It's great to look at studies by CDC and WHO, but it all needs to be taken in context.
This is a hot topic in my mind. I spent my first five years of backpacking without treating any water. Then a friend read an article about Giardia, USFS started posting warnings based on possibilities, and Katadyn stepped in with advertising in the magazines. In the 20+ years since I have always treated the water by microfiltration and/or chemical treatment. A few weeks ago I took my kids on their first backpack trip and I pumped all their water.
I have used the same protocol whether the water came from the Magdalena River downstream of Bogota Colombia, taps in Baja or 33 degree snowmelt at 12,000 feet in the Sierra.
Recent reading of articles specific to the high Sierra between Yosemite and Sequoia indicate that the panic for this region was mostly unfounded. Here are my conclusions:
Largest risk is poor sanitation habits by members of your own party. Using alcohol hand sanitizer after pooping and before touching food will eliminate more cases of the runs than all the water purification technology on earth. My solo hike eliminates this risk since I can't catch anything from myself.
For water borne pathogens these are some generalized risks:
Viruses: No risk. Nada. Zilch. This is 10,000 feet in the Sierra, not at the Ganges' mouth!
Cryptosporidia: No reported cases, no measured contamination.
Giardia: Drumroll please... Insignificant risk, or at least close to it.
Bacteria: Still low, but by far the most likely source of problems.
With this information, my decision whether or not to purify, and how to purify, has changed. Best sources for water are different with lake outlets having fewer bacteria than inlets. If you eliminate concern over viruses and cysts then the performance of chemical purification changes. Bacteria is killed quickly, and the reduced performance in colder water is offset by the lower liklihood that significant numbers of bacteria will be found in colder water.
Luckily there is no commercial cattle or sheep grazing upstream of the whole JMT. Tests of pack stock manure showed fairly low, but still significant rates of potentially harmful E-coli bacteria.
My plan for water treatment on my JMT hike is this:
1. Drink smart. Pay attention to the route water took and whether heavy human use, pack stock use, or pack stock grazing is likely upstream.
2. Chemically treat any suspect water, but use contact time based on killing bacteria not cysts.
3. Presume specific location contamination identified by Derlet to still exist, avoid these and similar areas.
4. Drink heavily from good water sources, avoid or treat suspect sources.
5. Treat all water between Yosemite Valley and Tuolume Meadows; near Blaney Meadows; and whenever I have to draw water from a source that has significant use and trail crossings upstream.
I'll let you all know how it worked out.
Here are my sources, plus lots of unsubstantiated forum banter. Remember this only applies to the national park and USFS wilderness areas near the John Muir Trail.
Abstract only for the following article free online- I haven't seen the full text:
Risk Factors for Coliform Bacteria in Backcountry Lakes and Streams in the Sierra Nevada Mountains: A 5-Year Study
Robert W. Derlet, MD; K. Ali Ger; John R. Richards, MD; James R. Carlson, PhD. Wilderness and Environmental Medicine: Vol. 19, No. 2, pp. 82–90.
Complete text for the following can be found online:
Giardia Lamblia and Giardiasis With Particular Attention to the Sierra Nevada By Robert L. Rockwell, PhD. Sierra Nature Notes, Volume 2, January 2002 (rev. May 2002)
High Sierra Water: What is in the H20? Robert W. Derlet, MD. Sierra Nature Notes, Volume 3, April 2004
Coliform Bacteria in Sierra Nevada Wilderness Lakes and Streams: What Is the Impact of Backpackers, Pack Animals, and Cattle?. Derlet, Robert W., Carlson, James R. 2006: Wilderness and Environmental Medicine: Vol. 17, No. 1, pp. 15–20.
An Analysis of Wilderness Water in Kings Canyon, Sequoia, and Yosemite National Parks for Coliform and Pathologic Bacteria. Derlet, Robert W., Carlson, James R. 2004: Wilderness and Environmental Medicine: Vol. 15, No. 4, pp. 238–244.
Coliform and Pathologic Bacteria in Sierra Nevada National Forest Wilderness Area Lakes and Streams. Derlet, Robert W., Carlson, James R., Noponen, Mikla N. 2004: Wilderness and Environmental Medicine: Vol. 15, No. 4, pp. 245–249
Derlet, Robert Wayne, Carlson, James Reynolds. 2002: An Analysis of Human Pathogens Found in Horse/Mule Manure Along the John Muir Trail in Kings Canyon and Sequoia and Yosemite National Parks. Wilderness and Environmental Medicine: Vol. 13, No. 2, pp. 113–118.