Estimated SARS-CoV-2 infection rate and fatality risk in Gauteng Province, South Africa: a population-based seroepidemiological survey

Abstract

Background Limitations in laboratory testing capacity undermine the ability to quantify the overall burden of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. Methods We undertook a population-based serosurvey for SARS-CoV-2 infection in 26 subdistricts, Gauteng Province (population 15.9 million), South Africa, to estimate SARS-CoV-2 infection, infection fatality rate (IFR) triangulating seroprevalence, recorded COVID-19 deaths and excess-mortality data. We employed three-stage random household sampling with a selection probability proportional to the subdistrict size, stratifying the subdistrict census-sampling frame by housing type and then selecting households from selected clusters. The survey started on 4 November 2020, 8 weeks after the end of the first wave (SARS-CoV-2 nucleic acid amplification test positivity had declined to <10% for the first wave) and coincided with the peak of the second wave. The last sampling was performed on 22 January 2021, which was 9 weeks after the SARS-CoV-2 resurgence. Serum SARS-CoV-2 receptor-binding domain (RBD) immunoglobulin-G (IgG) was measured using a quantitative assay on the Luminex platform. Results From 6332 individuals in 3453 households, the overall RBD IgG seroprevalence was 19.1% [95% confidence interval (CI): 18.1–20.1%] and similar in children and adults. The seroprevalence varied from 5.5% to 43.2% across subdistricts. Conservatively, there were 2 897 120 (95% CI: 2 743 907–3 056 866) SARS-CoV-2 infections, yielding an infection rate of 19 090 per 100 000 until 9 January 2021, when 330 336 COVID-19 cases were recorded. The estimated IFR using recorded COVID-19 deaths (n = 8198) was 0.28% (95% CI: 0.27–0.30) and 0.67% (95% CI: 0.64–0.71) assuming 90% of modelled natural excess deaths were due to COVID-19 (n = 21 582). Notably, 53.8% (65/122) of individuals with previous self-reported confirmed SARS-CoV-2 infection were RBD IgG seronegative. Conclusions The calculated number of SARS-CoV-2 infections was 7.8-fold greater than the recorded COVID-19 cases. The calculated SARS-CoV-2 IFR varied 2.39-fold when calculated using reported COVID-19 deaths (0.28%) compared with excess-mortality-derived COVID-19-attributable deaths (0.67%). Waning RBD IgG may have inadvertently underestimated the number of SARS-CoV-2 infections and conversely overestimated the mortality risk. Epidemic preparedness and response planning for future COVID-19 waves will need to consider the true magnitude of infections, paying close attention to excess-mortality trends rather than absolute reported COVID-19 deaths.

South African Population Immunity and Severe Covid-19 with Omicron Variant

“…We previously conducted a population-wide seroepidemiological survey in Gauteng that was completed on January 22, 2021. 9 We found that 19.1% of the population were anti-RBD IgG seropositive, a value that ranged from 5% to 43% across provincial sub-districts. 9 Since that time, South Africa has experienced a third wave of Covid-19 from April 7 to November 1 that was largely due to the Delta variant, which out-competed the Beta variant.…”

“…This survey included the same households sampled during our previous survey, which was undertaken from November 4, 2020, to January 22, 2021, 9 nine weeks after the onset of the second wave of Covid-19 in Gauteng Province, which was dominated by the Beta variant. Details of the previous survey, including the sampling framework used, have been published 9 and are summarized in the Supplementary Methods section of the Supplementary Appendix.…”

“…This survey included the same households sampled during our previous survey, which was undertaken from November 4, 2020, to January 22, 2021, 9 nine weeks after the onset of the second wave of Covid-19 in Gauteng Province, which was dominated by the Beta variant. Details of the previous survey, including the sampling framework used, have been published 9 and are summarized in the Supplementary Methods section of the Supplementary Appendix. In the survey reported here, which was conducted from October 22 to December 9, 2021, an additional 10% of households were sampled in the same clusters to accommodate for possible non-participation, out-migration, and death of individuals since the previous survey.…”

“…The survey was powered to evaluate seropositivity to SARS-CoV2 at the district and sub-district level. Demographic and epidemiologic data were collected using an electronic questionnaire, 9 as detailed in the Supplementary Methods.…”

“…Sample size justification and random household repeat sampling methods of households in our previous survey have been published 9 and are summarized in the Supplementary Methods section of the Supplementary Appendix, together with methodology for analyses of associations with seropositivity using generalized linear models with log link to estimate risk ratios (RR). These were unadjusted, univariable analyses for each risk factor.…”