Any time you look at cleaning products, you can probably find a message somewhere on it explaining that it's really quite effective. After all, it kills 99.99% of germs! That's practically all of them!
Well, it's not actually all of them. Germs are extremely tiny microorganisms, and you can have trillions upon trillions of them on your hands at any given time. In fact, it's pretty much guaranteed that you do. They live on every surface, they live in water, they live in the air. You can wash your hands or use hand sanitizer, but within a few minutes, the germ population on your hands will be just as high as it was before.
Of course, that's not harmful germs. There are thousands of different kinds of microorganisms out there, and most of them aren't harmful to humans at all. Even if you have harmful bacteria or viruses on your hands, they won't bother you or anyone else, simply because there aren't enough of them.
But wait, we said you have trillions on your hands, all the time. How is that not enough of them? Well, it's really because of your immune system. Your immune system is very good at fighting off viruses, bacteria, fungi, and other potential infections. There are generally a few reasons why you get sick with some kind of infection.
- The infection is present in such high quantities that it overwhelms your body's ability to fight it off.
- The infection is slightly mutated such that your immune system doesn't know how to fight it very well, and has to adapt.
- The infection is completely new to your body, such that your immune system doesn't have any idea how to fight it.
- The infection is resistant to common treatments, making it hard to fight.
If you think about it like war, you can draw an analogy. In the first case, it's like what you see in zombie movies; a small defending force fighting off overwhelming odds. Defenses get overwhelmed, they get tired and need to recharge, and that's when the constant press of attackers breaks through.
The second case is what happens with the seasonal flu. Your attackers start using different tactics that you haven't seen before. You can fight them off once you figure out what's going on, but you'll lose some soldiers along the way.
The third case is what's going on with the current coronavirus pandemic. Covid-19 comes from bats, and humans have not encountered it before. It mutated and infected humans, but since humans have never had to fight it off before, it can pretty much run rampant throughout our systems before the immune system develops a method to fight it off. In fact, much of the fatalities of Covid-19 come not from the virus itself, but from the immune system running out of control trying to fight it. It would be like your soldiers learning that eating a heavy meal made them more effective at fighting off enemies, and going all-in with binge eating until your regiment runs out of food.
The fourth case comes about with diseases like MRSA, which is a medication-resistant version of the staph infection. It's dangerous and aggressive, and your body has to struggle to fight it, and the help you give it in the form of antibiotics simply doesn't do anything. It's like giving the opponents in the war better armor.
All of this is illustrative of a particular point: bacteria and viruses on your hands rarely reach one of these points. You can have a tiny amount of MRSA on your hands and never get infected with the disease, for example.
Quantity of exposure is one of the most important factors in contracting an infection. Covid-19 is extremely contagious because even a single microscopic droplet of moisture from an infected person's breath is absolutely packed with the virus, such that breathing it in is dangerous. This is called "viral load" if you're interested in researching more about it.
This is why washing your hands or using hand sanitizer is so important, too. Keeping the viral and bacterial loads on your hands down helps to minimize any contact you could have with it.
Why Cleaners Say 99.9%
So why do hand sanitizers and other cleansers say they only kill 99.9% of germs and bacteria? There are a few different reasons for this.
The first reason is simply that cleansers can't kill everything. There are plenty of microorganisms that are not denatured – that is, torn apart – by alcohol, which is the primary ingredient in hand sanitizers. For example, norovirus, which is responsible for the stomach flu, and clostridium difficile, an intestinal germ that causes severe diarrhea, are not killed by alcohol. 
The same goes for pretty much every cleaning product or method. Bleach, for example, is very good at killing some kinds of bacteria and mold spores but doesn't do much of anything to others. Heat can kill a lot of organisms, but not all of them since some can survive temperatures that are not feasible to use to sterilize products that would, you know, melt. Even radiation, which can rip apart and kill just about anything given enough exposure, can't kill everything.
Therefore, a sanitizer cannot make the claim that it kills 100% of germs on a surface because it can't. Even the advanced formula hand sanitizers that have alcohol, soap, and other cleansers all worked into it, are not robust enough to kill everything.
There are certainly cleansers that can kill 100% of germs. The problem is, there's actually not all that much difference between germs and, say, skin cells. While you're killing germs, you can be killing your skin as well. That's why those kinds of chemicals aren't used as a hand wash.
The second reason why products say they only kill 99.9% of germs is marketing and legal liability. If a company claims that they can kill 100% of germs, and someone with an electron microscope decides to put that to the test and discovers germs on the cleansed surface, the company could be liable for false advertising. 
