Estimation of Shedding Time in Laboratoryconfirmed COVID-19 Cases in South Africa, 2020

ABSTRACT

Introduction/ Background: South Africa recorded its first COVID-19 case on 5 March 2020 and continues to report the largest number of cases in Africa. Determining viral shedding time is crucial in understanding COVID-19 transmission dynamics in South Africa. We aimed to estimate viral shedding time among laboratoryconfirmed COVID-19 cases in South Africa. Methods: We performed a cross-sectional analytic study using COVID-19 data collected in 2020, obtained from the NMCList and DATCOV systems. These platforms report laboratory-confirmed and hospitalized COVID-19 patients, respectively. The study consisted of laboratory-confirmed COVID-19 patients with repeat positive PCR tests (at least two positive PCR test results) and who subsequently tested negative. We defined shedding time as the period from the first positive PCR test to the last positive test prior to a first negative PCR test result. To determine the association between shedding time and predictor variables, multivariate analysis was conducted and a p-value <0.05 was considered statistically significant. Results: We included 2752 cases. About 39.9% (1099/2752) of participants were inpatients and 60.1% (1653/2752) outpatients. The median shedding time was 17 days (range 1-128). There was no significant difference in shedding time between males (median 16 days, range 1-128) and females (median 17 days, range 1- 94) and between inpatients (median 16 days, range 1-108) and outpatients (median 17 days, range 1- 128). Individuals aged 0-4 years had the lowest shedding time (median 14 days, range 1-72). After adjusting for age, sex and province, shedding time was shorter for admitted cases compared to outpatients (coefficient -0.14, CI -0.24 - -0.03, Pvalue 0.014). Impact Our results will assist in refining COVID-19 infection control strategies and assist in the interpretation of repeat positive COVID-19 PCR tests over time. These results may also be used in facilitating early treatment and intervention, leading to a decrease in the incidence and mortality due to coronavirus disease. Conclusion: The duration of viral shedding within the population of South Africa varies from 1 to 128 days. Admission status is associated with SARS-CoV-2 shedding time. Our findings indicate that infection control strategies should take into account factors affecting shedding time such as disease severity.