Moving from one region to another--hell, even migrating to a different area within the same region--sure leads to interesting things. At the job I just quit, two new guys both moved here from Texas and Florida, respectively, and the second cold weather hit, not even COLD cold by Plains standards, both of 'em were fending off nasty infections, one bronchial, the other more sinus related. The seasoned Midwesterners amongst us have been doing okay so far.
I moved to Kansas from Nebraska, which isn't exactly a huge move, but I definatly acquired some new allergies--or at least became aware of new ones--when I made the move.
Different bugs are common to different areas. When I went back home for a visit, I'd heard both Whooping Cough (2nd year in a row) and the Flu were going around pretty bad. Here, where I am now, it's just the Flu and mostly bronchial infections. When I mention Whooping Cough, most people look at me like I have 5 heads, but yes, Whooping Cough is alive and strong in that part of the country
These are some herbs native/can be found to the Plains that make good remedies, though it's a bit too late for foraging them now, you can probably find some at a local herb dealer (or your local witch doctor!):
Elderberries, good for keeping the Flu away and treating existing ailments. Make a tonic by pouring boiling water over some in a jar, screwing on the lid and letting set for 8 hours or overnight. I usually fill the jar 1/5th of the way with the berries and fill with water.
Echinacea root in tincture form, take at first sight of sickness, but for no more than 2 weeks straight since your body can develop an immunity to it. It boosts the immune system. I take lots of garlic along with it, as many have mentioned on here.
There are tons and I do mean tons of herbs good for bronchial issues. A few to consider are Coltsfoot, Slippery Elm, Mullein and Licorice. If you aren't repulsed to smoking, try smoking coltsfoot and mullein, if you are having a hard time with unproductive coughs. Otherwise, make an infusion or tonic.
And of course, eat tons of veggies!
edited to add: this isn't native to the midwest by any means, but a Japanese remedy to ward off the Flu has been to gargle with back tea. I drink black tea almost obsessively, and I haven't gotten the flu since I was a child, but if you like tea, it's an added benefit!