Faculty of Health Sciences

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Start date: 2000End date: 2017

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    CD4+ T-cell count at antiretroviral therapy initiation in the "Treat AII" era in South A: an interrupted time series analysis.
    (2012-11-05) Yapa HM; Kim H-y; Post FA; Jiamsakul A; de Neve J-W; Tanser F; Iwuji C; Baisley K; Shamanesh M; Pillay D; Siedner MJ; Barnighausen T; Bot J
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    Human respiratory syncytial virus diversity and epidemiology among patients hospitalized with severe respiratory illness in South Africa, 2012–2015
    (2015) Ziyaad Valley-Omar; Stefano Tempia; Orienka Hellferscee; Sibongile Walaza; Ebrahim Variava6; Halima Dawood; Kathleen Kahn; Meredith McMorrow; Marthi Pretorius; Senzo Mtshali; Ernest Mamorobela; Nicole Wolter; Marietjie Venter; Anne von Gottberg; Cheryl Cohen; Florette K. Treurnicht
    Background: We aimed to describe the prevalence of human respiratory syncytial virus (HRSV) and evaluate associations between HRSV subgroups and/or genotypes and epidemiologic characteristics and clinical outcomes in patients hospitalized with severe respiratory illness (SRI). Methods: Between January 2012 and December 2015, we enrolled patients of all ages admitted to two South African hospitals with SRI in prospective hospital-based syndromic surveillance. We collected respiratory specimens and clinical and epidemiological data. Unconditional random effect multivariable logistic regression was used to assess factors associated with HRSV infection. Results: HRSV was detected in 11.2% (772/6908) of enrolled patients of which 47.0% (363/772) were under the age of 6 months. There were no differences in clinical outcomes of HRSV subgroup A-infected patients compared with HRSV subgroup B-infected patients but among patients aged <5 years, children with HRSV subgroup A were more likely be coinfected with Streptococcus pneumoniae (23/208 11.0% vs. 2/90, 2.0%; adjusted odds ratio 5.7). No significant associations of HRSV A genotypes NA1 and ON1 with specific clinical outcomes were observed. Conclusions: While HRSV subgroup and genotype dominance shifted between seasons, we showed similar genotype diversity as noted worldwide. We found no association between clinical outcomes and HRSV subgroups or genotypes.
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    Estimates of HIV incidence among drug users in St. Petersburg, Russia: continued growth of a rapidly expanding epidemic
    (2010-07-30) Linda M. Niccolai; Sergei V. Verevochkin; Olga V. Toussova; Edward White; Russell Barbour; Andrei P. Kozlov; Robert Heimer
    Background: Russia has one of the world’s fastest growing HIV epidemics and it has been largely concentrated among injection drug users (IDU). St Petersburg, Russia’s second largest city, is one of the country’s regions that has been most affected by the HIV epidemic. To monitor the current epidemic situation, we sought to estimate recent HIV incidence among IDU in St Petersburg. Methods: In a cross-sectional study of 691 IDU recruited during 2005–08, HIV incidence was estimated by two methods: a retrospective cohort analysis and BED capture enzyme immunoassay (EIA) results. Socio-demographic and behavioural correlates of incident infections and spatial patterns were examined. Results: In the retrospective cohort analysis, the incidence rate was estimated to be 14.1/100 person-years [95% confidence interval (CI) 10.7–17.6]. Using results of BED EIA and two correction formulas for known misclassification, incidence estimates were 23.9 (95% CI 17.8–30.1) and 25.5 (95% CI 18.9–32.0) per 100 person-years. Independent correlates of being recently infected included current unemployment (P = 0.004) and not having injected drugs in the past 30 days (P = 0.03). HIV incident cases were detected in all but one district in the city, with focal areas of transmission observed to be expanding. Conclusions: High HIV incidence among IDU in St Petersburg attests to continued growth of the epidemic. The need for expansion of HIV prevention interventions targeted to vulnerable populations throughout the city is urgent. These results also suggest that the BED EIA may over-estimate incidence even after correction for low specificity.
