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1.  Community-based mental health support for orphans and vulnerable children in South Africa: A triangulation study 
Community-based care is receiving increasing global attention as a way to support children who are orphaned or vulnerable due to the HIV/AIDS pandemic. Using both qualitative and quantitative methodology, this study assesses community-based responses to the well-being of orphans and vulnerable children (OVC) and compares these responses with the actual mental health of OVC in order to evaluate the South African government's approach of funding community-based organisations (CBOs) that support and care for OVC. The study results show that the activities of CBOs mainly extend government services and address poverty. Although this should not be seen as insignificant, the paper argues that CBOs give very little attention to the mental health of OVC.
doi:10.1080/17450128.2013.855345
PMCID: PMC4007579  PMID: 24799952
2.  Details for Manuscript Number SSM-D-06-00290R2 “Internalized Stigma, Discrimination, and Depression among Men and Women Living with HIV/AIDS in Cape Town, South Africa” 
Social science & medicine (1982)  2007;64(9):1823-1831.
AIDS stigmas interfere with HIV prevention, diagnosis and treatment and can become internalized by people living with HIV/AIDS. However, the effects of internalized AIDS stigmas have not been investigated in Africa, home to two-thirds of the more than 40 million people living with AIDS in the world. The current study examined the prevalence of discrimination experiences and internalized stigmas among 420 HIV positive men and 643 HIV positive women recruited from AIDS services in Cape Town, South Africa. The anonymous surveys found that 40% of persons with HIV/AIDS had experienced discrimination resulting from having HIV infection and one in five had lost a place to stay or a job because of their HIV status. More than one in three participants indicated feeling dirty, ashamed, or guilty because of their HIV status. A hierarchical regression model that included demographic characteristics, health and treatment status, social support, substance use, and internalized stigma significantly predicted cognitive-affective depression. Internalized stigma accounted for 4.8% of the variance in cognitive-affective depression scores over and above the other variables. These results indicate an urgent need for social reform to reduce AIDS stigmas and the design of interventions to assist people living with HIV/AIDS to adjust and adapt to the social conditions of AIDS in South Africa.
doi:10.1016/j.socscimed.2007.01.006
PMCID: PMC4271649  PMID: 17337318
Internalized stigma; AIDS; coping; South Africa; Discrimination; Depression
3.  Australian graduating nurses’ knowledge, intentions and beliefs on infection prevention and control: a cross-sectional study 
BMC Nursing  2014;13(1):43.
Background
In recent year, national bodies have been actively addressing the increasing concern on the spread of healthcare-associated infections (HAIs). The current study measures the knowledge, intentions and beliefs of third-year Australian nursing students on key infection prevention and control (IPC) concepts.
Methods
A cross-sectional study of final-year undergraduate nursing students from Schools of Nursing at six Australian universities was undertaken. Students were asked to participate in an anonymous survey. The survey explored knowledge of standard precautions and transmission based precautions. In addition intentions and beliefs towards IPC were explored.
Results
349 students from six universities completed the study. 59.8% (95% CI 58.8–60.8%) of questions were answered correctly. Significantly more standard precaution questions were correctly answered than transmission-based precaution questions (p < 0.001). No association was found between self-reported compliance with IPC activities and gender or age. Certain infection control issues were correlated with the percentage of correctly answered transmission-based precaution questions. The participants were most likely to seek infection control information from an infection control professional.
Conclusion
Knowledge on transmission-based precautions was substandard. As transmission-based precautions are the foundation of IPC for serious organisms and infections, education institutions should reflect on the content and style of educational delivery on this topic.
Electronic supplementary material
The online version of this article (doi:10.1186/s12912-014-0043-9) contains supplementary material, which is available to authorized users.
doi:10.1186/s12912-014-0043-9
PMCID: PMC4266973  PMID: 25516721
4.  MATERNAL ALCOHOL CONSUMPTION PRODUCING FETAL ALCOHOL SPECTRUM DISORDERS (FASD): QUANTITY, FREQUENCY, AND TIMING OF DRINKING 
Drug and alcohol dependence  2013;133(2):10.1016/j.drugalcdep.2013.07.013.
Background
Concise, accurate measures of maternal prenatal alcohol use are needed to better understand fetal alcohol spectrum disorders (FASD).
Methods
Measures of drinking by mothers of children with specific FASD diagnoses and mothers of randomly-selected controls are compared and also correlated with physical and cognitive/behavioral outcomes.
Results
Measures of maternal alcohol use can differentiate maternal drinking associated with FASD from that of controls and some from mothers of alcohol-exposed normals. Six variables that combine quantity and frequency concepts distinguish mothers of FASD children from normal controls. Alcohol use variables, when applied to each trimester and three months prior to pregnancy, provide insight on critical timing of exposure as well. Measures of drinking, especially bingeing, correlate significantly with increased child dysmorphology and negative cognitive/behavioral outcomes in children, especially low non-verbal IQ, poor attention, and behavioral problems. Logistic regression links (p<.001) first trimester drinking (vs. no drinking) with FASD, elevating FASD likelihood 12 times; first and second trimester drinking increases FASD outcomes 61 times; and drinking in all trimesters 65 times. Conversely, a similar regression (p=.008) indicates that drinking only in the first trimester makes the birth of a child with an FASD 5 times less likely than drinking in all trimesters.
