Analysis of cytomegalovirus UL97 drug resistance mutations in patients receiving Ganciclovir

Introduction: Cytomegalovirus (CMV) drug resistance mutations, because of the widespread use of ganciclovir, have been widely reported in international literature, particularly in the post-transplant setting. However, a genotypic assay to detect CMV drug resistance is not available in South Africa and the prevalence of these mutations is therefore unknown. We aimed to document the prevalence and types of CMV UL97 mutations following exposure to ganciclovir in adult and paediatric oncology patients, transplant recipients and HIV-infected patients in the local tertiary level hospitals: Red Cross War Memorial Children's Hospital, Groote Schuur Hospital and Tygerberg Hospital. Methods: The study had two components, the first component being a retrospective cross-sectional study using stored extracted DNA from patients with serially elevated CMV viral load levels. Thirty-three samples were tested for this component. The second component was a prospective case series on patients who were referred by clinicians for genotypic testing in whom CMV drug resistance was suspected. Eight samples were tested for this component. The CMV UL97 gene was amplified by conventional nested polymerase chain reaction (PCR) and Sanger sequencing performed. Results: CMV UL97 mutations were identified in five of thirty-three (15%) retrospectively screened samples while the prospective testing of eight patient samples identified drug resistance mutations in three patients (38%). Overall 8/41 (20%) patients had CMV UL97 mutations. A trend of higher risk for development of drug resistance mutations among haematological oncology patients 7/23 (30%) compared to solid organ transplant recipients 1/10 (10%) was observed, however, this difference was not statistically significant (P=0.306). Conclusion: This study, the first of its nature in South Africa, identified the presence of CMV UL97 mutations conferring resistance to ganciclovir in the haematological oncology, primary immunodeficiency and solid organ transplant patients in the Western Cape. The assay successfully detected CMV UL97 drug resistance mutations in whole blood and cerebrospinal fluid clinical samples. Ongoing viral replication in the background of intensive immunosuppression and prolonged antiviral therapy selects for the emergence of CMV UL97 drug resistance mutations

Characterization and development of optical components for the Cassegrain telescope and laser beam coudé path of the lunar laser ranger of HartRAO.

Master of Science in Land Surveying. University of KwaZulu-Natal, Howard College 2015.The Observatoire de la Côte d’Azur (OCA) donated a 1-m Cassegrain telescope to be used for the dual satellite and lunar laser ranging system currently under development at the Hartebeesthoek Radio Astronomy in South Africa. As the very first of its kind in the Southern Hemisphere, the new system will be designed and developed as a permanent lunar laser ranging system with high precision laser and electronic equipment to achieve millimetre accuracy. Limited technical details of the telescope exist so tests were conducted to determine the optical characteristics and performance of the telescope and its mirrors. The optical performance of the telescope was validated through the analysis of transmission efficiency, structural efficiency and image quality. Spectroscopic measurements were conducted to determine the transmission efficiency of the telescope by taking into account all losses in light from the reflection of mirrors, transmission of lenses and the secondary spider central obstruction along the path of the proposed coudé optical path. A system transmission of ∼90% was obtained if a coudé path with no central obstruction is used. The primary mirror and its support structure was validated using finite element analysis software (ANSYS) to model the amount of deformation the mirror will experience under gravitational and external loading. Taking into account the lightweight nature (honeycomb structure) of the mirror, its material properties and multiple support mechanism, ANSYS was used to compute the gravity deformations experienced by the mirror as the telescope tracks from the horizon to zenith. The deformations when gravity acts along the axial support were in the range of 1/6th of the wavelength, which is below the maximum limit expected for such a structure at the given weight. In order to analyse the image quality of the system, an optical analysis software (OSLO) was used. Spot diagram analysis revealed coma as the dominant primary aberration in the system. The telescope is diffraction-limited for on-axis performance and yields a Strehl ratio of 0.78 for off-axis performance

Delays in HIV-1 infant polymerase chain reaction testing may leave children without confirmed diagnoses in the Western Cape province, South Africa

CITATION: Mahlakwane, K. L. et al. 2022. African Journal of Laboratory Medicine, 11(1):1485, doi:10.4102/ajlm.v11i1.1485.The original publication is available at https://ajlmonline.orgBackground: Early diagnosis and confirmation of HIV infection in newborns is crucial for expedited initiation of antiretroviral therapy. Confirmatory testing must be done for all children with a reactive HIV PCR result. There is no comprehensive data on confirmatory testing and HIV PCR test request rejections at National Health Laboratory Service laboratories in South Africa. Objective: This study assessed the metrics of routine infant HIV PCR testing at the Tygerberg Hospital Virology Laboratory, Cape Town, Western Cape, South Africa, including the proportion of rejected test requests, turn-around time (TAT), and rate of confirmatory testing. Methods: We retrospectively reviewed laboratory-based data on all HIV PCR tests performed on children ≤ 24 months old (n = 43 346) and data on rejected HIV PCR requests (n = 1479) at the Tygerberg virology laboratory over two years (2017–2019). Data from sample collection to release of results were analysed to assess the TAT and follow-up patterns. Results: The proportion of rejected HIV PCR requests was 3.3%; 83.9% of these were rejected for various pre-analytical reasons. Most of the test results (89.2%) met the required 96-h TAT. Of the reactive initial test results, 53.5% had a follow-up sample tested, of which 93.1% were positive. Of the initial indeterminate results, 74.7% were negative on follow-up testing. Conclusion: A high proportion of HIV PCR requests were rejected for pre-analytical reasons. The high number of initial reactive tests without evidence of follow-up suggests that a shorter TAT is required to allow confirmatory testing before children are discharged.https://ajlmonline.org/index.php/ajlm/article/view/1485Publisher's versio

