I know Egypt opened to tourists quite a while ago (although they may have closed again). I doubt any country is reporting a true number of cases as nowhere is testing 100% of its population daily and the tests aren’t fully accurate, so an accurate number is a gold-plated unicorn. (With my former medical scientist hat on there). We stayed in a variety of hotels, like you, we try to avoid the big chains and resort hotels, but to find Egyptian and clean, modern etc. is a big ask. Maybe if you found one of the old historic hotels like the one where Agatha Christie stayed (which we visited, it’s lovely). There must be some grand old hotels in Cairo. On the coast, it’s wall-to-wall resort hotels. We stayed in a Marriott. Everything is very modern in Hurghada although I know less developed places exist. Your problem will be finding flights and I have no idea what entry requirements Egypt has now with regards to negative tests, quarantine etc. As we’re stuck in Australia and not allowed out, at all, I’m very envious of anyone allowed to go anywhere.