We demonstrated previously that expression of simian virus 40 (SV40) large T antigen (LT), without a viral origin, is sufficient to induce the hallmarks of a cellular DNA damage response (DDR), such as focal accumulation of ␥-H2AX and 53BP1, via Bub1 binding. Here we expand our characterization of LT effects on the DDR. Using comet assays, we demonstrate that LT induces overt DNA damage. The Fanconi anemia pathway, associated with replication stress, becomes activated, since FancD2 accumulates in foci, and monoubiquitinated FancD2 is detected on chromatin. LT also induces a distinct set of foci of the homologous recombination repair protein Rad51 that are colocalized with Nbs1 and PML. The FancD2 and Rad51 foci require neither Bub1 nor retinoblastoma protein binding. Strikingly, wild-type LT is localized on chromatin at, or near, the Rad51/PML foci, but the LT mutant in Bub1 binding is not localized there. SV40 infection was previously shown to trigger ATM activation, which facilitates viral replication. We demonstrate that productive infection also triggers ATR-dependent Chk1 activation and that Rad51 and FancD2 colocalize with LT in viral replication centers. Using small interfering RNA (siRNA)-mediated knockdown, we demonstrate that Rad51 and, to a lesser extent, FancD2 are required for efficient viral replication in vivo, suggesting that homologous recombination is important for high-level extrachromosomal replication. Taken together, the interplay of LT with the DDR is more complex than anticipated, with individual domains of LT being connected to different subcomponents of the DDR and repair machinery.Simian virus 40 (SV40) carries genes encoding three early proteins: large T antigen (LT), small t antigen, and 17k. LT has served as a powerful model system for understanding cellular processes, such as DNA replication and malignant transformation (1, 16). An in vitro SV40 replication system based on purified cellular factors was established long ago, which in many ways recapitulates in vivo replication (33, 71). However, although very insightful, certain aspects of DNA replication cannot be reconstructed in a test tube and remain incompletely understood. Since SV40 relies extensively on cellular replication factors, it must reprogram the cellular environment to support viral DNA replication. A key component is cell cycle reprogramming, perhaps most importantly the potent induction of S phase in quiescent cells (19).The ability of LT to induce aberrant cellular proliferation depends on binding to and inactivating key tumor suppressors like p53 and the retinoblastoma protein (pRB) family (reviewed in references 1 and 16). These interactions are also critical for oncogenic transformation and induction of tumors in a wide variety of cell types and tissues. Additional functions contribute to transformation. A functional DnaJ domain resides within the first 70 amino acids, which directs binding of the Hsc70 molecular chaperone and contributes to both oncogenic transformation and viral replication proficiency (10, ...