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 This is one I've come around on over the past couple years

TLDR: Virology is pseuedoscientific and the viruses it finds are the products of the methods used

When Germ Theory failed (eg Koch himself failed to develop cholera after drinking a bunch of cholera bacteria) they decided the germ agent must be too small to see even with a microscope

The microscope images are from cells that are killed with antibiotics and antifungals, breaking down into a goop of sub-cellular items which are declared to be viruses (without proof)

The gene sequences are from basically the same thing - they take a whole bunch of DNA, cut it into tiny bits, and then the computer assembles the tiny bits into the virus

Experiments to spread contagious illness have failed, eg healthy volunteers spent time in a Spanish Flu (1918) ward and had sick mucus sprayed into their nose. None took ill.

An example of the pseudo-scientific process: Pasteur was not able to induce rabies (a supposed neurological virus) with the saliva of rabid dogs, and could produce similar symptoms only by injecting matter from the rabid dog directly into the brain of healthy dogs.

Maybe there are macro-parasites and thus contagion (eg ticks) but I am not aware of any germs which have been shown to cause illness. 
 Still can’t make sense of it. If viruses don’t exit, how do we get illnesses like flu? 
 3 causes of disease I can conceive:

1) Endogenous - the disease is somehow inside us all the time (eg genetic disorders)

2) Environmental - we are exposed to some sort of harmful condition (eg radiation, toxins, pathogens if any can be shown to exist)
For example, paralitic polio was probably caused by the pesticide lead arsenate.

3) Deficiency - we lack some element for ideal health (eg some vitamin/mineral, sunlight, fresh water, etc)

I suspect that in the case cold & flu illnesses the body is reacting to cold & diminished sunlight (and thus vitamin D conversion) during the winter months.

If flu is caused by a virus, why is it seasonal? Why does the virus care how sunny it is or whether it's 30C or 10C outside? 
 Another cause: psychosomatic - you observe people having a certain illness and interpret your own difficulties to mirror that illness

eg whether rabies "virus" causes you to fear water or to believe you are pregnant with a litter of puppies depends on what culture you're in

https://en.wikipedia.org/wiki/Puppy_pregnancy_syndrome

But I do think there is some root biological condition to cold & flu