How has the OSD affected our state hospitals?

The long-awaited occupation-specific dispensation (OSD) process for state-employed doctors has now been concluded. The final offer, signed and accepted in the bargaining chamber despite being rejected by 92% of doctors in a SAMA survey, has not received much attention or fanfare. At the conclusion of this process, which has been drawn out over several years, many points have emerged that are extremely worrying for the future of health care in this country

HIV false positive screening serology due to sample contamination reduced by a dedicated sample and platform in a high prevalence environment.

Automated testing of HIV serology on clinical chemistry analysers has become common. High sample throughput, high HIV prevalence and instrument design could all contribute to sample cross-contamination by microscopic droplet carry-over from seropositive samples to seronegative samples resulting in false positive low-reactive results. Following installation of an automated shared platform at our public health laboratory, we noted an increase in low reactive and false positive results. Subsequently, we investigated HIV serology screening test results for a period of 21 months. Of 485 initially low positive or equivocal samples 411 (85%) tested negative when retested using an independently collected sample. As creatinine is commonly requested with HIV screening, we used it as a proxy for concomitant clinical chemistry testing, indicating that a sample had likely been tested on a shared high-throughput instrument. The contamination risk was stratified between samples passing the clinical chemistry module first versus samples bypassing it. The odds ratio for a false positive HIV serology result was 4.1 (95% CI: 1.69-9.97) when creatinine level was determined first, versus not, on the same sample, suggesting contamination on the chemistry analyser. We subsequently issued a notice to obtain dedicated samples for HIV serology and added a suffix to the specimen identifier which restricted testing to a dedicated instrument. Low positive and false positive rates were determined before and after these interventions. Based on measured rates in low positive samples we estimate that before the intervention, of 44 117 HIV screening serology samples, 753 (1.71%) were false positive, declining to 48 of 7 072 samples (0.68%) post-intervention (p<0.01). Our findings showed that automated high throughput shared diagnostic platforms are at risk of generating false-positive HIV test results, due to sample contamination and that measures are required to address this. Restricting HIV serology samples to a dedicated platform resolved this problem

Molecular characterisation and epidemiology of enterovirus-associated aseptic meningitis in the Western and Eastern Cape Provinces, South Africa 2018–2019

BACKGROUND : Enteroviruses are amongst the most common causes of aseptic meningitis. Between November 2018 and May 2019, an outbreak of enterovirus-associated aseptic meningitis cases was noted in the Western and Eastern Cape Provinces, South Africa. OBJECTIVES : To describe the epidemiology and phylogeography of enterovirus infections during an aseptic meningitis outbreak in the Western and Eastern Cape Provinces of South Africa. METHODS : Cerebrospinal fluid samples from suspected cases were screened using a polymerase chain reaction targeting the 5’UTR. Confirmed enterovirus-associated meningitis samples underwent molecular typing through species–specific VP1/VP2 primers and pan-species VP1 primers. RESULTS : Between November 2018 and May 2019, 3497 suspected cases of aseptic meningitis were documented in the Western and Eastern Cape Provinces. Median age was 8 years (range 0–61), interquartile range (IQR=4–13 years), 405/735 (55%) male. 742/3497 (21%) cases were laboratory – confirmed enterovirus positive by routine diagnostic PCR targeting the 5’UTR. 128/742 (17%) underwent molecular typing by VP1 gene sequencing. Echovirus 4 (E4) was detected in 102/128 (80%) cases. Echovirus 9 was found in 7%, Coxsackievirus A13 in 3%. 10 genotypes contributed to the remaining 10% of cases. Synonymous mutations were found in most cases, with sporadic amino acid changes in 13 (12.7%) cases. CONCLUSION : The aseptic meningitis outbreak was associated with echovirus 4. Stool samples are valuable for molecular typing in CSF confirmed EV-associated aseptic meningitis.The National Health Laboratory Service Research Trust Development Grant and the Poliomyelitis Research Foundation.https://www.elsevier.com/locate/jcvam2022School of Health Systems and Public Health (SHSPH