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We define a second Steenrod square for virtual links, which is stronger than Khovanov homology for virtual links, toward constructing Khovanov-Lipshitz-Sarkar stable homotopy type for virtual links. This induces the first meaningful nontrivial example of the second Steenrod square operator on the Khovanov homology for links in a 3-manifold other than the 3-sphere.

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