This problem seems rampant and growing.
My tank experienced a complete clam wipeout 3 months ago. In light of how wide-spread this problem is, and that I can't think of how toxins were introduced, I highly doubt it was a clam-specific toxin/toxicant. Clam deaths were rapid, without much time between symptoms and death. A perfectly healthy clam will first begin gaping. Some people report mucus secretions through its exhalant, but I did not observe this. Shortly thereafter, the clam's mantle shows signs of detachment from the shell (severe gaping), and mortality ensues. The elasped time between symptom and death is between 2 and 48 hours .... very fast. And once one clam in a closed system succombs to the disease, all in the system quickly die within a very short amount of time (< two weeks). It's a devasting disease, whatever the origin may be.
People have blamed Phonapei clams as the vector. While this may be true, my clams died even although no new clams were introduced for several months. What led to my mass mortality was an introduction of a coral. This leads me to believe that the pathogen is water-bourne and can be transmitted via very small volume of saltwater or via other organisms. Further complicating the situation, it can exist in the water for weeks after the initial outbreak; I added 2 more clams about 5 weeks later, and both succumbed to the same disease in a short matter of time.
In light of my experiences, advice given on other boards for quarentine and/or not buying Phonapei clams as a safeguard against this disease would seem to be ineffective. If the infected clam's water touches any system's water during it's chain of custody (collector, distributor, wholesaler, LFS, etc.), I believe that water to be tainted. You can imagine how widespread this disease has become if this is true.
Now the important question remains: How long does this pathogen stay in the water without a proper host? And are there any effective treatments?
I hear analysis is currently being done on infected clams, and results will be available shortly. If I find out anything, i'll post them here. People have also suggested that this disease has been previously identified as a Vibrio bacterium (supposed Knop isolated the pathogen). I haven't verified this, but it seems plausible.