Naseem Cassim

Background: The COVID-19 pandemic required South African public sector HIV viral load (VL) laboratories to scale up Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) testing while maintaining essential HIV services. This placed additional pressure on diagnostic services. This dual mandate introduced significant occupational and environmental challenges (OEC) for staff that remain underexplored. Objective: This study aimed to investigate the OEC and effects that staff experienced during the implementation of COVID-19 testing at public sector VL laboratories in South Africa. Methods: A quantitative, cross-sectional study utilised a census approach among technical and support staff. Data were collected via a structured REDCap questionnaire using 5-point Likert scales. Pre- and post-implementation challenges were assessed across four domains: workload, environmental conditions (space, ventilation, waste), communication, and PPE availability. Statistical analyses included the Wilcoxon Signed-Rank and Spearman’s correlation tests. Results: Perceived occupational challenges increased significantly across all domains post-implementation. Staff workload saw the highest rise (mean score 3.02 to 3.53). Adverse health effects were pervasive; 80.2% of staff reported burnout/fatigue, and 76.5% reported increased anxiety/stress. A strong positive correlation was observed between post-COVID-19 challenges and adverse mental and physical health outcomes (rho = 0.449, p < 0.001). Furthermore, 35.8% of staff considered resigning due to increased job demands. Conclusion: Integrating COVID-19 testing exacerbated systemic weaknesses, causing measurable psychological injury and threatening workforce retention. Findings suggest that the diagnostic workforce requires formal crisis surge staffing models and institutionalised mental health support to safeguard personnel and maintain essential services during future health emergencies.

Background: In 2004, South Africa’s public health system faced the dual challenge of rapidly scaling up antiretroviral therapy (ART) while reducing the cost of laboratory monitoring. At the time, conventional CD4 testing methods were expensive, labour-intensive, and impractical for sustaining a national testing network. This study aimed to assess the financial impact and cost savings associated with the implementation of the PanLeucogated CD4 (PLG/CD4) enumeration method between 2004 and 2024 in the public-sector in South Africa. Methods: A longitudinal cost analysis was conducted using annual test volumes and state tariffs for PLG/CD4 testing and the 4-colour CD3/CD4/CD8/CD45 T-cell enumeration reference method. Annual cost savings were calculated in United States Dollars (USD) by applying historical South African Rands (ZAR) to United States Dollars (USD) exchange rates. The state prices for tariff codes PLG/CD4 and the reference method were provided by calendar year in ZAR and converted to USD based on the prevailing exchange rate. The USD test prices were multiplied by annual test volumes. Cost savings were calculated by multiplying annual test volumes and the difference in test prices in USD (difference between PLG/CD4 and the reference method). Results: There were 50,745,848 PLG/CD4 tests performed over 20-years. The cost-per-test of PLG/CD4 was consistently lower than the reference method, ranging from $4,06 to $9,40, compared to $13,06 to $28,21. Cumulative national savings amounted to USD 626 million. The peak annual savings of $64,6 million occurred in 2011, coinciding with the height of ART enrolment. Cost savings persisted despite a doubling in the exchange rate over the study period. Conclusion: The PLG/CD4 implementation enabled cost-efficient, scalable, quality-assured CD4 testing as part of the national HIV response, reducing reliance on complex/costly technologies while improving coverage. These findings support the critical role of context-specific diagnostic innovation to strengthen health system resilience.

Background: South Africa has the largest HIV epidemic globally. Despite the scale-up of antiretroviral therapy, people living with HIV still present with CD4 ≤ 200 cells/µL because of possible treatment interruptions and/or late presentation. Objectives: This study assessed the proportion of CD4 specimens with counts ≤ 200 cells/µL by health district, comparing 2013 to 2023. Method: This cross-sectional study analysed laboratory data. Annual test volumes, median CD4 and the percentage of specimens with a count ≤ 200 cells/µL were reported. The difference in the median CD4 between 2013 and 2023 was calculated. No de-duplication was possible because of the absence of unique identifiers. Results: Data are reported for 5 821 932 specimens, with a significant decline in absolute numbers, while the percentage of specimens with a count ≤ 200 cells/µL declined by 0.4%. The median CD4 increased from 396 cells/µL in 2013 to 465 cells/µL by 2023. Between 2013 and 2023, eight districts showed a decrease in the median CD4, while 44 reported an increase ranging from 2 cells/µL (Sedibeng) to 192 cells/µL (uThukela). A percentage point reduction for counts ≤ 200 cells/µL between 2013 and 2023 was reported for 23 districts (44.2%), while 29 (55.8%) showed a percentage point increase. Conclusion: Despite an upward trend in the national specimen-level CD4 count median over time, unacceptable levels of CD4 counts ≤ 200 cells/µL persisted. The analysis provides important insight into district burden of advanced HIV disease which warrants national attention and further investigation.

