At a Whole Foods in Manhattan on Wednesday, shelves were empty for the cheapest eggs — $3.39 for a carton of 12 large brown Grade A eggs. What remained were more expensive options like organic, cage-free eggs for more than $7. Prices of eggs across some countries are rising sharply. In January 2022, the average price for a dozen of large Grade A eggs in the U.S. was $1.39, according to the Bureau of Labor Statistics. Mr. Brey said that vehicles entering the farm were sprayed with disinfectant, another precaution to protect the farm, which produces 228,000 eggs daily.