The potential effect of an HIV/AIDS vaccine in South Africa

This paper presents a model for assessing the potential effect of an HIV/AIDS vaccine in South Africa, and for calculating the amount of vaccine that would be required. A number of different hypothetical vaccine profiles and vaccine distribution strategies are considered. Results suggest that a sterilising vaccine could reduce the HIV incidence between 2015 and 2025 by up to 50%, while a disease modifying vaccine would be unlikely to reduce HIV incidence by more than a third. The effect on AIDS mortality over the same period would be substantially smaller, and it is unlikely that any preventive vaccine would reduce AIDS mortality by more than 10% between 2015 and 2025

Development of a real-time full-field range imaging system

This article describes the development of a full-field range imaging system employing a high frequency amplitude modulated light source and image sensor. Depth images are produced at video frame rates in which each pixel in the image represents distance from the sensor to objects in the scene. The various hardware subsystems are described as are the details about the firmware and software implementation for processing the images in real-time. The system is flexible in that precision can be traded off for decreased acquisition time. Results are reported to illustrate this versatility for both high-speed (reduced precision) and high-precision operating modes

The potential effect of an HIV/AIDS vaccine in South Africa

This paper presents a model for assessing the potential effect of an HIV/AIDS vaccine in South Africa, and for calculating the amount of vaccine that would be required. A number of different hypothetical vaccine profiles and vaccine distribution strategies are considered. Results suggest that a sterilising vaccine could reduce the HIV incidence between 2015 and 2025 by up to 50%, while a disease modifying vaccine would be unlikely to reduce HIV incidence by more than a third. The effect on AIDS mortality over the same period would be substantially smaller, and it is unlikely that any preventive vaccine would reduce AIDS mortality by more than 10% between 2015 and 2025

Technical note: Development of a gradient tube method for examining microbial population structures in floating sulphur biofilms

Floating biofilms occur in thin layers of between 50 μm and 500 μm on the surface of certain organic, sulphidic aquatic environments and, at times, may only be several cells deep. While these structures may be important in terms of energy flow pathways, and possibly also in wastewater treatment operations, little is known about their structural/functional properties. This is due, in part, to their flimsy nature but also to methodological constraints related to their sampling and manipulation. We have investigated floating sulphur biofilms that appear as white layers on the surface of anoxic sulphidic organic wastewaters and describe here the development of a novel gradient tube method for investigating these systems. This approach enables testing of the hypothesis that these floating sulphur biofilms are complex well-differentiated structures rather than disordered dispersions of microbial biomass as has been previously thought. Furthermore, if the former is correct, they would seem to resemble the structure and functionality of comparable complex bioflms that are attached to solid substrates. The gradient tube method involves the establishment of apposing gradients of sulphide and oxygen that are expanded across a tube of agarose 10 cm in length; this simulates the oxic/anoxic interface that occurs over only several micrometres in the natural biofilm system. A plug of sulphide-enriched agarose is first placed in the base of the tube. Samples of the floating sulphur biofilm are then mixed into agarose growth medium and, before it sets, this is overlaid on top of the plug. The tubes are then open capped and incubated. A variety of different microbial populations may thus become established in the separate physiological niches that are set up in this way within the gradient tube. The populations may be quite robustly sampled by extruding and then sectioning the agarose plug. This expansion of the biofilm enables more detailed molecular phylogenetic studies of the populations found in the various niches within the biofilm and also measurement of physico-chemical parameters within the system.Keywords: gradient tube method, floating biofilms, floating sulphur biofilms, microbial ecology, sulphur biotechnology, acid mine drainage wastewater

Tracking mortality in near to real time provides essential information about the impact of the COVID-19 pandemic in South Africa in 2020

Background. Producing timely and accurate estimates of the impact of COVID-19 on mortality is challenging for most countries, but impossible for South Africa (SA) from cause-of-death statistics. Objectives. To quantify the excess deaths and likely magnitude of COVID-19 in SA in 2020 and draw conclusions on monitoring the epidemic in 2021. Methods. Basic details of deaths registered on the National Population Register by the Department of Home Affairs (DoHA) are provided to the South African Medical Research Council weekly. Adjustments are made to the numbers of weekly deaths to account for non-registration on the population register, as well as late registration of death with the DoHA. The weekly number of deaths is compared with the number predicted based on the Holt-Winters time-series analysis of past deaths for provinces and metropolitan areas. Excess deaths were calculated for all-causes deaths and natural deaths, using the predicted deaths as a baseline. In addition, an adjustment was made to the baseline for natural deaths to account for the drop in natural deaths due to lockdown. Results. We estimated that just over 550 000 deaths occurred among persons aged ≥1 year during 2020, 13% higher than the 485 000 predicted before the pandemic. A pronounced increase in weekly deaths from natural causes peaked in the middle of July across all ages except <20 years, and across all provinces with slightly different timing. During December, it became clear that SA was experiencing a second wave of COVID-19 that would exceed the death toll of the first wave. In 2020, there were 70 000 - 76 000 excess deaths from natural causes, depending on the base. Using the adjusted base, the excess death rate from natural causes was 122 per 100 000 population, with a male-to-female ratio of 0.78. Deaths from unnatural causes halved for both males and females during the stringent lockdown level 5. The numbers reverted towards the predicted number with some fluctuations as lockdown restrictions varied. Just under 5 000 unnatural deaths were averted. Conclusions. Tracking the weekly numbers of deaths in near to real time has provided important information about the spatiotemporal impact of the pandemic and highlights that the ~28 000 reported COVID-19 deaths during 2020 substantially understate the death toll from COVID-19. There is an urgent need to re-engineer the system of collecting and processing cause-of-death information so that it can be accessed in a timely way to inform public health actions

