Estimation of vaccine effectiveness against SARS-CoV-2-associated hospitalization using sentinel surveillance in South Africa.

BACKGROUND: COVID-19 vaccine effectiveness (VE) studies leveraging systematic surveillance in sub-Saharan Africa are limited. We assessed the effectiveness of two vaccines (Pfizer BNT162b2 and Johnson & Johnson Ad26.COV2.S) against SARS-CoV-2-associated hospitalization in South African adults aged ≥18 years. METHODS: We conducted a test-negative case-control study using pneumonia surveillance data in South Africa. Inpatients with physician-diagnosed lower respiratory tract infection or suspected COVID-19, testing SARS-CoV-2 positive or negative from June 2021-March 2022, were cases or controls, respectively. Fully vaccinated individuals received one Ad26.COV2.S dose or two BNT162b2 doses ≥14-days before enrollment. VE was estimated using multivariable logistic regression for Delta- and Omicron BA.1/BA.2-predominant periods, stratified by age and HIV status. RESULTS: The study included 925 cases and 1890 controls; 38 (4%) cases and 186 (10%) controls were fully vaccinated with BNT162b2, and 30 (3%) cases and 94 (5%) controls with Ad26.COV2.S. The vaccine effectiveness of BNT162b2 against SARS-CoV-2-associated hospitalization over Delta and Omicron BA.1/BA.2 periods was 91% (95% CI: 52%, 98%) and 33% (-16%, 86%), respectively. The vaccine effectiveness of Ad26.COV2.S against hospitalization over Delta and Omicron BA.1/BA.2 periods was 72% (-36% ,94%), and -19% (-130%, 39%), respectively. The vaccine effectiveness of BNT162b2 against hospitalization over the Delta period was 94% (50%, 99%) and 89% (27%, 98%) among adults aged ≥60 years and HIV-uninfected, respectively. CONCLUSIONS: The BNT162b2 vaccine was effective against SARS-CoV-2-associated hospitalization during the Delta period for adults aged ≥18 years, ≥60 years and those HIV-uninfected. VE for Ad26.COV2.S was inconclusive, potentially due to limited sample size or residual confounding. These findings highlight the utility of sentinel surveillance for estimating VE.

Changing Epidemiology of COVID-19 in Children and Adolescents Over Four Successive Epidemic Waves in South Africa, 2020-2022.

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 <1 year. Weekly admission rates for children <1 year (169/100,000) exceeded rates in adults (124/100,000) in the fourth wave. The odds of severe COVID-19 in all admitted cases were lower in the fourth wave versus the third wave in each age group, but they were twice as high in admitted cases with at least one comorbidity than those without. CONCLUSIONS: The admission rate for children <5 years was higher in the fourth wave than in previous waves, but the overall outcomes were less severe. However, children with at least one comorbidity had increased odds of severe disease, warranting consideration of prioritizing this group for vaccination.

Clinical severity of SARS-CoV-2 Omicron BA.4 and BA.5 lineages compared to BA.1 and Delta in South Africa.

Omicron lineages BA.4 and BA.5 drove a fifth wave of COVID-19 cases in South Africa. Here, we use the presence/absence of the S-gene target as a proxy for SARS-CoV-2 variant/lineage for infections diagnosed using the TaqPath PCR assay between 1 October 2021 and 26 April 2022. We link national COVID-19 individual-level data including case, laboratory test and hospitalisation data. We assess 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 (aOR 1.24, 95% CI 0.98-1.55) and severe outcome (aOR 0.72, 95% CI 0.41-1.26) compared to BA.1-infected individuals. Newly emerged Omicron lineages BA.4/BA.5 showed similar severity to the BA.1 lineage and continued to show reduced clinical severity compared to the Delta variant.

Early assessment of the clinical severity of the SARS-CoV-2 omicron variant in South Africa: a data linkage study.

BACKGROUND: The SARS-CoV-2 omicron variant of concern was identified in South Africa in November, 2021, and was associated with an increase in COVID-19 cases. We aimed to assess the clinical severity of infections with the omicron variant using S gene target failure (SGTF) on the Thermo Fisher Scientific TaqPath COVID-19 PCR test as a proxy. METHODS: We did data linkages for national, South African COVID-19 case data, SARS-CoV-2 laboratory test data, SARS-CoV-2 genome data, and COVID-19 hospital admissions data. For individuals diagnosed with COVID-19 via TaqPath PCR tests, infections were designated as either SGTF or non-SGTF. The delta variant was identified by genome sequencing. Using multivariable logistic regression models, we assessed disease severity and hospitalisations by comparing individuals with SGTF versus non-SGTF infections diagnosed between Oct 1 and Nov 30, 2021, and we further assessed disease severity by comparing SGTF-infected individuals diagnosed between Oct 1 and Nov 30, 2021, with delta variant-infected individuals diagnosed between April 1 and Nov 9, 2021. FINDINGS: From Oct 1 (week 39), 2021, to Dec 6 (week 49), 2021, 161 328 cases of COVID-19 were reported in South Africa. 38 282 people were diagnosed via TaqPath PCR tests and 29 721 SGTF infections and 1412 non-SGTF infections were identified. The proportion of SGTF infections increased from two (3·2%) of 63 in week 39 to 21 978 (97·9%) of 22 455 in week 48. After controlling for factors associated with hospitalisation, individuals with SGTF infections had significantly lower odds of admission than did those with non-SGTF infections (256 [2·4%] of 10 547 vs 121 [12·8%] of 948; adjusted odds ratio [aOR] 0·2, 95% CI 0·1-0·3). After controlling for factors associated with disease severity, the odds of severe disease were similar between hospitalised individuals with SGTF versus non-SGTF infections (42 [21%] of 204 vs 45 [40%] of 113; aOR 0·7, 95% CI 0·3-1·4). Compared with individuals with earlier delta variant infections, SGTF-infected individuals had a significantly lower odds of severe disease (496 [62·5%] of 793 vs 57 [23·4%] of 244; aOR 0·3, 95% CI 0·2-0·5), after controlling for factors associated with disease severity. INTERPRETATION: Our early analyses suggest a significantly reduced odds of hospitalisation among individuals with SGTF versus non-SGTF infections diagnosed during the same time period. SGTF-infected individuals had a significantly reduced odds of severe disease compared with individuals infected earlier with the delta variant. Some of this reduced severity is probably a result of previous immunity. FUNDING: The South African Medical Research Council, the South African National Department of Health, US Centers for Disease Control and Prevention, the African Society of Laboratory Medicine, Africa Centers for Disease Control and Prevention, the Bill & Melinda Gates Foundation, the Wellcome Trust, and the Fleming Fund.

Perceptions, risk and understandings of the COVID-19 pandemic in urban South Africa.

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 community-based 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.

Trends, prevalence and factors associated with hypertension and diabetes among South African adults living with HIV, 2005-2017.

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.