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

Background: 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.

Hematological findings in adult patients with SARS CoV-2 infection at Tygerberg Hospital Cape Town South Africa.

Background: Coronavirus disease 2019 (COVID-19) is associated with hematological abnormalities of variable severity. The full blood count (FBC) and leukocyte differential count (DIFF) could facilitate the prediction of disease severity and outcome in COVID-19. This study aimed to assess the hematological parameters in early severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and their correlation with disease outcome. Methods: A retrospective cross-sectional descriptive study was performed. Adults with a FBC and positive SARS-CoV-2 polymerase chain reaction results between March 1, and June 31, 2020 were reviewed. Basic hematological parameters (FBC, DIFF) and human immunodeficiency virus (HIV) status were recorded. Outcome measures were admission to a general ward or intensive care unit (ICU), recovery or death. Results: Six hundred and eighty-five cases median age 51 years, were analyzed. Forty-four percent were males and fourteen percent were HIV-positive with no association between death and/or ICU admission (p = 0.522 and p = 0.830, respectively). Leucocytosis was predictive of ICU admission (odds ratio [OR]: 2.4, confidence interval [CI]: 1.77-3.8186) and neutrophilia, of both mortality (OR: 1.5, CI: 1.0440-2.0899) and ICU admission (OR: 4, CI: 2.5933-6.475). Median lymphocyte count was decreased and d-dimer raised, showing no significant association with outcome. Raised neutrophil-to-lymphocyte-ratio (NLR) was associated with increased odds of mortality (OR: 2.5, CI: 1.3556-3.2503) and ICU admission (OR: 4.8, CI: 2.4307-9.5430) as was monocyte-to-lymphocyte-ratio (MLR) (OR: 2, CI: 1.3132-2.9064) and (OR: 2.3, CI: 1.0608-1.9935), respectively. Hospital admission and older age were significantly associated with mortality (p = 0.0008 and p < 0.0001), respectively. Conclusion: Evidence-based interpretation of routine laboratory parameters, readily available in resource-constrained settings, may identify patients at increased risk of mortality. The FBC, DIFF, NLR, and MLR should form part of the early COVID-19 investigation.

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.

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.

Rapid testing for respiratory syncytial virus in a resource-limited paediatric intensive care setting.

We analysed the performance characteristics of the respiratory syncytial virus lateral flow rapid antigen assay in use when compared to a multiplex polymerase chain reaction for detection of respiratory viruses. The study was conducted at a tertiary paediatric hospital in Port Elizabeth, South Africa, from 01 January 2017 to 31 December 2018. We found the clinical sensitivity (36.8%) of the rapid test to be too low for routine diagnostic use. Knowledge of assay performance characteristics of rapid tests are important for appropriate interpretation of rapid test results.