In real life, viruses are only tentatively referred to as an organisms because they cannot really exist comfortably or reproduce outside of the host. On TV, shows will consistently refer to any disease-causing pathogen as a virus. You could be more general and use the all-inclusive "pathogen", but "virus" just sounds cooler and scarier.
In Real Life, viral particles are basically stripped-down delivery packages for DNA; they don't have any ability to grow or replicate by themselves and need to hijack the host cells' replicative machinery to accomplish that. So spread of a virus is dependent on infecting 1) a living cell, 2) of the right species (most viruses are specialized to one or a few species). Furthermore, most viruses don't last very long outside of the cell, and thus require close contact between sick and healthy individuals. A few can be transmitted through the air (in the case of human diseases, usually in droplets of moisture produced when coughing or sneezing), but only for the distance of a few meters.
A major exception to this trope is any Made for TV Movie preying on the latest disease scare and, naturally, forensic medical shows.
- Inverted in a Dettol (cleaning product) advertisement. It claims to kill "99.9% of all bacteria", including, among others, the Flu Virus. Viruses are not Bacteria.
- If Thrax from Osmosis Jones were actually a virus, he would be about as tall as Jones's ankle.
- Spoofed in one Discworld novel: the Discworld's medical technology isn't advanced enough for the concept of viruses to exist, but this doesn't stop a doctor stumped for a diagnosis saying "it's probably a walrus". The Igors, however, have managed to arrive at the concept of 'tiny invithible biting creatureth' and have developed ointments to kill them before they can infect wounds.
- Pretty much all the various viruses in the Resident Evil series. For example, the T-Virus is able to infect humans, mammals, reptiles, birds, even invertebrates; real-life viruses are usually limited to a few, closely-related species due to messing with DNA. The third game and second movie even had it affect coffin bound dead bodies in a cemetery, all of which were six feet under and conveniently popped out of the ground. As you might imagine, RE viruses tend to discard the rule of biology whenever it interferes with the Rule of Cool.
- The third RE movie even goes so far as to have most of the world's water supplies go dry due to a virus. It apparently infected and killed the water. For your own sake, don't try thinking too hard about this.
- Trauma Center seemed determined to use every medical term possible to describe the main evil disease causing thing. The official name is the GUILT Virus, in which the T stands for "Toxin", but when you actually operate on it it tends to look like a tumor or parasite.
- Subverted in the Justice League episode "Fury", where Superman is felled by a cloud of airborne particles released at him by Aresia. It's assumed to be a fast-acting virus until J'onn's research shows that it is, in fact, an allergen which only affects men.
- Played straight on Batman Beyond, where one villain's scheme is to pass viruses around via credit cards.
- The Transformers Generation 1 cartoon had two such cases: the Cosmic Rust and Hate Plague spores were stated to be viral diseases, even though both were clearly specified as spores and could become airborne. Beast Wars and Beast Machines played this straight for the most part, with the former containing actual viruses that needed to be injected to be potent, and the latter's version of the Hate Plague acting more like a traditional virus with a specific carrier. Sadly, the latter's transformation lock "virus" was also airborne, meaning it was more likely a bacterial or spore-like agent. (Or, quite possibly, the other kind of virus).