Recently I took a short hike over Shepherds Pass in the Eastern Sierra. I had never been over the pass and wanted to see if for myself.
Anyway, as usual, I threw a bunch of my stuff together and took off. When I got to my first water source I took out my Steripen Opti. I have never used this one as my son had been using it this summer. I soon realized the batteries weren't strong enough to give a green light that shows all is well. The lamp lit up, however, it was real weak.
I had some chlorine dioxide with me but didn't want to dig it out. Also, looking at the source I figured it was fine to drink (pack animals probably aren't going up there due to the washout) and I like to drink untreated cold water whenever I can. So I drank up.
Here is my scenario: Lets say I take a drink of untreated water that has enough giardia in it to actually reproduce and cause the expected gastrointestinal problems. I now have a problem brewing that takes about 13-14 days to appear. (I have been home for over 2 weeks with no such effects). Let's assume I become less lazy, and at the next stop I use my drops and treat my water. After the waiting period I drink my properly treated water.
So, my question is this: when the treated water enters my stomach would it also have the ability to treat the infected water, killing the parasites I had earlier ingested?
Just wondering if anyone has an opinion or even better some actual knowledge of such things.