Background: Specimen losses across the pathology value chain (PVC) result in missed diagnostic opportunities. It is difficult to fully assess these due to the current paper-based systems, with tracking of specimens only possible on the laboratory information system (LIS). Aim: This study aimed to assess specimen losses using the paper-based register. Setting: Randomly selected Primary health care (PHC) facilities, City of Johannesburg, South Africa. Methods: The retrospective descriptive study design was used to scan 1,000 barcodes from facilities in sub-districts A to G. Data was limited to barcodes from the request form and excluded surveillance testing. Matching data from the laboratory repository was extracted. PVC losses were assessed by determining the percentage of scanned barcodes that had a registered, tested, reviewed and/or rejected date. The analysis was stratified according to sub-district, health facility type and test code. Results: The dataset analysed included 33 867 barcodes with 121 697 test codes, equating to 3.59 tests per barcode. Matching registered, tested and reviewed dates were detected for 33 107 (97.76%) barcodes. In total, a rejection for one or more test codes was detected for 1,961 barcodes (5.79%). At the sub-district level, between 95.95% (D) and 98.90% (E) of barcodes were reviewed. The rejection rate ranged from 3.27% (F) to 10.93% (D). For community health centres and clinics, 97.37% and 97.97% of the barcodes had a matching reviewed date. Conclusion: PVC losses reported were 4.05%, excluding rejections (5.79%), with slightly higher levels noted at the sub-district level. Contribution: The continuous audit of PVC losses is recommended.

Background: Reflexed cryptococcal antigenaemia (CrAg) testing has been offered on remnant CD4 specimens with a count < 100 cells/µL from 2017 in South Africa. The Western Cape is the only province to introduce CrAg testing for counts of 100 cells/µL to 200 cells/µL. Objectives: The objective of this study was to assess the reflexed CrAg detection rate in the Western Cape. Method: The retrospective analysis of laboratory data for reflexed CrAg testing was conducted between September 2022 and May 2024. The CrAg detection rate was reported for the following CD4 categories at the provincial, district, and sub-district levels: (1) < 100 cells/µL, (2) ≥ 100 cells/µL – ≤ 200 cells/µL, and (3) ≤ 200 cells/µL. Results: Data are reported for 80 809 specimens, with a CrAg detection rate of 4.0% for a CD4 ≤ 200 cells/µL compared to 6.2% for a count < 100 cells/µL. For a count of ≥ 100 cells/µL – ≤ 200 cells/µL, a CrAg detection rate of 2.1% was reported. The district CrAg detection rate for counts ≤ 200 cells/µL ranged from 1.4% (Central Karoo) to 5.9% (Cape Winelands). Excluding subdistricts without CrAg-positive specimens, the detection rate ranged from 1.3% (Beaufort West) to 8.3% (Swartland). Conclusion: The study findings of a CrAg detection rate of 4.0% in the Western Cape province justifies their decision to extend reflexed screening to a threshold of 200 cells/µL. However, most CrAg-positive specimens were identified for a count < 100 cells/µL. Intensified approaches to find CrAg-positive patients with a count ≤ 200 cells/µL are required.

Background: South Africa has the world’s largest human immunodeficiency virus (HIV) pandemic. Most service gaps for cluster of differentiation 4 (CD4) testing were previously addressed.Aim: This study aimed to assess the impact of a tiered service on interlaboratory referral distances.Setting: Data are reported for CD4 testing that are referred from a national network of laboratories.Methods: Test volumes were extracted for source and testing laboratories from 2012 to 2021. The Euclidean distances (EDs) were calculated, with the annual and provincial medians reported and categorised (50 km, 51 km – 99 km, 100 km – 199 km, 200 km – 299 km and ≥ 300 km). The relationship between ED, referrals and turnaround time (TAT) was analysed. The change in the provincial median ED between 2012 and 2021 was calculated.Results: Data included 14 487 006 referrals. The median ED ranged from 55 km to 60 km. An ED category of 51 km – 99 km, 100 km – 199 km, 200 km – 299 km and ≥ 300 km was reported for 35.1%, 13.2%, 3.5% and 0.3% of the specimens. A negative linear correlation was reported for ED with referral volumes (–0.1540) and TAT (–0.2305). The provincial median ED ranged from 16 km (Gauteng) to 186 km (Northern Cape). Excluding the Northern Cape, a provincial ED of ≤ 100 km was reported. The percentage change in median ED between 2012 and 2021 ranged from –55.7% (Free State) to 0.8% (Mpumalanga). Two source laboratories reported a median ED 300 km in 2021 (Springbok and Beaufort West).Conclusion: The study’s findings indicate that the decentralisation of services reduced the national median ED to below 60 km.Contribution: The tiered implementation improved accessibility, however, some coverage gaps still remain.

