School of Pathology (ETDs)
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Item Comparison of second and third generation parathyroid hormone (PTH) assays performed at Charlotte Maxeke Johannesburg Academic Hospital – Are they fit for purpose?(University of the Witwatersrand, Johannesburg, 2023-11) Nhlapo, Nokuthula; Jacob, Doreen; Maphayi, MphoBackground: Parathyroid hormone (PTH) measurement is crucial in the investigation of calcium and phosphate disorders and in the management of chronic kidney disease (CKD). Available PTH assays include second (intact PTH) and third generation (PTH 1-84) assays. Intact PTH assays are widely available and used for clinical guidelines but overestimate PTH in CKD. PTH 1-84 assays are more specific, but lack of standardisation has complicated clinical interpretation. The study aimed to compare the second and third generation assays to determine the difference in analytical performance and the effect on clinical interpretation. Methods: A method comparison was done on 481 patient samples with PTH requested at Charlotte Maxeke Johannesburg Academic Hospital. PTH was measured in each sample using both intact PTH and PTH 1-84 assays. Passing Bablok regression and Bland Altman plots were performed to determine method agreement and bias. Analytical performance was assessed using the European Federation of Clinical Chemistry and Laboratory Medicine biological variation specifications. Clinical performance was compared in the diagnosis of hypo- and hyperparathyroidism, and in predialysis and dialysis CKD based on current Kidney Disease Improving Global Outcomes guidelines. Results: Intact PTH had a higher median concentration than PTH 1-84 (9.93 vs 8.60 pmol/L, p<0.0001) but showed good correlation (r = 0.994 and p<0.0001). Regression analysis revealed significant systematic and proportional differences, with increased deviations at higher concentrations. The average bias was above allowable bias of 7.1%. Clinical interpretation of hypo- and hyperparathyroidism and predialysis and dialysis groups was unchanged. Conclusions: There was significant bias observed between the two PTH assays thus, they should not be used interchangeably. However, no significant changes in clinical interpretation were found when one assay was used over the other. The decision to use third over second generation PTH assay should consider the impact on clinical interpretation in the population.Item Epidemiology of laboratory-confirmed SARS-CoV-2 hospitalized cases in a tertiary hospital, Gauteng Province, South Africa, 1 April 2020 to 31 March 2021(University of the Witwatersrand, Johannesburg, 2021-12) Sikhosana, Mpho Lerato; Makatini, ZinhleGauteng Province (GP) was the most affected province in South Africa during the first year of the COVID-19 pandemic. We aimed to describe the epidemiology of COVID-19 cases admitted in one of the largest quaternary hospitals in the province during the two pandemic waves. We used data from the national hospital surveillance system, DATCOV, that recorded COVID-19 admissions at Charlotte Maxeke Johannesburg Academic Hospital in (GP) from 5 March 2020 to 27 March 2021. We used multivariable logistic regression to determine a) factors associated with hospitalization in the second compared to the first pandemic wave, and b) factors associated with in-hospital mortality. There were 1861 cases admitted during the study period. The mean age of the cases was 50 (IQR 37-61), 51.80% were females, and 58.68% were black. Of the total number of admissions, 2.10% were healthcare worker, 53.85% of whom were nurses. On admission, 91.99% of cases were admitted at a general ward while 5.86% were admitted at an intensive care unit. Overall, 10.59% of the cases required intensive care during their hospital stay. The case fatality ratio was the highest (28.54%) during wave 2 and lowest during pre-wave (11.49%). Compared to the first wave, factors associated with hospitalization during the second wave included age >80 years (adjusted odds ratio [aOR] 3.43, 95% CI 1.07-10.98) compared to ages 0-19 years, as well as being of other race (aOR 5.63, 95%CI 1.84-17.20) compared with White race. Regarding in-hospital mortality, associated factors included age groups 60-79 (aOR 4.53, 95%CI 1.03-19.86) and >80 (aOR 9.63, 95%CI 1.93-48.01) compared to ages 0-19 years; male sex (aOR 1.55, 95%CI 1.16-2.08); presence of an underlying comorbidity (aOR 1.99, 95%CI 1.45-2.71) 106 as well as being admitted during the second wave (aOR 1.54, 95%CI 1.12-2.10). Our study found that there was a higher risk of mortality during the second compared to the first wave, and other factors associated with mortality included older age, being male as well as having an existing comorbidity. These findings will help inform prevention strategies required to prevent high mortality rates during future waves of infection.Item Comparison of measured LDL cholesterol with