The goal of this study is to analyze and control the new variant JN.1 under generalized incidence rate for low immune individuals by taking combine measures of vaccination as well as quarantine. By incorporating vaccination and quarantine together with generalized incidence rate a new mathematical model is developed based on generated novel hypothesis. To ascertain the stable status of the recently constructed SEVIQR system which is analysis both qualitatively and quantitatively to understand the dynamics of spread as well as control under bounded domain including bifurcation analysis. Stability analysis have been derived on local as well as global scale using Lyapunov’s first derivative functions to evaluate the overall effects of disease propagation and control. The existence and positive solutions property is also derived under non local operator. To ensure reliable bounded findings, the boundedness and uniqueness are examined, those are necessary characteristics for epidemic models. We use Lipschit’z conditions and linear growth to fully validate the global derivative that characterizes the rate of change of disease impact on each sub-compartment. The bounded approximate solutions for new invariant JN.1 derived sing Mittag-Leffler kernel with fractal fractional operator for continuous monitoring. Simulations are derived using MATLAB coding to observe the real impact of spread as well as control of virus caused by new variant JN.1 with generalized incidence rate, a variety of factors are imposed with constant monitoring. To observe the asymptomatic and symptomatic consequences of the corona virus illness under new variant JN.1, simulations are developed with combine actions of vaccination as well as quarantine effects for low immunity people to capture the disease’s true behavior. To comprehend how the virus spreads for low immune individuals and to create efficient control plans based on the results that make sense such investigations are valuable.