Conclusions
There is significant variation in alcohol consumption both within and between diagnostic groupings of mothers bearing children diagnosed within the FASD continuum. Drinking measures are empirically identified and correlated with specific child outcomes. Alcohol use, especially heavy use, should be avoided throughout pregnancy.
doi:10.1016/j.drugalcdep.2013.07.013
PMCID: PMC3829200  PMID: 23932841
alcohol use and abuse; women; prenatal alcohol use; fetal alcohol spectrum disorders; South Africa; dysmorphology; cognition
5.  Facial affect recognition and exit examination performance in medical students: a prospective exploratory study 
BMC Medical Education  2014;14(1):245.
Background
Facial affect recognition (FAR) abilities underpin emotional intelligence (EI). The latter is suggested to predict academic success and to be important for clinician-patient interaction. It is therefore of interest to investigate the possible association between FAR and academic performance in undergraduate medical students.
Methods
We assessed the association between the ability to recognize emotions through facial expression and exit examination performance, a measure of clinical proficiency, in undergraduate medical students stratified by gender at a South African tertiary institution using a prospective descriptive design. Data on the perception of facial expressions and exit examination marks were obtained from 144 (61%) females and 93 (39%) males with a mean age of 24.1 ± 1.6 years. Facial affect recognition measures on the Hexagon and Animation tasks were individually correlated with academic performance indicators using Pearson correlation.
Results
The perceptual discrimination of anger was associated with improved performance in anaesthetics (r = .24; p = .004) and urology (r = .24; p = .001), while the recognition of happiness was associated with decreased performance in obstetrics (r = −.21, p = .002). Gender was an effect modifier in the relationship between perceptual discrimination of anger and urology performance (p = .03), with a strong positive relationship for males, but a non-significant relationship for females.
Conclusion
There was no overall correlation between FAR and overall academic performance or with gender. However, subject (specialty) specific findings with recognition of specific emotions and with gender as effect modifier poses interesting questions about EI and FAR and prompts further research into FAR as a useful tool. Being an objective test and offering a more focused assessment makes FAR worthy of further application.
doi:10.1186/s12909-014-0245-6
PMCID: PMC4261890  PMID: 25431251
Emotional intelligence; Facial affect recognition; Examination performance; Undergraduate medical students; Gender
6.  Housing conditions and mental health of orphans in South Africa 
Health & place  2013;24:10.1016/j.healthplace.2013.08.004.
Literature from the developed world suggests that poor housing conditions and housing environments contribute to poor mental health outcomes, although research results are mixed. This study investigates the relationship between housing conditions and the socio-emotional health of orphans and vulnerable children (OVC) in South Africa. The results of the study are mainly inconclusive, although it is suggested that methodological considerations play a vital role in explaining the mixed results. However, a positive relationship was found between living in informal settlements and better socio-emotional health of the OVC. We speculate that the historical context of informal settlement formation in South Africa helps to explain this unexpected result.
doi:10.1016/j.healthplace.2013.08.004
PMCID: PMC3834074  PMID: 24013088
housing conditions; orphans; mental health; informal settlements
7.  Distribution of Indigenous Bacterial Pathogens and Potential Pathogens Associated with Roof-Harvested Rainwater 
The harvesting of rainwater is gaining acceptance among many governmental authorities in countries such as Australia, Germany, and South Africa, among others. However, conflicting reports on the microbial quality of harvested rainwater have been published. To monitor the presence of potential pathogenic bacteria during high-rainfall periods, rainwater from 29 rainwater tanks was sampled on four occasions (during June and August 2012) in a sustainable housing project in Kleinmond, South Africa. This resulted in the collection of 116 harvested rainwater samples in total throughout the sampling period. The identities of the dominant, indigenous, presumptive pathogenic isolates obtained from the rainwater samples throughout the sampling period were confirmed through universal 16S rRNA PCR, and the results revealed that Pseudomonas (19% of samples) was the dominant genus isolated, followed by Aeromonas (16%), Klebsiella (11%), and Enterobacter (9%). PCR assays employing genus-specific primers also confirmed the presence of Aeromonas spp. (16%), Klebsiella spp. (47%), Legionella spp. (73%), Pseudomonas spp. (13%), Salmonella spp. (6%), Shigella spp. (27%), and Yersinia spp. (28%) in the harvested rainwater samples. In addition, on one sampling occasion, Giardia spp. were detected in 25% of the eight tank water samples analyzed. This study highlights the diverse array of pathogenic bacteria that persist in harvested rainwater during high-rainfall periods. The consumption of untreated harvested rainwater could thus pose a potential significant health threat to consumers, especially children and immunocompromised individuals, and it is recommended that harvested rainwater be treated for safe usage as an alternative water source.
doi:10.1128/AEM.04130-13
PMCID: PMC3993141  PMID: 24487540
8.  The influence of secondary structure, selection and recombination on rubella virus nucleotide substitution rate estimates 
Virology Journal  2014;11(1):166.
