SARS-CoV-2 reinfection trends in South Africa: analysis of routine surveillance data

ObjectiveTo examine whether SARS-CoV-2 reinfection risk has changed through time in South Africa, in the context of the emergence of the Beta and Delta variants DesignRetrospective analysis of routine epidemiological surveillance data SettingLine list data on SARS-CoV-2 with specimen receipt dates between 04 March 2020 and 30 June 2021, collected through South Africas National Notifiable Medical Conditions Surveillance System Participants1,551,655 individuals with laboratory-confirmed SARS-CoV-2 who had a positive test result at least 90 days prior to 30 June 2021. Individuals having sequential positive tests at least 90 days apart were considered to have suspected reinfections. Main outcome measuresIncidence of suspected reinfections through time; comparison of reinfection rates to the expectation under a null model (approach 1); empirical estimates of the time-varying hazards of infection and reinfection throughout the epidemic (approach 2) Results16,029 suspected reinfections were identified. The number of reinfections observed through the end of June 2021 is consistent with the null model of no change in reinfection risk (approach 1). Although increases in the hazard of primary infection were observed following the introduction of both the Beta and Delta variants, no corresponding increase was observed in the reinfection hazard (approach 2). Contrary to expectation, the estimated hazard ratio for reinfection versus primary infection was lower during waves driven by the Beta and Delta variants than for the first wave (relative hazard ratio for wave 2 versus wave 1: 0.75 (CI95: 0.59-0.97); for wave 3 versus wave 1: 0.70 (CI95: 0.55-0.90)). Although this finding may be partially explained by changes in testing availability, it is also consistent with a scenario in which variants have increased transmissibility but little or no evasion of immunity. ConclusionWe conclude there is no population-wide epidemiological evidence of immune escape and recommend ongoing monitoring of these trends. O_TEXTBOXBox 1O_ST_ABSWhat is already known on this topicC_ST_ABSO_LIPrior infection with SARS-CoV-2 is estimated to provide at least an 80% reduction in infection risk (1,2). C_LIO_LILaboratory-based studies indicate reduced neutralization by convalescent serum for the Beta and Delta variants relative to wild type virus (3-6); however, the impact of these reductions on risk of reinfection is not known. C_LI What this study addsO_LIWe provide two methods for monitoring reinfection trends to identify signatures of changes in reinfection risk. C_LIO_LIWe find no evidence of increased reinfection risk associated with circulation of Beta or Delta variants compared to the ancestral strain in routine epidemiological data from South Africa. C_LI C_TEXTBOX