South Africa’s experience with provision of quality HIV diagnostic services

No abstract available

Ability to develop broadly neutralizing HIV-1 antibodies is not restricted by the germline Ig gene repertoire.

CAPRISA, 2015.Abstract available in pdf

Biological indices to characterize community responses to drying in streams with contrasting flow permanence regimes

Many river networks include temporary reaches that stop flowing and may dry during unpredictable droughts (near-perennial) or more frequently (intermittent). A few biological indices have been developed to assess invertebrate community responses to hydrological variability, including the instream conditions associated with drought, but their performance in temporary streams remains poorly known. We evaluated the ability of two such indices, the Lotic-invertebrate Index for Flow Evaluation (LIFE) and the Drought Effect of Habitat Loss on Invertebrates (DEHLI), to predict responses to flow cessation and drying in temporary streams with contrasting flow permanence regimes. We used a 26-year dataset comprising spring-season invertebrate community samples and daily discharge measurements from 46 sites in a cool, wet temperate region, to examine relationships between hydrological variables and changes in index scores. We also identified taxon-specific thresholds at which occurrence changed with increasing drying and flowing durations. Both indices effectively characterized responses to increasing no-flow durations. DEHLI also reflected community changes following flow resumptions, identified differences in responses among flow permanence groups, and was particularly able to predict community responses at near-perennial sites. DEHLI scores at near-perennial sites took on average three years after a drying event to return to values typical of perennial sites, whereas responses to increasing flow duration were more erratic at intermittent sites. Lotic specialists declined whereas lentic and semi-aquatic taxa increased in occurrence with no-flow duration after summers with <50 days without flow, due to changes in the availability of preferred habitat types. Community responses to drying events were less predictable among intermittent than near-perennial sites, likely because differences in habitat conditions and connectivity may lead intermittent communities to harbour contrasting pools of species with strategies that promote persistence during and/or recolonization after drying. We identify DEHLI as an index that can characterize community responses to drying in temporary streams with contrasting flow permanence regimes. We also recommend the development of new indices that include lentic, semi-aquatic and terrestrial as well as lotic taxa, to more comprehensively describe and predict community responses to changing instream conditions

Options to Expand HIV Viral Load Testing in South Africa: Evaluation of the GeneXpert® HIV-1 Viral Load Assay.

Expansion of HIV viral load (VL) testing services are required to meet increased targets for monitoring patients on antiretroviral treatment. South Africa currently tests >4million VLs per annum in 16 highly centralised, automated high-throughput laboratories. The Xpert HIV-1 VL assay (Cepheid) was evaluated against in-country predicates, the Roche Cobas Taqmanv2 and Abbott HIV-1RT, to investigate options for expanding VL testing using GeneXpert's random access, polyvalent capabilities and already established footprint in South Africa with the Xpert MTB/RIF assay (207 sites). Additionally, the performance of Xpert HIV-1VL on alternative, off-label specimen types, Dried Blood Spots (DBS) and whole blood, was investigated.Precision, accuracy (agreement) and clinical misclassification (1000cp/ml) of Xpert HIV-1VL plasma was compared to Taqmanv2 (n = 155) and Abbott HIV-1 RT (n = 145). Misclassification of Xpert HIV-1VL was further tested on DBS (n = 145) and whole blood (n = 147).Xpert HIV-1VL demonstrated 100% concordance with predicate platforms on a standardised frozen, plasma panel (n = 42) and low overall percentage similarity CV of 1.5% and 0.9% compared to Taqmanv2 and Abbott HIV-1 RT, respectively. On paired plasma clinical specimens, Xpert HIV-1VL had low bias (SD 0.32-0.37logcp/ml) and 3% misclassification at the 1000cp/ml threshold compared to Taqmanv2 (fresh) and Abbott HIV-1 RT (frozen), respectively. Xpert HIV-1VL on whole blood and DBS increased misclassification (upward) by up to 14% with increased invalid rate. All specimen testing was easy to perform and compatible with concurrent Xpert MTB/RIF Tuberculosis testing on the same instrument.The Xpert HIV-1VL on plasma can be used interchangeably with existing predicate platforms in South Africa. Whole blood and DBS testing requires further investigation, but polyvalency of the GeneXpert offers a solution to extending VL testing services

Clinical misclassification of the Xpert VL assay tested on plasma, whole blood and DBS specimens.

<p>Clinical misclassification of the Xpert VL assay tested on plasma, whole blood and DBS specimens.</p

Scatter plots showing comparison of log VL values for Taqman v2, Abbott HIV-1 RT and Xpert VL assay.

<p>(A) Xpert HIV-1 (green) compared to Taqman v2 (blue) and Abbott HIV-1 RT (red) on plasma specimens. The vertical axis represents the log VL and the horizontal axis represents the sample number sorted by the Taqman v2 assay; B) Xpert HIV-1 plasma (blue) compared to Xpert HIV-1 whole blood (red) and Xpert HIV-1 DBS (green). The vertical axis respresents the log VL and the horizontal axis is sample number sorted by Xpert HIV-1 plasma VL values. The red dotted line in both plots highlights the 1000cp/ml clinical threshold.</p

Ultra-High-Throughput, Automated Nucleic Acid Detection of Human Immunodeficiency Virus (HIV) for Infant Infection Diagnosis Using the Gen-Probe Aptima HIV-1 Screening Assay▿

The early diagnosis of human immunodeficiency virus (HIV) infection in infants is critical to ensure the initiation of treatment before significant immunological compromise. Each year an estimated 300,000 HIV-exposed infants in South Africa require access to tests for the diagnosis of HIV infection. Currently, testing is performed at several facilities by using PCR amplification of HIV DNA at 6 weeks of age by the use of dried blood spots (DBSs) and whole blood (WB). The Gen-Probe Aptima HIV type 1 (HIV-1) screening assay (the Aptima assay) is a qualitative nucleic acid test based on transcription-mediated amplification (TMA), a technology routinely used in blood banks in South Africa. The performance characteristics of Gen-Probe's TMA technology compared well to those of the Roche Amplicor HIV-1 DNA (version 1.5) assay. The sensitivity of the assay with WB and DBS samples was 100%, and the specificities were 99.4% and 99.5% for DBSs and WB, respectively. The detection of HIV by the Aptima assay at greater levels of dilution in samples negative by the comparator assay indicates an improvement in sensitivity by the use of the TMA technology. The ability to process 1,900 samples in a 24-h period on the Tigris instrument makes the Aptima assay an attractive option for high-volume, centralized laboratories

Method comparison for the evaluation of Xpert VL compared to Taqman v2 and Abbott HIV-1 RT on the frozen SAVQA panel.

<p>Method comparison for the evaluation of Xpert VL compared to Taqman v2 and Abbott HIV-1 RT on the frozen SAVQA panel.</p