Background
Annually, rubella virus (RV) still causes severe congenital defects in around 100 000 children globally. An attempt to eradicate RV is currently underway and analytical tools to monitor the global decline of the last remaining RV lineages will be useful for assessing the effectiveness of this endeavour. RV evolves rapidly enough that much of this information might be inferable from RV genomic sequence data.
Methods
Using BEASTv1.8.0, we analysed publically available RV sequence data to estimate genome-wide and gene-specific nucleotide substitution rates to test whether current estimates of RV substitution rates are representative of the entire RV genome. We specifically accounted for possible confounders of nucleotide substitution rate estimates, such as temporally biased sampling, sporadic recombination, and natural selection favouring either increased or decreased genetic diversity (estimated by the PARRIS and FUBAR methods), at nucleotide sites within the genomic secondary structures (predicted by the NASP method).
Results
We determine that RV nucleotide substitution rates range from 1.19 × 10-3 substitutions/site/year in the E1 region to 7.52 × 10-4 substitutions/site/year in the P150 region. We find that differences between substitution rate estimates in different RV genome regions are largely attributable to temporal sampling biases such that datasets containing higher proportions of recently sampled sequences, will tend to have inflated estimates of mean substitution rates. Although there exists little evidence of positive selection or natural genetic recombination in RV, we show that RV genomes possess pervasive biologically functional nucleic acid secondary structure and that purifying selection acting to maintain this structure contributes substantially to variations in estimated nucleotide substitution rates across RV genomes.
Conclusion
Both temporal sampling biases and purifying selection favouring the conservation of RV nucleic acid secondary structures have an appreciable impact on substitution rate estimates but do not preclude the use of RV sequence data to date ancestral sequences. The combination of uniformly high substitution rates across the RV genome and strong temporal structure within the available sequence data, suggests that such data should be suitable for tracking the demographic, epidemiological and movement dynamics of this virus during eradication attempts.
Electronic supplementary material
The online version of this article (doi:10.1186/1743-422X-11-166) contains supplementary material, which is available to authorized users.
doi:10.1186/1743-422X-11-166
PMCID: PMC4175276  PMID: 25224517
Rubella virus; Congenital rubella syndrome; Nucleotide substitution rates; Synonymous substitution rates; Recombination; Nucleic acid secondary structure; Bayesian phylogenetic analyses
9.  Trauma exposure, posttraumatic stress disorder and the effect of explanatory variables in paramedic trainees 
Background
Emergency healthcare workers, including trainees and individuals in related occupations are at heightened risk of developing posttraumatic stress disorder (PTSD) and depression owing to work-related stressors.
We aimed to investigate the type, frequency, and severity of direct trauma exposure, posttraumatic stress symptoms and other psychopathology amongst paramedic trainees. In order to create a risk profile for individuals who are at higher occupational risk of developing PTSD, we examined risk and resilience factors that possibly contributed to the presence and severity of posttraumatic symptomatology.
Methods
Paramedic trainees (n = 131) were recruited from a local university. A logistic regression analysis was conducted using the explanatory variables age, gender, population group, trauma exposure, depression, alcohol abuse, alcohol dependence, resilience and social support.
Results
94% of paramedic trainees had directly experienced trauma, with 16% meeting PTSD criteria. A high rate of depression (28%), alcohol abuse (23%) and chronic perceived stress (7%) and low levels of social support was found. The number of previous trauma exposures, depression, resilience and social support significantly predicted PTSD status and depression had a mediating effect.
Conclusion
There is a need for efficient, ongoing screening of depressive and PTSD symptomatology in trauma exposed high risk groups so that early psychological supportive interventions can be offered.
doi:10.1186/1471-227X-14-11
PMCID: PMC4004503  PMID: 24755358
Trauma; Posttraumatic stress disorder; Paramedic trainees; Emergency medical workers
10.  Case Management Reduces Drinking During Pregnancy among High Risk Women 
Aim
Estimate the efficacy of Case Management (CM) for women at high risk for bearing a child with Fetal Alcohol Spectrum Disorders (FASD).
Design
Women were recruited from antenatal clinics and engaged in 18 months of CM.
Setting
A South African community with a subculture of heavy, regular, weekend, recreational drinking and high documented rates of FASD.
Participants
Forty-one women who were high risk for bearing a child with FASD.
Measures
Statistical analysis of trends in drinking and other risk factors.
Findings
At intake 87.8% were pregnant, most had previous alcohol-exposed pregnancies, most/all of their friends drink alcohol (67.5%), and 50.0% had stressful lives. CM was particularly valuable for pregnant women, as statistically significant reductions in alcohol risk were obtained for them in multiple variables: total drinks on weekends after six months of CM (p = .026) and estimated peak blood alcohol concentration (BAC) at six (p < .001) and 18 months (p < .001). For participants completing 18 months of CM, AUDIT scores improved significantly by 6-month follow-up (from 19.8 to 9.7, p = .000), and even though rising at 12 and 18 months, AUDIT scores indicate that problematic drinking remained statistically significantly lower than baseline throughout CM. Happiness scale scores correlated significantly with reduced drinking in most time periods.
