If someone wanted evidence that an intracellular pathogen was causing DNA damage, what assay would provide evidence to that effect (without sequencing the entire host genome)? The readout would have to be specific to DNA damage, and not a generalized response to an intracellular infection.
Take a look at this paper, it might help you: "Santos et al., 2006 Quantitative PCR-based measurement of nuclear and mitochondrial DNA damage and repair in mammalian cells".
Really depends on the type of DDR your looking for e.g. if your looking for DSB response then pS824-KAP1 is very specific to ATM activation in response to DSBs. There are similar phospho-subtrates you can look at in response to different types of DNA damage, so really just depends on what type of response your trying to measure...
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