calculated LDL-cholesterol using the Friedewald and Martin-Hopkins formulae in diabetic adults at Charlotte Maxeke Johannesburg Academic Hospital/NHLS Laboratory(University of the Witwatersrand, Johannesburg, 2023-01) Dintshi, Mogomotsi Portia; Kone, Ngalulawa; Khoza, SiyabongaBackground: National Cholesterol Education Programme Adult Treatment Panel III (NCEP ATP III) and the European Society of Cardiology recommends using low-density lipoprotein cholesterol (LDL-C) as a treatment target for cholesterol lowering therapy. The Friedewald formula underestimate LDL-C in non-fasted and hypertriglyceridemia patients. This study aimed to compare measured LDL-C to calculated LDL-C in diabetic patients using the Friedewald and Martin-Hopkins formulae. Methods: The data of 1 247 adult diabetes patients were retrospectively evaluated, and included triglycerides (TG), LDL-C, total cholesterol, and high-density lipoprotein cholesterol that were measured on the Roche Cobas® c702. Passing-Bablok regression analysis was used to determine the degree of agreement between measured LDL-C and calculated LDL-C using both formulae. The Bland-Altman plots were used to assess the bias at medical decision limits based on the 2021 European Society of Cardiology (ESC) guidelines on cardiovascular disease prevention in clinical practice. Results: Both formulae showed a good linear relationship against measured LDL-C. However, the Martin-Hopkins formula outperformed the Friedewald formula at LDL-C treatment target <1.4mmol/L. The Friedewald formula and the Martin-Hopkins formula had 14.9% and 10.9% mean positive bias, respectively. At TG-C ≥1.7 mmol/L, the Martin-Hopkins formula had a lower mean positive bias of 4.2 % (95 % CI 3.0-5.5) compared to the Friedewald formula, which had a mean positive bias of 21.8 % (95 % CI 19.9-23), which was higher than the NCEP ATP III recommended total allowable limit of 12%. Conclusion: The Martin-Hopkins formula performed better than the Friedewald formula at LDL-C of 1.4 mmol/L and showed the least positive bias in patients with hypertriglyceridemia.Item Validation of Roche immunoassay for severe acute respiratory virus 2/SARS-COV-2 in South Africa(University of the Witwatersrand, Johannesburg, 2023-01) Grove, Jurette Simone; George, Jaya; Mayne, ElizabethBackground: Serology testing is an important ancillary diagnostic to the reverse transcriptase polymerase chain reaction (RT-PCR) test for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We aimed to evaluate the performance of the Roche Elecsys™ chemiluminescent immunoassay (Rotkreuz, Switzerland), that detects antibodies against the SARS-CoV-2 nucleocapsid antigen, at an academic laboratory in South Africa. Methods: Serum samples were collected from 312 donors with confirmed positive SARS CoV-2 RT-PCR tests, with approval from a large university’s human research ethics committee. Negative controls included samples stored prior to December 2019 and from patients who tested negative for SARS-CoV-2 on RT-PCR and were confirmed negative using multiple serology methods (n = 124). Samples were stored at –80 °C and analysed on a Roche cobas™ 602 autoanalyser. Results: Compared with RT-PCR, our evaluation revealed a specificity of 100% and overall sensitivity of 65.1%. The sensitivity in individuals > 14 days’ post-diagnosis was 72.6%, with the highest sensitivity 31–50 days’ post-diagnosis at 88.6%. Results were also compared with in-house serology tests that showed high agreement in majority of categories. Conclusions: The sensitivity at all-time points post-diagnosis was lower than reported in other studies, but sensitivity in appropriate cohorts approached 90% with a high specificity. The lower sensitivity at earlier time points or in individuals without symptomatology may indicate failure to produce antibodies, which was further supported by the comparison against in-house serology tests.Item The stability of C-peptide and insulin in plasma and serum samples under different storage conditions(University of the Witwatersrand, Johannesburg, 2023-10) Nkuna, Delhia Xikombiso; Maphayi, MphoObjectives: C-peptide and insulin are peptide hormones and their stability is affected by a number of pre-analytical factors. The study aimed to investigate the impact of sample type, storage temperature and time delays before centri-fugation and analysis on the stability of C-peptide and insulin. Methods: Ten healthy non-diabetic adults in fasting and non-fasting state were enrolled. 