Severity and inpatient mortality of COVID-19 pneumonia from Beta variant infection: a clinical cohort study in Cape Town, South Africa (preprint)

ABSTRACT Background The SARS-CoV-2 Beta variant, associated with immune escape and higher transmissibility, drove a more severe second COVID-19 wave in South Africa. Individual patient level characteristics and outcomes with the Beta variant are not well characterized. Methods We performed a retrospective cohort study comparing disease severity and inpatient mortality of COVID-19 pneumonia between the first and second wave periods at a referral hospital in Cape Town, South Africa. Beta variant infection was confirmed by genomic sequencing. Outcomes were analyzed with logistic regression and accelerated failure time models. Results 1,182 patients were included: 571 during the first wave period and 611 from the second wave. Beta variant accounted for 97% of infections in the second wave. There was no difference in crude in-hospital mortality between wave periods (first wave 22.2%, second wave 22.1%; p = 0.9). Time to death was decreased with higher weekly hospital admissions (16%; 95% CI, 8 to 24 for every 50-patient increase), age (18%; 95% CI, 12 to 24 for every 10-year increase) and hypertension (31%; 95% CI, 12 to 46). Corticosteroid use delayed time to death by 2-fold (95% CI, 1.5 to 3.0). Admission during the second wave decreased time to death after adjustment for other predictors, but this did not reach statistical significance (24%; 95% CI, 47 to -2). There was no effect of HIV on survival. Conclusions There was a trend towards earlier mortality during the second COVID-19 wave driven by the Beta variant, suggesting a possible biological basis. Use of oral prednisone was strongly protective. Key points In Cape Town, South Africa, the second wave of COVID-19, dominated by the Beta variant, was associated with decreased time to inpatient death after adjustment for age, comorbidities, steroid use, and admission numbers. Use of oral prednisone was strongly protective.

Sentinel seroprevalence of SARS-CoV-2 in the Gauteng province, South Africa August to October 2020. (preprint)

Background: Estimates of prevalence of anti-SARS-CoV-2 antibody positivity (seroprevalence) are for tracking the Covid-19 epidemic and are lacking for most African countries. Objectives: To determine the prevalence of antibodies against SARS-CoV2 in a sentinel cohort of patient samples received for routine testing at tertiary laboratories in Johannesburg, South Africa Methods: This sentinel study was conducted using remnant serum samples received at three National Health Laboratory Services laboratories situated in the City of Johannesburg (COJ) district, South Africa. Collection was from 1 August until the 31 October 2020. We extracted accompanying laboratory results for haemoglobin A1c, creatinine, HIV, viral load, and CD4+ T cell count. An anti-SARS -CoV-2 targeting the nucleocapsid (N) protein of the coronavirus with higher affinity for IgM and IgG antibodies was used. We reported crude as well as population weighted and test adjusted seroprevalence. Multivariate logistic regression method was used to determine if age, sex, HIV and diabetic status were associated with increased risk for seropositivity. Results: A total of 6477 samples were analysed; the majority (5290) from the COJ region. After excluding samples with no age or sex stated, the model population weighted and test adjusted seroprevalence for COJ (N=4393) was 27.0 % (95% CI: 25.4-28.6%). Seroprevalence was highest in those aged 45-49 [29.8% (95% CI: 25.5-35.0 %)] and in those from the most densely populated areas of COJ. Risk for seropositivity was highest in those aged 18-49 as well as samples from diabetics (aOR =1.52; 95% CI: 1.13-2.13; p=0.0005) and (aOR=1.36; 95% CI: 1.13-1.63; p=0.001) respectively. Conclusion: Our study conducted during the first wave of the pandemic shows high levels of infection among patients attending public health facilities in Gauteng. 274/400 Words