Trends in Covid-19 Admissions and Deaths among People with Hiv in South Africa

Background: South Africa experienced five COVID-19 waves and over 90% of the population have developed immunity. HIV prevalence among adults is 19% and over 2 million people have uncontrolled viral loads, posing a risk for poor COVID-19 outcomes. Using national hospital surveillance data, we aimed to investigate trends in admission and factors associated with in-hospital COVID-19 mortality among people with HIV (PWH) in South Africa. Method(s): Data between March 5, 2020 and May 28, 2022 from the national COVID-19 hospital surveillance system, SARS-CoV-2 case linelist and Electronic Vaccine Data System were linked and analysed. A wave was defined as the period for which weekly incidence was >=30 cases/100,000 people. Descriptive statistics were employed for admissions and mortality trends. Postimputation random effect multivariable logistic regression models compared (a) characteristics of PWH and HIV-uninfected individuals, and (b) factors associated with mortality among PWH. Result(s): 68.7% (272,287/396,328) of COVID-19 admissions had a documented HIV status. PWH accounted for 8.4% (22,978/272,287) of total admissions, and 9.8%, 8.0%, 6.8%, 12.2% and 6.7% of admissions in the D614G, Beta, Delta, Omicron BA.1 and Omicron BA.4/BA.5 waves respectively. The case fatality ratio (CFR) among PWH and HIV-uninfected was 24.3% (5,584/22,978) vs 21.7% (54,110/249,309) overall, and in the respective waves was 23.7% vs 20.4% (D614G), 27.9% vs 26.6% (Beta), 26.2% vs 24.5% (Delta), 18.2% vs 9.1% (Omicron BA.1) and 16.8% vs 5.5% (Omicron BA.4/BA.5). Chronic renal disease, malignancy and past TB were more likely, and hypertension and diabetes were less likely in PWH compared to HIV-uninfected individuals. Among PWH, along with older age, male sex and presence of a comorbidity, there was a lower odds of mortality among individuals with prior SARS-CoV-2 infection (aOR 0.6;95% CI 0.4-0.8);>=1 dose vaccination (aOR 0.1;95% CI 0.1-0.1);and those admitted in the Delta (aOR 0.9;95% CI 0.8-0.9), Omicron BA.1 (aOR 0.5;95% CI 0.5-0.6) and Omicron BA.4/BA.5 (aOR 0.5;95% CI 0.4-0.7) waves compared to the D614G wave. PWH with CD4< 200 had higher odds of in-hospital mortality (aOR 1.9;95% CI 1.8-2.1). Conclusion(s): In South Africa, mortality among PWH was less likely in the Delta and Omicron waves but PWH had a disproportionate burden of mortality during the two Omicron waves. Prior immunity protected against mortality, emphasizing the importance of COVID-19 vaccination among PWH, particularly PWH with immunosuppression.

Leveraging epidemiology as a decision support tool during the COVID-19 epidemic in South Africa.

By May 2021, South Africa (SA) had experienced two 'waves' of COVID-19 infections, with an initial peak of infections reached in July 2020, followed by a larger peak of infections in January 2021. Public health decisions rely on accurate and timely disease surveillance and epidemiological analyses, and accessibility of data at all levels of government is critical to inform stakeholders to respond effectively. In this paper, we describe the adaptation, development and operation of epidemiological surveillance and modelling systems in SA in response to the COVID-19 epidemic, including data systems for monitoring laboratory-confirmed COVID-19 cases, hospitalisations, mortality and recoveries at a national and provincial level, and how these systems were used to inform modelling projections and public health decisions. Detailed descriptions on the characteristics and completeness of individual datasets are not provided in this paper. Rapid development of robust data systems was necessary to support the response to the SA COVID-19 epidemic. These systems produced data streams that were used in decision-making at all levels of government. While much progress was made in producing epidemiological data, challenges remain to be overcome to address gaps to better prepare for future waves of COVID-19 and other health emergencies.

