for Health and Population Studies

Abstract Introduction: Despite recent breakthroughs in the fight against the HIV/AIDS epidemic within South Africa, the transmission of the virus continues at alarmingly high rates. It is possible, with the use of phylogenetic methods, to uncover transmission events of HIV amongst local communities in order to identify factors that may contribute to the sustained transmission of the virus. The aim of this study was to uncover transmission events of HIV amongst the infected population of Cape Town

Trends in genotypic HIV-1 antiretroviral resistance between 2006 and 2012 in South African patients receiving first- and second-line antiretroviral treatment regimens

The original publication is available at http://www.plosone.org/Publication of this article was funded by the Stellenbosch University Open Access Fund.BibliographyObjectives: South Africa’s national antiretroviral (ARV) treatment program expanded in 2010 to include the nucleoside reverse transcriptase (RT) inhibitors (NRTI) tenofovir (TDF) for adults and abacavir (ABC) for children. We investigated the associated changes in genotypic drug resistance patterns in patients with first-line ARV treatment failure since the introduction of these drugs, and protease inhibitor (PI) resistance patterns in patients who received ritonavir-boosted lopinavir (LPV/r)-containing therapy. Methods: We analysed ARV treatment histories and HIV-1 RT and protease mutations in plasma samples submitted to the Tygerberg Academic Hospital National Health Service Laboratory. Results: Between 2006 and 2012, 1,667 plasma samples from 1,416 ARV-treated patients, including 588 children and infants, were submitted for genotypic resistance testing. Compared with 720 recipients of a d4T or AZT-containing first-line regimen, the 153 recipients of a TDF-containing first-line regimen were more likely to have the RT mutations K65R (46% vs 4.0%; p<0.001), Y115F (10% vs. 0.6%; p<0.001), L74VI (8.5% vs. 1.8%; p<0.001), and K70EGQ (7.8% vs. 0.4%) and recipients of an ABC-containing first-line regimen were more likely to have K65R (17% vs 4.0%; p<0.001), Y115F (30% vs 0.6%; p<0.001), and L74VI (56% vs 1.8%; p<0.001). Among the 490 LPV/r recipients, 55 (11%) had ≥1 LPV-resistance mutations including 45 (9.6%) with intermediate or high-level LPV resistance. Low (20 patients) and intermediate (3 patients) darunavir (DRV) cross resistance was present in 23 (4.6%) patients. Conclusions: Among patients experiencing virological failure on a first-line regimen containing two NRTI plus one NNRTI, the use of TDF in adults and ABC in children was associated with an increase in four major non- thymidine analogue mutations. In a minority of patients, LPV/r-use was associated with intermediate or high-level LPV resistance with predominantly low-level DRV cross-resistance.Stellenbosch University Open Access FundPublishers' Versio

Identifying Recent HIV Infections: From Serological Assays to Genomics

In this paper, we review serological and molecular based methods to identify HIV infection recency. The accurate identification of recent HIV infection continues to be an important research area and has implications for HIV prevention and treatment interventions. Longitudinal cohorts that follow HIV negative individuals over time are the current gold standard approach, but they are logistically challenging, time consuming and an expensive enterprise. Methods that utilize cross-sectional testing and biomarker information have become an affordable alternative to the longitudinal approach. These methods use well-characterized biological makers to differentiate between recent and established HIV infections. However, recent results have identified a number of limitations in serological based assays that are sensitive to the variability in immune responses modulated by HIV subtypes, viral load and antiretroviral therapy. Molecular methods that explore the dynamics between the timing of infection and viral evolution are now emerging as a promising approach. The combination of serological and molecular methods may provide a good solution to identify recent HIV infection in cross-sectional data. As part of this review, we present the advantages and limitations of serological and molecular based methods and their potential complementary role for the identification of HIV infection recency

Simian immunodeficiency viruses (SIVs) from eastern and southern Africa : detection of a SIVagm variant from a chacma baboon

