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We investigate the genealogy of a sample of $k\geq1$ particles chosen uniformly without replacement from a population alive at large times in a critical discrete-time Galton-Watson process in a varying environment (GWVE). We will show that subject to an explicit deterministic time-change involving only the mean and variances of the varying offspring distributions, the sample genealogy always converges to the same universal genealogical structure; it has the same tree topology as Kingman's coalescent, and the coalescent times of the $k-1$ pairwise mergers look like a mixture of independent identically distributed times. Our approach uses $k$ distinguished \emph{spine} particles and a suitable change of measure under which (a) the spines form a uniform sample without replacement, as required, but additionally (b) there is $k$-size biasing and discounting according to the population size. Our work significantly extends the spine techniques developed in Harris, Johnston, and Roberts \emph{[Annals Applied Probability, 2020]} for genealogies of uniform samples of size $k$ in near-critical continuous-time Galton-Watson processes, as well as a two-spine GWVE construction in Cardona and Palau \emph{[Bernoulli, 2021]}. Our results complement recent works by Kersting \emph{[Proc. Steklov Inst. Maths., 2022]} and Boenkost, Foutel-Rodier, and Schertzer \emph{[arXiv:2207.11612]}.