Yes, viruses like EBV, HIV, and some HHV (I forgot which one) produce proteins that can open endoplasmic reticulum (ER) receptors that release Calcium; if those stores are emptied the cell opens calcium channels in the plasma membrane (through which, I guess, the virus can send its DNA/RNA). The released calcium from the ER can be taken up by the mitochondrion which, in turn, can produce autophagy signals. I can't remember exactly (if increased or decreased), but ATP plays a role here. (If it was decreased ATP, that would mean inhibited kinases, amongst others, I guess.)
There are certainly other pathways that a virus can use. May depend on the virus.
I don't know how it is with bacteria though.
When I read this my sponatenous thought was viruses know exactly how the signaling pathways work - we don't (yet).