Association between SARS-CoV-2 gene specific Ct values and COVID-19 associated in-hospital mortality.

Background: Since there are currently no specific SARS-CoV-2 prognostic viral biomarkers for predicting disease severity, there has been interest in using SARS-CoV-2 polymerase chain reaction (PCR) cycle-threshold (Ct) values to predict disease progression. Objective: This study assessed the association between in-hospital mortality of hospitalized COVID-19 cases and Ct-values of gene targets specific to SARS-CoV-2. Methods: Clinical data of hospitalized COVID-19 cases from Gauteng Province from April 2020-July 2022 were obtained from a national surveillance system and linked to laboratory data. The study period was divided into pandemic waves: Asp614Gly/wave1 (7 June-22 Aug 2020); beta/wave2 (15 Nov 2020-6 Feb 2021); delta/wave3 (9 May-18 Sept 2021) and omicron/wave4 (21 Nov 2021-22 Jan 2022). Ct-value data of genes specific to SARS-CoV-2 according to testing platforms (Roche-ORF gene; GeneXpert-N2 gene; Abbott-RdRp gene) were categorized as low (Ct < 20), mid (Ct20-30) or high (Ct > 30). Results: There were 1205 recorded cases: 836(69.4%; wave1), 122(10.1%;wave2) 21(1.7%; wave3) and 11(0.9%;in wave4). The cases' mean age(±SD) was 49 years(±18), and 662(54.9%) were female. There were 296(24.6%) deaths recorded: 241(81.4%;wave1), 27 (9.1%;wave2), 6 (2%;wave3), and 2 (0.7%;wave4) (p < 0.001). Sample distribution by testing platforms was: Roche 1,033 (85.7%), GeneXpert 169 (14%) and Abbott 3 (0.3%). The median (IQR) Ct-values according to testing platform were: Roche 26 (22-30), GeneXpert 38 (36-40) and Abbott 21 (16-24). After adjusting for sex, age and presence of a comorbidity, the odds of COVID-19 associated death were high amongst patients with Ct values 20-30[adjusted Odds Ratio (aOR) 2.25; 95% CI: 1.60-3.18] and highest amongst cases with Ct-values <20 (aOR 3.18; 95% CI: 1.92-5.27), compared to cases with Ct-values >30. Conclusion: Although odds of COVID19-related death were high amongst cases with Ct-values <30, Ct values were not comparable across different testing platforms, thus precluding the comparison of SARS-CoV-2 Ct-value results.

Characteristics of hospitalised COVID-19 patients during the first two pandemic waves, Gauteng.

Background: Gauteng province (GP) was one of the most affected provinces in the country during the first two pandemic waves in South Africa. We aimed to describe the characteristics of coronavirus disease 2019 (COVID-19) patients admitted in one of the largest quaternary hospitals in GP during the first two waves. Objectives: Study objectives were to determine factors associated with hospital admission during the second wave and to describe factors associated with in-hospital COVID-19 mortality. Method: Data from a national hospital-based surveillance system of COVID-19 hospitalisations were used. Multivariable logistic regression models were conducted to compare patients hospitalised during wave 1 and wave 2, and to determine factors associated with in-hospital mortality. Results: The case fatality ratio was the highest (39.95%) during wave 2. Factors associated with hospitalisation included age groups 40-59 years (adjusted odds ratio [aOR]: 2.14, 95% confidence interval [CI]: 1.08-4.27), 60-79 years (aOR: 2.49, 95% CI: 1.23-5.02) and ≥ 80 years (aOR: 3.39, 95% CI: 1.35-8.49). Factors associated with in-hospital mortality included age groups 60-79 years (aOR: 2.55, 95% CI: 1.11-5.84) and ≥ 80 years (aOR: 5.66, 95% CI: 2.12-15.08); male sex (aOR: 1.56, 95% CI: 1.22-1.99); presence of an underlying comorbidity (aOR: 1.76, 95% CI: 1.37-2.26), as well as being admitted during post-wave 2 (aOR: 2.42, 95% CI: 1.33-4.42). Conclusion: Compared to the recent omicron-driven pandemic waves characterised by lower admission rates and less disease severity among younger patients, COVID-19 in-hospital mortality during the earlier waves was associated with older age, being male and having an underlying comorbidity. Contribution: This study showed how an active surveillance system can contribute towards identifying changes in disease trends.

Atypical presentation of herpes simplex virus type 1 infection in paediatric burns patients in a large tertiary hospital, South Africa.

INTRODUCTION: Herpes simplex virus has been reported in the literature to commonly complicate burn wounds. However, there is paucity of such data in the South African setting. CASE PRESENTATION: Eight paediatric burns patients with ages ranging between 10 months and 5 years presented with a febrile maculopapular rash illness in a paediatric ward of a large South African tertiary hospital. The rash became vesicular in three cases, involving the limbs and face. Varicella was suspected. MANAGEMENT AND OUTCOME: Medical records of suspected cases were reviewed. Blood, vesicular fluid and scab samples were collected. Electron microscopy of vesicular fluid revealed herpes virus particles. Laboratory testing confirmed herpes simplex virus type 1. CONCLUSION: Herpes simplex virus type 1 infection can present atypically in burns patients.

Characteristics of hospitalised COVID-19 patients during the first two pandemic waves, Gauteng

Background: Gauteng province (GP) was one of the most affected provinces in the country during the first two pandemic waves in South Africa. We aimed to describe the characteristics of coronavirus disease 2019 (COVID-19) patients admitted in one of the largest quaternary hospitals in GP during the first two waves. Objectives: Study objectives were to determine factors associated with hospital admission during the second wave and to describe factors associated with in-hospital COVID-19 mortality. Method: Data from a national hospital-based surveillance system of COVID-19 hospitalisations were used. Multivariable logistic regression models were conducted to compare patients hospitalised during wave 1 and wave 2, and to determine factors associated with in-hospital mortality.Results: The case fatality ratio was the highest (39.95%) during wave 2. Factors associated with hospitalisation included age groups 40­59 years (adjusted odds ratio [aOR]: 2.14, 95% confidence interval [CI]: 1.08­4.27), 60­79 years (aOR: 2.49, 95% CI: 1.23­5.02) and ≥ 80 years (aOR: 3.39, 95% CI: 1.35­8.49). Factors associated with in­hospital mortality included age groups 60­79 years (aOR: 2.55, 95% CI: 1.11­5.84) and ≥ 80 years (aOR: 5.66, 95% CI: 2.12­15.08); male sex (aOR: 1.56, 95% CI: 1.22­1.99); presence of an underlying comorbidity (aOR: 1.76, 95% CI: 1.37­2.26), as well as being admitted during post­wave 2 (aOR: 2.42, 95% CI: 1.33­4.42). Conclusion: Compared to the recent omicron-driven pandemic waves characterised by lower admission rates and less disease severity among younger patients, COVID-19 in-hospital mortality during the earlier waves was associated with older age, being male and having an underlying comorbidity.