Addressing social issues in a universal HIV test and treat intervention trial (ANRS 12249 TasP) in South Africa: methods for appraisal

Background: The Universal HIV Test and Treat (UTT) strategy represents a challenge for science, but is also a challenge for individuals and societies. Are repeated offers of provider-initiated HIV testing and immediate antiretroviral therapy (ART) socially-acceptable and can these become normalized over time? Can UTT be implemented without potentially adding to individual and community stigma, or threatening individual rights? What are the social, cultural and economic implications of UTT for households and communities? And can UTT be implemented within capacity constraints and other threats to the overall provision of HIV services? The answers to these research questions will be critical for routine implementation of UTT strategies. Methods/design: A social science research programme is nested within the ANRS 12249 Treatment-as-Prevention (TasP) cluster-randomised trial in rural South Africa. The programme aims to inform understanding of the (i) social, economic and environmental factors affecting uptake of services at each step of the continuum of HIV prevention, treatment and care and (ii) the causal impacts of the TasP intervention package on social and economic factors at the individual, household, community and health system level. We describe a multidisciplinary, multi-level, mixed-method research protocol that includes individual, household, community and clinic surveys, and combines quantitative and qualitative methods. Discussion: The UTT strategy is changing the overall approach to HIV prevention, treatment and care, and substantial social consequences may be anticipated, such as changes in social representations of HIV transmission, prevention, HIV testing and ART use, as well as changes in individual perceptions and behaviours in terms of uptake and frequency of HIV testing and ART initiation at high CD4. Triangulation of social science studies within the ANRS 12249 TasP trial will provide comprehensive insights into the acceptability and feasibility of the TasP intervention package at individual, community, patient and health system level, to complement the trial's clinical and epidemiological outcomes. It will also increase understanding of the causal impacts of UTT on social and economic outcomes, which will be critical for the long-term sustainability and routine UTT implementation. Trial registration: Clinicaltrials.gov: NCT01509508; South African Trial Register: DOH-27-0512-3974

Consistent phenological shifts in the making of a biodiversity hotspot: the Cape flora

Background The best documented survival responses of organisms to past climate change on short (glacial-interglacial) timescales are distributional shifts. Despite ample evidence on such timescales for local adaptations of populations at specific sites, the long-term impacts of such changes on evolutionary significant units in response to past climatic change have been little documented. Here we use phylogenies to reconstruct changes in distribution and flowering ecology of the Cape flora - South Africa's biodiversity hotspot - through a period of past (Neogene and Quaternary) changes in the seasonality of rainfall over a timescale of several million years. Results Forty-three distributional and phenological shifts consistent with past climatic change occur across the flora, and a comparable number of clades underwent adaptive changes in their flowering phenology (9 clades; half of the clades investigated) as underwent distributional shifts (12 clades; two thirds of the clades investigated). Of extant Cape angiosperm species, 14-41% have been contributed by lineages that show distributional shifts consistent with past climate change, yet a similar proportion (14-55%) arose from lineages that shifted flowering phenology. Conclusions Adaptive changes in ecology at the scale we uncover in the Cape and consistent with past climatic change have not been documented for other floras. Shifts in climate tolerance appear to have been more important in this flora than is currently appreciated, and lineages that underwent such shifts went on to contribute a high proportion of the flora's extant species diversity. That shifts in phenology, on an evolutionary timescale and on such a scale, have not yet been detected for other floras is likely a result of the method used; shifts in flowering phenology cannot be detected in the fossil record

Mobile HIV Screening in Cape Town, South Africa: Clinical Impact, Cost and Cost-Effectiveness

Background: Mobile HIV screening may facilitate early HIV diagnosis. Our objective was to examine the cost-effectiveness of adding a mobile screening unit to current medical facility-based HIV testing in Cape Town, South Africa. Methods and Findings: We used the Cost Effectiveness of Preventing AIDS Complications International (CEPAC-I) computer simulation model to evaluate two HIV screening strategies in Cape Town: 1) medical facility-based testing (the current standard of care) and 2) addition of a mobile HIV-testing unit intervention in the same community. Baseline input parameters were derived from a Cape Town-based mobile unit that tested 18,870 individuals over 2 years: prevalence of previously undiagnosed HIV (6.6%), mean CD4 count at diagnosis (males 423/µL, females 516/µL), CD4 count-dependent linkage to care rates (males 31%–58%, females 49%–58%), mobile unit intervention cost (includes acquisition, operation and HIV test costs, $29.30 per negative result and$31.30 per positive result). We conducted extensive sensitivity analyses to evaluate input uncertainty. Model outcomes included site of HIV diagnosis, life expectancy, medical costs, and the incremental cost-effectiveness ratio (ICER) of the intervention compared to medical facility-based testing. We considered the intervention to be “very cost-effective” when the ICER was less than South Africa's annual per capita Gross Domestic Product (GDP) ($8,200 in 2012). We projected that, with medical facility-based testing, the discounted (undiscounted) HIV-infected population life expectancy was 132.2 (197.7) months; this increased to 140.7 (211.7) months with the addition of the mobile unit. The ICER for the mobile unit was$2,400/year of life saved (YLS). Results were most sensitive to the previously undiagnosed HIV prevalence, linkage to care rates, and frequency of HIV testing at medical facilities. Conclusion: The addition of mobile HIV screening to current testing programs can improve survival and be very cost-effective in South Africa and other resource-limited settings, and should be a priority

