Orbit-following simulations of fast-ion transport and losses with time-dependent electromagnetic perturbations are performed to clarify the roles of Alfvén eigenmodes (AEs) and the low-frequency magnetohydrodynamic (MHD) mode observed in the kinetic-MHD hybrid simulation of AE bursts in the Large Helical Device. Fast-ion pressure profile flattening in the kinetic-MHD hybrid simulation can be reproduced by an orbit-following simulation with only the primary single AE of the time-dependent amplitude following the kinetic-MHD hybrid simulation result, while orbit-following simulations with constant AE amplitude of average level during AE burst cannot reproduce the fast-ion pressure profile flattening observed. The effects of other modes are negligible on the fast-ion pressure profile flattening. The fast-ion losses in kinetic-MHD hybrid simulation can be reproduced by an orbit-following simulation with time-dependent amplitude when the low-frequency MHD mode is considered in addition to multiple AEs. This indicates the synergetic effect of multiple AEs and the low-frequency MHD mode on fast-ion losses.