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    Performance of four computer-coded verbal autopsy methods for cause of death assignment compared with physician coding on 24,000 deaths in low- and middle-income countries
    (2014) Nikita Desai; Lukasz Aleksandrowicz; Pierre Miasnikof; Ying Lu; Jordana Leitao; Peter Byass; Stephen Tollman; Paul Mee; Dewan Alam; Suresh Kumar Rathi; Abhishek Singh; Rajesh Kumar; Faujdar Ram; Prabhat Jha
    Background: Physician-coded verbal autopsy (PCVA) is the most widely used method to determine causes of death (CODs) in countries where medical certification of death is uncommon. Computer-coded verbal autopsy (CCVA) methods have been proposed as a faster and cheaper alternative to PCVA, though they have not been widely compared to PCVA or to each other. Methods: We compared the performance of open-source random forest, open-source tariff method, InterVA-4, and the King-Lu method to PCVA on five datasets comprising over 24,000 verbal autopsies from low- and middle-income countries. Metrics to assess performance were positive predictive value and partial chance-corrected concordance at the individual level, and cause-specific mortality fraction accuracy and cause-specific mortality fraction error at the population level. Results: The positive predictive value for the most probable COD predicted by the four CCVA methods averaged about 43% to 44% across the datasets. The average positive predictive value improved for the top three most probable CODs, with greater improvements for open-source random forest (69%) and open-source tariff method (68%) than for InterVA-4 (62%). The average partial chance-corrected concordance for the most probable COD predicted by the open-source random forest, open-source tariff method and InterVA-4 were 41%, 40% and 41%, respectively, with better results for the top three most probable CODs. Performance generally improved with larger datasets. At the population level, the King-Lu method had the highest average cause-specific mortality fraction accuracy across all five datasets (91%), followed by InterVA-4 (72% across three datasets), open-source random forest (71%) and open-source tariff method (54%). Conclusions: On an individual level, no single method was able to replicate the physician assignment of COD more than about half the time. At the population level, the King-Lu method was the best method to estimate cause-specific mortality fractions, though it does not assign individual CODs. Future testing should focus on combining different computer-coded verbal autopsy tools, paired with PCVA strengths. This includes using open-source tools applied to larger and varied datasets (especially those including a random sample of deaths drawn from the population), so as to establish the performance for age- and sex-specific CODs
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    A radiation dose review for paediatric fluoroscopy in an Academic South African referral hospital
    (2017) Venter, Mauritz
    INTRODUCTION Children are more sensitive to radiation and it is therefore important to reduce their exposure. There are currently no published data on South African paediatric fluoroscopic upper GIT, contrasted enemas and vesico-urethrogram dosage reference levels. AIM To determine the dose area product (DAP) values in common paediatric fluoroscopic examinations: Upper GIT studies, contrasted enemas and vesico-urethrograms. The primary endpoint was comparing our median and upper third quartile DAP values to international standards. METHOD We adhere to the Radiological Society of South Africa (RSSA)/South African Society of Paediatric Imaging’s (SASPI) guidelines to minimise radiation exposure. The upper third quartile and mean DAP values were collected between March 2013 and March 2016 for each study, categorised into four age groups (0–1, 2–5, 6–10 and 11–15 years) and stratified by our three major examinations. The data were compared to literature from the National UK Radiological Protection Board. RESULTS DAP values for upper GIT studies were significantly lower in the three younger age groups. There was no significant difference in the oldest age group. DAP values for vesico-urethrograms were significantly lower in the youngest age group. There was no significant difference in the three older age groups. For our contrasted enemas, there were no suitable data for comparison. CONCLUSION By following the RSSA / SASPI guidelines, our overall DAP values compared better than the UK National Patient Dose Database in the younger age groups and no worse in the older age groups.
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    Variation by Geographic Scale in the Migration-Environment Association: Evidence from Rural South Africa
    (Federal Institute for Population Research, 2017) Hunter, L.M.; Leyk, S.; Maclaurin, G.J.; Nawrotzki, R.; Twine, W.; Erasmus, B.F.N.; Collinson, M.
