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Omicron lineages BA.4 and BA.5 drove a fifth wave of COVID-19 cases in South Africa. We assessed the severity of BA.4/BA.5 infections using the presence/absence of the S-gene target for infections diagnosed using the TaqPath PCR assay between 1 October 2021 and 26 April 2022. We linked national COVID-19 individual-level data including case, laboratory test and hospitalisation data. We assessed severity using multivariable logistic regression comparing the risk of hospitalisation and risk of severe disease, once hospitalised, for Delta, BA.1, BA.2 and BA.4/BA.5 infections. After controlling for factors associated with hospitalisation and severe outcome respectively, BA.4/BA.5-infected individuals had a similar odds of hospitalisation (aOR1.24, 95% CI 0.98–1.55) and severe outcome (aOR 0.71, 95%CI 0.41–1.25) compared to BA.1-infected individuals. Newly emerged Omicron lineages BA.4/BA.5 continue to show reduced clinical severity compared to previous variants, as observed for Omicron BA.1.

Early data indicated that infection with Omicron BA.1 sub-lineage was associated with a lower risk of hospitalisation and severe illness, compared to Delta infection. Recently, the BA.2 sub-lineage has increased in many areas globally. We aimed to assess the severity of BA.2 infections compared to BA.1 in South Africa. We performed data linkages for (i) national COVID-19 case data, (ii) SARS-CoV-2 laboratory test data, and (iii) COVID-19 hospitalisations data, nationally. For cases identified using TaqPath COVID-19 PCR, infections were designated as S-gene target failure (SGTF, proxy for BA.1) or S-gene positive (proxy for BA.2). Disease severity was assessed using multivariable logistic regression models comparing individuals with S-gene positive infection to SGTF-infected individuals diagnosed between 1 December 2021 to 20 January 2022. From week 49 (starting 5 December 2021) through week 4 (ending 29 January 2022), the proportion of S-gene positive infections increased from 3% (931/31,271) to 80% (2,425/3,031). The odds of being admitted to hospital did not differ between individuals with S-gene positive (BA.2 proxy) infection compared to SGTF (BA.1 proxy) infection (adjusted odds ratio (aOR) 0.96, 95% confidence interval (CI) 0.85-1.09). Among hospitalised individuals, after controlling for factors associated with severe disease, the odds of severe disease did not differ for individuals with S-gene positive infection compared to SGTF infection (aOR 0.91, 95%CI 0.68-1.22). These data suggest that while BA.2 may have a competitive advantage over BA.1 in some settings, the clinical profile of illness remains similar.

Background South Africa experienced four waves of SARS-CoV-2 infection, dominated by Wuhan-Hu, Beta, Delta, and Omicron (BA.1/BA.2). We describe the trends in SARS-CoV-2 testing, cases, admissions, and deaths among children and adolescents in South Africa over successive waves. Methods We analyzed national SARS-CoV-2 testing, case, and admissions data from March 2020 to February 2022 and estimated cumulative rates by age group for each endpoint. The severity in the third versus the fourth wave was assessed using multivariable logistic regression. Results Individuals ≤18 years comprised 35% (21,008,060/60,142,978) of the population but only 12% (424,394/3,593,644) of cases and 6% (26,176/451,753) of admissions. Among individuals ≤18 years, infants had the highest admission (505/100,000) rates. Testing, case, and admission rates generally increased successively in the second (Beta) and third (Delta) waves among all age groups. In the fourth (Omicron BA.1/BA.2) wave, the case rate dropped among individuals ≥1 year but increased among those Conclusions The admission rate for children

