(Technicalities: viruses are not form of lives, since they cannot replicate without a host cell; bacteria are living organisms, perfectly able to replicate on their own, but they are limited to one cell).
Viruses are particularly dangerous because they don't seem to serve any useful purpose for us (unless you count "selecting the fittest humans" as a useful purpose). It is estimated that there are 10 to the 31st power viruses on this planet, compared with 10 to the 10th human beings. We are outnumbered big time. If you have trouble killing all the dozen flies that fly into your living room when you leave the patio door open, imagine trying to kill your quota of 10 to the 21st viruses. It is foolish to think that we can kill all viruses. There are only two winning strategies: 1. quarantine humans from the natural world (e.g. confining cities inside artificial domes), 2. engineer such a strong immune system that the human body will resist any virus attack of any kind.
Ironically, human society has been moving in the opposite direction. On one hand humans travel a lot more than ever, therefore getting in touch with many more viruses than ever. On the other hand, by keeping alive millions of children who would have died of all sorts of diseases and by "protecting" people with all sorts of vaccinations, we are creating a immune system that is now vulnerable to anything, from the dirt in your backyard to the water of mountain creeks.
In other words, we have both of the worst worlds: the human body is getting weaker, and it is getting easier to spread diseases.
Bacteria are far less dangerous than viruses. In fact, most bacteria are useful to us (the "commensal bacteria"). Our body contains many more bacteria cells than human cells, and we need them: they carry out vital functions for us helping us digest and even... fight viruses. Unfortunately, we tend to kill them by the millions when we use (and abuse of) antibiotics. "Antibiotic" basically means "anti-life": it kills life. An antibiotic does not discriminate between friend and foe: it kills all bacteria in your body. In the old days you would replenish your body simply by breathing them in the air and by drinking natural water (no, the water that is labeled "natural" at the supermarket is not "natural" at all). These days we diligently kill bacteria in the air and in the water so there is virtually no way to replenish our body after we exterminated them with antibiotics. (See also Revising the Myth of Longevity). Whichever term you want to use for the beneficial work of bacteria, that thing is being weakened generation after generation.
Meanwhile, the process of vaccinating people from childhood to old age is certainly saving a lot of lives but it is also making everybody's immune system much weaker. The immune system works like a muscle: the more you use it, the stronger it gets. Vaccinations that prevent the spread of a disease have a downside: de facto they prevent your immune system from "exercising". This makes your immune system more vulnerable to that kind of disease, and this means that vaccinating becomes even more vital. This is an infinite loop: the less prepared your immune system is, the more you need to vaccinate, the less prepared your immune system will be.
Ultimately, our strategy can be summed up as: we are smarter than them and we will find ways (medicines) to defeat them. This is a strategy that works with animals that are similar to us, whose lives are controlled by brains: we discover smarter ways to tame them, domesticate them, repel them, contain them, and sometimes kill them and eat them. When the battle is between brains, human brains win.
However, the longest living beings on the planet have no brain: bacteria and trees. That in itself could be an important clue. Framing the problem as a battle between human intelligence versus virus/bacteria intelligence might be completely misguided: they don't have any. This fight is not about who is smarter, just like a lion can be misguided if it thinks that the fight with the villagers that chased it away is about physical strength. Your brain does not help you live a long life: it was designed to help you woo a mate and then feed your children, and then quietly fade away. For reasons that are obscure to us, brain-less beings have been designed to live a long life. Our brains, designed for short lifespans, are fighting an uphill battle against organism designed for a long lifespan. Our strategy to defeat viruses and bacteria by devising ever smarter medicines might be as misguided as the strategy of a group of lions trying to fight humans on the basis of physical strength.
