I recognized the symptoms from the MOFGA Pest Report as Purple Blotch. It seems the humid wet weather we had this summer was the perfect environment for the disease.
PURPLE BLOTCH ON ONION (Alternaria porri)
Purple blotch is a very common and sometime destructive disease that effects onions, garlic, shallots and leeks. Lesions begin as whitish sunken areas that elongate and develop purplish centers. Under favorable conditions (warm with wet leaves) the purple blotch lesions grow large and oval with concentric rings. The lesions may merge and take down whole leaves, and may become covered with brownish spores. The older leaves are more susceptible than the younger leaves.
Onion residue is the source of the disease in the spring. The fungal mycelium and conidia spores persist as long as the onion debris in the field or in cull piles. New conidia are produce on infected tissue in the spring and wind blown or carried in water to the new crop. The leaves have to have liquid water on them for the spores to germinate, but germination is very quick, less than an hour.
Symptoms may appear in less than a week after germination and new conidia spores are quickly produced.
Sanitation is very important to limiting spread. Infected crop debris should be destroyed or buried after harvest. Cull piles should not be kept near the new onion field. Onions should be grown in rotation with non host crops.
I didn't want the infection to move down into the bulbs, so I harvested all the onions and hung from the fence to dry for a few days.
Once the roots were dry, I cut the tops of the foliage off leaving a few inches above the bulb so the neck can dry. Then they were spread out in the shed to cure further.
I have never had this disease before and keep a pretty clean garden. I suspect the disease blew in or was seed born. Either way, I am trying to make sure it doesn't reoccur. The diseased foliage was bagged up and disposed of with the household trash. I am going to keep these out of the basement so as not to infect my seed starting area.
Most of these onions will be used up quickly for canned sauce and salsa once the tomatoes begin ripening. I may slice and freeze the extras instead of storing them in the basement this year because Purple Blotch can affect the bulbs and cause them to rot.