Because DRACOs contain a non-human component, it is very likely that they will induce a strong immune response.
On the theory side, DRACOs are mostly made from parts of two existing human proteins. The only non-human component is a very short peptide (roughly 9 to 11 amino acids), which is a transduction tag. Based on this, while some immunogenic response is possible, as with all drugs, the odds of it being significant are small. It's certainly much safer and less immunogenic than current approaches that use entire active viruses to deliver payloads inside cells.
On the practical side, the mice that were treated with DRACO in the 2011 study showed no signs of either toxicity or immunogenecity, in spite of the relatively high doses they received.
Viruses sometimes infect large numbers of cells. If DRACOs succeeded in killing all human cells with viruses in them, that could mean killing very large numbers of human cells, potentially posing substantial health risks.
This is a valid concern. One of the ways that VTose is different from DRACO is that we have several potential solutions. I can't say too much more at the moment, though, other that this is something we've given considerable thought and attention to.
Nature could have evolved a mechanism for triggering apoptosis in cells with dsRNA, but appears not do it naturally.
Yes, nature could have done that -- and it did:
You can see PKR in the middle of the diagram, attached to dsRNA, which triggers FADD, then Caspase 8, which causes apoptosis.
The problem with this pathway is that viruses like to interfere with it. For example, Caspase 8 is a common target:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4515451/
There is a risk that some cells may naturally have enough dsRNA that they could potentially be attacked by DRACO despite being healthy. The proteins used in the DRACO system are most strongly activated by long dsRNA which is intended to make the mechanism specific for viruses. However, short dsRNA of 11-16 nucleotides can bind to the dsRNA binding sites and activate the proteins under some conditions.
Activation of the apoptosis requires binding of two molecules of DRACO to dsRNA, as shown in the above diagram for "regular" PKR. This requires at least 30 to 50 base pairs of dsRNA. Short segments don't and can't bind. If they did, they would activate PKR in healthy cells, along with all of its downstream effects. Uninfected mammalian cells generally do not produce dsRNA longer than 21 to 23 base pairs.
Harmless viruses in cells could be targeted by DRACOs as well, posing additional risk (i.e., widespread cell death).
I would like to know which viruses the author considers harmless. There are viruses like CMV and EBV that often produce subclinical symptoms, but there's also clear evidence that they're harmful. The widespread cell death issue was addressed earlier.
Bacteriophages are viruses that attack bacteria, and may be helpful as a result. DRACO doesn't affect bacteriophages.