Conclusions
An enduring change in drinking behavior is difficult in this social setting. Yet, CM provided by skilled and empathic case managers reduced maternal drinking at critical times, and therefore, alcohol exposure levels to the fetus.
doi:10.7895/ijadr.v2i3.79
PMCID: PMC3981106  PMID: 24729823
fetal alcohol spectrum disorders (FASD); prevention; case management; alcohol abuse
11.  Prevalence of Virulence Genes Associated with Pathogenic Escherichia coli Strains Isolated from Domestically Harvested Rainwater during Low- and High-Rainfall Periods 
The possible health risks associated with the consumption of harvested rainwater remains one of the major obstacles hampering its large-scale implementation in water limited countries such as South Africa. Rainwater tank samples collected on eight occasions during the low- and high-rainfall periods (March to August 2012) in Kleinmond, South Africa, were monitored for the presence of virulence genes associated with Escherichia coli. The identity of presumptive E. coli isolates in rainwater samples collected from 10 domestic rainwater harvesting (DRWH) tanks throughout the sampling period was confirmed through universal 16S rRNA PCR with subsequent sequencing and phylogenetic analysis. Species-specific primers were also used to routinely screen for the virulent genes, aggR, stx, eae, and ipaH found in enteroaggregative E. coli (EAEC), enterohemorrhagic E. coli (EHEC), enteropathogenic E. coli (EPEC), and enteroinvasive E. coli, respectively, in the rainwater samples. Of the 92 E. coli strains isolated from the rainwater using culture based techniques, 6% were presumptively positively identified as E. coli O157:H7 using 16S rRNA. Furthermore, virulent pathogenic E. coli genes were detected in 3% (EPEC and EHEC) and 16% (EAEC) of the 80 rainwater samples collected during the sampling period from the 10 DRWH tanks. This study thus contributes valuable information to the limited data available regarding the ongoing prevalence of virulent pathotypes of E. coli in harvested rainwater during a longitudinal study in a high-population-density, periurban setting.
doi:10.1128/AEM.03061-13
PMCID: PMC3957612  PMID: 24375127
12.  Correction: Dietary Plasticity of Generalist and Specialist Ungulates in the Namibian Desert: A Stable Isotopes Approach 
PLoS ONE  2013;8(9):10.1371/annotation/89fe804f-20cc-40cc-99af-d42751676d36.
doi:10.1371/annotation/89fe804f-20cc-40cc-99af-d42751676d36
PMCID: PMC3782397
13.  Dietary Plasticity of Generalist and Specialist Ungulates in the Namibian Desert: A Stable Isotopes Approach 
PLoS ONE  2013;8(8):e72190.
Desert ungulates live in adverse ecosystems that are particularly sensitive to degradation and global climate change. Here, we asked how two ungulate species with contrasting feeding habits, grazing gemsbok (Oryx g. gazella) and browsing springbok (Antidorcas marsupialis), respond to an increase in food availability during a pronounced rain period. We used a stable isotope approach to delineate the feeding habits of these two ungulates in the arid Kunene Region of Namibia. Our nineteen months field investigation included two time periods of drought when food availability for ungulates was lowest and an intermediate period with extreme, unusual rainfalls. We documented thirteen isotopically distinct food sources in the isotopic space of the study area. Our results indicated a relatively high dietary plasticity of gemsbok, which fed on a mixture of plants, including more than 30% of C3 plants during drought periods, but almost exclusively on C4 and CAM plant types when food was plentiful. During drought periods, the inferred gemsbok diets also consisted of up to 25% of Euphorbia damarana; an endemic CAM plant that is rich in toxic secondary plant compounds. In contrast, springbok were generalists, feeding on a higher proportion of C3 than C4/CAM plants, irrespective of environmental conditions. Our results illustrate two dietary strategies in gemsbok and springbok which enable them to survive and coexist in the hostile Kunene arid ecosystem.
doi:10.1371/journal.pone.0072190
PMCID: PMC3745446  PMID: 23977249
14.  HLA-A*7401–Mediated Control of HIV Viremia Is Independent of Its Linkage Disequilibrium with HLA-B*5703 
The potential contribution of HLA-A alleles to viremic control in chronic HIV type 1 (HIV-1) infection has been relatively understudied compared with HLA-B. In these studies, we show that HLA-A*7401 is associated with favorable viremic control in extended southern African cohorts of >2100 C-clade–infected subjects. We present evidence that HLA-A*7401 operates an effect that is independent of HLA-B*5703, with which it is in linkage disequilibrium in some populations, to mediate lowered viremia. We describe a novel statistical approach to detecting additive effects between class I alleles in control of HIV-1 disease, highlighting improved viremic control in subjects with HLA-A*7401 combined with HLA-B*57. In common with HLA-B alleles that are associated with effective control of viremia, HLA-A*7401 presents highly targeted epitopes in several proteins, including Gag, Pol, Rev, and Nef, of which the Gag epitopes appear immunodominant. We identify eight novel putative HLA-A*7401–restricted epitopes, of which three have been defined to the optimal epitope. In common with HLA-B alleles linked with slow progression, viremic control through an HLA-A*7401–restricted response appears to be associated with the selection of escape mutants within Gag epitopes that reduce viral replicative capacity. These studies highlight the potentially important contribution of an HLA-A allele to immune control of HIV infection, which may have been concealed by a stronger effect mediated by an HLA-B allele with which it is in linkage disequilibrium. In addition, these studies identify a factor contributing to different HIV disease outcomes in individuals expressing HLA-B*5703.
