Modelling the transmission dynamics of a multi-strain SARS-CoV-2  epidemic with vaccination for an emerging strain

Abstract Background: The SARS-CoV-2 virus that causes COVID-19 has severely impacted the health, economic and social status of Ugandans and people globally. Its mutations result into numerous deadly variants which are constantly emerging in short time intervals. The rise of these variants has led to increased virus transmissibility, disease severity and reduction in vaccine effectiveness. To-date, it is unclear which direction the pandemic is likely to take in the next few years.Methods: This study developed a deterministic two strain Susceptible-Exposed-Infectious-Recovered-Vaccinated (SEIR-V) mathematical model to describe the transmission dynamics of these SARS-CoV-2 variants. The model considers 10 compartments to deal with both strain one and strain two (emerging strain). Basic reproductive number R0 is computed and both local and global stability analysis of the disease free equilibrium investigated qualitatively. The model's bifurcation analysis revealed a forward type.Results: Simulation results indicate a 17.17 % increase in peak infections for strain two dominance as compared to strain one dominance. Further, a 10-fold increase in vaccination rate would lead to 16.98 % reduction in strain two peak infections. Furthermore, periodically administering booster doses within 18-24 months is recommended. Compulsory face mask usage and early hospitalization/isolation of symptomatic individuals would lead to 14.2 % and 16.98 % decrease in symptomatic infections respectively.Conclusions: Our results suggest that continuous vaccination (at a higher rate) of populations is still vital in the fight against COVID-19. Besides, results on face mask usage and hospitalization of symptomatic individuals provides valuable information that can be used to support emergency preparedness for future SARS-CoV-2 outbreaks.