Now, suing a company over .01% of germs making it through a cleaning is kind of ridiculous, but one should never underestimate the limits people will go to if they think they can get a payday from a company. If slightly changing some text on a label can prevent a company from losing a lawsuit, they're certainly going to do it.
The third reason is one of physical reach. Look at your hands. You can see tiny textures to your skin, right? Little micro-wrinkles, pores where hair grows, the deep grooves around and under your nails. To you, these are tiny. To a germ, they're larger than the grand canyon. Bacteria, viruses, and other microorganisms can hide deep in these cracks, where an application of hand sanitizer might not be thorough enough to get them.
Part of the CDC's hand-washing guide (which is a process you can follow when applying hand sanitizer as well, to be thorough with its application), is making sure you give soap (or hand sanitizer) plenty of time to work its way deep into these cracks. 
The fourth reason actually has something to do with what 99.9% means. It's not actually a flat percentage; it's measuring something called the D-value, or the "decimal reduction time" for the cleaner.
The decimal reduction time is the amount of time (or the dose of a substance) necessary to kill or remove 90% of the microorganisms on a surface. A value of 1 D means a 90% reduction in germs. 1 D could be an amount of time under UV light or in a heat cleaner, it could mean exposure to ethyl alcohol or soap, or it could be another sterilization method.
90% is very different from 99.9%, though. It's based on a logarithmic scale, which is some complicated math you don't really need to know to understand the system. Think about it like this: if you leave hand sanitizer on your hands for 3 seconds, it kills 90% of the germs on your hands. If you leave it for another 3 seconds, it will kill 90% of what's left, for a total of 99% killed. If you leave it in place for yet another 3 seconds, it kills another 9%, for 99.9%. This is why hand sanitizer instructions have you rubbing the gel all over your hands for 15+ seconds, to make sure it kills as much as it can.
You might note, of course, that adding another 9 to the end of the decimal never quite brings it to 100%. There will always be some leftover germs, whether it's hidden in deep crevasses beneath your nails or in wrinkles in the skin, or it's just microorganisms that aren't killed by alcohol.
Is 99.9% Okay?
Other than the legal liability, all of those reasons indicate that hand sanitizer simply can't kill every germ on your hands. So, is that okay? Is that fine, or is it something you should worry about?
The fact is, it's fine in almost every case. Hand sanitizer is broadly used in hospital settings for a reason, and that reason is that it's generally sufficient to prevent the spread of most diseases between patients and healthcare workers.
The hand sanitizer you get for carrying around on your daily errands might not be the same kind of hand sanitizer a hospital is using, of course. Theirs tend to have foaming agents and soaps as well as alcohol. There are also plenty of hand sanitizers that don't actually contain alcohol, or that contain a low enough concentration that it's not effective. This is why you should look for hand sanitizers with at least 60-80% alcohol concentrations. 
As with any product, it's important to get the right kind of product for the job you want it to do. A hand sanitizer that doesn't have alcohol in it can work against many types of germs, and if you're generally concerned about things like the flu, they can be fine. If you're concerned about the pandemic – which many of us are – you need a product with plenty of alcohol, full stop.
Hand sanitizer also has one major drawback, and that's the fact that you aren't rinsing your hands after using it. You may kill most of the germs on your hands, but some remain, and even if they're bound up in dirt and grime, they're still there. Using soap and water is particularly effective; not just because soap destroys bacteria and viruses, but because it also rinses away the bound but not killed microorganisms as well.
Hand sanitizers also have one other limitation, which is that they only work on your hands. For germs you pick up on contact with surfaces, that's fine. The coronavirus, however, is largely spread through aerosolized moisture; that is, infected droplets that come from breathing, coughing, sneezing, sweating, and other ways your body sheds moisture into the air. This is why masks are so important; breathing in those particles bypasses your hands, so all the hand sanitizer in the world won't help you.
So, yes. A product that kills "only" 99.9% of germs is perfectly acceptable. You need to use it properly – that is, long enough for it to work – and you should still keep up with washing your hands whenever you get the chance, but there's nothing wrong with a product that kills 99.9% of germs. To fully protect yourself, you need to take every precaution you can, though. That means hand sanitizer when you can't wash your hands with soap and water (when you can, making sure to use a full 20+ second washing procedure), wearing a mask whenever you go out, and isolating yourself as much as possible.