doi:10.4049/jimmunol.1003711
PMCID: PMC3738002  PMID: 21498667
15.  Development and evaluation of a de-identification procedure for a case register sourced from mental health electronic records 
Background
Electronic health records (EHRs) provide enormous potential for health research but also present data governance challenges. Ensuring de-identification is a pre-requisite for use of EHR data without prior consent. The South London and Maudsley NHS Trust (SLaM), one of the largest secondary mental healthcare providers in Europe, has developed, from its EHRs, a de-identified psychiatric case register, the Clinical Record Interactive Search (CRIS), for secondary research.
Methods
We describe development, implementation and evaluation of a bespoke de-identification algorithm used to create the register. It is designed to create dictionaries using patient identifiers (PIs) entered into dedicated source fields and then identify, match and mask them (with ZZZZZ) when they appear in medical texts. We deemed this approach would be effective, given high coverage of PI in the dedicated fields and the effectiveness of the masking combined with elements of a security model. We conducted two separate performance tests i) to test performance of the algorithm in masking individual true PIs entered in dedicated fields and then found in text (using 500 patient notes) and ii) to compare the performance of the CRIS pattern matching algorithm with a machine learning algorithm, called the MITRE Identification Scrubber Toolkit – MIST (using 70 patient notes – 50 notes to train, 20 notes to test on). We also report any incidences of potential breaches, defined by occurrences of 3 or more true or apparent PIs in the same patient’s notes (and in an additional set of longitudinal notes for 50 patients); and we consider the possibility of inferring information despite de-identification.
Results
True PIs were masked with 98.8% precision and 97.6% recall. As anticipated, potential PIs did appear, owing to misspellings entered within the EHRs. We found one potential breach. In a separate performance test, with a different set of notes, CRIS yielded 100% precision and 88.5% recall, while MIST yielded a 95.1% and 78.1%, respectively. We discuss how we overcome the realistic possibility – albeit of low probability – of potential breaches through implementation of the security model.
Conclusion
CRIS is a de-identified psychiatric database sourced from EHRs, which protects patient anonymity and maximises data available for research. CRIS demonstrates the advantage of combining an effective de-identification algorithm with a carefully designed security model. The paper advances much needed discussion of EHR de-identification – particularly in relation to criteria to assess de-identification, and considering the contexts of de-identified research databases when assessing the risk of breaches of confidential patient information.
doi:10.1186/1472-6947-13-71
PMCID: PMC3751474  PMID: 23842533
De-identification; Anonymisation; Electronic health records; Psychiatric case register; Medical health records security; Medical information database security
16.  HIV Control through a Single Nucleotide on the HLA-B Locus 
Journal of Virology  2012;86(21):11493-11500.
Genetic variation within the HLA-B locus has the strongest impact on HIV disease progression of any polymorphisms within the human genome. However, identifying the exact mechanism involved is complicated by several factors. HLA-Bw4 alleles provide ligands for NK cells and for CD8 T cells, and strong linkage disequilibrium between HLA class I alleles complicates the discrimination of individual HLA allelic effects from those of other HLA and non-HLA alleles on the same haplotype. Here, we exploit an experiment of nature involving two recently diverged HLA alleles, HLA-B*42:01 and HLA-B*42:02, which differ by only a single amino acid. Crucially, they occur primarily on identical HLA class I haplotypes and, as Bw6 alleles, do not act as NK cell ligands and are therefore largely unconfounded by other genetic factors. We show that in an outbred cohort (n = 2,093) of HIV C-clade-infected individuals, a single amino acid change at position 9 of the HLA-B molecule critically affects peptide binding and significantly alters the cytotoxic T lymphocyte (CTL) epitopes targeted, measured directly ex vivo by gamma interferon (IFN-γ) enzyme-linked immunospot (ELISPOT) assay (P = 2 × 10−10) and functionally through CTL escape mutation (P = 2 × 10−8). HLA-B*42:01, which presents multiple Gag epitopes, is associated with a 0.52 log10 lower viral-load set point than HLA-B*42:02 (P = 0.02), which presents no p24 Gag epitopes. The magnitude of this effect from a single amino acid difference in the HLA-A*30:01/B*42/Cw*17:01 haplotype is equivalent to 75% of that of HLA-B*57:03, the most protective HLA class I allele in this population. This naturally controlled experiment represents perhaps the clearest demonstration of the direct impact of a particular HIV-specific CTL on disease control.
doi:10.1128/JVI.01020-12
PMCID: PMC3486337  PMID: 22896606
17.  Where is the game? Wild meat products authentication in South Africa: a case study 
Background
Wild animals’ meat is extensively consumed in South Africa, being obtained either from ranching, farming or hunting. To test the authenticity of the commercial labels of meat products in the local market, we obtained DNA sequence information from 146 samples (14 beef and 132 game labels) for barcoding cytochrome c oxidase subunit I and partial cytochrome b and mitochondrial fragments. The reliability of species assignments were evaluated using BLAST searches in GenBank, maximum likelihood phylogenetic analysis and the character-based method implemented in BLOG. The Kimura-2-parameter intra- and interspecific variation was evaluated for all matched species.