40 mL of blood was collected from each participant into SST and dipotassium EDTA tubes. Samples were centrifuged immediately or at timed intervals (8, 12, 48 and 72 h). After baseline measurements on the Roche Cobas e602 analyzer using electrochemiluminescence immunoassays, aliquots were stored at room temperature (RT), 2–8 and −20 °C for 4 h to 30 days. The percentage deviation (PD) from baseline was calculated and a change greater than desirable biological variation total error was considered clinically significant. Results: C-peptide was more stable in separated serum than plasma (PD of −5 vs. −13 %) samples stored at 2–8 °C for 7 days and was most unstable at RT when centrifugation was delayed (PD −46 % in plasma and −74 % in serum after 48 h). Insulin was more stable in plasma than in serum under the different storage conditions with a minimum PD of −1% when stored at −20 °C for 30 days. When samples were kept unspun at RT for 72 h, PD was −23 and −80 % in plasma and serum, respectively. Conclusions: C-peptide was more stable in serum provided the sample was centrifuged immediately and stored in the fridge or freezer while insulin was found to be more stable in EDTA plasma.Item The usefulness of monocyte fluorescence as a biomarker of Tuberculosis infection at Chris Hani Baragwanath Academic Hospital(University of the Witwatersrand, Johannesburg, 2023-11) Moosa, Aamina Yunus; Vaughan, Jenifer; Hodkinson, KatherineIntroduction: South Africa has the 5th highest burden of Tuberculosis (TB) as well as coinfection with Human immunodeficiency virus (HIV) worldwide. Routine laboratory methods have varying sensitivity and specificity. The Xpert MTB/RIF (GXPU) (Cepheid, Sunnyvale, CA), has lower sensitivity in sputum smear negative cases and poor quality sputum samples. A robust, non-sputum based, inexpensive biomarker of TB would be of value in such cases. Monocytes are the major leucocyte involved in the immune response to TB. The Sysmex haematology analysers (Sysmex, Kobe, Japan) measure monocyte activation via monocyte fluorescence (MO-Y). This study aimed to evaluate the MO-Y and other Sysmex extended differential parameters (EDPs) as biomarkers of TB infection in the local setting. Methods: The MO-Y and EDPs were retrieved from the analyser for 121 adult cases (56 with TB, 65 controls). Further information was obtained from the laboratory information system, including patient demographics and other laboratory results; TB culture, SARS-CoV-2 results, C-reactive protein level, HIV status, bone marrow biopsies and the cycle threshold (CT) values on positive GXPU analysis. The MO-Y, EDPs and full blood count (FBC) values were compared among patients with and without TB (HIV positive and negative). Statistical significance was assessed (P-value of <0.05). Results: The MO-Y did not show utility in identifying patients with TB. A sub-population of patients living with HIV (PLWH) with a CD4 <100 cells/ul showed significantly higher MO-Y levels, due to other opportunistic infections affecting monocytes. Neutrophil surface fluorescence (a marker of neutrophil activation), was significantly higher in PLWH and with concomitant TB infection, possibly due to immune activation, worse illness, or increased bacterial infection. Among the PLWH, those with TB had significantly lower CD4 counts, absolute lymphocyte counts and mean cell volume (MCV) values. The MCV (cut-off value 87 fL) showed the strongest diagnostic utility for discriminating PLWH with and without TB (AUC 0.79). Conclusion: The MO-Y is not a useful biomarker of TB, but is significantly elevated in PLWH with low CD4 counts. The MCV showed adequate discriminatory power for differentiating patients with and without TB, at a cut-off level of 87fL.Item The contribution of common genetic variants to breast cancer risk in South African black populations(University of the Witwatersrand, Johannesburg, 2023-08) Hayat, Mahtaab; Brandenburg, Jean-Tristan; Ramsay, Michèle; Mathew, ChristopherBreast cancer is the second most common cancer in South African black women. The contribution of common genetic variants to breast cancer risk is well studied in non-African populations, but little is known about their role in resident African populations, and there are no published genome-wide association studies (GWAS) on breast cancer in Africa. This PhD thesis aimed to determine the contribution of common genetic variants to breast cancer in a South African black population. A GWAS was carried out in 2,573 black female breast cancer patients from the Johannesburg Cancer Study and 744 population-matched, female controls from the AWI-Gen study. All participants were from Soweto, Johannesburg, South Africa. Samples were genotyped on the H3Africa SNP array. Replication testing was done of existing loci from European and African American (AA) populations in the resident African data, and loci from the resident African data in European and AA populations. A meta-analysis was carried out with an AA population. Finally, existing polygenic risk scores (PRSs) were tested in the resident African dataset. Three variants at two loci were strongly associated with breast cancer in this study. Two variants (rs77422433, p-value=2.89x10-08, odds ratio (OR):0.46, 95% confidence interval (95%CI): 0.40-0.52 and rs112410019, p-value=3.01x10-08, OR: 0.47, 95%CI: 