    Scholarly understanding of human migration’s environmental dimensions has greatly advanced in the past several years, motivated in large part by public and policy dialogue around “climate migrants”. The research presented here advances current demographic scholarship both through its substantive interpretations and conclusions, as well as its methodological approach. We examine temporary rural South African outmigration as related to household-level availability of proximate natural resources. Such “natural capital” is central to livelihoods in the region, both for sustenance and as materials for market-bound products. The results demonstrate that the association between local environmental resource availability and outmigration is, in general, positive: households with higher levels of proximate natural capital are more likely to engage in temporary migration. In this way, the general findings support the “environmental surplus” hypothesis that resource security provides a foundation from which households can invest in migration as a livelihood strategy. Such insight stands in contrast to popular dialogue, which tends to view migration as a last resort undertaken only by the most vulnerable households. As another important insight, our findings demonstrate important spatial variation, complicating attempts to generalize migration-environment findings across spatial scales. In our rural South African study site, the positive association between migration and proximate resources is actually highly localized, varying from strongly positive in some villages to strongly negative in others. We explore the socio-demographic factors underlying this “operational scale sensitivity”. The cross-scale methodologies applied here offer nuance unavailable within more commonly used global regression models, although also introducing complexity that complicates story-telling and inhibits generalizability.
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    The impact of antiretroviral therapy on symptom burden among HIV outpatients with low CD4 count in rural Uganda: nested longitudinal cohort study
    (Springer Nature, 2017-07-13) Wakeham, Katie; Harding, Richard; Levin, Jonathan; Parkes-Ratanshi, Rosalind; Kamali, Anatoli; Lalloo, David G
    Individuals with HIV have a high prevalence of physical and psychological symptoms throughout their disease course. Despite the clinical and public health implications of unresolved pain and symptoms, little is known about the effect of anti-retroviral therapy (ART) on these outcomes. This study aimed to assess the impact on symptom burden for the year after ART initiation in individuals with a CD4 count <200 cells/uL in Uganda.
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    Zinc oxide-eugenol and calcium hydroxide pulpectomies in baboon primary molars: histological responses
    (2004) Cleaton-Jones, P.; Duggal, M.; Parak, R.; et al
    AIM: To compare histological responses to zinc oxide-eugenol (ZOE) and calcium hydroxide (CH) pulpectomies in primary molar teeth with inflamed pulps. STUDY DESIGN:This was an experimental study in 17 juvenile baboons (Papio ursinus). METHODS: Pulpitis was induced with fresh human carious dentine or Streptococcus mutans placed into occlusal cavities in 78 primary molars; after 14 days a pulpectomy was performed on the same primary molars with the two root fillings randomly allocated. The root canal openings were then covered with IRM and the cavity filled with amalgam. After 90 days specimens were harvested and examined under the light microscope with the examiner blind to the treatment. RESULTS:Reaction frequencies in the ZOE-treated versus CH-treated teeth were: no recognisable pulp 89% and 82%, internal root resorption 0% and 1%, external root resorption 11% and 24%, presence of bacteria 5% and 18%, periapical abscesses 24% and 52%. STATISTICS:Fisher's exact probability test showed a statistically significant higher prevalence of periapical abscesses in the CH-treated group (P=0.03, relative risk 2.2). CONCLUSIONS: ZOE pulpectomy is preferred to CH for the treatment of infected pulps in primary molars
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    Ferric sulphate and formocresol pulpotomies in baboon primary molars: histological responses
    (2002) Cleaton-Jones, P.; Duggal, M.; Parak, R.; Et al
    Aim: To compare pulpal reactions to ferric sulphate and formocresol pulpotomies in primary molar teeth with inflamed pulps. Study design: An experimental study in 15 juvenile baboons (Papio ursinus). Materials and methods: Pulpitis was induced with fresh human carious dentine or Streptococcus mutans placed into occlusal cavities in 57 primary molars; after 14 days a pulpotomy was performed on the same primary molars with the two pulp medicaments randomly allocated; the pulp was covered with IRM and the cavity filled with amalgam. After 90 days specimens were harvested and examined under the light microscope with the examiner blind to the treatment. Results: Reaction frequencies in the ferric sulphate-treated and formocresol-treated teeth were: recognisable pulp 52% and 50%, dentine bridges 16% and 12%, internal root resorption 12% and 4%, external resorption 28% and 31%, bacteria 12% and 23%, peri-apical abscesses 32% and 38%. Statistics: Fisher’s exact probability test showed no statistically significant differences between reaction frequencies in the two treatment groups. Conclusion: A pulpotomy in a primary tooth may be clinically successful in the presence of adverse histological reactions.
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