Barcoding a Quantified Food Web: Crypsis, Concepts, Ecology and Hypotheses

The efficient and effective monitoring of individuals and populations is critically dependent on correct species identification. While this point may seem obvious, identifying the majority of the more than 100 natural enemies involved in the spruce budworm (Choristoneura fumiferana – SBW) food web remains a non-trivial endeavor. Insect parasitoids play a major role in the processes governing the population dynamics of SBW throughout eastern North America. However, these species are at the leading edge of the taxonomic impediment and integrating standardized identification capacity into existing field programs would provide clear benefits. We asked to what extent DNA barcoding the SBW food web would alter our understanding of the diversity and connectence of the food web and the frequency of generalists vs. specialists in different forest habitats. We DNA barcoded over 10% of the insects collected from the SBW food web in three New Brunswick forest plots from 1983 to 1993. For 30% of these specimens, we amplified at least one additional nuclear region. When the nodes of the food web were estimated based on barcode divergences (using molecular operational taxonomic units (MOTU) or phylogenetic diversity (PD) – the food web became much more diverse and connectence was reduced. We tested one measure of food web structure (the “bird feeder effect”) and found no difference compared to the morphologically based predictions. Many, but not all, of the presumably polyphagous parasitoids now appear to be morphologically-cryptic host-specialists. To our knowledge, this project is the first to barcode a food web in which interactions have already been well-documented and described in space, time and abundance. It is poised to be a system in which field-based methods permit the identification capacity required by forestry scientists. Food web barcoding provided an effective tool for the accurate identification of all species involved in the cascading effects of future budworm outbreaks. Integrating standardized barcodes within food webs may ultimately change the face of community ecology. This will be most poignantly felt in food webs that have not yet been quantified. Here, more accurate and precise connections will be within the grasp of any researcher for the first time

Life form and species diversity on abandoned croplands, Roggeveld, South Africa

The Roggeveld consists of an island of Mountain Renosterveld (Fynbos biome) surrounded by Succulent Karoo biome vegetation. Since management of abandoned croplands depends on a better understanding of their succession sequences, vegetation recovery on abandoned croplands in the Roggeveld was studied using species and life form diversity parameters. Abandoned croplands of different ages were compared with each other and to the natural vegetation. Therophytes and chamaephytes were the most abundant life forms. Chamaephytes made an overwhelming contribution to the relative cover. Species-area curves (exponential function) differed significantly between the abandoned croplands and natural vegetation. Species richness increased with time since abandonment but no similar increase in species evenness, Shannon or Simpson indices were found. A regression of species richness against age of abandoned cropland predicted that an abandoned cropland of approximately 33 years should be as species rich as the natural vegetation, but a principal cooordinate analysis of floristic data indicated that all the plots were floristically still extremely different from the natural vegetation. Across all nine survey plots only 15 species contributed to a high cover on the plots. Vegetation recovery on abandoned croplands in the Roggeveld occurs naturally, yet the rate of recovery varies among the life forms.Keywords: diversity indices, Fynbos biome, old fields, species richness, Succulent Karoo biomeAfrican Journal of Range & Forage Science 2011, 28(2): 99–11

Seasonal nutrient fluctuation in selected plant species in the Kalahari

Seasonal changes in crude protein, phosphorus and calcium contents of five common plant species in the south-western Kalahari were investigated. Three species that are browsed by springbok (Acacia erioloba, Grewia flava and Rhigozum trichotomum) and two grass species (Schmidtia kalahariensis and Stipagrostis obtusa), were included in the study. Browse species had higher crude protein, phosphorus and calcium contents than the grass species, but the fluctuation range was similar to that of the grass species. In general, the crude protein content of the food plant species sampled in the present study was above the level required by African ungulates for maintenance. However, the diet of springbok in the south-western Kalahari appeared to be phosphorus deficient. Crude protein and phosphorus levels in plant food were especially low during the cold-dry season, when the crude protein content of the grass species was at or below that which is required by springbok for sustenance. The phosphorus content was below ruminant requirements in all plant species in all habitats during the cold-dry season. Faecal crude protein and phosphorus percentages higher than that of the selected plant species investigated imply that springbok have the ability to select the most nutrient-rich plant species and plant parts available. The Ca:P ratio of the plant species that were sampled in the present study fell outside the range that is considered to be healthy for ruminants in all instances, with calcium in excess. Keywords: calcium, Kalahari, nitrogen content, nutritional value, phosphorus, seasonal variationAfrican Journal of Range & Forage Science 2008, 25(3): 111–11

Modelling dimensional growth of three street tree species in the urban forest of the City of Tshwane, South Africa

Tree height, crown height, crown diameter and stem diameter were measured for 282 trees of the indigenous species Combretum erythrophyllum, Searsia lancea and S. pendulina. Growth relationships were modelled using age as explanatory variable for stem diameter and subsequently stem diameter as explanatory variable for tree height, crown height and crown diameter. Coefficients are presented for predicting tree dimensions using a logarithmic function. There were strong correlations for stem diameter and age (r2 ≥ 0.75), and crown diameter and stem diameter (r2 ≥ 0.74) for all three of the species investigated. Correlations were weaker for tree height and stem diameter (r2 ≥ 0.63), and crown height and stem diameter (r2 ≥ 0.60) for S. pendulina but stronger for both C. erythrophyllum (r2 ≥ 0.83) and S. lancea (r2 ≥ 0.70) in both instances. The results can be used in forecasting the physical dimensions of these species as a function of time. The results could also be used in the process of modelling energy use reduction, air pollution uptake, rainfall interception, carbon sequestration and microclimate modification of urban forests such as those found in the City of Tshwane. Keywords: allometry; regression; size relationships; tree growth; urban forestsSouthern Forests 2009, 71(4): 273–27