The spread of infectious diseases in Indonesia has become a significant concern in health. COVID-19 contagious disease has difficulties in infection because some individuals are infected asymptomatically. Infectious diseases are modeled with a SEIR model modification with vaccinations 1 and 2, and Quarantine will produce a new approach by considering the variables and parameters of prevention so that it can suppress the rate of spread of the infectious disease COVID-19. The study will simulate a numerical analysis of the transmission model of contagious diseases solved using the Runge-Kutta order 4. The results achieved a new model with the SEIAR-V1V2Q modification, this model can predict the acceleration of the spread of the COVID-19 transmitted disease by considering asymptomatic conditions. Based on the research, modifying the SEIR model with 2-stage vaccination and quarantine measures can reduce the percentage of infection cases of susceptible individuals, especially cases of asymptomatic infection, which are cases of infected individuals without showing symptoms. Discipline in accelerating 2-stage vaccination will increase the formation of individual body immunity to strengthen unique antibodies to minimize infection with the COVID-19 virus. It can be a reference in similar cases requiring vaccination and Quarantine of infected individuals.