HIV/AIDS mortality trends pre and post ART for 1997 - 2012 in South Africa – have we turned the tide?

Background. South Africa (SA) has one of the largest HIV/AIDS epidemics in the world and the most extensive antiretroviral therapy (ART) programme globally, which was rolled out from 2004. This paper reports the trends in HIV/AIDS mortality pre and post ART rollout in SA. Methods. Vital registration cause-of-death data from Statistics South Africa were adjusted for under-reporting of deaths using demographic methods. Misattributed HIV/AIDS deaths were identified by regressing excess mortality on a lagged indicator HIV antenatal clinic prevalence for causes found to be associated with HIV/AIDS. Background trends in the source-cause mortality rates were estimated from the trend in cause-specific mortality experienced among 75 - 84-year-olds. Mortality rates were calculated using mid-year population estimates and the World Health Organization world standard age-weights. Results. We estimated over 3 189 000 HIV/AIDS deaths for 1997 - 2012. In 1997, 60 336 (14.5%) of deaths were attributed to HIV/AIDS; this number peaked in 2006 at 283 564 (41.9%) and decreased to 153 661 (29.1%) by 2012; female mortality rates peaked in 2005 and those of males in 2006. Men aged 35 years and older had higher mortality rates than did women. While the rates at ages below 65 years in 2012 were lower than those in 2006, rates of those age 65 years and older remained unchanged. Conclusion. The number of HIV/AIDS deaths has almost halved since the ART rollout. Of concern is the high mortality in men 45 years and older and the high mortality of men compared with women in the older ages by 2012; this gap has increased with age. Treatment and prevention programmes should strategise how to target men

South African Annuitant Standard Mortality Tables 1996-2000 (SAIML98 and SAIFL98)

This paper describes the data and the processes used to produce the first standard tables of mortality of South African immediate annuitants. A parametric curve was fitted to the data from the normal retirement ages up to age 85. Below the normal retirement ages the rates increasingly reflected the impact of higher mortality due to ill health retirements and so the curve was blended into that of the most recent standard table of life assured mortality (SA85 90). Above age 85 the estimates were thought to be unreliable and the extrapolation of the curve fit to the younger ages did not allow for the expected fall in the rate of increase in the rates with age. Thus rates above this age were estimated using a relationship proposed by Coale and Kisker. It was not possible to produce select rates or to decide on a trend in these rates over time

The burden of disease attributable to sexually transmitted infections in South Africa in 2000

Objectives. 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. South African Medical Journal Vol. 97 (8) Part 2 2007: pp. 658-66

Issues in public health: Unnatural deaths, alcohol bans and curfews: Evidence from a quasi-natural experiment during COVID-19

Background. Coronavirus disease-19 (COVID-19) restrictions, particularly relating to the sale of alcohol and hours of curfew, have had a marked effect on the temporal pattern of unnatural deaths in South Africa. Methods. Death data were collected over 68 weeks from January 2020 to April 2021, together with information on the nature of restrictions (if any) on the sale of alcohol, and hours of curfew. Data were analysed using a simple ordinary least square (OLS) regression model to estimate the relative contribution of restrictions on the sale of alcohol and hours of curfew to the pattern of excess unnatural deaths. Results. The complete restriction on the sale of alcohol resulted in a statistically significant reduction in unnatural deaths regardless of the length of curfew. To the contrary, periods where no or limited restrictions on alcohol were in force had no significant effect, or resulted in significantly increased unnatural deaths. Conclusion. The present study highlights an association between alcohol availability and the number of unnatural deaths and demonstrates the extent to which those deaths might be averted by disrupting the alcohol supply. While this is not a long-term solution to addressing alcohol-related harm, it further raises the importance of implementing evidence-based alcohol control measures