ANATIONAL SEROPREVALENCE SURVEY of SARS-CoV-2 ANTIBODIES in SOUTH AFRICA: 2020-2021

Background: South Africa is one of the African countries most affected by the COVID-19 pandemic. SARS-CoV-2 seroprevalence surveys provide valuable epidemiological information given the existence of asymptomatic cases. We report the findings of the first nationwide household-based population estimates of SARS-CoV-2 seroprevalence among people aged 12 years and older in South Africa. Methods: The survey used a cross-sectional multi-stage stratified cluster design undertaken over two separate time periods (November 2020-February 2021 and April-June 2021) which coincided with the second and third waves of the pandemic in South Africa. The Abbott® and Euroimmun® ani-SARS CoV-2 antibody assays were used to test for SARS-CoV-2 antibodies, the latter being the final result. The survey data was weighted with final individual weights benchmarked against 2020 mid-year population estimates by age, race, sex, and province. Frequencies were used to describe characteristics of the study population and SARS-CoV-2 seroprevalence. Bivariate and multivariate logistics regression analysis were used to identify factors associated with SARS-CoV-2 seropositivity. Results: 13640 participants gave a blood sample. The SARS-CoV-2 seroprevalence using the Euroimmun assay was 19.6% (95% CI 17.9-21.3) over the study period, translating to an estimated 8 675 265 (95% CI 7 508 393-9 842 137) estimated infections among people aged 12 years and older across South Africa by June 2021. Seroprevalence was higher in the Free State (26.8%), and Eastern Cape (26.0%) provinces (Figure). Increased odds of seropositivity were associated with prior PCR testing [aOR=1.29 (95% CI: 0.99-1.66)], being female [aOR=1.28 (95% CI 1.00-1.64), p=0.048] and hypertension, [aOR=1.28 (95% CI 1.00-1.640, p=0.048]. Conclusion: These findings highlight the burden of infection in South Africa by June 2021, and support testing strategies that focus on individuals with known exposure or symptoms since universal testing is not feasible. Females and younger people were more likely to be infected suggesting need for additional strategies targeting these populations. The estimated number of infections was 6.5 times higher than the number of SARS-CoV-2 cases reported nationally, suggesting that the country's testing strategy and capacity partly explain the dynamics of the pandemic. It is therefore essential to bolster testing capacity and to rapidly scale up vaccinations in order to contain the spread of the virus in the country.

PERFORMANCE of SARS-CoV-2 ANTIBODY ASSAYS in A NATIONAL SEROSURVEY in SOUTH AFRICA

Background: Accurate and reliable serological assays are essential for epidemiological surveillance of SARS-CoV-2. Several commercial anti-SARS assays are available and use cases for serological testing includes surveillance. However, there is growing evidence of varying performance of SARS-CoV-2 assays dependent of their format. We compare the performance of 3 different assays used in a national serosurvey undertaken between April and June 2021, in South Africa before widescale vaccination roll out. Methods: Venous blood samples from participants ≥12 years were transported under cold chain to a central testing laboratory within 24 hours of collection. Samples were tested for SARS CoV-2 antibodies with the Abbott nucleocapsid (NC)-based Architect anti-SARS CoV-2 chemiluminescent microparticle immunoassay (CMIA), the EuroImmun Spike (S)-based assay and the Roche total IgG NC-based Elecsys Anti-SARS-CoV-2 electrochemiluminescence immunoassay (ECLIA) on the Cobas e411 platform. We compared antibody detection proportions. Results: 8146 participants (median age 40 years, IQR 26-55) 5.6% of whom reported ≥1 SARS-CoV-2 symptom in the preceding 3 months gave a blood sample. Samples were tested on the Abbott assay with different cut-offs:-15.5% tested positive at the 1.40 cut-off and 26.8% at the 0.49 lower cut-off. 21.6% of the samples tested positive on the Euroimmun and 39.0% tested positive on the Roche assay (Table). 286 samples were from respondents self-reporting a prior positive PCR test, and among them 149(52.1%), 156(54.6%), and 206(72.3%) were positive on the Abbott (1.40 cut-off), Euroimmun and Roche assays respectively. 116/286(40.6%) of these were positive on all three assays and with 21(7.3%) positive on Roche only. 224/286(78.3%) of those reporting prior PCR test positivity were positive at the lower Abbott cut-off, with 47(16.4%) positive on Abbott only. Conclusion: These samples collected before wide scale vaccination roll out in South Africa show variable performance of these assays with the Roche NC assay detecting more infections that both the Abbott NC assay(0.40 cut-off) and the Euroimmun S assay.This could be reflective of seroreversion previously reported with Abbott and Euroimmun, and the greater sensitivity of Roche assay targeting the more abundant NC as an epitope. Use of direct, double Antigen-sandwich-based assays that are stable and have increased sensitivity over time may be optimal to detect both natural and vaccine-induced immunity in serosurveys.