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Physics based control variates are widely used to reduce the numerical noise and, consequently, the computational cost, of global particle-in-cell simulations. Nevertheless, when plasma profiles change significantly during the nonlinear evolution of the system, control variates based on fixed background distribution functions become less and less effective. Recently, an adaptive scheme has been proposed for the code ORB5, based on an adaptive Maxwellian with time-evolving density and temperature profiles. In this work, we propose an alternative time-varying control variate to study deviation from Maxwellian equilibria based on the Phase-Space Zonal Structures (PSZS) transport theory. In particular, we show how the information provided by the finite element projection of the full distribution function can be used to adjust and update the control variate, i.e. the background distribution function, during the nonlinear evolution of the system for Maxwellian and non-Maxwellian plasma reference states.