It's not a virus. It's either fungal (most likely) or bacterial.

Both fungi and bacteria need moisture to thrive. Anything you can do to keep foliage dry will reduce these problems. This could be more spacing for better air flow, orienting plants to get most morning sun (to dry out dew faster) or using a soaker hose buried under mulch to prevent water from getting on the foliage.

What effects the tomatoes may not be the same pathogen that effects the zinnias etc. But those simple techniques will help reduce the pathogens.

The soil will be a source for pathogens. However, spores can still come in from the air. So 100% prevention will not always be obtainable especially in high humidity or frequent rainfall situations.

One can chose to remove infected foliage. It will help some.

There are a few organic choices for sprays. One would be a product called MilStop. It won't be perfect but coupled with keeping foliage dry, that one is broad spectrum (covers many foliar diseases) enough to cover most of the problems for that range of plant families. It is not cheap but the amount and form it is sold in should last a long time.

Copper based sprays may also help. Most consider them to be organic. The copper can build up in the soil over time.

Here is a link that might be useful: MilStop

also adding some mycorrhizal inoculant to your seeds/starts will help improve the plants ability to fight off pathogens