Introduction: To ensure there is adequate investment into diagnostics, an understanding of the magnitude of impact and return on investment is necessary. We, therefore, sought to understand the health and economic impacts of the molecular diagnostic programme in South Africa, to deepen the understanding of the broad value of diagnostics and guide future healthcare investments. Methods: We calculated the 10-year (where data were available) total cost and disability-adjusted life-years (DALYs) averted associated with molecular testing for tuberculosis diagnosis (2013–2022), HIV viral load monitoring (2013–2022), early infant diagnosis of HIV infection (2013–2022) and SARS-CoV-2 testing (2020–2022), based on the actual number of molecular tests conducted in South Africa for the respective time periods. We then calculated the economic value associated with those health gains and subsequent return on investment. Results: Since the inception of the molecular diagnostics programme in South Africa, approximately 4.3 million DALYs (uncertainty range (UR): 2.8–5.8 million) have been averted as a direct consequence of this programme. This has generated an estimated US$28.3 billion in economic value due to these health gains (UR$18.4–UR$38.7 billion). The return on investment varied by specific diagnostic test (20.3 (UR 15.2–25.4) for tuberculosis, 7.7 (UR 1.6–13.9) for HIV viral load testing, 63.0 (UR 63.0–65.5) for early infant diagnosis of HIV and 2.5 (UR 0.7–4.6) for SARS-CoV-2), for an average of 13.9 (UR 9.0–18.9) for the entire molecular diagnostics programme or US$13.9 of value for each UR$1 invested. Conclusions: The molecular diagnostics programme in South Africa generated a significant amount of health gains and economic value associated with these health gains. The return on investment rivals other high-impact public health interventions such as childhood vaccination. The molecular diagnostics programme in South Africa is highly impactful and will continue to be an excellent investment in South African public health expenditure.

SUMMARY: INTRODUCTION: In South Africa, Xpert ^® MTB/RIF Ultra (Ultra) is the recommended diagnostic assay for TB with line-probe assays for first- (LPAfl) and second-line drugs (LPAsl) providing additional drug susceptibility testing (DST) for samples that were rifampicin-resistant (RR-TB). To guide implementation of the recently launched Xpert ^® MTB/XDR (MTB/XDR) assay, a cost-outcomes analysis was conducted comparing total costs for genotypic DST (gDST) for persons diagnosed with RR-TB considering three strategies: replacing LPAfl/LPAsl (centralised level) with MTB/XDR vs. Ultra reflex testing (decentralised level). Further, DST was performed using residual specimen following RR-TB diagnosis. METHODS: The total cost of gDST was determined for three strategies, considering loss to follow-up (LTFU), unsuccessful test rates, and specimen volume. RESULTS: For 2019, 9,415 persons were diagnosed with RR-TB. A 35% LTFU rate between RR-TB diagnosis and LPAfl/LPAsl-DST was estimated. Unsuccessful test rates of 37% and 23.3% were reported for LPAfl and LPAsl, respectively. The estimated total costs were $191,472 for the conventional strategy, $122,352 for the centralised strategy, and $126,838 for the decentralised strategy. However, it was found that sufficient residual volume for reflex MTB/XDR testing is a limiting factor at the decentralised level. CONCLUSION: Centralising the implementation of XDR testing, as compared to LPAfl/LPAsl, leads to significant cost savings.

Background: South Africa has the largest HIV epidemic globally. Despite the scale-up of antiretroviral therapy, people living with HIV are still presenting with low CD4 counts. Objectives: This study assessed CD4 trends. Method: A retrospective analysis of laboratory data from 2013 to 2023 was conducted. Annual test volumes, the median CD4, and the percentage of specimens with a count ≤ 200 cells/μL and > 500 cells/μL were reported at the national and provincial levels, and by age and gender. The percentage change in both CD4 categories between 2013 and 2023 was assessed, and the CD4 counts per 100 000 population reported. Results: Data are reported for 32 154 644 specimens. The overall median CD4 increased from 396 cells/μL to 473 cells/μL. The percentage of specimens with CD4 counts > 500 cells/μL increased over time but the percentage with CD4 counts ≤ 200 cells/μL remained stable. Men had lower CD4 median and higher percentage of specimens with counts ≤ 200 cells/μL than women. However, the rate of, CD4 ≤ 200 cells/μL decreased from 1411 to 700 per 100 000 population; this decrease occurred in all provinces except the Western Cape. Conclusion: This study found high percentage of specimens with CD4 counts ≤ 200 cells/μL despite an increase in median CD4 count. Men had lower CD4 counts than women.