Memai wa Madoi no Tsugai

On the day of the earthquake, Hato, an Omega unable to return home, finds shelter for the night in a secondhand bookstore run by a man named Kazumi. "In times like these, I guess you could say we're in the same boat." Touched by Kazumi’s quiet kindness, Hato begins to feel a faint affection for him. A few days later, Hato happens to visit a bar where Kazumi works part-time. But as an Alpha, Kazumi instantly senses that Hato is not only an Omega, but also someone deeply compatible with him...!?

(Source: Shinshokan, translated)

Note: Includes one extra chapter.