Using the MuPyV CNS infection model to explore early events in the pathogenesis of JCPyV-PML, we determined that brain-infiltrating CD4+ and CD8+ T cells co-express the CXCR4 and CXCR6 chemokine receptors, which act in concert to limit T cell aggregation at the infected ependyma. Here, CD4 is linked to progressive multifocal leukoencephalopathy.