0.41-0.53) were located within the DNA repair gene XRCC5. These variants were not previously associated with breast cancer, suggesting that it may be an African specific risk locus. The second locus is on chromosome 16 in CES5A (rs3859109, p-value=4.54x10-08, OR=0.70, 95%CI: 0.68-0.73), and had not previously been associated with breast cancer. None of these SNPs were replicated in European and AA populations. The meta-analysis with AA data revealed strong association of an intergenic SNP with breast cancer (rs139299680, pmeta=7.25x10-08) on chromosome 3. A polygenic risk score (PRS) developed in European populations demonstrated poor transferability to this African dataset. This GWAS is the first to be conducted in a resident black African population. This study suggests that there may be African-specific genetic risk factors for African breast cancer, and that large genome-wide studies in African populations are essential to develop a comprehensive understanding of the genetics of breast cancer in Africa.Item Development of an Anopheles arabiensis sex separation strain and optimisation of mosquito handling, packaging and transport conditions for the South African Mosquito Sterile Insect Technique programme(University of the Witwatersrand, Johannesburg, 2023) Mashatola, Thabo; Munhenga, Givemore; Koekemoer, LizetteSouth Africa is taking significant strides towards eliminating malaria transmission within its borders. However, existing vector control strategies that focus on indoor mosquito management face challenges with Anopheles arabiensis, the primary malaria vector. To bolster these efforts, the sterile insect technique (SIT) is being considered as an additional vector control strategy. SIT involves mass-rearing and sterilising specific pest insects, which are then released to mate with wild insects, effectively reducing the pest population. The South African SIT project faces a crucial challenge of efficiently separating female mosquitoes from the production line. This is because female mosquitoes are capable of transmitting the malaria parasite, making their elimination vital. Current methods like manual separation and resistance-based sorting have operational limitations and require further optimisation for field trials. To address this challenge, this thesis conducted optimisation and acclimatisation experiments on adult Anopheles arabiensis females, aiming to transition them to an artificial membrane feeding technique. Comparative assessments demonstrated that artificial blood-feeding methods utilising a Hemotek® membrane feeding system and hog casing could effectively replace conventional methods without significant detriment to reproductive fitness. Subsequently, the study explored the use of ivermectin, a toxicant, to spike blood during artificial feeding to target and eliminate females. An optimal concentration of ivermectin (7.5 ppm) was identified, showing potential for segregating females from males during laboratory rearing. However, complete female elimination within the desired timeframe was not achieved, indicating that this method serves as a secondary phase for female elimination. The study also investigated the use of genetic sexing strains (GSSs) to selectively eliminate females. Although efforts to induce temperature-sensitive lethal mutations temperature sensitive lethality mutations and random morphological variations were unsuccessful, further cross mating studies and insights from previous studies on thermosensitive strains from Cameroon informed future research aimed at developing GSSs tailored to the South African genetic background Another challenge addressed was the optimal temperature and compaction conditions for chilling and immobilising sterile males during handling and transport. This is crucial for maintaining the quality of sterile males. Optimal knockdown temperature ranges (4°C – 8°C for 20 minutes) and packaging conditions (1000 sterile, marked adult males per 27000 cm³ Bugdorm-1® cage) were identified for laboratory handling and transport, facilitating recent small-scale pilot trials with successful packaging and transportation of sterile males to field sites. These advancements signify significant strides in South Africa's malaria elimination endeavours, while also playing a pivotal role in shaping the development of efficient operational protocols for SIT. Furthermore, as the country remains steadfast in its commitment to eliminating malaria, these innovative approaches offer a promising trajectory forward and establish a robust framework for orchestrating the SIT operational phase.Item Equitable access to vaccines: exploring the role of accessability, acceptability, affordabilityand availability with a focus on COVID-19(University of the Witwatersrand, Johannesburg, 2024) Schwalbe, Nina; Cutland, ClareThe coronavirus disease (COVID-19) crisis brought to light many challenges, including “vaccine equity”. In