Modelling the spread of COVID-19 in South Africa using stratified compartmental models in the period March 2020 - August 2020

Abstract

The novel coronavirus strand (SARS-CoV-2) first appeared in Wuhan, China in December 2019 and caused the respiratory syndrome COVID-19. A unique feature of COVID-19 is its non-uniform effect on populations. The effects of COVID-19 are more severe amongst older age groups and people with co-morbidities as seen by the higher mortality, infection and hospitali sation rates observed amongst these groups. This study models the spread of COVID-19 in South Africa between March-August 2020 using stratified compartmental models to capture this population heterogeneity. To understand the unique dynamics of COVID-19, an age stratified and co morbidity stratified compartmental model was built with additional com partments and parameters. A sensitivity analysis was then performed to determine the models’ sensitivity to initialisation date and lockdown level to determine the optimal pandemic start date and to identify the effects of harsh lockdown restrictions on infections, hospitalisations and deaths. A parameter sensitivity analysis was also conducted to determine the pa rameters that needed to be re-estimated to improve model accuracy and to identify the age groups which were driving infections, hospitalisations, and deaths. These analyses showed that a prolonged harsh lockdown would have reduced infections by approximately 46% and delayed the infection peak by 4-6 months. The analyses also showed that hospitalisations were driven by the 61-75 age group while infections and deaths were driven by the 76-90 age group. In addition, the model was most sensitive to infection duration, death rate and proportion of asymptomatic infection. These parameters were then re-estimated using Gauteng hospitalisation data and literature to account for the effects of age and co-morbidity and a χ 2 Goodness of Fit test proved that making parameters age/co-morbidity dependent improved the accuracy of all models