Let $X$ and $Y$ be compact hyper-Kähler manifolds deformation equivalent to the Hilbert scheme of length $n$ subschemes of a $K3$ surface. A class in $H^{p,p}(X\times Y,{\mathbb {Q}})$ is an analytic correspondence, if it belongs to the subring generated by Chern classes of coherent analytic sheaves. Let $f:H^2(X,{\mathbb {Q}})\rightarrow H^2(Y,{\mathbb {Q}})$ be a rational Hodge isometry with respect to the Beauville–Bogomolov–Fujiki pairings. We prove that $f$ is induced by an analytic correspondence. We furthermore lift $f$ to an analytic correspondence $\tilde {f}: H^*(X,{\mathbb {Q}})[2n]\rightarrow H^*(Y,{\mathbb {Q}})[2n]$, which is a Hodge isometry with respect to the Mukai pairings and which preserves the gradings up to sign. When $X$ and $Y$ are projective, the correspondences $f$ and $\tilde {f}$ are algebraic.

We prove that any hyper-Kähler sixfold $K$ of generalized Kummer type has a naturally associated manifold $Y_K$ of $\mathrm {K}3^{[3]}$ type. It is obtained as crepant resolution of the quotient of $K$ by a group of symplectic involutions acting trivially on its second cohomology. When $K$ is projective, the variety $Y_K$ is birational to a moduli space of stable sheaves on a uniquely determined projective $\mathrm {K}3$ surface $S_K$. As an application of this construction we show that the Kuga–Satake correspondence is algebraic for the K3 surfaces $S_K$, producing infinitely many new families of $\mathrm {K}3$ surfaces of general Picard rank $16$ satisfying the Kuga–Satake Hodge conjecture.

Moduli spaces of stable objects in the derived category of a $K3$ surface provide a large class of holomorphic symplectic varieties. In this paper, we study the interplay between Chern classes of stable objects and zero-cycles on holomorphic symplectic varieties which arise as moduli spaces. First, we show that the second Chern class of any object in the derived category lies in a suitable piece of O’Grady’s filtration on the $\text{CH}_{0}$-group of the $K3$ surface. This solves a conjecture of O’Grady and improves on previous results of Huybrechts, O’Grady, and Voisin. Second, we propose a candidate for the Beauville–Voisin filtration on the $\text{CH}_{0}$-group of the moduli space of stable objects. We discuss its connection with Voisin’s recent proposal via constant cycle subvarieties, and prove a conjecture of hers on the existence of special algebraically coisotropic subvarieties for the moduli space.