Results
The combined application of similarity, phylogenetic and character-based methods proved successful in species identification. Game meat samples showed 76.5% substitution, no beef samples were substituted. The substitutions showed a variety of domestic species (cattle, horse, pig, lamb), common game species in the market (kudu, gemsbok, ostrich, impala, springbok), uncommon species in the market (giraffe, waterbuck, bushbuck, duiker, mountain zebra) and extra-continental species (kangaroo). The mountain zebra Equus zebra is an International Union for Conservation of Nature (IUCN) red listed species. We also detected Damaliscus pygargus, which is composed of two subspecies with one listed by IUCN as ‘near threatened’; however, these mitochondrial fragments were insufficient to distinguish between the subspecies. The genetic distance between African ungulate species often overlaps with within-species distance in cases of recent speciation events, and strong phylogeographic structure determines within-species distances that are similar to the commonly accepted distances between species.
Conclusions
The reliability of commercial labeling of game meat in South Africa is very poor. The extensive substitution of wild game has important implications for conservation and commerce, and for the consumers making decisions on the basis of health, religious beliefs or personal choices.
Distance would be a poor indicator for identification of African ungulates species. The efficiency of the character-based method is reliant upon availability of large reference data. The current higher availability of cytochrome b data would make this the marker of choice for African ungulates. The encountered problems of incomplete or erroneous information in databases are discussed.
doi:10.1186/2041-2223-4-6
PMCID: PMC3621286  PMID: 23452350
Biltong; conservation; Cytb; DNA barcoding; Food forensics; Meat; Species identification
18.  Co-Operative Additive Effects between HLA Alleles in Control of HIV-1 
PLoS ONE  2012;7(10):e47799.
Background
HLA class I genotype is a major determinant of the outcome of HIV infection, and the impact of certain alleles on HIV disease outcome is well studied. Recent studies have demonstrated that certain HLA class I alleles that are in linkage disequilibrium, such as HLA-A*74 and HLA-B*57, appear to function co-operatively to result in greater immune control of HIV than mediated by either single allele alone. We here investigate the extent to which HLA alleles - irrespective of linkage disequilibrium - function co-operatively.
Methodology/Principal Findings
We here refined a computational approach to the analysis of >2000 subjects infected with C-clade HIV first to discern the individual effect of each allele on disease control, and second to identify pairs of alleles that mediate ‘co-operative additive’ effects, either to improve disease suppression or to contribute to immunological failure. We identified six pairs of HLA class I alleles that have a co-operative additive effect in mediating HIV disease control and four hazardous pairs of alleles that, occurring together, are predictive of worse disease outcomes (q<0.05 in each case). We developed a novel ‘sharing score’ to quantify the breadth of CD8+ T cell responses made by pairs of HLA alleles across the HIV proteome, and used this to demonstrate that successful viraemic suppression correlates with breadth of unique CD8+ T cell responses (p = 0.03).
Conclusions/Significance
These results identify co-operative effects between HLA Class I alleles in the control of HIV-1 in an extended Southern African cohort, and underline complementarity and breadth of the CD8+ T cell targeting as one potential mechanism for this effect.
doi:10.1371/journal.pone.0047799
PMCID: PMC3477121  PMID: 23094091
19.  Task shifting of antiretroviral treatment from doctors to primary-care nurses in South Africa (STRETCH): a pragmatic, parallel, cluster-randomised trial 
Lancet  2012;380(9845):889-898.
Summary
Background
Robust evidence of the effectiveness of task shifting of antiretroviral therapy (ART) from doctors to other health workers is scarce. We aimed to assess the effects on mortality, viral suppression, and other health outcomes and quality indicators of the Streamlining Tasks and Roles to Expand Treatment and Care for HIV (STRETCH) programme, which provides educational outreach training of nurses to initiate and represcribe ART, and to decentralise care.
Methods
We undertook a pragmatic, parallel, cluster-randomised trial in South Africa between Jan 28, 2008, and June 30, 2010. We randomly assigned 31 primary-care ART clinics to implement the STRETCH programme (intervention group) or to continue with standard care (control group). The ratio of randomisation depended on how many clinics were in each of nine strata. Two cohorts were enrolled: eligible patients in cohort 1 were adults (aged ≥16 years) with CD4 counts of 350 cells per μL or less who were not receiving ART; those in cohort 2 were adults who had already received ART for at least 6 months and were being treated at enrolment. The primary outcome in cohort 1 was time to death (superiority analysis). The primary outcome in cohort 2 was the proportion with undetectable viral loads (<400 copies per mL) 12 months after enrolment (equivalence analysis, prespecified difference <6%). Patients and clinicians could not be masked to group assignment. The interim analysis was blind, but data analysts were not masked after the database was locked for final analysis. Analyses were done by intention to treat. This trial is registered, number ISRCTN46836853.