other words, it raised the question: was the distribution of vaccines “fair”? While, on the one hand, there have been unprecedented advances in the science and technologies associated with vaccines, including extraordinary speed and scale-up of manufacturing, there were also significant barriers related to rollout and reaching those most at risk of severe COVID-19. These challenges have disproportionately affected low- and middle-income countries and low-income populations in high-income countries. Building on evidence from other vaccine preventable diseases, this thesis describes the challenges and opportunities concerning vaccine access with a focus on production and distribution (the “supply side”). It explores access using a “4A's” framework to conceptualise the components of access to medicines: affordability, availability, acceptability, and accessibility. The research identifies a range of access policy levers across the end-to-end process of vaccine research, development, and rollout (affordability, acceptability, accessibility, acceptability); reviews these levers as they apply to vaccine manufacturing (affordability, availability); explores the lever of financial incentives to increase coverage (acceptability); and explores the potential of using precision public health to improve vaccine impact by targeting vaccine distribution to groups most risk (accessibility). This thesis identifies several policy and program interventions ranging from regulatory harmonisation and intellectual property sharing, to using precision public health to target the delivery of vaccines to those most at risk. It also shows that while financial incentives may help, governments cannot “buy” coverage. It proposes that in future, vaccine development and deployment should start and end with a “4A’s” strategy and provides practical recommendations on how that can be achievedItem The development and value assessment of an integrated cardiovascular disease risk score in an African setting(University of the Witwatersrand, Johannesburg, 2024) Kamp, Michelle; Ramsay, Michѐle; Lewis, Cathryn; Pain, OliverCardiovascular diseases (CVD) are a significant health threat in Africa and are a leading cause of mortality and morbidity in the region. Risk stratification is the preferred approach to disease prevention but is challenging to apply due to scarce data and current scores not being validated in African populations. CVD risk is influenced by genetic and environmental factors, with the latter mostly considered in risk calculators. Precision medicine (PM) aims to tailor medical diagnostics and therapeutics by leveraging the genetics, environment, and lifestyle of individual patients. Polygenic scores (PGS) can quantify an individual’s genetic burden for CVD and improve the predictive value of risk tools when included with conventional risk factors. PGS for European ancestry populations are reaching the point where they may be useful in clinical care. However, transferability of European-derived PGS to African populations is limited and may hamper application in clinical practice. The overarching aim of the study was to develop and evaluate an integrated CVD risk score incorporating both genetic and non-genetic factors for continental African populations. This comprised of developing ancestry-aligned PGS for various cardiometabolic traits, and then deriving, evaluating, and comparing the predictive utility of genetic, non-genetic, and integrated (genetic + non-genetic) CVD risk prediction models using elastic net regression with nested 10-fold cross validation. Furthermore, we aimed to contextualise the potential utility of such PM-based tools in Africa through an assessment of the current landscape of translational genomics on the continent and by gauging clinician’s perceptions on implementing the derived CVD-risk stratification tool in South Africa’s public health setting. This study demonstrated the potential of genetic information to enhance disease risk stratification among continental African populations. Results revealed PGS provide both independent and complementary information in predicting dyslipidaemia, hypertension, and obesity - integrated scores improved prediction by at least 2.5% compared to models consisting of non-genetic factors alone. The study also highlights the challenges limiting the advancement of PM in Africa – 1. the paucity of genetic and phenotypic data within continental African populations limits the development and validation of robust and clinically useful models. This challenge is exacerbated by Euro-centric genomic and computational tools and echoes the call for more inclusive methodological approaches. 2. Despite positive perceptions of PM, there is an urgent need to address complex structural and operational barriers, including insufficient funding, lack of political will, healthcare infrastructure deficits, and training and education gaps