It took two months for JoAnn Clevenger to reopen Upperline, a traditional Creole restaurant in New Orleans, after Hurricane Katrina devastated that city in 2005. This time, a virus has closed the place, probably for a lot longer.

It didn’t take long for her to realize that a takeout operation wouldn’t keep the business alive, and the odds that she will reopen anytime soon are against her. On Thursday, Ms. Clevenger wrote out the last paychecks to her 24 employees, some of whom had been with her for more than 25 years.

“Stay safe, stay in touch,” she wrote on each one. “You’re what makes the Upperline great.”

The prognosis for independent operations like hers seem dire. From big cities like New York to smaller ones like Birmingham, Ala., restaurants have been forced to close their dining rooms; many have simply shuttered, while others are relying on takeout and delivery. Cities like Omaha and Tempe, Ariz., have limited the number of guests, but closings are on the horizon.

Large chains and well-funded restaurant groups have the resources to ride out a protracted shutdown, but the independent restaurants that make up about two-thirds of the American dining landscape — noodle shops, diners and that charming urban restaurant that always had a line out the door — may not survive.