BackgroundThe SARS-CoV-2 Omicron variant of concern (VOC) almost completely replaced other variants in South Africa during November 2021, and was associated with a rapid increase in COVID-19 cases. We aimed to assess clinical severity of individuals infected with Omicron, using S Gene Target Failure (SGTF) on the Thermo Fisher Scientific TaqPath COVID-19 PCR test as a proxy.MethodsWe performed data linkages for (i) SARS-CoV-2 laboratory tests, (ii) COVID-19 case data, (iii) genome data, and (iv) the DATCOV national hospital surveillance system for the whole of South Africa. For cases identified using Thermo Fisher TaqPath COVID-19 PCR, infections were designated as SGTF or non-SGTF. Disease severity was assessed using multivariable logistic regression models comparing SGTF-infected individuals diagnosed between 1 October to 30 November to (i) non-SGTF in the same period, and (ii) Delta infections diagnosed between April and November 2021.ResultsFrom 1 October through 6 December 2021, 161,328 COVID-19 cases were reported nationally; 38,282 were tested using TaqPath PCR and 29,721 SGTF infections were identified. The proportion of SGTF infections increased from 3% in early October (week 39) to 98% in early December (week 48). On multivariable analysis, after controlling for factors associated with hospitalisation, individuals with SGTF infection had lower odds of being admitted to hospital compared to non-SGTF infections (adjusted odds ratio (aOR) 0.2, 95% confidence interval (CI) 0.1-0.3). Among hospitalised individuals, after controlling for factors associated with severe disease, the odds of severe disease did not differ between SGTF-infected individuals compared to non-SGTF individuals diagnosed during the same time period (aOR 0.7, 95% CI 0.3-1.4). Compared to earlier Delta infections, after controlling for factors associated with severe disease, SGTF-infected individuals had a lower odds of severe disease (aOR 0.3, 95% CI 0.2-0.5).ConclusionEarly analyses suggest a reduced risk of hospitalisation among SGTF-infected individuals when compared to non-SGTF infected individuals in the same time period. Once hospitalised, risk of severe disease was similar for SGTF- and non-SGTF infected individuals, while SGTF-infected individuals had a reduced risk of severe disease when compared to earlier Delta-infected individuals. Some of this reducton is likely a result of high population immunity.

Background: How people perceive the coronavirus disease 2019 (COVID-19) pandemic and understand their risk can influence their health, behaviours and overall livelihood. The disease’s novelty and severity have elicited a range of attitudes and perspectives countrywide, which consequently influence the public’s adherence to public health prevention and treatment guidelines.Aim: To investigate perceptions, experiences and knowledge on COVID-19 in a communitybased cohort study.Setting: Adults living in Soweto in South Africa’s Gauteng province during the first six weeks of the national lockdown regulations (i.e. Alert Level 5 lockdown from end of March to beginning of May 2020).Methods: Participants completed a series of surveys and answered open-ended questions through telephonic interviews (n = 391). We queried their perceptions of the origins of COVID-19, understandings of the disease, personal and communal risks and its relations with the existing disease burden.Results: Findings from our sample of 391 adults show that perceptions and knowledge of COVID-19 vary across several demographic characteristics. We report moderate levels of understanding about COVID-19, prevention methods and risk, as well as exposure to major physical, psychosocial and financial stressors. Depressive symptoms, perceived infection risk and concern about COVID-19 significantly predicted COVID-19 prevention knowledge.Conclusion: Public health communication campaigns should focus on continuing to improve knowledge and reduce misinformation associated with the virus. Policymakers should consider the mental health- and non-health-related impact of the pandemic on their citizens in order to curb the pandemic in a manner that maximises well-being.

Background Many people are now living longer with HIV due to access to antiretroviral treatment. In turn, there has been an increase in the burden of hypertension and diabetes. The paucity of data on the burden of hypertension and diabetes in adults living with HIV in South Africa is a public health concern. The paper aimed to describe the prevalence and factors associated with hypertension and diabetes among adults living with HIV (ALHIV). Methods This was a secondary data analysis of the population based on the South African National HIV Prevalence, Incidence, Behaviour and Communication surveys for 2005, 2008 and 2017. Descriptive statistics were used to summarise the characteristics of the study sample. Bivariate and multivariate logistic regression analyses were used to determine factors associated with hypertension and diabetes. Results The total study population of ALHIV aged 25 years and older was 978, 1023 and 2483 for 2005, 2008 and 2017. The prevalence of hypertension showed an increasing trend at 11.8% in 2005, 9.5% in 2008 and 14.3% in 2017. The prevalence of diabetes was 3.3% in 2005, 2.8% in 2008 and 3.2% in 2017. Increased odds of hypertension among adults living with HIV were consistently associated with being female and the age group 45 years older across all the survey years, including pensioners and the sick, living in urban areas, high risk of hazardous alcohol consumption, diabetes and heart disease. Increased odds of diabetes were consistently associated with hypertension across all the survey years, including age group 45 years and older, and poor health. While having a secondary level of education and above was protective against diabetes. Conclusion The study showed that the prevalence of hypertension is high and has increased over time among adults living with HIV while the prevalence of diabetes has remained constant. Findings identified factors consistently associated with the prevalence of both diseases overtime, including contemporary risk factors that should be targeted in the integrated management of chronic disease and HIV care model.