Findings
5390 patients in cohort 1 and 3029 in cohort 2 were in the intervention group, and 3862 in cohort 1 and 3202 in cohort 2 were in the control group. Median follow-up was 16·3 months (IQR 12·2–18·0) in cohort 1 and 18·0 months (18·0–18·0) in cohort 2. In cohort 1, 997 (20%) of 4943 patients analysed in the intervention group and 747 (19%) of 3862 in the control group with known vital status at the end of the trial had died. Time to death did not differ (hazard ratio [HR] 0·94, 95% CI 0·76–1·15). In a preplanned subgroup analysis of patients with baseline CD4 counts of 201–350 cells per μL, mortality was slightly lower in the intervention group than in the control group (0·73, 0·54–1.00; p=0·052), but it did not differ between groups in patients with baseline CD4 of 200 cells per μL or less (0·94, 0·76–1·15; p=0·577). In cohort 2, viral load suppression 12 months after enrolment was equivalent in intervention (2156 [71%] of 3029 patients) and control groups (2230 [70%] of 3202; risk difference 1·1%, 95% CI −2·4 to 4·6).
Interpretation
Expansion of primary-care nurses' roles to include ART initiation and represcription can be done safely, and improve health outcomes and quality of care, but might not reduce time to ART or mortality.
Funding
UK Medical Research Council, Development Cooperation Ireland, and Canadian International Development Agency.
doi:10.1016/S0140-6736(12)60730-2
PMCID: PMC3442223  PMID: 22901955
20.  Comparative Analysis of Mycobacterium tuberculosis pe and ppe Genes Reveals High Sequence Variation and an Apparent Absence of Selective Constraints 
PLoS ONE  2012;7(4):e30593.
Mycobacterium tuberculosis complex (MTBC) genomes contain 2 large gene families termed pe and ppe. The function of pe/ppe proteins remains enigmatic but studies suggest that they are secreted or cell surface associated and are involved in bacterial virulence. Previous studies have also shown that some pe/ppe genes are polymorphic, a finding that suggests involvement in antigenic variation. Using comparative sequence analysis of 18 publicly available MTBC whole genome sequences, we have performed alignments of 33 pe (excluding pe_pgrs) and 66 ppe genes in order to detect the frequency and nature of genetic variation. This work has been supplemented by whole gene sequencing of 14 pe/ppe (including 5 pe_pgrs) genes in a cohort of 40 diverse and well defined clinical isolates covering all the main lineages of the M. tuberculosis phylogenetic tree. We show that nsSNP's in pe (excluding pgrs) and ppe genes are 3.0 and 3.3 times higher than in non-pe/ppe genes respectively and that numerous other mutation types are also present at a high frequency. It has previously been shown that non-pe/ppe M. tuberculosis genes display a remarkably low level of purifying selection. Here, we also show that compared to these genes those of the pe/ppe families show a further reduction of selection pressure that suggests neutral evolution. This is inconsistent with the positive selection pressure of “classical” antigenic variation. Finally, by analyzing such a large number of genes we were able to detect large differences in mutation type and frequency between both individual genes and gene sub-families. The high variation rates and absence of selective constraints provides valuable insights into potential pe/ppe function. Since pe/ppe proteins are highly antigenic and have been studied as potential vaccine components these results should also prove informative for aspects of M. tuberculosis vaccine design.
doi:10.1371/journal.pone.0030593
PMCID: PMC3319526  PMID: 22496726
21.  Progression to AIDS in South Africa Is Associated with both Reverting and Compensatory Viral Mutations 
PLoS ONE  2011;6(4):e19018.
We lack the understanding of why HIV-infected individuals in South Africa progress to AIDS. We hypothesised that in end-stage disease there is a shifting dynamic between T cell imposed immunity and viral immune escape, which, through both compensatory and reverting viral mutations, results in increased viral fitness, elevated plasma viral loads and disease progression. We explored how T cell responses, viral adaptation and viral fitness inter-relate in South African cohorts recruited from Bloemfontein, the Free State (n = 278) and Durban, KwaZulu-Natal (n = 775). Immune responses were measured by γ-interferon ELISPOT assays. HLA-associated viral polymorphisms were determined using phylogenetically corrected techniques, and viral replication capacity (VRC) was measured by comparing the growth rate of gag-protease recombinant viruses against recombinant NL4-3 viruses. We report that in advanced disease (CD4 counts <100 cells/µl), T cell responses narrow, with a relative decline in Gag-directed responses (p<0.0001). This is associated with preserved selection pressure at specific viral amino acids (e.g., the T242N polymorphism within the HLA-B*57/5801 restricted TW10 epitope), but with reversion at other sites (e.g., the T186S polymorphism within the HLA-B*8101 restricted TL9 epitope), most notably in Gag and suggestive of “immune relaxation”. The median VRC from patients with CD4 counts <100 cells/µl was higher than from patients with CD4 counts ≥500 cells/µl (91.15% versus 85.19%, p = 0.0004), potentially explaining the rise in viral load associated with disease progression. Mutations at HIV Gag T186S and T242N reduced VRC, however, in advanced disease only the T242N mutants demonstrated increasing VRC, and were associated with compensatory mutations (p = 0.013). These data provide novel insights into the mechanisms of HIV disease progression in South Africa. Restoration of fitness correlates with loss of viral control in late disease, with evidence for both preserved and relaxed selection pressure across the HIV genome. Interventions that maintain viral fitness costs could potentially slow progression.
