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.

Association between preeclampsia and HIV: a case-control study in urban South Africa.

BACKGROUND: Preeclampsia is a considerable cause of maternal and infant morbidity and mortality. Although its etiology is unknown, preeclampsia has been described as a state of exaggerated maternal inflammatory response. Therefore, it has been hypothesized that preeclampsia would occur less commonly in states of immune deficiency. OBJECTIVE: This study aimed to compare the prevalence of treated and untreated HIV infections among preeclamptic cases and controls, determine infant outcomes, and evaluate the association between HIV and preeclampsia after adjusting for known predictor variables, including maternal age, gravidity, body mass index, and smoking. STUDY DESIGN: This case-control study investigated the association between preeclampsia and HIV infection using secondary data from an unrelated study. We defined preeclamptic cases as pregnant women who were normotensive until 20 weeks of gestation and thereafter had at least 1 high blood pressure measurement either before or at delivery and proteinuria, defined as protein excretion of ≥300 mg within 24 hours or >2 protein on dipstick urinalysis. The prevalence of HIV infection was compared between cases and controls. Multivariate logistic regression analysis was used to assess the association between preeclampsia and potential confounding variables and reported using odds ratios and 95% confidence intervals. RESULTS: There were 571 cases with preeclampsia and 596 normotensive controls included in this study. The median age was 27 years for cases and 26 years for controls (P=.008). Most participants (69%) had ≥2 previous pregnancies with no difference between the cases and controls (P=.176). Overall, 43% of the participants were obese, with a mean body mass index of 29 (interquartile range, 24.5-34.2), with higher proportions of women who were overweight and obese in the group with preeclampsia (P=.031). The prevalence of HIV was significantly lower in cases than in controls (24% vs 30%, respectively; P=.014). Compared with 16% of infants born preterm to normotensive controls, 48% of infants were born preterm born to women with preeclampsia (P<.001). Compared with 14% of infants born with low birthweight to normotensive controls, 53% of infants were born with low birthweight to women with preeclampsia (P<.0001). Untreated HIV infection was negatively associated with preeclampsia (unadjusted odds ratio, 0.330; 95% confidence interval, 0.197-0.552; P<.0001), whereas factors associated with preeclampsia were advanced maternal age (odds ratio, 1.673; 95% confidence interval, 1.209-2.316; P=.002) and obesity (odds ratio, 1.611; 95% confidence interval, 1.023-2.537; P=.040). After adjusting for maternal age, gravidity, smoking, and body mass index in the multivariate regression, only obesity remained significantly associated with preeclampsia (adjusted odds ratio, 1.624; 95% confidence interval, 1.024-2.575; P=.039). CONCLUSION: Before the large-scale rollout of antiretroviral therapy in a setting with a high burden of HIV and preeclampsia, untreated HIV infection was found to have a protective effect against preeclampsia. The protective effect against preeclampsia was not apparent for HIV infection treated with antiretroviral therapy.

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.

Vaccine Efficacy of ALVAC-HIV and Bivalent Subtype C gp120-MF59 in Adults.

BACKGROUND: A safe, effective vaccine is essential to eradicating human immunodeficiency virus (HIV) infection. A canarypox-protein HIV vaccine regimen (ALVAC-HIV plus AIDSVAX B/E) showed modest efficacy in reducing infection in Thailand. An analogous regimen using HIV-1 subtype C virus showed potent humoral and cellular responses in a phase 1-2a trial in South Africa. Efficacy data and additional safety data were needed for this regimen in a larger population in South Africa. METHODS: In this phase 2b-3 trial, we randomly assigned 5404 adults without HIV-1 infection to receive the vaccine (2704 participants) or placebo (2700 participants). The vaccine regimen consisted of injections of ALVAC-HIV at months 0 and 1, followed by four booster injections of ALVAC-HIV plus bivalent subtype C gp120-MF59 adjuvant at months 3, 6, 12, and 18. The primary efficacy outcome was the occurrence of HIV-1 infection from randomization to 24 months. RESULTS: In January 2020, prespecified criteria for nonefficacy were met at an interim analysis; further vaccinations were subsequently halted. The median age of the trial participants was 24 years; 70% of the participants were women. The incidence of adverse events was similar in the vaccine and placebo groups. During the 24-month follow-up, HIV-1 infection was diagnosed in 138 participants in the vaccine group and in 133 in the placebo group (hazard ratio, 1.02; 95% confidence interval, 0.81 to 1.30; P = 0.84). CONCLUSIONS: The ALVAC-gp120 regimen did not prevent HIV-1 infection among participants in South Africa despite previous evidence of immunogenicity. (HVTN 702 ClinicalTrials.gov number, NCT02968849.).

Epidemiology of laboratory-confirmed mumps infections in South Africa, 2012-2017: a cross-sectional study.

BACKGROUND: Data on the burden of mumps in South Africa are limited and the epidemiology of mumps in this setting is not well understood. We present an analysis of mumps data in South Africa from 2012 to 2017. METHODS: This cross-sectional study included secondary data on laboratory-confirmed mumps infections from 2012 to 2017, archived at the South African National Health Laboratory Services' data repository as well as from four private laboratories. Mumps-specific immunoglobulin M (IgM) and/or viral nucleic acid positive results represented acute infections. We used age-specific mid-year population estimates for each study year as denominators when calculating annual cumulative incidence. Seasonality was based on the season that showed a peak in infections. RESULTS: Out of 48,580 records obtained from the public and private sectors, 46,713 (96.2%) were from the private sector. Over the study period, there were 7494 acute infections, 7085 (94.5%) of which were recorded in the private sector. Of these 7494 infections, 3924 (52.4%) occurred in males. The proportion of samples tested that were IgM positive was 18.6% (1058/5682) in 2012, 15% (1016/6790) in 2013, 15.8% (1280/8093) in 2014, 15.5% (1384/8944) in 2015, 13.1% (1260/9629) in 2016 and 15.8% (1496/9442) in 2017. The cumulative incidence rate per 100,000 was highest in children between one and 9 years throughout the study period. The cumulative incidence of infections was highest in the Western Cape, Gauteng and the Northern Cape. Infections peaked in June and November. CONCLUSION: Laboratory-confirmed mumps infections predominantly occurred in spring, affecting children below 10 years of age and individuals who were male. There were fewer tests performed in the public sector compared to the private sector. Since only laboratory data was analysed our results represent and underestimate of disease burden. Further studies that include clinical data are required to provide better estimates of disease burden in South Africa.

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.