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The focus of our work is dispersive, second-order effective model describing the low-frequency wave motion in heterogeneous (e.g.~functionally-graded) media endowed with periodic microstructure. For this class of quasi-periodic medium variations, we pursue homogenization of the scalar wave equation in $\mathbb{R}^d$, $d\geqslant 1$ within the framework of multiple scales expansion. When either $d=1$ or $d=2$, this model problem bears direct relevance to the description of (anti-plane) shear waves in elastic solids. By adopting the lengthscale of microscopic medium fluctuations as the perturbation parameter, we synthesize the germane low-frequency behavior via a fourth-order differential equation (with smoothly varying coefficients) governing the mean wave motion in the medium, where the effect of microscopic heterogeneities is upscaled by way of the so-called cell functions. In an effort to demonstrate the relevance of our analysis toward solving boundary value problems (deemed to be the ultimate goal of most homogenization studies), we also develop effective boundary conditions, up to the second order of asymptotic approximation, applicable to one-dimensional (1D) shear wave motion in a macroscopically heterogeneous solid with periodic microstructure. We illustrate the analysis numerically in 1D by considering (i) low-frequency wave dispersion, (ii) mean-field homogenized description of the shear waves propagating in a finite domain, and (iii) full-field homogenized description thereof. In contrast to (i) where the overall wave dispersion appears to be fairly well described by the leading-order model, the results in (ii) and (iii) demonstrate the critical role that higher-order corrections may have in approximating the actual waveforms in quasi-periodic media.