One of the biggest misconceptions is that COVID is "like the flu". It was never "like the flu". Traditional upper respiratory diseases get into the respiratory system and then stop. They just aren't very good at getting into other cells. COVID, however, gets into cells via the ACE2 receptor, and there are ACE2 receptors in almost every cell.
https://www.donotpanic.news/p/why-covid-can-never-be-just-a-cold
In autopsy studies, they have found SARS-CoV-2 virus just about everywhere they have looked: lungs, heart, brain, kidney, gut, testicles, ovarian fluid, etc. It is true that in many of the research papers, they only look for RNA (because it's easy), which can't tell if it's infectious or just fragments of no-longer-dangerous virus. HOWEVER, there have also been a fair number of studies which have found infectious viruses in human tissues, including this one which found infectious virus in skull sawdust that came from sawing open skulls to do brain autopsies:
https://wwwnc.cdc.gov/eid/article/30/8/24-0145_article