To decide which water purification system will work for you, you need to match capabilities with requirements—horses for courses, as they say. For example, if viruses are a concern then a typical .1-micron backpacking filter wouldn't be a good choice. Say, if you were an international traveler or you worry about norovirus. Viruses are the most common cause of water-born intestinal illness and filters won't remove them and don't claim to.
There are two modern ways to kill all pathogens, including viruses. The SteriPens are one. The other is the Aquamira Water Treatment Drops. The Aquamira drops work by reacting to produce an oxygenated chemical that does the work. The reacting and treatment can easily be done in the backcountry. The whole process takes at least 20 minutes but you can keep hiking for most of that. The SteriPens work by producing sterilizing UV light and take only a few minutes. The Classic 3 can use any type of AA battery, including rechargeables or, in an emergency, readily available alkalines. You get about 150 liters from a set of lithiums. The SteriPen weighs 141 g with batteries. The 1 oz Aquamira kit weighs about 75 g and treats 115 liters; you can adjust the mix for different volumes, such as 20 oz instead of a liter.
Another option would be to use Aquatab tablets. These create the same oxygenated chemical as Aquamira drops and also take about a half hour to work. They cost about ten cents per quart of treated water whereas Aquamira costs about a penny.
The SteriPen pre-filter is a nice addition, even though it's relatively heavy. It connects to the nifty Nalgene On-The-Fly 22-oz water bottle, but imperfectly. The 40-micron filter won't remove cloudiness and certainly not pathogens. You could also use a coffee filter or even a bandanna. If you don't need to filter out pine needles and chipmunks you can jam the SteriPen directly into the filled bottle's drinking tube. If you use repurposed 590 ml energy drink bottles to hold your water, as many thru-hikers do, you can drill a 7/8” hole in a spare cap and wedge the SteriPen into it during treatment—a perfect solution, except you'll have to decide whether to use the half liter or full liter treatment options depending on clarity and source of the water.
You have to be aware that no system works on water that's in the threads of containers, and both are less effective at treating the bacterial biofilms that form on tiny particles in cloudy water. You have to take care not contaminate your purified drinking water with even a drop of untreated water in your apparatus, as some pathogens need only a few organisms to cause an infection. Be sure to dry out those threads, and don't brush your teeth with untreated water. Aquamira treated water kills pathogens that it comes into contact with during the time it is working, so you can use that to your advantage, but SteriPen treated water is always inert.
One worry about the SteriPens used to be the life of the UV discharge tube. SteriPen has addressed that with their Premium Lamp Life Pledge. When the number of treatments with your registered unit approaches 8,000 SteriPen will send you a brand new unit. That's one reason I have decided to use a SteriPen when appropriate: not because I think that I will ever use it up, but because I admire a company that stands behind its products.
You should understand some things about acquired intestinal distress. Water-born illness doesn't come on immediately; most infections take about a week or so to manifest. If illness comes on more quickly, the most likely cause is food poisoning. If illness appears on an outing, you probably were infected beforehand. The most common mode of acquiring intestinal distress is, ahem, fecal-oral transmission. Avoiding that transmission process requires diligent hand washing when preparing food in the back country, something that is seldom assiduously practiced. I suspect that nearly all clear back country water is OK to drink without treatment except that downstream from persistent human habitation, but even if you become infected, you'll be home before it hits you.
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