams, Alex Welte, Bertran Auvert, and John Hargrove (2009) Consequences of Early Treatment for Individuals at Risk of Human Immunodeficiency Virus Infection Clin Infect Dis. (2009) 49 (7). doi: 10.1086/605598

Alex Welte, Thomas A. McWalter, and Till B?rnighausen. (2009) Reply to ?Should biomarker estimates of HIV incidence be adjusted??. AIDS 23(15). doi: 10.1097/QAD.0b013e32832eff59.

Hankins C, Hargrove Jw, Williams Bg, Raddad La, Auvert B, Bollinger L, Dorrington R, Ghani A, Gray R, Hallet T, Kahn Jg, Lohse N, Nagelkerke N, Porco T, Schmid G, Stover J, Weiss H, Welte A, White P, White R. (2009) Male Circumcision for HIV Prevention in High HIV Prevalence Settings: What Can Mathematical Modelling Contribute to Informed Decision Making? PLoS Med 6(9): e1000109. doi:10.1371/journal.pmed.1000109.

Alex Welte, Thomas A. McWalter, and Till Bärnighausen (2009) A Simplified Formula for Inferring HIV Incidence from Cross-Sectional Surveys Using a Test for Recent Infection AIDS Res Hum Retroviruses. 25(1): doi: 10.1089/aid.2008.0150

Till Bärnighausen , Claudia Wallrauch, Alex Welte, Thomas A. McWalter, Nhlanhla Mbizana, Johannes Viljoen, Natalie Graham, Frank Tanser, Adrian Puren, Marie-Louise Newell (2009) HIV incidence in rural South Africa: comparison of estimates from longitudinal surveillance and cross-sectional cBED assay testing. PLoS ONE 3(11): e3640. doi:10.1371/journal.pone.0003640

Brian Gerard Williams, David Ginsburg, Julio Montaner, Tienie Stander, Alex Welte (2009) Achieving South Africa's national strategic plan for HIV/AIDS. The Lancet 373(9667). doi/10.1016/S0140-6736(09)60547-X.

Tinevimbo Shiri and Alex Welte (2008) Transient antiretroviral therapy selecting for common HIV-1 mutations substantially accelerates the appearance of rare mutations Theoretical Biology and Medical Modelling 5(25). doi:10.1186/1742-4682-5-25

R. Ouifki, A. Welte, and C. Pretorius (2008) A model of HIV infection with two viral strains and cytotoxic T-lymphocyte response under structured treatment interruptions South African Journal of Science 104(5-6).

Alex Welte (2008) Relating incidence to recent infection prevelance: Application to HIV. South African Journal of Science 104.

DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis