Browsing by Author "Johnson, Leigh"
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- ItemOpen AccessChildren 'in need of care' or in need of cash? Questioning social security provisions for orphans in the context of the South African AIDS pandemic(Children's Institute, 2003-12) Meintjes, Helen; Budlender, Debbie; Giese, Sonja; Johnson, LeighJoint working paper of the Children's Institute and Centre for Actuarial Research, University of Cape Town.
- ItemOpen AccessA comparison of South African national HIV incidence estimates: A critical appraisal of different methods(Public Library of Science, 2015) Rehle, Thomas; Johnson, Leigh; Hallett, Timothy; Mahy, Mary; Kim, Andrea; Odido, Helen; Onoya, Dorina; Jooste, Sean; Shisana, Olive; Puren, AdrianBACKGROUND: The interpretation of HIV prevalence trends is increasingly difficult as antiretroviral treatment programs expand. Reliable HIV incidence estimates are critical to monitoring transmission trends and guiding an effective national response to the epidemic. Methods and FINDINGS: We used a range of methods to estimate HIV incidence in South Africa: (i) an incidence testing algorithm applying the Limiting-Antigen Avidity Assay (LAg-Avidity EIA) in combination with antiretroviral drug and HIV viral load testing; (ii) a modelling technique based on the synthetic cohort principle; and (iii) two dynamic mathematical models, the EPP/Spectrum model package and the Thembisa model. Overall, the different incidence estimation methods were in broad agreement on HIV incidence estimates among persons aged 15-49 years in 2012. The assay-based method produced slightly higher estimates of incidence, 1.72% (95% CI 1.38 - 2.06), compared with the mathematical models, 1.47% (95% CI 1.23 - 1.72) in Thembisa and 1.52% (95% CI 1.43 - 1.62) in EPP/Spectrum, and slightly lower estimates of incidence compared to the synthetic cohort, 1.9% (95% CI 0.8 - 3.1) over the period from 2008 to 2012. Among youth aged 15-24 years, a declining trend in HIV incidence was estimated by all three mathematical estimation methods. CONCLUSIONS: The multi-method comparison showed similar levels and trends in HIV incidence and validated the estimates provided by the assay-based incidence testing algorithm. Our results confirm that South Africa is the country with the largest number of new HIV infections in the world, with about 1 000 new infections occurring each day among adults aged 15-49 years in 2012.
- ItemOpen AccessInitial burden of disease estimates for South Africa, 2000(2003) Bradshaw, Debbie; Groenewald, Pam; Laubscher, Ria; Nannan, Nadine; Nojilana, Beatrice; Rosana, Norman; Pieterse, Desiréé; Schneider, Michelle; Bourne, David E; Timæus, Ian M; Dorrington, Rob; Johnson, LeighBackground. This paper describes the first national burden of disease study for South Africa. The main focus is the burden due to premature mortality, i.e. years of life lost (YLLs). In addition, estimates of the burden contributed by morbidity, i.e. the years lived with disability (YLDs), are obtained to calculate disability-adjusted life years (DALYs); and the impact of AIDS on premature mortality in the year 2010 is assessed. Method. Owing to the rapid mortality transition and the lack of timely data, a modelling approach has been adopted. The total mortality for the year 2000 is estimated using a demographic and AIDS model. The non-AIDS cause-of-death profile is estimated using three sources of data: Statistics South Africa, the National Department of Home Affairs, and the National Injury Mortality Surveillance System. A ratio method is used to estimate the YLDs from the YLLestimates. Results. The top single cause of mortality burden was HIV/AIDS followed by homicide, tuberculosis, road traffic accidents and diarrhoea. HIV/AIDS accounted for 38% of total YLLs, which is proportionately higher for females (47%) than for males (33%). Pre-transitional diseases, usually associated with poverty and underdevelopment, accounted for 25%, non-communicable diseases 21% and injuries 16% of YLLs. The DALY estimates highlight the fact that mortality alone underestimates the burden of disease, especially with regard to unintentional injuries, respiratory disease, and nervous system, mental and sense organ disorders. The impact of HIV/AIDS is expected to more than double the burden of premature mortality by the year 2010. Conclusion. This study has drawn together data from a range of sources to develop coherent estimates of premature mortality by cause. South Africa is experiencing a quadruple burden of disease comprising the pre-transitional diseases, the emerging chronic diseases, injuries, and HIV/AIDS. Unless interventions that reduce morbidity and delay morbidity become widely available, the burden due to HIV/AIDS can be expected to grow very rapidly in the next few years. An improved base of information is needed to assess the morbidity impact more accurate.
- ItemOpen AccessMathematical modelling of the population impact of screening for Chlamydia Trachomatis and Neisseria gonorrhoeae in South Africa(2018) Esra, Rachel; Johnson, LeighA large proportion of chlamydial and gonococcal infections are asymptomatic. In lower- and middle-income countries like South Africa, where syndromic management is practiced, it is likely that a large proportion of curable STIs go untreated, as screening for asymptomatic STIs is rarely conducted. Due to the lack of empirical data on the efficacy of STI screening programs, dynamic mathematical modelling has been used to assess the impact of screening, but most previous modelling studies have focused on high-income settings. Here we utilize dynamic mathematical modelling to evaluate the potential impact of opportunistic STI screening programs on the incidence and prevalence of Chlamydia trachomatis and Neisseria gonorrhea in South Africa. We extended an existing agent-based model of heterosexual HIV and STI transmission in South Africa to investigate the impact of targeted screening strategies directed at high risk groups including youth, female sex workers, pregnant women and patients in HIV care. All four screening strategies resulted in reductions in general and key population STI transmission. Opportunistic STI screening of youth and ART patients were shown to be most effective and represent viable interventions for reducing STI transmission in the South African population. Additionally, we compared the modelled impact of a standardized screening program to results obtained from other published mathematical models of chlamydia screening. Differences between models could be attributed to differences in the modelled heterogeneity in sexual behaviour as well as differences in assumptions about immunity following chlamydia recovery.
- ItemOpen AccessModelling the impact of prevention strategies on cervical cancer incidence in South Africa(2021) van Schalkwyk, Catherina; Johnson, Leigh; Moodley, JenniferBackground: In 2019, the World Health Organisation called for the elimination of cervical cancer as a public health concern. In South Africa, despite having a national screening policy in place since 2000, diagnosed cervical cancer incidence has shown no signs of decline. Since 2014, girls aged 9 have been vaccinated against HPV infection using the bivalent vaccine, with high coverage. However, due to the long delay between HPV infection and progression to cancer, the impact that vaccination will have on cervical cancer incidence will be unobservable in the near future. This thesis sets out to quantify this impact using a mathematical model, and will estimate the impact of scaling up current cancer prevention strategies, as well as proposed alternative strategies. Methods: This research extends a previously developed individual-based model for HIV to include infection with 13 high-risk HPV types and progression to cervical cancer. HPV infection and cervical disease parameters were calibrated to a wide range of South African data sources using a likelihood based approach. In the process of developing an appropriate model for cervical cancer incidence in South Africa, important aspects related to HIV/HPV co-infection dynamics, the natural history of HPV and the current and historic levels of cervical cancer prevention in the Western Cape were investigated. The calibrated and validated model was used to estimate the impact of current and proposed alternative prevention strategies on cervical cancer incidence in the next century. Findings: Using a model structure that does not include a biological transmission co-factor, we show that simulated associations between HIV and HPV transmission are similar to corresponding empirical estimates and therefore these associations may result from residual confounding by sexual behavioural factors and network-level effects. Using simulated vaccine trials, we show that viral latency and reactivation of latent infections is necessary in the natural history of HPV to match results from empirical trials. The model's screening algorithm reflects findings from the Western Cape's public health sector – low levels of screening coverage and linkage to treatment facilities, and poor adherence to screening schedules. The model matches stable trends in diagnosed cervical cancer incidence in South Africa, but it estimates increases in cervical cancer incidence over the last number of years (due to increased life expectancy of women on ART), which will result in sharp increases in diagnoses. While decreasing HIV prevalence and HPV vaccination will substantially reduce cervical cancer incidence in the long term, improvements in South Africa's current screening strategy, as well as switching to new screening technologies, will have significant impact in the short term. Conclusions: This thesis presents an epidemiological model of cervical cancer in South Africa – the first to dynamically simulate infection with both HIV and HPV at national level. It allows for estimation of the impact of both HIV and cervical cancer prevention on cancer incidence, and provides the opportunity to identify the vaccination and screening strategies with the greatest public health significance.
- ItemOpen AccessModelling the South African tuberculosis epidemic: the effect of HIV, sex differences, and the impact of interventions(2023) Kubjane, Mmamapudi; Johnson, Leigh; Boulle, AndrewThe South African tuberculosis (TB) epidemic is driven mainly by HIV, and the TB disease burden is greater in males than females. Additional factors that drive the epidemic include undiagnosed and untreated TB, contributing to transmission; and highly prevalent TB risk factors such as alcohol misuse, smoking, diabetes, and undernutrition, which increase the risk of progression to TB disease. These factors are distributed differently by sex and likely explain the observed sex disparities in TB. The South African TB control programme has implemented multiple interventions, including directly observed therapy strategy (DOTS), antiretroviral therapy (ART), intensified screening activities, the provision of isoniazid preventative therapy (IPT) and the implementation of Xpert MTB/RIF as a first-line diagnostic tool. However, few analyses have quantified the historical impact of HIV and the combined impact of TB interventions on the South African TB epidemic at a national level. In addition, factors that influence sex disparities in the South African TB burden have not been explored thoroughly. Also, it remains uncertain whether, with existing interventions, it would be feasible for South Africa to meet the End TB targets to reduce TB incidence and mortality by 80% and 90% respectively (relative to 2015 levels) by 2030. This thesis aims to address the abovementioned gaps in knowledge and provide insights into understanding the population-level TB dynamics, using a mathematical model. The first objective is to quantify TB incidence and mortality due to HIV and assess the impact of interventions mentioned above on TB incidence and mortality between 1990 and 2019. The second objective is to explore the extent to which the following factors contribute to sex differences in TB: HIV, ART uptake, smoking, alcohol abuse, undernutrition, diabetes, health-seeking patterns, social contact rates and TB treatment discontinuation. The third objective is to project the future impact of increasing screening, improving linkage to TB care and retention, increasing preventative therapy, and reducing ART interruptions. An age- and sex-stratified dynamic tuberculosis transmission model for South Africa was developed. To dynamically model the effect of HIV and ART on TB incidence and mortality, the TB model was integrated into the Thembisa model, a previously developed HIV and demographic model. In addition, age- and sex-specific relative risks were applied to rates of progression to TB disease to capture age and sex differences in tuberculosis incidence. The model also included a diagnostic pathway representing health-seeking patterns and the sensitivity and specificity of the diagnostic algorithm. A Bayesian approach was used to calibrate the model to the numbers of people starting treatment from the electronic tuberculosis register, deaths from the vital register, microbiological tests, and the national tuberculosis prevalence survey. The model estimated rapid increases in TB incidence and mortality in the mid-to-late 1990s, influenced by HIV. Between 1990 and 2019, approximately eight million people developed tuberculosis, and two million died from TB; HIV accounted for at least half and two-thirds of the TB incidence and mortality, respectively. The TB epidemic peaked in the mid-to-late 2000s, followed by declines until 2019. The ART program and TB screening efforts, which were expanded in the mid-2000s, contributed the most to reductions in TB incidence and mortality, while other interventions had minor impacts. Due to the heavier HIV burden in women than men, women experienced greater HIV-associated TB incidence and mortality than men. However, because of the higher ART uptake among women than men, women experienced greater relative reductions in TB incidence and mortality over the period 2005– 2019. Consequently, the higher TB burden among men has been sustained; the estimated male-to-female ratios of TB incidence and mortality in 2019 were 1.7 and 1.65, respectively. Additional factors explaining the excess TB in men are smoking, alcohol abuse and delays in health-seeking patterns. Sex differences in undernutrition, social contact patterns, and treatment discontinuation had minimal effect on TB sex disparities. Projections of the model to 2030, considering the effects of COVID-19-related disruptions to TB care, suggest that increasing TB screening would be the most impactful among all interventions explored. However, the model also suggests that the 2030 End TB milestone is unlikely to be met by scaling up existing interventions. Other interventions that need to be explored include targeted universal TB testing and other diagnostic tests such as digital chest x-rays, urine Lipoarabinomannan, and biomarkers to identify individuals at risk of TB disease. Accelerating progress toward TB incidence and mortality reductions will require developing affordable and efficient rapid diagnostic tools to identify potential and active TB cases. Research and innovation efforts towards finding a vaccine effective in preventing TB disease are also critical. In addition, it is essential to improve the uptake of TB preventative therapy in HIV-positive individuals and perhaps further expand provision to other TB risk groups
- ItemOpen AccessOptimal uses of antiretrovirals for prevention in HIV-1 serodiscordant heterosexual couples in South Africa: a modelling study(Public Library of Science, 2011) Hallett, Timothy B; Baeten, Jared M; Heffron, Renee; Barnabas, Ruanne; De Bruyn, Guy; Cremin, Íde; Delany, Sinead; Garnett, Geoffrey P; Gray, Glenda; Johnson, LeighHallett et al use a mathematical model to examine the long-term impact and cost-effectiveness of different pre-exposure prophylaxis (PrEP) strategies for HIV prevention in serodiscordant couples.
- ItemOpen AccessSocial security for children in the context of AIDS: questioning the State's response(Children's Institute, 2004-07) Meintjes, Helen; Budlender, Debbie; Giese, Sonja; Johnson, Leigh
- ItemOpen AccessThe burden of disease attributable to sexually transmitted infections in South Africa in 2000(2007) Johnson, Leigh; Bradshaw, Debbie; Dorrington, Rob; South African Comparative Risk Assessment Collaborating GroupObjectives. To estimate the burden of disease attributable to sexually transmitted infections (STIs) in South Africa, to identify the factors contributing to this burden, and to review successes and failures in reducing this burden. Design. Years of life lost (YLL) and years lived with disability (YLD) were estimated using different approaches for HIV/AIDS, other STIs and cervical cancer. Burden in respect of HIV/ AIDS was estimated using the ASSA2002 model, and for the other diseases the revised national burden of disease estimates for 2000 based on 1996 cause-of-death data were used. The ASSA2002 model was used to estimate numbers of AIDS deaths under different prevention and treatment scenarios. Setting. South Africa. Outcome measures. Deaths, YLL and disability-adjusted life years (DALYs) associated with HIV/AIDS, other STIs and cervical cancer. Results. STIs accounted for more than 26% of all deaths and over 5 million DALYs in 2000 and over 98% of this burden was due to HIV/AIDS. A combination of social, behavioural and biological conditions contribute to this burden. HIV/AIDS mortality and morbidity are estimated to have increased significantly since 2000, and the future change in this burden is largely dependent on the extent to which antiretroviral treatment and HIV prevention programmes are introduced. 2.5 million AIDS deaths could be prevented by 2015 if high levels of access to antiretroviral treatment are achieved. Conclusion. South Africa faces one of the largest STI epidemics in the world. A multifaceted strategy to prevent and treat STIs is needed, and burden of disease assessments should look beyond the role of ‘unsafe sex’ when attributing this disease burden to risk factors.