Simian immunodeficiency viruses (SIVs) have been shown to infect many old world African primate species. Thus far, no work has been published on southern African primates. In this study we investigated the genetic diversity between SIV strains from Kenyan and South African vervets (Cercopithecus aethiops pygerythrus). We amplified and sequenced a 1113 bp region of the env gene. Phylogenetic analysis of these sequences showed that all strains clustered with members of the vervet subgroup of SIVagm. The SIVs from South African vervets differed by 7% from each other and by 8–14% from the Kenyan SIV strains, while the Kenyan SIV strains differed by 10–21% from SIVagm of other east African vervets. We also isolated and sequenced, for the first time, a SIV strain from a healthy chacma baboon (Papio ursinus), caught in South Africa. Phylogenetic analysis of the env region showed the virus to be closely related to the South African vervet SIV strains, while analysis of its pol region confirmed the virus to be a SIVagm variant

Peripheral blood lymphocyte proviral DNA predicts neurocognitive impairment in clade C HIV

CITATION: Ruhanya, V. et al. 2020. Peripheral blood lymphocyte proviral DNA predicts neurocognitive impairment in clade C HIV. Journal of NeuroVirology, 26:920–928, doi:10.1007/s13365-020-00882-9.The original publication is available at https://link.springer.comIt is not known if proviral DNA in the periphery corresponds to cognitive status in clade C as it does in clade B and recombinant forms. A cross-sectional study was conducted on participants investigated for HIV-associated neurocognitive impairment in South Africa. HIV-1 proviral DNA was quantified using a PCR assay targeting a highly conserved HIV-1 LTR-gag region. Fifty-four (36.7%) participants were cognitively impaired and 93 (63.3%) were not impaired. Forty-three (79.6%) of the cognitively impaired participants were female and 11 (20.4%) were male. There was no significant age difference between cognitively impaired and unimpaired participants (p = 0.42). HIV-1 DNA in cognitively impaired PLWH was significantly higher than in cognitively normal individuals (p = .016). Considering impaired participants, lymphocyte HIV-1 DNA was significantly higher in males than females (p = 0.02). There was a modest positive correlation between lymphocyte HIV-1 DNA and global deficit scores (GDS) r = 0.176; p = 0.03). The two measures of viral load, lymphocyte HIV-1 DNA copies/million and plasma RNA copies/ml, were positively correlated (r = 0.39; p < .001). After adjusting for other covariates, age, sex, treatment status, and the interactions between impairment and treatment, the multivariate regression showed association between proviral load and neurocognitive impairment; omega effect size was 0.04, p value = 0.010. The burden of HIV-1 peripheral blood lymphocyte proviral DNA corresponds to neurocognitive impairment among individuals infected with clade C disease. Therefore, therapeutic strategies to reduce the HIV-1 proviral DNA reservoir in lymphocytes may improve neurocognitive outcomes in PLWH.Poliomyelitis Research Foundation (PRF)National Research Foundation (NRF)South African Medical Research Council (SAMRC)Publisher's versio