doi:10.1371/journal.pone.0019018
PMCID: PMC3081339  PMID: 21544209
22.  Integrated Gender-Based Violence and HIV Risk Reduction Intervention for South African Men: Results of a Quasi-Experimental Field Trial 
South Africa is in the midst of one of the world’s most devastating HIV/AIDS epidemics and there is a well documented association between violence against women and HIV transmission. Interventions that target men and integrate HIV prevention with gender-based violence prevention may demonstrate synergistic effects. A quasi-experimental field intervention trial was conducted with two communities randomly assigned to receive either: (a) a five session integrated intervention designed to simultaneously reduce gender-based violence (GBV) and HIV risk behaviors (N=242) or (b) a single 3-hour alcohol and HIV risk reduction session (N=233). Men were followed for 1, 3, and 6-months post intervention with 90% retention. Results indicated that the GBV/HIV intervention reduced negative attitudes toward women in the short term and reduced violence against women in longer term. Men in the GBV/HIV intervention also increased their talking with sex partners about condoms and were more likely to have been tested for HIV at the follow-ups. There were few differences between conditions on any HIV transmission risk reduction behavioral outcomes. Further research is needed to examine the potential synergistic effects of alcohol use, gender violence, and HIV prevention interventions.
doi:10.1007/s11121-009-0129-x
PMCID: PMC3015088  PMID: 19353267
23.  Challenges Faced by People Living with HIV/AIDS in Cape Town, South Africa: Issues for Group Risk Reduction Interventions 
AIDS Research and Treatment  2010;2010:420270.
This paper presents the findings of an exploratory study to investigate the challenges faced by people living with HIV/AIDS (PLWHA) in communities in Cape Town, South Africa. The primary goal of the study was to gather data to inform the adaptation of a group risk reduction intervention to the South African context. Qualitative methods were used to examine the experiences of PLWHA. Eight focus group discussions (FGDs) were conducted with 83 HIV-positive participants and 14 key informants (KIs) involved in work with PLWHA were interviewed. Findings revealed that AIDS-related stigma was still pervasive in local communities. This was associated with the difficulty of disclosure of their status for fear of rejection. Also notable was the role of risky behaviours such as lack of condom use and that PLWHA considered their HIV/AIDS status as secondary to daily life stressors like poverty, unemployment, and gender-based violence. These findings have implications for the adaptation or development of behavioural risk reduction interventions for PLWHA.
doi:10.1155/2010/420270
PMCID: PMC3065817  PMID: 21490904
24.  Disclosure of HIV status to sex partners and sexual risk behaviours among HIV‐positive men and women, Cape Town, South Africa 
Background
The HIV epidemic continues to amplify in southern Africa and there is a growing need for HIV prevention interventions among people who have tested HIV positive.
Methods
Anonymous surveys were completed by 413 HIV‐positive men and 641 HIV‐positive women sampled from HIV/AIDS services; 73% were <35 years old, 70% Black African, 70% unemployed, 75% unmarried, and 50% taking antiretroviral treatment.
Results
Among the 903 (85%) participants who were currently sexually active, 378 (42%) had sex with a person to whom they had not disclosed their HIV status in the previous 3 months. Participants who had not disclosed their HIV status to their sex partners were considerably more likely to have multiple partners, HIV‐negative partners, partners of unknown HIV status and unprotected intercourse with non‐concordant sex partners. Not disclosing their HIV status to partners was also associated with having lost a job or a place to stay because of being HIV positive and feeling less able to disclose to partners.
Conclusions
HIV‐related stigma and discrimination are associated with not disclosing HIV status to sex partners, and non‐disclosure is closely associated with HIV transmission risk behaviours. Interventions are needed in South Africa to reduce the AIDS stigma and discrimination and to assist people with HIV to make effective decisions on disclosure.
doi:10.1136/sti.2006.019893
PMCID: PMC2598581  PMID: 16790562
25.  [N,N-Bis(diphenyl­phosphino)propyl­amine-κ2 P,P′]dichloridoplatinum(II) 
The Pt(II) atom in the title compound, [PtCl2(C27H27NP2)], has a highly distorted square-planar geometry, as evidenced by the P—Pt—P bite angle [72.4 (1)°]. The strain in the complex is further illustrated by the distorted tetra­hedral angles of the P atoms, which range between 93.5 (1) and 122.2 (1)°. It is of inter­est to note that the N atom has to adopt an almost planar geometry with the two P atoms and the C atom attached to it [it is displaced by 0.093 (2) Å from the CP2 plane] in order to accommodate the steric bulk of the phenyl groups and the alkyl group of the ligand coordinated to the PtII centre. The mol­ecules pack in horizontal rows across the bc plane. C—H⋯Cl hydrogen bonds stabilize the crystal packing.
doi:10.1107/S160053680905301X
PMCID: PMC2980280  PMID: 21579949

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