Stellenbosch Media Forum 2008

Stellenbosch Media Forum is an annual publication written and produced by the BPhil (Journalism) class of that specific year in the Department of Journalism, Stellenbosch University.Earlier this year Koos Bekker, owner of Media24, said he would not buy the New York Times even though his company could afford it. According to Moneyweb.co.za Bekker said the days of print media are numbered and the New York Times is old news. Die afgelope klompie jare het die media 'n transformasie ondergaan. In Suid-Afrika spesifiek is talle beperkinge op die media in die post-94-era opgehef. Die media funksioneer in 'n vryemark-stelsel en die algemene persepsie is dat dit meer fokus op die kommersiele as tevore. Met die ekonomiese afplatting is daar boonop gerugte van personeelverminderings en word selfs meer verwag van die Gideonsbende wat in die nuuskantore oorbly. Exposure to a variety of TV channels and internet websites is increasing the visual stimulation of media audiences. Media products are being redesigned to satisfy specific needs, in specific niches. One big change in terms of design is that more - and bigger - visuals and less text are being used. Vanjaar het e.tv die eerste 24-uur-nuuskanaal in Suid-Afrika geloods en al hoe meer drukmediaprodukte fokus op hul aanlyn-teenwoordigheid. Die Mail & Guardian het in Junie sy webtuiste herontwerp en sy groepblog, Thoughtleader, het die prys vir die Beste Suid-Afrikaanse Blog in die 2008 Suid-Afrikaanse Blogtoekennnings gekry. The Times, die Sunday Times se interaktiewe dagblad, het vanjaar sy eerste verjaarsdag gevier en bewys (sover) dat die konsep van 'n koerant wat met 'n webblad geintegreer is, wel werk. We are living in exciting times as far as development in the media is concerned. And that is why this year's edition of SMF has as its theme "Change in the media". Die veranderende media is hoofsaaklik te danke aan die ontwikkeling van tegnologie, soos dat jy jou nuus op jou selfoon kan kry. Nuttig, veral in Suid-Afrika waar die toegang tot breebandinternet gebrekkig is. Die koms van blogs noop koerante nou om onmiddellikheid en interaksie na te volg. These developments also influence journalists, sources and their audiences. With the advent of democracy in South Africa, changes in the consumer demographics of certain media products have occurred. And, oh yes, women have also advanced in the media since 1994, both as producers of media, and how they are represented. And then there is the youth, who "owns" new media technologies. And the disabled, who can get access to a new world through media technology. But, there are still many people in South Africa who do not have access to media, because of socio-economic circumstances: too poor to own the latest technology; illiterate and forgotten by the media elites. Die rol van die media, om debat te stimuleer, as waghond op te tree en die stem van die stemloses te wees, word deur al hierdie veranderings uitgedaag. Toenemende kommersialisering kan mediavryheid van binne erodeer. En dan is daar steeds die moontlikheid van politieke inmenging, al is mediavryheid grondwetlik verskans. Tradisionele kunsvorme in die media, soos kortverhale, radiodramas en boekresensies word gemarginaliseer, maar tog is daar die moontlikheid dat hulle kan aanpas en bly voortbestaan. Another challenge is the media's coverage of environmental issues, which has to be in sync with the phenomenon of global warming. Sport reporting also has to adapt to new developments, with sport writers now needing to have a knowledge of economics and politics as well. Een ding is seker: maatskappye, mense, produkte en onderwerpe wat by die media betrokke is, sal soos 'n verkleurmannetjie moet aanpas om te kan oorleef

Too few staff, too many patients: A qualitative study of the impact on obstetric care providers and on quality of care in Malawi

Background: Shortages of staff have a significant and negative impact on maternal outcomes in low-income countries, but the impact on obstetric care providers in these contexts is less well documented. Despite the government of Malawi's efforts to increase the number of human resources for health, maternal mortality rates remain persistently high. Health workers' perceptions of insufficient staff or time to carry out their work can predict key variables concerning motivation and attrition, while the resulting sub-standard care and poor attitudes towards women dissuade women from facility-based delivery. Understanding the situation from the health worker perspective can inform policy options that may contribute to a better working environment for staff and improved quality of care for Malawi's women. Methods: A qualitative research design, using critical incident interviews, was used to generate a deep and textured understanding of participants' experiences. Eligible participants had performed at least one of the emergency obstetric care signal functions a in the previous three months and had experienced a demotivating critical incident within the same timeframe. Data were analysed using NVivo software. Results: Eighty-four interviews were conducted. Concerns about staff shortages and workload were key factors for over 40% of staff who stated their intention to leave their current post and for nearly two-thirds of the remaining health workers who were interviewed. The main themes emerging were: too few staff, too many patients; lack of clinical officers/doctors; inadequate obstetric skills; undermining performance and professionalism; and physical and psychological consequences for staff. Underlying factors were inflexible scheduling and staff allocations that made it impossible to deliver quality care. Conclusion: This study revealed the difficult circumstances under which maternity staff are operating and the professional and emotional toll this exacts. Systems failures and inadequate human resource management are key contributors to the gaps in provision of obstetric care and need to be addressed. Thoughtful strategies that match supply to demand, coupled with targeted efforts to support health workers, are necessary to mitigate the effects of working in this context and to improve the quality of obstetric care for women in Malawi

Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic in southern Africa has been characterised by three distinct waves. The first was associated with a mix of SARS-CoV-2 lineages, whilst the second and third waves were driven by the Beta and Delta variants, respectively1-3. In November 2021, genomic surveillance teams in South Africa and Botswana detected a new SARS-CoV-2 variant associated with a rapid resurgence of infections in Gauteng Province, South Africa. Within three days of the first genome being uploaded, it was designated a variant of concern (Omicron) by the World Health Organization and, within three weeks, had been identified in 87 countries. The Omicron variant is exceptional for carrying over 30 mutations in the spike glycoprotein, predicted to influence antibody neutralization and spike function4. Here, we describe the genomic profile and early transmission dynamics of Omicron, highlighting the rapid spread in regions with high levels of population immunity